title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2022-01
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Identification of key genes and biological pathways in Chinese lung cancer population using bioinformatics analysis
link: https://peerj.com/articles/12731
last-modified: 2022-01-31
description: BackgroundIdentification of accurate prognostic biomarkers is still particularly urgent for improving the poor survival of lung cancer patients. In this study, we aimed to identity the potential biomarkers in Chinese lung cancer population via bioinformatics analysis.MethodsIn this study, the differentially expressed genes (DEGs) in lung cancer were identified using six datasets from Gene Expression Omnibus (GEO) database. Subsequently, enrichment analysis was conducted to evaluate the underlying molecular mechanisms involved in progression of lung cancer. Protein-protein interaction (PPI) and CytoHubba analysis were performed to determine the hub genes. The GEPIA, Human Protein Atlas (HPA), Kaplan-Meier plotter, and TIMER databases were used to explore the hub genes. The receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic value of hub genes. Reverse transcription quantitative PCR (qRT-PCR) was used to validate the expression levels of hub genes in 10 pairs of lung cancer paired tissues.ResultsA total of 499 overlapping DEGs (160 upregulated and 339 downregulated genes) were identified in the microarray datasets. DEGs were mainly associated with pathways in cancer, focal adhesion, and protein digestion and absorption. There were nine hub genes (CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A, UBE2C, CHEK1 and BIRC5) identified by PPI and module analysis. In GEPIA database, the expression levels of these genes in lung cancer tissues were significantly upregulated compared with normal lung tissues. The results of prognostic analysis showed that relatively higher expression of hub genes was associated with poor prognosis of lung cancer. In HPA database, most hub genes were highly expressed in lung cancer tissues. The hub genes have good diagnostic efficiency in lung cancer and normal tissues. The expression of any hub gene was associated with the infiltration of at least two immune cells. qRT-PCR confirmed that the expression level of CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A were highly expressed in lung cancer tissues.ConclusionsThe hub genes and functional pathways identified in this study may contribute to understand the molecular mechanisms of lung cancer. Our findings may provide new therapeutic targets for lung cancer patients.
creator: Ping Liu
creator: Hui Li
creator: Chunfeng Liao
creator: Yuling Tang
creator: Mengzhen Li
creator: Zhouyu Wang
creator: Qi Wu
creator: Yun Zhou
uri: https://doi.org/10.7717/peerj.12731
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Liu et al.

title: The effect of 2,4-dichlorophenoxyacetic acid on the production of oat (Avena sativa L.) doubled haploid lines through wide hybridization
link: https://peerj.com/articles/12854
last-modified: 2022-01-31
description: BackgroundDevelopment of new cultivars is one of the vital options for adapting agriculture to climate change, and the production of doubled haploid (DH) plants can make a significant contribution to accelerating the breeding process. Oat is one of the cereals with particular health benefits, but it unfortunately still remains recalcitrant to haploidization. Our previous studies have clearly demonstrated that post-pollination with hormone treatment is a key step in haploid production through wide hybridization and indicated it as the most effective method for this species. Therefore, we subsequently addressed the problem of the influence of 2,4-dichlorophenoxyacetic acid (2,4-D) concentration on consecutive stages of DH production.MethodsTwenty-nine genotypes were tested, 9,465 florets were pollinated with maize pollen 2 days after emasculation and then treated with 2,4-D at 50 mg/L and 100 mg/L.ResultsThe applied treatments did not reveal any differences in the number of obtained haploid embryos. However, almost twice as many haploid plants formed on MS medium after applying a higher auxin concentration and 20% more successfully acclimatized. Moreover, 100 mg/L 2,4-D treatment resulted in twice as many DH lines that produced almost three times more seeds compared to 50 mg/L treatment. Nevertheless, the results have confirmed the existence of strong genotypic variation, which may significantly limit the development of an effective and economically feasible method that could be incorporated into breeding programs.
creator: Katarzyna Juzoń
creator: Marzena Warchoł
creator: Kinga Dziurka
creator: Ilona Mieczysława Czyczyło-Mysza
creator: Izabela Marcińska
creator: Edyta Skrzypek
uri: https://doi.org/10.7717/peerj.12854
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Juzoń et al.

title: Effect of biological treatment used before harvesting and storage methods on the quality, health and microbial characteristics of unripe hazelnut in the husk (Corylus avellana L.)
link: https://peerj.com/articles/12760
last-modified: 2022-01-28
description: BackgroundThe hazelnut (Corylus avellana) is still one of the most profitable nut crop species. In recent years, however, there has been growing interest in this species in the form of “fresh nuts” that are picked before falling out of the fruit cover. The aim of this study was to evaluate the effect of storage conditions for hazelnuts protected with biological preparations on selected morphological features of the fruits, their health status and the count of bacteria and fungi colonizing the fruits.ResultsThe hazelnuts harvested from the trees protected with a preparation containing Pythium oligandrum and stored for 2 months under the controlled atmosphere conditions and in Xtend® bags (MAP) had the greatest weight and the highest percentage of the kernel. After 3 months of storage, the hazelnuts had reduced commercial value. Only a few hazelnuts displayed symptoms of infectious diseases caused by species of Botrytis and Monilia. The protection applied before the hazelnut harvesting contributed to a multiple increase in the bacterial and yeasts count on the husks and shells of the hazelnuts stored for 3 months. The bacterial count on the nuts stored under the controlled atmosphere (CA, 3%O2:3%CO2, a temperature of 0–1 °C, humidity of 85–95%) and under the controlled atmosphere conditions and in Xtend® bags (MAP) increased significantly. An analysis of the ITS region sequence revealed the presence of bacteria Arthrobacter luteolus and Pantoea agglomerans. A Koch test proved that both non-pathogenic bacteria and pathogenic fungi can cause the browning of the C. avellana leaf under conditions of high humidity. The application of a controlled atmosphere is recommended for a short-term storage of hazelnuts in the husk.ConclusionThis research showed that 2 months’ storage of hazelnuts under controlled atmosphere conditions and Xtend® bags (MAP) prevented a reduction in the weight of hazelnuts in the husk, without the husk, and of the kernel and prevented the nut separation from the husk. In general, the application of biopreparations for the protection of the hazelnut had a positive effect on the kernel weight and size.
creator: Bogumił Markuszewski
creator: Anna Adriana Bieniek
creator: Urszula Wachowska
creator: Arkadiusz Bieniek
creator: Izabela Krzymińska
uri: https://doi.org/10.7717/peerj.12760
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Markuszewski et al.

title: Dimensional changes of commercial and novel polyvinyl siloxane impression materials following sodium hypochlorite disinfection
link: https://peerj.com/articles/12812
last-modified: 2022-01-28
description: BackgroundDental impressions are used to record anatomy of teeth and surrounding oral structures. Impression materials become contaminated with saliva and blood requiring disinfection, which may have negative impact on dimensional stability of materials.ObjectiveComparatively evaluate linear dimensional changes of synthesized Tetra-functional (dimethylsilyl) orthosilicate (TFDMOS) containing Polyvinylsiloxane (PVS) impressions following sodium hypochlorite disinfection.MethodsPercentage dimensional changes of three commercial PVS (Elite HD Monophase, Extrude and Aquasil Ultra Monophase) and five experimental PVS impression materials were measured. Experimental material contained novel cross-linking agent (TFDMOS) and a non-ionic surfactant (Rhodasurf CET-2) that is Exp-A (without TFDMOS), Exp-B (with TFDMOS), Exp-C (TFDMOS+ 2% Rhodasurf CET-2), Exp-D (TFDMOS+ 2.5% Rhodasurf CET-2) Exp-E (TFDMOS+ 3% Rhodasurf CET-2). Samples were made using rectangular stainless-steel molds (40 × 10 × 3 mm3) and linear dimensional changes were measured using a calibrated travelling microscope at 10× magnification after immersion in distilled water (D.W) and 1% Sodium Hypochlorite solution at two different time intervals i.e., 30 min and 24 h.ResultsSamples immersed in 1% NaOCl showed significant (p < 0.05) dimensional changes after 30 min of immersion. Exp-E showed significantly greater dimensional changes than their control (Exp-A and Exp-B). In distilled water, there were no significant difference among the tested materials. Aquasil exhibited highest expansion (0.06%) in both solutions. At 24 h, among the commercial materials, Extrude had the greatest expansion followed by Aquasil and Elite in DW while Aquasil showed the greatest expansion followed by Extrude and Elite in NaOCl.ConclusionExperimental PVS had linear dimensional changes within the ISO 4823; 2015 recommended range. However, extended immersion can negatively affect the linear dimensions.
creator: Shahab Ud Din
creator: Muhammad Sajid
creator: Asfia Saeed
creator: Farooq Ahmad Chaudhary
creator: Mohammad Khursheed Alam
creator: Juneda Sarfraz
creator: Bilal Ahmed
creator: Mangala Patel
uri: https://doi.org/10.7717/peerj.12812
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Ud Din et al.

title: Factors of influence in prisoner’s dilemma task: a review of medical literature
link: https://peerj.com/articles/12829
last-modified: 2022-01-28
description: The Prisoner’s Dilemma (PD) is one of the most popular concepts amongst the scientific literature. The task is used in order to study different types of social interactions by giving participants the choice to defect or cooperate in a specific social setting/dilemma. This review focuses on the technical characteristics of the PD task as it is used in medical literature and describes how the different PD settings could influence the players’ behaviour. We identify all the studies that have used the PD task in medical research with human participants and distinguish, following a heuristic approach, seven parameters that can differentiate a PD task, namely (a) the opponent parties’ composition; (b) the type of the opponent as perceived by the players; (c) the interaction flow of the game; (d) the number of rounds; (e) the instructions narrative and options that are given to players; (f) the strategy and (g) the reward matrix and payoffs of the game. We describe how each parameter could influence the final outcome of the PD task and highlight the great variability concerning the settings of these parameters in medical research. Our aim is to point out the heterogeneity of such methods in the past literature and to assist future researchers with their methodology design.
creator: Vasileios Mantas
creator: Artemios Pehlivanidis
creator: Vasileia Kotoula
creator: Katerina Papanikolaou
creator: Georgia Vassiliou
creator: Anthoula Papaiakovou
creator: Charalambos Papageorgiou
uri: https://doi.org/10.7717/peerj.12829
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Mantas et al.

title: Response of Pinus tabuliformis saplings to continuous autumn fertilization treatments in the mountains of Eastern Liaoning Province, China
link: https://peerj.com/articles/12853
last-modified: 2022-01-28
description: Autumn fertilization is an important cultivation and management measure used to provide nutrients at the hardening stage during the end of the growing season—bolstering nutrient reserves and promoting additional growth in the following spring. Previous studies mainly focused on short-term or one-time fertilization treatment of container seedlings, and few studies have observed the effects of autumn fertilization of large-area forests over multiple continuous years. The growth dynamics and nutrient changes during autumn in 324 Pinus tabuliformis saplings in the temperate zone of China (in the eastern Liaoning mountains) were studied under field conditions with different fertilizer treatments for three consecutive years. The second year of autumn fertilization promoted the growth of tree height and annual leaf length more significantly than that in the first year, the change in diameter at breast height (DBH) was significant. Tree height (TH) in spring increased at a faster rate than in autumn, while DBH stably increased throughout the year. The increase in TH, DBH, and annual leaf length (ALL) under all fertilization treatments was higher than that of the control group, and the decrease in annual branch length (ABL) was higher than that of the control group. High N significantly increased the concentration of new coniferous N (NLN), soil total N (STN), and soil alkali-hydrolyzable N (SAHN) in P. tabuliformis saplings. High P significantly increased the concentration of P in annual needles and soil total P (STP), and decreased the concentration of N in new needles. In addition, there is a certain correlation between the N and P concentration in the needles and soil, representing the competition and interactions between plant nutrient demand and soil nutrient supply. The most favorable fertilizer treatment consisted of high N and low P (urea 204 g, calcium superphosphate 104 g), which provide support for the formulation of a reasonable fertilization technology for P. tabuliformis in the mountains of Eastern Liaoning Province, China.
creator: Yiming Zhang
creator: Jincheng Han
creator: Lijiao Wang
creator: Xin Jing
creator: Yutao Wang
creator: Ping Liu
uri: https://doi.org/10.7717/peerj.12853
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Zhang et al.

title: Leopard and spotted hyena densities in the Lake Mburo National Park, southwestern Uganda
link: https://peerj.com/articles/12307
last-modified: 2022-01-27
description: Robust measures of animal densities are necessary for effective wildlife management. Leopards (Panthera pardus) and spotted hyenas (Crocuta Crocuta) are higher order predators that are data deficient across much of their East African range and in Uganda, excepting for one peer-reviewed study on hyenas, there are presently no credible population estimates for these species. A lack of information on the population status and even baseline densities of these species has ramifications as leopards are drawcards for the photo-tourism industry, and along with hyenas are often responsible for livestock depredations from pastoralist communities. Leopards are also sometimes hunted for sport. Establishing baseline density estimates for these species is urgently needed not only for population monitoring purposes, but in the design of sustainable management offtakes, and in assessing certain conservation interventions like financial compensation for livestock depredation. Accordingly, we ran a single-season survey of these carnivores in the Lake Mburo National Park of south-western Uganda using 60 remote camera traps distributed in a paired format at 30 locations. We analysed hyena and leopard detections under a Bayesian spatially explicit capture-recapture (SECR) modelling framework to estimate their densities. This small national park (370 km2) is surrounded by Bahima pastoralist communities with high densities of cattle on the park edge (with regular park incursions). Leopard densities were estimated at 6.31 individuals/100 km2 (posterior SD = 1.47, 95% CI [3.75–9.20]), and spotted hyena densities were 10.99 individuals/100 km2, but with wide confidence intervals (posterior SD = 3.35, 95% CI [5.63–17.37]). Leopard and spotted hyena abundance within the boundaries of the national park were 24.87 (posterior SD 7.78) and 39.07 individuals (posterior = SD 13.51) respectively. Leopard densities were on the middle end of SECR studies published in the peer-reviewed literature over the last 5 years while spotted hyena densities were some of the first reported in the literature using SECR, and similar to a study in Botswana which reported 11.80 spotted hyenas/100 km2. Densities were not noticeably lower at the park edge, and in the southwest of our study site, despite repeated cattle incursions into these areas. We postulate that the relatively high densities of both species in the region could be owed to impala Aepyceros melampus densities ranging from 16.6–25.6 impala/km2. Another, potential explanatory variable (albeit a speculative one) is the absence of interspecific competition from African lions (Panthera leo), which became functionally extinct (there is only one male lion present) in the park nearly two decades ago. This study provides the first robust population estimate of these species anywhere in Uganda and suggests leopards and spotted hyenas continue to persist in the highly modified landscape of Lake Mburo National Park.
creator: Aleksander Braczkowski
creator: Ralph Schenk
creator: Dinal Samarasinghe
creator: Duan Biggs
creator: Allie Richardson
creator: Nicholas Swanson
creator: Merlin Swanson
creator: Arjun Dheer
creator: Julien Fattebert
uri: https://doi.org/10.7717/peerj.12307
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Braczkowski et al.

title: Effects of media multitasking frequency on a novel volitional multitasking paradigm
link: https://peerj.com/articles/12603
last-modified: 2022-01-27
description: The effect of media multitasking (e.g., listening to podcasts while studying) on cognitive processes has seen mixed results thus far. To date, the tasks used in the literature to study this phenomenon have been classical paradigms primarily used to examine processes such as working memory. While perfectly valid on their own, these paradigms do not approximate a real-world volitional multitasking environment. To remedy this, as well as attempt to further validate previously found effects in the literature, we designed a novel experimental framework that mimics a desktop computer environment where a “popup” associated with a secondary task would occasionally appear. Participants could choose to attend to the popup, or to ignore it. Attending to the popup would prompt a word stem completion task, while ignoring it would continue the primary math problem verification task. We predicted that individuals who are more impulsive, more frequent media multitaskers, and individuals who prefer to multitask (quantified with the Barratt Impulsiveness Scale, a modified version of the Media Use Questionnaire, and the Multitasking Preference Inventory) would be more distracted by popups, choose to switch tasks more often and more quickly, and be slower to return to the primary task compared to those who media multitask to a lesser degree. We found that as individuals media multitask to a greater extent, they are slower to return to the previous (primary) task set and are slower to complete the primary task overall whether a popup was present or not, among other task performance measures. We found a similar pattern of effects within individuals who prefer to multitask. Our findings suggest that overall, more frequent media multitaskers show a marginal decrease in task performance, as do preferential multitaskers. Attentional impulsivity was not found to influence any task performance measures, but was positively related to a preference for multitasking. While our findings may lack generalizability due to the modifications to the Media Use Questionnaire, and this initial study is statically underpowered, this paradigm is a crucial first step in establishing a more ecologically valid method to study real-world multitasking.
creator: Jesus J. Lopez
creator: Joseph M. Orr
uri: https://doi.org/10.7717/peerj.12603
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Lopez and Orr

title: Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities
link: https://peerj.com/articles/12701
last-modified: 2022-01-27
description: Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.
creator: Julian A. Liber
creator: Douglas H. Minier
creator: Anna Stouffer-Hopkins
creator: Judson Van Wyk
creator: Reid Longley
creator: Gregory Bonito
uri: https://doi.org/10.7717/peerj.12701
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Liber et al.

title: Conservation paleobiology on Minami-Daito Island, Okinawa, Japan: anthropogenic extinction of cave-dwelling bats on a tropical oceanic island
link: https://peerj.com/articles/12702
last-modified: 2022-01-27
description: BackgroundWith strong environmental and geographic filtration, vertebrates incapable of flying and swimming are often extirpated from island ecosystems. Minami-Daito Island is an oceanic island in Okinawa, Japan that harbors the Daito flying fox (Pteropus dasymallus daitoensis), a subspecies of the fruit bat and the only extant mammal endemic to the island. However, the skeleton of a cave-dwelling bat Rhinolophus sp. and fossil guano were briefly reported in a previous study.MethodsHere, we present evidence for the anthropogenic extirpation of two species of cave-dwelling bats (Miniopterus sp. & Rhinolophus sp.) from Minami-Daito Island. Our goal is to reliably constrain the ages of the extirpated bat species by a multiproxy approach. Because skeletal materials did not preserve sufficient bone collagen for direct radiocarbon dating, we alternatively examined guano-like deposits based on SEM observation and Fourier-transform infrared spectroscopy (FTIR) along with stable carbon and nitrogen isotope analyses for possible indirect dating. We also examined stable carbon isotopes in bone apatite, assuming that an isotopic signal of C4 plants on the bat bones links to sugarcane plantation on the island based on the historical knowledge that early human settlers quickly replaced the island’s native C3 forests with sugarcane (C4 perennial grass) plantation from 1900 onward.ResultsOur cave survey documents the remains of Miniopterus sp. from the island for the first time. Based on the unique taphonomic conditions (unpermineralized bones, disarticulated skeletons closely scattered without sediment cover, various degrees of calcite crystal growth around bones) and a radiocarbon age of a humic sample, we suggest that the maximum age constraint of Miniopterus sp. and Rhinolophus sp. is 4,640 calBP. Based on a series of analyses, we conclude that the guano-like deposits are composed not of bat guano but mainly of humic substances; however, a hydroxyapatite crust associated with bat-lying stalagmites may be derived from bat feces. Stable carbon isotope analysis of bone apatite revealed C4 signals in various degrees, confirming that small populations of cave-dwelling bats persisted on Minami-Daito Island after 1900.ConclusionsThe results of this study indicate that these populations remained rather small and did not leave many generations and that the estimated ages can be bracketed from 4,640 calBP to the post-1900 (perhaps, until the 1950s). They likely faced a continuously high mortality risk due to severe anthropogenic stresses on the island, where most of the forests were turned into sugarcane plantations within a few decades in the early 20th century. A result of hearing surveys to local residents suggests the latest remnants most likely disappeared on the island concurrently with the introduction of chemical pesticides after World War II.
creator: Yuri Kimura
creator: Dai Fukui
creator: Mizuko Yoshiyuki
creator: Kazuaki Higashi
uri: https://doi.org/10.7717/peerj.12702
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Kimura et al.

title: Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone
link: https://peerj.com/articles/12706
last-modified: 2022-01-27
description: BackgroundPseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites.MethodsWater from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3–6, 7–9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots.ResultsA total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance.
creator: José Alan Herrera-García
creator: Mahinda Martinez
creator: Pilar Zamora-Tavares
creator: Ofelia Vargas-Ponce
creator: Luis Hernández-Sandoval
creator: Fabián Alejandro Rodríguez-Zaragoza
uri: https://doi.org/10.7717/peerj.12706
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Herrera-García et al.

title: Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants
link: https://peerj.com/articles/12791
last-modified: 2022-01-27
description: BackgroundThe recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL.MethodsOur study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages.ResultsThe reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta’ subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway.
creator: Claudio Casola
creator: Jingjia Li
uri: https://doi.org/10.7717/peerj.12791
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Casola and Li

title: Soil health and nutrient density: preliminary comparison of regenerative and conventional farming
link: https://peerj.com/articles/12848
last-modified: 2022-01-27
description: Several independent comparisons indicate regenerative farming practices enhance the nutritional profiles of crops and livestock. Measurements from paired farms across the United States indicate differences in soil health and crop nutrient density between fields worked with conventional (synthetically-fertilized and herbicide-treated) or regenerative practices for 5 to 10 years. Specifically, regenerative farms that combined no-till, cover crops, and diverse rotations—a system known as Conservation Agriculture—produced crops with higher soil organic matter levels, soil health scores, and levels of certain vitamins, minerals, and phytochemicals. In addition, crops from two regenerative no-till vegetable farms, one in California and the other in Connecticut, had higher levels of phytochemicals than values reported previously from New York supermarkets. Moreover, a comparison of wheat from adjacent regenerative and conventional no-till fields in northern Oregon found a higher density of mineral micronutrients in the regenerative crop. Finally, a comparison of the unsaturated fatty acid profile of beef and pork raised on one of the regenerative farms to a regional health-promoting brand and conventional meat from local supermarkets, found higher levels of omega-3 fats and a more health-beneficial ratio of omega-6 to omega-3 fats. Despite small sample sizes, all three crop comparisons show differences in micronutrient and phytochemical concentrations that suggest soil health is an under appreciated influence on nutrient density, particularly for phytochemicals not conventionally considered nutrients but nonetheless relevant to chronic disease prevention. Likewise, regenerative grazing practices produced meat with a better fatty acid profile than conventional and regional health-promoting brands. Together these comparisons offer preliminary support for the conclusion that regenerative soil-building farming practices can enhance the nutritional profile of conventionally grown plant and animal foods.
creator: David R. Montgomery
creator: Anne Biklé
creator: Ray Archuleta
creator: Paul Brown
creator: Jazmin Jordan
uri: https://doi.org/10.7717/peerj.12848
license: https://creativecommons.org/licenses/by-nc/4.0
rights: © 2022 Montgomery et al.

title: Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects
link: https://peerj.com/articles/12573
last-modified: 2022-01-26
description: BackgroundIn comparison to organic mercury (MeHg), the environmental inorganic mercury (IHg) can be found in some skin-lightening cosmestics were considered “harmless” for a long time. However, recent studies have shown that long-term exposure to low doses of IHg may affect biological systems. Therefore, this study investigated the effects of IHg long-term exposure to the alveolar bone of adult rats.MethodsAdult Wistar rats were distributed in control and HgCl2 exposed (0.375 mg/kg/day). After 45 days, the rats were euthanized and both blood and hemimandibles were collected. Total blood Hg levels were measured and both inorganic and organic components of the alveolar bone were determined through XRD and ATR-FTIR. The microstructure of the alveolar bone was assessed by using micro-CT and the morphometric analysis was performed by using stereomicroscopy.ResultsAlterations in the physicochemical components of the alveolar bone of exposed animals were observed. The bone changes represented a tissue reaction at the microstructural level, such as bone volume increase. However, no significant dimensional changes (bone height) were observed.ConclusionExposure to IHg at this dose can promote microstructural changes and alteration in the organic and inorganic components in the alveolar bone.
creator: Paula Beatriz de Oliveira Nunes
creator: Maria Karolina Martins Ferreira
creator: Deborah Ribeiro Frazão
creator: Leonardo Oliveira Bittencourt
creator: Victória dos Santos Chemelo
creator: Márcia Cristina Freitas Silva
creator: Armando Lopes Pereira-Neto
creator: Alan Rodrigo Leal Albuquerque
creator: Simone Patricia Aranha Paz
creator: Rômulo Simões Angélica
creator: Sofia Pessanha
creator: Rafael Rodrigues Lima
uri: https://doi.org/10.7717/peerj.12573
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Nunes et al.

title: miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1
link: https://peerj.com/articles/12724
last-modified: 2022-01-26
description: PurposeTo investigate the mechanism of miR-148a-3p regulating the proliferation and migration of bladder tumor cells.Materials and MethodsWe conducted a preliminary study to detect the relative expression of miR-148a-3p in bladder cancer and para-cancerous tissue samples. Three bladder tumor cell lines, T24, 5,637 and UM-UC-3, were selected. The expression levels of miR-148a-3p were artificially regulated with miR-148a-3p mimics and the miR-148a-3p inhibitor. The relative expression levels of miR-148a-3p in the samples of each cell line were determined. Cell Counting Kit-8 (CCK-8) was used to detect cell proliferation, while the effect of the miR-148a-3p mimics and inhibitor on tumor cell migration was detected by wound healing assay. Flow cytometry assay was carried out to explore the effect of miR-148a-3p on cell apoptosis. Dual-luciferase reporter assay was performed in order to verify miR-148a-3p’s target gene. The expressions of ROCK-1 and Bcl-2 were analyzed by western blot.ResultsThe relative expression of miR-148a-3p in tumor and adjacent tissues was assessed with qRT-PCR (P < 0.05) and found to be significantly lower in the tumor tissues than the adjacent tissues. The data obtained from the CCK-8 and wound healing assay showed that intracellular transfection of miR-148a-3p mimics could inhibit cell proliferation and migration, while the miR-148a-3p inhibitor promoted them. Overexpression of miR-148a-3p promoted cell apoptosis in the T24 and 5,637 cell lines. The dual-luciferase reporter assay verified that ROCK-1 is a direct target of miR-148a-3p. Western blot showed that miR-148a-3p overexpression downregulated the expression of ROCK-1 and Bcl-2, while miR-148a-3p knockdown upregulated the expression of ROCK-1 and Bcl-2.ConclusionsWe confirmed that miR-148a-3p was significantly decreased in bladder cancer cells. miR-148a-3p overexpression inhibited bladder cancer cell proliferation and migration, whereas miR-148a-3p knockdown promoted bladder cancer cell proliferation and migration. Moreover, we found that ROCK-1 was a downstream target of miR-148a-3p. We also found that miR-148a-3p induced cell apoptosis by regulating the expression of Bcl-2. However, the deeper mechanism of this regulatory relationship needs further study.
creator: Chao Xu
creator: Guanwen Zhou
creator: Zhuang Sun
creator: Zhaocun Zhang
creator: Haifeng Zhao
creator: Xianzhou Jiang
uri: https://doi.org/10.7717/peerj.12724
license: https://creativecommons.org/licenses/by-nc/4.0
rights: © 2022 Xu et al.

title: The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women
link: https://peerj.com/articles/12745
last-modified: 2022-01-26
description: BackgroundBody composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women.MethodsThe sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated.ResultsThe cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32).ConclusionBMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predicting injury among men. In contrast, indices with a higher contribution of fat are better for women. It indicates sex differentiation of injury risk conditions. Men should focus on developing muscle mass, whereas women should reduce body fat to decrease injury risk. However, widespread use seemed to be limited to the specific examined group. Therefore, cut-off points should be used with caution, and calculated values should be verified and confirmed in subsequent studies.
creator: Jarosław Domaradzki
creator: Dawid Koźlenia
uri: https://doi.org/10.7717/peerj.12745
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Domaradzki and Koźlenia

title: Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals
link: https://peerj.com/articles/12840
last-modified: 2022-01-26
description: In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, whereas the hydrocoral Millepora species had the highest BTI. Within each heating regime, the BTI of different species were ranked and used to indicate susceptibility. In the FHP, the three Pocilloporidae species could be divided into two groups in terms of bleaching susceptibility. FHP not only displayed a higher differentiating capability on coal bleaching susceptibility than SHP, but also had a faster completion time, thus reducing the likelihood of unforeseen complications during the tank experiments. Our color-based method is easier and less effort-intensive than methods involving the assessment of zooxanthellae densities. Moreover, it requires much fewer replicates and all samples in one large tank (e.g., 300 L) for the studies considering multiple species comparisons. This method opens opportunities for studying the effects of species types, acclimatization (e.g., seasons), and environmental factors other than temperature on coral bleaching.
creator: Jih-Terng Wang
creator: Chi-Wei Chu
creator: Keryea Soong
uri: https://doi.org/10.7717/peerj.12840
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wang et al.

title: Potential impacts from simulated vessel noise and sonar on commercially important invertebrates
link: https://peerj.com/articles/12841
last-modified: 2022-01-26
description: Human usage of coastal water bodies continues to increase and many invertebrates face a broad suite of anthropogenic stressors (e.g., warming, pollution, acidification, fishing pressure). Underwater sound is a stressor that continues to increase in coastal areas, but the potential impact on invertebrates is not well understood. In addition to masking natural sound cues which may be important for behavioral interactions, there is a small but increasing body of scientific literature indicating sublethal physiological stress may occur in invertebrates exposed to high levels of underwater sound, particularly low frequency sounds such as vessel traffic, construction noise, and some types of sonar. Juvenile and sub-adult blue crabs (Callinectes sapidus) and American lobsters (Homarus americanus) were exposed to simulated low-frequency vessel noise (a signal was low-pass filtered below 1 kHz to ensure low-frequency content only) and mid-frequency sonar (a 1-s 1.67 kHz continuous wave pulse followed by a 2.5 to 4.0 kHz 1-s linear frequency modulated chirp) and behavioral response (the animal’s activity level) was quantified during and after exposure using EthoVision XT™ from overhead video recordings. Source noise was quantified by particle acceleration and pressure. Physiological response to the insults (stress and recovery) were also quantified by measuring changes in hemolymph heat shock protein (HSP27) and glucose over 7 days post-exposure. In general, physiological indicators returned to baseline levels within approximately 48 h, and no observable difference in mortality between treatment and control animals was detected. However, there was a consistent amplified hemolymph glucose signal present 7 days after exposure for those animals exposed to mid-frequency sound and there were changes to C. sapidus competitive behavior within 24 h of exposure to sound. These results stress the importance of considering the impacts of underwater sound among the suite of stressors facing marine and estuarine invertebrates, and in the discussion of management actions such as protected areas, impact assessments, and marine spatial planning efforts.
creator: David M. Hudson
creator: Jason S. Krumholz
creator: Darby L. Pochtar
creator: Natasha C. Dickenson
creator: Georges Dossot
creator: Gillian Phillips
creator: Edward P. Baker
creator: Tara E. Moll
uri: https://doi.org/10.7717/peerj.12841
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Hudson et al.

title: Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production
link: https://peerj.com/articles/12677
last-modified: 2022-01-25
description: BackgroundCassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha−1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria.MethodsWe screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL−1 h−1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed.ResultsThe experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL−1h−1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
creator: Xiao Zhang
creator: Juanjuan Tong
creator: Mengmeng Dong
creator: Kashif Akhtar
creator: Bing He
uri: https://doi.org/10.7717/peerj.12677
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Zhang et al.

title: Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels
link: https://peerj.com/articles/12778
last-modified: 2022-01-25
description: Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The interactions in microbial communities also influence the healthy growth of Fritillaria ussuriensis.
creator: Ning Jiao
creator: Xiaoshuang Song
creator: Ruiqing Song
creator: Dachuan Yin
creator: Xun Deng
uri: https://doi.org/10.7717/peerj.12778
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Jiao et al.

title: A newly recognized theropod assemblage from the Lewisville Formation (Woodbine Group; Cenomanian) and its implications for understanding Late Cretaceous Appalachian terrestrial ecosystems
link: https://peerj.com/articles/12782
last-modified: 2022-01-25
description: While the terrestrial fossil record of the mid-Cretaceous interval (Aptian to Cenomanian) in North America has been poorly studied, the recent focus on fossil localities from the western United States has offered a more detailed picture of vertebrate diversity, ecosystem dynamics and faunal turnover that took place on the western landmass of Laramidia. This is in stark contrast to the terrestrial record from the eastern landmass of Appalachia, where vertebrate fossils are rare and consist mostly of isolated and fragmentary remains. However, a detailed understanding of these fossil communities during this interval is necessary for comparison of the faunal patterns that developed during the opening of the Western Interior Seaway (WIS). The Woodbine Group of Texas is a Cenomanian age (95–100 mya) deposit consisting of shallow marine, deltaic, and terrestrial communities, which were only recently separated from their western counterparts. These deposits have yielded a wealth of vertebrate remains, yet non-avian theropods are still largely unknown. Recently, multiple localities in the Lewisville Formation of the Woodbine Group have yielded new non-avian theropod material, including numerous isolated teeth and postcranial remains. While largely fragmentary, this material is sufficiently diagnostic to identify the following taxa: a large-bodied carcharodontosaur, a mid-sized tyrannosauroid, a large ornithomimosaur, a large dromaeosaurine, a small dromaeosaurid, a small troodontid, and a small coelurosaur. Some of these groups represent the first occurrence for Appalachia and provide a broader understanding of a newly expanded faunal diversity for the Eastern landmass. The Lewisville Formation theropod fauna is similar in taxonomic composition to contemporaneous deposits in Laramidia, confirming that these groups were widespread across the continent prior to extension of the WIS. The Lewisville Formation documents the transitional nature of Cenomanian coastal ecosystems in Texas while providing additional details on the evolution of Appalachian communities shortly after WIS extension.
creator: Christopher R. Noto
creator: Domenic C. D’Amore
creator: Stephanie K. Drumheller
creator: Thomas L. Adams
uri: https://doi.org/10.7717/peerj.12782
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Noto et al.

title: Seasonal and diel variations in the vertical distribution, composition, abundance and biomass of zooplankton in a deep Chilean Patagonian Fjord
link: https://peerj.com/articles/12823
last-modified: 2022-01-25
description: Comau Fjord is a stratified Chilean Patagonian Fjord characterized by a shallow brackish surface layer and a >400 m layer of aragonite-depleted subsurface waters. Despite the energetic burden of low aragonite saturation levels to calcification, Comau Fjord harbours dense populations of cold-water corals (CWC). While this paradox has been attributed to a rich supply of zooplankton, supporting abundance and biomass data are so far lacking. In this study, we investigated the seasonal and diel changes of the zooplankton community over the entire water column. We used a Nansen net (100 µm mesh) to take stratified vertical hauls between the surface and the bottom (0-50-100-200-300-400-450 m). Samples were scanned with a ZooScan, and abundance, biovolume and biomass were determined for 41 taxa identified on the web-based platform EcoTaxa 2.0. Zooplankton biomass was the highest in summer (209 g dry mass m−2) and the lowest in winter (61 g dry mass m−2). Abundance, however, peaked in spring, suggesting a close correspondence between reproduction and phytoplankton spring blooms (Chl a max. 50.86 mg m−3, 3 m depth). Overall, copepods were the most important group of the total zooplankton community, both in abundance (64–81%) and biovolume (20–70%) followed by mysids and chaetognaths (in terms of biovolume and biomass), and nauplii and Appendicularia (in terms of abundance). Throughout the year, diel changes in the vertical distribution of biomass were found with a daytime maximum in the 100–200 m depth layer and a nighttime maximum in surface waters (0–50 m), associated with the diel vertical migration of the calanoid copepod family Metridinidae. Diel differences in integrated zooplankton abundance, biovolume and biomass were probably due to a high zooplankton patchiness driven by biological processes (e.g., diel vertical migration or predation avoidance), and oceanographic processes (estuarine circulation, tidal mixing or water column stratification). Those factors are considered to be the main drivers of the zooplankton vertical distribution in Comau Fjord.
creator: Nur Garcia-Herrera
creator: Astrid Cornils
creator: Jürgen Laudien
creator: Barbara Niehoff
creator: Juan Höfer
creator: Günter Försterra
creator: Humberto E. González
creator: Claudio Richter
uri: https://doi.org/10.7717/peerj.12823
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Garcia-Herrera et al.

title: The relationship between endorsing reporting guidelines or trial registration and the impact factor or total citations in surgical journals
link: https://peerj.com/articles/12837
last-modified: 2022-01-25
description: BackgroundA journal’s impact factor (IF) and total citations are often used as indicators of its publication quality. Furthermore, journals that require authors to abide by reporting guidelines or conduct trial registration generally have a higher quality of reporting. In this study, we sought to explore the potential associations between the enforcement of reporting guidelines or trial registration and a surgical journal’s IF or total citations in order to find new approaches and ideas to improve journal publication quality.MethodsWe examined surgical journals from the 2018 Journal Citation Report’s Expanded Scientific Citation Index to quantify the use of reporting guidelines or study registration. We reviewed the “instructions for authors” from each journal and used multivariable linear regression analysis to determine which guidelines were associated with the journal IF and total citations. The dependent variable was the logarithm base 10 of the IF in 2018 or the logarithm base 10 of total citations in 2018 (the results were presented as geometric means, specifically the ratio of the “endorsed group” results to “not endorsed group” results). The independent variable was one of the requirements (endorsed and not endorsed). Models adjust for the publication region, language, start year, publisher and journal size (only used to adjust total citations).ResultsWe included 188 surgical journals in our study. The results of multivariable linear regression analysis showed that journal IF was associated (P < 0.01) with the following requirements: randomized controlled trial (RCT) registration (geometric means ratio (GR) = 1.422, 95% CI [1.197–1.694]), Consolidated Standards of Reporting Trials (CONSORT) statement (1.318, [1.104–1.578]), Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) statement (1.390, [1.148–1.683]), Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement (1.556, [1.262–1.919]), Standards for Reporting Diagnostic Accuracy (STARD) statement (1.585, [1.216–2.070]), and Meta-analysis of Observational Studies in Epidemiology (MOOSE) statement (2.113, [1.422–3.133]). We found associations between the endorsement of RCT registration (GR = 1.652, 95% CI [1.268–2.153]), CONSORT (1.570, [1.199–2.061]), PRISMA (1.698, [1.271–2.270]), STROBE (2.023, [1.476–2.773]), STARD (2.173, [1.452–3.243]), and MOOSE statements (2.249, [1.219–4.150]) and the number of total citations.ConclusionThe presence of reporting guidelines and trial registration was associated with higher IF or more total citations in surgical journals. If more surgical journals incorporate these policies into their submission requirements, this may improve publication quality, thus increasing their IF and total citations.
creator: Jing Zhou
creator: Jianqiang Li
creator: Jingao Zhang
creator: Bo Geng
creator: Yao Chen
creator: Xiaobin Zhou
uri: https://doi.org/10.7717/peerj.12837
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Zhou et al.

title: Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer
link: https://peerj.com/articles/12843
last-modified: 2022-01-25
description: BackgroundBladder cancer (BC) is a common urinary tract system tumor with high recurrence rate and different populations show distinct response to immunotherapy. Novel biomarkers that can accurately predict prognosis and therapeutic responses are urgently needed. Here, we aim to identify a novel prognostic and therapeutic responses immune-related gene signature of BC through a comprehensive bioinformatics analysis.MethodsThe robust rank aggregation was conducted to integrate differently expressed genes (DEGs) in datasets of the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO). Lasso and Cox regression analyses were performed to formulate a novel mRNA signature that could predict prognosis of BC patients. Subsequently, the prognostic value and predictive value of the signature was validated with two independent cohorts GSE13507 and IMvigor210. Finally, quantitative Real-time PCR (qRT-PCR) analysis was conducted to determine the expression of mRNAs in BC cell lines (UM-UC-3, EJ-1, SW780 and T24).ResultsWe built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1. Our prognostic signature could be used to stratify BC population into two risk groups with distinct immune profile and responsiveness to immunotherapy. The results of qRT-PCR demonstrated that the eight mRNAs exhibited different expression levels in BC cell lines.ConclusionOur study constructed a convenient and reliable 8-mRNA gene signature, which might provide prognostic prediction and aid treatment decision making of BC patients in clinical practice.
creator: Yichi Zhang
creator: Yifeng Lin
creator: Daojun Lv
creator: Xiangkun Wu
creator: Wenjie Li
creator: Xueqing Wang
creator: Dongmei Jiang
uri: https://doi.org/10.7717/peerj.12843
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Zhang et al.

title: Perceived physical activity during stay-at-home COVID-19 pandemic lockdown March–April 2020 in Polish adults
link: https://peerj.com/articles/12779
last-modified: 2022-01-24
description: BackgroundLockdowns amid the COVID-19 pandemic drastically reduced the possibility of undertaking physical activity (PA) in gyms, swimming pools, or work-related PA, e.g., active commuting. However, the stay-at-home order could have reduced PA the most, i.e., the ban of unnecessary outdoor activities. It affected free walking, running, skiing, active tourism, etc. It is, therefore, crucial to estimate how the stay-at-home order affected PA. We estimated how the stay-at-home order affected perceived PA and sedentary behavior compared to the pre-pandemic time in Poland.MethodsWe used a self-reported International Physical Activity Questionnaire—Long Form (IPAQ-LF) to estimate the time (minutes per day) of vigorous and moderate PA and walking and sitting time.ResultsWe gathered data from 320 Polish participants. Bayesian approaches, including t-test and Bayesian correlations, were used to find differences and correlations between PA before and during the stay-at-home lockdown. Our data supported the hypotheses that vigorous PA, as well as walking, declined during the lockdown. Surprisingly, our data did not support the hypothesis that moderate physical activity was reduced. We found that moderate PA during lockdown increased compared to the pre-lockdown PA. As hypothesized, our data strongly evinced that sitting time inclined during the lockdown. PA decline was not correlated with the available living space. People who had access to gardens did not demonstrate a higher PA level than those without.DiscussionWalking and sitting time have drastically changed during the stay-at-home lockdown, decreasing and increasing, respectively. Given results from studies focusing on lockdowns without the stay-at-home restriction, it may be assumed that letting people go outside is crucial in keeping them more active and less sedentary. Authorities should take into account the effect the stay-at-home order may have on PA and sedentary behavior and as a result, on health. Stay-at-home orders should be the last considered restriction, given its detrimental consequences.
creator: Stanisław H. Czyż
creator: Wojciech Starościak
uri: https://doi.org/10.7717/peerj.12779
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Czyż and Starościak

title: Almost all known sauropod necks are incomplete and distorted
link: https://peerj.com/articles/12810
last-modified: 2022-01-24
description: Sauropods are familiar dinosaurs, immediately recognisable by their great size and long necks. However, their necks are much less well known than is often assumed. Surprisingly few complete necks have been described in the literature, and even important specimens such as the Carnegie Diplodocus and Apatosaurus, and the giant Berlin brachiosaur, in fact have imperfectly known necks. In older specimens, missing bone is often difficult to spot due to over-enthusiastic restoration. Worse still, even those vertebrae that are complete are often badly distorted—for example, in consecutive cervicals of the Carnegie Diplodocus CM 84, the aspect ratio of the posterior articular facet of the centrum varies so dramatically that C14 appears 35% broader proportionally than C13. And even in specimens where the cervicodorsal sequence is preserved, it is often difficult or impossible to confidently identify which vertebra is the first dorsal. Widespread incompleteness and distortion are both inevitable due to sauropod anatomy: large size made it almost impossible for whole individuals to be preserved because sediment cannot be deposited quickly enough to cover a giant carcass on land; and distortion of presacral vertebrae is common due to their lightweight hollow construction. This ubiquitous incompleteness and unpredictable distortion compromise attempts to mechanically analyze necks, for example to determine habitual neck posture and range of motion by modelling articulations between vertebrae.
creator: Michael P. Taylor
uri: https://doi.org/10.7717/peerj.12810
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Taylor

title: Impervious surface and local abiotic conditions influence arthropod communities within urban greenspaces
link: https://peerj.com/articles/12818
last-modified: 2022-01-24
description: The abundance of arthropods is declining globally, and human-modification of natural habitat is a primary driver of these declines. Arthropod declines are concerning because arthropods mediate critical ecosystem functions, and sustained declines may lead to cascading trophic effects. There is growing evidence that properly managed urban environments can provide refugium to arthropods, but few cities have examined arthropods within urban greenspaces to evaluate their management efforts. In this study, we surveyed arthropod communities within a medium-sized, growing city. We investigated arthropod communities (abundance, richness, diversity, community composition) within 16 urban greenspaces across metropolitan Grand Rapids, Michigan (USA). We focused our efforts on urban gardens and pocket prairies, and measured environmental variables at each site. We collected 5,468 individual arthropods that spanned 14 taxonomic orders and 66 morphospecies. The results showed that community composition was influenced by impervious surface, white flower abundance, and humidity. Total arthropod abundance and diversity were positively associated with humidity. For specific orders, Hymenoptera (bees, ants, wasps) abundance was negatively associated with temperature, and positively associated with site perimeter-area ratio. Hemiptera (true bugs) were negatively associated with impervious surface and positively associated with humidity. These findings show that impervious surfaces impact arthropod communities, but many of the observed changes were driven by local abiotic conditions like temperature and humidity. This suggests that management decisions within urban greenspaces are important in determining the structure of arthropod communities. Future studies on arthropods in cities should determine whether manipulating the abiotic conditions of urban greenspaces influences the composition of arthropod communities. These results should inform city planners and homeowners of the need to properly manage urban greenspaces in cities to maintain diverse arthropod assemblages.
creator: Garrett M. Maher
creator: Graham A. Johnson
creator: Justin D. Burdine
uri: https://doi.org/10.7717/peerj.12818
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Maher et al.

title: Characterization of transcriptional landscape in bone marrow-derived mesenchymal stromal cells treated with aspirin by RNA-seq
link: https://peerj.com/articles/12819
last-modified: 2022-01-24
description: IntroductionAspirin is a common antipyretic, analgesic, and anti-inflammatory drug, which has been reported to extend life in animal models and application in the treatment of aging-related diseases. However, it remains unclear about the effects of aspirin on bone marrow-derived mesenchymal stromal cells (BM-MSCs). Here, we aimed to analyze the influence of aspirin on senescence and young BM-MSCs.MethodsBM-MSCs were serially passaged to construct a replicative senescence model. SA-β-gal staining, PCR, western blot, and RNA-sequencing were performed on BM-MSCs with or without aspirin treatment, to examine aspirin’s impact on bone marrow-derived mesenchymal stem cells.ResultsSA-β-gal staining, PCR, and western blot revealed that aspirin could alleviate the cellular expression of senescence-related indicators of BM-MSCs, including a decrease of SA-β-gal-positive cells and staining intensity, and downregulation of p16, p21, and p53 expression after aspirin treatment. RNA-sequencing results shown in the biological processes related to aging, aspirin could influence cellular immune response and lipid metabolism.ConclusionThe efficacy of aspirin for retarding senescence of BM-MSCs was demonstrated. Our study indicated that the mechanisms of this delay might involve influencing immune response and lipid metabolism.
creator: Xinpeng Liu
creator: Yuanbo Zhan
creator: Wenxia Xu
creator: Lixue Liu
creator: Xiaoyao Liu
creator: Junlong Da
creator: Kai Zhang
creator: Xinjian Zhang
creator: Jianqun Wang
creator: Ziqi Liu
creator: Han Jin
creator: Bin Zhang
creator: Ying Li
uri: https://doi.org/10.7717/peerj.12819
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Liu et al.

title: Retrogene survival is not impacted by linkage relationships
link: https://peerj.com/articles/12822
last-modified: 2022-01-24
description: In retrogene evolution, the out-of-the-X pattern is the retroduplication of X-linked housekeeping genes to autosomes, hypothesized to be driven by meiotic sex chromosome inactivation during spermatogenesis. This pattern suggests that some retrogene survival is driven by selection on X-linkage. We asked if selection on linkage constitutes an important evolutionary force in retrogene survival, including for autosomal parents. Specifically, is there a correlation between retrogene survival and changes in linkage with parental gene networks? To answer this question, we compiled data on retrogenes in both Homo sapiens and Drosophila melanogaster and using Monte Carlo methods, we tested whether retrogenes exhibit significantly different linkage relationships than expected under a null assumption of uniform distribution in the genome. Overall, after excluding genes involved in the out-of-the-X pattern, no general pattern was found associating genetic linkage and retrogene survival. This demonstrates that selection on linkage may not represent an overarching force in retrogene survival. However, it remains possible that this type of selection still influences the survival of specific retrogenes.
creator: Johnathan Lo
creator: Heath Blackmon
uri: https://doi.org/10.7717/peerj.12822
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Lo and Blackmon

title: Identification and validation of an epithelial mesenchymal transition-related gene pairs signature for prediction of overall survival in patients with skin cutaneous melanoma
link: https://peerj.com/articles/12646
last-modified: 2022-01-21
description: BackgroundWe aimed to construct a novel epithelial-mesenchymal transition (EMT)-related gene pairs (ERGPs) signature to predict overall survival (OS) in skin cutaneous melanoma (CM) patients.MethodsExpression data of the relevant genes, corresponding clinicopathological parameters, and follow-up data were obtained from The Cancer Genome Atlas database. Univariate Cox regression analysis was utilized to identify ERGPs significantly associated with OS, and LASSO analysis was used to identify the genes used for the construction of the ERGPs signature. The optimal cutoff value determined by the receiver operating characteristic curve was used to classify patients into high-risk and low-risk groups. Survival curves were generated using the Kaplan–Meier method, and differences between the two groups were estimated using the log-rank test. The independent external datasets GSE65904 and GSE19234 were used to verify the performance of the ERGPs signature using the area under the curve (AUC) values. In addition, we also integrated clinicopathological parameters and risk scores to develop a nomogram that can individually predict the prognosis of patients with CM.ResultsA total of 104 ERGPs related to OS were obtained, of which 21 ERGPs were selected for the construction of the signature. All CM patients were stratified into high-and low-risk groups based on an optimal risk score cutoff value of 0.281. According to the Kaplan–Meier analysis, the mortality rate in the low-risk group was lower than that in the high-risk group in the TCGA cohort (P < 0.001), GSE65904 cohort (P = 0.006), and GSE19234 cohort (P = 0.002). Multivariate Cox regression analysis indicated that our ERGP signature was an independent risk factor for OS in CM patients in the three cohorts (for TCGA: HR, 2.560; 95% CI [1.907–3.436]; P < 0.001; for GSE65904: HR = 2.235, 95% CI [1.492–3.347], P < 0.001; for GSE19234: HR = 2.458, 95% CI [1.065–5.669], P = 0.035). The AUC value for predicting the 5-year survival rate of patients with CM of our developed model was higher than that of two previously established prognostic signatures. Both the calibration curve and the C-index (0.752, 95% CI [0.678–0.826]) indicated that the developed nomogram was highly accurate. Most importantly, the decision curve analysis results showed that the nomogram had a higher net benefit than that of the American Joint Committee on Cancer stage system.ConclusionOur study established an ERGPs signature that could be potentially used in a clinical setting as a genetic biomarker for risk stratification of CM patients. In addition, the ERGPs signature could also predict which CM patients will benefit from PD-1 and PD-L1 inhibitors.
creator: Yucang Shi
creator: Zhanpeng Li
creator: Zhihong Zhou
creator: Simu Liao
creator: Zhiyuan Wu
creator: Jie Li
creator: Jiasheng Yin
creator: Meng Wang
creator: Meilan Weng
uri: https://doi.org/10.7717/peerj.12646
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Shi et al.

title: Antimicrobial peptides properties beyond growth inhibition and bacterial killing
link: https://peerj.com/articles/12667
last-modified: 2022-01-21
description: Antimicrobial peptides (AMPs) are versatile molecules with broad antimicrobial activity produced by representatives of the three domains of life. Also, there are derivatives of AMPs and artificial short peptides that can inhibit microbial growth. Beyond killing microbes, AMPs at grow sub-inhibitory concentrations also exhibit anti-virulence activity against critical pathogenic bacteria, including ESKAPE pathogens. Anti-virulence therapies are an alternative to antibiotics since they do not directly affect viability and growth, and they are considered less likely to generate resistance. Bacterial biofilms significantly increase antibiotic resistance and are linked to establishing chronic infections. Various AMPs can kill biofilm cells and eradicate infections in animal models. However, some can inhibit biofilm formation and promote dispersal at sub-growth inhibitory concentrations. These examples are discussed here, along with those of peptides that inhibit the expression of traits controlled by quorum sensing, such as the production of exoproteases, phenazines, surfactants, toxins, among others. In addition, specific targets that are determinants of virulence include secretion systems (type II, III, and VI) responsible for releasing effector proteins toxic to eukaryotic cells. This review summarizes the current knowledge on the anti-virulence properties of AMPs and the future directions of their research.
creator: Israel Castillo-Juárez
creator: Blanca Esther Blancas-Luciano
creator: Rodolfo García-Contreras
creator: Ana María Fernández-Presas
uri: https://doi.org/10.7717/peerj.12667
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Castillo-Juárez et al.

title: Chondrochelia Guţu, 2016 (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) from North America: new species, redescription and distribution using morphological and molecular data
link: https://peerj.com/articles/12773
last-modified: 2022-01-21
description: Until now, four species of the genus ChondrocheliaGuţu, 2016 have been recorded from America. Using morphological and molecular data, we were able to recognize and describe two new species, Chondrochelia caribensis sp. nov. from the Mexican Caribbean and Chondrochelia winfieldi sp. nov. from the Gulf of Mexico. We found significant genetic divergence values between species based on the nucleotide sequences of cytochrome oxidase subunit I to support the morphological data. Also, the range of distribution of two species: Chondrochelia mexicana (Jarquín-González, García-Madrigal & Carrera-Parra, 2015) and Chondrochelia ortizi (Jarquín-González, 2016), were expanded within their described geographic regions. In contrast, the supposed distribution of the Brazilian C. dubia in the Mexican Caribbean and the Gulf of Mexico was rejected. Additionally, Chondrochelia algicola (Harger, 1878) was redescribed based upon type material. Minute details and ornamentation of some structures of three species were examined using SEM.
creator: Jani Jarquín-González
creator: Luis F. Carrera-Parra
uri: https://doi.org/10.7717/peerj.12773
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Jarquín-González and Carrera-Parra

title: Measuring mass: variation among 3,161 species of Canadian Coleoptera and the prospects of a mass registry for all insects
link: https://peerj.com/articles/12799
last-modified: 2022-01-21
description: Although biomass values are critical for diverse ecological and evolutionary analyses, they are unavailable for most insect species. Museum specimens have the potential to address this gap, but the variation introduced by sampling and preservation methods is uncertain. This study quantifies species-level variation in the body mass of Canadian Coleoptera based on the analysis of 3,744 specimens representing 3,161 Barcode Index Number (BIN) clusters. Employing the BIN system as a proxy for species allows the inclusion of groups where the taxonomic impediment prevents the assignment of specimens to a Linnaean species. By validating the reproducibility of measurements and evaluating the error introduced by operational complexities such as curatorial practice and the loss of body parts, this study demonstrates that museum specimens can speed the assembly of a mass registry. The results further indicate that congeneric species of Coleoptera generally have limited variation in mass, so a genus-level identification allows prediction of the body mass of species that have not been weighed or measured. Building on the present results, the construction of a mass registry for all insects is feasible.
creator: Jingchan Hu
creator: Mikko Pentinsaari
creator: Paul D.N. Hebert
uri: https://doi.org/10.7717/peerj.12799
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Hu et al.

title: Effectiveness of interactive teaching intervention on medical students’ knowledge and attitudes toward stem cells, their therapeutic uses, and potential research applications
link: https://peerj.com/articles/12824
last-modified: 2022-01-21
description: BackgroundStem cell science is rapidly developing with the potential to alleviate many non-treatable diseases. Medical students, as future physicians, should be equipped with the proper knowledge and attitude regarding this hopeful field. Interactive teaching, whereby the teachers actively involve the students in the learning process, is a promising approach to improve their interest, knowledge, and team spirit. This study aims to evaluate the effectiveness of an interactive teaching intervention on medical students’ knowledge and attitudes about stem cell research and therapy.MethodsA pre-post test study design was employed. A six-session interactive teaching course was conducted for a duration of six weeks as an intervention. Pre- and post-intervention surveys were used. The differences in the mean scores of students’ knowledge and attitudes were examined using paired t-test, while gender differences were examined using an independent t-test.ResultsOut of 71 sixth-year medical students from different nationalities invited to participate in this study, the interactive teaching course was initiated by 58 students resulting in a participation rate of 81.7%. Out of 58 students, 48 (82.8%) completed the entire course. The mean age (standard deviation) of students was 24 (1.2) years, and 32 (66.7%) were males. The results showed poor knowledge about stem cells among the medical students in the pre-intervention phase. Total scores of stem cell-related knowledge and attitudes significantly improved post-intervention. Gender differences in knowledge and attitudes scores were not statistically significant post-intervention.ConclusionsIntegrating stem cell science into medical curricula coupled with interactive learning approaches effectively increased students’ knowledge about recent advances in stem cell research and therapy and improved attitudes toward stem cell research and applications.
creator: Fayez Abdulrazeq
creator: Khalid A. Kheirallah
creator: Abdel-Hameed Al-Mistarehi
creator: Samir Al Bashir
creator: Mohammad A. ALQudah
creator: Abdallah Alzoubi
creator: Jomana Alsulaiman
creator: Mazhar S. Al Zoubi
creator: Abdulwahab Al-Maamari
uri: https://doi.org/10.7717/peerj.12824
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Abdulrazeq et al.

title: Genome-wide identification and expression analysis of the VQ gene family in Cucurbita pepo L.
link: https://peerj.com/articles/12827
last-modified: 2022-01-21
description: VQ protein is a plant specific protein, which plays an important role in plant growth and development and biological and abiotic stress response. This study aimed to systematically analyze for the first time the VQ of Cucurbita pepo and understand their expression patterns in response to different stimuli. Herein, 44 VQ genes were identified, which were divided into eight groups (I–VIII) based on phylogenetic analysis. Two genes (CpVQ1 and CpVQ2) could not be located on the chromosome, whereas the remaining CpVQ genes were randomly distributed on the chromosomes, except for chromosomes 15 and 18. Noteworthy, the main event driving the expansion of the VQ gene family was chromosome fragment duplication. Based on qRT-PCR analysis, VQ genes are expressed in different tissues, and VQ genes are differentially regulated under a variety of abiotic stresses and powdery mildew stress, indicating that they play an important role in plant stress response and other aspects. This report presents the first systematic analysis of VQ genes from C. pepo and provides a solid foundation for further research of the specific functions of VQ proteins.
creator: Ke Xu
creator: Ping Wang
uri: https://doi.org/10.7717/peerj.12827
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Xu and Wang

title: Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo
link: https://peerj.com/articles/12637
last-modified: 2022-01-20
description: Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.
creator: Aïcha Edith Soara
creator: Essodina Talaki
creator: Guiguigbaza-Kossigan Dayo
creator: Isidore Houaga
creator: Kokou Tona
creator: Mohammed Bakkali
uri: https://doi.org/10.7717/peerj.12637
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Soara et al.

title: Galapagos land iguanas as ecosystem engineers
link: https://peerj.com/articles/12711
last-modified: 2022-01-20
description: BackgroundDeclines of large-bodied herbivorous reptiles are well documented, but the consequences for ecosystem function are not. Understanding how large-bodied herbivorous reptiles engineer ecosystems is relevant given the current interest in restoration of tropical islands where extinction rates are disproportionately high and reptiles are prominent as herbivores.MethodsIn this study, we measured the ecosystem-level outcomes of long-term quasi-experiment represented by two adjacent islands within the Galapagos Archipelago, one with and the other without Galapagos land iguanas (Conolophus subcristatus), large-bodied herbivores known to feed on many plant species. We characterized plant communities on each island by developing high-resolution (<1 cm2) aerial imagery and delineating extent of plant associations and counting individual plants on each.ResultsIn the presence of iguanas there was dramatically less woody plant cover, more area with seasonal grasses, and many fewer cacti. Cacti had a more clumped distribution where iguanas were absent than where iguanas were present.DiscussionThis study provided strong evidence that Galapagos land iguanas can substantially engineer the structure of terrestrial plant communities; therefore, restoration of large-bodied reptilian herbivores, such as land iguanas and giant tortoises, should be regarded as an important component of overall ecosystem restoration, especially for tropical islands from which they have been extirpated.
creator: Washington Tapia
creator: James P. Gibbs
uri: https://doi.org/10.7717/peerj.12711
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Tapia and Gibbs

title: Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems
link: https://peerj.com/articles/12785
last-modified: 2022-01-20
description: Ecosystem Design (ED) is an approach for constructing habitats that places human needs for ecosystem services at the center of intervention, with the overarching goal of establishing self-sustaining habitats which require limited management. This concept was originally developed for use in mangrove ecosystems, and is understandably controversial, as it markedly diverges from other protection approaches that assign human use a minor priority or exclude it. However, the advantage of ED lies within the considered implementation of these designed ecosystems, thus preserving human benefits from potential later disturbances. Here, we outline the concept of ED in tropical carbonate depositional systems and discuss potential applications to aid ecosystem services such as beach nourishment and protection of coastlines and reef islands at risk from environmental and climate change, CO2 sequestration, food production, and tourism. Biological carbonate sediment production is a crucial source of stability of reef islands and reef-rimmed coastlines. Careful implementation of designed carbonate depositional ecosystems could help counterbalance sea-level rise and manage documented erosion effects of coastal constructions. Importantly, adhering to the core ethos of ED, careful dynamic assessments which provide a balanced approach to maximizing ecosystem services (e.g., carbonate production), should identify and avoid any potential damages to existing functioning ecosystems.
creator: Hildegard Westphal
creator: Gary N. Murphy
creator: Steve S. Doo
creator: Thomas Mann
creator: Alexander Petrovic
creator: Christiane Schmidt
creator: Marleen Stuhr
uri: https://doi.org/10.7717/peerj.12785
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Westphal et al.

title: Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?
link: https://peerj.com/articles/12794
last-modified: 2022-01-20
description: As linear mixed-effects models (LMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of the grouping variable associated with a random effect. Having so few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one’s ability to estimate fixed effects terms—which are often of primary interest in ecology. Here, I simulate datasets and fit simple models to show that having few random effects levels does not strongly influence the parameter estimates or uncertainty around those estimates for fixed effects terms—at least in the case presented here. Instead, the coverage probability of fixed effects estimates is sample size dependent. LMMs including low-level random effects terms may come at the expense of increased singular fits, but this did not appear to influence coverage probability or RMSE, except in low sample size (N = 30) scenarios. Thus, it may be acceptable to use fewer than five levels of random effects if one is not interested in making inferences about the random effects terms (i.e. when they are ‘nuisance’ parameters used to group non-independent data), but further work is needed to explore alternative scenarios. Given the widespread accessibility of LMMs in ecology and evolution, future simulation studies and further assessments of these statistical methods are necessary to understand the consequences both of violating and of routinely following simple guidelines.
creator: Dylan G.E. Gomes
uri: https://doi.org/10.7717/peerj.12794
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Gomes

title: Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean
link: https://peerj.com/articles/12815
last-modified: 2022-01-20
description: BackgroundStrigolactones (SLs) play a key role in modulating plant root growth, shoot branching, and plant-symbiont interaction. However, despite their significance, the components of SL biosynthesis and signaling in soybean and their role in soybean-rhizobia interaction is unknown.MethodsIn this study, we identified and functionally characterized the GmD53a from soybean. The GmD53a ORFs were amplified from root cDNA using primers for GmD53a RNA interference. To induce transgenic hairy roots of soybean, electric shock was used to transform pB7WG1WG2 vectors containing GmD53a knockdown and GUS into K599 strains of Agrobacterium rhizogenes. The hairy roots and nodules were collected and examined for root nodules ratio and RNA was extracted after 4 weeks of rhizobia inoculation.ResultsA tissue-specific expression assay showed that GmD53a was differentially expressed in plant parts, predominantly in the stem and nodule. Furthermore, its expression was significantly up-regulated during rhizobia infection and varied with nodule formation. The GmD53a-knockdown chimerical plants were produced to further check its role in soybean nodulation in comparison with control GUS. In knockdown lines, the GmD53a (suppressor of strigolactone MAX2) has a higher number of nodules compared to control lines. Furthermore, the expression levels of several nodulation genes essential for initiation and formation of nodules were altered in GmD53a-knockdown lines.ConclusionThe results revealed that SL biosynthesis and signaling are not conserved but also have close interaction between SL and legume rhizobia.
creator: Naveed Rehman
creator: Fahim Ullah Khan
creator: Muhammad Imran
creator: Shahid Ali Rajput
creator: Yiming Li
creator: Ihteram Ullah
creator: Rana waseem Akhtar
creator: Muhammad Imran
creator: Arwa Abdulkreem AL-Huqail
creator: Ahmad El Askary
creator: Amany Salah Khalifa
creator: Muhammad Tehseen Azhar
uri: https://doi.org/10.7717/peerj.12815
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Rehman et al.

title: Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants
link: https://peerj.com/articles/12828
last-modified: 2022-01-20
description: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
creator: Jiang-Ping Shu
creator: Yue-Hong Yan
creator: Rui-Jiang Wang
uri: https://doi.org/10.7717/peerj.12828
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Shu et al.

title: Fast, low-memory detection and localization of large, polymorphic inversions from SNPs
link: https://peerj.com/articles/12831
last-modified: 2022-01-20
description: BackgroundLarge (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed.MethodsWe propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time.ResultsWhen evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks.ConclusionWith these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
creator: Ronald J. Nowling
creator: Fabian Fallas-Moya
creator: Amir Sadovnik
creator: Scott Emrich
creator: Matthew Aleck
creator: Daniel Leskiewicz
creator: John G. Peters
uri: https://doi.org/10.7717/peerj.12831
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Nowling et al.

title: Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills
link: https://peerj.com/articles/12836
last-modified: 2022-01-20
description: BackgroundAttention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder affecting numerous executive functioning skills, such as organizational skills. While the relationship between the inattention aspect of ADHD and poor organizational skills is well documented, it is still unclear if lower organizational skills are only associated with ADHD or if they are also associated with other comorbid disorders commonly diagnosed in conjunction with ADHD. The purpose of the present study is to investigate the relationship between organizational skills and ADHD in adults, as well as the impact of comorbid disorders on ADHD in relation to organizational skills.MethodsFour hundred seven (n = 201 with a diagnosis of ADHD) adults from the general population were recruited online. Participants completed a measure of organizational skills, measures assessing levels of ADHD, depression, and anxiety, and extensive demographic information related to their diagnosis of ADHD or other possible diagnosis.ResultsParticipants with a diagnosis of ADHD were significantly more likely to have a comorbid diagnosis of depression and/or anxiety. Organizational skills were significantly lower in individuals who reported having received a diagnosis of ADHD, but not in those with a past diagnosis of depression and anxiety. However, organizational skills were lower in individuals currently experiencing higher levels of depression and anxiety. The results of regression analyses suggest that levels of organizational skills are most strongly predicted by inattention and more weakly predicted by comorbid disorders.DiscussionThese results highlight the centrality of organizational skills deficit in ADHD as well as the influence of the inattention component over other components commonly observed in ADHD on organizational skills. Suggestions for treatment of ADHD in adults are discussed.
creator: Guillaume Durand
creator: Ioana-Smarandita Arbone
uri: https://doi.org/10.7717/peerj.12836
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Durand and Arbone

title: Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups
link: https://peerj.com/articles/12721
last-modified: 2022-01-19
description: Fire and herbivores are two important drivers of changes in vegetation composition, quality and dynamics and both are highly related to each other. Herbivores are known to respond to fire both in terms of foraging decisions and distribution. However, little is known about the actual changes in plant chemistry following a fire event and how long these changes will last. We investigated the effect of fire on two different plant functional groups (grasses and woody species) in a woodland savanna of southern Africa. We studied chemical compounds known to be important for palatability of five perennial grass and seven woody species (trees and shrubs) common in the woodland savanna and known to be utilized by herbivores. We wanted to know if plant chemistry differs between a recently burned site (burned 2 years ago) and a control site, burned 16 years ago, and if grasses and woody species show similar relative differences between sites (i.e., the plants’ response to fire). We found a clear difference in chemical composition patterns between the plant functional groups, with an almost homogenous response to fire among woody species, but higher variability in response among grass species. Furthermore, we found that woody species maintained a higher nutritional value even 2 years after burning, whereas grasses did not show clear differences among the two investigated sites. Hence, few years after burning, woody plants might still serve as an attraction for herbivores, especially browsers, in contrast to grasses. The knowledge about these differences between the two functional groups in response to fire is beneficial for the development of management strategies for large herbivores whether domestic or wild.
creator: Caroline Stolter
creator: David F. Joubert
creator: Nekulilo Uunona
creator: Elise Nghalipo
creator: Vistorina Amputu
creator: Annika M. Felton
uri: https://doi.org/10.7717/peerj.12721
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Stolter et al.

title: Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods
link: https://peerj.com/articles/12589
last-modified: 2022-01-19
description: BackgroundMany coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific.MethodsMethods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health.ResultsThere were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
creator: Sohyoung Kim
creator: Christian Wild
creator: Arjen Tilstra
uri: https://doi.org/10.7717/peerj.12589
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Kim et al.

title: A novel nutritional index as a predictor of mortality in dilated cardiomyopathy: a retrospective study
link: https://peerj.com/articles/12704
last-modified: 2022-01-19
description: BackgroundResearch has associated nutritional status with the prognosis of cardiovascular diseases. This study aimed to investigate the prognostic value of a novel nutritional index, triglycerides × total cholesterol × body weight index (TCBI), in patients with dilated cardiomyopathy (DCM).MethodsThis retrospective cohort study enrolled 445 patients with DCM. The median follow-up period was 2.8 years, and the primary endpoint was all-cause death.ResultsDuring follow-up, the all-cause mortality was observed in 135 out of 445 patients (30.3%). In Kaplan–Meier survival analysis, the third TCBI tertile had a lower mortality risk (T3 vs. T2 vs. T1: 16.9% vs. 35.1% vs. 38.9%; log-rank P < 0.001). In the multivariable Cox regression analysis, patients in the third tertile were associated with a decreased mortality, whereas there was no significant difference between the T2 and T1 groups. Moreover, TCBI could significantly improve risk stratification (continuous net reclassification improvement and integrated discrimination improvement) over the Geriatric Nutritional Risk Index (GNRI) and N-terminal pro-brain natriuretic peptide (NT-proBNP).ConclusionsTCBI is independently associated with long-term survival in patients with DCM. Combination of TCBI and other biomarkers, such as GNRI and NT-proBNP, can significantly improve prognostic prediction. Further studies with larger sample size are required to validate our results.
creator: Can Wang
creator: Yali Qing
creator: Wuxian Chen
creator: Gaoye Li
uri: https://doi.org/10.7717/peerj.12704
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Plasma FGF21 concentrations are regulated by glucose independently of insulin and GLP-1 in lean, healthy humans
link: https://peerj.com/articles/12755
last-modified: 2022-01-19
description: BackgroundFibroblast growth factor 21 (FGF21) treatment improves metabolic homeostasis in diverse species, including humans. Physiologically, plasma FGF21 levels increase modestly after glucose ingestion, but it is unclear whether this is mediated by glucose itself or due to a secondary effect of postprandial endocrine responses. A refined understanding of the mechanisms that control FGF21 release in humans may accelerate the development of small-molecule FGF21 secretagogues to treat metabolic disease. This study aimed to determine whether FGF21 secretion is stimulated by elevations in plasma glucose, insulin, or glucagon-like peptide-1 (GLP-1) in humans.MethodsThree groups of ten healthy participants were included in a parallel-group observational study. Group A underwent a hyperglycemic infusion; Group B underwent a 40 mU/m2/min hyperinsulinemic euglycemic clamp; Group C underwent two pancreatic clamps (to suppress endogenous insulin secretion) with euglycemic and hyperglycemic stages with an infusion of either saline or 0.5 pmol/kg/min GLP-1. Plasma FGF21 concentrations were measured at baseline and during each clamp stage by ELISA.ResultsPlasma FGF21 was unaltered during hyperglycemic infusion and hyperinsulinemic euglycemic clamps, compared to baseline. FGF21 was, however, increased by hyperglycemia under pancreatic clamp conditions (P < 0.05), while GLP-1 infusion under pancreatic clamp conditions did not change circulating FGF21 levels.ConclusionIncreases in plasma FGF21 are likely driven directly by changes in plasma glucose independent of changes in insulin or GLP-1 secretion. Ecologically valid postprandial investigations are now needed to confirm our observations from basic science infusion models.
creator: Thomas P.J. Solomon
creator: Steven Carter
creator: Jacob M. Haus
creator: Kristian Karstoft
creator: Stephanie von Holstein-Rathlou
creator: Mette S. Nielsen
creator: Matthew P. Gillum
uri: https://doi.org/10.7717/peerj.12755
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Solomon et al.

title: DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
link: https://peerj.com/articles/12758
last-modified: 2022-01-19
description: DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
creator: Adrià Antich
creator: Creu Palacín
creator: Xavier Turon
creator: Owen S. Wangensteen
uri: https://doi.org/10.7717/peerj.12758
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Antich et al.

title: Optimized nitrogen rate, plant density, and irrigation level reduced ammonia emission and nitrate leaching on maize farmland in the oasis area of China
link: https://peerj.com/articles/12762
last-modified: 2022-01-19
description: Nitrogen fertilizers play a key role in crop production to meet global food demand. Inappropriate application of nitrogen fertilizer coupled with poor irrigation and other crop management practices threaten agriculture and environmental sustainability. Over application of nitrogen fertilizer increases nitrogen gas emission and nitrate leaching. A field experiment was conducted in China’s oasis irrigation area in 2018 and 2019 to determine which nitrogen rate, plant density, and irrigation level in sole maize (Zea mays L.) cropping system reduce ammonia emission and nitrate leaching. Three nitrogen rates of urea (46-0-0 of N-P2O5-K2O), at (N0 = 0 kg N ha−1, N1 = 270 kg N ha−1, and N2 = 360 kg N ha−1) were combined with three plant densities (D1 = 75,000 plants/ha−1, D2 = 97,500 plants/ha−1, and D3 = 120,000 plants/ha−1) with two irrigation levels (W1 = 5,250 m3/hm2 and W2 = 4,740 m3/hm2) using a randomized complete block design. The results showed that, both the main and interaction effects of nitrogen rate, plant density, and irrigation level reduced nitrate leaching (p < 0.05). In addition, irrigation level × nitrogen rate significantly (p < 0.05) reduced ammonia emission. Nitrate leaching and ammonia emission decreased with higher irrigation level and higher plant density. However, high nitrogen rates increased both nitrate leaching and ammonia emission. The study found lowest leaching (0.35 mg kg−1) occurring at the interaction of 270 kg N ha−1 × 120,000 plants/ha−1 × 4,740 m3/hm2, and higher plant density of 120,000 plants/ha−1 combined with 0 kg N ha−1 and irrigation level of 5,250 m3/hm2 recorded the lowest ammonia emission (0.001 kg N)−1. Overall, ammonia emission increased as days after planting increased while nitrate leaching decreased in deeper soil depths. These findings show that, though the contributory roles of days after planting, soil depth, amount of nitrogen fertilizer applied and year of cultivation cannot be undermined, it is possible to reduce nitrate leaching and ammonia emission through optimized nitrogen rate, plant density and regulated irrigation for agricultural and environmental sustainability.
creator: Aziiba Emmanuel Asibi
creator: Wen Yin
creator: Falong Hu
creator: Zhilong Fan
creator: Zhiwen Gou
creator: Hongwei Yang
creator: Yao Guo
creator: Qiang Chai
uri: https://doi.org/10.7717/peerj.12762
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Asibi et al.

title: Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection
link: https://peerj.com/articles/12767
last-modified: 2022-01-19
description: BackgroundIn Japan, routine two-dose immunization against varicella has been conducted among children at ages of 12 and 36 months since 2014, and the vaccination coverage has reached around 90%. To understand the impact of routine varicella vaccination, we reconstructed the epidemiological dynamics of varicella in Japan.MethodsEpidemiological and demographic datasets over the past three decades were analyzed to reconstruct the number of susceptible individuals by age and year. To estimate the annual risk of varicella infection, we fitted a balance equation model to the annual number of cases from 1990 to 2019. Using parameter estimates, we reconstructed varicella dynamics starting from 1990 and modeled future dynamics until 2033.ResultsOverall varicella incidence declined over time and the annual risk of infection among children younger than 10 years old decreased monotonically starting in 2014. Conversely, varicella incidence among teenagers (age 10 to 14 years) has increased each year since 2014. A substantial number of unvaccinated individuals born before the routine immunization era remained susceptible and aged without contracting varicella, while the annual risk of infection among teenagers aged 10 to 14 years increased starting in 2011 despite gradual expansion of varicella vaccine coverage. The number of susceptible individuals decreased over time in all age groups. Modeling indicated that susceptibility rates among pre-school children aged 1 to 4 years will remain low.ConclusionRoutine varicella vaccination has successfully reduced infections in pre-school and early primary school age children, but has also resulted in increased infection rates among adolescents. This temporary increase was caused both by the increased age of susceptible individuals and increased transmission risk among adolescents resulting from the dynamic nature of varicella transmission. Monitoring susceptibility among adolescents will be important to prevent outbreaks over the next decade.
creator: Ayako Suzuki
creator: Hiroshi Nishiura
uri: https://doi.org/10.7717/peerj.12767
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Suzuki and Nishiura

title: The value of diffusion weighted imaging-alberta stroke program early CT score in predicting stroke-associated pneumonia in patients with acute cerebral infarction: a retrospective study
link: https://peerj.com/articles/12789
last-modified: 2022-01-19
description: BackgroundIn this study, we aimed to investigate the value of Diffusion-Weighted Imaging-Alberta Stroke Program Early CT Score (DWI-ASPECTS) in predicting stroke-associated pneumonia (SAP) in patients with acute ischemic stroke.MethodsA total of 291 patients who suffered acute cerebral infarction for the first time were included in this retrospective study. DWI-ASPECTS was assessed and clinical data were collected in order to find the risk factors of SAP, and a logistic regression model was used to investigate the effect of predicting SAP. Furthermore, correlation analysis was used to explore the relationship between DWI-ASPECTS and the immume status of the body.ResultsAmong the 291 patients, 74 (25.4%) subjects were diagnosed with SAP. Compared with non-SAP, the patients with SAP were older and had a higher rate of atrial fibrillation (AF), National Institutes of Health Stroke Scale (NIHSS) scores. The SAP group also had a significantly lower DWI-ASPECTS than did the non-SAP group (P < 0.01). In the multivariable logistic regression analysis, the DWI-ASPECTS (adjusted odds ratio [aOR] = 1.438; 95% CI [1.158–1.787]; P < 0.01) remained significant after adjusting for confounders. What’s more, the predictive ability of DWI-ASPECTS (AUC = 0.743 >0.7, 95% CI [0.678–0.800]) had acceptable discriminatory abilities. By the correlation analysis, DWI-ASPECTS was found to be negatively correlated with the count of white blood cell, neutrophils, monocytes, neutrophil-to-monocyte ratio and neutrophil-to-lymphocyte ratio, and positively correlated with the count of lymphocytes.ConclusionsDWI-ASPECTS grades could predict stroke-associated pneumonia for patients with acute ischemic stroke, and combining grade with age, AF, or NIHSS could predict SAP events more accurately.
creator: Dong Zhao
creator: Jing Zhu
creator: Qiang Cai
creator: Feifei Zeng
creator: Xiujuan Fu
creator: Ke Hu
uri: https://doi.org/10.7717/peerj.12789
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhao et al.

title: Biological effects of gamma-ray radiation on tulip (Tulipa gesneriana L.)
link: https://peerj.com/articles/12792
last-modified: 2022-01-19
description: Tulip, being an important ornamental plant, generally requires lengthy and laborious procedures to develop new varieties using traditional breeding methods requires. But ionizing radiation potentially accelerates the breeding process of ornamental plant species. The biological effects of γ-ray irradiation on tulip, therefore, were investigated through establishing an irradiation-mediated mutation breeding protocol to accelerate its breeding process. ISSR-PCR molecular marker technique was further used to identify the mutants of phenotypic variation plants. This study showed that low irradiation doses (5 Gy) stimulated bulb germination to improve the survival rate of tulip, while high irradiation doses (20 to 100 Gy) significantly (P < 0.05) inhibited its seed germination and growth, and decreased the flowering rate, petal number, flower stem length and flower diameter. More than 40 Gy significantly (P < 0.05) decreased the total chlorophyll content and increased the malondialdehyde (MDA) content in tulips. Interestingly, three types of both stigma variations and flower pattern variations, and four types of flower colour variations were observed. With increasing the irradiation dose from 5 to 100 Gy, the anthocyanin and flavonoid contents continuously decreased. Scanning electron microscopy (SEM) analysis evidenced that high irradiation doses altered the micromorphology of leaf stomata. Microscopic observations of tulip root apical mitosis further showed the abnormal chromosomal division behaviour occurring at different mitotic phases under irradiation treatment (80 Gy). Increasing the irradiation dose from 20 to 100 Gy enhanced the micronucleus rate. Moreover, the suspected genetic variation in tulips was evaluated by inter-simple sequence repeat (ISSR) analysis, and the percentage of polymorphic bands was 68%. Finally, this study concludes that that 80 Gy may be an appropriate radiation does to better enhance the efficiency of mutagenic breeds in tulip plants. Using γ-ray irradiation, therefore, is expected to offer a theoretical basis for mutation breeding in tulips.
creator: Yirui Li
creator: Li Chen
creator: Xiaodie Zhan
creator: Liang Liu
creator: Feihong Feng
creator: Zihua Guo
creator: Dan Wang
creator: Hao Chen
uri: https://doi.org/10.7717/peerj.12792
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Li et al.

title: Prokaryotic expression, purification and evaluation of anti-cardiac fibrosis activity of recombinant TGF-β latency associated peptide
link: https://peerj.com/articles/12797
last-modified: 2022-01-19
description: BackgroundCardiac fibrosis refers to the abnormal accumulation of extracellular matrix in the heart, which leads to the formation of cardiac scars. It causes systolic and diastolic dysfunction, and ultimately leads to cardiac dysfunction and arrhythmia. TGF-β1 is an important regulatory factor involved in cardiac fibrosis. Studies have shown that the N-terminal latency associated peptide (LAP) must be removed before TGF-β1 is activated. We hypothesize that recombinant LAP may inhibit cardiac fibrosis induced by TGF-β1. To evaluate anti-cardiac fibrosis activity of recombinant LAP, an experimental study was carried out and is reported here.MethodsThe pET28a-LAP plasmid was constructed and transformed into E. coli C43 (DE3) competent cells. The recombinant LAP protein was purified by Ni affinity chromatography. The cells were treated with TGF-β1 at different concentrations for 24 h. The expression of α-SMA was detected by Western blot. RTCA was used to detect the effect of recombinant LAP on the proliferation of H9C2 cells induced by 10 ng/mL TGF-β1. To detect the effect of LAP on the expression of fibrosis-related proteins, H9C2 cells were treated with 10 ng/mL TGF-β1 for 24 h, then added 60 μg/mL recombinant LAP for 48 h. The LAP group was treated with 60 μg/mL recombinant LAP alone. The LAP pre-protection group was treated with 10 ng/mL TGF-β1 and 60 μg/mL recombinant LAP at the same time. Western blot and immunofluorescence were used to detect the expression of α-SMA, collagen I and fibronectin and p-Smad2.ResultsThe recombinant LAP was prokaryotic expressed and purified. 10 ng/mL was determined as the optimal working concentration of TGF-β1 to induce H9C2 cells fibrosis. RTCA results showed that 60 μg/mL LAP could effectively inhibit the proliferation of H9C2 cells induced by TGF-β1. Immunofluorescence results showed that compared with the control group, the fluorescence intensities of α-SMA, collagen I and FN increased significantly after TGF-β1 treatment. The fluorescence intensities in the TGF-β1+LAP group decreased significantly. Western blot results showed that 60 μg/mL LAP could inhibit the increase of α-SMA, collagen I and FN expression in H9C2 cells induced by TGF-β1. Compared with the control, the LAP alone group has no significant difference in α-SMA and p-Smad2 expression level. The expression of α-SMA and p-Smad2 in the TGF-β1 model group was significantly increased compared with the control group. Compared with the TGF-β1 group, both TGF-β1+LAP group and LAP pre-protection group significantly reduced the increase in α-SMA and p-Smad2 levels.ConclusionsRecombinant LAP was prokaryotic expressed and purified. The results showed that recombinant LAP can inhibit the cell proliferation and expression increase of α-SMA, collagen I, fibronectin and p-Smad2 in H9C2 cells induced by TGF-β1. These results suggested that recombinant LAP might inhibit TGF-β1-induced fibrosis of H9C2 cells through the TGF-β/Smad pathway.
creator: Xudong Song
creator: Yufei Qiu
creator: Jiayi Shi
creator: Luxin Li
creator: Xiaohuan Yuan
creator: Dan Wu
creator: Yanhui Chu
uri: https://doi.org/10.7717/peerj.12797
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Song et al.

title: Segmentation of multi-temporal polarimetric SAR data based on mean-shift and spectral graph partitioning
link: https://peerj.com/articles/12805
last-modified: 2022-01-19
description: AbstractPolarimetric SAR (PolSAR) image segmentation is a key step in its interpretation. For the targets with time series changes, the single-temporal PolSAR image segmentation algorithm is difficult to provide correct segmentation results for its target recognition, time series analysis and other applications. For this, a new algorithm for multi-temporal PolSAR image segmentation is proposed in this paper. Firstly, the over-segmentation of single-temporal PolSAR images is carried out by the mean-shift algorithm, and the over-segmentation results of single-temporal PolSAR are combined to get the over-segmentation results of multi-temporal PolSAR images. Secondly, the edge detectors are constructed to extract the edge information of single-temporal PolSAR images and fuse them to get the edge fusion results of multi-temporal PolSAR images. Then, the similarity measurement matrix is constructed based on the over-segmentation results and edge fusion results of multi-temporal PolSAR images. Finally, the normalized cut criterion is used to complete the segmentation of multi-temporal PolSAR images. The performance of the proposed algorithm is verified based on three temporal PolSAR images of Radarsat-2, and compared with the segmentation algorithm of single-temporal PolSAR image. Experimental results revealed the following findings: (1) The proposed algorithm effectively realizes the segmentation of multi-temporal PolSAR images, and achieves ideal segmentation results. Moreover, the segmentation details are excellent, and the region consistency is good. The objects which can’t be distinguished by the single-temporal PolSAR image segmentation algorithm can be segmented. (2) The segmentation accuracy of the proposed multi-temporal algorithm is up to 86.5%, which is significantly higher than that of the single-temporal PolSAR image segmentation algorithm. In general, the segmentation result of proposed algorithm is closer to the optimal segmentation. The optimal segmentation of farmland parcel objects to meet the needs of agricultural production is realized. This lays a good foundation for the further interpretation of multi-temporal PolSAR image.
creator: Caiqiong Wang
creator: Lei Zhao
creator: Wangfei Zhang
creator: Xiyun Mu
creator: Shitao Li
uri: https://doi.org/10.7717/peerj.12805
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wang et al.

title: High fitness areas drive the aggregation of the sea urchin Mesocentrotus nudus
link: https://peerj.com/articles/12820
last-modified: 2022-01-19
description: Sea urchin aggregation is a common phenomenon in coastlines. However, it remains controversial whether sea urchins form resource aggregations or behavioral aggregations in a non-spawning season. To clarify, we studied the aggregative responses to food and predators in the sea urchin Mesocentrotus nudus when high fitness areas (HFAs) were scarce versus sufficient. By taking the occupied area of each sea urchin (test diameter + spines =  4.5 cm) as a square (4.5 cm × 4.5 cm), we set scarce HFAs for the sea urchins in Experiment 1 (the squares of HFAs: the area occupied by experimental sea urchins = 1:1) and sufficient HFAs for the sea urchins in Experiment 2 (the squares of HFAs: the area occupied by experimental sea urchins = 2:1). If M. nudus form resource aggregations, they would aggregate passively under the scarce HFAs conditions, but not in the sufficient HFAs conditions. Conversely, if M. nudus form behavioral aggregation, aggregation would occur in both scarce and sufficient HFAs. The present results showed that in the scarce HFAs, M. nudus in the food and predator groups were significantly closer to the food and further from predators, and had significantly more aggregated numbers in HFAs than those in the control group. Sea urchins did not aggregate in response to food or predators under the sufficient HFAs, although significantly more sea urchins of the experimental group was found in HFAs than that of the control group. Sea urchins (at least M. nudus) form resource aggregations that are driven by the scarce HFAs. This provides valuable information into the mechanisms of the aggregation of sea urchins.
creator: Yushi Yu
creator: Jiangnan Sun
creator: Yaqing Chang
creator: Chong Zhao
uri: https://doi.org/10.7717/peerj.12820
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Yu et al.

title: A survey of Cryptosporidium prevalence among birds in two zoos in China
link: https://peerj.com/articles/12825
last-modified: 2022-01-19
description: BackgroundCryptosporidiosis is an important zoonotic protozoan disease worldwide, but few studies on this disease have been performed in wild birds; thus, our knowledge of this disease is insufficient, even in zoo birds. Animals in zoos are possible zoonotic disease reservoirs, potentially resulting in zoonotic agent spillover to humans; accordingly, our understanding of such phenomena should be improved.MethodsA total of 263 fresh fecal samples from 43 avian species were randomly collected from the Beijing Zoo and Harbin North Forest Zoo and screened for the prevalence of Cryptosporidium by 18S rRNA gene sequencing. Cryptosporidium species were distinguished based on the combined results of phylogenetic tree and genetic distance analyses conducted with the inclusion of seven avian Cryptosporidium species and 13 avian Cryptosporidium genotypes. The genetic diversity of Cryptosporidium parvum among different hosts, including humans, cattle, dogs, and birds, and the genetic diversity of avian C. parvum among avian hosts in China, Iraq and Brazil were determined based on C. parvum 18S rRNA haplotypes.ResultsThe results of PCR targeting the 18S rRNA gene revealed that 1.9% (5/263) of the samples were Cryptosporidium-positive. Four of the five Cryptosporidium-positive samples originated from white cranes (Grus leucogeranus), and one originated from a flamingo (Phoenicopteridae). Avian C. parvum isolates, including the isolates examined in the present study, showed gene flow with other isolates from different types of hosts, including humans, cattle and dogs, indicating that zoo birds potentially pose zoonotic and pathogenic risks to humans and animals. Additionally, gene flow between avian C. parvum isolates from China and Brazil was detected.ConclusionsTo the best of our knowledge, our results demonstrate C. parvum infection in a flamingo (Phoenicopteridae) and white cranes (Grus leucogeranus) for the first time. The results of our study provide an important reference for understanding the host range, biological characteristics, and molecular epidemiology of C. parvum.
creator: Yaxian Lu
creator: Tianchun Pu
creator: Baohua Ma
creator: Lixin Wang
creator: Mengchao Zhou
creator: Yu Chen
creator: Xiuyun Li
creator: Changming Zheng
creator: Hetong Liu
creator: Jinpeng Liu
creator: Chunyu Guan
creator: Hongyan Yu
creator: Chunkuo Dai
creator: Yuan Huang
creator: Yuling Yang
creator: Zhiwei Peng
creator: Lei Han
creator: Hongliang Chai
creator: Zhijun Hou
uri: https://doi.org/10.7717/peerj.12825
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Lu et al.

title: Bioinformatics analysis and identification of hub genes and immune-related molecular mechanisms in chronic myeloid leukemia
link: https://peerj.com/articles/12616
last-modified: 2022-01-18
description: BackgroundChronic myeloid leukemia (CML) is a malignant hyperplastic tumor of the bone marrow originating from pluripotent hematopoietic stem cells. The advent of tyrosine kinase inhibitors (TKIs) has greatly improved the survival rate of patients with CML. However, TKI-resistance leads to the disease recurrence and progression. This study aimed to identify immune-related genes (IRGs) associated with CML progression.MethodsWe extracted the gene’s expression profiles from the Gene Expression Omnibus (GEO). Bioinformatics analysis was used to determine the differentially expressed IRGs of CML and normal peripheral blood mononuclear cells (PBMCs). Functional enrichment and gene set enrichment analysis (GSEA) were used to explore its potential mechanism. Hub genes were identified using Molecular Complex Detection (MCODE) and the CytoHubba plugin. The hub genes’ diagnostic value was evaluated using the receiver operating characteristic (ROC). The relative proportions of infiltrating immune cells in each CML sample were evaluated using CIBERSORT. Quantitative real-time PCR (RT-qPCR) was used to validate the hub gene expression in clinical samples.ResultsA total of 31 differentially expressed IRGs were identified. GO analyses revealed that the modules were typically enriched in the receptor ligand activity, cytokine activity, and endopeptidase activity. KEGG enrichment analysis of IRGs revealed that CML involved Th17 cell differentiation, the NF-kappa B signaling pathway, and cytokine-cytokine receptor interaction. A total of 10 hub genes were selected using the PPI network. GSEA showed that these hub genes were related to the gamma-interferon immune response, inflammatory response, and allograft rejection. ROC curve analysis suggested that six hub genes may be potential biomarkers for CML diagnosis. Further analysis indicated that immune cells were associated with the pathogenesis of CML. The RT-qPCR results showed that proteinase 3 (PRTN3), cathepsin G (CTSG), matrix metalloproteinase 9 (MMP9), resistin (RETN), eosinophil derived neurotoxin (RNase2), eosinophil cationic protein (ECP, RNase3) were significantly elevated in CML patients’ PBMCs compared with healthy controls.ConclusionThese results improved our understanding of the functional characteristics and immune-related molecular mechanisms involved in CML progression and provided potential diagnostic biomarkers and therapeutic targets.
creator: Fangyi Yao
creator: Cui Zhao
creator: Fangmin Zhong
creator: Tingyu Qin
creator: Shuqi Li
creator: Jing Liu
creator: Bo Huang
creator: Xiaozhong Wang
uri: https://doi.org/10.7717/peerj.12616
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Yao et al.

title: Exploring the nitrogen reservoir of biodegradable household garbage and its potential in replacing synthetic nitrogen fertilizers in China
link: https://peerj.com/articles/12621
last-modified: 2022-01-18
description: Biodegradable household garbage contains a large amount of nitrogen, which could be used as organic fertilizer to produce organic food and significantly reduce synthetic nitrogen fertilizers. There is limited information on how large the nitrogen reservoir of biodegradable household garbage is in a certain country or region. Here we took China as a case, analyzed the amount of biodegradable household garbage resources and their nitrogen reservoirs. It was noted that the biodegradable household garbage mainly included food waste, waste paper and wood chips, with the amount being 31.56, 29.55, and 6.45 × 106 t·a−1, respectively. Accordingly, the nitrogen reservoirs were 65.31 × 104, 6.80 × 104, and 3.81 × 104 t·a−1 in China. The nitrogen reservoir of food waste accounted for 86% of the total nitrogen reservoir of biodegradable household garbage, which was equivalent to 11% of the amount of actual absorption for synthetic nitrogen fertilizers (6.20 × 106 t·a−1) by agriculture plants in China. Our findings provided a scientific basis for the classification and utilization of biodegradable household garbage.
creator: Lan Wang
creator: Tianyu Qin
creator: Jianshe Zhao
creator: Yicheng Zhang
creator: Zhiyuan Wu
creator: Xiaohui Cui
creator: Gaifang Zhou
creator: Caihong Li
creator: Liyue Guo
creator: Gaoming Jiang
uri: https://doi.org/10.7717/peerj.12621
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wang et al.

title: Prediction of active ingredients in Salvia miltiorrhiza Bunge. based on soil elements and artificial neural network
link: https://peerj.com/articles/12726
last-modified: 2022-01-18
description: The roots of Salvia miltiorrhiza Bunge. are commonly used in the treatment of cardiovascular diseases, and tanshinones and salvianolic acids are its main active ingredients. However, the composition and content of active ingredients of S. miltiorrhiza planted in different regions of the soil environment are also quite different, which adds new difficulties to the large-scale and standardization of artificial cultivation. Therefore, in this study, we measured the active ingredients in the roots of S. miltiorrhiza and the contents of rhizosphere soil elements from 25 production areas in eight provinces in China, and used the data to develop a prediction model based on BP (back propagation) neural network. The results showed that the active ingredients had different degrees of correlation with soil macronutrients and trace elements, the prediction model had the best performance (MSE = 0.0203, 0.0164; R2 = 0.93, 0.94). The artificial neural network model was shown to be a method that can be used to screen the suitable cultivation sites and proper fertilization. It can also be used to optimize the fertilizer application at specific sites. It also suggested that soil testing formula fertilization should be carried out for medicinal plants like S. miltiorrhiza, which is grown in multiple origins, rather than promoting the use of “special fertilizer” on a large scale. Therefore, the model is helpful for efficient, rational, and scientific guidance of fertilization management in the cultivation of S. miltiorrhiza.
creator: Yu Liu
creator: Ke Wang
creator: Zhu-Yun Yan
creator: Xiaofeng Shen
creator: Xinjie Yang
uri: https://doi.org/10.7717/peerj.12726
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Liu et al.

title: A review of the common crab genus Macromedaeus Ward, 1942 (Brachyura, Xanthidae) from China Seas with description of a new species using integrative taxonomy methods
link: https://peerj.com/articles/12735
last-modified: 2022-01-18
description: Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and M. orientalis (Takeda & Miyake, 1969) from Hainan Island, South China Sea. M. hainanensis is most related to M. distinguendus (De Haan, 1833-1850) and M. orientalis on the carapace shape and granular appearance, but can be distinguished by unique morphological characteristics especially its front, pereopods and male first gonopod. Taxonomic identities of the six Macromedaeus species recorded from China seas are discussed, and a phylogenetic analyzation is performed on Macromedaeus and related taxa based on three mitochondrial and two nuclear markers (12S, 16S, COI, H3, 18S). Integrated taxonomic evidence is used to support the taxonomic status of each species.
creator: Ziming Yuan
creator: Wei Jiang
creator: Zhongli Sha
uri: https://doi.org/10.7717/peerj.12735
license: https://creativecommons.org/licenses/by-nc/4.0
rights: ©2022 Yuan et al.

title: Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus
link: https://peerj.com/articles/12749
last-modified: 2022-01-18
description: BackgroundHoplolaimus galeatus is a plant-parasite nematode with a broad range of hosts. This nematode is known to damage cotton, corn, and soybean crops. Hoplolaimus galeatus is also an economically important pest of turfgrasses. Despite its economical importance, no genomic resources exist for this parasite.MethodsUsing 300 bp paired-end short read sequencing, this study estimated genome size, analyzed a nearly complete mitochondrial chromosome, and explored nuclear repetitive elements, including microsatellites, in H. galeatus for the first time. The phylogenetic placement of H. galeatus in the superfamily Tylenchoidea was also examined.ResultsThe average haploid genome size estimated using a k-mer approach was 517.69 Mbp. The partially assembled mitochondrial genome of H. galeatus is 16,578 bp in length and comprised of 11 protein-coding genes, two ribosomal RNA genes, and 16 transfer RNA genes. A maximum likelihood phylogenetic analysis confirmed the monophyly of the genus Hoplolaimus and the superfamily Tylenchoidea. Repetitive elements constituted  50% of the nuclear genome while half of the genome represented single- or low-copy sequences. A large portion of repetitive sequences could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous belonged to Class II- Subclass 2-Maverick elements, Class I-LTR-Ty-3/Bel-Pao elements, and satellites. 45S ribosomal DNA was also abundant and a total of 36 SSRs were identified.This study developed genomic resources for the plant-parasitic nematode Hoplolaimus galeatus that will contribute to the better understanding of meta-population connectivity and putative genomic mechanisms involved in the exploitation of the broad range of host plants used by H. galeatus.
creator: Xinyuan Ma
creator: Paula Agudelo
creator: Vincent P. Richards
creator: J. Antonio Baeza
uri: https://doi.org/10.7717/peerj.12749
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Ma et al.

title: Exploring the potential biomarkers for prognosis of glioblastoma via weighted gene co-expression network analysis
link: https://peerj.com/articles/12768
last-modified: 2022-01-18
description: BackgroundGlioblastoma (GBM) is the most common malignant tumor in the central system with a poor prognosis. Due to the complexity of its molecular mechanism, the recurrence rate and mortality rate of GBM patients are still high. Therefore, there is an urgent need to screen GBM biomarkers to prove the therapeutic effect and improve the prognosis.ResultsWe extracted data from GBM patients from the Gene Expression Integration Database (GEO), analyzed differentially expressed genes in GEO and identified key modules by weighted gene co-expression network analysis (WGCNA). GSE145128 data was obtained from the GEO database, and the darkturquoise module was determined to be the most relevant to the GBM prognosis by WGCNA (r =  − 0.62, p = 0.01). We performed enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal the interaction activity in the selected modules. Then Kaplan-Meier survival curve analysis was used to extract genes closely related to GBM prognosis. We used Kaplan-Meier survival curves to analyze the 139 genes in the darkturquoise module, identified four genes (DARS/GDI2/P4HA2/TRUB1) associated with prognostic GBM. Low expression of DARS/GDI2/TRUB1 and high expression of P4HA2 had a poor prognosis. Finally, we used tumor genome map (TCGA) data, verified the characteristics of hub genes through Co-expression analysis, Drug sensitivity analysis, TIMER database analysis and GSVA analysis. We downloaded the data of GBM from the TCGA database, the results of co-expression analysis showed that DARS/GDI2/P4HA2/TRUB1 could regulate the development of GBM by affecting genes such as CDC73/CDC123/B4GALT1/CUL2. Drug sensitivity analysis showed that genes are involved in many classic Cancer-related pathways including TSC/mTOR, RAS/MAPK.TIMER database analysis showed DARS expression is positively correlated with tumor purity (cor = 0.125, p = 1.07e−02)), P4HA2 expression is negatively correlated with tumor purity (cor =−0.279, p = 6.06e−09). Finally, GSVA analysis found that DARS/GDI2/P4HA2/TRUB1 gene sets are closely related to the occurrence of cancer.ConclusionWe used two public databases to identify four valuable biomarkers for GBM prognosis, namely DARS/GDI2/P4HA2/TRUB1, which have potential clinical application value and can be used as prognostic markers for GBM.
creator: Mengyuan Zhang
creator: Zhike Zhou
creator: Zhouyang Liu
creator: Fangxi Liu
creator: Chuansheng Zhao
uri: https://doi.org/10.7717/peerj.12768
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhang et al.

title: Association between perceived life stress and subjective well-being among Chinese perimenopausal women: a moderated mediation analysis
link: https://peerj.com/articles/12787
last-modified: 2022-01-18
description: BackgroundThe impact of perceived life stress on subjective well-being has been well-established; while few studies have explored the mediating and moderating mechanisms of the association between perceived life stress and subjective well-being among perimenopausal women. This study is aimed at exploring the mediating effect of depressive symptoms and the role of interests/hobbies as a moderator in the association between perceived life stress and subjective well-being among perimenopausal women.MethodsThe participants were 1,104 perimenopausal women at the age of 40 to 60, who were asked to complete a paper-based questionnaire. A single item was used to measure self-perceived life stress and interests/hobbies. The Zung Self-rating Depression Scale (SDS) and Subjective Well-being Scale for Chinese Citizens (SWBS-CC) were applied to assess both depressive symptoms and subjective well-being. Multiple linear regression analysis and the PROCESS macro were adopted to analyse not only the mediating effect of depressive symptoms but also the moderating role of interests/hobbies.ResultsPerceived life stress was negatively associated with subjective well-being (B =  − 1.424, β =  − 0.101, P < 0.001). The impact of perceived life stress on subjective well-being was partially mediated by depressive symptoms (mediation effect = −0.760, 95% confidence intervals (CI) [−1.129, −0.415]). In addition, the interaction term between depressive symptoms and interests/hobbies was significantly related to subjective well-being (β =  − 0.060, P < 0.05), indicating moderating effect. Moderated mediation had a significant index (Index = −0.220, SE = 0.099, 95% CI [−0.460, −0.060]).ConclusionsPerceived life stress was negatively related to subjective well-being. The impact of perceived life stress on subjective well-being was mediated by depressive symptoms. Besides, interests/hobbies moderated the indirect effect of depressive symptoms on the relationship between perceived life stress and subjective well-being.
creator: Xiangrong Li
creator: Zheng Ren
creator: Tianliang Ji
creator: Hong Shi
creator: Hanfang Zhao
creator: Minfu He
creator: Xinwen Fan
creator: Xia Guo
creator: Shuang Zha
creator: Shuyin Qiao
creator: Yuyu Li
creator: Yajiao Pu
creator: Hongjian Liu
creator: Xiumin Zhang
uri: https://doi.org/10.7717/peerj.12787
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Li et al.

title: A new ancient lineage of ablepharine skinks (Sauria: Scincidae) from eastern Himalayas with notes on origin and systematics of the group
link: https://peerj.com/articles/12800
last-modified: 2022-01-18
description: The Himalayas represent a renowned biodiversity hotspot and an important biogeographic realm that has influenced origin and diversification of multiple taxa. A recent herpetological investigation of the eastern Himalayas of the Indian state of Arunachal Pradesh led to the discovery of a unique lineage of ablepharine skink, which is herein described as a new genus along with a new species. The findings are based an integrated taxonomic approach incorporating data from external morphology, microCT scans of the skull and molecular data. The molecular phylogeny of ablepharine skinks is also presented that suggests taxonomic amendments. Discovery of this unique lineage of skinks further highlights the biogeographic importance of the eastern Himalayas as a source for origin of several relic biota.
creator: Zeeshan A. Mirza
creator: Andrey M. Bragin
creator: Harshal Bhosale
creator: Gaurang G. Gowande
creator: Harshil Patel
creator: Nikolay A. Poyarkov
uri: https://doi.org/10.7717/peerj.12800
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Mirza et al.

title: In vitro anti-Leishmania activity of 8-hydroxyquinoline and its synergistic effect with amphotericin B deoxycholate against Leishmania martiniquensis
link: https://peerj.com/articles/12813
last-modified: 2022-01-18
description: Leishmania (Mundinia) martiniquensis is responsible for visceral leishmaniasis in patients with no known underlying immunodeficiency, and visceral or disseminated cutaneous leishmaniasis in HIV-infected patients. The available anti-Leishmania drugs for treatment have limitations such as high toxicity and variable efficacy. To improve the therapeutic index of anti-Leishmania drugs, the search for a new drug or a new natural compound in combination therapy instead of using monotherapy to reduce drug side effect and have high efficacy is required. In this study, anti-Leishmania activity of 8-hydroxyquinoline (8HQN) and its synergistic effect with amphotericin B (AmB) against L. martiniquensis were evaluated in vitro for the first time. These results showed that 8HQN presented anti-Leishmania activity against L. martiniquensis with IC50 1.60 ± 0.28 and 1.56 ± 0.02 µg/mL for promastigotes and intracellular amastigotes, respectively. The selectivity index (SI) value of 8HQN was 79.84 for promastigotes and 82.40 for intracellular amastigotes, which highlight promising results for the use of 8HQN in the treatment of L. martiniquensis-infected host cells. Interestingly, four combinations of 8HQN and AmB provided synergistic effects for intracellular amastigotes and showed no toxic effects to host cells. These results provided information of using a combination therapy in treating this Leishmania species leads to further development of therapy and can be considered as an alternative treatment for leishmaniasis.
creator: Wetpisit Chanmol
creator: Padet Siriyasatien
creator: Nuchpicha Intakhan
uri: https://doi.org/10.7717/peerj.12813
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Chanmol et al.

title: Functional genetic variants in complement component 7 confer susceptibility to gastric cancer
link: https://peerj.com/articles/12816
last-modified: 2022-01-18
description: BackgroundComplement system plays an important role in innate immunity which involved in the changes tumor immune microenvironment by mediating the inflammatory response. This study aims to explore the relationship between complement component 7 (C7) polymorphisms and the risk of gastric cancer (GC).Materials and MethodsAll selected SNPs of C7 were genotyped in 471 patients and 471 controls using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by unconditional Logistic regression to analyze the relationship between each genotype and the genetic susceptibility to gastric cancer. The level of C7 expression in GC was analyzed by Gene Expression Profiling Interactive Analysis (GEPIA) and detected by Enzyme Linked Immunosorbent Assay. Kaplan–Meier plotter were used to reveal C7 of prognostic value in GC. We examined SNPs associated with the expression of C7 using the GTEx database. The effect of C7 polymorphisms on the regulatory activity of C7 was detected by luciferase reporter assay.ResultsUnconditional logistic regression showed that individuals with C7rs1376178 AA or CA genotype had a higher risk of GC with OR (95% CI) of 2.09 (1.43–3.03) and 1.88 (1.35–2.63), respectively. For C7rs1061429 C > A polymorphism, AA genotype was associated with the elevated risk for developing gastric cancer (OR = 2.16, 95% CI [1.37–3.38]). In stratified analysis, C7rs1376178 AA genotype increased the risk of GC among males (OR = 2.88, 95% CI [1.81–4.58]), but not among females (OR = 1.06, 95% CI [0.55–2.06]). Individuals carrying rs1061429 AA significantly increased the risk of gastric cancer among youngers (OR = 2.84, 95% CI [1.39–5.80]) and non-smokers (OR = 2.79, 95% CI [1.63–4.77]). C7 was overexpressed in gastric cancer tissues and serum of cancer patients and was significantly associated with the prognosis. C7rs1061429 C > A variant contributed to reduced protein level of C7 (P = 0.029), but rs1376178 didn’t. Luciferase reporter assay showed that rs1376178C-containing plasmid exhibited 2.86-fold higher luciferase activity than rs1376178 A-containing plasmid (P < 0.001). We also found that rs1061429A allele contributed 1.34-fold increased luciferase activity than rs1061429C allele when co-transfected with miR-591 (P = 0.0012).ConclusionsThese findings highlight the role of C7 in the development of gastric cancer.
creator: Siyue Wang
creator: Wenqian Hu
creator: Yuning Xie
creator: Hongjiao Wu
creator: Zhenxian Jia
creator: Zhi Zhang
creator: Xuemei Zhang
uri: https://doi.org/10.7717/peerj.12816
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Morphological and biochemical responses of tropical seagrasses (Family: Hydrocharitaceae) under colonization of the macroalgae Ulva reticulata Forsskål
link: https://peerj.com/articles/12821
last-modified: 2022-01-18
description: BackgroundCoastal land development has deteriorated the habitat and water quality for seagrass growth and causes the proliferation of opportunist macroalgae that can potentially affect them physically and biochemically. The present study investigates the morphological and biochemical responses of seagrass from the Hydrocharitaceae family under the macroalgal bloom of Ulva reticulata, induced by land reclamation activities for constructing artificial islands.MethodsFive seagrass species, Enhalus acoroides, Thalassia hemprichii, Halophila ovalis, Halophila major, and Halophila spinulosa were collected at an Ulva reticulata-colonized site (MA) shoal and a non-Ulva reticulata-colonized site (MC) shoal at Sungai Pulai estuary, Johor, Malaysia. Morphometry of shoots comprising leaf length (LL), leaf width (LW), leaf sheath length (LSL), leaflet length (LTL), leaflet width (LTW), petiole length (PL), space between intra-marginal veins (IV) of leaf, cross vein angle (CVA) of leaf, number of the cross vein (NOC), number of the leaf (NOL) and number of the leaflet (NOLT) were measured on fresh seagrass specimens. Moreover, in-situ water quality and water nutrient content were also recorded. Seagrass extracts in methanol were assessed for total phenolic content (TPC), total flavonoid content (TFC), 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH), 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid radical cation scavenging activity (ABTS), and ferric reducing antioxidant power (FRAP).ResultsSeagrasses in the U. reticulata-colonized site (MA) had significantly higher (t-test, p < 0.05) leaf dimensions compared to those at the non-U. reticulata colonized site (MC). Simple broad-leaved seagrass of H. major and H. ovalis were highly sensitive to the colonization of U. reticulata, which resulted in higher morphometric variation (t-test, p < 0.05) including LL, PL, LW, and IV. Concerning the biochemical properties, all the seagrasses at MA recorded significantly higher (t-test, p < 0.05) TPC, TFC, and ABTS and lower DPPH and FRAP activities compared to those at MC. Hydrocharitaceae seagrass experience positive changes in leaf morphology features and metabolite contents when shaded by U. reticulata. Researching the synergistic effect of anthropogenic nutrient loads on the interaction between seagrasses and macroalgae can provide valuable information to decrease the negative effect of macroalgae blooms on seagrasses in the tropical meadow.
creator: Lau Sheng Hann Emmclan
creator: Muta Harah Zakaria
creator: Shiamala Devi Ramaiya
creator: Ikhsan Natrah
creator: Japar Sidik Bujang
uri: https://doi.org/10.7717/peerj.12821
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Emmclan et al.

title: An exploratory assessment of human and animal health concerns of smallholder farmers in rural communities of Chimborazo, Ecuador
link: https://peerj.com/articles/12208
last-modified: 2022-01-17
description: BackgroundLivestock play important economic and cultural roles in smallholder communities of Ecuador, yet they also serve as potential sources of zoonotic infections. Understanding the animal and human health concerns of smallholder farmers is important in guiding strategies for improvement of the health and livelihoods of these resource-poor farmers. Therefore, the objectives of this study were to: (a) assess the health concerns of smallholder farmers; (b) explore animal and waste management practices; and (c) identify predictors of pediatric and livestock diarrhea on smallholder farms in Ecuador.MethodsThis is a cross-sectional survey of 58 smallholder farmers in three communities of Chimborazo province, Ecuador. Data were collected on household demographics, smallholding characteristics, type of animals owned, human-animal interactions, health concerns, and 30-day occurrence of human as well as animal diarrhea. Summary statistics were computed and logistic models used to investigate predictors of pediatric and animal diarrhea.ResultsAll respondents reported keeping animals. Animals kept included cattle, pigs, poultry, dogs, guinea pigs, cats, sheep, horses, rabbits, donkeys, or other livestock. More than half of the respondents named diseases as their greatest personal (55.2%) or family (58.6%) health concern, while an even greater percentage (60.3%) reported physiological stress as the primary health concern for their animals. Occurrence of diarrhea in the 30 days prior to the study was reported by 12.1% of the respondents. Additionally, 15.2% and 55.2% of the households reported diarrhea among children and animals, respectively. The majority (65.5%) of the households had toilets, while the remainder had either latrines (27.6%) or no sanitation facilities (6.9%). However, only 9.1% of the smallholdings had either a toilet (3.6%) or a latrine (5.5%) onsite and yet the farmers tended to spend most of the day at the smallholdings. Potential exposures to gastrointestinal pathogens included food- or water-borne sources (93.5% of children; 91.4% of adults) and blood-borne or fecal sources (80.4% of children; 100% of adults). Although 98.3% of the respondents kept cattle, only 27.6% had animal enclosures and even fewer (15.5%) had animal waste management plans. The odds of animal diarrhea were significantly higher (Odds Ratio [OR] = 8.7; 95% Confidence Interval [1.0–75.0]; p = .049) among households that had animal waste management plans compared to those that did not. None of the variables investigated were significant predictors of pediatric diarrhea.ConclusionsOngoing surveillance is needed to develop estimates of diarrhea incidence among smallholder families and their livestock. The impact of different animal management strategies on the potential pathogen exposure of smallholders warrants further investigations. Improving sanitation infrastructure and animal waste management strategies is recommended.
creator: Tamara L. Chavez-Lindell
creator: Ana L. Moncayo
creator: María Fernanda Vinueza Veloz
creator: Agricola Odoi
uri: https://doi.org/10.7717/peerj.12208
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Chavez-Lindell et al.

title: Hybridization of green synthesized silver nanoparticles with poly(ethylene glycol) methacrylate and their biomedical applications
link: https://peerj.com/articles/12540
last-modified: 2022-01-17
description: In the present research, a rapid, simple and efficient green method is used for the incorporation of silver nanoparticles (AgNPs) into poly(ethylene glycol) methacrylate (PEGMA) to create biocatalysts with excellent properties for pharmaceutical purpose. In the first phase, Caralluma tuberculata capped AgNPs (Ca-AgNPs) were prepared using green synthetic approach and in the second phase Caralluma tuberculata capped AgNPs were hybridized with poly(ethylene glycol) methacrylate to form PEGMA-AgNPs. Both the virgin (naked or uncapped) and polymer-capped materials were characterized spectroscopically and their results were compared. Fourier transform infrared spectroscopy showed no new peak after the capping procedure, showing that only physical interactions takes place during capping. After PEGMA capping, the spectra of the AgNPs red shifted (from 450 nm to 520 nm) and the overall particle size of AgNPs increased. Catalytic activity of the nanoparticles and hybrid system were tested by choosing the catalytic reduction of 4-nitrophenol (4-NP) as a model reaction. Both synthesized NPs and polymer capped NPs exhibits catalytic activity for the reduction of 4-NP to 4-aminophenol. The polymer hybrid exhibits remarkable antiproliferative, antioxidant, cytotoxic, antidiabetic and antileishmanial activities.
creator: Natasha Anwar
creator: Abbas Khan
creator: Mohib Shah
creator: John J. Walsh
creator: Samreen Saleem
creator: Zeeshan Anwar
creator: Sobia Aslam
creator: Muhammad Irshad
uri: https://doi.org/10.7717/peerj.12540
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Anwar et al.

title: Screening and identification of differentially expressed long non-coding RNAs in multidrug-resistant tuberculosis
link: https://peerj.com/articles/12776
last-modified: 2022-01-17
description: BackgroundEfforts to eradicate tuberculosis are largely threatened by drug-resistant tuberculosis, particularly, multidrug-resistant tuberculosis (MDR-TB). Screening and identification potential biomarkers for MDR-TB is crucial to diagnose early and reduce the incidence of MDR-TB.MethodsTo screen the differentially expressed long non-coding RNAs in MDR-TB, the lncRNA and mRNA expression profiles in serum derived from healthy controls (HCs), individuals with MDR-TB and drug-sensitive tuberculosis (DS-TB) were analyzed by microarray assay and 10 lncRNAs were randomly selected for further validation by reverse transcription-quantitative real-time PCR(RT-qPCR). The biological functions of differentially expressed mRNAs as well as relationships between genes and signaling pathways were investigated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively.ResultsA total of 353 differentially expressed lncRNAs (312 upregulated) and 202 mRNAs (99 upregulated) were found in the MDR-TB group compared to HCs. And compared with the DS-TB group, 442 differentially expressed lncRNAs (115 upregulated) and 190 mRNAs (87 upregulated) were found in the MDR-TB group. The expression levels of lncRNA n335659 were found to differ significantly between each group by RT-qPCR. Compared with DS-TB group, the GO analysis showed that the differential mRNAs were mainly enriched in the processes associated with the detection of the chemical stimulus, the regulation of mRNA metabolic process and neutrophil activation in the MDR-TB group; the KEGG analysis indicated that the differential mRNAs between DS-TB and MDR-TB were mainly enriched in proteasome and Notch signaling pathway, which might reveal a fraction of the mechanism of MDR-TB. The discovery of the serum lncRNA n335659 might serve as a potential biomarker for MDR-TB and Notch signaling pathway provided a new clue for the investigation of the pathological mechanism of MDR-TB.
creator: Junwei Zhao
creator: ShuHui Gao
creator: Chunguang Chen
creator: Hui Li
creator: Shaohua Wang
creator: Yongmin Yu
creator: Liang Ming
uri: https://doi.org/10.7717/peerj.12776
license: https://creativecommons.org/licenses/by-nc/4.0
rights: ©2022 Zhao et al.

title: Sixteenth-century tomatoes in Europe: who saw them, what they looked like, and where they came from
link: https://peerj.com/articles/12790
last-modified: 2022-01-17
description: BackgroundSoon after the Spanish conquest of the Americas, the first tomatoes were presented as curiosities to the European elite and drew the attention of sixteenth-century Italian naturalists. Despite of their scientific interest in this New World crop, most Renaissance botanists did not specify where these ‘golden apples’ or ‘pomi d’oro’ came from. The debate on the first European tomatoes and their origin is often hindered by erroneous dating, botanical misidentifications and inaccessible historical sources. The discovery of a tomato specimen in the sixteenth-century ‘En Tibi herbarium’ kept at Leiden, the Netherlands, triggered research on its geographical provenance and morphological comparison to other tomato specimens and illustrations from the same time period.MethodsRecent digitization efforts greatly facilitate research on historic botanical sources. Here we provide an overview of the ten remaining sixteenth-century tomato specimens, early descriptions and 13 illustrations. Several were never published before, revealing what these tomatoes looked like, who saw them, and where they came from. We compare our historical findings with recent molecular research on the chloroplast and nuclear DNA of the ‘En Tibi’ specimen.ResultsOur survey shows that the earliest tomatoes in Europe came in a much wider variety of colors, shapes and sizes than previously thought, with both simple and fasciated flowers, round and segmented fruits. Pietro Andrea Matthioli gave the first description of a tomato in 1544, and the oldest specimens were collected by Ulisse Aldrovandi and Francesco Petrollini in c. 1551, possibly from plants grown in the Pisa botanical garden by their teacher Luca Ghini. The oldest tomato illustrations were made in Germany and Switzerland in the early 1550s, but the Flemish Rembert Dodoens published the first image in 1553. The names of early tomatoes in contemporary manuscripts suggest both a Mexican and a Peruvian origin. The ‘En Tibi’ specimen was collected by Petrollini around 1558 and thus is not the oldest extant tomato. Recent molecular research on the ancient nuclear and chloroplast DNA of the En Tibi specimen clearly shows that it was a fully domesticated tomato, and genetically close to three Mexican landraces and two Peruvian specimens that probably also had a Mesoamerican origin. Molecular research on the other sixteenth-century tomato specimens may reveal other patterns of genetic similarity, past selection processes, and geographic origin. Clues on the ‘historic’ taste and pest resistance of the sixteenth-century tomatoes will be difficult to predict from their degraded DNA, but should be rather sought in those landraces in Central and South America that are genetically close to them. The indigenous farmers growing these traditional varieties should be supported to conserve these heirloom varieties in-situ.
creator: Tinde van Andel
creator: Rutger A. Vos
creator: Ewout Michels
creator: Anastasia Stefanaki
uri: https://doi.org/10.7717/peerj.12790
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 van Andel et al.

title: Impact of dialysis modality conversion on the health-related quality of life of peritoneal dialysis patients: a retrospective cohort study in China
link: https://peerj.com/articles/12793
last-modified: 2022-01-17
description: BackgroundTo analyze the health-related quality of life associated with the conversion of dialysis modality among end-stage renal disease patients in China.MethodsPatients were recruited from hospitals and a dialysis center in Kunshan, China. Patients converting from continuous ambulatory peritoneal dialysis to automated peritoneal dialysis were recruited as the observation group (n = 64), and patients continuing with continuous ambulatory peritoneal dialysis treatment were included in the control group (n = 64) after matching in this retrospective cohort study. Their health-related quality of life was measured using the kidney disease quality of life instrument in 2019 and 2020, respectively. Baseline socio-demographic characteristics and clinical data were collected in 2019. The before-and-after cross-group comparisons of subscale scores of two groups were conducted using a Student‘s t-test. Multiple linear regression models were fitted to identify the factors associated with the change of each scale.ResultsThe health-related quality of life scores of the two groups was comparable in baseline, while the observation group had higher scores in Physical Component Summary (51.92 ± 7.50), Kidney Disease Component Summary (81.21 ± 8.41), Symptoms (90.76 ± 6.30), Effects (82.86 ± 11.42), and Burden (69.04 ± 15.69) subscales after one year. In multivariate regression analysis, the change of Physical Component Summary was significantly associated with conversion to APD (β = 11.54, 95% CI [7.26–15.82]); the change of Mental Component Summary with higher education (β =  − 5.96, 95% CI [−10.18–−1.74]) and CCI (>2) (β = 5.39, 95% CI [1.05–9.73]); the change of Kidney Disease Component Summary with conversion to APD (β = 15.95, 95% CI [10.19–21.7]) and age (>60 years) (β =  − 7.36, 95% CI [−14.11–−0.61]); the change of Symptoms with CCI (>2) (β = 7.96, 95% CI [1.49–14.44]); the change of Effects with conversion to APD (β = 19.23, 95% CI [11.57–26.88]); and the change of Burden with conversion to APD (β = 22.40, 95% CI [13.46–31.34]), age (>60 years) (β =  − 12.12, 95% CI [−22.59–−1.65]), and higher education (β =  − 10.38, 95% CI [−19.79–−0.98]).ConclusionsThe conversion of dialysis modality had a significant impact on the scores of most subscales. Patients converting from continuous ambulatory peritoneal dialysis to automated peritoneal dialysis generally had improved health-related quality of life scores.
creator: Heqi Sun
creator: Ye Zhuang
creator: Lanying Gao
creator: Ningze Xu
creator: Yan Xiong
creator: Min Yuan
creator: Jun Lu
creator: Jianming Ye
uri: https://doi.org/10.7717/peerj.12793
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Sun et al.

title: Post-mortem enamel surface texture alteration during taphonomic processes—do experimental approaches reflect natural phenomena?
link: https://peerj.com/articles/12635
last-modified: 2022-01-14
description: Experimental approaches are often used to better understand the mechanisms behind and consequences of post-mortem alteration on proxies for diet reconstruction. Dental microwear texture analysis (DMTA) is such a dietary proxy, using dental wear features in extant and extinct taxa to reconstruct feeding behaviour and mechanical food properties. In fossil specimens especially, DMTA can be biased by post-mortem alteration caused by mechanical or chemical alteration of the enamel surface. Here we performed three different dental surface alteration experiments to assess the effect of common taphonomic processes by simplifying them: (1) tumbling in sediment suspension to simulate fluvial transport, (2) sandblasting to simulate mechanical erosion due to aeolian sediment transport, (3) acid etching to simulate chemical dissolution by stomach acid. For tumbling (1) we found alteration to be mainly dependent on sediment grain size fraction and that on specimens tumbled with sand fractions mainly post-mortem scratches formed on the dental surface, while specimens tumbled with a fine-gravel fraction showed post-mortem formed dales. Sandblasting (2) with loess caused only negligible alteration, however blasting with fine sand quartz particles resulted in significant destruction of enamel surfaces and formation of large post-mortem dales. Acid etching (3) using diluted hydrochloric acid solutions in concentrations similar to that of predator stomachs led to a complete etching of the whole dental surface, which did not resemble those of teeth recovered from owl pellets. The experiments resulted in post-mortem alteration comparable, but not identical to naturally occurring post-mortem alteration features. Nevertheless, this study serves as a first assessment and step towards further, more refined taphonomic experiments evaluating post-mortem alteration of dental microwear texture (DMT).
creator: Katrin Weber
creator: Daniela E. Winkler
creator: Ellen Schulz-Kornas
creator: Thomas M. Kaiser
creator: Thomas Tütken
uri: https://doi.org/10.7717/peerj.12635
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Weber et al.

title: Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?
link: https://peerj.com/articles/12763
last-modified: 2022-01-14
description: BackgroundCommunity assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates.AimsThis paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate.ResultsIt can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.
creator: Zoltán Botta-Dukát
uri: https://doi.org/10.7717/peerj.12763
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Botta-Dukát

title: Using InVEST to evaluate water yield services in Shangri-La, Northwestern Yunnan, China
link: https://peerj.com/articles/12804
last-modified: 2022-01-14
description: Water yield is an ecosystem service that is vital to not only human life, but also sustainable development of the social economy and ecosystem. This study used annual average precipitation, potential evapotranspiration, plant available water content, soil depth, biophysical parameters, Zhang parameter, and land use/land cover (LULC) as input data for the Integrated Valuation of Ecosystem Service Tradeoffs (InVEST) model to estimate the water yield of Shangri-La City from 1974 to 2015. The spatiotemporal variations and associated factors (precipitation, evapotranspiration, LULC, and topographic factors) in water yield ecosystem services were then analyzed. The result showed that: (1) The water yield of Shangri-La City decreases from north and south to the center and showed a temporal trend from 1974 to 2015 of an initial decrease followed by an increase. Areas of higher average water yield were mainly in Hutiaoxia Town, Jinjiang Town, and Shangjiang Township. (2) Areas of importance for water yield in the study area which need to be assigned priority protection were mainly concentrated in the west of Jiantang Town, in central Xiaozhongdian Town, in central Gezan Township, in northwestern Dongwang Township, and in Hutiaoxia Town. (3) Water yield was affected by precipitation, evapotranspiration, vegetation type, and topographic factors. Water yield was positively and negatively correlated with precipitation and potential evapotranspiration, respectively. The average water yield of shrubs exceeded that of meadows and forests. Terrain factors indirectly affected the ecosystem service functions of water yield by affecting precipitation and vegetation types. The model used in this study can provide references for relevant research in similar climatic conditions.
creator: Yuanhe Yu
creator: Xingqi Sun
creator: Jinliang Wang
creator: Jianpeng Zhang
uri: https://doi.org/10.7717/peerj.12804
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Yu et al.

title: ChiroVox: a public library of bat calls
link: https://peerj.com/articles/12445
last-modified: 2022-01-13
description: Recordings of bat echolocation and social calls are used for many research purposes from ecological studies to taxonomy. Effective use of these relies on identification of species from the recordings, but comparative recordings or detailed call descriptions to support identification are often lacking for areas with high biodiversity. The ChiroVox website (https://www.chirovox.org) was created to facilitate the sharing of bat sound recordings together with their metadata, including biodiversity data and recording circumstances. To date, more than 30 researchers have contributed over 3,900 recordings of nearly 200 species, making ChiroVox the largest open-access bat call library currently available. Each recording has a unique identifier that can be cited in publications; hence the acoustic analyses are repeatable. Most of the recordings available through the website are from bats whose species identities are confirmed, so they can be used to determine species in recordings where the bats were not captured or could not be identified. We hope that with the help of the bat researcher community, the website will grow rapidly and will serve as a solid source for bat acoustic research and monitoring.
creator: Tamás Görföl
creator: Joe Chun-Chia Huang
creator: Gábor Csorba
creator: Dorottya Győrössy
creator: Péter Estók
creator: Tigga Kingston
creator: Kriszta Lilla Szabadi
creator: Ellen McArthur
creator: Juliana Senawi
creator: Neil M. Furey
creator: Vuong Tan Tu
creator: Vu Dinh Thong
creator: Faisal Ali Anwarali Khan
creator: Emy Ritta Jinggong
creator: Melissa Donnelly
creator: Jayaraj Vijaya Kumaran
creator: Jian-Nan Liu
creator: Shiang-Fan Chen
creator: Mao-Ning Tuanmu
creator: Ying-Yi Ho
creator: Heng-Chia Chang
creator: Nurul-Ain Elias
creator: Nur-Izzati Abdullah
creator: Lee-Sim Lim
creator: C Daniel Squire
creator: Sándor Zsebők
uri: https://doi.org/10.7717/peerj.12445
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Görföl et al.

title: Identifying changes in immune cells and constructing prognostic models using immune-related genes in post-burn immunosuppression
link: https://peerj.com/articles/12680
last-modified: 2022-01-13
description: BackgroundBurn patients are prone to infection as well as immunosuppression, which is a significant cause of death. Currently, there is a lack of prognostic biomarkers for immunosuppression in burn patients. This study was conducted to identify immune-related genes that are prognosis biomarkers in post-burn immunosuppression and potential targets for immunotherapy.MethodsWe downloaded the gene expression profiles and clinical data of 213 burn patients and 79 healthy samples from the Gene Expression Omnibus (GEO) database. Immune infiltration analysis was used to identify the proportion of circulating immune cells. Functional enrichment analyses were carried out to identify immune-related genes that were used to build miRNA-mRNA networks to screen key genes. Next, we carried out correlation analysis between immune cells and key genes that were then used to construct logistic regression models in GSE77791 and were validated in GSE19743. Finally, we determined the expression of key genes in burn patients using quantitative reverse transcription polymerase chain reaction (qRT-PCR).ResultsA total of 745 differently expressed genes were screened out: 299 were up-regulated and 446 were down-regulated. The number of Th-cells (CD4+) decreased while neutrophils increased in burn patients. The enrichment analysis showed that down-regulated genes were enriched in the T-cell activation pathway, while up-regulated genes were enriched in neutrophil activation response in burn patients. We screened out key genes (NFATC2, RORA, and CAMK4) that could be regulated by miRNA. The expression of key genes was related to the proportion of Th-cells (CD4+) and survival, and was an excellent predictor of prognosis in burns with an area under the curve (AUC) value of 0.945. Finally, we determined that NFATC2, RORA, and CAMK4 were down-regulated in burn patients.ConclusionWe found that NFATC2, RORA, and CAMK4 were likely prognostic biomarkers in post-burn immunosuppression and potential immunotherapeutic targets to convert Th-cell dysfunction.
creator: Peng Wang
creator: Zexin Zhang
creator: Bin Yin
creator: Jiayuan Li
creator: Cheng Xialin
creator: Wenqin Lian
creator: Yingjun Su
creator: Chiyu Jia
uri: https://doi.org/10.7717/peerj.12680
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wang et al.

title: Genome-wide identification and evolution of WNK kinases in Bambusoideae and transcriptional profiling during abiotic stress in Phyllostachys edulis
link: https://peerj.com/articles/12718
last-modified: 2022-01-13
description: With-no-lysine (WNK) kinases play vital roles in abiotic stress response, circadian rhythms, and regulation of flowering time in rice, Arabidopsis, and Glycine max. However, there are no previous reports of WNKs in the Bambusoideae, although genome sequences are available for diploid, tetraploid, and hexaploid bamboo species. In the present study, we identified 41 WNK genes in five bamboo species and analysed gene evolution, phylogenetic relationship, physical and chemical properties, cis-elements, and conserved motifs. We predicted the structure of PeWNK proteins of moso bamboo and determined the exposed, buried, structural and functional amino acids. Real-time qPCR analysis revealed that PeWNK5, PeWNK7, PeWNK8, and PeWNK11 genes are involved in circadian rhythms. Analysis of gene expression of different organs at different developmental stages revealed that PeWNK genes are tissue-specific. Analysis of various abiotic stress transcriptome data (drought, salt, SA, and ABA) revealed significant gene expression levels in all PeWNKs except PeWNK11. In particular, PeWNK8 and PeWNK9 were significantly down- and up-regulated, respectively, after abiotic stress treatment. A co-expression network of PeWNK genes also showed that PeWNK2, PeWNK4, PeWNK7, and PeWNK8 were co-expressed with transcriptional regulators related to abiotic stress. In conclusion, our study identified the PeWNKs of moso bamboo involved in circadian rhythms and abiotic stress response. In addition, this study serves as a guide for future functional genomic studies of the WNK genes of the Bambusoideae.
creator: RongXiu Liu
creator: Naresh Vasupalli
creator: Dan Hou
creator: Antony Stalin
creator: Hantian Wei
creator: Huicong Zhang
creator: Xinchun Lin
uri: https://doi.org/10.7717/peerj.12718
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Liu et al.

title: Therapeutic targeting of ARID1A and PI3K/AKT pathway alterations in cholangiocarcinoma
link: https://peerj.com/articles/12750
last-modified: 2022-01-13
description: BackgroundGenetic alterations in ARID1A were detected at a high frequency in cholangiocarcinoma (CCA). Growing evidence indicates that the loss of ARID1A expression leads to activation of the PI3K/AKT pathway and increasing sensitivity of ARID1A-deficient cells for treatment with the PI3K/AKT inhibitor. Therefore, we investigated the association between genetic alterations of ARID1A and the PI3K/AKT pathway and evaluated the effect of AKT inhibition on ARID1A-deficient CCA cells.MethodsAlterations of ARID1A, PI3K/AKT pathway-related genes, clinicopathological data and overall survival of 795 CCA patients were retrieved from cBio Cancer Genomics Portal (cBioPortal) databases. The association between genetic alterations and clinical data were analyzed. The effect of the AKT inhibitor (MK-2206) on ARID1A-deficient CCA cell lines and stable ARID1A-knockdown cell lines was investigated. Cell viability, apoptosis, and expression of AKT signaling were analyzed using an MTT assay, flow cytometry, and Western blots, respectively.ResultsThe analysis of a total of 795 CCA samples revealed that ARID1A alterations significantly co-occurred with mutations of EPHA2 (p < 0.001), PIK3CA (p = 0.047), and LAMA1 (p = 0.024). Among the EPHA2 mutant CCA tumors, 82% of EPHA2 mutant tumors co-occurred with ARID1A truncating mutations. CCA tumors with ARID1A and EPHA2 mutations correlated with better survival compared to tumors with ARID1A mutations alone. We detected that 30% of patients with PIK3CA driver missense mutations harbored ARID1A-truncated mutations and 60% of LAMA1-mutated CCA co-occurred with truncating mutations of ARID1A. Interestingly, ARID1A-deficient CCA cell lines and ARID1A-knockdown CCA cells led to increased sensitivity to treatment with MK-2206 compared to the control. Treatment with MK-2206 induced apoptosis in ARID1A-knockdown KKU-213A and HUCCT1 cell lines and decreased the expression of pAKTS473 and mTOR.ConclusionThese findings suggest a dependency of ARID1A-deficient CCA tumors with the activation of the PI3K/AKT-pathway, and that they may be more vulnerable to selective AKT pathway inhibitors which can be used therapeutically.
creator: Supharada Tessiri
creator: Anchalee Techasen
creator: Sarinya Kongpetch
creator: Achira Namjan
creator: Watcharin Loilome
creator: Waraporn Chan-on
creator: Raynoo Thanan
creator: Apinya Jusakul
uri: https://doi.org/10.7717/peerj.12750
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Tessiri et al.

title: Filtered mud improves sugarcane growth and modifies the functional abundance and structure of soil microbial populations
link: https://peerj.com/articles/12753
last-modified: 2022-01-13
description: BackgroundExploring high-quality organic amendments has been a focus of sustainable agriculture. Filtered mud (FM), a sugar factory waste derived from sugarcane stems, could be an alternative organic amendment for sugarcane production. However, the effects of its application proportions on soil fertility, nutrient cycling, structure of soil bacterial and fungal communities, and the growth of sugarcane in clay-loam soils remain unexplored.MethodsThree application proportions of FM: (FM1-(FM: Soil at 1:4), FM2-(FM: Soil at 2:3), and FM3-(FM: Soil at 3:2)) were evaluated on sugarcane growth and soil nutrient cycling. High throughput sequencing was also employed to explore soil microbial dynamics.ResultsWe observed that FM generally increased the soil’s nutritional properties while improving NO3− retention compared to the control, resulting in increased growth parameters of sugarcane. Specifically, FM1 increased the concentration of NH4+−N, the N fraction preferably taken up by sugarcane, which was associated with an increase in the plant height, and more improved growth properties, among other treatments. An increase in the proportion of FM also increased the activity of soil nutrient cycling enzymes; urease, phosphatase, and β-glucosidase. High throughput sequencing revealed that FM reduced the diversity of soil bacteria while having insignificant effects on fungal diversity. Although increasing FM rates reduced the relative abundance of the phyla Proteobacteria, its class members, the Gammaproteobacteria and Betaproteobacteria containing some N-cycling related genera, were stimulated. Also, FM stimulated the abundance of beneficial and lignocellulose degrading organisms. These included the bacterial phyla Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and the fungal phylum Ascomycota. The distribution of the soil microbial community under FM rates was regulated by the changes in soil pH and the availability of soil nutrients. Since FM1 showed more promise in improving the growth properties of sugarcane, it could be more economical and sustainable for sugarcane production in clay-loam soils.
creator: Ahmad Yusuf Abubakar
creator: Muhammed Mustapha Ibrahim
creator: Caifang Zhang
creator: Muhammad Tayyab
creator: Nyumah Fallah
creator: Ziqi Yang
creator: Ziqin Pang
creator: Hua Zhang
uri: https://doi.org/10.7717/peerj.12753
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Abubakar et al.

title: Trophic niche but not abundance of Collembola and Oribatida changes with drought and farming system
link: https://peerj.com/articles/12777
last-modified: 2022-01-13
description: Higher frequencies of summer droughts are predicted to change soil conditions in the future affecting soil fauna communities and their biotic interactions. In agroecosystems drought effects on soil biota may be modulated by different management practices that alter the availability of different food resources. Recent studies on the effect of drought on soil microarthropods focused on measures of abundance and diversity. We here additionally investigated shifts in trophic niches of Collembola and Oribatida as indicated by stable isotope analysis (13C and 15N). We simulated short-term summer drought by excluding 65% of the ambient precipitation in conventionally and organically managed winter wheat fields on the DOK trial in Switzerland. Stable isotope values suggest that plant litter and root exudates were the most important resources for Collembola (Isotoma caerulea, Isotomurus maculatus and Orchesella villosa) and older plant material and microorganisms for Oribatida (Scheloribates laevigatus and Tectocepheus sarekensis). Drought treatment and farming systems did not affect abundances of the studied species. However, isotope values of some species increased in organically managed fields indicating a higher proportion of microorganisms in their diet. Trophic niche size, a measure of both isotope values combined, decreased with drought and under organic farming in some species presumably due to favored use of plants as basal resource instead of algae and microorganisms. Overall, our results suggest that the flexible usage of resources may buffer effects of drought and management practices on the abundance of microarthropods in agricultural systems.
creator: Svenja Meyer
creator: Dominika Kundel
creator: Klaus Birkhofer
creator: Andreas Fliessbach
creator: Stefan Scheu
uri: https://doi.org/10.7717/peerj.12777
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Meyer et al.

title: RNA-seq and phytohormone analysis reveals the culm color variation of Bambusa oldhamii Munro
link: https://peerj.com/articles/12796
last-modified: 2022-01-13
description: BackgroundThe clumping bamboo Bambusa oldhamii Munro, known as “green bamboo”, is famous for its edible bamboo shoots and fast-growing timber. The green and yellow striped-culm B. oldhamii variety, named B. oldhamii f. revoluta W.T. Lin & J. Y. Lin, is an attractive system for researching the culm color variation of B. oldhamii.MethodsMillions of clean reads were generated and assembled into 604,900 transcripts, and 383,278 unigenes were acquired with RNA-seq technology. The quantification of ABA, IAA, JA, GA1, GA3, GA4, and GA7 was performed using HPLC–MS/MS platforms.ResultsDifferential expression analysis showed that 449 unigenes were differentially expressed genes (DEGs), among which 190 DEGs were downregulated and 259 DEGs were upregulated in B. oldhamii f. revoluta. Phytohormone contents, especially GA1 and GA7, were higher in B. oldhamii. Approximately 21 transcription factors (TFs) were differentially expressed between the two groups: the bZIP, MYB, and NF-YA transcription factor families had the most DEGs, indicating that those TFs play important roles in B. oldhamii culm color variation. RNA-seq data were confirmed by quantitative RT-PCR analysis of the selected genes; moreover, phytohormone contents, especially those of ABA, GA1 and GA7, were differentially accumulated between the groups. Our study provides a basal gene expression and phytohormone analysis of B. oldhamii culm color variation, which could provide a solid fundamental theory for investigating bamboo culm color variation.
creator: Yulian Jiao
creator: Hu Zeng
creator: Haitao Xia
creator: Yueying Wang
creator: Jinwang Wang
creator: Chuan Jin
uri: https://doi.org/10.7717/peerj.12796
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Jiao et al.

title: Old trees are perceived as a valuable element of the municipal forest landscape
link: https://peerj.com/articles/12700
last-modified: 2022-01-12
description: Urban trees are important to maintain biodiversity and, therefore, need public acceptance. Few studies, however, have addressed the topic of social acceptability of old trees. The aim of this research was to examine city residents’ perception of old trees, including hollow-bearing ones, mainly in the aspect of safety and aesthetics. A total of 448 Warsaw municipal forest’ users expressed their opinions by completing an online questionnaire. Several methods were used to analyse the results of the study: the Chi-square test of independence, the Kruskal–Wallis H test, the Mann–Whitney U test and the Quartimax method of factor rotation analysis. The results revealed a correlation between the frequency of forest visits and the level of sensitivity toward old trees, which translates to less radical notion of danger and less radical decisions about cutting such trees down. Age of the respondents (56+) was a factor contributing to higher willingness to protect and care for old trees. The results also indicated that outdoor activity in the urban forest may increase ancient trees acceptance by developing emotional connection with them, and eventually contribute to their protection.
creator: Marzena Suchocka
creator: Magdalena Wojnowska-Heciak
creator: Magdalena Błaszczyk
creator: Agnieszka Gawłowska
creator: Joanna Ciemniewska
creator: Agata Jarska
creator: Jakub Heciak
creator: Beata Pachnowska
uri: https://doi.org/10.7717/peerj.12700
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Suchocka et al.

title: Waterlogging tolerance and recovery capability screening in peanut: a comparative analysis of waterlogging effects on physiological traits and yield
link: https://peerj.com/articles/12741
last-modified: 2022-01-12
description: Fifteen peanut varieties at the pod filling stage were exposed to waterlogging stress for 7 days, the enzyme activities and fluorescence parameters were measured after 7 days of waterlogging and drainage. The waterlogging tolerance and recovery capability of varieties were identified. After waterlogging, waterlogging tolerance coefficient (WTC) of relative electrolyte linkage (REL), malondialdehyde (MDA) content, superoxide dismutase (SOD) activity, and catalase (CAT) activity, non-photochemical quenching (NPQ) and photochemical quenching (qL) of leaves of most peanut varieties were increased, while the WTC of the soil and plant analysis development (SPAD) value, PS II actual quantum yield (ΦPS II), maximum photochemical efficiency (Fv/Fm) were decreased. After drainage, the WTC of REL, MDA content, SOD and CAT activity of leaves were decreased compared with that of after waterlogging, but these indicators of a few cultivars were increased. ΦPS II, Fv/Fm and qL can be used as important indexes to identify waterlogging recovery capability. There was a significant negative correlation between recovery capability and the proportion of reduction in yield, while no significant correlation was found between waterlogging tolerance and the proportion of reduction in yield. Therefore, it is recommended to select varieties with high recovery capability and less pod number reduction under waterlogging in peanut breeding and cultivation.
creator: Ruier Zeng
creator: Jing Cao
creator: Xi Li
creator: Xinyue Wang
creator: Ying Wang
creator: Suzhe Yao
creator: Yu Gao
creator: Jing Hu
creator: Mingzhu Luo
creator: Lei Zhang
creator: Tingting Chen
uri: https://doi.org/10.7717/peerj.12741
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zeng et al.

title: Extra high superoxide dismutase in host tissue is associated with improving bleaching resistance in “thermal adapted” and Durusdinium trenchii-associating coral
link: https://peerj.com/articles/12746
last-modified: 2022-01-12
description: Global warming threatens reef-building corals with large-scale bleaching events; therefore, it is important to discover potential adaptive capabilities for increasing their temperature resistance before it is too late. This study presents two coral species (Platygyra verweyi and Isopora palifera) surviving on a reef having regular hot water influxes via a nearby nuclear power plant that exhibited completely different bleaching susceptibilities to thermal stress, even though both species shared several so-called “winner” characteristics (e.g., containing Durusdinium trenchii, thick tissue, etc.). During acute heating treatment, algal density did not decline in P. verweyi corals within three days of being directly transferred from 25 to 31 °C; however, the same treatment caused I. palifera to lose < 70% of its algal symbionts within 24 h. The most distinctive feature between the two coral species was an overwhelmingly higher constitutive superoxide dismutase (ca. 10-fold) and catalase (ca. 3-fold) in P. verweyi over I. palifera. Moreover, P. verweyi also contained significantly higher saturated and lower mono-unsaturated fatty acids, especially a long-chain saturated fatty acid (C22:0), than I. palifera, and was consistently associated with the symbiotic bacteria Endozoicomonas, which was not found in I. palifera. However, antibiotic treatment and inoculation tests did not support Endozoicomonas having a direct contribution to thermal resistance. This study highlights that, besides its association with a thermally tolerable algal symbiont, a high level of constitutive antioxidant enzymes in the coral host is crucial for coral survivorship in the more fluctuating and higher temperature environments.
creator: Jih-Terng Wang
creator: Yi-Ting Wang
creator: Chaolun Allen Chen
creator: Pei-Jei Meng
creator: Kwee Siong Tew
creator: Pei-Wen Chiang
creator: Sen-Lin Tang
uri: https://doi.org/10.7717/peerj.12746
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Communities of T4-like bacteriophages associated with bacteria in Lake Baikal: diversity and biogeography
link: https://peerj.com/articles/12748
last-modified: 2022-01-12
description: Lake Baikal phage communities are important for lake ecosystem functioning. Here we describe the diversity of T4-bacteriophage associated with the bacterial fraction of filtered water samples collected from the pelagic zone, coastal zone and shallow bays. Although the study of the diversity of phages for the g23 gene has been carried out at Lake Baikal for more than ten years, shallow bays that comprise a significant part of the lake’s area have been neglected, and this gene has not previously been studied in the bacterial fraction. Phage communities were probed using amplicon sequencing methods targeting the gene of major capsid protein (g23) and compared phylogenetically across sample locations and with sequences previously retrieved from non-bacterial fractions (<0.2 um) and biofilms (non-fractionated). In this study, we examined six water samples, in which 24 to 74 viral OTUs were obtained. The sequences from shallow bays largely differed from those in the pelagic and coastal samples and formed individual subcluster in the UPGMA tree that was obtained from the comparison of phylogenetic distances of g23 sequence sets from various ecosystems, reflecting differences in viral communities depending on the productivity of various sites of Lake Baikal. According to the RefSeq database, from 58.3 to 73% of sequences of each sample had cultivated closest relatives belonging to cyanophages. In this study, for phylogenetic analysis, we chose the closest relatives not only from the RefSeq and GenBank NR databases but also from two marine and one freshwater viromes: eutrophic Osaka Bay (Japan), oligotrophic area of the Pacific Ocean (Station ALOHA) and mesotrophic and ancient Lake Biwa (Japan), which allowed us to more fully compare the diversity of marine and freshwater phages. The identity with marine sequences at the amino acid level ranged from 35 to 80%, and with the sequences from the viral fraction and bacterial one from Lake Biwa—from 35.3 to 98% and from 33.9 to 89.1%, respectively. Therefore, the sequences from marine viromes had a greater difference than those from freshwater viromes, which may indicate a close relationship between freshwater viruses and differences from marine viruses.
creator: Sergey Anatoljevich Potapov
creator: Irina Vasilievna Tikhonova
creator: Andrey Yurjevich Krasnopeev
creator: Maria Yurjevna Suslova
creator: Natalia Albertovna Zhuchenko
creator: Valentin Valerianovich Drucker
creator: Olga Ivanovna Belykh
uri: https://doi.org/10.7717/peerj.12748
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Potapov et al.

title: Effects of different intensities of long-term grazing on plant diversity, biomass and carbon stock in alpine shrubland on the Qinghai-Tibetan Plateau
link: https://peerj.com/articles/12771
last-modified: 2022-01-12
description: Grazing is the main grassland management strategy applied in alpine shrubland ecosystems on the Qinghai-Tibetan Plateau. However, how different intensities of long-term grazing affect plant diversity, biomass accumulation and carbon (C) stock in these ecosystems is poorly understood. In this study, alpine shrubland with different long-term (more than 30 years) grazing intensities (excluded from grazing for 5 years (EX), light grazing (LG), moderate grazing (MG) and heavy grazing (HG)) on the Qinghai-Tibetan Plateau were selected to study changes in plant diversity, aboveground biomass and C accumulation, as well as distribution of C stock among biomass components and soil depths. A structural equation model was used to illustrate the impact of grazing on the soil carbon stock (SOC). The results showed that the Shannon–Wiener diversity index and richness index of herbaceous plants, shrubs, and communities first significantly increased and then decreased with increasing grazing intensity, reaching maxima at the LG site. The aboveground and belowground and litter biomass of understory herbaceous plants, shrubs and communities decreased with increasing grazing intensity, reaching maxima at the EX site. The aboveground and belowground biomass C storage decreased with increasing grazing intensity, reaching maxima at the EX site. The SOC stock and total ecosystem C stock decreased with increasing grazing intensity, reaching maxima at the EX and LG sites. A structural equation model showed that grazing-induced changes in the belowground biomass of understory herbaceous plants greatly contributed to the SOC stock decrease. Thus, considering the utilization and renewal of grassland resources, as well as local economic benefits and ecological effects, LG may be a more rational grazing intensity for species diversity conservation and ecosystem C sequestration in alpine shrubland. Our results provide new insights for incorporating grazing intensity into shrub ecosystem C stock and optimizing grazing management and grassland ecosystem C management.
creator: Jinlan Wang
creator: Wen Li
creator: Wenxia Cao
creator: Shilin Wang
uri: https://doi.org/10.7717/peerj.12771
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Differences in the expression profiles of lncRNAs and mRNAs in partially injured anterior cruciate ligament and medial collateral ligament of rabbits
link: https://peerj.com/articles/12781
last-modified: 2022-01-12
description: Long noncoding RNAs (lncRNAs), as a novel regulatory factor, are considered to play a vital role in various biological processes and diseases. However, the overall expression profile and biological functions of lncRNAs in the partially injured anterior cruciate ligament (ACL) and medial collateral ligament (MCL) have not been clearly explored. Partially injured models of ACL and MCL were established in 3-month-old healthy male New Zealand white rabbits. Expression of lncRNAs and mRNAs in the ligament tissue was detected by high-throughput sequencing technology, and biological functions of differentially expressed RNAs were evaluated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Validation of several differentially expressed RNAs was performed using quantitative real-time PCR (qRT-PCR). Protein-protein interaction (PPI) analysis and competitive endogenous RNA (ceRNA) prediction were used to identify interactions among hub genes and the interaction among lncRNAs, miRNAs, and mRNAs. The results showed that compared with the normal group, there were 267 mRNAs and 329 lncRNAs differentially expressed in ACL and 726 mRNAs and 609 lncRNAs in MCL in the injured group. Compared with MCL, 420 mRNAs and 470 lncRNAs were differentially expressed in ACL in the normal group; 162 mRNAs and 205 lncRNAs were differentially expressed in ACL in the injured group. Several important lncRNAs and genes were identified, namely, COL7A1, LIF, FGFR2, EPHA2, CSF1, MMP2, MMP9, SOX5, LOX, MSTRG.1737.1, MSTRG.26038.25, MSTRG.20209.5, MSTRG.22764.1, and MSTRG.18113.1, which are closely related to inflammatory response, tissue damage repair, cell proliferation, differentiation, migration, and apoptosis. Further study of the functions of these genes may help to better understand the specific molecular mechanisms underlying the occurrence of endogenous repair disorders in ACL, which may provide new ideas for further exploration of effective means to promote endogenous repair of ACL injury.
creator: Huining Gu
creator: Siyuan Chen
creator: Mingzheng Zhang
creator: Yu Wen
creator: Bin Li
uri: https://doi.org/10.7717/peerj.12781
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Gu et al.

title: CTRP3 as a novel biomarker in the plasma of Saudi children with autism
link: https://peerj.com/articles/12630
last-modified: 2022-01-11
description: BackgroundC1q/tumor necrosis factor-related protein-3 (CTRP3) has diverse functions: anti-inflammation, metabolic regulation, and protection against endothelial dysfunction.MethodsThe plasma level of CTRP3 in autistic patients (n = 32) was compared to that in controls (n = 37) using ELISA.ResultsCTRP3 was higher (24.7% with P < 0.05) in autistic patients than in controls. No association was observed between CTRP3 and the severity of the disorder using the Childhood Autism Rating Scale (CARS). A positive correlation between CARs and the age of patients was reported. Receiver operating characteristic (ROC) analysis demonstrated a low area under the curve (AUC) for all patients (0.636). Low AUCs were also found in the case of severe patients (0.659) compared to controls, but both values were statistically significant (P ≤ 0.05). Despite the small sample size, we are the first to find an association between CTRP3 and autism spectrum disorder (ASD).
creator: Manan Alhakbany
creator: Laila Al-Ayadhi
creator: Afaf El-Ansary
uri: https://doi.org/10.7717/peerj.12630
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Alhakbany et al.

title: Biochemical profile in mixed martial arts athletes
link: https://peerj.com/articles/12708
last-modified: 2022-01-11
description: The study aimed to evaluate changes in selected biochemical indicators among mixed martial arts competitors in subsequent periods of the training cycle. The research involved 12 mixed martial arts athletes aged 25.8 ± 4.2 years competing in the intermediate category. Selected somatic indicators were measured twice. Biochemical indicators were assessed five times during the 14-week study period. Serum concentrations of testosterone, cortisol, uric acid, myoglobin, total protein, interleukin 6, and tumor necrosis factor, as well as creatine kinase activity were determined. One hour after sparring completion, there were significant increases in cortisol (by 54.9%), uric acid (22.0%), myoglobin (565.0%), and interleukin 6 (280.3%) as compared with the values before the simulated fight. The highest creatine kinase activity (893.83 ± 139.31 U/l), as well as tumor necrosis factor (3.93 ± 0.71 pg/ml) and testosterone (5.83 ± 0.81 ng/ml) concentrations (p = 0.00) were recorded 24 hours after the simulation. Systematic observation of selected blood biochemical indicators in the training process periodization in mixed martial arts helps understand adaptive, compensatory, and regenerative mechanisms occurring in training athletes.
creator: Łukasz Marcin Tota
creator: Szczepan Stanisław Wiecha
uri: https://doi.org/10.7717/peerj.12708
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Tota and Wiecha

title: A decision support system for primary headache developed through machine learning
link: https://peerj.com/articles/12743
last-modified: 2022-01-11
description: BackgroundPrimary headache is a disorder with a high incidence and low diagnostic accuracy; the incidence of migraine and tension-type headache ranks first among primary headaches. Artificial intelligence (AI) decision support systems have shown great potential in the medical field. Therefore, we attempt to use machine learning to build a clinical decision-making system for primary headaches.MethodsThe demographic data and headache characteristics of 173 patients were collected by questionnaires. Decision tree, random forest, gradient boosting algorithm and support vector machine (SVM) models were used to construct a discriminant model and a confusion matrix was used to calculate the evaluation indicators of the models. Furthermore, we have carried out feature selection through univariate statistical analysis and machine learning.ResultsIn the models, the accuracy, F1 score were calculated through the confusion matrix. The logistic regression model has the best discrimination effect, with the accuracy reaching 0.84 and the area under the ROC curve also being the largest at 0.90. Furthermore, we identified the most important factors for distinguishing the two disorders through statistical analysis and machine learning: nausea/vomiting and photophobia/phonophobia. These two factors represent potential independent factors for the identification of migraines and tension-type headaches, with the accuracy reaching 0.74 and the area under the ROC curve being at 0.74.ConclusionsApplying machine learning to the decision-making system for primary headaches can achieve a high diagnostic accuracy. Among them, the discrimination effect obtained by the integrated algorithm is significantly better than that of a single learner. Second, nausea/vomiting, photophobia/phonophobia may be the most important factors for distinguishing migraine from tension-type headaches.
creator: Fangfang Liu
creator: Guanshui Bao
creator: Mengxia Yan
creator: Guiming Lin
uri: https://doi.org/10.7717/peerj.12743
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Liu et al.

title: Genome-wide identification and expression analysis of the cucumber PYL gene family
link: https://peerj.com/articles/12786
last-modified: 2022-01-11
description: Abscisic acid (ABA) is a very important hormone in plants. It regulates growth and development of plants and plays an important role in biotic and abiotic stresses. The Pyrabactin resistance 1-like (PYR/PYL) proteins play a central role in ABA signal transduction pathways. The working system of PYL genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. Through bioinformatics, a total of 14 individual PYL genes were identified in Chinese long ‘9930’ cucumber. Fourteen PYL genes were distributed on six chromosomes of cucumber, and their encoded proteins predicted to be distributed in cytoplasm and nucleus. Based on the phylogenetic analysis, the PYL genes of cucumber, Arabidopsis, rice, apple, Brachypodium distachyon and soybeancould be classified into three groups. Genetic structures and conserved domains analysis revealed that CsPYL genes in the same group have similar exons and conserved domains. By predicting cis-elements in the promoters, we found that all CsPYL members contained hormone and stress-related elements. Additionally, the expression patterns of CsPYL genes were specific in tissues. Finally, we further examined the expression of 14 CsPYL genes under ABA, PEG, salt stress. The qRT-PCR results showed that most PYL gene expression levels were up-regulated. Furthermore, with different treatments about 3h, the relative expression of PYL8 was up-regulated and more than 20 times higher than 0h. It indicated that this gene may play an important role in abiotic stress.
creator: Zeyu Zhang
creator: Shilei Luo
creator: Zeci Liu
creator: Zilong Wan
creator: Xueqin Gao
creator: Yali Qiao
creator: Jihua Yu
creator: Guobin Zhang
uri: https://doi.org/10.7717/peerj.12786
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhang et al.

title: Spatiotemporal variations in length-weight relationship, growth pattern and condition factor of Periophthalmus variabilis Eggert, 1935 in Vietnamese Mekong Delta
link: https://peerj.com/articles/12798
last-modified: 2022-01-11
description: Length-weight relationship (LWR), growth pattern and condition factor (CF) play a vital role in fish resource evaluation and management but data on this is limited for Periophthalmus variabilis. This is an amphibious fish that lives in the mudflats of the mangrove forests in the Western Pacific regions, including the Vietnamese Mekong Delta (VMD). This paper contributes to the understanding of the LWR, growth pattern and CF of P. variabilis. Fish specimens were collected by hand at four sites in the VMD from April 2020 to March 2021. The analysis of 495 individual fish (259 females and 236 males) showed that fish weight could be estimated from a given fish length due to high determination values (r2 = 0.70 − 0.97). Dusky-gilled mudskippers of the VMD exhibited positive allometry, as indicated by their larger than 3 b value (b = 3.094 ± 0.045, p = 0.04). However, the growth pattern of the mudskipper between the sex and maturation stage (immature versus mature) showed isometry. These fish displayed positive allometry in the dry season (b = 3.138 ± 0.065) (>3, p = 0.04) but isometry in the wet season (b = 3.058 ± 0.061) (≈3, p = 0.34). Fish growth ranged from isometry to positive allometry and varied by site (b = 2.850 ± 0.103–3.370 ± 0.114) and month (b = 2.668 ± 0.184–3.588 ± 0.299) based on the b value. The CF of P. variabilis was not affected by sex (p = 0.29), body size (p = 0.64) or season (p = 0.43), but was affected by site (p = 0.01) and month (p = 0.01). The CF of this species (1.05 ± 0.02) was higher than 1 (p < 0.001), indicating that the fish adapted well to their habitat.
creator: Quang Minh Dinh
creator: Ton Huu Duc Nguyen
creator: Tien Thi Kieu Nguyen
creator: Giang Van Tran
creator: Ngon Trong Truong
uri: https://doi.org/10.7717/peerj.12798
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Dinh et al.

title: Validity and reliability evidence for the Behavioral Regulation in Sport Questionnaire with Romanian professional athletes
link: https://peerj.com/articles/12803
last-modified: 2022-01-11
description: BackgroundDespite the importance attributed to athletes’ motivation in sports performance and well-being; no measures of motivation toward sport were found in the Romanian sport context.ObjectiveGrounded in self-determination theory, this research aimed to adapt and to gather validity and reliability evidence supporting the use of the Behavioral Regulation in Sport Questionnaire (BRSQ) in the Romanian sport domain.MethodThe participants were 596 Romanian professional athletes (age: M = 22.91, SD = 5.84; sports experience: M = 11.14, SD = 5.03), who 273 practiced individual sports and 323 team sports. They completed an online questionnaire survey assessing their perception of behavioral regulation, resilience and burnout in sport.ResultsConfirmatory factor analysis supported the six-factor correlated model, which was invariant across age and sport. Correlations among latent factors configured a simplex structure, underpinning the self-determination continuum. Average variance extracted values from .50 to .70 endorsed convergent validity. Scores for heterotrait-monotrait ratio of correlations as high as .88, as well as 95% confidence intervals of each interfactor correlation that did not include 1.00 supported discriminant validity. Values over .70 for Cronbach’s alpha, McDonald’s omega and Raykov’s coefficients showed a good level of reliability for each factor. Linear regression analysis revealed that while intrinsic motivation, integrated regulation and identified regulation positively predicted resilience, introjected regulation, external regulation and amotivation positively predicted burnout.ConclusionsThe BRSQ is shown to be a valid and reliable measure of the six types of behavioral regulation in the Romanian sport context.
creator: Cristina Ioana Alexe
creator: Dan Iulian Alexe
creator: Gabriel Mareş
creator: Dragoş Ioan Tohănean
creator: Ioan Turcu
creator: Rafael Burgueño
uri: https://doi.org/10.7717/peerj.12803
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Alexe et al.

title: Medical cannabis use in Thailand after its legalization: a respondent-driven sample survey
link: https://peerj.com/articles/12809
last-modified: 2022-01-11
description: BackgroundMany countries now allow the consumption of cannabis or cannabinoids for medical purposes with varying approaches concerning products allowed and the regulatory frameworks prevailing their endowment. On 18 February 2019 Thailand passed legislation allowing the use of cannabis for medical purposes. This study aimed to examine patterns and purposes for consumption of medical cannabis, and consumers’ perceptions and opinions towards benefits and harms of cannabis and related policies in 2019–2020.MethodsA cross-sectional study using a respondent-driven sampling (RDS) method was conducted in four sites across Thailand. Participants were 485 adults aged 18 years and over, living in the study region, who had used cannabis for medical purposes within the past 12 months. Face-to-face interviews using a structured questionnaire were used to collect data on (1) demographic characteristics, (2) pattern of consumption, (3) source of information and perception of benefits and harms of medical cannabis, and (4) opinion towards cannabis policies. Data were analyzed using RDS Analyst and presented as percentage and mean with 95% confidence interval (CI).ResultsMost participants (84.7%, 95% CI [78.9–90.5]) used an oral form of crude oil extract while 9.2% (95% CI [4.1–14.2]) used the raw form. The most common uses were for treatment of cancers (23.3%, 95% CI [16.1–30.4]), neuropsychiatric symptoms (22.8%, 95% CI [17.5–28.0]), and musculoskeletal pains (21.6%, 95% CI [16.7–26.6]). Illegal sources such as underground traders (54.5%, 95% CI [40.8–68.3]), friends and relatives (12.2%, 95% CI [6.2–18.3]), not-for-profit provider groups (5.2%, 95% CI [0.5–10.9]), and clandestine growers or producers (2.9%, 95% CI [0.6–5.3]) were the main suppliers. Most (>80%) perceived cannabis could treat cancers, chronic pains, insomnia, Parkinson’s disease and generalized anxiety disorder. Less than half perceived that cannabis could cause adverse conditions e.g., palpitation, panic, memory impairment and schizophrenic-like psychosis. Most respondents agreed or strongly agreed with the policies regarding permission to use cannabis for medical purposes (95.1%, 95% CI [92.0–98.2]), for the legal sale of medical cannabis products (95.9%, 95% CI [93.7–98.2]), and for people to grow cannabis for medical use (94.2%, 95% CI [91.8–96.5]). However, only two-thirds agreed with policies concerning the sales of cannabis (65.3%, 95% CI [56.9–73.7]) and home-grown cannabis for recreational purposes (61.3%, 95% CI [52.7–69.9]).ConclusionOur study reports the experiences of consumers of medical cannabis in the first year after its legalization in Thailand. Consumers reported various patterns and indications of consumption that were not supported by scientific evidence, but had positive perception of the results of consumption. These findings highlight ongoing policy challenges for Thailand and can be a lesson to be learned for other countries in the region.
creator: Sawitri Assanangkornchai
creator: Kanittha Thaikla
creator: Muhammadfahmee Talek
creator: Darika Saingam
uri: https://doi.org/10.7717/peerj.12809
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Assanangkornchai et al.

title: Postural stability disorders—early signs of aging—in physically non-active prisoners
link: https://peerj.com/articles/12489
last-modified: 2022-01-10
description: BackgroundThere is a need for a study of possible relationship between serving a prison sentence and developing postural stability dysfunction. The aim of the study was to analyze postural stability of physically inactive prisoners. The study group consisted of 24 male prisoners aged 34.6 ± 7.02 years, imprisoned in closed prison and 30 healthy, non-active physically, aged 36.9 ± 7.5 years, who consisted control group. The subjects were imprisoned for a mean of 105.43 ± 58.48 months.MethodsThe static balance test was conducted on bi-modular stabilometric platform CQStab2P.ResultsWe found statistically significant differences in several stability parameters. Prisoners results were significantly worse in parameters measured with eyes open: MA (mean amplitude p < 0.01), MAAP (mean amplitude in anterio–posterior plane p < 0.03), MAML (mean amplitude in medio—lateral plane p < 0.04), MaxAP (maximal sway in AP p < 0.01), MaxML (p < 0.01). With eyes closed the prisoner’s results were significantly worse in SPML (sway path in medio-lateral plane p = 0.01), better in MAML (p < 0.01) and MaxML (p < 0.01), and faster in MVML (mean velocity in medio-lateral plane p < 0.01).Conclusions(1) Diagnostics aimed at early diagnoses of ageing symptoms should be performed in prisons. It would allow for better prisoner management in terms of assessment of ability to work, free time activity offer and falls prevention. (2) In prisons, in addition to counteracting the typical causes of balance disorders, action should be taken to counteract the causes for balance disorders typical for prison environment, inter alia: sensory deprivation—by implementing programmes comprehensively activating prisoners, and hypokinesis—by implementing physical activity programmes that cater for the needs of older prisoners.
creator: Piotr Łapiński
creator: Aleksandra Truszczyńska-Baszak
creator: Justyna Drzał-Grabiec
creator: Adam Tarnowski
uri: https://doi.org/10.7717/peerj.12489
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Łapiński et al.

title: An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina
link: https://peerj.com/articles/12713
last-modified: 2022-01-10
description: Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the “upstream” colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
creator: Nikolay A. Poyarkov
creator: Tan Van Nguyen
creator: Parinya Pawangkhanant
creator: Platon V. Yushchenko
creator: Peter Brakels
creator: Linh Hoang Nguyen
creator: Hung Ngoc Nguyen
creator: Chatmongkon Suwannapoom
creator: Nikolai Orlov
creator: Gernot Vogel
uri: https://doi.org/10.7717/peerj.12713
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Poyarkov et al.

title: DNA barcoding and morphological identification of spiny lobsters in South Korean waters: a new record of Panulirus longipes and Panulirus homarus homarus
link: https://peerj.com/articles/12744
last-modified: 2022-01-10
description: To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.
creator: Sachithra Amarin Hettiarachchi
creator: Ji-Yeon Hyeon
creator: Angka Mahardini
creator: Hyung-Suk Kim
creator: Jun-Hwan Byun
creator: Han-Jun Kim
creator: Jong-Gyun Jeong
creator: Jung-Kyu Yeo
creator: Shin-Kwon Kim
creator: Se-Jae Kim
creator: Youn-Seong Heo
creator: Jonathan Sathyadith
creator: Do-Hyung Kang
creator: Sung-Pyo Hur
uri: https://doi.org/10.7717/peerj.12744
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Hettiarachchi et al.

title: Effects of soil fauna on litter decomposition in Chinese forests: a meta-analysis
link: https://peerj.com/articles/12747
last-modified: 2022-01-10
description: Litter quality and climate have been presumed to be the dominant factors regulating litter decomposition rates on broad spatial scales. However, the role of soil fauna on litter decomposition is poorly understood, despite the fact that it could strongly influence decomposition by fragmentation and subsequent modification of the activities of microorganisms.In this study, we carried out a meta-analysis on the effects of soil fauna on litter decomposition rates in Chinese forests, ranging from boreal to tropical forests, based on data from 20 studies. The effects of climatic factors on decomposition rate were assessed by comparing the contribution of soil fauna to litter decomposition from studies carried out at different latitudes.The degree of influence of the soil fauna was in the order tropical (200%) > subtropical (47%) > temperate forest (28%). Comparing the effect size of soil fauna, it was found that when soil fauna was excluded, the decomposition rate, calculated using Olson’s equation, was most affected in tropical forest (−0.77), while the litter decomposition rate both subtropical (−0.36) and temperate forest (−0.19) were also suppressed to varying degrees (P < 0.001). These results highlight that soil fauna could promote litter decomposition to different extents. Using stepwise multiple linear regression, the effect size of the soil fauna was negatively correlated with the cellulose and nitrogen concentrations of the initial litter material. In Chinese forests, litter decomposition rates were reduced, on average, by 65% when soil fauna was excluded. The impact of soil fauna on decomposition was shown to be closely related to climate and litter quality.
creator: Peng Zan
creator: Zijun Mao
creator: Tao Sun
uri: https://doi.org/10.7717/peerj.12747
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zan et al.

title: The speed of information propagation in the scientific network distorts biomedical research
link: https://peerj.com/articles/12764
last-modified: 2022-01-10
description: Delays in the propagation of scientific discoveries across scientific communities have been an oft-maligned feature of scientific research for introducing a bias towards knowledge that is produced within a scientist’s closest community. The vastness of the scientific literature has been commonly blamed for this phenomenon, despite recent improvements in information retrieval and text mining. Its actual negative impact on scientific progress, however, has never been quantified. This analysis attempts to do so by exploring its effects on biomedical discovery, particularly in the discovery of relations between diseases, genes and chemical compounds. Results indicate that the probability that two scientific facts will enable the discovery of a new fact depends on how far apart these two facts were originally within the scientific landscape. In particular, the probability decreases exponentially with the citation distance. Thus, the direction of scientific progress is distorted based on the location in which each scientific fact is published, representing a path-dependent bias in which originally closely-located discoveries drive the sequence of future discoveries. To counter this bias, scientists should open the scope of their scientific work with modern information retrieval and extraction approaches.
creator: Raul Rodriguez-Esteban
uri: https://doi.org/10.7717/peerj.12764
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Rodriguez-Esteban

title: Tentacle patterning during Exaiptasia diaphana pedal lacerate development differs between symbiotic and aposymbiotic animals
link: https://peerj.com/articles/12770
last-modified: 2022-01-10
description: Exaiptasia diaphana, a tropical sea anemone known as Aiptasia, is a tractable model system for studying the cellular, physiological, and ecological characteristics of cnidarian-dinoflagellate symbiosis. Aiptasia is widely used as a proxy for coral-algal symbiosis, since both Aiptasia and corals form a symbiosis with members of the family Symbiodiniaceae. Laboratory strains of Aiptasia can be maintained in both the symbiotic (Sym) and aposymbiotic (Apo, without algae) states. Apo Aiptasia allow for the study of the influence of symbiosis on different biological processes and how different environmental conditions impact symbiosis. A key feature of Aiptasia is the ease of propagating both Sym and Apo individuals in the laboratory through a process called pedal laceration. In this form of asexual reproduction, small pieces of tissue rip away from the pedal disc of a polyp, then these lacerates eventually develop tentacles and grow into new polyps. While pedal laceration has been described in the past, details of how tentacles are formed or how symbiotic and nutritional state influence this process are lacking. Here we describe the stages of development in both Sym and Apo pedal lacerates. Our results show that Apo lacerates develop tentacles earlier than Sym lacerates, while over the course of 20 days, Sym lacerates end up with a greater number of tentacles. We describe both tentacle and mesentery patterning during lacerate development and show that they form through a single pattern in early stages regardless of symbiotic state. In later stages of development, Apo lacerate tentacles and mesenteries progress through a single pattern, while variable patterns were observed in Sym lacerates. We discuss how Aiptasia lacerate mesentery and tentacle patterning differs from oral disc regeneration and how these patterning events compare to postembryonic development in Nematostella vectensis, another widely-used sea anemone model. In addition, we demonstrate that Apo lacerates supplemented with a putative nutrient source developed an intermediate number of tentacles between un-fed Apo and Sym lacerates. Based on these observations, we hypothesize that pedal lacerates progress through two different, putatively nutrient-dependent phases of development. In the early phase, the lacerate, regardless of symbiotic state, preferentially uses or relies on nutrients carried over from the adult polyp. These resources are sufficient for lacerates to develop into a functional polyp. In the late phase of development, continued growth and tentacle formation is supported by nutrients obtained from either symbionts and/or the environment through heterotrophic feeding. Finally, we advocate for the implementation of pedal lacerates as an additional resource in the Aiptasia model system toolkit for studies of cnidarian-dinoflagellate symbiosis.
creator: Jason S. Presnell
creator: Elizabeth Wirsching
creator: Virginia M. Weis
uri: https://doi.org/10.7717/peerj.12770
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Presnell et al.

title: Identifying and prioritising climate change adaptation actions for greater one-horned rhinoceros (Rhinoceros unicornis) conservation in Nepal
link: https://peerj.com/articles/12795
last-modified: 2022-01-10
description: Climate change has started impacting species, ecosystems, genetic diversity within species, and ecological interactions and is thus a serious threat to conserving biodiversity globally. In the absence of adequate adaptation measures, biodiversity may continue to decline, and many species will possibly become extinct. Given that global temperature continues to increase, climate change adaptation has emerged as an overarching framework for conservation planning. We identified both ongoing and probable climate change adaptation actions for greater one-horned rhinoceros conservation in Nepal through a combination of literature review, key informant surveys (n = 53), focus group discussions (n = 37) and expert consultation (n = 9), and prioritised the identified adaptation actions through stakeholder consultation (n = 17). The majority of key informants (>80%) reported that climate change has been impacting rhinoceros, and more than 65% of them believe that rhinoceros habitat suitability in Nepal has been shifting westwards. Despite these perceived risks, climate change impacts have not been incorporated well into formal conservation planning for rhinoceros. Out of 20 identified adaptation actions under nine adaptation strategies, identifying and protecting climate refugia, restoring the existing habitats through wetland and grassland management, creating artificial highlands in floodplains to provide rhinoceros with refuge during severe floods, and translocating them to other suitable habitats received higher priority. These adaptation actions may contribute to reducing the vulnerability of rhinoceros to the likely impacts of climate change. This study is the first of its kind in Nepal and is expected to provide a guideline to align ongoing conservation measures into climate change adaptation planning for rhinoceros. Further, we emphasise the need to integrating likely climate change impacts while planning for rhinoceros conservation and initiating experimental research and monitoring programs to better inform adaptation planning in the future.
creator: Ganesh Pant
creator: Tek Maraseni
creator: Armando Apan
creator: Benjamin L. Allen
uri: https://doi.org/10.7717/peerj.12795
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Pant et al.

title: Identification and expression analysis of the sucrose synthase gene family in pomegranate (Punica granatum L.)
link: https://peerj.com/articles/12814
last-modified: 2022-01-10
description: BackgroundSucrose synthase (SUS, EC 2.4.1.13) is one of the major enzymes of sucrose metabolism in higher plants. It has been associated with C allocation, biomass accumulation, and sink strength. The SUS gene families have been broadly explored and characterized in a number of plants. The pomegranate (Punica granatum) genome is known, however, it lacks a comprehensive study on its SUS genes family.MethodsPgSUS genes were identified from the pomegranate genome using a genome-wide search method. The PgSUS gene family was comprehensively analyzed by physicochemical properties, evolutionary relationship, gene structure, conserved motifs and domains, protein structure, syntenic relationships, and cis-acting elements using bioinformatics methods. The expression pattern of the PgSUS gene in different organs and fruit development stages were assayed with RNA-seq obtained from the NCBI SRA database as well as real-time quantitative polymerase chain reaction (qPCR).ResultsFive pomegranate SUS genes, located on four different chromosomes, were divided into three subgroupsaccording to the classification of other seven species. The PgSUS family was found to be highly conserved during evolution after studying the gene structure, motifs, and domain analysis. Furthermore, the predicted PgSUS proteins showed similar secondary and tertiary structures. Syntenic analysis demonstrated that four PgSUS genes showed syntenic relationships with four species, with the exception of PgSUS2. Predictive promoter analysis indicated that PgSUS genes may be responsive to light, hormone signaling, and stress stimulation. RNA-seq analysis revealed that PgSUS1/3/4 were highly expressed in sink organs, including the root, flower, and fruit, and particularly in the outer seed coats. qPCR analysis showed also that PgSUS1, PgSUS3, and PgSUS4 were remarkably expressed during fruit seed coat development. Our results provide a systematic overview of the PgSUS gene family in pomegranate, developing the framework for further research and use of functional PgSUS genes.
creator: Longbo Liu
creator: Jie Zheng
uri: https://doi.org/10.7717/peerj.12814
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Liu and Zheng

title: KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
link: https://peerj.com/articles/12692
last-modified: 2022-01-07
description: The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance and clearing viral infections. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Inferring KIR gene content from genetic variant data is therefore desirable for immunogenetic analysis, particularly in the context of growing biobank genome data collections that rely on genotyping by microarray. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 807 Finnish biobank samples genotyped for 5900 KIR-region SNPs and analysed for KIR gene content with targeted sequencing. Cross-validation results demonstrate a high mean overall accuracy of 98.5% (95% CI [97.0–99.2]%) which compares favourably with previous methods including short-read sequencing based approaches.
creator: Jarmo Ritari
creator: Kati Hyvärinen
creator: Jukka Partanen
creator: Satu Koskela
uri: https://doi.org/10.7717/peerj.12692
license: https://creativecommons.org/licenses/by-nc/4.0/
rights: ©2022 Ritari et al.

title: Antigenic properties of the SARS-CoV-2 nucleoprotein are altered by the RNA admixture
link: https://peerj.com/articles/12751
last-modified: 2022-01-07
description: Determining the presence of antibodies to the SARS-CoV-2 antigens is the best way to identify infected people, regardless of the development of symptoms of COVID-19. The nucleoprotein (NP) of the SARS-CoV-2 is an immunodominant antigen of the virus; anti-NP antibodies are detected in persons previously infected with the virus with the highest titers. Many test systems for detecting antibodies to SARS-CoV-2 contain NP or its fragments as antigen. The sensitivity and specificity of such test systems differ significantly, which can be explained by variations in the antigenic properties of NP caused by differences in the methods of its cultivation, isolation and purification. We investigated this effect for the Escherichia coli-derived SARS-CoV-2 NP, obtained from the cytoplasm in the soluble form. We hypothesized that co-purified nucleic acids that form a strong complex with NP might negatively affect NP’s antigenic properties. Therefore, we have established the NP purification method, which completely eliminates the RNA in the NP preparation. Two stages of RNA removal were used: treatment of the crude lysate of E. coli with RNase A and subsequent selective RNA elution with 2 M NaCl solution. The resulting NP without RNA has a significantly better signal-to-noise ratio when used as an ELISA antigen and tested with a control panel of serum samples with antibodies to SARS-CoV-2; therefore, it is preferable for in vitro diagnostic use. The same increase of the signal-to-noise ratio was detected for the free N-terminal domain of the NP. Complete removal of RNA complexed with NP during purification will significantly improve its antigenic properties, and the absence of RNA in NP preparations should be controlled during the production of this antigen.
creator: Denis E. Kolesov
creator: Maria V. Sinegubova
creator: Irina V. Safenkova
creator: Ivan I. Vorobiev
creator: Nadezhda A. Orlova
uri: https://doi.org/10.7717/peerj.12751
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Kolesov et al.

title: Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon
link: https://peerj.com/articles/12614
last-modified: 2022-01-06
description: BackgroundThe Ebo Forest area is a highly threatened centre of diversity in the Littoral Region of Cameroon, globally important for conservation with many threatened species including 68 threatened species of plant, yet not formally protected. The tropical African evergreen forest tree genus Uvariopsis Engl. & Diels (Annonaceae) is characterised by unisexual, usually cauliflorous flowers with a uniseriate corolla of four petals, and two sepals. Cameroon is the centre of diversity of the genus with 14 of the 19 known species.MethodsThe herbarium collection MacKinnon 51 from Ebo is hypothesized to represent a new species to science of Uvariopsis. This hypothesis is tested by the study of herbarium specimens from a number of herbaria known to hold important collections from Cameroon and surrounding countries.ResultsWe test the hypothesis that MacKinnon 51 represents a new species to science, using the most recent dichotomous identification key, and comparing it morphologically with reference material of all known species of the genus. We make a detailed comparative morphological study focussing on three other Cameroonian species, Uvariopsis solheidii, U. korupensis and the sympatric U. submontana. In the context of a review of the pollination biology of Uvariopsis, we speculate that in a genus otherwise with species with dull, flesh-coloured (pink, red to brown) flowers pollinated (where known) by diptera, orthoptera and blattodea (flies, crickets and cockroaches), the glossy, pale yellow-green flowers of Uvariopsis dicaprio, with additional traits unique in the genus, may be pollinated by nocturnal moths. Based on MacKinnon 51, we formally name Uvariopsis dicaprio Cheek & Gosline (Annonaceae) as new to science, and we describe, and illustrate, and map it. Restricted so far to a single site in evergreen forest in the Ebo Forest, Littoral Region, Cameroon, Uvariopsis dicaprio is provisionally assessed as Critically Endangered using the IUCN, 2012 standard because the forest habitat of this species remains unprotected, and there exist imminent threats of logging and conversion to plantations.DiscussionWe show that the highest density of species of the genus (12), and of narrow endemics (5), is found in the Cross-Sanaga Interval of SE Nigeria and Western Cameroon. A revised key to the 14 Cameroonian species of Uvariopsis is presented. We review the other seven narrowly endemic and threatened species unique to the Ebo forest of Cameroon and discuss the phytogeographic affinities of the area.ConclusionsUvariopsis dicaprio adds to the growing list of species threatened with extinction at Ebo Forest due to current anthropogenic pressures.
creator: George Gosline
creator: Martin Cheek
creator: Jean Michel Onana
creator: Eric Ngansop Tchatchouang
creator: Xander M. van der Burgt
creator: Lorna MacKinnon
creator: Léo-Paul M. J. Dagallier
uri: https://doi.org/10.7717/peerj.12614
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Gosline et al.

title: Psychometric properties of the Valuing Questionnaire in a Spaniard sample and factorial equivalence with a Colombian sample
link: https://peerj.com/articles/12670
last-modified: 2022-01-06
description: BackgroundThe Valuing Questionnaire (VQ) is considered as one of the most psychometrically robust instruments to measure valued living according to the acceptance and commitment therapy model. It consists of 10 items that are responded to on a 7-point Likert-type scale and has two factors: Progression and Obstruction. The Spanish version of the VQ showed good psychometric properties in Colombian samples. However, there is no evidence of the psychometric properties of the VQ in Spaniard samples. This study aims to analyze the validity of the VQ in a large Spaniard sample and analyze the measurement invariance with a similar Colombian sample.MethodThe VQ was administered to a Spaniard sample of 846 adult participants from general online population. Cronbach’s alpha and McDonald’s omega were computed to analyze the internal consistency of the VQ. The fit of the VQ’s two-factor model was tested through a confirmatory factor analysis with a robust maximum likelihood (MLR) estimation method. Afterward, we analyzed the measurement invariance across countries and gender. Convergent construct validity was analyzed with a package of questionnaires that evaluated experiential avoidance (Acceptance and Action Questionnaire-II, AAQ-II), emotional symptoms (Depression Anxiety and Stress Scale-21, DASS-21), life satisfaction (Satisfaction with Life Scale, SWLS), and cognitive fusion (Cognitive Fusion Questionnaire, CFQ).ResultsThe internal consistency across samples was adequate (alphas and omegas were .85 for VQ-Progress and .84 for VQ-Obstruction). The two-factor model obtained a good fit to the data (RMSEA = 0.073, 90% CI [0.063, 0.083], CFI = 0.98, NNFI = 0.97, and SRMR = 0.053). The VQ showed strict invariance across countries and gender and showed theoretically coherent correlations with emotional symptoms, life satisfaction, experiential avoidance, and cognitive fusion. In conclusion, the Spanish version of the VQ demonstrated good psychometric properties in a large Spaniard sample.
creator: Francisco J. Ruiz
creator: Paula Odriozola-González
creator: Juan C. Suárez-Falcón
creator: Miguel A. Segura-Vargas
uri: https://doi.org/10.7717/peerj.12670
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Ruiz et al.

title: Assessment of microbiota diversity in dental unit waterline contamination
link: https://peerj.com/articles/12723
last-modified: 2022-01-06
description: BackgroundDental unit waterlines (DUWLs) provide water for handpieces, air/water syringes, and mouth-rinse water outlets. DUWL contamination can negatively affect the operating environment and public health. Therefore, it is important to elucidate the bacterial concentrations and microbial composition in the DUWLs from different dental specialties.MethodsWe collected 350 5-mL dental water samples (from high-speed handpieces, air/water syringes, and mouth-rinse water outlets) from 60 dental chair units (DCUs) at a dental hospital to determine the bacterial concentrations by culture methods. Meanwhile, to investigate the diversity and community structure of microbe in the DUWLs, 17 high-quality DNA from 60 250-mL air/water syringe water samples, which were collected from the same 60 DCUs, were analyzed using 16S rDNA high-throughput sequencing.ResultsThe median bacterial concentration was 166 (31.5, 672.5) CFU/mL and the range was 0–3,816,000 CFU/mL. Only 42.6% of the water samples had bacterial concentrations below 100 CFU/mL. The Kruskal–Wallis H-test revealed that the water samples from three dental specialties had significantly different bacterial concentrations (H = 27.441, P < 0.01). High-throughput sequencing results showed significant differences in bacterial community structure between periodontics and the other two dental specialties. In the samples from three dental specialties, 508 OTUs were detected, with 160, 182 and 176 OTUs unique to the periodontics, endodontics and prosthodontics specialties, respectively. Linear discriminant analysis (LDA) effect size (LEfSe) suggested that Hydrocarboniphaga, Zoogloea, Aquabacterium, and Hydrogenophaga were enriched in the periodontics specialty; Acinetobacter, Geothrix, and Desulfovibrio were enriched in the prosthodontics specialty; and Alistipes, Clostridium XIVa, and Serratia were enriched in the endodontics specialty. Seven potentially human-pathogenic genera (Pseudomonas, Acinetobacter, Sphingomonas, Ochrobactrum, Rhizobium, Brevundimonas, and Methylobacterium) with relative abundance exceeding 1% were also detected in the DUWLs.ConclusionsThe bacterial concentrations and microbial composition were influenced by different dental specialties, so a validated disinfection protocol should be used to control DUWL contamination in different dental specialties.
creator: Yun Dang
creator: Qian Zhang
creator: Jing Wang
creator: Qian Wang
creator: Meng Han
creator: Yuting Niu
creator: Hua Li
creator: Xiue Li
uri: https://doi.org/10.7717/peerj.12723
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Dang et al.

title: Corticospinal excitability remains unchanged in the presence of residual force enhancement and does not contribute to increased torque production
link: https://peerj.com/articles/12729
last-modified: 2022-01-06
description: BackgroundFollowing stretch of an active muscle, muscle force is enhanced, which is known as residual force enhancement (rFE). As earlier studies found apparent corticospinal excitability modulations in the presence of rFE, this study aimed to test whether corticospinal excitability modulations contribute to rFE.MethodsFourteen participants performed submaximal plantar flexion stretch-hold and fixed-end contractions at 30% of their maximal voluntary soleus muscle activity in a dynamometer. During the steady state of the contractions, participants either received subthreshold or suprathreshold transcranial magnetic stimulation (TMS) of their motor cortex, while triceps surae muscle responses to stimulation were obtained via electromyography (EMG), and net ankle joint torque was recorded. B-mode ultrasound imaging was used to confirm muscle fascicle stretch during stretch-hold contractions in a subset of participants.ResultsFollowing stretch of the plantar flexors, an average rFE of 7% and 11% was observed for contractions with subthreshold and suprathreshold TMS, respectively. 41–46 ms following subthreshold TMS, triceps surae muscle activity was suppressed by 19–25%, but suppression was not significantly different between stretch-hold and fixed-end contractions. Similarly, the reduction in plantar flexion torque following subthreshold TMS was not significantly different between contraction conditions. Motor evoked potentials, silent periods and superimposed twitches following suprathreshold TMS were also not significantly different between contraction conditions.DiscussionAs TMS of the motor cortex did not result in any differences between stretch-hold and fixed-end contractions, we conclude that rFE is not linked to changes in corticospinal excitability.
creator: Jasmin Frischholz
creator: Brent J. Raiteri
creator: Andrew G. Cresswell
creator: Daniel Hahn
uri: https://doi.org/10.7717/peerj.12729
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Frischholz et al.

title: Influence of environmental factors on the spread of COVID-19 in Saudi Arabia
link: https://peerj.com/articles/12732
last-modified: 2022-01-06
description: BackgroundCoronavirus disease 2019 (COVID-19) has affected millions of people worldwide. The infection is mostly spread through the inhalation of infected droplets. Saudi Arabia is a vast country having different climatic conditions.MethodsThe study evaluated the influence of environmental factors on the spread of COVID-19. Six zones (A to F) were classified depending on the climatic conditions. The study was conducted by retrospective analysis of COVID-19 records from the ministry of health between the months of September 2020 and August 2021. The environmental data such as average temperature (°C), humidity (%), wind speed (m/s) and sun exposure (kwh/m2) were retrieved from official sites. The data was analyzed to determine the effect of these factors on the spread of COVID-19. SPSS IBM 25 software was used to conduct the analysis and p < 0.05 was considered to indicate the significance of the results.ResultsAccording to the findings, the rate of infection was greater between April and July 2021. Six climatic zones experienced high temperatures, little humidity, consistent wind flow, and intense sun exposure throughout this time. The correlation study revealed a significant (p < 0.05) relationship between the environmental factors and the spread of COVID-19. The data suggested that during summer condition when the weather is hot, less humid, and steady wind flow with lots of sun exposure, the COVID-19 infection rate got augmented in Saudi Arabia. Poor ventilation and closed-door habitats in an air-conditioned atmosphere during this period could have played a role in human transmission. More research on air quality, population mobility and diseased condition is essential, so that precise proactive measures can be designed to limit the spread of infection in specific climatic seasons.
creator: Syed Mohammed Basheeruddin Asdaq
creator: Syed Imam Rabbani
creator: Abdulhakeem S. Alamri
creator: Wala F. Alsanie
creator: Majid Alhomrani
creator: Mohammad J. Al-Yamani
uri: https://doi.org/10.7717/peerj.12732
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Asdaq et al.

title: Prior exposure to weathered oil influences foraging of an ecologically important saltmarsh resident fish
link: https://peerj.com/articles/12593
last-modified: 2022-01-05
description: Estuarine ecosystem balance typically relies on strong food web interconnectedness dependent on a relatively low number of resident taxa, presenting a potential ecological vulnerability to extreme ecosystem disturbances. Following the Deepwater Horizon (DwH) oil spill disaster of the northern Gulf of Mexico (USA), numerous ecotoxicological studies showed severe species-level impacts of oil exposure on estuarine fish and invertebrates, yet post-spill surveys found little evidence for severe impacts to coastal populations, communities, or food webs. The acknowledgement that several confounding factors may have limited researchers’ abilities to detect negative ecosystem-level impacts following the DwH spill drives the need for direct testing of weathered oil exposure effects on estuarine residents with high trophic connectivity. Here, we describe an experiment that examined the influence of previous exposure to four weathered oil concentrations (control: 0.0 L oil m−2; low: 0.1 L oil m−2; moderate: 0.5–1 L oil m−2; high: 3.0 L oil m−2) on foraging rates of the ecologically important Gulf killifish (Fundulus grandis). Following exposure in oiled saltmarsh mesocosms, killifish were allowed to forage on grass shrimp (Palaeomonetes pugio) for up to 21 h. We found that previous exposure to the high oil treatment reduced killifish foraging rate by ~37% on average, compared with no oil control treatment. Previous exposure to the moderate oil treatment showed highly variable foraging rate responses, while low exposure treatment was similar to unexposed responses. Declining foraging rate responses to previous high weathered oil exposure suggests potential oil spill influence on energy transfer between saltmarsh and off-marsh systems. Additionally, foraging rate variability at the moderate level highlights the large degree of intraspecific variability for this sublethal response and indicates this concentration represents a potential threshold of oil exposure influence on killifish foraging. We also found that consumption of gravid vs non-gravid shrimp was not independent of prior oil exposure concentration, as high oil exposure treatment killifish consumed ~3× more gravid shrimp than expected. Our study findings highlight the sublethal effects of prior oil exposure on foraging abilities of ecologically valuable Gulf killifish at realistic oil exposure levels, suggesting that important trophic transfers of energy to off-marsh systems may have been impacted, at least in the short-term, by shoreline oiling at highly localized scales. This study provides support for further experimental testing of oil exposure effects on sublethal behavioral impacts of ecologically important estuarine species, due to the likelihood that some ecological ramifications of DwH on saltmarshes likely went undetected.
creator: Ashley M. McDonald
creator: Charles W. Martin
creator: Guillaume Rieucau
creator: Brian J. Roberts
uri: https://doi.org/10.7717/peerj.12593
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 McDonald et al.

title: A critical review on modulators of Multidrug Resistance Protein 1 in cancer cells
link: https://peerj.com/articles/12594
last-modified: 2022-01-05
description: Multidrug resistance protein 1 (MRP1/ABCC1) is an ATP-dependent efflux transporter, and responsible for the transport of a broad spectrum of xenobiotics, toxins, and physiological substrates across the plasma membrane. As an efflux pump, it plays a significant role in the absorption and disposition of drugs including anticancer drugs, antivirals, antimalarials, and antibiotics and their metabolites across physiological barriers in cells. MRP1 is also known to aid in the regulation of several physiological processes such as redox homeostasis, steroid metabolism, and tissue defense. However, its overexpression has been reported to be a key clinical marker associated with multidrug resistance (MDR) of several types of cancers including lung cancer, childhood neuroblastoma, breast and prostate carcinomas, often resulting in a higher risk of treatment failure and shortened survival rates in cancer patients. Aside MDR, overexpression of MRP1 is also implicated in the development of neurodegenerative and cardiovascular diseases. Due to the cellular importance of MRP1, the identification and biochemical/molecular characterization of modulators of MRP1 activity and expression levels are of key interest to cancer research and beyond. This review primarily aims at highlighting the physiological and pharmacological importance of MRP1, known MRP1 modulators, current challenges encountered, and the potential benefits of conducting further research on the MRP1 transporter.
creator: Vivian Osei Poku
creator: Surtaj Hussain Iram
uri: https://doi.org/10.7717/peerj.12594
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Poku and Iram

title: Hyaluronic acid plasma levels during high versus low tidal volume ventilation in a porcine sepsis model
link: https://peerj.com/articles/12649
last-modified: 2022-01-05
description: BackgroundShedding of the endothelial glycocalyx can be observed regularly during sepsis. Moreover, sepsis may be associated with acute respiratory distress syndrome (ARDS), which requires lung protective ventilation with the two cornerstones of application of low tidal volume and positive end-expiratory pressure. This study investigated the effect of a lung protective ventilation on the integrity of the endothelial glycocalyx in comparison to a high tidal volume ventilation mode in a porcine model of sepsis-induced ARDS.MethodsAfter approval by the State and Institutional Animal Care Committee, 20 male pigs were anesthetized and received a continuous infusion of lipopolysaccharide to induce septic shock. The animals were randomly assigned to either low tidal volume ventilation, high tidal volume ventilation, or no-LPS-group groups and observed for 6 h. In addition to the gas exchange parameters and hematologic analyses, the serum hyaluronic acid concentrations were determined from central venous blood and from pre- and postpulmonary and pre- and postcerebral circulation. Post-mortem analysis included histopathological evaluation and determination of the pulmonary and cerebral wet-to-dry ratios.ResultsBoth sepsis groups developed ARDS within 6 h of the experiment and showed significantly increased serum levels of hyaluronic acid in comparison to the no-LPS-group. No significant differences in the hyaluronic acid concentrations were detected before and after pulmonary and cerebral circulation. There was also no significant difference in the serum hyaluronic acid concentrations between the two sepsis groups. Post-mortem analysis showed no significant difference between the two sepsis groups.ConclusionIn a porcine model of septic shock and ARDS, the serum hyaluronic acid levels were significantly elevated in both sepsis groups in comparison to the no-LPS-group. Intergroup comparison between lung protective ventilated and high tidal ventilated animals revealed no significant differences in the serum hyaluronic acid levels.
creator: Rainer Thomas
creator: Tanghua Liu
creator: Arno Schad
creator: Robert Ruemmler
creator: Jens Kamuf
creator: René Rissel
creator: Thomas Ott
creator: Matthias David
creator: Erik K. Hartmann
creator: Alexander Ziebart
uri: https://doi.org/10.7717/peerj.12649
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Thomas et al.

title: Highly divergent isolates of chrysanthemum virus B and chrysanthemum virus R infecting chrysanthemum in Russia
link: https://peerj.com/articles/12607
last-modified: 2022-01-05
description: BackgroundChrysanthemum is a popular ornamental and medicinal plant that suffers from many viruses and viroids. Among them, chrysanthemum virus B (CVB, genus Carlavirus, family Betaflexiviridae) is widespread in all chrysanthemum-growing regions. Another carlavirus, chrysanthemum virus R (CVR), has been recently discovered in China. Information about chrysanthemum viruses in Russia is very scarce. The objective of this work was to study the prevalence and genetic diversity of CVB and CVR in Russia.MethodsWe surveyed the chrysanthemum (Chrysanthemum morifolium Ramat.) germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. To detect CVB and CVR, we used RT-PCR with virus-specific primers. To reveal the complete genome sequences of CVB and CVR isolates, metatransciptomic analysis of the cultivars Ribonette, Fiji Yellow, and Golden Standard plants, naturally co-infected with CVB and CVR, was performed using Illumina high-throughput sequencing. The recombination detection tool (RDP4) was employed to search for recombination in assembled genomes.ResultsA total of 90 plants of 23 local and introduced chrysanthemum cultivars were surveyed. From these, 58 and 43% plants tested positive for CVB and CVR, respectively. RNA-Seq analysis confirmed the presence of CVB and CVR, and revealed tomato aspermy virus in each of the three transcriptomes. Six near complete genomes of CVB and CVR were assembled from the RNA-Seq reads. The CVR isolate X21 from the cultivar Golden Standard was 92% identical to the Chinese isolate BJ. In contrast, genomes of the CVR isolates X6 and X13 (from the cultivars Ribonette and Fiji Yellow, respectively), were only 76% to 77% identical to the X21 and BJ, and shared 95% identity to one another and appear to represent a divergent group of the CVR. Two distantly related CVB isolates, GS1 and GS2, were found in a plant of the cultivar Golden Standard. Their genomes shared from 82% to 87% identity to each other and the CVB genome from the cultivar Fiji Yellow (isolate FY), as well as to CVB isolates from Japan and China. A recombination event of 3,720 nucleotides long was predicted in the replicase gene of the FY genome. It was supported by seven algorithms implemented in RDP4 with statistically significant P-values. The inferred major parent was the Indian isolate Uttar Pradesh (AM765837), and minor parent was unknown.ConclusionWe found a wide distribution of CVB and CVR in the chrysanthemum germplasm collection of the Nikita Botanical Gardens, which is the largest in Russia. Six near complete genomes of CVR and CVB isolates from Russia were assembled and characterized for the first time. This is the first report of CVR in Russia and outside of China thus expanding the information on the geographical distribution of the virus. Highly divergent CVB and CVR isolates have been identified that contributes the better understanding the genetic diversity of these viruses.
creator: Sergei N. Chirkov
creator: Anna Sheveleva
creator: Anastasiya Snezhkina
creator: Anna Kudryavtseva
creator: George Krasnov
creator: Alexander Zakubanskiy
creator: Irina Mitrofanova
uri: https://doi.org/10.7717/peerj.12607
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Chirkov et al.

title: Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus
link: https://peerj.com/articles/12654
last-modified: 2022-01-05
description: The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.
creator: Qiangqiang Ding
creator: Hongyuan Zhao
creator: Peilei Zhu
creator: Xiangting Jiang
creator: Fan Nie
creator: Guoqing Li
uri: https://doi.org/10.7717/peerj.12654
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Ding et al.

title: Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct
link: https://peerj.com/articles/12664
last-modified: 2022-01-05
description: The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species’ triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
creator: Sen Zhang
creator: Shaoping Wu
creator: Chunhua Hu
creator: Qiaosong Yang
creator: Tao Dong
creator: Ou Sheng
creator: Guiming Deng
creator: Weidi He
creator: Tongxin Dou
creator: Chunyu Li
creator: Chenkang Sun
creator: Ganjun Yi
creator: Fangcheng Bi
uri: https://doi.org/10.7717/peerj.12664
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhang et al.

title: Cancer types with high numbers of driver events are largely preventable
link: https://peerj.com/articles/12672
last-modified: 2022-01-05
description: There is a long-standing debate on whether cancer is predominantly driven by extrinsic risk factors such as smoking, or by intrinsic processes such as errors in DNA replication. We have previously shown that the number of rate-limiting driver events per tumor can be estimated from the age distribution of cancer incidence using the gamma/Erlang probability distribution. Here, we show that this number strongly correlates with the proportion of cancer cases attributable to modifiable risk factors for all cancer types except the ones inducible by infection or ultraviolet radiation. The correlation was confirmed for three countries, three corresponding incidence databases and risk estimation studies, as well as for both sexes: USA, males (r = 0.80, P = 0.002), females (r = 0.81, P = 0.0003); England, males (r = 0.90, P < 0.0001), females (r = 0.67, P = 0.002); Australia, males (r = 0.90, P = 0.0004), females (r = 0.68, P = 0.01). Hence, this study suggests that the more driver events a cancer type requires, the more of its cases are due to preventable anthropogenic risk factors.
creator: Aleksey V. Belikov
creator: Sergey V. Leonov
uri: https://doi.org/10.7717/peerj.12672
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Belikov and Leonov

title: Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects
link: https://peerj.com/articles/12676
last-modified: 2022-01-05
description: Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the clone CCN 51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao industry will be discussed highlighting the major challenges for flavor enhancement and its relevance as a platform for the identification of novel genetic markers for cultivar improvement in breeding programs.
creator: Ramon E. Jaimez
creator: Luigy Barragan
creator: Miguel Fernández-Niño
creator: Ludger A. Wessjohann
creator: George Cedeño-Garcia
creator: Ignacio Sotomayor Cantos
creator: Francisco Arteaga
uri: https://doi.org/10.7717/peerj.12676
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Jaimez et al.

title: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog
link: https://peerj.com/articles/12712
last-modified: 2022-01-05
description: The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection.
creator: Roland A. Knapp
creator: Maxwell B. Joseph
creator: Thomas C. Smith
creator: Ericka E. Hegeman
creator: Vance T. Vredenburg
creator: James E. Erdman Jr
creator: Daniel M. Boiano
creator: Andrea J. Jani
creator: Cheryl J. Briggs
uri: https://doi.org/10.7717/peerj.12712
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Knapp et al.

title: Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study
link: https://peerj.com/articles/12715
last-modified: 2022-01-05
description: BackgroundImproved detection of hepatocellular carcinoma (HCC) is needed, as current detection methods, such as alpha fetoprotein (AFP) and ultrasound, suffer from poor sensitivity. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate many cellular functions and impact cancer development and progression. Notably, miRNAs are detectable in saliva and have shown potential as non-invasive biomarkers for a number of cancers including breast, oral, and lung cancers. Here, we present, to our knowledge, the first report of salivary miRNAs in HCC and compare these findings to patients with cirrhosis, a high-risk cohort for HCC.MethodsWe performed small RNA sequencing in 20 patients with HCC and 19 with cirrhosis. Eleven patients with HCC had chronic liver disease, and analyses were performed with these samples combined and stratified by the presence of chronic liver disease. P values were adjusted for multiple comparisons using a false discovery rate (FDR) approach and miRNA with FDR P < 0.05 were considered statistically significant. Differential expression of salivary miRNAs was compared to a previously published report of miRNAs in liver tissue of patients with HCC vs cirrhosis. Support vector machines and leave-one-out cross-validation were performed to determine if salivary miRNAs have predictive potential for detecting HCC.ResultsA total of 4,565 precursor and mature miRNAs were detected in saliva and 365 were significantly different between those with HCC compared to cirrhosis (FDR P < 0.05). Interestingly, 283 of these miRNAs were significantly downregulated in patients with HCC. Machine-learning identified a combination of 10 miRNAs and covariates that accurately classified patients with HCC (AUC = 0.87). In addition, we identified three miRNAs that were differentially expressed in HCC saliva samples and in a previously published study of miRNAs in HCC tissue compared to cirrhotic liver tissue.ConclusionsThis study demonstrates, for the first time, that miRNAs relevant to HCC are detectable in saliva, that salivary miRNA signatures show potential to be highly sensitive and specific non-invasive biomarkers of HCC, and that additional studies utilizing larger cohorts are needed.
creator: Arshiya Mariam
creator: Galen Miller-Atkins
creator: Amika Moro
creator: Alejandro I. Rodarte
creator: Shirin Siddiqi
creator: Lou-Anne Acevedo-Moreno
creator: J. Mark Brown
creator: Daniela S. Allende
creator: Federico Aucejo
creator: Daniel M. Rotroff
uri: https://doi.org/10.7717/peerj.12715
license: https://creativecommons.org/licenses/by-nc/4.0
rights: © 2022 Mariam et al.

title: Genome-wide sequence identification and expression analysis of N6-methyladenosine demethylase in sugar beet (Beta vulgaris L.) under salt stress
link: https://peerj.com/articles/12719
last-modified: 2022-01-05
description: In eukaryotes, N6-methyladenosine (m6A) is the most abundant and highly conserved RNA modification. In vivo, m6A demethylase dynamically regulates the m6A level by removing the m6A marker where it plays an important role in plant growth, development and response to abiotic stress. The confirmed m6A demethylases in Arabidopsis thaliana include ALKBH9B and ALKBH10B, both belonging to the ALKB family. In this study, BvALKB family members were identified in sugar beet genome-wide database, and their conserved domains, gene structures, chromosomal locations, phylogeny, conserved motifs and expression of BvALKB genes were analyzed. Almost all BvALKB proteins contained the conserved domain of 2OG-Fe II-Oxy. Phylogenetic analysis suggested that the ten proteins were clustered into five groups, each of which had similar motifs and gene structures. Three Arabidopsis m6A demethylase-homologous proteins (BvALKBH6B, BvALKBH8B and BvALKBH10B) were of particular interest in our study. Expression profile analysis showed that almost all genes were up-regulated or down-regulated to varying degrees under salt stress. More specifically, BvALKBH10B homologous to AtALKBH10B was significantly up-regulated, suggesting that the transcriptional activity of this gene is responsive to salt stress. This study provides a theoretical basis for further screening of m6A demethylase in sugar beet, and also lays a foundation for studying the role of ALKB family proteins in growth, development and response to salinity stress.
creator: Jie Cui
creator: Junli Liu
creator: Junliang Li
creator: Dayou Cheng
creator: Cuihong Dai
uri: https://doi.org/10.7717/peerj.12719
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Cui et al.

title: Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma
link: https://peerj.com/articles/12736
last-modified: 2022-01-05
description: Pancreatic ductal adenocarcinoma (PDAC) is one of the common malignant tumors with high lethal rate and poor prognosis. Dysregulation of many genes have been reported to be involved in the occurrence and development of PDAC. However, as a highly conserved gene in eukaryotes, the role of Fasciculation and Elongation protein Zeta 2 (FEZ2) in pancreatic cancer progression is not clear. In this study, we identified the oncogenic effect of FEZ2 on PDAC. By mining of The Cancer Genome Atlas (TCGA) database, we found that FEZ2 was upregulated in PDAC tissues and FEZ2 expression was negatively regulated by its methylation. Moreover, high expression and low methylation of FEZ2 correlated with poor prognosis in PDAC patients. Besides, we found that FEZ2 could promote PDAC cells proliferation, migration and 5-FU resistance in vitro. Furthermore, Gene pathway enrichment analysis demonstrated a positive correlation between Wnt signaling activation and FEZ2 expression in PDAC patients. Western blot showed that FEZ2 knockdown significantly suppressed β-catenin expression. Collectively, our finding revealed that FEZ2 functioned as a potential oncogene on PDAC progression and migration, and the expression of FEZ2 had guidance value for the treatment and chemotherapy program of PDAC patients.
creator: Chaozhi Yang
creator: Xuebing Wang
creator: Chenjie Qiu
creator: Ziruo Zheng
creator: Kai Lin
creator: Min Tu
creator: Kai Zhang
creator: Kuirong Jiang
creator: Wentao Gao
uri: https://doi.org/10.7717/peerj.12736
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Yang et al.

title: Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach
link: https://peerj.com/articles/12740
last-modified: 2022-01-05
description: Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.
creator: Kantinan Leetanasaksakul
creator: Sittiruk Roytrakul
creator: Narumon Phaonakrop
creator: Suthathip Kittisenachai
creator: Siriwan Thaisakun
creator: Nitiya Srithuanok
creator: Klanarong Sriroth
creator: Laurent Soulard
uri: https://doi.org/10.7717/peerj.12740
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Leetanasaksakul et al.

title: Beyond the prey: male spiders highly invest in silk when producing worthless gifts
link: https://peerj.com/articles/12757
last-modified: 2022-01-05
description: In the spider Paratrechalea ornata, males have two gift-giving mating tactics, offering either a nutritive (prey) or a worthless (prey leftovers) silk wrapped gift to females. Both gift types confer similar mating success and duration and afford males a higher success rate than when they offer no gift. If this lack of difference in the reproductive benefits is true, we would expect all males to offer a gift but some males to offer a worthless gift even if prey are available. To test this, we allowed 18 males to court multiple females over five consecutive trials. In each trial, a male was able to produce a nutritive gift (a live housefly) or a worthless gift (mealworm exuviae). We found that, in line with our predictions, 20% of the males produced worthless gifts even when they had the opportunity to produce a nutritive one. However, rather than worthless gifts being a cheap tactic, they were related to a higher investment in silk wrapping. This latter result was replicated for worthless gifts produced in both the presence and absence of a live prey item. We propose that variation in gift-giving tactics likely evolved initially as a conditional strategy related to prey availability and male condition in P. ornata. Selection may then have favoured silk wrapping as a trait involved in female attraction, leading worthless gift-giving to invade.
creator: Camila Pavón-Peláez
creator: Valentina Franco-Trecu
creator: Irene Pandulli-Alonso
creator: Therésa M. Jones
creator: Maria J. Albo
uri: https://doi.org/10.7717/peerj.12757
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Pavón-Peláez et al.

title: Protection of catalpol against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway
link: https://peerj.com/articles/12759
last-modified: 2022-01-05
description: Catalpol significantly reduces triptolide-induced hepatotoxicity, which is closely related to autophagy. The aim of this study was to explore the unclear protective mechanism of catalpol against triptolide. The detoxification effect of catalpol on triptolide was investigated in HepaRG cell line. The detoxification effects were assessed by measuring cell viability, autophagy, and apoptosis, as well as the endoplasmic reticulum stress protein and mRNA expression levels. We found that 5–20 µg/L triptolide treatments increased the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH), as well as the expression of autophagy proteins including LC3 and Beclin1. The expression of P62 was downregulated and the production of autophagosomes was increased, as determined by transmission electron microscope and monodansylcadaverine staining. In contrast, 40 µg/L catalpol reversed these triptolide-induced changes in the liver function index, autophagy level, and apoptotic protein expression, including Cleaved-caspase3 and Cleaved-caspase9 by inhibiting excessive autophagy. Simultaneously, catalpol reversed endoplasmic reticulum stress, including the expression of PERK, which regulates autophagy. Moreover, we used the PERK inhibitor GSK2656157 to prove that the PERK-ATF4-CHOP pathway of the unfolded protein response is an important pathway that could induce autophagy. Catalpol inhibited excessive autophagy by suppressing the PERK pathway. Altogether, catalpol protects against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway. The results of this study are beneficial to clarify the detoxification mechanism of catalpol against triptolide-induced hepatotoxicity and to promote the application of triptolide.
creator: Linluo Zhang
creator: Changqing Li
creator: Ling Fu
creator: Zhichao Yu
creator: Gengrui Xu
creator: Jie Zhou
creator: Meiyu Shen
creator: Zhe Feng
creator: Huaxu Zhu
creator: Tong Xie
creator: Lingling Zhou
creator: Xueping Zhou
uri: https://doi.org/10.7717/peerj.12759
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhang et al.

title: Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma
link: https://peerj.com/articles/12493
last-modified: 2022-01-04
description: BackgroundClear cell renal cell carcinoma (ccRCC) is a tumor that frequently shows the hematogenous pathway and tends to be resistant to radiotherapy and chemotherapy. However, the exact mechanism of ccRCC metastasis remains unknown.MethodsDifferentially expressed genes (DEGs) of three gene expression profiles (GSE85258, GSE105288 and GSE22541) downloaded from the Gene Expression Omnibus (GEO) database were analyzed by GEO2R analysis, and co-expressed DEGs among the datasets were identified using a Venn drawing tool. The co-expressed DEGs were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and hub genes were determined based on the protein-protein interaction network established by STRING. After survival analysis performed on UALCAN website, possible key genes were selected and verified in ccRCC cell lines and ccRCC tissues (n = 44). Statistical analysis was conducted using GraphPad Prism (Version 8.1.1).ResultsA total of 104 co-expressed DEGs were identified in the three datasets. Pathway analysis revealed that these genes were enriched in the extracellular matrix (ECM)–receptor interaction, protein digestion and absorption and focal adhesion. Survival analysis on 17 hub genes revealed that four key genes with a significant impact on survival: procollagen C-endopeptidase enhancer (PCOLCE), prolyl 4-hydroxylase subunit beta (P4HB), collagen type VI alpha 2 (COL6A2) and collagen type VI alpha 3 (COL6A3). Patients with higher expression of these key genes had worse survival than those with lower expression. In vitro experiments revealed that the mRNA expression levels of PCOLCE, P4HB and COL6A2 were three times higher and that of COL6A3 mRNA was 16 times higher in the metastatic ccRCC cell line Caki-1 than the corresponding primary cell line Caki-2. Immunohistochemistry revealed higher expression of the proteins encoded by these four genes in metastatic ccRCC compared with tumors from the corresponding primary sites, with statistical significance.ConclusionPCOLCE, P4HB, COL6A2 and COL6A3 are upregulated in metastatic ccRCC and might be related to poor prognosis and distant metastases.
creator: Tingting Zhong
creator: Zeying Jiang
creator: Xiangdong Wang
creator: Honglei Wang
creator: Meiyi Song
creator: Wenfang Chen
creator: Shicong Yang
uri: https://doi.org/10.7717/peerj.12493
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhong et al.

title: Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola
link: https://peerj.com/articles/12558
last-modified: 2022-01-04
description: BackgroundMembers of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available.MethodsIn the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed.ResultsEight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.
creator: Chengru Li
creator: Na Dong
creator: Liming Shen
creator: Meng Lu
creator: Junwen Zhai
creator: Yamei Zhao
creator: Lei Chen
creator: Zhiting Wan
creator: Zhongjian Liu
creator: Hui Ren
creator: Shasha Wu
uri: https://doi.org/10.7717/peerj.12558
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Li et al.

title: Metabolomics of a cell line-derived xenograft model reveals circulating metabolic signatures for malignant mesothelioma
link: https://peerj.com/articles/12568
last-modified: 2022-01-04
description: BackgroundMalignant mesothelioma (MM) is a rare and highly aggressive cancer. Despite advances in multidisciplinary treatments for cancer, the prognosis for MM remains poor with no effective diagnostic biomarkers currently available. The aim of this study was to identify plasma metabolic biomarkers for better MM diagnosis and prognosis by use of a MM cell line-derived xenograft (CDX) model.MethodsThe MM CDX model was confirmed by hematoxylin and eosin staining and immunohistochemistry. Twenty female nude mice were randomly divided into two groups, 10 for the MM CDX model and 10 controls. Plasma samples were collected two weeks after tumor cell implantation. Gas chromatography-mass spectrometry analysis was conducted. Both univariate and multivariate statistics were used to select potential metabolic biomarkers. Hierarchical clustering analysis, metabolic pathway analysis, and receiver operating characteristic (ROC) analysis were performed. Additionally, bioinformatics analysis was used to investigate differential genes between tumor and normal tissues, and survival-associated genes.ResultsThe MM CDX model was successfully established. With VIP > 1.0 and P-value < 0.05, a total of 23 differential metabolites were annotated, in which isoleucine, 5-dihydrocortisol, and indole-3-acetamide had the highest diagnostic values based on ROC analysis. These were mainly enriched in pathways for starch and sucrose metabolism, pentose and glucuronate interconversions, galactose metabolism, steroid hormone biosynthesis, as well as phenylalanine, tyrosine and tryptophan biosynthesis. Further, down-regulation was observed for amino acids, especially isoleucine, which is consistent with up-regulation of amino acid transporter genes SLC7A5 and SLC1A3 in MM. Overall survival was also negatively associated with SLC1A5, SLC7A5, and SLC1A3.ConclusionWe found several altered plasma metabolites in the MM CDX model. The importance of specific metabolic pathways, for example amino acid metabolism, is herein highlighted, although further investigation is warranted.
creator: Yun Gao
creator: Ziyi Dai
creator: Chenxi Yang
creator: Ding Wang
creator: Zhenying Guo
creator: Weimin Mao
creator: Zhongjian Chen
uri: https://doi.org/10.7717/peerj.12568
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Gao et al.

title: Development and validation of a novel risk score to predict 5-year mortality in patients with acute myocardial infarction in China: a retrospective study
link: https://peerj.com/articles/12652
last-modified: 2022-01-04
description: BackgroundThe disease burden from ischaemic heart disease remains heavy in the Chinese population. Traditional risk scores for estimating long-term mortality in patients with acute myocardial infarction (AMI) have been developed without sufficiently considering advances in interventional procedures and medication. The goal of this study was to develop a risk score comprising clinical parameters and intervention advances at hospital admission to assess 5-year mortality in AMI patients in a Chinese population.MethodsWe performed a retrospective observational study on 2,722 AMI patients between January 2013 and December 2017. Of these patients, 1,471 patients from Changsha city, Hunan Province, China were assigned to the development cohort, and 1,251 patients from Xiangtan city, Hunan Province, China, were assigned to the validation cohort. Forty-five candidate variables assessed at admission were screened using least absolute shrinkage and selection operator, stepwise backward regression, and Cox regression methods to construct the C2ABS2-GLPK score, which was graded and stratified using a nomogram and X-tile. The score was internally and externally validated. The C-statistic and Hosmer-Lemeshow test were used to assess discrimination and calibration, respectively.ResultsFrom the 45 candidate variables obtained at admission, 10 potential predictors, namely, including Creatinine, experience of Cardiac arrest, Age, N-terminal Pro-Brain Natriuretic Peptide, a history of Stroke, Statins therapy, fasting blood Glucose, Left ventricular end-diastolic diameter, Percutaneous coronary intervention and Killip classification were identified as having a close association with 5-year mortality in patients with AMI and collectively termed the C2ABS2-GLPK score. The score had good discrimination (C-statistic = 0.811, 95% confidence intervals (CI) [0.786–0.836]) and calibration (calibration slope = 0.988) in the development cohort. In the external validation cohort, the score performed well in both discrimination (C-statistic = 0.787, 95% CI [0.756–0.818]) and calibration (calibration slope = 0.976). The patients were stratified into low- (≤148), medium- (149 to 218) and high-risk (≥219) categories according to the C2ABS2-GLPK score. The predictive performance of the score was also validated in all subpopulations of both cohorts.ConclusionThe C2ABS2-GLPK score is a Chinese population-based risk assessment tool to predict 5-year mortality in AMI patients based on 10 variables that are routinely assessed at admission. This score can assist physicians in stratifying high-risk patients and optimizing emergency medical interventions to improve long-term survival in patients with AMI.
creator: Yan Tang
creator: Yuanyuan Bai
creator: Yuanyuan Chen
creator: Xuejing Sun
creator: Yunmin Shi
creator: Tian He
creator: Mengqing Jiang
creator: Yujie Wang
creator: Mingxing Wu
creator: Zhiliu Peng
creator: Suzhen Liu
creator: Weihong Jiang
creator: Yao Lu
creator: Hong Yuan
creator: Jingjing Cai
uri: https://doi.org/10.7717/peerj.12652
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Tang et al.

title: Pecan agroforestry systems improve soil quality by stimulating enzyme activity
link: https://peerj.com/articles/12663
last-modified: 2022-01-04
description: BackgroundForest and plantation intercropping are efficient agroforestry systems that optimize land use and promote agroforestry around the world. However, diverse agroforestry systems on the same upper-plantation differently affect the physical and chemical properties of the soil.MethodsThe treatments for this study included a single cultivation (CK) pecan control and three agroforestry systems (pecan + Paeonia suffruticosa + Hemerocallis citrina, pecan + Paeonia suffruticosa, and pecan + Paeonia lactiflora). Soil samples were categorized according to the sampling depth (0–20 cm, 20–40 cm, 40–60 cm).ResultsThe results demonstrated that the bulk density (BD) of soil under the pecan agroforestry system (PPH and PPL) was reduced by 16.13% and 7.10%, respectively, and the soil moisture content (MC) and total soil porosity (TPO) increased. Improvements in the physical properties of the soil under the PPS agroforestry system were not obvious when compared with the pecan monoculture. The soil total phosphorus (TP), total nitrogen (TN), available potassium (AK), and total carbon (TC) increased significantly, while the soil urease (S-UE), alkaline phosphatase (S-AKP), and 1,4-β-N-acetylglucosamines (S-NAG) enzyme activity also increased significantly, following agroforestry. Overall, the pecan agroforestry system significantly improved the physical properties of the pecan plantation soil, enriched the soil nutrients, and increased the activity of soil enzymes related to TC, TN, and TP cycles.
creator: Zhaocheng Wang
creator: Mengyu Zhou
creator: Hua Liu
creator: Cheng Huang
creator: Yuhua Ma
creator: Hao xin Ge
creator: Xiang Ge
creator: Songling Fu
uri: https://doi.org/10.7717/peerj.12663
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Measuring evidence-based practice in physical therapy: a mix-methods study
link: https://peerj.com/articles/12666
last-modified: 2022-01-04
description: BackgroundEvidence-based practice (EBP) is considered the “holy grail” to manage patients by health practitioners (such as physical therapists). However, sometimes, patients are not treated with the best interventions for their condition. Although studies already explored the facilitators and barriers for this issue, they increase in the level of importance if the information gathered are context appropriated. As the profession is relatively new in Portugal, currently little is known about the implementation of EBP in Portuguese physical therapists context. So, the aim of this study is to know if the Portuguese physical therapists use an EBP, and collect and deeper understand the factors, barriers and facilitators associated with EBP.MethodsThis study incorporated a mixed-methods design (quantitative and qualitative). In an attempt to ensure the correct population sample, a national professional association e-mail database and the e-mails of past students from national schools were requested. For the quantitative data it was choose an e-survey, adapted from the EBP: Beliefs, Attitudes, Knowledge, and Behaviors of Physical Therapists Portuguese version questionnaire, consisted of 55 close-ended questions. It was analyzed response frequencies and associations between variables with logistic regression analyses. For the qualitative data, it was choose to perform semi-structured interviews in purposefully selected physical therapists to include different sociodemographic factors (especially those found to be statistically significant in the logistic regression) and survey responses regarding the physical therapists’ beliefs, attitudes, knowledge, and behaviors. The interviews were performed in an online software, where only audio contact was performed. The audios were anonymized and verbatim transcribed, and the texts explored by the thematic approach.ResultsFrom the 277 physical therapists that shown interest in participating in the study, 193 fully completed the questionnaire and, from those, 10 participated in the interviews. The Portuguese physical therapists reported positive beliefs, attitudes, knowledge, and behaviors regarding EBP. Among the physical therapists characteristics it seems that age (younger therapists), education (participating in continuing education courses; belonging to practice-orientated organizations; having a doctorate degree; pursuing a higher academic degree; and being a clinical instructor), and workplace (working for someone else account; and academic sector) are the main factors in the Portuguese EBP implementation. The Portuguese physical therapists, beyond the physical therapists individual characteristics and workplace, also stated that evidence, patients, clinical experience, schools, country and physical therapy characteristics, may behave as facilitators or barriers when performing an EBP.
creator: Ricardo M. Ferreira
creator: Pedro N. Martins
creator: Nuno Pimenta
creator: Rui S. Gonçalves
uri: https://doi.org/10.7717/peerj.12666
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Ferreira et al.

title: RNA sequencing-based exploration of the effects of blue laser irradiation on mRNAs involved in functional metabolites of D. officinales
link: https://peerj.com/articles/12684
last-modified: 2022-01-04
description: Dendrobium officinale Kimura et Migo (D. officinale) has promising lung moisturizing, detoxifying, and immune boosting properties. Light is an important factor influencing functional metabolite synthesis in D. officinale. The mechanisms by which lasers affect plants are different from those of ordinary light sources; lasers can effectively address the shortcomings of ordinary light sources and have significant interactions with plants. Different light treatments (white, blue, blue laser) were applied, and the number of red leaves under blue laser was greater than that under blue and white light. RNA-seq technology was used to analyze differences in D. officinale under different light treatments. The results showed 465, 2,107 and 1,453 differentially expressed genes (DEGs) in LB-B, LB-W and W-B, respectively. GO, KEGG and other analyses of DEGs indicated that D. officinale has multiple blue laser response modes. Among them, the plasma membrane, cutin, suberine and wax biosynthesis, flavone and flavonol biosynthesis, heat shock proteins, etc. play central roles. Physiological and biochemical results verified that blue laser irradiation significantly increases POD, SOD, and PAL activities in D. officinale. The functional metabolite results showed that blue laser had the greatest promoting effect on total flavonoids, polysaccharides, and alkaloids. qPCR verification combined with other results suggested that CRY DASH, SPA1, HY5, and PIF4 in the blue laser signal transduction pathway affect functional metabolite accumulation in D. officinale through positively regulated expression patterns, while CO16 and MYC2 exhibit negatively regulated expression patterns. These findings provide new ideas for the efficient production of metabolites in D. officinale.
creator: Hansheng Li
creator: Yuqiang Qiu
creator: Gang Sun
creator: Wei Ye
uri: https://doi.org/10.7717/peerj.12684
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Li et al.

title: Human-wildlife conflicts with crocodilians, cetaceans and otters in the tropics and subtropics
link: https://peerj.com/articles/12688
last-modified: 2022-01-04
description: Conservation of freshwater biodiversity and management of human-wildlife conflicts are major conservation challenges globally. Human-wildlife conflict occurs due to attacks on people, depredation of fisheries, damage to fishing equipment and entanglement in nets. Here we review the current literature on conflicts with tropical and subtropical crocodilians, cetaceans and otters in freshwater and brackish habitats. We also present a new multispecies case study of conflicts with four freshwater predators in the Western Amazon: black caiman (Melanosuchus niger), giant otter (Pteronura brasiliensis), boto (Inia geoffrensis) and tucuxi (Sotalia fluviatilis). Documented conflicts occur with 34 crocodilian, cetacean and otter species. Of the species reviewed in this study, 37.5% had conflicts frequently documented in the literature, with the saltwater crocodile (Crocodylus porosus) the most studied species. We found conflict severity had a positive relationship with species body mass, and a negative relationship with IUCN Red List status. In the Amazonian case study, we found that the black caiman was ranked as the greatest ‘problem’ followed by the boto, giant otter and tucuxi. There was a significant difference between the responses of local fishers when each of the four species were found entangled in nets. We make recommendations for future research, based on the findings of the review and Amazon case study, including the need to standardise data collection.
creator: Patrick Cook
creator: Joseph E. Hawes
creator: João Vitor Campos-Silva
creator: Carlos A. Peres
uri: https://doi.org/10.7717/peerj.12688
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Cook et al.

title: Seasonal variations and co-occurrence networks of bacterial communities in the water and sediment of artificial habitat in Laoshan Bay, China
link: https://peerj.com/articles/12705
last-modified: 2022-01-04
description: Marine bacteria in the seawater and seafloor are essential parts of Earth’s biodiversity, as they are critical participants of the global energy flow and the material cycles. However, their spatial-temporal variations and potential interactions among varied biotopes in artificial habitat are poorly understood. In this study, we profiled the variations of bacterial communities among seasons and areas in the water and sediment of artificial reefs using 16S rRNA gene sequencing, and analyzed the potential interaction patterns among microorganisms. Distinct bacterial community structures in the two biotopes were exhibited. The Shannon diversity and the richness of phyla in the sediment were higher, while the differences among the four seasons were more evident in the water samples. The seasonal variations of bacterial communities in the water were more distinct, while significant variations among four areas were only observed in the sediment. Correlation analysis revealed that nitrite and mud content were the most important factors influencing the abundant OTUs in the water and sediment, respectively. Potential interactions and keystone species were identified based on the three co-occurrence networks. Results showed that the correlations among bacterial communities in the sediment were lower than in the water. Besides, the abundance of the top five abundant species and five keystone species had different changing patterns among four seasons and four areas. These results enriched our understanding of the microbial structures, dynamics, and interactions of microbial communities in artificial habitats, which could provide new insights into planning, constructing and managing these special habitats in the future.
creator: Guangjie Fang
creator: Haolin Yu
creator: Huaxiang Sheng
creator: Chuanxi Chen
creator: Yanli Tang
creator: Zhenlin Liang
uri: https://doi.org/10.7717/peerj.12705
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Fang et al.

title: Developmental exposure to the DE-71 mixture of polybrominated diphenyl ether (PBDE) flame retardants induce a complex pattern of endocrine disrupting effects in rats
link: https://peerj.com/articles/12738
last-modified: 2022-01-04
description: Polybrominated diphenyl ethers (PBDEs) are legacy compounds with continued widespread human exposure. Despite this, developmental toxicity studies of DE-71, a mixture of PBDEs, are scarce and its potential for endocrine disrupting effects in vivo is not well covered. To address this knowledge gap, we carried out a developmental exposure study with DE-71. Pregnant Wistar rat dams were exposed to 0, 40 or 60 mg/kg bodyweight/day from gestation day 7 to postnatal day 16, and both sexes were examined. Developmental exposure affected a range of reproductive toxicity endpoints. Effects were seen for both male and female anogenital distances (AGD), with exposed offspring of either sex displaying around 10% shorter AGD compared to controls. Both absolute and relative prostate weights were markedly reduced in exposed male offspring, with about 40% relative to controls. DE-71 reduced mammary gland outgrowth, especially in male offspring. These developmental in vivo effects suggest a complex effect pattern involving anti-androgenic, anti-estrogenic and maybe estrogenic mechanisms depending on tissues and developmental stages. Irrespective of the specific underlying mechanisms, these in vivo results corroborate that DE-71 causes endocrine disrupting effects and raises concern for the effects of PBDE-exposure on human reproductive health, including any potential long-term consequences of disrupted mammary gland development.
creator: Louise Ramhøj
creator: Karen Mandrup
creator: Ulla Hass
creator: Terje Svingen
creator: Marta Axelstad
uri: https://doi.org/10.7717/peerj.12738
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Ramhøj et al.

title: Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution
link: https://peerj.com/articles/12752
last-modified: 2022-01-04
description: BackgroundGround reaction forces (GRFs) are important for understanding human movement, but their measurement is generally limited to a laboratory environment. Previous studies have used neural networks to predict GRF waveforms during running from wearable device data, but these predictions are limited to the stance phase of level-ground running. A method of predicting the normal (perpendicular to running surface) GRF waveform using wearable devices across a range of running speeds and slopes could allow researchers and clinicians to predict kinetic and kinematic variables outside the laboratory environment.PurposeWe sought to develop a recurrent neural network capable of predicting continuous normal (perpendicular to surface) GRFs across a range of running speeds and slopes from accelerometer data.MethodsNineteen subjects ran on a force-measuring treadmill at five slopes (0°, ±5°, ±10°) and three speeds (2.5, 3.33, 4.17 m/s) per slope with sacral- and shoe-mounted accelerometers. We then trained a recurrent neural network to predict normal GRF waveforms frame-by-frame. The predicted versus measured GRF waveforms had an average ± SD RMSE of 0.16 ± 0.04 BW and relative RMSE of 6.4 ± 1.5% across all conditions and subjects.ResultsThe recurrent neural network predicted continuous normal GRF waveforms across a range of running speeds and slopes with greater accuracy than neural networks implemented in previous studies. This approach may facilitate predictions of biomechanical variables outside the laboratory in near real-time and improves the accuracy of quantifying and monitoring external forces experienced by the body when running.
creator: Ryan S. Alcantara
creator: W. Brent Edwards
creator: Guillaume Y. Millet
creator: Alena M. Grabowski
uri: https://doi.org/10.7717/peerj.12752
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Alcantara et al.

title: Efficacy of bakuchiol-garlic combination against virulent genes of Candida albicans
link: https://peerj.com/articles/12251
last-modified: 2022-01-03
description: BackgroundPolymicrobial biofilms are notorious for causing intraoral tissue destruction. Streptococcus sanguinis and Streptococcus mitis, commensals of oral cavities, have been found co-existing with C. albicans in resistant oral infections. There is an urgent need to find alternative treatment options. This study aims to assess the efficacy of garlic (G) and bakuchiol (Bk) combination against candida virulent genes and their subsequently secreted proteins.MethodsIn vitro single species biofilms of C. albicans, and mixed species biofilms formed in combination with streptococci were exposed to bakuchiol and garlic extract (Bk+G). Gene expression of agglutinin-like sequence (ALS1), (ALS3), adhesin-like wall proteins (HWP1) and aspartyl proteinases (SAP5) were determined using qPCR and their subsequent proteins were assessed through Western blotting.ResultsVirulent genes were significantly downregulated in single species biofilms when they were treated with Bk+G combination. However, Bk+G did not have significant effect on ALS1 and HWP1 gene in polymicrobial biofilms. ALS3 and SAP5 were significantly downregulated in Bk+G treated polymicrobial biofilm. Similar results were portrayed in Western blotting.ConclusionBk+G combination exhibited antimicrobial effects against single and mixed species biofilms. The findings might provide insights for treating resistant candida infections. This combination could potentially serve as an herbal alternative to traditional antifungals following further research.
creator: Ayesha Fahim
creator: Wan Harun Himratul-Aznita
creator: Puteri Shafinaz Abdul-Rahman
creator: Mohammad K. Alam
uri: https://doi.org/10.7717/peerj.12251
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Fahim et al.

title: Role of miR-100-5p and CDC25A in breast carcinoma cells
link: https://peerj.com/articles/12263
last-modified: 2022-01-03
description: ObjectiveTo inquiry about mechanism of miR-100-5p/CDC25A axis in breast carcinoma (BC), thus offering a new direction for BC targeted treatment.MethodsqRT-PCR was employed to explore miR-100-5p and CDC25A mRNA levels. Western blot was employed for detecting protein expression of CDC25A. Targeting relationship of miR-100-5p and CDC25A was verified by dual-luciferase assay. In vitro experiments were used for assessment of cell functions.ResultsIn BC tissue and cells, miR-100-5p was significantly lowly expressed (P < 0.05) while CDC25A was highly expressed. Besides, miR-100-5p downregulated CDC25A level. miR-100-5p had a marked influence on the prognosis of patients. The forced miR-100-5p expression hindered BC cell proliferation, migration and invasion, and facilitated cell apoptosis. Upregulated miR-100-5p weakened promotion of CDC25A on BC cell growth.ConclusionTogether, these findings unveiled that CDC25A may be a key target of miR-100-5p that mediated progression of BC cells. Hence, miR-100-5p overexpression or CDC25A suppression may contribute to BC diagnosis.
creator: Xiaoping Li
creator: Yanli Ren
creator: Donghong Liu
creator: Xi Yu
creator: Keda Chen
uri: https://doi.org/10.7717/peerj.12263
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Li et al.

title: Characteristics of Central American brocket deer resting sites in a tropical mountain cloud forest in eastern Mexico
link: https://peerj.com/articles/12587
last-modified: 2022-01-03
description: The Central American brocket deer is a vulnerable species. Geographically isolated populations have been affected by poaching and habitat fragmentation, leading to local extinctions. It is therefore important to understand this species’ habitat characteristics, particularly of resting sites, which play a crucial role in survival and fitness. We describe the characteristics and distribution patterns of Central American brocket deer resting sites at the microhabitat and landscape scales in San Bartolo Tutotepec, Hidalgo, México. We conducted eight bimonthly field surveys between November 2017 and March 2019, consisting of 32 transects of 500 m length to search for fecal pellets, footprints, scrapes, and browsed plants. At each resting site we identified, we measured canopy closure, horizontal thermal cover, protection from predators for fawns and adults, escape routes, slope from the ground, presence of scrapes, cumulative importance value of the edible plant species, and distance from the resting site to the nearest water resource to characterize the site at the microhabitat scale. At the landscape scale, we identified the type of biotope, elevation, aspect, and slope. We compared all of these parameters from resting sites with a paired randomly selected site to serve as a control. We performed a multiple logistic regression to identify the parameters associated with the resting sites and a point pattern analysis to describe their distribution. We characterized 43 resting sites and their corresponding control plots. At the microhabitat scale, resting sites were associated with higher vertical thermal cover, more concealment cover, more escape routes, more edible plant species, higher slope from the ground, and closer distance to water resources. At the landscape scale, resting sites were associated with beech forest, oak forest, secondary forest, and ravine biotopes and negatively associated with pine forest, houses, and roads. Resting sites had an aggregated spatial pattern from 0 to 900 m, but their distribution was completely random at larger scales. Our study revealed that Central American brocket deer selected places with specific characteristics to rest, at both microhabitat and landscape scales. We therefore suggest that existing habitat be increased by reforesting with native species—particularly Mexican beech forest and oak forest—to improve the deer’s conservation status in the study area.
creator: Brenda Muñoz Vazquez
creator: Sonia Gallina Tessaro
creator: Livia León-Paniagua
uri: https://doi.org/10.7717/peerj.12587
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Muñoz Vazquez et al.

title: Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles
link: https://peerj.com/articles/12632
last-modified: 2022-01-03
description: Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic Xanthomonas strains on Xcc infections.
creator: Stephen D. B. Jr. Ramnarine
creator: Jayaraj Jayaraman
creator: Adesh Ramsubhag
uri: https://doi.org/10.7717/peerj.12632
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Ramnarine et al.

title: Assessment of health-related quality of life in hypertensive hemodialysis patients
link: https://peerj.com/articles/12690
last-modified: 2022-01-03
description: Background and ObjectivesGlobally, the prevalence of hypertension (HTN) with the coexistence of chronic kidney disease (CKD) is increasing, resulting in poor quality of life. The main objective of the study was to measure the health-related quality of life (HRQoL) of hypertensive hemodialysis patients.MethodsA multicenter follow-up study was carried out in six public and two private dialysis centers in Pakistan. A total of 517 hypertensive hemodialysis patients responded by completing the questionnaire at baseline and two subsequent phases. The quality of life of these patients was assessed using the EQ-5D-5L questionnaire (a standardized instrument for measuring generic health status). Statistical analysis was done using a multivariate linear regression model, Friedman test and Kruskal Wallis test.ResultsThe majority of patients (58.2%) had normal body mass index and about 60.5% of the patients were taking less salt due to HTN. Friedman test gave the statistically significant results (p ≤ 0.001) in systolic blood pressure (BP), diastolic BP and EQ-5D visual analogue scale (VAS) score between three phases (initial visit, first follow-up and second follow-up). A significant improvement was observed in self-care and usual activities from initial visit to first follow-up (p < 0.05). The most problematic dimension among the hypertensive patients with CKD was pain/discomfort (86.5%).ConclusionsHTN with coexisting CKD in hemodialysis patients severely affected HRQoL. Pain/discomfort was the most problematic dimension among the participants.
creator: Ayesha Aslam
creator: Shahid Shah
creator: Ghulam Abbas
creator: Anees ur Rehman
creator: Tauqeer Hussain Malhi
creator: Nasser Hadal Alotaibi
creator: Abdulaziz Ibrahim Alzarea
creator: Muhammad Fawad Rasool
creator: Haris Khurram
creator: Sibgha Noureen
creator: Muhammad Talha Saeed Bokhari
uri: https://doi.org/10.7717/peerj.12690
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Aslam et al.

title: Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot
link: https://peerj.com/articles/12693
last-modified: 2022-01-03
description: Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010–2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to describe the composition and structure of the woody plants in this plot, assess their spatial associations within and among the dominant species using univariate and bivariate spatial point-pattern analysis, and examine the interactions between land-use history and ecological processes. The plot includes 108,632 live stems ≥ 1 cm in diameter (2,215 individuals/ha) and 7,595 standing dead stems ≥ 5 cm in diameter. Live tree basal area averaged 42.25 m2/ha, of which 84% was represented by Tsuga canadensis (14.0 m2/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), Acer rubrum (7.2 m2/ ha) and Pinus strobus (eastern white pine; 4.4 m2/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha. Across all species and size classes, the forest contains a preponderance (> 80,000) of small stems (<10-cm diameter) that exhibit a reverse-J size distribution. Significant spatial clustering of abundant overstory species was observed at all spatial scales examined. Spatial distributions of A. rubrum and Q. rubra showed negative intraspecific correlations in diameters up to at least a 150-m spatial lag, likely indicative of crowding effects in dense forest patches following intensive past land use. Bivariate marked point-pattern analysis, showed that T. canadensis and Q. rubra diameters were negatively associated with one another, indicating resource competition for light. Distribution and abundance of the common overstory species are predicted best by soil type, tree neighborhood effects, and two aspects of land-use history: when fields were abandoned in the late 19th century and the succeeding forest types recorded in 1908. In contrast, a history of intensive logging prior to 1950 and a damaging hurricane in 1938 appear to have had little effect on the distribution and abundance of present-day tree species. Our findings suggest that current day composition and structure are still being influenced by anthropogenic disturbances that occurred over a century ago.
creator: David A. Orwig
creator: Jason A. Aylward
creator: Hannah L. Buckley
creator: Bradley S. Case
creator: Aaron M. Ellison
uri: https://doi.org/10.7717/peerj.12693
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Orwig et al.

title: Identification of the occurrence and potential mechanisms of heterotopic ossification associated with 17-beta-estradiol targeting MKX by bioinformatics analysis and cellular experiments
link: https://peerj.com/articles/12696
last-modified: 2022-01-03
description: BackgroundTendon heterotopic ossification (HO) is a common condition occurring secondary to tendon injury or surgical trauma that significantly affects the patient’s quality of life. The treatment of tendon HO remains challenging due to a lack of clarity regarding the pathological mechanism. Mohawk (MKX) is a key factor in preventing tendon HO; however, its upstream regulatory mechanism remains to be understood. This study aimed to identify potential compounds that target and regulate MKX and explore their functional mechanisms.MethodsBioinformatics analysis of MKX-related compounds and proteins was performed based on data from the STITCH and OncoBinder databases. Subsequently, the SymMap database was used to study MKX-related traditional Chinese medicine drugs and symptoms. Next, the OncoBinder genomic and proteomic discovery model was applied to identify potential regulators of MKX. The analytical tool Expert Protein Analysis System for proteomics was used to predict the three-dimensional structure of MKX, and the AutoDockTools software was used to identify pockets of activity at potential sites for molecular docking. Furthermore, we evaluated the effect of different doses of 17-beta-estradiol on bone marrow-derived mesenchymal stem cells (BM-MSCs).ResultsBy predicting the three-dimensional structure of MKX and simulating molecular docking, Pro-Tyr and 17-beta-Estradiol were found to target and bind to MKX. Analysis of the STITCH and OncoBinder databases showed that MKX had a significant regulatory correlation with suppressor interacting 3 A/histone deacetylase 1 (SIN3A/HDAC1). The GO and KEGG pathway enrichment analysis revealed that the functions of MKX and its associated proteins were mainly enriched in osteogenic-related pathways. Assessment of the proliferation of BM-MSCs revealed that 17-beta-estradiol possibly upregulated the mRNA expression of the HDAC1-SIN3A/BMP pathway-related RUNX2, thereby promoting the proliferation of BM-MSCs.ConclusionsThe compounds Pro-Tyr and 17-beta-Estradiol may bind to MKX and thus affect the interaction of MKX with SIN3A/HDAC1.
creator: Yunpeng Zhang
creator: Jingwei Zhang
creator: Chenyu Sun
creator: Fan Wu
uri: https://doi.org/10.7717/peerj.12696
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Zhang et al.

title: First report of fatty acids in Mimosadiplotricha bee pollen with in vitro lipase inhibitory activity
link: https://peerj.com/articles/12722
last-modified: 2022-01-03
description: Bee pollen (BP) is full of nutrients and phytochemicals, and so it is widely used as a health food and alternative medicine. Its composition and bioactivity mainly depend on the floral pollens. In this work, BP collected by Apis mellifera with different monoculture flowering crops (BP1-6) were used. The types of floral pollen in each BP were initially identified by morphology, and subsequently confirmed using molecular phylogenetic analysis. Data from both approaches were consistent and revealed each BP to be monofloral and derived from the flowers of Camellia sinensis L., Helianthus annuus L., Mimosa diplotricha, Nelumbo nucifera, Xyris complanata, and Ageratum conyzoides for BP1 to BP6, respectively. The crude extracts of all six BPs were prepared by sequential partition with methanol, dichloromethane (DCM), and hexane. The crude extracts were then tested for the in vitro (i) α-amylase inhibitory, (ii) acetylcholinesterase inhibitory (AChEI), and (iii) porcine pancreatic lipase inhibitory (PPLI) activities in terms of the percentage enzyme inhibition and half maximum inhibitory concentration (IC50). The DCM partitioned extract of X. complanata BP (DCMXBP) had the highest active α-amylase inhibitory activity with an IC50 value of 1,792.48 ± 50.56 µg/mL. The DCM partitioned extracts of C. sinensis L. BP (DCMCBP) and M. diplotricha BP (DCMMBP) had the highest PPLI activities with an IC50 value of 458.5 ± 13.4 and 500.8 ± 24.8 µg/mL, respectively), while no crude extract showed any marked AChEI activity. Here, the in vitro PPLI activity was focused on. Unlike C. sinensis L. BP, there has been no previous report of M. diplotricha BP having PPLI activity. Hence, DCMMBP was further fractionated by silica gel 60 column chromatography, pooling fractions with the same thin layer chromatography profile. The pooled fraction of DCMMBP2-1 was found to be the most active (IC50 of 52.6 ± 3.5 µg/mL), while nuclear magnetic resonance analysis revealed the presence of unsaturated free fatty acids. Gas chromatography with flame-ionization detection analysis revealed the major fatty acids included one saturated acid (palmitic acid) and two polyunsaturated acids (linoleic and linolenic acids). In contrast, the pooled fraction of DCMMBP2-2 was inactive but pure, and was identified as naringenin, which has previously been reported to be present in M. pigra L. Thus, it can be concluded that naringenin was compound marker for Mimosa BP. The fatty acids in BP are nutritional and pose potent PPLI activity.
creator: Phanthiwa Khongkarat
creator: Prapun Traiyasut
creator: Preecha Phuwapraisirisan
creator: Chanpen Chanchao
uri: https://doi.org/10.7717/peerj.12722
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Khongkarat et al.

title: Genome-wide identification and characterization of the CLASP_N gene family in upland cotton (Gossypium hirsutum L.)
link: https://peerj.com/articles/12733
last-modified: 2022-01-03
description: BackgroundCytoplasmic linker–associated proteins (CLASPs) are tubule proteins that can bind to microtubules and participate in regulating the structure and function of microtubules, which significantly affects the development and growth of plants. These proteins have been identified in Arabidopsis; however, little research has been performed in upland cotton.MethodsIn this study, the whole genome of the CLASP_N family was analyzed to provide theoretical support for the function of this gene family in the development of upland cotton fiber. Bioinformatics was used to analyze the family characteristics of CLASP_N in upland cotton, such as member identification, sequence characteristics, conserved domain structure and coevolutionary relationships. Real-time fluorescent quantitative PCR (qRT-PCR) was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber.ResultsAt the genome-wide level, we identified 16 upland cotton CLASP_N genes. A chromosomal localization analysis revealed that these 16 genes were located on 13 chromosomes. The motif results showed that all CLASP_N proteins have the CLASP_N domain. Gene structure analysis showed that the structure and length of exons and introns were consistent in the subgroups. In the evolutionary analysis with other species, the gene family clearly diverged from the other species in the evolutionary process. A promoter sequence analysis showed that this gene family contains a large number of cis-acting elements related to a variety of plant hormones. qRT-PCR was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber and leaves, and Gh210800 was found to be highly expressed in the later stages of fiber development. The results of this study provide a foundation for further research on the molecular role of the CLASP_N genes in cotton fiber development.
creator: Meijun Ji
creator: Kangtai Sun
creator: Hui Fang
creator: Zhimin Zhuang
creator: Haodong Chen
creator: Qi Chen
creator: Ziyi Cao
creator: Yiting Wang
creator: Allah Ditta
creator: Muhammad Kashif Riaz Khan
creator: Kai Wang
creator: Baohua Wang
uri: https://doi.org/10.7717/peerj.12733
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Ji et al.

title: Investigation of lipolytic activity of the red king crab hepatopancreas homogenate by NMR spectroscopy
link: https://peerj.com/articles/12742
last-modified: 2022-01-03
description: The digestive gland of craboids (hepatopancreas) is rich in a huge number of various enzymes (collagenases, nucleases, hyaluronidases, proteases), which are well studied at the moment. However, little is known about crustacean lipases. In this work, using 1H NMR spectroscopy, it was found that the hepatopancreas homogenate of the red king crab Paralithodes camtschaticus demonstrates high lipolytic activity against triacetin in a wide pH range and shows moderate activity against the caprylic/capric triglyceride emulsion. Under the action of the hepatopancreas homogenate, triacylglycerols are converted into 1,2-diacylglycerol, and then into 2-monoacylglycerol and 1-monoacylglycerol. The 1-monoacylglycerol predominates in the reaction products. The use of NMR spectroscopy makes it possible to quickly detect hydrolysis products and evaluate the reaction direction.
creator: Maria Timchenko
creator: Vladislav Molchanov
creator: Maxim Molchanov
creator: Alexander Timchenko
creator: Evgeny Sogorin
uri: https://doi.org/10.7717/peerj.12742
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Timchenko et al.