Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
Gill et al. (2022) Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 10:e12835 https://doi.org/10.7717/peerj.12835
Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy
Iberian natural steppes have traditionally been used for extensive sheep grazing, which has been noted to be positively associated with steppe bird abundance and diversity. Sheep numbers in Spain, which harbors the largest European populations of many steppe bird species, decreased by 9.2 million (37.3%) between 1992 and 2020. Steppe birds in Spain have faced dramatic declines during the same period, but there is a lack of knowledge about the potential association between sheep and open-habitat bird declines. We used sheep data from the Spanish Ministry of Agriculture and bird data (1998–2018) from the Spanish Common Bird Monitoring Program to assess the association at the Spanish scale between sheep decline and the Farmland Bird Index (FBI) and the Natural Shrub-steppe Bird Index (SBI). We also used an independent dataset on population trends of the Dupont’s Lark (Chersophilus duponti) to assess the relationship between sheep numbers and the decline of this threatened steppe specialist passerine in Spain, whose European population is restricted to Iberian natural steppes. To test for a spurious relationship between temporal series, variables were tested for cointegration. After confirming cointegration, we found a strong positive relationship between sheep abundance and the trends of the FBI and SBI indices during the period 1998–2018. The association between sheep abundance and trends of the Dupont’s Lark (2004–2015) was positive although it was not statistically significant. Although the main causes of decline of farmland and steppe birds are mainly related to agricultural intensification and land use changes, the correlation found, using two independent cointegrated datasets, between the reduction in farmland and shrub-steppe birds and sheep numbers at the country scale suggests that the decline of steppe birds in Spain may be also associated with the decline in sheep numbers. This agrees with previous studies that found a positive relationship between intermediate levels of sheep grazing and steppe bird abundance in Iberian steppes. Further research (e.g. experimental studies) is needed to corroborate our study and identify the most appropriate level of grazing intensity for protecting the most farmland and shrub-steppe birds. Our results suggest that the promotion of extensive grazing should be considered as a key factor in future Common Agricultural Policy reforms and conservation programmes to protect steppe birds.
Traba et al. (2022) Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy. PeerJ 10:e12870 https://doi.org/10.7717/peerj.12870
Analysis and comparison of protein secondary structures in the rachis of avian flight feathers
Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.
Lin et al. (2022) Analysis and comparison of protein secondary structures in the rachis of avian flight feathers. PeerJ 10:e12919 https://doi.org/10.7717/peerj.12919
Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)
Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to decipher the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found high abundance proteins related to nitrate and amino acids metabolismsin the salt-tolerant cultivars. The significant increase in abundance of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. Moreover, the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including sterol side chain reductase, gamma aminobutyrate transaminase and starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future.
Wang et al. (2022) Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium). PeerJ 10:e12955 https://doi.org/10.7717/peerj.12955
Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)
Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful information for the understanding of the complex mechanisms of plant hormones in controlling pod size by regulating the cell size in peanuts and will facilitate the improvement of peanut breeding.
Wang et al. (2022) Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.). PeerJ 10:e12965 https://doi.org/10.7717/peerj.12965
Response of bacterial community structure to different ecological niches and their functions in Korean pine forests
A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.
Ji et al. (2022) Response of bacterial community structure to different ecological niches and their functions in Korean pine forests. PeerJ 10:e12978 https://doi.org/10.7717/peerj.12978
Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China
Background With the exacerbating effects of the global climate change and the more and more attention to the study of plant carbon sink, an increasing number of researches on plant carbon sinks has grown. Although many studies exist on shrub vegetation, soil and litters, most studies focus on the community structure, biomass, surface soil of single plant and shrub layer vegetation, and lack the studies which included the potential relationships between climate change and ecological stoichiometric elements, comprehensive research on main species, even herb and litter layer. In order to provide relevant theoretical basis and data support, it is necessary to take the main terrestrial shrub ecosystem in Central Yunnan as the starting point to analyze and explore its carbon sink distribution characteristics, formation causes, the correlation between climatic factors (temperature and precipitation) and stoichiometric elements, which from community and species levels. Methods Plants which originated from 12 main shrub species, litter and soil samples which collected in 69 plots were from 23 plots (Q1–Q23) of 11 cities (countries) in the central Yunnan, China. The biomass and carbon density distribution pattern of each shrub ecosystem and the potential correlations with main climate factors was explored and identified. Some indexes were analyzed such as biomass and carbon density of each part of the shrub ecosystem distribution pattern, correlation, significant changes, formation reasons with the mean value (±standard deviation: SD). Through the redundancy analysis(RDA) of carbon (c), nitrogen (n), phosphorus (P) and main climate factors (precipitation and temperature), the distribution pattern of stoichiometric elements in shrub ecosystem can be judged. Results (1) The above-ground biomass (AGB), under-ground biomass (UGB) and root-shoot ratio (R/S) were between 1.13–2.03 t/hm2, 0.62–1.49 t/hm2, and 0.38–0.84, the carbon element was distributed in herb layer under-ground part and rhizomes of the shrub layer mostly. (2) The fitting slope of AGB and UGB of shrub communities and species was in accordance with the allometric distribution growth relationship, the R/S of shrubs was smaller than other vegetation types. Mean annual temperature (MAT) and mean annual precipitation (MAP) are not the main factors which affect the biomass and R/S. (3) The contents of C, N and P elements in leaves were significantly higher than other parts in shrub layer. P in shrub layer above-ground part is much higher than under-ground part. The surface soil layer has the highest C content, and decreased with the depth, so as the impact of vegetation and litter on the content of soil elements. Both of the correlation of MAT with N content of leaf, C/N of stem, the correlation of MAP with C content, C/N of soil is the greatest.
Guo et al. (2022) Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China. PeerJ 10:e13005 https://doi.org/10.7717/peerj.13005
Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants
Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.
Li et al. (2022) Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants. PeerJ 10:e13012 https://doi.org/10.7717/peerj.13012
Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.
The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant’s adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
Gu et al. (2022) Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.. PeerJ 10:e12882 https://doi.org/10.7717/peerj.12882
Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury
MicroRNAs (miRNAs or miRs) are non-coding RNAs that contribute to pathological processes of various kidney diseases. Renal function injury represents a final common outcome of congenital obstructive nephropathy and has attracted a great deal of attention. However the molecular mechanisms are still not fully established. In this study, we compared transcriptome sequencing data of miRNAs of renal tissues from congenital hydronephrosis children with or without renal functional injury, in order to better understand whether microRNAs could play important roles in renal functional injury after ureteropelvic junction obstruction. A total of 22 microRNAs with significant changes in their expression were identified. Five microRNAs were up-regulated and 17 microRNAs were down-regulated in the renal tissues of the hydronephrosis patients with renal function injury compared with those without renal function injury. MicroRNA target genes were predicted by three major online miRNA target prediction algorithms, and all these mRNAs were used to perform the gene ontology analysis and Kyoto Encyclopedia of Gene and Genomes pathway analysis. Then, twelve candidate human and rat homologous miRNAs were selected for validation using RT-qPCR in vitro and in vivo; only miR-187-3p had a trend identical to that detected by the sequencing results among the human tissues, in vivo and in vitro experimental models. In addition, we found that the change of miR-187-3p in vivo was consistent with results in vitro models and showed a decrease trend in time dependence. These results provided a detailed catalog of candidate miRNAs to investigate their regulatory role in renal injury of congenital hydronephrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.
Liu et al. (2022) Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury. PeerJ 10:e12962 https://doi.org/10.7717/peerj.12962
Applications and limitations of current markerless motion capture methods for clinical gait biomechanics
Background Markerless motion capture has the potential to perform movement analysis with reduced data collection and processing time compared to marker-based methods. This technology is now starting to be applied for clinical and rehabilitation applications and therefore it is crucial that users of these systems understand both their potential and limitations. This literature review aims to provide a comprehensive overview of the current state of markerless motion capture for both single camera and multi-camera systems. Additionally, this review explores how practical applications of markerless technology are being used in clinical and rehabilitation settings, and examines the future challenges and directions markerless research must explore to facilitate full integration of this technology within clinical biomechanics. Methodology A scoping review is needed to examine this emerging broad body of literature and determine where gaps in knowledge exist, this is key to developing motion capture methods that are cost effective and practically relevant to clinicians, coaches and researchers around the world. Literature searches were performed to examine studies that report accuracy of markerless motion capture methods, explore current practical applications of markerless motion capture methods in clinical biomechanics and identify gaps in our knowledge that are relevant to future developments in this area. Results Markerless methods increase motion capture data versatility, enabling datasets to be re-analyzed using updated pose estimation algorithms and may even provide clinicians with the capability to collect data while patients are wearing normal clothing. While markerless temporospatial measures generally appear to be equivalent to marker-based motion capture, joint center locations and joint angles are not yet sufficiently accurate for clinical applications. Pose estimation algorithms are approaching similar error rates of marker-based motion capture, however, without comparison to a gold standard, such as bi-planar videoradiography, the true accuracy of markerless systems remains unknown. Conclusions Current open-source pose estimation algorithms were never designed for biomechanical applications, therefore, datasets on which they have been trained are inconsistently and inaccurately labelled. Improvements to labelling of open-source training data, as well as assessment of markerless accuracy against gold standard methods will be vital next steps in the development of this technology.
Wade et al. (2022) Applications and limitations of current markerless motion capture methods for clinical gait biomechanics. PeerJ 10:e12995 https://doi.org/10.7717/peerj.12995
Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study
Background Anemia is a common health issue among adolescents. Anemic conditions could affect physical performance; however, the actual profiles of anemia in adolescent students in sports clubs have not been well documented. Methods We conducted a retrospective chart review of individuals aged 13–22 years who belonged to sports clubs in schools and visited an outpatient clinic between August 1, 2016, and August 31, 2020. The medical and laboratory records, including serum levels of ferritin, folate, vitamin B12, and creatinine kinase at their first visit were assessed. Results A total of 485 individuals (231 male (48%) and 254 female (52%) patients) were eligible for the study. The most common club activity was track and field (n = 171 (35%)). The overall prevalence of the World Health Organization-defined anemia was 16.5% (95% CI [13.1–20.4]; 9.0% [5.4–13.8] and 23.1% [17.8–29.2] in males and females, respectively) after excluding pre-treated individuals. Hypoferritinemia and elevation of serum creatinine kinase levels were identified as independent contributors to anemia in both sexes (odds ratios: 13.2 (95% CI [4.2–41.1]), p < 0.001 and 14.7 (95% CI [1.8–118.4]), p = 0.012, respectively for males; odds ratios: 6.6 (95% CI [1.3–13.9]), p < 0.001 and 2.7 (95% CI [1.4–5.5]), p = 0.004, respectively for females). Discussion Anemia is prevalent in both male and female adolescent students in sports clubs. Iron deficiency and excessive training indicated by elevated creatinine kinase levels may contribute to the risk of anemia. Physicians should assess the amount of exercise, and not merely iron storage, in clinical practice.
Yamamoto et al. (2022) Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study. PeerJ 10:e13004 https://doi.org/10.7717/peerj.13004
Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau
Background The microbial decomposition of soil organic carbon (SOC) is a major source of carbon loss, especially in ecologically fragile regions (e.g., the Tibetan Plateau), which are also affected by global warming and anthropogenic activities (e.g., fertilization). The inherent differences between bacteria and fungi indicate that they are likely to play distinct roles in the above processes. However, there still have been no reports on that, which is restricting our knowledge about the mechanisms underlying SOC decomposition. Methods A long-term nitrogen (N) and phosphorus (P) addition field experiment was conducted to assess their effects on soil microbial, fungal, and bacterial respiration (RM, RF, and RB, respectively) and temperature sensitivity (Q10; at 15 °C, 25 °C, and 35 °C) using cycloheximide and streptomycin to inhibit the growth of fungi and bacteria. Results We found that N suppressed RM and RF at all temperatures, but RB was only suppressed at 15 °C, regardless of the addition of P. The addition of N significantly decreased the ratio of RF/RM at 35 °C, and the combined NP treatment increased the Q10 of RB but not that of RF. Results of the redundancy analysis showed that variations in soil respiration were linked with NO3−-N formation, while the variations in Q10 were linked with SOC complexity. Long-term N addition suppressed RM by the formation of NO3−-N, and this was mediated by fungi rather than bacteria. The contribution of fungi toward SOC decomposition was weakened by N addition and increasing temperatures. Combined NP addition increased the Q10 of RB due to increased SOC complexity. The present study emphasizes the importance of fungi and the soil environment in SOC decomposition. It also highlights that the role of bacteria and SOC quality will be important in the future due to global warming and increasing N deposition.
Chen et al. (2022) Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau. PeerJ 10:e12851 https://doi.org/10.7717/peerj.12851
Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives
The need for comprehensive and effective coral restoration projects, as part of a broader conservation management strategy, is accelerating in the face of coral reef ecosystem decline. This study aims to expand the currently limited knowledge base for restoration techniques in the Maldives by testing the performance of mid-water rope nurseries in a lagoon and a reef habitat. We examined whether different coral farming habitats impacted fragment survival, health and growth of two coral genera and how the occurrence of mutualistic fauna, predation and disease influenced coral rearing success. Two nurseries were stocked with a total of 448 Pocillopora verrucosa and 96 Acropora spp. fragments, divided into different groups (four Pocillopora groups: lagoon nursery at 5 m; reef nursery at 5, 10 and 15 m; two Acropora groups: lagoon nursery at 5 m and reef nursery at 5 m). Eight fragment replicates from the same donor colony (Pocillopora genets: N = 14, Acropora genets N = 6) were used in each group and monitored for one year. Our results show that fragment survival was high in both farming habitats (>90%), with P. verrucosa surviving significantly better in the lagoon and Acropora spp. surviving and growing significantly faster in the reef nursery. P. verrucosa growth rates were similar between reef and lagoon habitat. Different rearing depths in the reef nursery had no impact on the survival of P. verrucosa but coral growth decreased considerably with depth, reducing fragments’ ecological volume augmentation and growth rates by almost half from 5 to 15 m depth. Further, higher fish predation rates on fragments were recorded on the reef, which did not impact overall nursery performance. Mutualistic fauna, which correlated positively with fragment survival, was more frequently observed in the lagoon nursery. The occurrence of disease was noted in both habitats, even though implications for fragment health were more severe in the lagoon. Overall, our study demonstrates that lagoon and reef nurseries are suitable for rearing large numbers of coral fragments for transplantation. Nevertheless, we recommend considering the specific environmental conditions of the farming habitat, in particular water quality and year-round accessibility, in each case and to adjust the coral farming strategy accordingly. We hope that this novel research encourages the increased application of mid-water rope nurseries for ‘coral gardening’ to advance coral reef recovery and climate resilience in the Maldives.
Dehnert et al. (2022) Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives. PeerJ 10:e12874 https://doi.org/10.7717/peerj.12874
Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes
Background Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss. Methods Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress. Results It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.
Shang et al. (2022) Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes. PeerJ 10:e12954 https://doi.org/10.7717/peerj.12954
AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis
Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. ‘Jinnan Shiqin’ . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in ‘Jinnan Shiqin’ were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.
Liu et al. (2022) AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis. PeerJ 10:e12976 https://doi.org/10.7717/peerj.12976
Biomarkers of non-communicable chronic disease: an update on contemporary methods
Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic diseases was discussed. Recently, multivariate biomarkers analysis approach has been employed with promising prospect. A brief discussion of the multivariate approach for the early diagnosis of the most common chronic diseases was highlighted in this review. The use of diagnostic algorithms might show the way for novel criteria and enhanced diagnostic effectiveness inpatients with one or numerous non-communicable chronic diseases. The search for new relevant biomarkers for the better diagnosis of patients with non-communicable chronic diseases according to the risk of progression, sickness, and fatality is ongoing. It is important to determine whether the newly identified biomarkers are purely associations or real biomarkers of underlying pathophysiological processes. Use of multivariate analysis could be of great importance in this regard.
Al-hadlaq et al. (2022) Biomarkers of non-communicable chronic disease: an update on contemporary methods. PeerJ 10:e12977 https://doi.org/10.7717/peerj.12977
Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
Cruz et al. (2022) Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard. PeerJ 10:e12761 https://doi.org/10.7717/peerj.12761
Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trapeziformis were identified as Holothuria (Halodeima) inornata Semper, 1868; the presence of the crab in the host’s coelomic cavity was confirmed, and for the first time we found it within the intestine. The geographical distribution is the Pacific coast of Mexico. Based on the data presented here, the taxonomic status of Holothuriophilus trapeziformis is now complete.
Cortés-Carrasco et al. (2022) Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy. PeerJ 10:e12774 https://doi.org/10.7717/peerj.12774
Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support for the range-shift hypothesis, they also highlight the dual effect of distinct factors on spatial patterns in population dynamics and can explain the overall difficulty to find general evidence for geographic gradients in natural populations. We propose that considering the separate contribution of the factors affecting population dynamics could help better understand the drivers of abundance-distribution patterns.
Chevalier et al. (2022) Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species. PeerJ 10:e12857 https://doi.org/10.7717/peerj.12857
Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints showed early inflammatory changes, which later decreased.
Syed Sulaiman et al. (2022) Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits. PeerJ 10:e12897 https://doi.org/10.7717/peerj.12897
Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
Mei et al. (2022) Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis. PeerJ 10:e12975 https://doi.org/10.7717/peerj.12975
Disentangling bias for non-destructive insect metabarcoding
A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
Martoni et al. (2022) Disentangling bias for non-destructive insect metabarcoding. PeerJ 10:e12981 https://doi.org/10.7717/peerj.12981
Microbial biogeography of the wombat gastrointestinal tract
Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.
Eisenhofer et al. (2022) Microbial biogeography of the wombat gastrointestinal tract. PeerJ 10:e12982 https://doi.org/10.7717/peerj.12982
A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift
Cerebral blood flow (CBF) monitoring is of great significance for treating and preventing strokes. However, there has not been a fully accepted method targeting continuous assessment in clinical practice. In this work, we built a noninvasive continuous assessment system for cerebral blood flow pulsation (CBFP) that is based on magnetic induction phase shift (MIPS) technology and designed a physical model of the middle cerebral artery (MCA). Physical experiments were carried out through different simulations of CBF states. Four healthy volunteers were enrolled to perform the MIPS and ECG synchronously monitoring trials. Then, the components of MIPS related to the blood supply level and CBFP were investigated by signal analysis in time and frequency domain, wavelet decomposition and band-pass filtering. The results show that the time-domain baseline of MIPS increases with blood supply level. A pulse signal was identified in the spectrum (0.2–2 Hz in 200–2,000 ml/h groups, respectively) of MIPS when the simulated blood flow rate was not zero. The pulsation frequency with different simulated blood flow rates is the same as the squeezing frequency of the feeding pump. Similar to pulse waves, the MIPS signals on four healthy volunteers all had periodic change trends with obvious peaks and valleys. Its frequency is close to that of the ECG signal and there is a certain time delay between them. These results indicate that the CBFP component can effectively be extracted from MIPS, through which different blood supply levels can be distinguished. This method has the potential to become a new solution for non-invasive and comprehensive monitoring of CBFP.
Zeng et al. (2022) A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift. PeerJ 10:e13002 https://doi.org/10.7717/peerj.13002
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum
Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including ‘translation’, ‘folding, sorting and degradation’, ‘transcription’, ‘signal transduction’ and ‘cell growth and death’, eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease.
Huang et al. (2022) Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PeerJ 10:e12756 https://doi.org/10.7717/peerj.12756
Estimation of Coregonus ussuriensis age, growth, and maturation in China’s Amur River
This study examined the age, growth, and maturation of 1,064 Coregonus ussuriensis individuals that were collected monthly from the middle section of the Amur River, China between 2016 and 2018. The fork length (FL) ranged from 14.9 to 49.1 cm for males and 21.5 to 58.8 cm for females, and the body weight (BW) ranged from 72.6 to 1,348.7 g for males and 107.9 to 2,854.9 g for females. The relationship of BW and FL was expressed as: BW♂ = 0.0324 × FL2.708; BW♀ = 0.014 × FL2.963. The sample ages ranged from 2 to 8 years for males and 2 to 9 years for females. We used the von Bertalanffy function based on otolith reading and observed FL data to simulate Coregonus ussuriensis growth, which has been suggested to be similar to that of other Salmonidae fishes. No significant difference in growth was determined between males and females. The monthly gonad somatic index (GSI) value ranged from 0.16% to 1.69% for males and from 0.73% to 16.15% for females, with a peak in November. Additionally, the reproductive staging suggested that the Coregonus ussuriensis spawning season was mainly in November and December. The size at maturity (FL50%) for males and females was 34.9 cm and 37.9 cm respectively, and the corresponding age (T50%) was 4.5 and 5.1, respectively. This study provides basic information for understanding the biological characteristics of Coregonus ussuriensis and should aid in the assessment and management of fishery resources.
Wang et al. (2022) Estimation of Coregonus ussuriensis age, growth, and maturation in China’s Amur River. PeerJ 10:e12817 https://doi.org/10.7717/peerj.12817
A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia
Background Carbapenem resistant Enterobacteriaceae (CRE) has rapidly disseminated worldwide and has become a global threat to the healthcare system due to its resistance towards “last line” antibiotics. This study aimed to investigate the prevalence of CRE and the resistance mechanism as well as the risk factors associated with in-hospital mortality. Methods A total of 168 CRE strains isolated from a tertiary teaching hospital from 2014–2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains were characterised by PFGE. The risk factors of patients infected by CRE associated with in-hospital mortality were determined statistically. Results The predominant CRE species isolated was K. pneumoniae. The carbapenemases detected were blaOXA-48, blaOXA-232, blaVIM and blaNDM of which blaOXA-48 was the predominant carbapenemase detected among 168 CRE strains. A total of 40 CRE strains harboured two different carbapenemase genes. A total of seven clusters and 48 pulsotypes were identified among 140 CRKp strains. A predominant pulsotype responsible for the transmission from 2014 to 2015 was identified. Univariate statistical analysis identified that the period between CRE isolation and start of appropriate therapy of more than 3 days was statistically associated with in-hospital mortality.
Kong et al. (2022) A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia. PeerJ 10:e12830 https://doi.org/10.7717/peerj.12830
Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands
Background Urbanization and global warming are generating ecological degradation and land pattern alteration problems in natural wetlands. These changes are greatly affecting the ecological services of wetlands. Therefore, there is an urgent need to explore the relationship between pollutants and land-use type for wetland restoration purposes. Zaozhadian Lake is a freshwater wetland in the North China Plain, which is facing degradation and land-use types changes. An experiment for analyzing soil pollutants was conducted in three land-use types of farmland, lake, and ditch in the Zaozhadian Lake. The aims of this study were to identify the distribution, pollution degree, and sources of pollutants in different land-use types, and to explore the influence of land-use type changes on contamination. Methods In this study, surface sediments (0–10 cm) of three land types (farmland, lake, and ditch) in Zaozhadian Lake were collected, and heavy metals (Cu, Ni, Zn, Pb, Cd, Cr, Hg), As, total nitrogen (TN), total phosphorus (TP) and organic matter (OM) were determined. Kriging interpolation was used to visualize the pollutants distribution. The pollution degree of TN and TP was evaluated by the Nemerow pollution index. The pollution of heavy metals and As was evaluated by the geological accumulation index (Igeo) and the potential ecological risk index (RI). Then, dual hierarchical clustering analysis and the principal component analysis were performed to further analyze the impact of land type changes on pollutants. Results The heavy metal contents in the farmland were higher than other areas, while the TN (3.71 ± 1.03 g kg-1) and OM (57.17 ± 15.16 g kg−1) in lake sediments were higher than that in other regions. Farmland, lake, and ditches had low ecological risks, with RI values of 84.21, 71.34, and 50.78, respectively. The primary heavy metal pollutants are Pb, Cu, and Ni. Furthermore, Cu, As, Ni, Pb, and Zn were primarily derived from agriculture pollution, the source of Cd was the industrial pollution, and Cr mainly originated from natural sources. Nutrients primarily came from the decomposition of aquatic animals, plants, and human-related activities. When the lake area was converted into farmland, the heavy metal concentrations in the soils increased and the TN and OM decreased. Based on the results, this study put forward key strategies including the adjustment of the land-use type and restriction of the entry of pollutants into the wetland ecosystems in the Zaozhadian Lake. More attention should be paid to the impact of land-use type change on pollutants in wetlands.
Environmental Contamination and Remediation
Han et al. (2022) Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands. PeerJ 10:e12885 https://doi.org/10.7717/peerj.12885
Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia
Background Investigating the land use and land cover (LULC) dynamics and the status of traditional agroforestry practices provide important data for policymakers. The main objective of this study was to assess the LULC dynamics and traditional agroforestry practices among smallholder farmers across the two agro-ecological zones in Wonchi District of Ethiopia. Methods Landsat images were acquired from Earth Explorer, and changes in LULC were quantified with three Landsat sensors in the three time-series (1985, 2001, and 2019). Supervised classification with maximum likelihood technique was employed using ERDAS Imagine and ArcGIS. A ground survey was conducted with 100 key informants who were selected from 10 sites using a purposive sampling method. The collected data were subjected to direct matrix ranking, use-value analysis of most important multipurpose plant species, and semi-structured interviews were conducted for qualitative analysis. Results In total, 103 agroforestry plant species belonging to 44 families were identified in Wonchi District, of which 74 were indigenous including seven endemic and 29 exotic species. The highest species (13) were recorded in the Fabaceae family. About 61% of species were reported in the midland agro-ecological zone. A mixed farming system was the most frequently (56%) reported source of income. The results of LULC changes from 1985 to 2019 showed that the agroforestry cover increased from 31.1% to 34.9% and settlement including road construction increased from 12.5% to 31.6% of the total area with an annual rate change of 0.3% and 2.7%, respectively. These changes corresponded with a decreasing trend of the forest, cropland, water body, and shrub at a rate of 4.7%, 1.3%, 0.8%, and 0.5%, respectively. The LULC changes were more pronounced in the highlands than in the midlands of Wonchi District. Expansion of settlement and tenure policy change are the main drivers for these changes in the area. The authors recommended that protecting and planting indigenous and multipurpose plant species is essential as restoration techniques for all degraded land-use types. Therefore, strengthening agroforestry practices and land-use planning is urgently needed for achieving multiple goals.
Spatial and Geographic Information Science
Meragiaw et al. (2022) Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia. PeerJ 10:e12898 https://doi.org/10.7717/peerj.12898
Methodological approaches for estimating populations of the endangered dhole Cuon alpinus
Large carnivores are important for maintaining ecosystem integrity and attract much research and conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings for individual identification. This hinders status assessments for many threatened species, and calls for testing new methodological approaches. We examined past efforts to assess the population status of the endangered dhole (Cuon alpinus), and explored the application of a suite of recently developed models for estimating their populations using camera-trap data from India’s Western Ghats. We compared the performance of Site-Based Abundance (SBA), Space-to-Event (STE), and Time-to-Event (TTE) models against current knowledge of their population size in the area. We also applied two of these models (TTE and STE) to the co-occurring leopard (Panthera pardus), for which density estimates were available from Spatially Explicit Capture–Recapture (SECR) models, so as to simultaneously validate the accuracy of estimates for one marked and one unmarked species. Our review of literature (n = 38) showed that most assessments of dhole populations involved crude indices (relative abundance index; RAI) or estimates of occupancy and area of suitable habitat; very few studies attempted to estimate populations. Based on empirical data from our field surveys, the TTE and SBA models overestimated dhole population size beyond ecologically plausible limits, but the STE model produced reliable estimates for both the species. Our findings suggest that it is difficult to estimate population sizes of unmarked species when model assumptions are not fully met and data are sparse, which are commonplace for most ecological surveys in the tropics. Based on our assessment, we propose that practitioners who have access to photo-encounter data on dholes across Asia test old and new analytical approaches to increase the overall knowledge-base on the species, and contribute towards conservation monitoring of this endangered carnivore.
Punjabi et al. (2022) Methodological approaches for estimating populations of the endangered dhole Cuon alpinus. PeerJ 10:e12905 https://doi.org/10.7717/peerj.12905
SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.
Background Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. Methods To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. Results In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” and “monoterpene biosynthesis”. Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in P. cablin.
Zhang et al. (2022) SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.. PeerJ 10:e12940 https://doi.org/10.7717/peerj.12940
Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study
Background In the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida. Methods Vaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions. Results Total exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high median income (p = 0.001), high percentage of Hispanic population (p = 0.046), and low percentage of population with a college education (p = 0.013). A predictor of high risk of non-medical vaccination exemptions was high percentage of White population (p = 0.045). However, predictors of low risks of non-medical exemptions were high percentages of population: living in rural areas (p = 0.023), with college education (p = 0.013), with high school education (p = 0.009), and with less than high school education (p < 0.001). Conclusions There is evidence of county-level geographic disparities in both total and non-medical vaccination exemption risks in Florida. These disparities are explained by differences in county-level socioeconomic and demographic factors. Study findings are important in guiding resource allocation for health planning aimed at improving vaccination rates and reducing incidence of vaccine-preventable diseases.
Tandy et al. (2022) Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study. PeerJ 10:e12973 https://doi.org/10.7717/peerj.12973
Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition
Background Oral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism. Methods Two OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography. Results Our results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment. Conclusions Our study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis.
Zang et al. (2022) Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition. PeerJ 10:e12991 https://doi.org/10.7717/peerj.12991
Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish
The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
Nyholm et al. (2022) Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish. PeerJ 10:e12992 https://doi.org/10.7717/peerj.12992
Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)
Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.
Lan et al. (2022) Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PeerJ 10:e12993 https://doi.org/10.7717/peerj.12993
Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow
Objective The purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow. Methods To determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight. Results Soluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments. Conclusion A diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation.
Choi et al. (2022) Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow. PeerJ 10:e12998 https://doi.org/10.7717/peerj.12998
Functional network motifs defined through integration of protein-protein and genetic interactions
Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
Sahoo et al. (2022) Functional network motifs defined through integration of protein-protein and genetic interactions. PeerJ 10:e13016 https://doi.org/10.7717/peerj.13016
Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat
Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.
Yasin et al. (2022) Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat. PeerJ 10:e12808 https://doi.org/10.7717/peerj.12808
Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1
Inorganic and synthetic flocculants are widely investigated for removing harmful microalgae, such as Microcystis aeruginosa. However, their toxicity and non-biodegradability are shortcomings. Bioflocculants based on extracellular polysaccharides have attracted much attention as alternative flocculants. However, its high production cost is a limiting factor for applying bioflocculants. Here, we investigate the potential of the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1, as a novel flocculant on M. aeruginosa cells. The removal efficiency of M. aeruginosa cells by the dead cells was measured by mixing and shaking both components in a buffer with 5 mM CaCl2 in different incubation times and concentrations of the dead cells. After that, the minimum effective concentration of CaCl2 was determined. The combination effect of FeCl3 and the dead cells on the removal efficiency was tested. The structure of cell aggregates consisted of the dead cells and M. aeruginosa cells were also observed using a scanning electron microscope. The maximum removal efficiency (75.39%) was reached within 3 min in the presence of CaCl2 when 5 mg/ml of the dead cells (wet cells) were added. The optimal concentration of CaCl2 was 5 mM. The combination of the dead cells and a low concentration of FeCl3 (10 mg/L) with 5 mM of CaCl2 significantly improved the removal efficiency by about 1.2 times (P < 0.05). This result indicates that the combination usage of the dead cells can reduce the use of FeCl3. These results indicated that the dead cells could potentially be a novel biolfocculant to remove M. aeruginosa cells.
Furusawa et al. (2022) Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1. PeerJ 10:e12867 https://doi.org/10.7717/peerj.12867
Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.)
Laccase, as a copper-containing polyphenol oxidase, primarily functions in the process of lignin, anthocyanin biosynthesis, and various abiotic/biotic stresses. In this study, forty-eight laccase members were identified in the eggplant genome. Only forty-two laccase genes from eggplant (SmLACs) were anchored unevenly in 12 chromosomes, the other six SmLACs were mapped on unanchored scaffolds. Phylogenetic analysis indicated that only twenty-five SmLACs were divided into six different groups on the basis of groups reported in Arabidopsis. Gene structure analysis revealed that the number of exons ranged from one to 13. Motif analysis revealed that SmLACs included six conserved motifs. In aspects of gene duplication analysis, twenty-one SmLACs were collinear with LAC genes from Arabidopsis, tomato or rice. Cis-regulatory elements analysis indicated many SmLACs may be involved in eggplant morphogenesis, flavonoid biosynthesis, diverse stresses and growth/development processes. Expression analysis further confirmed that a few SmLACs may function in vegetative and reproductive organs at different developmental stages and also in response to one or multiple stresses. This study would help to further understand and enrich the physiological function of the SmLAC gene family in eggplant, and may provide high-quality genetic resources for eggplant genetics and breeding.
Wan et al. (2022) Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.). PeerJ 10:e12922 https://doi.org/10.7717/peerj.12922
Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations
Background Fuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated. Methods This study used next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China. Results The results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.
Miao et al. (2022) Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations. PeerJ 10:e12927 https://doi.org/10.7717/peerj.12927
Drivers of phenotypic divergence in a Mesoamerican highland bird
Animals derive their coloration from a variety of pigments as well as non-pigmentary structural features. One of the most widespread types of pigments are carotenoids, which are used by all invertebrate taxa and most vertebrate orders to generate red, pink, orange and yellow coloration. Despite their widespread use by diverse animal groups, animals obligately obtain carotenoid pigments from diet. Carotenoid-based coloration is therefore modulated by evolutionary and ecological processes that affect the acquisition and deposition of these pigments into tegumentary structures. The Flame-colored Tanager (Piranga bidentata) is a highland songbird in the cardinal family (Cardinalidae) that is distributed from Mexican sierras through Central America up to western Panama. While female plumage throughout its entire range is predominantly yellow, males exhibit a noticeable split in ventral plumage color, which is bright orange on the West slope and the Tres Marias Islands and blood red in Eastern Mexico and Central America. We used Multiple Regression on Matrices (MRM) to evaluate the relative contributions of geographic distance, climate and genetic distance on color divergence and body differences between geographically disjunct populations. We found that differentiation in carotenoid plumage coloration was mainly explained by rainfall differences between disjunct populations, whereas body size differences was best explained by variation in the annual mean temperature and temperature of coldest quarter. These results indicate that climate is a strong driver of phenotypic divergence in Piranga bidentata.
Robles-Bello et al. (2022) Drivers of phenotypic divergence in a Mesoamerican highland bird. PeerJ 10:e12901 https://doi.org/10.7717/peerj.12901
Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast
Background Many migrant birds have been returning to Europe earlier in spring since the 1980s. This has been attributed mostly to an earlier onset of spring in Europe, but we found the timing of Willow Warblers’ passage to be influenced by climate indices for Africa as much as those for Europe. Willow Warblers’ spring passage through northern Europe involves populations from different wintering quarters in Africa. We therefore expected that migration timing in the early, middle and late periods of spring would be influenced sequentially by climate indices operating in different parts of the winter range. Methods Using data from daily mistnetting in 1 April–15 May over 1982–2017 at Bukowo (Poland, Baltic Sea coast), we derived an Annual Anomaly (AA, in days) of Willow Warbler spring migration. We decomposed this anomaly into three main periods (1–26 April, 27 April–5 May, 6–15 May); one-third of migrants in each period. We modelled three sequential time series of spring passage using calendar year and 15 large-scale climate indices averaged over the months of Willow Warblers’ life stages in the year preceding spring migration as explanatory variables in multiple regression models. Nine climate variables were selected in the best models. We used these nine explanatory variables and calculated their partial correlations in models for nine overlapping sub-periods of AA. The pattern of relationships between AA in these nine sub-periods of spring and the nine climate variables indicated how spring passage had responded to the climate. We recommend this method for the study of birds’ phenological responses to climate change. Results The Southern Oscillation Index and Indian Ocean Dipole in Aug–Oct showed large partial correlations early in the passage, then faded in importance. For the Sahel Precipitation Index (PSAH) and Sahel Temperature Anomaly (TSAH) in Aug–Oct partial correlations occurred early then peaked in mid-passage; for PSAH (Nov–March) correlations peaked at the end of passage. NAO and local temperatures (April–May) showed low correlations till late April, which then increased. For the Scandinavian Index (Jun–Jul) partial correlations peaked in mid-passage. Year was not selected in any of the best models, indicating that the climate variables alone accounted for Willow Warblers’ multiyear trend towards an earlier spring passage. Discussion Climate indices for southern and eastern Africa dominated relationships in early spring, but western African indices dominated in mid- and late spring. We thus concluded that Willow Warblers wintering in southern and eastern Africa dominated early arrivals, but those from western Africa dominated later. We suggest that drivers of phenological shifts in avian migration are related to changes in climate at remote wintering grounds and at stopovers, operating with climate change in the north, especially for species with complex and long-distance migration patterns.
Remisiewicz et al. (2022) Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast. PeerJ 10:e12964 https://doi.org/10.7717/peerj.12964
Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types
Grain filling affects grain weight and quality and is among the most critical factors in determining the yield and quality of cereal crops. Though hybrids have larger panicles and numerous spikelets with a larger sink capacity than conventional varieties, data on the grain filling commonalities and differences between foxtail millet varieties with different panicle types remain sparse. In this study, we found that “Zhang Gu 13” (ZG, large panicle) exhibits a significantly higher panicle weight than “Yu Gu 18” (YG, conventional panicle) at the early stage of grain filling, but the weight of YG increased rapidly and gradually overtook ZG during the middle stages. A temporal expression pattern analysis demonstrated that the genes involved in photosynthesis, metabolic pathways, and phenylpropanoid biosynthesis were downregulated, while those related to peroxisome function, purine metabolism, and zeatin biosynthesis were upregulated during grain filling in both varieties. A total of 6,832 differentially expressed genes (DEGs) were identified in both varieties, with the majority identified at the early and late stages. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that the upregulated DEGs in YG were associated with gibberellin (GA) biosynthesis, ATP-binding cassette (ABC) transporters, and plant hormone signal transduction. Photosynthesis-related DEGs, such as photosystem and antenna proteins, were significantly upregulated in ZG. This study provides preliminary insights into the differences in gene expression and molecular mechanisms of grain filling between ZG and YG in the North China summer-sowing region.
Song et al. (2022) Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types. PeerJ 10:e12968 https://doi.org/10.7717/peerj.12968
A neuronal theta band signature of error monitoring during integration of facial expression cues
Error monitoring is the metacognitive process by which we are able to detect and signal our errors once a response has been made. Monitoring when the outcome of our actions deviates from the intended goal is crucial for behavior, learning, and the development of higher-order social skills. Here, we explored the neuronal substrates of error monitoring during the integration of facial expression cues using electroencephalography (EEG). Our goal was to investigate the signatures of error monitoring before and after a response execution dependent on the integration of facial cues. We followed the hypothesis of midfrontal theta as a robust neuronal marker of error monitoring since it has been consistently described as a mechanism to signal the need for cognitive control. Also, we hypothesized that EEG frequency-domain components might bring advantage to study error monitoring in complex scenarios as it carries information from locked and non-phase-locked signals. A challenging go/no-go saccadic paradigm was applied to elicit errors: integration of facial emotional signals and gaze direction was required to solve it. EEG data were acquired from twenty healthy participants and analyzed at the level of theta band activity during response preparation and execution. Although theta modulation has been consistently demonstrated during error monitoring, it is still unclear how early it starts to occur. We found theta power differences at midfrontal channels between correct and error trials. Theta was higher immediately after erroneous responses. Moreover, before response initiation we observed the opposite: lower theta preceding errors. These results suggest theta band activity not only as an index of error monitoring, which is needed to enhance cognitive control, but also as a requisite for success. This study adds to previous evidence for the role of theta band in error monitoring processes by revealing error-related patterns even before response execution in complex tasks, and using a paradigm requiring the integration of facial expression cues.
Dias et al. (2022) A neuronal theta band signature of error monitoring during integration of facial expression cues. PeerJ 10:e12627 https://doi.org/10.7717/peerj.12627
Deciphering the Heteropterys pannosa species complex (Malpighiaceae)
We describe three new species of Malpighiaceae that are endemic to central Brazil and related to the Heteropterys pannosa complex, a group of xylopodiferous, unbranched subshrubs with fruit in mericarps that have a strongly reduced or no dorsal wing. Heteropterys tocantinensis is more common in eastern Tocantins State and on the border with Bahia State, and there are a few records from Mato Grosso State. Heteropterys veadeirensis is restricted to northern Goiás State and H. walteri has a wider distribution, occurring in some municipalities in northern Goiás and southern Tocantins. Additionally, we also provide detailed redescriptions of H. pannosa and H. rosmarinifolia, the two previously known species in this complex. All species are considered Endangered (EN) based on IUCN criteria, especially due to the low area of occupancy. Illustrations, distribution maps, and information about phenology and habitat are also provided for all taxa.
Amorim et al. (2022) Deciphering the Heteropterys pannosa species complex (Malpighiaceae). PeerJ 10:e12937 https://doi.org/10.7717/peerj.12937
Characterizing the suckling behavior by video and 3D-accelerometry in humpback whale calves on a breeding ground
Getting maternal milk through nursing is vital for all newborn mammals. Despite its importance, nursing has been poorly documented in humpback whales (Megaptera novaeangliae). Nursing is difficult to observe underwater without disturbing the whales and is usually impossible to observe from a ship. We attempted to observe nursing from the calf’s perspective by placing CATS cam tags on three humpback whale calves in the Sainte Marie channel, Madagascar, Indian Ocean, during the breeding seasons. CATS cam tags are animal-borne multi-sensor tags equipped with a video camera, a hydrophone, and several auxiliary sensors (including a 3-axis accelerometer, a 3-axis magnetometer, and a depth sensor). The use of multi-sensor tags minimized potential disturbance from human presence. A total of 10.52 h of video recordings were collected with the corresponding auxiliary data. Video recordings were manually analyzed and correlated with the auxiliary data, allowing us to extract different kinematic features including the depth rate, speed, Fluke Stroke Rate (FSR), Overall Body Dynamic Acceleration (ODBA), pitch, roll, and roll rate. We found that suckling events lasted 18.8 ± 8.8 s on average (N = 34) and were performed mostly during dives. Suckling events represented 1.7% of the total observation time. During suckling, the calves were visually estimated to be at a 30–45° pitch angle relative to the midline of their mother’s body and were always observed rolling either to the right or to the left. In our auxiliary dataset, we confirmed that suckling behavior was primarily characterized by a high average absolute roll and additionally we also found that it was likely characterized by a high average FSR and a low average speed. Kinematic features were used for supervised machine learning in order to subsequently detect suckling behavior automatically. Our study is a proof of method on which future investigations can build upon. It opens new opportunities for further investigation of suckling behavior in humpback whales and the baleen whale species.
Ratsimbazafindranahaka et al. (2022) Characterizing the suckling behavior by video and 3D-accelerometry in humpback whale calves on a breeding ground. PeerJ 10:e12945 https://doi.org/10.7717/peerj.12945
Sarcopenia is not associated with inspiratory muscle strength but with expiratory muscle strength among older adults requiring long-term care/support
Background Recently, the concept of respiratory sarcopenia has been advocated, but evidence is lacking regarding which respiratory parameters are appropriate indicators. Therefore, we investigated the association between sarcopenia, respiratory function, and respiratory muscle strength to identify the most appropriate parameters for respiratory sarcopenia. Methods We included 124 older adults (67 men, 57 women; average age 77.2 ± 8.3 years) requiring long-term care/support who underwent Day Care for rehabilitation. Handgrip strength, usual gait speed, and skeletal muscle mass were measured using bioelectrical impedance analysis. Participants were then diagnosed with sarcopenia using the algorithm of the Asian Working Group for Sarcopenia 2019. Parameters of respiratory function (forced vital capacity, forced expiratory volume in one second [FEV1.0], FEV1.0%, and peak expiratory flow rate) and respiratory muscle strength (maximal expiratory pressure [MEP] and maximal inspiratory pressure) were also measured according to American Thoracic Society guidelines. Respiratory parameters significantly related to sarcopenia were identified using binomial logistic regression and receiver operating characteristic analyses. Results Seventy-seven participants were classified as having sarcopenia. Binomial logistic regression analysis showed that MEP was the only respiratory parameter significantly associated with sarcopenia. The cut-off MEP value for predicting sarcopenia was 47.0 cmH20 for men and 40.9 cmH20 for women. Conclusions The most appropriate parameter for assessing respiratory sarcopenia may be MEP, which is an indicator of expiratory muscle strength, rather than FVC, MIP, or PEFR, as suggested in previous studies. Measuring MEP is simpler than measuring respiratory function parameters. Moreover, it is expected to have clinical applications such as respiratory sarcopenia screening.
Sawaya et al. (2022) Sarcopenia is not associated with inspiratory muscle strength but with expiratory muscle strength among older adults requiring long-term care/support. PeerJ 10:e12958 https://doi.org/10.7717/peerj.12958
Prevalence of iron deficiency anemia in Brazilian women of childbearing age: a systematic review with meta-analysis
Background Iron deficiency anemia (IDA) is among the most common micronutrient deficiencies in women of childbearing age and may affect children’s development. Brazil has several national programs to tackle this condition, such as food fortification and supplementation for pregnant women, but IDA prevalence in this population has not been systematically reviewed. We sought to determine the prevalence of IDA in Brazilian women of childbearing age through a systematic review with metanalysis. Methodology A protocol was previously published on the PROSPERO platform under the code CRD42020200960. A panel of the National Council for Scientific and Technological Development (CNPq) approved the protocol of this study under the public call number 26/2019. The main databases searched were MEDLINE, Web of Science, Scopus, Lilacs, and SciELO. In gray literature, the Brazilian Digital Library of Theses and Dissertations and the annals of the Brazilian Congress of Epidemiology and the Brazilian Congress of Public Health were accessed. The search strategy involved terms related to the condition (IDA) and the age group of the population of interest (teenagers and adults). Studies that had assessed the prevalence of IDA in Brazilian women of childbearing age (10–49 years) were included. Three independent reviewers read all titles and abstracts and extracted data from the included studies. Random effects meta-analyses using the Freeman-Tukey arcsine transformation were carried out with prevalence data, and meta-regression was conducted to test for subgroup differences. The quality of the studies was assessed using the Newcastle-Ottawa Scale. Results From 21,210 unique records screened, 237 full-texts were retrieved, of which 91 were included in the qualitative synthesis, and 83 were included in the meta-analysis. The overall IDA prevalence was 25% (95% CI [23–28], 83 studies). The subgroup of studies that used random sampling showed a prevalence of 22% (95% CI [17–27], 22 studies), whereas in those with non-random sampling, the prevalence was 27% (95% CI [23–30], 61 studies), without significant differences between subgroups in the metaregression (P = 0.13). High prevalence of IDA were found in the subgroups of studies conducted in the North and Northeast regions (30%; 95% CI [24–37]; seven studies, and 30%; 95% CI [26–34]; 27 studies, respectively), in studies conducted with indigenous population (53%; 95% CI [27–78], four studies), and with studies that had their collections after 2015 (28%; 95% CI [23–34], nine studies). Conclusions IDA in women of childbearing age remains a public health problem in Brazil, especially in the North and Northeast region. The national programs should be strengthened and more thoroughly supervised to decrease this condition nationally.
Macena et al. (2022) Prevalence of iron deficiency anemia in Brazilian women of childbearing age: a systematic review with meta-analysis. PeerJ 10:e12959 https://doi.org/10.7717/peerj.12959
PCAtest: testing the statistical significance of Principal Component Analysis in R
Principal Component Analysis (PCA) is one of the most broadly used statistical methods for the ordination and dimensionality-reduction of multivariate datasets across many scientific disciplines. Trivial PCs can be estimated from data sets without any correlational structure among the original variables, and traditional criteria for selecting non-trivial PC axes are difficult to implement, partially subjective or based on ad hoc thresholds. PCAtest is an R package that implements permutation-based statistical tests to evaluate the overall significance of a PCA, the significance of each PC axis, and of contributions of each observed variable to the significant axes. Based on simulation and empirical results, I encourage R users to routinely apply PCAtest to test the significance of their PCA before proceeding with the direct interpretation of PC axes and/or the utilization of PC scores in subsequent evolutionary and ecological analyses.
Camargo (2022) PCAtest: testing the statistical significance of Principal Component Analysis in R. PeerJ 10:e12967 https://doi.org/10.7717/peerj.12967
Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon
Transformer 2 (tra 2) and fruitless (fru) genes have been proven to play a key role in sex determination pathways in many Arthropods, including insects and crustaceans. In this study, a paralog of P. monodon tra 2 (Pmtra 2), P. monodon ovarian associated transformer 2 (PmOvtra 2) and 2 isoforms of P. monodon fruitless-like gene (Pmfru-1 and Pmfru-2) were identified and characterized. The full cDNA sequence of PmOvtra 2 consisted of 1,774 bp with the longest open reading frame (ORF) of 744 bp encoding for 247 amino acids. The PmOvtra 2 exhibited a predicted RNA-recognition motif (RRM) domain and two arginine-serine (RS) regions, suggesting its function in RNA splicing. The full cDNA sequence of Pmfru-1 consisted of 1,306 bp with 1,182 bp ORF encoding for 393 amino acids, whereas the full cDNA sequence of Pmfru-2 consisted of 1,858 bp with 1,437 bp ORF encoding 478 amino acids. The deduced amino acid sequences of Pmfru-1 and Pmfru-2 exhibited highly conserved domains of Fru proteins, including Broad-complex, Tramtrack and Bric-a-brac (BTB), and zinc finger (ZF) domains. In addition, Pmfru-1 and Pmfru-2 were suggestively originated from the same single genomic locus by genomic sequence analysis. Specifically, Pmfru pre-mRNA was alternatively spliced for Pmfru-1 and Pmfru-2 to include mutually exclusive exon 7 and exon 6, respectively. Temporal and spatial expression of PmOvtra 2, Pmfru-1, and Pmfru-2 were also investigated by qPCR. The results showed that all were expressed in early developmental stages with undifferentiated gonads starting from nauplius until postlarvae. The expression of PmOvtra 2 started at nauplius stage and gradually increased from mysis to postlarvae (PL) 1. However, the expression of Pmfru-1 was low at the nauplii stage and slightly increased from protozoea to PL5, whereas the expression of Pmfru-2 maintained a low level from nauplius to mysis and then gradually increased at the PL stages. Expressions of PmOvtra 2, Pmfru-1, and Pmfru-2 were detected in various tissues including nervous tissue, gill, heart, hepatopancreas, gut, and gonads. Interestingly, the sexually dimorphic expression of PmOvtra 2, Pmfru-1, and Pmfru-2 was demonstrated in fully developed gonads in which the ovary showed significantly higher expressions than the testis. The great difference in the expression pattern of PmOvtra 2, Pmfru-1, and Pmfru-2 in the ovary and testis suggested their roles in the female sex determination in P. monodon.
Thaijongrak et al. (2022) Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon. PeerJ 10:e12980 https://doi.org/10.7717/peerj.12980
The relationships between toad behaviour, antipredator defences, and spatial and sexual variation in predation pressure
Background Animal behaviour is under strong selection. Selection on behaviour, however, might not act in isolation from other fitness-related traits. Since predators represent outstanding selective forces, animal behaviour could covary with antipredator defences, such that individuals better suited against predators could afford facing the costs of riskier behaviours. Moreover, not all individuals undergo equivalent degrees of predation pressure, which can vary across sexes or habitats. Individuals under lower predation pressure might also exhibit riskier behaviours. Methods In this work, I tested these hypotheses on natterjack toads (Epidalea calamita). Specifically, I gauged activity time, exploratory behaviour and boldness in standard laboratory conditions, and assessed whether they correlated with body size and antipredator strategies, namely sprint speed, parotoid gland area and parotoid gland colour contrast. Additionally, I compared these traits between sexes and individuals from an agrosystem and pine grove, since there is evidence that males and agrosystem individuals are subjected to greater predation pressure. Results Sprint speed as well as parotoid gland contrast and size appeared unrelated to the behavioural traits studied. In turn, body mass was negatively related to activity time, boldness and exploration. This trend is consistent with the fact that larger toads could be more detectable to their predators, which are mostly gape unconstrained and could easily consume them. As predicted, females exhibited riskier behaviours. Nonetheless, agrosystem toads did not differ from pine grove toads in the behavioural traits measured, despite being under stronger predation pressure.
Zamora-Camacho (2022) The relationships between toad behaviour, antipredator defences, and spatial and sexual variation in predation pressure. PeerJ 10:e12985 https://doi.org/10.7717/peerj.12985
Measurement of dispersion of PM 2.5 in Thailand using confidence intervals for the coefficient of variation of an inverse Gaussian distribution
Air pollution is a growing concern for the general public in Thailand with PM 2.5 (particulate matter ≤ 2.5 µm) having the greatest impact on health. The inverse Gaussian (IG) distribution is used for examining the frequency of high concentration events and has often been applied to analyze pollution data, with the coefficient of variation (CV) being used to calculate the quantitative difference in PM 2.5 concentrations. Herein, we propose confidence intervals for the CV of an IG distribution based on the generalized confidence interval (GCI), the adjusted generalized confidence interval (AGCI), the bootstrap percentile confidence interval (BPCI), the fiducial confidence interval (FCI), and the fiducial highest posterior density confidence interval (F-HPDCI). The performance of the proposed confidence intervals was evaluated by using their coverage probabilities and average lengths from various scenarios via Monte Carlo simulations. The simulation results indicate that the coverage probabilities of the AGCI and FCI methods were higher than or close to the nominal level in all of test case scenarios. Moreover, FCI outperformed the others for small sample sizes by achieving the shortest average length. The efficacies of the confidence intervals were demonstrated by using PM 2.5 data from the Din Daeng and Bang Khun Thian districts in Bangkok, Thailand.
Chankham et al. (2022) Measurement of dispersion of PM 2.5 in Thailand using confidence intervals for the coefficient of variation of an inverse Gaussian distribution. PeerJ 10:e12988 https://doi.org/10.7717/peerj.12988
Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe
Background After implementing of the “Grain-for-Green” project, Caragana korshinskii Kom. has been widely planted in China’s arid regions. Although natural restoration grassland and artificial Caragana plantations measures have long been focuses in carbon research, the combined influence of natural restoration grassland and artificial Caragana plantation measures on aggregate stability and the aggregate-associated organic carbon (OC) remains unclear. Method We selected natural grassland (NG) and three different densities of Caragana plantations (high planting density, HG; middle planting density, MD; low planting density, LD) on desert steppe. The soil aggregate distribution and stability index such as fractal dimension (D), mean weight diameter (MWD), geometric mean diameter (GMD), percentage of aggregation destruction (PAD), as well as aggregate-associated OC concentration and stock were measured. Results Results shows that the soil aggregates were primarily macroaggregates (>2 mm) and mesoaggregates (0.25–2 mm) under dry sieving while microaggregates (<0.25 mm) were preponderant under wet sieving (more than 57%). Overall, compared with Caragana plantations, the MWD (4.43 and 4.51 mm) and GMD (1.72 and 1.83 mm) were both highest in two soil layers under the NG and the D (2.77 and 2.71) was lowest. Compared with the NG, the aggregate-associated OC stocks in the 0–40 cm depths in the LD, MD, and HD decreased by 41.54%, 46.93%, and 42.03%, respectively. SOC stock was mainly concentrated in the soil aggregate with sizes of >2 mm and <0.25 mm. These results suggested that natural grassland restoration measures could improve the soil aggregate stability and aggregate-associated OC concentration better than Caragana plantation restoration measures, which NG may be optimal for increasing carbon sequestration and stabilizing soil aggregates on desert steppe.
Lu et al. (2022) Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe. PeerJ 10:e12507 https://doi.org/10.7717/peerj.12507
Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets
Background Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. Methods Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. Results Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
Canário Viana et al. (2022) Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PeerJ 10:e12662 https://doi.org/10.7717/peerj.12662
Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs
Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3–V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.
Thomson et al. (2022) Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs. PeerJ 10:e12695 https://doi.org/10.7717/peerj.12695
Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey
To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38).
Caple et al. (2022) Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey. PeerJ 10:e12887 https://doi.org/10.7717/peerj.12887
Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension
Background Gene-environment interaction is related to the prevalence of hypertension, but the impact of genetic polymorphisms on hypertension may vary due to different geography and population. Objective To explore the impact of the interaction among occupational stress and MTHFR gene and SELE gene polymorphism on the prevalence of hypertension in Xinjiang oil workers. Methods A case-control study was conducted on 310 oil workers. In an oilfield base in Karamay City, Xinjiang, 155 hypertensive patients aged 18~60 years old with more than one year of service were selected as the case group, and 155 oil workers without hypertension were selected as the control group according to the 1:1 matching principle (matching conditions: the gender and shift were the same. The age is around 2 years old). The Occupational Stress Scale was used to evaluate the degree of occupational stress, PCR technique was used to detect MTHFR and SELE gene polymorphism, Logistic regression analysis was used to analyze the effects of gene and occupational stress on hypertension, and gene-gene and gene-environment interactions were analyzed by generalized multi-factor dimension reduction method. Results The G98T polymorphism of SELE gene (χ2 = 6.776, P = 0.034), the C677T (χ2 = 7.130, P = 0.028) and A1298C (χ2 = 12.036, P = 0.002) loci of MTHFR gene and the degree of occupational stress (χ2 = 11.921, P = 0.003) were significantly different between the case group and the control group. The genotypes GT at the G98T polymorphism of the SELE gene (OR = 2.151, 95% CI [1.227–3.375]), and the dominant model (AC/CC vs AA, OR = 1.925, 95% CI [1.613–3.816]); AC and CC at the A1298C polymorphism of the MTHFR gene (ORAC = 1.917, 95% CI [1.064–3.453]; ORCC = 2.233, 95% CI [1.082–4.609]), the additive model (CC vs AA, OR = 2.497, 95% CI [1.277–4.883]) and the dominant model (AC/CC vs AA, OR = 2.012, 95% CI [1.200–3.373]); at the C677T polymorphism of the MTHFR gene CT and TT (ORCT = 1.913, 95% CI [1.085–3.375]; ORTT = 3.117, 95% CI [1.430–6.795]), the additive model (CC vs AA, OR = 1.913, 95% CI [1.085–3.375]) and the dominant model (AC/CC vs AA, OR = 2.012, 95% CI [1.200–3.373]), which could increase hypertension risk (P < 0.05). The gene-gene interaction showed that there was a positive interaction between the A1298C and C677T sites of the MTHFR gene, and the gene-occupational stress interaction showed that there was a positive interaction between the A1298C and C677T sites of the MTHFR gene and the occupational stress. Conclusion The interaction of gene mutation and occupational stress in Xinjiang oil workers maybe increase the risk of hypertension.
Yang et al. (2022) Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension. PeerJ 10:e12914 https://doi.org/10.7717/peerj.12914
Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey desert soil, a 1% CSB addition increased the RL (48.6%), SRL (58%), and RV (18.6%) in the aeolian sandy soil, while a 3% further increased the RL (54.8%), SRL (84.2%), RV (21.9%), and soluble sugar content (233%). The mechanisms by which CSB addition improves the two soils differ: root morphology changed from coarse and short to fine and long in the grey desert soil, and from fine and long to longer in the aeolian sandy soil. Overall, a 3% CSB addition may be a promising and sustainable strategy for maintaining cotton productivity in aeolian sandy soil in the Xinjiang region.
Dong et al. (2022) Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China. PeerJ 10:e12928 https://doi.org/10.7717/peerj.12928
New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
Zograf et al. (2022) New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea). PeerJ 10:e12946 https://doi.org/10.7717/peerj.12946
The impact of COVID-19 and control measures on public health in Thailand, 2020
Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
Yorsaeng et al. (2022) The impact of COVID-19 and control measures on public health in Thailand, 2020. PeerJ 10:e12960 https://doi.org/10.7717/peerj.12960
In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid peroxidation, and inhibition of inflammation and cardiac cell death.
Elsawy et al. (2022) In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury. PeerJ 10:e12986 https://doi.org/10.7717/peerj.12986
A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
Vaidya et al. (2022) A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ 10:e12618 https://doi.org/10.7717/peerj.12618
Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?
Background The Oral Impacts on Daily Performances (OIDP) index asks the respondents to indicate both, the frequency and severity of the impact. However, it is not clear if the two scaling methods are correlated, and if using one scale is sufficient. The purpose of the study was to investigate the correlation between frequency and severity rating scales of the OIDP instrument, and whether only one of the rating scales can be used instead of both. Methods A battery of patient-reported outcome questionnaires were administered to a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,115). Only those who responded to any of the OIDP items were included in the analysis for this study (N = 873). We assessed correlations between the frequency and severity scales for all OIDP items, and for the summary scores of the two OIDP response scales. We additionally fit a categorical structural equation model (SEM) (or an item factor analysis model) and examined the correlation between two latent variables (Frequency and Severity). Results The correlation estimates for all OIDP items were greater than 0.50, indicating large correlations between the frequency and severity scores for each OIDP item. The correlation estimate between the two summary scores was 0.85 (95% CI [0.82–0.86]). When we calculated the correlation coefficient using a latent variable model, the value increased to 0.96 (95% CI [0.93–1.00]). Conclusion Our study findings show that OIDP frequency and severity scores are highly correlated, which indicates the use of one scale only. Based on previous evidence, we recommend applying the frequency rating scale only in research and clinical settings.
Pattanaik et al. (2022) Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?. PeerJ 10:e12717 https://doi.org/10.7717/peerj.12717
Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure
Dogs and wolves both show attachment-like behaviors to their owners/caregivers, including exploring more in the presence of the owner/caregiver, and greeting the owner/caregiver more effusively after an absence. Concurrent choice studies can elucidate dogs’ and wolves’ relationship to their owners/caregivers by assessing their preference for the owner/caregiver compared to other stimuli. While previous research has used concurrent choice paradigms to evaluate dogs’ and wolves’ preference between humans giving social interaction or humans giving food, no research has explored their preferences for an owner/caregiver compared to food when the food is not delivered by a human. In the current study, we investigated whether dogs and hand-reared wolves preferred their owner/caregiver or food, unassociated with a human, when they had been equally deprived of each stimulus (at least 4 hours). Each canid experienced four trials; we measured first choice and time spent with each alternative. Dogs overall did not show a preference for the owner or food. Wolves, on the other hand, tended to show a preference for food in both measures. We observed a range of individual variation in both measures, although dogs showed more individual variation. The differences we observed between dogs and wolves align with prior research comparing wolf and dog behavior directed towards humans; however, the reasons for this differential responding could be due to a variety of factors beyond phylogeny.
Isernia et al. (2022) Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure. PeerJ 10:e12834 https://doi.org/10.7717/peerj.12834
From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation
Liver cirrhosis (LC) involves multiple systems throughout the body, and patients with LC often die of multiple organ failure. However, few drugs are useful to treat LC. Hair follicle mesenchymal stem cells (HF-MSCs) are derived from the dermal papilla and the bulge area of hair follicles and are pluripotent stem cells in the mesoderm with broad prospects in regenerative medicine. As an emerging seed cell type widely used in skin wound healing and plastic surgery, HF-MSCs show considerable prospects in the treatment of LC due to their proliferation and multidirectional differentiation capabilities. We established an LC model in C57BL/6J mice by administering carbon tetrachloride (CCl4) and injected HF-MSCs through the tail vein to explore the therapeutic effects and potential mechanisms of HF-MSCs on LC. Here, we found that HF-MSCs improved liver function and ameliorated the liver pathology of LC. Notably, PKH67-labeled HF-MSCs were detected in the injured liver and expressed the hepatocyte-specific markers cytokeratin 18 (CK18) and albumin (ALB). In addition, in contrast to that in the LC group, the α-SMA expression showed a decreasing trend in the treatment group in vitro and in vivo, indicating that the pathological activation of hepatic stellate cells (HSCs) was inhibited by HF-MSC treatment. Moreover, the levels of transforming growth factor β (TGF-β1) and p-Smad3, a signaling molecule downstream of TGF-β1, were increased in mice with LC, while HF-MSC treatment reversed these changes in vivo and in vitro. Based on these findings, HF-MSCs may reverse LC by blocking the TGF-β/Smad pathway and inhibiting the pathological activation of HSCs, which may provide evidence for the application of HF-MSCs to treat LC.
Liu et al. (2022) From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation. PeerJ 10:e12872 https://doi.org/10.7717/peerj.12872
New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans
We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m−2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
Langer et al. (2022) New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans. PeerJ 10:e12884 https://doi.org/10.7717/peerj.12884
7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway
Background 7,8-dihydroxyflavone (7,8-DHF), a selective agonist of tropomyosin related kinase receptor B (TrkB), is known to exert protective effects in neurodegenerative diseases. However, the role of 7,8-DHF in TrkB signaling after ischemic stroke has remained elusive. Methods In the vitro model of ischemic stroke, we investigated the neuroprotective effect of 7,8-DHF through activation of TrkB signaling. Neurons subjected to oxygen and glucose deprivation/reperfusion were treated with the protein kinase inhibitor K252a and a knockdown of TrkB. Cell counting kit-8 (CCK-8) assay, Flow Cytometric Analysis (FACS), TdT-mediated dUTP nick end labeling (TUNEL) assay were conducted for measuring cell viability and numbers of apoptotic cells. And apoptosis-associated proteins were analyzed by Western blotting. Results Compared with the Control group, OGD/R group revealed lower cell viability by CCK-8 assay FACS and TUNEL assay showed increased rates of neuronal apoptosis. However, 7,8-DHF treatment increased cell viability and reduced neuronal apoptosis. Western blotting indicated upregulated Bax and cleaved caspase-3 and but downregulated Bcl-2 following OGD/R. Whereas 7,8-DHF treatment downregulated Bax and cleaved caspase-3 but upregulated Bcl-2. These changes were accompanied by a significant increase in the phosphorylation of TrkB and Akt following 7,8-DHF administration. However, the administration of K252a and knockdown of TrkB could alleviate those effects. Conclusion Our study demonstrates that activation of TrkB signaling by 7,8-DHF protects neurons against OGD/R injury via the TrkB/Akt pathway, which provides the evidence for the role of TrkB signaling in OGD-induced neuronal damage and may become a potential therapeutic target for ischemic stroke.
Zhou et al. (2022) 7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway. PeerJ 10:e12886 https://doi.org/10.7717/peerj.12886
Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study
Bactericera gobica is the major pest of Goji berry plants and causes severe damage. Psyllids mainly use the antennal sensilla to recognize olfactory cues necessary to find host plants and mates. However, the structure and function of the antenna and the antennal sensilla of B. gobica remains previously unexplored. Here, we identify the external and internal morphology of the antennal sensilla of B. gobica using both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). We found seven types of sensilla on the filiform antennae, including apical setae (LAS, SAS), sensilla basiconica (SB1, SB2), sensilla campaniform (SCA), sensilla chaetica (ChS1, ChS2), cavity sensilla (CvS1, CvS2), antennal rhinaria (AR1, AR2), and sensilla trichodea (ST). Five of these sensilla types—apical setae, sensilla basiconica, sensilla chaetica, cavity sensilla, and antennal rhinaria—may have olfactory functions based on their porous surfaces and internal dendritic outer segments (DOS). We also found several differences between the two sexes of B. gobica in the sensilla array and internal structure. ChS and DOS in the protrusions of AR were more abundant in males than females. Altogether, we comprehensively revealed the fine structure and probable function of B. gobica antennae and identified differences in the distribution and structure between psyllid sexes. Our findings provide important insights for future studies on defining the olfactory function of psyllid antenna using electrophysiological methods.
Ge et al. (2022) Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study. PeerJ 10:e12888 https://doi.org/10.7717/peerj.12888
The coalescent with replication-independent mutations
We develop the mathematical structure of the neutral coalescent with both replication-dependent and replication-independent mutations. This allows us to explain and quantify empirical results that explore differences in genetic diversity in bacterial cultures with different growth rates. We also derive an unbiased and consistent estimator for the replication-independent mutation rate that is based on a comparison of total single nucleotide polymorphism counts for two independent well-mixed cultures with different growth rates. In addition to explaining differences in genetic diversity between well-mixed cultures with different (but constant) growth rates, our coalescent also quantifies the effects of fluctuating growth rates—a situation that can be common in natural populations.
Krone et al. (2022) The coalescent with replication-independent mutations. PeerJ 10:e12926 https://doi.org/10.7717/peerj.12926
Wei2GO: weighted sequence similarity-based protein function prediction
Background Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases. Methods This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations. Results Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes. Availability Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
Reijnders (2022) Wei2GO: weighted sequence similarity-based protein function prediction. PeerJ 10:e12931 https://doi.org/10.7717/peerj.12931
Human cytomegalovirus infection and its association with gestational diabetes mellitus during pregnancy
Background Infection is an important risk factor for gestational diabetes mellitus (GDM), while infection of human cytomegalovirus (HCMV) with GDM remains unclear and rarely reported. This study aimed to investigate the association of HCMV infection and serum inflammatory factor levels in pregnancy with GDM. Methods This prospective study included pregnant women who attended at Affiliated Hospital of Qingdao Hospital and Zibo Maternal and Child Health Hospital between December 2018 and August 2020. HCMV specific IgM and serum levels of inflammatory factors, including TNF-α, IL-6, and IL-1β, were analyzed. Results A total of 5,316 pregnant women were included (415 with GDM (107 with HCMV+GDM+ and 308 with HCMV-GDM+) and 4901 GDM-free (759 with HCMV+GDM- and 4142 with HCMV-GDM-)). The prevalence of GDM was 7.81%. The rate of activation of HCMV was 16.29%. Specifically, 107 and 759 women in the GDM and control group exhibited HCMV infection, with positive rates of25.78% and 15.48%, respectively (P < 0.01). TNF-α, IL-6, and IL-1β at 24–28 weeks of gestation were significantly higher in women with GDM and HCMV infection than inthe other groups (all P < 0.01). Multivariable analysis showed that HCMV positive (OR = 1.851; 95% CI [1.425–2.403]; P < 0.001), IL-6 (OR = 1.010; 95% CI [1.002–1.018]; P = 0.013), and IL-1β (OR = 1.410; 95% CI [1.348–1.474]; P < 0.001) were all significantly correlated with GDM. Conclusion This study suggests HCMV infection during pregnancy is an independent risk factor of GDM and could significantly increase its incidence. Further studies are needed to elucidate possible mechanisms underlying associations between HCMV infection and GDM.
Wang et al. (2022) Human cytomegalovirus infection and its association with gestational diabetes mellitus during pregnancy. PeerJ 10:e12934 https://doi.org/10.7717/peerj.12934
Exploring the mechanism of cordycepin combined with doxorubicin in treating glioblastoma based on network pharmacology and biological verification
Background Glioblastoma is the most common and fatal primary malignant tumor in the central nervous system, and the prognosis is poor. Currently, there are no effective treatments for glioblastoma. Cordycepin is a natural active substance with significant anticancer activity and doxorubicin is a broad-spectrum anticancer drug. Cordycepin administered with doxorubicin is a potential drug combination for the treatment of glioblastoma. However, the mechanism of action for this drug combination has not yet been elucidated. Aim of the study To explore the complex mechanism of cordycepin combined with doxorubicin against glioblastoma using network pharmacology and biological verification. Materials and methods We used an MTT assay, colony formation assay, and scratch healing to detect the growth, proliferation, and migration of LN-229, U251 and T98G cells. Putative targets and the potential mechanism of action for the drug combination in glioblastoma were obtained through online databases, network construction, and enrichment analyses. We verified the expression of EMT-related genes and identified important therapeutic targets by western blot. Results In this study, the combination of doxorubicin and cordycepin was found to significantly inhibit cell proliferation and migration and can induce apoptosis. These effects are better together than with either drug alone. The drug combination inhibited EMT by upregulating the expression of E-cadherin protein and downregulating the expression of N-cadherin, ZEB1, and Twist1 proteins. There were 71 potential targets for the drug combination in glioblastoma, and Kyoto Encyclopedia of Genes and Genome analysis suggested that the anticancer process may be mediated by proteoglycans in cancer, the tumor necrosis factor signaling pathway, microRNA in cancer, pathways in cancer, and other pathways. To study the molecular mechanism of anticancer activity, we detected the expression of target proteins with downregulated expression of NFKB1, MAPK8, MYC, and MMP-9 proteins and upregulated expression of cleaved caspase 3 that promoted the apoptosis of LN-229 cells. Conclusions This study shows that the drug combination of doxorubicin and cordycepin effectively inhibits the growth and proliferation of LN-229 cells through multiple targets and multiple pathways, and the combination inhibits cell invasion and migration by regulating the EMT switch of tumor cells. Our findings provide new ideas about, and a theoretical basis for, the treatment of glioblastoma.
Chen et al. (2022) Exploring the mechanism of cordycepin combined with doxorubicin in treating glioblastoma based on network pharmacology and biological verification. PeerJ 10:e12942 https://doi.org/10.7717/peerj.12942
No evidence of conditioning of pupillary constriction despite overtraining
Eyeblink conditioning is the most popular paradigm for studying classical conditioning in humans. But the fact that eyelids are under voluntary control means it is ultimately impossible to ascertain whether a blink response is ‘conditioned’ or a timed ‘voluntary’ blink response. In contrast, the pupillary response is an autonomic response, not under voluntary control. By conditioning the pupillary response, one might avoid potential volition-related confounds. Several attempts have been made to condition the pupillary constriction and dilation responses, with the earliest published attempts dating back to the beginning of the 20th century. While a few early studies reported successful conditioning of pupillary constriction, later studies have failed to replicate this. The apparatus for recording pupil size, the type of stimuli used and the interval between the stimuli has varied in previous attempts—which may explain the inconsistent results. Moreover, measuring the pupil size used to be cumbersome compared with today when an eyetracker can continuously measure pupil size non-invasively. Here we used an eyetracker to test whether it is possible to condition the autonomic pupillary constriction response by pairing a tone (CS) and a light (US) with a 1s CS-US interval. Unlike in previous studies, our subjects went through multiple training sessions to ensure that any potential lack of conditioning would not be due to too little training. A total of 10 participants went through 2–12 conditioning sessions, each lasting approximately 20 min. One training session consisted of 75 paired, tone + light, trials and 25 randomly interspersed CS alone trials. The eyetracker (Tobii Pro Nano), continuously measured participants’ pupil size. To test statistically whether conditioning of the pupillary response occurred we compared the pupil size after the tone on the first session and the last session. The results showed a complete lack of evidence of conditioning. Though the pupil size varied slightly between participants, the size did not change as a result of the training—irrespective of the number of training sessions. The data replicate previous findings that pupillary constriction does not show conditioning. We conclude that it is not possible to condition pupillary constriction—at least not by pairing a tone and a light. One hypothesis is that when pupillary conditioning has been observed in previous studies, it has been mediated by conditioning of an emotional response.
Niehorster et al. (2022) No evidence of conditioning of pupillary constriction despite overtraining. PeerJ 10:e12948 https://doi.org/10.7717/peerj.12948
Factors of balance determining the risk of falls in physically active women aged over 50 years
Background Balance disorders are believed to be one of the main reasons for falls in older adults. They are related to natural processes of ageing, resulting in deterioration of information integration and processing from the vestibular, somatosensory and visual systems. The consequence is an increased number of postural sways, which are some of balance factors. Balance control in static and dynamic activities is an essential element of daily functioning of older citizens. It seems that balance assessment is essential to determine the risk of falls, as well as to determine which factors of balance have greatest impact on the risk of falls. Methods The study involved physically active female students (n = 36, mean age 67,11 ± 5,35) of a University of the Third Age. We used the Balance System SD platform to assess their balance in four tests with eyes open and with eyes closed and to determine the risk of falls. We assessed the relationships between individual balance indices (overall stability index, anterior/posterior stability index, medial/lateral stability index) and the falls risk index. We also determined those factors which predicted the risk of falls the most. Results The studied subjects had low risk of falls for their age category. In most measurements there were relationships between the risk of falls and the size of sways in the coronal plane and the overall stability index. We also found that the overall stability index calculated in measurements with eyes closed predicted the risk of falls of the studied physically active females most accurately (R2 0.391 F(1.34)=23.475; <0.000). The subjects were physically active and their falls risk index was low - this allowed us to presume that there was a relationship between these two factors. Preventive programmes should include exercise performed with eyes closed, and tests conducted with eyes closed seem to be most sensitive in determining balance disorders in physically active women.
Bednarczuk et al. (2022) Factors of balance determining the risk of falls in physically active women aged over 50 years. PeerJ 10:e12952 https://doi.org/10.7717/peerj.12952
Identification of novel prophage regions in Xenorhabdus nematophila genome and gene expression analysis during phage-like particle induction
Background Entomopathogenic Xenorhabdus bacteria are endosymbionts of Steinernema nematodes and together they form an insecticidal mutualistic association that infects a wide range of insect species. Xenorhabdus produce an arsenal of toxins and secondary metabolites that kill the insect host. In addition, they can induce the production of diverse phage particles. A few studies have focused on one integrated phage responsible for producing a phage tail-like bacteriocin, associated with an antimicrobial activity against other Xenorhabdus species. However, very little is known about the diversity of prophage regions in Xenorhabdus species. Methods In the present study, we identified several prophage regions in the genome of Xenorhabdus nematophila AN6/1. We performed a preliminary study on the relative expression of genes in these prophage regions. We also investigated some genes (not contained in prophage region) known to be involved in SOS bacterial response (recA and lexA) associated with mitomycin C and UV exposure. Results We described two integrated prophage regions (designated Xnp3 and Xnp4) not previously described in the genome of Xenorhabdus nematophila AN6/1. The Xnp3 prophage region appears very similar to complete Mu-like bacteriophage. These prophages regions are not unique to X. nematophila species, although they appear less conserved among Xenorhabdus species when compared to the previously described p1 prophage region. Our results showed that mitomycin C exposure induced an up-regulation of recA and lexA suggesting activation of SOS response. In addition, mitomycin C and UV exposure seems to lead to up-regulation of genes in three of the four integrated prophages regions.
Lefoulon et al. (2022) Identification of novel prophage regions in Xenorhabdus nematophila genome and gene expression analysis during phage-like particle induction. PeerJ 10:e12956 https://doi.org/10.7717/peerj.12956
Validity and inter-rater reliability of ankle motion observed during a single leg squat
Background The single leg squat (SLS) test is a clinical functional test commonly used to evaluate clinically aberrant movement patterns of the knee. The SLS could be an interesting option to analyze ankle control in the frontal plane during dynamic load analysis. However, to date, there are no studies that have analyzed the associations between the increased subtalar joint pronation by navicular drop (ND) test and ankle control with single leg squat (SLSankle) using a three-point scale. The purpose of this study was to evaluate the reliability of a clinical observation method to assess and determine the relationship between navicular drop (ND) and ankle control on the SLSankle score. Methods A total of fifty-five healthy, physically active (31 females and 24 males) volunteers participated in this study. The degree of subtalar pronation was assessed through the ND test, and the ankle control was defined as the ankle displacement in the frontal plane during the SLS. Results We found good intra-rater and inter-rater agreement during SLSankle, with Kappa values from 0.731 to 0.750. The relationship between the SLSankle and ND was significant ; the Spearman’s rank correlation coefficient was 0.504 (p < 0.05). Conclusions The SLSankle score supplied the clinical practice with a reliable and valid alternative for quantifying foot mobility in comparison to the ND test.
Guillén-Rogel et al. (2022) Validity and inter-rater reliability of ankle motion observed during a single leg squat. PeerJ 10:e12990 https://doi.org/10.7717/peerj.12990
The shadow model: how and why small choices in spatially explicit species distribution models affect predictions
The use of species distribution models (SDMs) has rapidly increased over the last decade, driven largely by increasing observational evidence of distributional shifts of terrestrial and aquatic populations. These models permit, for example, the quantification of range shifts, the estimation of species co-occurrence, and the association of habitat to species distribution and abundance. The increasing complexity of contemporary SDMs presents new challenges—as the choices among modeling options increase, it is essential to understand how these choices affect model outcomes. Using a combination of original analysis and literature review, we synthesize the effects of three common model choices in semi-parametric predictive process species distribution modeling: model structure, spatial extent of the data, and spatial scale of predictions. To illustrate the effects of these choices, we develop a case study centered around sablefish (Anoplopoma fimbria) distribution on the west coast of the USA. The three modeling choices represent decisions necessary in virtually all ecological applications of these methods, and are important because the consequences of these choices impact derived quantities of interest (e.g., estimates of population size and their management implications). Truncating the spatial extent of data near the observed range edge, or using a model that is misspecified in terms of covariates and spatial and spatiotemporal fields, led to bias in population biomass trends and mean distribution compared to estimates from models using the full dataset and appropriate model structure. In some cases, these suboptimal modeling decisions may be unavoidable, but understanding the tradeoffs of these choices and impacts on predictions is critical. We illustrate how seemingly small model choices, often made out of necessity or simplicity, can affect scientific advice informing management decisions—potentially leading to erroneous conclusions about changes in abundance or distribution and the precision of such estimates. For example, we show how incorrect decisions could cause overestimation of abundance, which could result in management advice resulting in overfishing. Based on these findings and literature gaps, we outline important frontiers in SDM development.
Commander et al. (2022) The shadow model: how and why small choices in spatially explicit species distribution models affect predictions. PeerJ 10:e12783 https://doi.org/10.7717/peerj.12783
Uptake of a plasticizer (di-n-butyl phthalate) impacts the biochemical and physiological responses of barley
Background DBP is one of the most commonly used plasticizers for imparting desirable properties to polymers. The introduction of phthalates is reported to have occurred in the late 1920s, and there has been a significant rise in their release into the environment in past decades due to a lack of covalent bonding with the parent matrix. Because of their numerous applications in day-to-day life, phthalates have become ubiquitous and also classified as endocrine disruptors. Hence, several studies have been conducted to investigate the phthalate-mediated toxicities in animals; however, plants have not been explored to the same amount. Methods Therefore, in the present study, the accumulation and translocation along with morpho-physiological perturbations in barley plants after 15, 30, 60, and 120 days of exposure to di-n-butyl phthalate (DBP) are investigated using standard protocols. Results The maximal accumulation and translocation of DBP in the roots and shoots of barley plants was observed after 60 days of exposure. The exposure of DBP from 15 to 120 days was recorded to decline all the morphological indices (i.e., dry weight, net primary productivity, seed number per spike, and seed weight) of barley plants. The pigments content declined under DBP treatment for all exposure durations except 120 days exposure. Carbohydrate content increased after 15–30 days of exposure afterward it was observed to be decreased under 60 and 120 days of exposure. The protein content was declined in DBP stressed plants for 15–120 days. Proline content was increased in all exposure durations and maximal percent increase was recorded in 120 days of exposure. MDA content showed an increase at earlier exposure durations then followed by a decline in long-term exposure. Hydrogen peroxide content increased at all exposure durations. There were significant alterations observed in the activities of all antioxidative enzymes in comparison to the control. Furthermore, DBP stressed plants after 60 days were analyzed for the macromolecular variations using Fourier transform infrared spectroscopy (FTIR). Conclusion Thus, the outcomes of the current work provide an appraisal of phthalates’ uptake and translocation mediated phytotoxic responses in barley plants. These observations can help in developing genetically modified edible plants that are resistant to phthalates uptake, thereby ensuring food security.
Kumari et al. (2022) Uptake of a plasticizer (di-n-butyl phthalate) impacts the biochemical and physiological responses of barley. PeerJ 10:e12859 https://doi.org/10.7717/peerj.12859
Assessment of the effects of storage temperature on fatty acid analysis using dried blood spot cards from managed southern white rhinoceroses (Ceratotherium simum simum): implications for field collection and nutritional care
Background Southern white rhinoceroses (Ceratotherium simum simum) are an endangered species in decline due to poaching and negative habitat changes. Conservation of the species has become increasingly important and a focus on better human management has become prevalent. One area of management that impacts southern white rhinoceroses is nutritional health monitoring, which is often conducted through blood analysis. Blood analysis conducted during field research can be difficult due to temperature, distance, and limited technological resources, so new methods of fast, and relatively stable blood collection are being pursued. One method that has been used in humans for many years is beginning to make its way into wildlife studies: the use of dried blood spot (DBS) cards. These cards are used as a tool to store single drops of whole blood on specialized filter paper and, once dried, can be used for nutritional biomarker analysis. An area of interest for southern white rhinoceroses and nutrition is monitoring fatty acid percentages for cardiovascular, immune, and reproductive health. The time and temperature limitations for storing blood fractions or liquid whole blood when analyzing fatty acids have been investigated, but few studies have performed storage studies on DBS cards colder than −20 °C or in non-human species. Methods In order to better understand the limitations of DBS cards and the impact of temperature on fatty acid DBS samples in long-term storage, triplicate samples from seven adult southern white rhinoceroses at the North Carolina Zoo were collected and subjected to three storage treatments (immediate, room temperature (23 °C), or frozen (−80 °C) for 1 year). Results Stearidonic (18:4w3) (Δ 0.3%), arachdic (20:0) (Δ 0.1%), eicosatetraenoic (20:4w3) (Δ 0.2%), and erucic acid (22:1w9) (Δ 0.1%) were in higher concentration in frozen than initial. Fatty acids in higher concentrations in the initial samples than frozen were myristic (14:0) (Δ 0.2%), mead (20:3w9) (Δ 0.1%), docosatetraenoic (22:4w6) (Δ 0.2%), nervonic (24:1) (Δ 0.1%), and total highly unsaturated fatty acids (HUFAs) (Δ 0.7%). Stearic (18:0) (Δ 2.2%), stearidonic (18:4w3) (Δ 0.3%), arachdic (20:0) (Δ 0.2%), paullinic (20:1w7) (Δ 0.4%), eicosatetraenoic (20:4w3) (Δ 0.1%), eicosapentaenoic (20:5w3) (Δ 0.1%), docosatetraenoic (22:4w6) (Δ 0.2%), nervonic acid (24:1) (Δ 0.2%), monoenes (Δ 1.9%), and total saturates (Δ 3.6%) had higher concentrations in room temperature than initial. Linoleic (18:2w6) (Δ 4.9%), mead acid (20:3w9) (Δ 0.1%), total polyunsaturated fatty acids (5.3%), and total omega-6 fatty acids (Δ 4.8%) had higher concentrations in initial compared to room temperature. Arachidonic (20:4w6) (Δ 0.4%) and omega-3 docosapentaenoic acid (22:5w3) (Δ 0.1%), had higher concentrations in frozen than in room temperature. Discussion The frozen samples had the fewest statistical differences compared to room temperature samples and essential omega-3 and -6 fatty acids were stable with freezing up to 1 year. While more research is still warranted, current results suggest that DBS samples are best utilized when immediate analysis or −80 °C storage is available.
Wood et al. (2022) Assessment of the effects of storage temperature on fatty acid analysis using dried blood spot cards from managed southern white rhinoceroses (Ceratotherium simum simum): implications for field collection and nutritional care. PeerJ 10:e12896 https://doi.org/10.7717/peerj.12896
Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes
We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used confidently as complementary viral indicators of human fecal pollution.
Garcia et al. (2022) Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes. PeerJ 10:e12957 https://doi.org/10.7717/peerj.12957
The COVID-19 pandemic has had a wide range of negative physical and mental impacts. This review begins with a theoretical explanation of the psychological defense mechanisms used to deal with the pandemic. It then discusses different categories of defense mechanisms and their roles in managing the impacts of psychological distress. The aim of this review is to highlight the various psychological defense mechanisms individuals use to deal with the pandemic and to discuss how adjustment mechanisms can protect individuals from internal and external threats by shielding the integrity of the ego (the mind) and helping individuals maintain their self-schema.
Altwaijri et al. (2022) Defense mechanism responses to COVID-19. PeerJ 10:e12811 https://doi.org/10.7717/peerj.12811
A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida)
Since 2010, the trypanorhynch tapeworm family Rhinoptericolidae Carvajal & Campbell, 1975 has housed just two distinctive, monotypic genera (Rhinoptericola Carvajal & Campbell, 1975 and Nataliella Palm, 2010). However, global collections of tapeworms from sharks and rays over the last more than three decades brought to light the need for major revision of the family by suggesting a much greater species-level diversity for the nominal genus Rhinoptericola. Through synonymy and the description of new species, the number of species in the genus is increased from one to eight. A phylogenetic analysis of the D1–D3 gene region of 28S rRNA (28S), including seven of the now nine species of rhinoptericolids, and a broad sampling of the other Trypanobatoida is the first to recover a monophyletic Rhinoptericolidae. In addition to systematic revision, this study allowed for the first evaluation of the degree of intraspecific vs interspecific variation in 28S for adult trypanorhynchs across the various hosts and geographic localities from which they have been reported, suggesting a relatively consistent boundary for Rhinoptericola. It is further suggested that detailed scanning electron microscopy (SEM) images of both the basal and metabasal armatures greatly aid in the interpretation of hook arrangement and shape. A schematic to streamline determination of the tentacular surface presented in scanning electron micrographs and line drawings of trypanorhynchs is presented for species with both two and four bothria. In combination, these methodological refinements can now be used as a model to resolve issues of classification and non-monophyly within both major lineages of the Trypanorhyncha. As a result of the taxonomic work, Rhinoptericola megacantha Carvajal & Campbell, 1975 (previously only known from the American cownose ray from the Chesapeake Bay and the Ticon cownose ray from the Gulf of Mexico, Venezuela, and Brazil) is now known from an additional species of cownose ray and a species of stingray, and is revealed to have a transatlantic distribution. Data from SEM suggest a simpler interpretation of hook arrangement in the metabasal armature for Rhinoptercola and—in combination with 28S sequence data—support Shirleyrhynchus Beveridge & Campbell, 1988 (a former rhinoptericolid) as its junior synonym. The three species formerly assigned to Shirleyrhynchus are thus transferred to Rhinoptericola. Data from light microscopy on whole-mounted specimens and histological sections, SEM, and 28S showed the eutetrarhynchid Prochristianella jensenae Schaeffner & Beveridge, 2012b to be morphologically consistent with species of Rhinoptericola and it is thus transferred to the genus. The type series of P. jensenae was determined to be mixed, representing two distinct species which are here redescribed and described as new, respectively. Two additional novel species of Rhinoptericola are described from cownose rays from off Mozambique and the Gulf of California.
Herzog et al. (2022) A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida). PeerJ 10:e12865 https://doi.org/10.7717/peerj.12865
Carbon isotope discrimination and the factors affecting it in a summer maize field under different tillage systems
Based on two years of field experiments, under different soil tillage methods and straw management practices, which included conventional tillage (CT), subsoiling (SS), rotary tillage (RT), and no-tillage (NT), combined with either straw return (S) or straw removal (0), we characterized the dynamic changes in Δ13C among three height layers [upper (U, 240 cm above the ground), middle (M, 120 cm above the ground), and lower (L, 30 cm above the ground)] of the summer maize canopy. The Δ13C, the factors affecting it, and the relationships between Δ13C and soil water content (SWC), the leaf area index (LAI), canopy microclimate, and the CO2 concentration were elucidated. The results indicated that the Δ13C of summer maize at the pre-filling stage was greater than that at the post-filling stage. Δ13C also varied at different heights, with the order of the Δ13C values being L > U > M. Among the different tillage methods, the Δ13C values were ordered SSS > CTS > RTS > NTS. SSS and NTS significantly increased the LAI; air temperature and relative humidity tended to gradually decrease with the increase in height of summer maize. Correlation analyses of the various influencing factors and Δ13C showed that SWC, LAI, air temperature, and CO2 concentration were all positively correlated with Δ13C, in which LAI and air temperature were significantly or extremely significantly positively correlated with Δ13C. In addition, we show that Δ13C can be used as a prediction index for summer maize yield, providing a theoretical basis for future yield research that may save precious time in summer maize breeding efforts.
Cui et al. (2022) Carbon isotope discrimination and the factors affecting it in a summer maize field under different tillage systems. PeerJ 10:e12891 https://doi.org/10.7717/peerj.12891
Genetic variability studies for tuber yield and yield attributes in Ethiopian released potato (Solanum tuberosum L.) varieties
Information on the extent of genetic variability and association among quantitative traits are vital for any crop improvement program and the development of suitable selection strategies. Limited research has been carried out thus far on potato genetic variability and trait association. This study on genetic variability and association among quantitative traits was conducted to assess the extent of genetic variability among yield and agronomic traits to identify superior varieties for the breeding program. To this effect, 20 improved varieties and a local cultivar were planted at two locations in central Ethiopia during the main cropping season of 2017/18 in a randomized complete block design using three replications. Analysis of variance of tuber yield and yield traits at each location and over locations, revealed the existence of highly significant (P < 0.01) differences among varieties in all agronomic and yield traits. Phenotypic coefficient of variation values ranged from 0.75% (specific gravity) to 32.22% (total starch yield) while the genotypic coefficient of variation values ranged between 0.70% (specific gravity) to 30.22% (total starch yield). Maximum difference between phenotypic and genotypic coefficient of variation values were noted for stem number, average tuber number, average tuber weight, number of leaves per plant and tuber yield. Hence, these traits are substantially influenced by the physiological status of the seed tuber at planting and by the environment, post emergence. Range of variability for most of the traits was high, indicating ample scope for selection and improvement in these traits. The estimated values for broad sense heritability and genetic advance, as percent of mean, ranged from 33.52% to 98.66% and 1.35% to 58.26%, respectively. All the traits had high heritability values, except average tuber number per hill, days to physiological maturity, average tuber weight and number of leaves per plant with moderate heritability values.
Tessema et al. (2022) Genetic variability studies for tuber yield and yield attributes in Ethiopian released potato (Solanum tuberosum L.) varieties. PeerJ 10:e12860 https://doi.org/10.7717/peerj.12860
Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem
Soil microbes are an essential component of terrestrial ecosystems and drive many biogeochemical processes throughout the soil profile. Prior field studies mainly focused on the vertical patterns of soil microbial communities, meaning their temporal dynamics have been largely neglected. In the present study, we investigated the vertical and temporal patterns of soil bacterial and archaeal communities in a wheat-soybean rotation agroecosystem at a depth of millions of sequences per sample. Our results revealed different vertical bacterial and archaeal richness patterns: bacterial richness was lowest in the deep soil layer and peaked in the surface or middle soil layer. In contrast, archaeal richness did not differ among soil layers. PERMANOVA analysis indicated that both bacterial and archaeal community compositions were significantly impacted by soil depth but unaffected by sampling time. Notably, the proportion of rare bacteria gradually decreased along with the soil profile. The rare bacterial community composition was the most important indicator for soil nutrient fertility index, as determined by random forest analysis. The soil prokaryotic co-occurrence networks of the surface and middle soil layers are more connected and harbored fewer negative links than that of the deep soil layer. Overall, our results highlighted soil depth as a more important determinant than temporal variation in shaping the soil prokaryotic community and interspecific interactions and revealed a potential role of rare taxa in soil biogeochemical function.
Yokota et al. (2022) Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem. PeerJ 10:e12868 https://doi.org/10.7717/peerj.12868
Determinants of quality of life and well-being in cognitively unimpaired older adults: a systematic review
Objective It is important to know the psychological variables that are related to quality of life and well-being in healthy elderly people. The main objective of the present review is to analyse which factors, through psychological variables, are determinant on the adaptive processes that acquire relevance in the last stage of life. Data sources An electronic search was conducted in WOS, Science Direct, PsycARTICLES, Psychology Database and Psycinfo. Study selection The search terms used were derived from the combination of the following search string: ((“Emotional Factors” OR “Emotional Effects”) AND (“Emotional Intelligence” OR “Emotional Regulation”) AND (“Quality of Life” OR “Personal Satisfaction”) AND (“Healthy Old People” OR “Healthy Old Adults”) AND (“Healthy Aging” OR “Successful Aging”)). Data extraction 11th April 2021. Data synthesis In total, 13 articles were selected. Conclusions The articles showed the importance of social support, proactive coping strategies (emotional regulation) and emotional intelligence as key factors in the elderly population for their positive influence on variables such as quality of life and well-being. Prospero ID: CRD42021224789
© 2022 Frías-Luque and Toledano-González
Frías-Luque et al. (2022) Determinants of quality of life and well-being in cognitively unimpaired older adults: a systematic review. PeerJ 10:e12900 https://doi.org/10.7717/peerj.12900
The effect of farmland on the surface water of the Aral Sea Region using Multi-source Satellite Data
Background The improper land utilization has brought tremendous pressure on the surface water of the Aral Sea Region in the past decades. It was seriously hindered for construction of the Green Silk Road Economic Belt by the fragile environment. Therefore, it is of great necessity for environmental protection and social development to monitor the change of surface water in the Aral Sea Region. Methods In this study, LandTrendr algorithm was used on Landsat time-series data to characterize the change in farmland on the Google Earth Engine platform. Based on multi-source data, the water area changes of the Aral Sea were extracted based on the Google Earth Engine, and the mean method was utilized to extract the changes in water level and water storage. Finally, a water-farmland coupling degree model was utilized to evaluate the impact of farmland changes on the surface water in the Aral Sea Region. Results As a result, the change of farmland is as follows: the farmland area of the Aral Sea Region has abandoned 3,129 km2 from 1987 to 2019, with overall accuracy of 85.3%. The farmland change had increased the drainage downstream of the Amu Darya River and the Syr Darya River. It has led area of the Aral Sea to decrease each year continuously. The area of the Aral Sea shrank by 1,606.36 km2 per year from 1987 to 2019. Furthermore, Aral Sea’s water level decreased by 0.13 m per year from 2003 to 2009. The amount of water storage in the Aral Sea Region also showed a downward trend from 2002 to 2016. There was a high-quality coupling coordination 0.903 relationship between surface water and farmland. It will increase the burden of water for people’s normal daily life by the water loss resources caused by abandoned farmland. This study emphasized threat of unreasonable farmland management to surface water of the Aral Sea Region. The findings contributed for decision makers to formulating effective reasonable policies to protect surface water and use land of the Aral Sea Region. Meanwhile, the application of coupling degree model can provide a new method for studying the connection of independent systems in the farmland, water, environment and more.
Shi et al. (2022) The effect of farmland on the surface water of the Aral Sea Region using Multi-source Satellite Data. PeerJ 10:e12920 https://doi.org/10.7717/peerj.12920
Clinical predictors and electrodiagnostic characteristics in patients with Guillain-Barré syndrome with respiratory failure: a retrospective, matched case-control study
Background Respiratory failure is a common complication of Guillain-Barré syndrome (GBS). This study aimed to determine the clinical predictors and electrodiagnostic (EDx) characteristics in patients with Guillain-Barré syndrome (GBS) with respiratory failure. Methods The retrospective study included 29 confirmed GBS cases with respiratory failure and age- (±5 years) and sex-matched controls (1:1). The dependent t-test and McNemar–Bowker test were used to analyse the continuous and categorical data, respectively. In addition, a multiple logistic regression analysis was used to analyse the predictive factors for respiratory failure. Results Among both cases and controls, the majority were male (72.4%), and the average age was 50.9 years. The data showed that patients with respiratory failure had higher GBS disability scores, lower motor power (≤3) of the hip flexors and ankle dorsiflexors, and experienced facial and bulbar palsy. In the multivariate analysis, the significant predictive factors were bulbar palsy (AOR 10.4 [95% CI [2.6–41.4]) and motor power of hip flexors ≤ 3 (AOR 31.4 [95% CI [3.1–314.5]). Patients with respiratory failure had lower compound muscle action potential amplitude of the ulnar and tibial nerves. The median, ulnar, and tibial nerve conduction studies were more likely to reflect inexcitability. The GBS subtypes in GBS patients with and without respiratory failure were not significantly different. Conclusions Bulbar palsy and motor power of the hip flexors ≤ 3 were significant predictors for respiratory failure. The GBS subtypes in patients with and without respiratory failure were not significantly different.
Charoentanyarak et al. (2022) Clinical predictors and electrodiagnostic characteristics in patients with Guillain-Barré syndrome with respiratory failure: a retrospective, matched case-control study. PeerJ 10:e12930 https://doi.org/10.7717/peerj.12930
Depletion of RIPK4 parallels higher malignancy potential in cutaneous squamous cell carcinoma
Background The RIPK4 (receptor-interacting protein kinase 4), a member of the RIPK family, acts as an important regulator of epidermal differentiation, cutaneous inflammation, and cutaneous wound repair. However, Until now, the role of RIPK4 in tumorigenesis remains elusive. There have been no studies exploring the effects of RIPK4 on the signaling pathway in cutaneous squamous cell carcinoma (SCC). It remains unknown whether RIPK4 expression, which can affect the degree of epidermal differentiation can also influence the radiosensitivity of skin SCC. It is urgent to fully elucidate the biological mechanism by which RIPK4 promotes carcinogenesis in skin SCC and determine whether RIPK4 expression levels predicts the sensitivity to radiotherapy in skin SCC. Methods Human skin SCC cell line, A431, was transfected with either small interfering RNAs (siRNAs) targeting RIPK4 (siR-RIPK4) or negative control siRNA (siR-NC). Western blotting was used to detect the expression of RIPK4 and Raf/MEK/ERK pathway-related proteins. The cells were irradiated using an X-ray irradiator at 6 MV with different radiation doses (0, 2, 6, and 10 Gy). Cell proliferation analysis, colony formation assay, transwell cell migration and invasion assay, cell cycle and apoptosis analysis were conducted to investigate the effect of RIPK4 silencing on skin SCC malignancy and radiosensitivity. Results RIPK4 protein expression was significantly decreased in the A431 cells transfected with siR-RIPK4, compared with the A431 cells transfected with siR-NC. RIPK4 silencing facilitated the proliferation, colony formation, migration, and invasion ability of A431 cell line, while cell cycle progression or cell apoptosis were not significantly influenced. In contrast with the previous literature, Raf/MEK/ERK pathway was not effected by RIPK4 knockdown in skin SCC. RIPK4 knockdown could not reverse the radiation resistance of A431 cells to irradiation in vitro. Conclusions In general, although depletion of RIPK4 cannot reverse the radiation resistance of A431 cells in vitro, it parallels higher malignancy potential in cutaneous SCC. To our knowledge, this is the first report of the effects of RIPK4 expression on the Raf/MEK/ERK signaling pathway and radiosensitivity in cutaneous SCC. The better understanding of the molecular mechanism of RIPK4 in cutaneous SCC may provide a promising biomarker for skin SCC prognosis and treatment.
Xu et al. (2022) Depletion of RIPK4 parallels higher malignancy potential in cutaneous squamous cell carcinoma. PeerJ 10:e12932 https://doi.org/10.7717/peerj.12932
Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)
Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H2O2, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.
Liu et al. (2022) Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum). PeerJ 10:e12943 https://doi.org/10.7717/peerj.12943
A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L.
Background Shading is an important factor affecting the cultivation of American ginseng, as it influences crop quality and yield. Rhizosphere microorganisms are also crucial for normal plant growth and development. However, whether different shade types significantly change American ginseng rhizosphere microorganisms is unknown. Methods This study evaluated the rhizosphere soils of American ginseng under traditional, high flag and high arch shade sheds. High-throughput 16S rRNA gene sequencing determined the change of rhizosphere bacterial communities. Results The microbial diversity in rhizosphere soils of American ginseng significantly changed under different shading conditions. The bacteria diversity was more abundant in the high arch shade than flat and traditional shades. Different bacterial genera, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira, showed significantly different abundances. Different shading conditions changed the microbial metabolic function in the American ginseng rhizosphere soils. The three types of shade sheds had specific enriched functional groups. The abundance of ATP-binding cassette (ABC) transporters consistently increased in the bacterial microbiota. These results help understand the influence of shading systems on the rhizosphere microecology of American ginseng, and contribute to the American ginseng cultivation.
Wang et al. (2022) A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L.. PeerJ 10:e12807 https://doi.org/10.7717/peerj.12807
Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland
Most previous publications on Devonian crinoids from the Holy Cross Mountains in Poland have concentrated on crinoid columns, and until now, little has been published about crinoid cups and calyxes. Herein, five crinoid taxa are described from an abundant occurrence of aboral cups and partial crowns from the Bukowa Góra Member (Emsian) in the Holy Cross Mountains of southern Poland. The following taxa are described: Bactrocrinites sp., Codiacrinus sevastopuloi sp. nov., Halocrinites geminatus (Bohatý, 2005), Halocrinites schlotheimii Steininger, 1831, and a single brachial plate from a flexible crinoid placed in Flexibilia incertae sedis. Simple discoid holdfasts are also present encrusted to cylindrical stromatoporoids. These taxa are the first crinoids described from the remains of partial crowns from Emsian strata of Poland.
Ausich et al. (2022) Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland. PeerJ 10:e12842 https://doi.org/10.7717/peerj.12842
Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates
Inhibitory control, the ability to override an inappropriate prepotent response, is crucial in many aspects of everyday life. However, the various paradigms designed to measure inhibitory control often suffer from a lack of systematic validation and have yielded mixed results. Thus the nature of this ability remains unclear, is it a general construct or a family of distinct sub-components? Therefore, the aim of this study was first to demonstrate the content validity and the temporal repeatability of a battery of inhibitory control tasks. Then we wanted to assess the contextual consistency of performances between these tasks to better understand the structure of inhibitory control. We tested 21 rhesus macaques (Macaca mulatta, 12 males, nine females) in a battery of touchscreen tasks assessing three main components of inhibitory control: inhibition of a distraction (using a Distraction task), inhibition of an impulsive action (using a Go/No-go task) and inhibition of a cognitive set (using a Reversal learning task). All tasks were reliable and effective at measuring the inhibition of a prepotent response. However, while there was consistency of performance between the inhibition of a distraction and the inhibition of an action, representing a response-driven basic form of inhibition, this was not found for the inhibition of a cognitive set. We argue that the inhibition of a cognitive set is a more cognitively demanding form of inhibition. This study gives a new insight in the multifaceted structure of inhibitory control and highlights the importance of a systematic validation of cognitive tasks in animal cognition.
Loyant et al. (2022) Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates. PeerJ 10:e12863 https://doi.org/10.7717/peerj.12863
Autophagy-related prognostic signature for survival prediction of triple negative breast cancer
Background Triple-negative breast cancer (TNBC) is a highly aggressive type of cancer with few available treatment methods. The aim of the current study was to provide a prognostic autophagy-related gene (ARG) model to predict the outcomes for TNBC patients using bioinformatic analysis. Methods mRNA expression data and its clinical information for TNBC samples obtained from The Cancer Genome Atlas (TCGA) and Metabric databases were extracted for bioinformatic analysis. Differentially expressed autophagy genes were identified using the Wilcoxon rank sum test in R software. ARGs were downloaded from the Human Autophagy Database. The Kaplan–Meier plotter was employed to determine the prognostic significance of the ARGs. The sample splitting method and Cox regression analysis were employed to establish the risk model and to demonstrate the association between the ARGs and the survival duration. The corresponding ARG-transcription factor interaction network was visualized using the Cytoscape software. Results A signature-based risk score model was established for eight genes (ITGA3, HSPA8, CTSD, ATG12, CLN3, ATG7, MAP1LC3C, and WIPI1) using the TCGA data and the model was validated with the GSE38959 and Metabric datasets, respectively. Patients with high risk scores had worse survival outcomes than those with low risk scores. Of note, amplification of ATG12 and reduction of WIPI were confirmed to be significantly correlated with the clinical stage of TNBC. Conclusion An eight-gene autophagic signature model was developed in this study to predict the survival risk for TNBC. The genes identified in the study may favor the design of target agents for autophagy control in advanced TNBC.
Yang et al. (2022) Autophagy-related prognostic signature for survival prediction of triple negative breast cancer. PeerJ 10:e12878 https://doi.org/10.7717/peerj.12878
Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses
Background The ability to maintain sufficient oxygen levels in the belowground tissues and the rhizosphere is crucial for the growth and survival of seagrasses in habitats with highly reduced sediment. Such ability varies depending on plant anatomical features and environmental conditions. Methods In the present study, we compared anatomical structures of roots, rhizomes and leaves of the tropical intertidal seagrasses, Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis, followed by an investigation of their gas exchange both in the belowground and aboveground tissues and photosynthetic electron transport rates (ETR) in response to experimental manipulations of O2 level (normoxia and root hypoxia) and temperature (30 °C and 40 °C). Results We found that C. rotundata and T. hemprichii displayed mostly comparable anatomical structures, whereas H. ovalis displayed various distinctive features, including leaf porosity, number and size of lacunae in roots and rhizomes and structure of radial O2 loss (ROL) barrier. H. ovalis also showed unique responses to root hypoxia and heat stress. Root hypoxia increased O2 release from belowground tissues and overall photosynthetic activity of H. ovalis but did not affect the other two seagrasses. More pronounced warming effects were detected in H. ovalis, measured as lower O2 release in the belowground tissues and overall photosynthetic capacity (O2 release and dissolved inorganic carbon uptake in the light and ETR). High temperature inhibited photosynthesis of C. rotundata and T. hemprichii but did not affect their O2 release in belowground tissues. Our data show that seagrasses inhabiting the same area respond differently to root hypoxia and temperature, possibly due to their differences in anatomical and physiological attributes. Halophila ovalis is highly dependent on photosynthesis and appears to be the most sensitive species with the highest tendency of O2 loss in hypoxic sediment. At the same time, its root oxidation capacity may be compromised under warming scenarios.
Soonthornkalump et al. (2022) Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses. PeerJ 10:e12899 https://doi.org/10.7717/peerj.12899
Cyber-victimization and its association with depression among Vietnamese adolescents
Background Cyberbullying has become an alarming social issue, but little is known about its prevalence and consequences in many countries. This study investigated the prevalence of cyber-victimization and its association with depression among students in Ho Chi Minh City, Vietnam. Methods A cross-sectional study was conducted in 1,492 students from eight secondary schools and high schools in four urban and suburban areas. Multi-stage cluster sampling approach was used to recruit participants. Students participated in this study on a voluntary basis and completed a self-report questionnaire that included validated scales to measure their experience of cyber-bullying (Cyber Bullying Scale) and symptoms of depression (Center for Epidemiologic Studies–Depression Scale). Weighted logistic regression analysis was used to adjust for the cluster effect and sampling probability. Results Almost all (92.4%) students reported using the internet everyday and nearly 40% used internet for more than four hours per day. Cyber-victimization was identified in 36.5% of students and almost 25% experienced multiple types of cyber-victimization. Nearly half of students reported symptoms of depression. After adjusting for other covariates, students who experienced cyber-victimization were found to have 1.81 times (95% CI [1.42–2.30]) higher in odds of having symptoms of depression. Conclusions Cyber victimization and depression are both common in Vietnamese adolescents. Those who experienced cyber bullying have a higher likelihood of having symptoms of depression. These findings indicate an urgent need for interventions and policies targeting this emerging type of bullying in Vietnam and similar settings due to its potential harmful effects on adolescents’ health.
Thai et al. (2022) Cyber-victimization and its association with depression among Vietnamese adolescents. PeerJ 10:e12907 https://doi.org/10.7717/peerj.12907
On the Andean genus Leschenius (Coleoptera: Curculionidae: Entiminae): Updated phylogeny, with a new species from Ecuador, discovery of males, and larval description of the potato weevil Leschenius vulcanorum
The weevil genus Leschenius del Río (Curculionidae: Entiminae: Naupactini) is distributed in the northern Andes, in Colombia and Ecuador. Among its species, L. vulcanorum stands out as an important pest of potatoes in its parthenogenetic form, which is known as “tiroteador de la papa”. In this study, the adult male and the larval stage (first and mature larvae) of L. vulcanorun are described and illustrated for the first time. A description of the male of Leschenius bifurcatus is also provided. A new bisexual species was discovered, Leschenius ventrilingulatus sp. nov., and is described from Ecuador. An updated phylogenetic analysis was performed, including the new species, with results indicating a sister group relationship between L. ventrilingulatus and L. vulcanorum. They can be distinguished because the former is usually of smaller size and is covered by denser and thicker setae, has shorter antennae, a subcylindrical shape of the pronotum, shorter elytra (about 1.5×longer than wide at base), the female has ventrite 4 with a posterior rounded projection, and posterior margin of ventrite 5 subacute, not excavated. This paper also includes lectotype designations, a revised key to all known species of Leschenius, habitus photos of males and females, illustrations of genitalia, and a distribution map.
del Río et al. (2022) On the Andean genus Leschenius (Coleoptera: Curculionidae: Entiminae): Updated phylogeny, with a new species from Ecuador, discovery of males, and larval description of the potato weevil Leschenius vulcanorum. PeerJ 10:e12913 https://doi.org/10.7717/peerj.12913
Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma
Purpose Multiple myeloma (MM), a kind of malignant neoplasm of clonal plasma cells in the bone marrow, is a refractory disease. Understanding the metabolism disorders and identification of metabolomics pathways as well as key metabolites will provide new insights for exploring diagnosis and therapeutic targets of MM. Methods We conducted nontargeted metabolomics analysis of MM patients and normal controls (NC) using ultra-high-performance liquid chromatography (UHPLC) combined with quadrupole time-of-flight mass spectrometry (Q-TOF-MS) in 40 cases of cohort 1 subjects. The targeted metabolomics analysis of amino acids using multiple reaction monitoring-mass spectrometry (MRM-MS) was also performed in 30 cases of cohort 1 and 30 cases of cohort 2 participants, to comprehensively investigate the metabolomics disorders of MM. Results The nontargeted metabolomics analysis in cohort 1 indicated that there was a significant metabolic signature change between MM patients and NC. The differential metabolites were mainly enriched in metabolic pathways related to amino acid metabolism, such as protein digestion and absorption, and biosynthesis of amino acids. Further, the targeted metabolomics analysis of amino acids in both cohort 1 and cohort 2 revealed differential metabolic profiling between MM patients and NC. We identified 12 and 14 amino acid metabolites with altered abundance in MM patients compared to NC subjects, in cohort 1 and cohort 2, respectively. Besides, key differential amino acid metabolites, such as choline, creatinine, leucine, tryptophan, and valine, may discriminate MM patients from NC. Moreover, the differential amino acid metabolites were associated with clinical indicators of MM patients. Conclusions Our findings indicate that amino acid metabolism disorders are involved in MM. The differential profiles reveal the potential utility of key amino acid metabolites as diagnostic biomarkers of MM. The alterations in metabolome, especially the amino acid metabolome, may provide more evidences for elucidating the pathogenesis and development of MM.
Yue et al. (2022) Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma. PeerJ 10:e12918 https://doi.org/10.7717/peerj.12918
External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection
Background No postoperative cardiopulmonary morbidity models have been developed or validated in Chinese patients with lung resection. This study aims to externally validate five predictive models, including Eurolung models, the Brunelli model and the Age-adjusted Charlson Comorbidity Index, in a Chinese population. Methods Patients with lung cancer who underwent anatomic lung resection between 2018/09/01 and 2019/08/31 in our center were involved. Model discrimination was assessed by the area under the receiver operating characteristic curve. Model calibration was evaluated by the Hosmer–Lemeshow test. Calibration curves were plotted. Specificity, sensitivity, negative predictive value, positive predictive value and accuracy were calculated. Model updating was achieved by re-estimating the intercept and/or the slope of the linear predictor and re-estimating all coefficients. Results Among 1085 patients, 91 patients had postoperative cardiopulmonary complications defined by the European Society of Thoracic Surgeons. For original models, only parsimonious Eurolung1 had acceptable discrimination (area under the receiver operating characteristic curve = 0.688, 95% confidence interval 0.630–0.745) and calibration (p = 0.23 > 0.05) abilities simultaneously. Its sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 0.700, 0.649, 0.153, 0.960 and 0.653, respectively. In the secondary analysis, increased pleural effusion (n = 94), which was nonchylous and nonpurulent, was labeled as a kind of postoperative complication. The area under the receiver operating characteristic curve of the models increased slightly, but all models were miscalibrated. The original Eurolung1 model had the highest discrimination ability but poor calibration, and thus it was updated by three methods. After model updating, new models showed good calibration and small improvements in discrimination. The discrimination ability was still merely acceptable. Conclusions Overall, none of the models performed well on postoperative cardiopulmonary morbidity prediction in this Chinese population. The original parsimonious Eurolung1 and the updated Eurolung1 were the best-performing models on morbidity prediction, but their discrimination ability only achieved an acceptable level. A multicenter study with more relevant variables and sophisticated statistical methods is warranted to develop new models among Chinese patients in the future.
Huang et al. (2022) External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection. PeerJ 10:e12936 https://doi.org/10.7717/peerj.12936
Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889
For many years an undescribed species of the genus Bathypathes has been misidentified as Bathypathes alternata Brook, 1889 (a species currently re-assigned to the genus Alternatipathes). This new species is rather common at mid- and lower bathyal depths of the Pacific, Atlantic and Indian oceans, often in areas with high concentrations of commercially valuable cobalt-rich ferromanganese crusts, where it was observed in underwater photo and video transects to occur in high densities. Under the name B. alternata this species is recorded in several inventories and databases. There is an urgent need for a formal description of this misidentified and widely distributed species to avoid further confusion. The new species is superficially similar to A. alternata in having a monopodial corallum and simple, bilateral and alternately arranged pinnules. However, it differs from the former in that it has an upright corallum with a straight pinnulated part (vs. a horizontally bent pinnulated part), pinnules of uniform length and density (vs. decreasing regularly distally), and a constant distal angle formed by the pinnules and the stem along different parts of the corallum (vs. a decreasing distal angle near the top). The new species can therefore be easily distinguished from A. alternata in underwater imagery. We formally describe this new species in the genus Bathypathes and assign it the new name B. pseudoalternata. An extensive synonymy list with previous misidentified records is provided. To evaluate the distributional patterns of the new species we review the geographic distribution of antipatharians reported below 800 m. The majority of the hitherto described lower bathyal and abyssal species have been recorded from one biogeographic province; however, 20 species are known from more than two provinces, and only three species are widely distributed (>5 provinces), including the newly described Bathypathes pseudoalternata. Members of the family Schizopathidae, to which the new species belongs, represent the majority of the lower bathyal (50.54%) and abyssal (82.35%) species.
Molodtsova et al. (2022) Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889. PeerJ 10:e12638 https://doi.org/10.7717/peerj.12638
A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus
A new species of Diasporus is described from the lowlands of southwestern Colombia. The new species exhibits a yellowish coloration in life, a character that it shares with other three species in the genus—Diasporus citrinobapheus, D. gularis, and D. tigrillo. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II–IV and toes II–IV. Further, the new species differs from all congeners by an uncorrected p-distance of > 5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within Diasporus, which may be recognized as the Diasporus diastema species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in Diasporus, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of Diasporus. Regarding pointed disc covers (ungual flap) present in some species of Diasporus, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus Diasporus.
Ospina Sarria et al. (2022) A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus. PeerJ 10:e12765 https://doi.org/10.7717/peerj.12765
Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments
Background Atherosclerosis emerges as a result of multiple dynamic cell processes including endothelial damage, inflammatory and immune cell infiltration, foam cell formation, plaque rupture, and thrombosis. Animal experiments have indicated that cathepsins (CTSs) mediate the antigen transmission and inflammatory response involved in the atherosclerosis process, but the specific signal pathways and target cells of the CTSs involved in atherosclerosis are unknown. Methods We used the GEO query package to download the dataset GSE28829 from the Gene Expression Omnibus (GEO) and filtered the data to check the standardization of the samples through the box chart. We then used the ‘limma’ package to analyze between-group differences and selected the corresponding differentially expressed genes of CTSs from the protein-protein interaction (PPI) network constructed with the STRING database, and then visualized the CTS-target genes. The best matching pathway and target cells were verified by a male mouse ligation experiment, single-sample GSEA (ssGSEA) analysis, and vitro experiment. Results There were 275 differentially expressed genes (DEGs) selected from the GSE28829 dataset, and the DEGs were identified mainly in the PPI network; 58 core genes (APOE, CD74, CP, AIF1, etc.) target three selected CTS family members (CTSS, CTSB, and CTSC). After the enriched analysis, 15 CTS-target genes were markedly enriched in the phagosome signaling pathway. The mouse experiment results revealed that the percentages and numbers of monocytes and neutrophils and the number of CD68+ cells in CTSS deficiency (CatS−/−) group were lower than those in the wildtype (CatS+/+) group. CTSS mediating phagosome via macrophage were further verified by ssGSEA analysis and vitro experiment. Conclusions CTSS are the main target molecules in the CTS family that are involved in atherosclerosis. The molecule participate in the progression of atherosclerosis by mediating the phagosome via macrophage.
Wang et al. (2022) Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments. PeerJ 10:e12846 https://doi.org/10.7717/peerj.12846
Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays
Background Tumor Treating Fields (TTFields), are a novel, non-invasive tissue ablation technology for treatment of cancer. Tissue ablation is achieved through the continuous delivery of a narrow range of electromagnetic fields across a tumor, for a period of months. TTFields are designed to affect only cells that divide and to interfere with the cell division process. The therapy is monitored with MRI imaging, performed every couple of months. Current technology is unable to assess the treatment effectiveness in real time. Methods We propose that the effect of the treatment can be assessed, in real time, by continuously measuring the change in electrical impedance across the TTFields delivery electrode arrays. An in vitro anatomic skull experimental study, with brain and tumor mimics phantom tissues was conducted to confirm the potential value of the proposed monitoring system. Results Experiments show that measuring the change in the impedance amplitude between opposite TTFields electrode arrays, at a typical TTFields treatment frequency of (200 kHz), can detect changes in the tumor radius with a sensitivity that increases with the radius of the tumor. The study shows that TTFields electrode arrays can be used to assess the effectiveness of TTFields treatment on changes in the tumor dimensions in real time, throughout the treatement. This monitoring system may become a valuable addition to the TTFields cancer treatment technology. It could provide the means to continuously assess the effectiveness of the treatment, and thereby optimize the design of the treatment protocol.
Li et al. (2022) Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays. PeerJ 10:e12877 https://doi.org/10.7717/peerj.12877
Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense
Background Calcium dependent protein kinases (CDPKs) are a class of important calcium signal sensing response proteins, which play an important regulatory role in response to abiotic stress. However, researchers have not been excavated CDPKs’ role in drought in sea-island cotton(Gossypium barbadense L. ‘H7124’). Results Eighty-four CDPK genes have been identified in G. barbadense. These GbCDPK genes are unevenly distributed on 26 chromosomes, and segmental duplication is the significant way for the extension of CDPK family. Also, members within the same subfamily share a similar gene structure and motif composition. There are a large number of cis-elements involved in plant growth and response to stresses in the promoter regions of GbCDPKs. Additionally, these GbCDPKs show differential expression patterns in cotton tissues. The transcription levels of most genes were markedly altered in cotton under heat, cold, salt and PEG treatments, while the expressions of some GbCDPKs were induced in cotton under drought stress. Among these drought-induced genes, we selected GbCDPK32, GbCDPK68, GbCDPK74, GbCDPK80 and GbCDPK83 for further functional characterization by virus-induced gene silencing (VIGS) method. Conclusions In conclusion, the principal findings of this prospective study are that CDPKs were associated with drought. These findings provide a solid foundation for the development of future molecular mechanism in sea-island cotton.
Shi et al. (2022) Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense. PeerJ 10:e12883 https://doi.org/10.7717/peerj.12883
Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields
Background Microplastic (MP) contamination has been discovered in aquatic systems throughout the world. They are well known as contaminants in aquatic species, but there is a gap in understanding about pathways of MP contamination into humans (i.e., through aquatic animals). The goal of this study is to assess MP contamination in an edible aquatic insect (Pantala sp.) living in rice fields. Methods A dragonfly larva, Pantala sp. (Odonata: Libellulidae), was tested for MPs. The study concentrated on three distinct anatomical compartments (whole body, gastrointestinal tract, and body without gastrointestinal tract), each of which was examined separately. For the physical identification and chemical analysis of MPs, a stereomicroscope and a Fourier transformed infrared spectroscope (FT-IR) were used, respectively. Results and Discussion The microplastics content was 121 in the whole body, 95 in the gastrointestinal tract, and 66 in the body without the gastrointestinal tract, with an average of 1.34 ± 1.11, 1.06 ± 0.77, and 0.73 ± 0.51 abundance/ individual, respectively. The most common MPs discovered during this study were fragments, followed by fibers and rods. The chemical analysis by FT-IR confirmed three different polymers, including polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polypropylene (PP). There was no significant difference in MP abundances among the sample types (Kruskal-Wallis chi-squared = 2.774, df = 2, p = 0.250). The findings suggest that eating an edible aquatic insect (Odonata: Pantala sp.) could be one way for humans to ingest MPs.
Maneechan et al. (2022) Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields. PeerJ 10:e12902 https://doi.org/10.7717/peerj.12902
Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond
Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn (Macrobrachium rosenbergii) and the white leg shrimp (Litopenaeus vannamei) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were predominant, and white/transparent MPs were most prevalent (63.67%). Furthermore, regarding the morphotypes of the MPs, fibers, fragments, films, and spheres were frequently observed, with fibers shows predominance. Specifically, the proportions of fibers in the GTs of female Macrobrachium rosenbergii, male Macrobrachium rosenbergii, and Litopenaeus vannamei were 83.3, 79.91, and 46.06%, respectively. Four MP polymer types, polyethylene, polycaprolactone, polyvinyl alcohol, and acrylonitrile butadiene styrene, were also identified via FTIR spectroscopy, which further confirmed the presence of MPs in the GT of the freshwater-cultured species. Discussion Our findings indicated that consuming shrimps and prawns without first removing the MPs from their GTs is one of the mean by which humans get exposed to MPs. Thus, MPs in freshwater species can be passed down the food chain to humans.
Reunura et al. (2022) Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond. PeerJ 10:e12916 https://doi.org/10.7717/peerj.12916
Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease
The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than −102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
Kandeel et al. (2022) Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease. PeerJ 10:e12929 https://doi.org/10.7717/peerj.12929
Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana
Background Bark storage protein (BSP) plays an important role in seasonal nitrogen cycling in perennial deciduous trees. However, there is no report on the function of BSP in the perennial woody oil plant Jatropha curcas. Methods In this study, we identified six members of JcBSP gene family in J. curcas genome. The patterns, seasonal changes, and responses to nitrogen treatment in gene expression of JcBSPs were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Overexpression of JcBSP1 in transgenic Arabidopsis thaliana was driven by a constitutive cauliflower mosaic virus (CaMV) 35S RNA promoter. Results JcBSP members were found to be expressed in various tissues, except seeds. The seasonal changes in the total protein concentration and JcBSP1 expression in the stems of J. curcas were positively correlated, as both increased in autumn and winter and decreased in spring and summer. In addition, the JcBSP1 expression in J. curcas seedlings treated with different concentrations of an NH4NO3 solution was positively correlated with the NH4NO3 concentration and application duration. Furthermore, JcBSP1 overexpression in Arabidopsis resulted in a phenotype of enlarged rosette leaves, flowers, and seeds, and significantly increased the seed weight and yield in transgenic plants.
Zhang et al. (2022) Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana. PeerJ 10:e12938 https://doi.org/10.7717/peerj.12938
Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss
Background Parental chromosomal aberrations are important causes of recurrent pregnancy loss (RPL). Some immunological factors such as antiphospholipid antibodies and interleukin-6 (IL-6) also contribute to this complication. The aim of this study was to determine the frequency of chromosomal abnormalities and to evaluate some of the immunological factors in couples with RPL from different cities in Iraq. Methods This study was conducted on 25 couples (50 individuals) who had more than two first trimester abortions in the past and 25 healthy females as controls. Karyotyping was performed on peripheral blood of all participants. Anticardiolipin (IgG and IgM), antiphosopholipid (IgG and IgM), lupus anticoagulant, and IL-6 were assayed. Data were analyzed using appropriate statistical tests. Results Chromosomal abnormalities were found in 28.0% (n = 7/25) of RPL couples. Of these five (10.0%) were female and two (4.0%) were male. The types of structural abnormalities were as follows: 45, XX, t(21; 21); 45, XX, rob (14, 15); 46, XX, add (21) (p13); 46 XY, add (21)(p13); 46, XX, 21ps+; 46, XY, per inv (9) (p11q12) and 45, XX, t(13q, 13q). No chromosomal abnormalities were found in the control group. Also, no significant differences were found in the immunological parameters of the couples with RPL and the control group. Conclusion In this study, karyotyping revealed a high number of chromosomal abnormalities associated with the RPL in Iraqi couples. Since identification of genetic causes of miscarriage is important for genetic counseling and educating couples about the risk of future pregnancies, it is recommended that conventional karyotyping be investigated in patients with RPL.
Khamees et al. (2022) Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss. PeerJ 10:e12801 https://doi.org/10.7717/peerj.12801
Using virtual reality for anatomical landmark annotation in geometric morphometrics
To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.
Messer et al. (2022) Using virtual reality for anatomical landmark annotation in geometric morphometrics. PeerJ 10:e12869 https://doi.org/10.7717/peerj.12869
Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis
The intensity of a pathogen infection plays a key role in determining how the host responds to infection. Hosts with high infections are more likely to transmit infection to others, and are may be more likely to experience progression from infection to disease symptoms, to being physiologically compromised by disease. Understanding how and why hosts exhibit variation in infection intensity therefore plays a major part in developing and implementing measures aimed at controlling infection spread, its effects, and its chance of persisting and circulating within a population of hosts. To track the relative importance of a number of variables in determining the level of infection intensity, we ran field-surveys at two breeding sites over a 12 month period using marked larvae of the common midwife toad (Alyes obstetricans) and their levels of infection with the amphibian pathogen Batrachochytrium dendrobatidis (Bd). At each sampling occasion we measured the density of larvae, the temperature of the water in the 48 h prior to sampling, the period of time the sampled individual had been in the water body, the developmental (Gosner) stage and the intensity of Bd infection of the individual. Overall our data suggest that the temperature and the duration of time spent in the water play a major role in determining the intensity of Bd infection within an individual host. However, although the duration of time spent in the water was clearly associated with infection intensity, the relationship was negative: larvae that had spent less than 3–6 months in the water had significantly higher infection intensities than those that had spent over 12 months, although this infection intensity peaked between 9 and 12 months. This could be due to animals with heavier infections developing more quickly, suffering increased mortality or, more likely, losing their mouthparts (the only part of anuran larvae that can be infected with Bd). Overall, our results identify drivers of infection intensity, and potentially transmissibility and spread, and we attribute these differences to both host and pathogen biology.
Bielby et al. (2022) Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis. PeerJ 10:e12889 https://doi.org/10.7717/peerj.12889
Micropropagation of pokeweed (Phytolacca americana L.) and comparison of phenolic, flavonoid content, and antioxidant activity between pokeweed callus and other parts
Background Pokeweed (Phytolacca americana L.) is regarded as an invasive plant in many parts of the world but possesses therapeutic characteristics used for antitumor and rheumatism treatment. This study investigated the effects of auxins and four explants on pokeweed callus induction. The effects of cytokinins and combinations between cytokinins and NAA on shoot and root induction were also studied. TPC, TFC and antioxidant activity of calli were screened and compared with other pokeweed plant parts. Methods Four explants were used to induce callus using 2,4-D and IBA at 1, 2, 3 and 4 mg/l for each auxin. Direct shoot organogenesis from nodal explants was investigated using BAP, kinetin and TDZ (1, 2 and 4 mg/l for each cytokinin). Combined effects between cytokinins and NAA at 0.1, 0.2 and 0.3 mg/l were further simultaneously estimated with root induction. Calli derived from the leaves were compared with other plant parts for TPC, TFC and antioxidant activity using the Folin-Ciocalteu, AlCl3 colorimetric assay and DPPH assays, respectively. Results Results showed that MS medium containing 2 mg/l 2,4-D induced callus formation on leaf explants that provided highest fresh and dry weights. Three types of synthetic cytokinins as kinetin, TDZ and BAP were used for direct shoot organogenesis from pokeweed nodes. MS medium containing 2 mg/l kinetin was effective in stimulating normal shoots, with the largest number of shoots and leaves and the longest shoots. The combination between cytokinins and NAA showed no positive effect on shoot and root induction from pokeweed nodal explants. For TPC and TFC determination, pokeweed seeds and leaves possessed the highest phenolic and flavonoid contents, respectively. Highest phenolic content of pokeweed seeds led to lowest IC50 by DPPH assay. Phenolic content was higher than flavonoid content. Conclusion Results suggested promising conditions for callus induction. Leaf explants cultured on MS medium with 2 mg/l 2,4-D and nodal explants cultured on MS medium with 2 mg/l kinetin provided the largest number of normal shoots and leaves. NAA did not show positive effects on shoot and root induction when combined with cytokinins. Chemical constituent screening indicated that seeds and leaves provided highest TPC and TFC, respectively, while pokeweed calli contained higher phenolic than flavonoid content. This is the first report describing chemical constituent screening and antioxidant activity of calli and other parts of the pokeweed plant. Results provided significant information to further enhance bioactive compound contents of pokeweed calli using elicitation methods.
Trunjaruen et al. (2022) Micropropagation of pokeweed (Phytolacca americana L.) and comparison of phenolic, flavonoid content, and antioxidant activity between pokeweed callus and other parts. PeerJ 10:e12892 https://doi.org/10.7717/peerj.12892
Effects of substituting soybean meal with corn on immune function and gene expression of gut TLR4 pathway of growing goats
Background Protein malnutrition remains a severe problem in ruminant production and can increase susceptibility to infection, especially during the growth stage. This study aimed to explore substituting soybean meal with corn on activation of the TLR pathway and potential impact on immune response bias towards Type 1 or Type 2 using growing female goats as experimental animals. Methods Twenty-four Xiangdong black goats (initial BW = 19.83 ± 0.53 kg, about 8 ± 0.3 months old) were selected and randomly divided into the corn-soybean meal basal diet group (CON, 10.77% protein) and replacing soybean meal with 100% of corn group (CRS, 5.52% protein). EDTA whole blood and serum samples were collected prior to slaughter for determinations of blood cell counts, anti-inflammatory cytokines and antibodies. The duodenum, jejunum, ileum and colon tissues were collected after formal trial to study the effect of CRS diet on the expression of TLR4 pathway. Results Our results showed CRS diet did not induce a significant change in immune function, as evidenced by the observations that white blood cell (WBC), neutrophil (Neu), lymphocyte (Lym), monocyte (Mon), eosinophil (Eos), interleukin-4 (IL-4), IL-5, IL-13, immunoglobin G (IgG), IgA, and IgM levels in serum were similar between the two groups. RT-PCR results showed the expression of tumor necrosis factor-α (TNF-α) (P < 0.01) and interferon-β (IFN-β) (P < 0.01) were up-regulated in the colon of goats in the CRS group. No differences in the expression of myeloid differentiation factor 88 (MyD88) adaptor-like protein (TIRAP), IL-1 receptor–associated kinase 1 (IRAK1), TNF receptor related factor 6 (TRAF6), NF-kappa B (NF-κB), mitogen-activated protein kinase 1 (MAPK1) or activator protein-1 (AP-1) in the TLR4/MyD88 dependent pathway were observed between the two groups for any of the tested tissue. However, the expression of NF-κB activator (TANK) binding kinase 1 (TBK1) in TLR4/MyD88 independent pathway was up-regulated in the duodenum and colon (P < 0.01), and the expression of interferon regulatory factor-3 (IRF3) was up-regulated (P < 0.01) in colon. Conclusions Our results suggested that the CRS diet failed to induce a significant change in innate immunity and adaptive immunity in growing goats. However, the up-regulated TBK1 and IRF3 in the colon from the CRS goats suggests that the CRS diet may induce the expression of Th1-type proinflammatory cytokines and inflammatory response through a TLR4-MyD88-independent pathway, and the colon may be the easiest targeted section in the intestinal tract.
Cheng et al. (2022) Effects of substituting soybean meal with corn on immune function and gene expression of gut TLR4 pathway of growing goats. PeerJ 10:e12910 https://doi.org/10.7717/peerj.12910
Antioxidant and anti-inflammatory activities of durian (Durio zibethinus Murr.) pulp, seed and peel flour
The unripe pulp, inner peel and seed of durian were used in this study. These are generally not considered edible and must be disposed of as waste. However, they are good sources of bioactive compounds. Flour extracts from the unripe pulp, inner peel, and seed of two durian (Durio zibethinus Murr.) varieties, namely, Monthong and Chanee, were analyzed chemically to determine their total phenolic content (TPC), antioxidant, and anti-inflammatory capacities. Chanee pulp (CPu) contained a higher TPC (5285.37 ± 517.65 mg GAE/g) than Monthong pulp (MPu), Monthong peel (MP), Monthong seed (MS), Chanee peel (CP) and Chanee seed (CS) (p = 0.0027, 0.0042, 0.0229, 0.0069 and 0.36), respectively. The antioxidant activity of each durian extract was determined against ABTS, nitric oxide, superoxide, hydroxyl, and metal ions. The results indicated that the pulp, inner peel and seed of these durian varieties had antioxidant capacities. Murine Raw 264.7 macrophages were used to determine the cytotoxicity of the flour extracts. The extract of CS flour had the lowest cytotoxicity followed by MP, CPu, CP, MPu and MS (p = 0.5926, 0.44, 0.3191, 0.1471 and 0.0014), respectively. The anti-inflammatory activity was tested by anti-nitric oxide (NO) production in lipopolysaccharide (LPS) stimulated cells by co-treating the Raw 264.7 cells with each durian flour extract and LPS. The extract of MP flour had the lowest IC50 against NO production, indicating the highest anti-NO production activity followed by CS, CPu, MPu, CP and MS (p = 0.7473, 0.0104, < 0.0001, 0.0002 and < 0.0001, respectively). The information obtained in this study is useful for researchers to explore more durian varieties in Southeast Asia to find bioactive compounds that might be novel nutraceuticals for antioxidant, anti-inflammation and therapeutic functional food.
Charoenphun et al. (2022) Antioxidant and anti-inflammatory activities of durian (Durio zibethinus Murr.) pulp, seed and peel flour. PeerJ 10:e12933 https://doi.org/10.7717/peerj.12933
Assessing the impact of workaholism and work engagement on medical university employee stress and satisfaction levels
Background Workaholism (WH) is related with high mental trouble and physical objections, low employment and family fulfillment, and low occupation execution; however, work commitment is related with job and life satisfaction. This study aimed to assess the impact of WH and work engagement (WE) on medical university employee job stress and satisfaction. Methods This descriptive analytical study was conducted on workers employed in medical universities using validated questionnaires for data collection. The sample size was 330, from which 305 responded with completed questionnaire. The employees were the direct workers of different accessible medical universities in Karachi, Pakistan. The employee enrolment and distribution of the questionnaire was performed using non-probability convenient sampling. The Brief Job Questionnaire (BJQ), Dutch Work Addiction Scale (DUWAS) and Utrecht Work Engagement Scale (UWES) were used to assess the impact of job stress on job satisfaction and WE. The data was analyzed by applying descriptive statistics, Spearman correlation and regression analysis. A p-value of ≤ 0.05 was taken as significant. Results The study consisted of 117 (38.4%) male and 188 (61.6%) female participants; the mean age of participating employee was 28.50 ± 6.192. The mean score for WE was 3.78 ± 0.467, that of WH was 3.42 ± 0.559, for JS was 4.29 ± 0.400, whereas JSF was 3.10 ± 0.591. A positive correlation was observed between job stress, WH and WE. WH had a strong correlation with job stress and weak correlation with job satisfaction and performance. A significant difference was observed between WE and WH among males and females. Conclusions The study presented with a significant effect of job satisfaction with WH and WE with job stress. Hence, indicating the importance of social skills and WE with fellow employees to increase the work productivity and performance. However, in case of over work and WH, an increase of job stress is inevitable.
Sarfaraz et al. (2022) Assessing the impact of workaholism and work engagement on medical university employee stress and satisfaction levels. PeerJ 10:e12565 https://doi.org/10.7717/peerj.12565
Analysis of metabolites in young and mature Docynia delavayi (Franch.) Schneid leaves using UPLC-ESI-MS/MS
Docynia delavayi (Franch.) Schneid is a plant used both as food and traditional folk medicine. The leaves of D. delavayi are rich in polyphenols, plants with phenolic content are known to be extremely beneficial in terms of human nutrition. In the present study, we used metabolome technology (UPLC-ESI-MS/MS) to examine the young and mature D. delavayi leaves on metabolites changes, which were then analyzed and compared. As a result, 477 metabolites (including 111 flavonoids, 47 others (consisted of nine vitamin, 18 saccharides and alcohols, and 20 unassigned metabolites), 71 phenolic acids, 52 amino acids and derivatives, 18 alkaloids, 61 lipids, 24 terpenoids, 33 nucleotides and derivatives, 18 lignans and coumarins, 12 tannins, 30 organic acids) were identified, of which 281 differentially accumulated metabolites, including 146 up-regulated metabolites and 135 down-regulated metabolites. The result of clustering and PCA analyses showed that young and mature leaves were separated, which indicated that there was a great difference in metabolites between young and mature leaves. Meanwhile, we also found that both young and mature leaves displayed unique metabolites with important biological functions. KEGG enrichment analysis showed that 90 of the differential metabolites were mainly concentrated in 68 KEGG pathways. The result will greatly complement the existing knowledge on the D. delavayi leaves for lays a foundation for subsequent development and utilization.
Xia et al. (2022) Analysis of metabolites in young and mature Docynia delavayi (Franch.) Schneid leaves using UPLC-ESI-MS/MS. PeerJ 10:e12844 https://doi.org/10.7717/peerj.12844
Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies
Background Exercise elicits a range of adaptive responses in skeletal muscle, which include changes in mRNA expression. To better understand the health benefits of exercise training, it is important to investigate the underlying molecular mechanisms of skeletal muscle adaptation to exercise. However, most studies have assessed the molecular events at only a few time-points within a short time frame post-exercise, and the variations of gene expression kinetics have not been addressed systematically. Methods We assessed the mRNA expression of 23 gene isoforms implicated in the adaptive response to exercise at six time-points (0, 3, 9, 24, 48, and 72 h post exercise) over a 3-day period following a single session of high-intensity interval exercise. Results The temporal patterns of target gene expression were highly variable and the expression of mRNA transcripts detected was largely dependent on the timing of muscle sampling. The largest fold change in mRNA expression of each tested target gene was observed between 3 and 72 h post-exercise. Discussion and Conclusions Our findings highlight an important gap in knowledge regarding the molecular response to exercise, where the use of limited time-points within a short period post-exercise has led to an incomplete understanding of the molecular response to exercise. Muscle sampling timing for individual studies needs to be carefully chosen based on existing literature and preliminary analysis of the molecular targets of interest. We propose that a comprehensive time-course analysis on the exercise-induced transcriptional response in humans will significantly benefit the field of exercise molecular biology.
Kuang et al. (2022) Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies. PeerJ 10:e12856 https://doi.org/10.7717/peerj.12856
Bayesian computation for the common coefficient of variation of delta-lognormal distributions with application to common rainfall dispersion in Thailand
Rainfall fluctuation makes precipitation and flood prediction difficult. The coefficient of variation can be used to measure rainfall dispersion to produce information for predicting future rainfall, thereby mitigating future disasters. Rainfall data usually consist of positive and true zero values that correspond to a delta-lognormal distribution. Therefore, the coefficient of variation of delta-lognormal distribution is appropriate to measure the rainfall dispersion more than lognormal distribution. In particular, the measurement of the dispersion of precipitation from several areas can be determined by measuring the common coefficient of variation in the rainfall from those areas together. Herein, we compose confidence intervals for the common coefficient of variation of delta-lognormal distributions by employing the fiducial generalized confidence interval, equal-tailed Bayesian credible intervals incorporating the independent Jeffreys or uniform priors, and the method of variance estimates recovery. A combination of the coverage probabilities and expected lengths of the proposed methods obtained via a Monte Carlo simulation study were used to compare their performances. The results show that the equal-tailed Bayesian based on the independent Jeffreys prior was suitable. In addition, it can be used the equal-tailed Bayesian based on the uniform prior as an alternative. The efficacies of the proposed confidence intervals are demonstrated via applying them to analyze daily rainfall datasets from Nan, Thailand.
Yosboonruang et al. (2022) Bayesian computation for the common coefficient of variation of delta-lognormal distributions with application to common rainfall dispersion in Thailand. PeerJ 10:e12858 https://doi.org/10.7717/peerj.12858
Cytokinin and gibberellic acid-mediated waterlogging tolerance of mungbean (Vigna radiata L. Wilczek)
Background Mungbean (Vigna radiata L. Wilczek) is one of the most important pulse crops, well-known for its protein-rich seeds. Growth and productivity are severely undermined by waterlogging. Methods In this study, we aim to evaluate how two promising phytohormones, namely cytokinin (CK) and gibberellic acid (GA3), can improve waterlogging tolerance in mungbean by investigating key morphological, physiological, biochemical, and yield-related attributes. Results Our results showed that foliar application of CK and GA3 under 5-day of waterlogged conditions improved mungbean growth and biomass, which was associated with increased levels of photosynthetic rate and pigments. Waterlogged-induced accumulation of reactive oxygen species and the consequently elevated levels of malondialdehyde were considerably reduced by CK and GA3 treatments. Mungbean plants sprayed with either CK or GA3 suffered less oxidative stress due to the enhancement of total phenolics and flavonoids levels. Improvement in the contents of proline and total soluble sugars indicated a better osmotic adjustment following CK and GA3 treatments in waterlogged‐exposed plants. Most fundamentally, CK or GA3-sprayed waterlogged-stressed mungbean plants demonstrated better performance in the aforementioned parameters after the 15-day recovery period as compared to water-sprayed waterlogged-exposed plants. Our results also revealed that CK and GA3 treatments increased yield-associated features in the waterlogged-stressed plant. Here, both phytohormones are efficient in improving mungbean resistance to waterlogging. However, CK was found to be more effective. Overall, our findings suggested that CK or GA3 could be used for managing waterlogging-induced damage to mungbean and perhaps in other cash crops.
Islam et al. (2022) Cytokinin and gibberellic acid-mediated waterlogging tolerance of mungbean (Vigna radiata L. Wilczek). PeerJ 10:e12862 https://doi.org/10.7717/peerj.12862
Involvement of TOB1 on autophagy in gastric cancer AGS cells via decreasing the activation of AKT/mTOR signaling pathway
Background We previously identified the tumor suppressor gene TOB1 as related to gastric cancer. The purpose of this study was to explore whether TOB1 induces autophagy through the AKT/mTOR signaling pathway in gastric cancer. Methods Western blotting was used to detect the protein levels of TOB1, LC3, AKT, mTOR, phosphorylated (p) AKT, and p-mTOR. A double fluorescent GFP-RFP-LC3 fusion protein was used to trace autophagy by laser confocal microscopy. Autophagosomes were observed by transmission electron microscopy. Results The conversion of LC3-I to LC3-II and the LC3-II/LC3-I ratio were significantly increased in AGS cells overexpressing TOB1 compared with control cells. Fluorescence imaging showed LC3 puncta at 48 h, and these puncta increased significantly at 72 h after TOB1 transfection compared with control tumor cells. The presence of autophagosomes in AGS cells was observed at 72 h after TOB1 transfection by transmission electron microscopy, and no autophagosomes were found in the control cells. Moreover, the levels of p-AKT and p -mTOR were lower in AGS cells than in control cancer cells. Conclusion Our results provide novel insight that TOB1 might suppress gastric cancer by inducing autophagy, possibly through decreasing phosphorylation and the subsequent activation of the AKT/mTOR signaling pathway.
Wang et al. (2022) Involvement of TOB1 on autophagy in gastric cancer AGS cells via decreasing the activation of AKT/mTOR signaling pathway. PeerJ 10:e12904 https://doi.org/10.7717/peerj.12904
Testosterone and estradiol affect adolescent reinforcement learning
During adolescence, gonadal hormones influence brain maturation and behavior. The impact of 17β-estradiol and testosterone on reinforcement learning was previously investigated in adults, but studies with adolescents are rare. We tested 89 German male and female adolescents (mean age ± sd = 14.7 ± 1.9 years) to determine the extent 17β-estradiol and testosterone influenced reinforcement learning capacity in a response time adjustment task. Our data showed, that 17β-estradiol correlated with an enhanced ability to speed up responses for reward in both sexes, while the ability to wait for higher reward correlated with testosterone primary in males. This suggests that individual differences in reinforcement learning may be associated with variations in these hormones during adolescence, which may shift the balance between a more reward- and an avoidance-oriented learning style.
Kohne et al. (2022) Testosterone and estradiol affect adolescent reinforcement learning. PeerJ 10:e12653 https://doi.org/10.7717/peerj.12653
Functional mechanism of hsa-miR-128-3p in epithelial-mesenchymal transition of pancreatic cancer cells via ZEB1 regulation
Pancreatic cancer (PC) often correlates with high mortality due to late diagnosis, rapid metastasis, and resistance to chemotherapy. miR-128-3p has been validated as a tumor suppressor in PC. This study explored the functional mechanism of miR-128-3p in epithelial-mesenchymal transition (EMT) of PC cells. Four PC cancer cell lines with different degrees of malignancy and normal pancreatic cells were selected to detect expressions of hsa-miR-128-3p and ZEB1 by RT-qPCR and Western blot. miR-128-3p mimic or si-ZEB1 was delivered into PANC-1 cells and miR-128-3p inhibitor or oe-ZEB1 was delivered into AsPC-1 cells. Expressions of epithelial and mesenchymal markers were analyzed by Western blot and cell fluorescence staining. The binding relationship between miR-128-3p and ZEB1 was examined by bioinformatics analysis and dual-luciferase assay, and verified by RT-qPCR and Western blot. PC cell invasion and migration were assessed by Transwell assays. Generally, hsa-miR-128-3p was poorly-expressed in PC cells. However, it was relatively more expressed in AsPC-1 cells with epithelial phenotypes relative to PANC-1 cells with mesenchymal phenotype, whereas ZEB1 expression showed opposite tendencies. PANC-1 cells transfected with miR-128-3p mimic or si-ZEB1 showed upregulated E-cadherin and downregulated N-cadherin, and transformed from mesenchymal phenotypes to epithelial phenotypes, with decreased invasion and migration, while opposite results occurred in AsPC-1 cells transfected with miR-128-3p inhibitor or oe-ZEB1. miR-128-3p targeted ZEB1. oe-ZEB1 antagonized the inhibition of miR-128-3p mimic on PANC-1 cell EMT, invasion, and migration, while si-ZEB1 reversed the facilitation of miR-128-3p inhibitor in AsPC-1 cells. In conclusion, miR-128-3p inhibited PC cell EMT, invasion, and migration by targeting ZEB1.
Zheng et al. (2022) Functional mechanism of hsa-miR-128-3p in epithelial-mesenchymal transition of pancreatic cancer cells via ZEB1 regulation. PeerJ 10:e12802 https://doi.org/10.7717/peerj.12802
Identification and expression profiles of the YABBY transcription factors in wheat
Background YABBY is a plant-specific transcription factor (TF) that belongs to the zinc finger protein superfamily and is composed of a C2–C2 domain at the N-terminus and a YABBY domain at the C-terminus. It plays a role in plant development and growth. Methods In this study, 20 YABBY TFs were identified in the wheat genome. Phylogenetic relationships, collinearity relationships, gene structures, conserved motifs, and expression patterns were analyzed. Results Twenty TaYABBY TFs were distributed unevenly on 15 chromosomes. Collinearity analysis showed that these genes have a close relationship with monocot plants. The phylogenetic tree of wheat YABBYs classified these TaYABBYs into FIL, YAB2, INO, and CRC clades. Gene structure and conserved motif analyses showed that they share similar components in the same clades. Expression profile analysis showed that many TaYABBY genes have high expression levels in leaf tissues and are regulated by abiotic stresses, especially salt stress. Our results provide a basis for further functional characterization of the YABBY gene family.
Hao et al. (2022) Identification and expression profiles of the YABBY transcription factors in wheat. PeerJ 10:e12855 https://doi.org/10.7717/peerj.12855
Comparative transcriptomic analysis reveals potential mechanisms for high tolerance to submergence in arbor willows
Background Submergence threatens plant growth and survival by decreasing or eliminating oxygen supply. Uncovering the complex regulatory network underlying the tolerance of Salix to submergence and identifying the key regulators are important for molecular-assisted breeding of Salix. Methods In this study, we screened germplasm resources of arbor willows and discovered both submergence-tolerant and submergence-sensitive varieties. Then, by performing RNA-seq, we compared the differences between the transcriptomes of two varieties, i.e., the submergence-tolerant variety “Suliu 795” and the submergence-sensitive variety “Yanliu No. 1,” and the different submergence treatment time points to identify the potential mechanisms of submergence in Salix and the unique approaches by which the variety “Suliu 795” possessed a higher tolerance compared to “Yanliu No. 1”. Results A total of 22,790 differentially expressed genes were identified from 25 comparisons. Using gene ontology annotation and pathway enrichment analysis, the expression pattern of transcriptional factors, important players in hormone signaling, carbohydrate metabolism, and the anaerobic respiration pathway were found to differ significantly between the two varieties. The principal component analysis and qRT-PCR results verified the reliability of the RNA sequencing data. The results of further analysis indicated that “Suliu 795” had higher submergence tolerant activity than “Yanliu No. 1” because of three characteristics: (1) high sensitivity to the probable low oxygen stress and initiation of appropriate responding mechanisms in advance; (2) maintenance of energy homeostasis to prevent energy depletion under hypoxic stress; and (3) keep “quiescence” through fine-tuning the equilibrium between phytohormones GA, SA and ethylene.
Chen et al. (2022) Comparative transcriptomic analysis reveals potential mechanisms for high tolerance to submergence in arbor willows. PeerJ 10:e12881 https://doi.org/10.7717/peerj.12881
Arbuscular mycorrhizal fungi improve the growth and performance in the seedlings of Leymus chinensis under alkali and drought stresses
Alkali and drought stresses are increasing severe environmental problems throughout the world, especially in the Songnen grassland of northern China. Leymus chinensis is the dominant grass species in the Songnen grassland of northern China and the most promising species for grassland restoration. Arbuscular mycorrhizal fungi (AMF) can colonize 80% of vascular plants, which can enhance the growth of host plants and provide extrinsic protection against abiotic stresses. However, little is known about the interaction effect of alkali and drought stresses on plant-AM symbionts. Here, seedlings of Leymus chinensis inoculated with or without mycorrhizae were cultivated in soil with 0, 100 or 200 mM NaHCO3 under 0, 5 or 10% (w/v) PEG treatment, and the changes in growth, osmotic adjustment substances and ions were measured. The results showed that the interaction of alkali and drought stresses caused greater seedling growth inhibition than either single alkali or drought stress due to ion toxicity and oxidative damage. Mycorrhizae could alleviate the growth inhibition of seedlings under alkali or drought stress. The interaction of alkali and drought stresses did not affect the alleviating effect of mycorrhizae on seedling growth but improved the osmotic regulation ability and ionic balance of the seedlings. Our results clearly show different effects of the interaction of alkali and drought stresses versus a single stress (alkali or drought) on plant development and provide new insights into the positive effect of arbuscular mycorrhizal fungi on host plants under such stress conditions.
Wang et al. (2022) Arbuscular mycorrhizal fungi improve the growth and performance in the seedlings of Leymus chinensis under alkali and drought stresses. PeerJ 10:e12890 https://doi.org/10.7717/peerj.12890
Overexpression of the LcCUC2-like gene in Arabidopsis thaliana alters the cotyledon morphology and increases rosette leaf number
Background The unique ‘mandarin jacket’ leaf shape is the most famous trait of Liriodendron chinense and this characteristic gives L. chinense aesthetic and landscaping value. However, the underlying regulatory mechanism of genes involved in the leaf development of L. chinense has remained unclear. Methods Based on transcriptome data of leaves at different developmental stages from L. chinense, we identified differentially expression genes (DEGs) functioning in leaf development. A candidate gene named LcCUC2-like (LcCUC2L) had high similarity in sequence with Arabidopsis thaliana CUC2, and used for further research. We isolated the full-length LcCUC2L gene and its promoter from L. chinense. Subsequently, we analyzed the function of the LcCUC2L gene and its promoter activity via transformation into A. thaliana. Results In this study, we found that the LcCUC2L and AtCUC2 are homologous in sequence but not homologous in function. Unlike the role of AtCUC2 in leaf serration and SAM formation, the LcCUC2L mainly regulates cotyledon development and rosette leaf number. Histochemical β-glucuronidase (GUS) staining revealed that LcCUC2L was expressed in the cotyledons of A. thaliana seedlings, indicating that the LcCUC2L may play a role in cotyledon development. Ectopic expression of LcCUC2L resulted in long, narrow cotyledons without petioles, abnormal lamina epidermis cells and defective vascular tissue in cotyledons, and these results were consistent with the LcCUC2L expression pattern. Further analysis showed that overexpression of LcCUC2L also induced numerous rosette leaves. Also, LcCUC2L and other related genes showed a severe response in L. chinense by introducing exogenous auxin stimulation, partly revealed that LcCUC2L affects the leaf development by regulating the auxin content. Conclusions These results suggest that LcCUC2L may play a critical role in leaf development and morphogenesis in L. chinense, and our findings provide insight into the molecular mechanisms of leaf development in L. chinense.
Wen et al. (2022) Overexpression of the LcCUC2-like gene in Arabidopsis thaliana alters the cotyledon morphology and increases rosette leaf number. PeerJ 10:e12615 https://doi.org/10.7717/peerj.12615
The effect of internet addiction and smartphone addiction on sleep quality among Turkish adolescents
Background: Sleep quality plays a principal role in the protection of health. There is an increasing number of studies in the literature demonstrating that internet addiction and smartphone addiction impair sleep quality. However, the number of studies on Turkish adolescents is very limited. Therefore, this study examined the effects of internet addiction and smartphone addiction on sleep quality among Turkish adolescents. Methods: Participants in this cross-sectional study were 910 adolescents aged 13–18 years. Data were collected with the Short Internet Addiction Test, Smartphone Addiction Scale, and Pittsburgh Sleep Quality Index. In addition, a questionnaire was used to gather information about the demographic, socioeconomic, and health-related characteristics. Pearson’s Chi-square test, Chi-square test for trend, Mann–Whitney U test, logistic regression analysis, and Spearman’s correlation analysis were used in the analysis. Results: The sleep quality of 58.7% of the adolescents was poor. Additionally, girls and adolescents ≥16 years old had poor sleep quality. Sleep quality deteriorated as perceived health status and perceived economic status of family deteriorated. Compared to participants with normal internet addiction scores, poor sleep quality was 1.83 (95% CI [1.22–2.74]) times higher in those with problematic internet addiction and 1.99 (95% CI [1.23–3.87]) times higher in those with pathological internet addiction. One point increase in Smartphone Addiction Scale total score increased poor sleep quality 1.01 (95% CI [1.00–1.02]) times. Sleep quality scale were positively correlated with the smartphone addiction and internet addiction. However, there was no positive correlation between habitual sleep efficiency subcomponent of sleep quality and smartphone addiction and internet addiction. Conclusions: Internet addiction and smartphone addiction were associated with poor sleep quality in adolescents. Older adolescents (≥16 years), gender (female), poor health perception, and perception of moderate economic status of the family were other factors associated with poor sleep quality.
Acikgoz et al. (2022) The effect of internet addiction and smartphone addiction on sleep quality among Turkish adolescents. PeerJ 10:e12876 https://doi.org/10.7717/peerj.12876
Transcriptome analysis reveals the potential biological function of FSCN1 in HeLa cervical cancer cells
Fascin actin-bundling protein 1 (FSCN1), an actin-bundling protein associated with cell migration and invasion, is highly expressed in various tumor tissues. FSCN1 has also been reported to be a marker of increased invasive potential in cervical cancers. However, the functions of FSCN1 are still not fully understood in cervical cancers. Here, the gene expression profile of HeLa cells transfected with FSCN1 shRNA (shFSCN1) was compared with that of cells transfected with empty vector (shCtrl). The results showed that shFSCN1 extensively affected the transcription level of 5,043 genes in HeLa cells. In particular, Gene Ontology (GO) analysis showed that a large number of upregulated genes were annotated with terms including transcription regulation and DNA binding. The downregulated genes were enriched in some cancer pathways, including angiogenesis and cell adhesion. qPCR validation confirmed that FSCN1 knockdown significantly affected the expression of selected genes in HeLa cells either negatively or positively. Expression analysis in TCGA (The Cancer Genome Atlas) revealed that FSCN1 had negative correlations with several transcription factors and a positive correlation with an angiogenic factor (angiopoietin like 4, ANGPTL4) in cervical tumor tissue. In particular, validation by Western blotting showed that FSCN1 knockdown decreased the protein level of ANGPTL4. Our results demonstrated that FSCN1 is not only an actin-binding protein but also a transcriptional regulator and an angiogenic factor in cervical cancer. Thus, our study provides important insights for further study on the regulatory mechanism of FSCN1 in cervical cancer.
Guo et al. (2022) Transcriptome analysis reveals the potential biological function of FSCN1 in HeLa cervical cancer cells. PeerJ 10:e12909 https://doi.org/10.7717/peerj.12909
Spatial distribution and ecological risk assessment of heavy metals in karst soils from the Yinjiang County, Southwest China
Background Soil heavy metals (HMs) under different land-use types have diverse effects, which may trigger the ecological risk. To explore the potential sources of HMs in karst soils, the spatial distribution and geochemical behavior of HMs based on different land-use types are employed in this study. Methods Soil samples (n = 47) were collected in three suites of karst soil profiles from the secondary forest, abandoned cropland and shrubland in Yinjiang, Southwest China. The concentrations of Ni, Mn, Cr, Pb, Cd and Mo were determined to give a comprehensive understanding of the possible sources of these HMs and evaluate the potential ecological risk in Yinjiang County. Results The mean concentrations of HMs in all profiles followed the same order: Mn > Cr > Ni > Pb > Mo > Cd. Meanwhile, the concentrations of most HMs roughly increased with the depth. Additionally, the concentrations of HMs were mostly correlated with soil pH and SOC, rather than with clay and silt proportions. By contrast, with the enrichment factors (EF), geo-accumulation (Igeo) and potential ecological risk index (PERI) of HMs in soil under different land-use types, the results indicated that these HMs exhibited non-pollution (Igeo < 0) and no ecological risk (PERI < 30) to human health in soils of Yinjiang County. Conclusions The distribution of HMs is dominated by weathering in the karst area, and the effects of agricultural inputs on the enrichment of soil HMs in Yinjiang County are limited. This further state that the arrangement of the local agricultural structure is reasonable.
Han et al. (2022) Spatial distribution and ecological risk assessment of heavy metals in karst soils from the Yinjiang County, Southwest China. PeerJ 10:e12716 https://doi.org/10.7717/peerj.12716
Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte
Background New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. Methods Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium “black”, and the morphology of a species previously reported as Diversibipalium “blue”. Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. Results The new species Humbertium covidum n. sp. (syn: Diversibipalium “black” of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium “blue” of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position. Conclusion Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.
Justine et al. (2022) Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte. PeerJ 10:e12725 https://doi.org/10.7717/peerj.12725
Dispersal into the Qinghai–Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum
Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai–Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (FST = 0.654 for cpDNA, FST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis “dispersal into the QTP,” proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.
Liu et al. (2022) Dispersal into the Qinghai–Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum. PeerJ 10:e12754 https://doi.org/10.7717/peerj.12754
Pain threshold in selected trigger points of superficial muscles of the back in young adults
Background Monitoring of pain threshold is the basis for verification of the effectiveness of therapy or assessment of the patient’s condition. This study aimed to determine the pain threshold of selected superficial muscles of the back taking into account trigger point activity in young and healthy males and females, with the evaluation of intrarater reliability of algometric measurements. Material and methods The study examined 30 young adult participants (15 males and 15 females) aged 26.23 ± 3.21, and BMI of 23.80 ± 3.43. The Pain Test FPX Algometer (Wagner) was used for the study. Trigger points on the levator scapulae and trapezius muscles (superior and inferior portion) on both sides were examined. It was also verified whether the trigger points studied are active or inactive. Furthermore, an author’s survey questionnaire was used. Results Within the trigger points of the right (p = 0.04) and left (p = 0.02) superior trapezius muscle and the left (p = 0.04) levator scapulae muscle, the pain threshold values were higher in the male group. There was a statistically significantly higher number of active trigger points in the female group compared to that in the male group (2.49 ± 1.51 vs. 1.07 ± 1.16, respectively), p = 0.01. For all muscles tested, mean pain threshold values were significantly higher for inactive trigger points. A greater number of active trigger points is associated with lower pain thresholds at these points (left: the superior trapezius, r = −0.597, the inferior trapezius, r = −0.609; the levator scapulae, r = −0.746; right: the superior trapezius, r = −0.610, the inferior trapezius, r = −0.604; the levator scapulae, r = −0.747). The evaluation of the intrarater reliability showed excellent agreement between the first and second measurements, ICC > 0.987 for all examined trigger points. Conclusions (1) Women who reported pain more than once a week in the studied muscles showed a greater number of active trigger points. (2) A greater number of active trigger points in female is related to a lower pain threshold (which is associated with greater pain sensitivity) in female than in male. (3) A sample size of 30 people seems sufficient to detect variations in the pain threshold at active and inactive trigger points of selected back muscles, especially when the frequency of occurrence of both types of points is comparable.
Cygańska et al. (2022) Pain threshold in selected trigger points of superficial muscles of the back in young adults. PeerJ 10:e12780 https://doi.org/10.7717/peerj.12780
Characterization of habitat requirements of European fishing spiders
Wetlands are among the most threatened habitats in the world, and so are their species, which suffer habitat loss due to climate and land use changes. Freshwater species, and especially arthropods, receive comparatively little attention in conservation plans, and the goals to stop and reverse the destruction of wetlands published 25 years ago in a manifesto by the Union of Concerned Scientists have not been reached. In this study, we investigated the occurrence and habitat requirements at two spatial scales of two species of European fishing spiders Dolomedes, which rely heavily on declining wetland habitats in Sweden and southern Norway. We collected occurrence data for Dolomedes plantarius and Dolomedes fimbriatus, using a live-determination method. We modelled the placement of nursery webs to describe fine-scale habitat requirements related to vegetation and micro-climate. Using a machine learning approach, we described the habitat features for each species and for co-occurrence sites, thus providing insight into variables relevant for the presence and detectability of Dolomedes. Nursery placement is mostly dependent on proximity to water, presence of Carex sp. (Sedges) and crossing vegetation structures, and on humidity, while detection can be affected by weather conditions. Furthermore, co-occurrence sites were more similar to D. plantarius sites than to D. fimbriatus sites, whereby surrounding forest, water type and velocity, elevation and latitude were of importance for explaining which species of Dolomedes was present. Overall, habitat requirements were narrower for D. plantarius compared to D. fimbiratus.
Dickel et al. (2022) Characterization of habitat requirements of European fishing spiders. PeerJ 10:e12806 https://doi.org/10.7717/peerj.12806
In leukemia, knock-down of the death inducer-obliterator gene would inhibit the proliferation of endothelial cells by inhibiting the expression of CDK6 and CCND1
Background Endothelial cells (ECs) are a critical component of the hematopoietic niche, and the cross-talk between ECs and leukemia was reported recently. This study aimed to determine the genes involved in the proliferation inhibition of endothelial cells in leukemia. Methods Human umbilical vein endothelial cells (HUVEC) were cultured alone or co-cultured with K562 cell lines. GeneChip assays were performed to identify the differentially expressed genes. The Celigo, MTT assay, and flow cytometric analysis were used to determine the effect of RNAi DIDO on cell growth and apoptosis. The differently expressed genes were verified by qRT-PCR (quantitative real-time PCR) and western-blot. Results In K562-HUVEC co-cultured cell lines, 323 down-regulated probes were identified and the extracellular signal-regulated kinase 5 (ERK5) signaling pathway was significantly inhibited. Among the down-regulated genes, the death inducer-obliterator gene (DIDO) is a part of the centrosome protein and may be involved in cell mitosis. As shown in the public data, leukemia patients with lower expression of DIDO showed a better overall survival (OS). The HUVEC cells were infected with shDIDO lentivirus, and reduced expression, inhibited proliferation, and increased apoptosis was observed in shDIDO cells. In addition, the expression of Cyclin-Dependent Kinase 6 (CDK6) and Cyclin D1 (CCND1) genes was inhibited in shDIDO cells. Finally, the public ChIP-seq data were used to analyze the regulators that bind with DIDO, and the H3K4me3 and PolII (RNA polymerase II) signals were found near the Exon1 and exon2 sites of DIDO. Conclusion The knock-down of DIDO will inhibit the proliferation of endothelial cells in the leukemia environment. The expression of DIDO may be regulated by H3K4me3 and the inhibition of DIDO may lead to the down-regulation of CDK6 and CCND1. However, how DIDO interacts with CDK6 and CCND1 requires further study.
Cao et al. (2022) In leukemia, knock-down of the death inducer-obliterator gene would inhibit the proliferation of endothelial cells by inhibiting the expression of CDK6 and CCND1. PeerJ 10:e12832 https://doi.org/10.7717/peerj.12832
Unearthing soil arthropod diversity through DNA metabarcoding
DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna–the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
Young et al. (2022) Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 10:e12845 https://doi.org/10.7717/peerj.12845
Adult bonobos show no prosociality in both prosocial choice task and group service paradigm
Previous studies reported contrasting conclusions concerning bonobo prosociality, which are likely due to differences in the experimental design, the social dynamics among subjects and characteristics of the subjects themselves. Two hypotheses have been proposed to explain the occurrence of prosociality in animals: the cooperative breeding hypothesis and the self-domestication hypothesis. While the former predicts low levels of prosociality in bonobos because they are non-cooperative breeders, the latter predicts high levels of prosociality because self-domestication has been proposed to select for high levels of tolerance in this species. Here, we presented a group of thirteen bonobos with two platform food-provisioning tasks: the prosocial choice task (PCT) and the group service paradigm (GSP). The latter has so far never been applied to bonobos. To allow for free choice of participation and partner, we implemented both tasks in a group setting. Like in previous PCT studies, bonobos did not choose the prosocial option more often when a group member could benefit vs not benefit. In the GSP, where food provisioning is costly, only subadult bonobos showed a limited amount of food provisioning, which was much lower than what was previously reported for chimpanzees. In both experiments, adult subjects were highly motivated to obtain rewards for themselves, suggesting that bonobos behaved indifferently to the gains of group members. We suggest that previous positive food-provisioning prosociality results in bonobos are mainly driven by the behaviour of subadult subjects. The lack of prosociality in this study corresponds to the hypothesis that proactive food provisioning co-occurs with cooperative breeding and suggests that proactive prosociality might not be part of the self-domestication syndrome in bonobos.
Verspeek et al. (2022) Adult bonobos show no prosociality in both prosocial choice task and group service paradigm. PeerJ 10:e12849 https://doi.org/10.7717/peerj.12849
B-box containing protein 1 from Malus domestica (MdBBX1) is involved in the abiotic stress response
B-box proteins (BBXs), which act as transcription factors, mainly regulate photomorphogenesis. However, the molecular functions underlying the activity of plant BBXs in response to abiotic stress remain largely unclear. In this investigation, we found that a BBX from Malus domestica (MdBBX1) was involved in the response to various abiotic stresses. The expression of MdBBX1 was significantly upregulated in response to abiotic stresses and abscisic acid (ABA). Recombinant MdBBX1 increased stress tolerance in Escherichia coli cells. In addition, overexpression of MdBBX1 in Arabidopsis decreased sensitivity to exogenous ABA, resulting in a germination rate and root length that were greater and longer, respectively, than those of wild-type (WT) plants. Moreover, the expression of ABI5 was decreased in MdBBX1-overexpressing lines under ABA treatment. After salt and drought treatments, compared with the WT plants, the MdBBX1 transgenic plants displayed enhanced tolerance and had a higher survival rate. Furthermore, under salt stress, increased proline (PRO) contents, decreased levels of malondialdehyde (MDA), increased activity of antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX)) and decreased accumulation of reactive oxygen species (ROS) were observed in the MdBBX1-overexpressing plants. Overall, our results provide evidence that MdBBX1 might play a critical role in the regulation of abiotic stress tolerance by reducing the generation of ROS.
Dai et al. (2022) B-box containing protein 1 from Malus domestica (MdBBX1) is involved in the abiotic stress response. PeerJ 10:e12852 https://doi.org/10.7717/peerj.12852
Arbuscular mycorrhizal fungi increase crop yields by improving biomass under rainfed condition: a meta-analysis
Background Rainfed agriculture plays key role in ensuring food security and maintain ecological balance. Especially in developing areas, most grain food are produced rainfed agricultural ecosystem. Therefore, the increase of crop yields in rainfed agricultural ecosystem becomes vital as well as ensuring global food security. Methods The potential roles of arbuscular mycorrhizal fungi (AMF) in improving crop yields under rainfed condition were explored based on 546 pairs of observations published from 1950 to 2021. Results AMF inoculation increased 23.0% crop yields based on 13 popular crops under rainfed condition. Not only was crop biomass of shoot and root increased 24.2% and 29.6% by AMF inocula, respectively but also seed number and pod/fruit number per plant were enhanced markedly. Further, the effect of AMF on crop yields depended on different crop groups. AMF improved more yield of N-fixing crops than non-N-fixing crops. The effect of AMF changed between grain and non-grain crops with the effect size of 0.216 and 0.352, respectively. AMF inoculation enhances stress resistance and photosynthesis of host crop in rainfed agriculture. Conclusion AMF increased crop yields by enhancing shoot biomass due to the improvement of plant nutrition, photosynthesis, and stress resistance in rainfed field. Our findings provide a new view for understanding the sustainable productivity in rainfed agroecosystem, which enriched the theory of AMF functional diversity. This study provided a theoretical and technical way for sustainable production under rainfed agriculture.
Wu et al. (2022) Arbuscular mycorrhizal fungi increase crop yields by improving biomass under rainfed condition: a meta-analysis. PeerJ 10:e12861 https://doi.org/10.7717/peerj.12861
C. elegans as an in vivo model system for the phenotypic drug discovery for treating paraquat poisoning
Background Paraquat (PQ) is an effective and widely used herbicide and causes numerous fatalities by accidental or voluntary ingestion. However, neither the final cytotoxic mechanism nor effective treatments for PQ poisoning have been discovered. Phenotypic drug discovery (PDD), which does not rely on the molecular mechanism of the diseases, is having a renaissance in recent years owing to its potential to address the incompletely understood complexity of diseases. Herein, the C. elegans PDD model was established to pave the way for the future phenotypic discovery of potential agents for treating PQ poisoning. Methods C. elegans were treated with PQ-containing solid medium followed by statistical analysis of worm survival, pharyngeal pumping, and movement ability. Furthermore, coenzyme Q10 (CoQ10) was used to test the C. elegans model of PQ poisoning by measuring the levels of reactive oxygen species (ROS) and malondialdehyde (MDA), mitochondrial morphology, and worm survival rate. Additionally, we used the classic mice model of PQ intoxication to evaluate the validity of the C. elegans model of PQ poisoning by measuring the effect of CoQ10 as a potential antidote for PQ poisoning. Results In the C. elegans model of PQ poisoning, 5 mg/mL PQ increased the levels of ROS, MDA content, mitochondrial fragments, which significantly shortened the lifespan, while CoQ10 alleviated these phenotypes. In the mice model of PQ poisoning, CoQ10 increased the chance of survival in PQ poisoned mice while reducing ROS, MDA content in lung tissue and inhibiting PQ-induced lung edema. Moreover, CoQ10 alleviated the lung morphopathological changes induced by PQ. Conclusion Here we established a C. elegans model of PQ poisoning, whose validity was confirmed by the classic mice model of PQ intoxication.
Ji et al. (2022) C. elegans as an in vivo model system for the phenotypic drug discovery for treating paraquat poisoning. PeerJ 10:e12866 https://doi.org/10.7717/peerj.12866
BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma
Background Laryngeal squamous cell carcinoma (LSCC) remains one of the most common respiratory tumors worldwide. Baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5) is a member of the inhibitor-of-apoptosis protein family. BIRC5 plays an important role in various types of cell proliferation, differentiation, migration and invasion. However, the specific role of BIRC5 in LSCC remains unclear. Methods To provide a prognostic biomarker for LSCC, we screened the prognostic genes of LSCC via bioinformatics. PPI network and KEGG pathways were used to select hub genes. Clinical prognoses were performed using a Kaplan–Meier plotter and Cox proportional-hazard analysis. BIRC5 expression in LSCC tissues and cell lines were detected by RT-PCR, Western blot and Immunohistochemistry (IHC). Cell proliferation, cell cycle and cell apoptosis were detected with Cell Counting Kit-8 (CCK-8) and Flow Cytometry assay, respectively. Results Here, BIRC5 was strongly correlated with higher tumor grade and differentiation. BIRC5 was highly expressed in LSCC tissues when compared with normal tissues and increased expression of BIRC5 was associated with overall survival in LSCC patients. The suppression of BIRC5 induced cell apoptosis and cell cycle arrest, thereby inhibiting the proliferation of LSCC cells. The survival analysis confirmed that higher level of BIRC5 expression predicted poor prognosis of LSCC patients. BIRC5 may act as an oncogene of LSCC development and was suggested as a promising prognostic biomarker for LSCC.
Wang et al. (2022) BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma. PeerJ 10:e12871 https://doi.org/10.7717/peerj.12871
A revision of Plectanocotyle (Monogenea, Plectanocotylidae), with molecular barcoding of three species and the description of a new species from the streaked gurnard Chelidonichthys lastoviza off Algeria
Background The family Plectanocotylidae includes parasites of the gills of marine fish; although nine genera and about 20 species have been described, almost no molecular information is available. Putting aside Plectanocotyle elliptica Diesing, 1850, supposedly a parasite of the white perch Morone americana, never found again since its original description, two species were valid within Plectanocotyle Diesing, 1850 before this work: Plectanocotyle gurnardi (Van Beneden & Hesse, 1863) Llewellyn, 1941 and Plectanocotyle major Boudaya, Neifar & Euzet, 2006. Methods In this paper, we describe the third species of the genus Plectanocotyle and perform a comparative morphological and molecular analysis of the three species and of Triglicola obscura (Euzet & Suriano, 1974) Mamaev, 1976. Host fishes were also barcoded (COI) for confirmation of host identifications. Results Plectanocotyle lastovizae n. sp. is described from the gills of the streaked gurnard Chelidonichthys lastoviza collected off Algeria. The species is compared with specimens of Plectanocotyle cf. gurnardi (from C. lastoviza) from the same locality and P. major and T. obscura (both from the longfin gurnard C. obscurus). Molecules from Plectanocotyle cf. gurnardi could not be compared with P. gurnardi from the type-host and type-locality and we kept the status of the Mediterranean specimens as pending. Algeria is a new geographic record for P. major and T. obscura. Plectanocotyle lastovizae n. sp. is distinguished from the other species found in the Mediterranean by the measurements of clamps, number of testes, and COI sequences, with notable divergence (7.8–11.8%) from the other two species of the genus. Discussion We briefly present a list of currently known members of the family Plectanocotylidae, their biology and their hosts.
Ayadi et al. (2022) A revision of Plectanocotyle (Monogenea, Plectanocotylidae), with molecular barcoding of three species and the description of a new species from the streaked gurnard Chelidonichthys lastoviza off Algeria. PeerJ 10:e12873 https://doi.org/10.7717/peerj.12873
Differential modulation of behavior by infraslow activities of different brain regions
The oscillation phase of electroencephalograms (EEGs) is associated with behavioral performance. Several studies have demonstrated this association for relatively fast oscillations (>1 Hz); a similar finding has also been reported for slower oscillations, showing that behavioral performance is correlated with the phase of infraslow activity (ISA, 0.01–0.1 Hz) of electroencephalography (EEG). However, the previous study only investigated ISA in a local brain region using a relatively simple task (somatosensory discrimination task), leaving it difficult to determine how the EEG ISA for various brain regions is associated with behavioral performance. In addition, it is not known whether the EEG ISA phase modulates more complex behavioral task performance. In the present study, we analyzed the ISA of whole-brain EEG of participants performing various behaviors while playing video games. We found that behavior was associated with the specific oscillation phase of EEG ISA when that behavior was independent of other behaviors. In addition, we found that the EEG ISA oscillation phases modulating the different behaviors varied across brain regions. Our results suggest that the EEG ISA for different brain regions modulates behavioral performance in different ways and such modulation of EEG ISA can be generalized to diverse behaviors. This study may deepen the understanding of how EEG ISA modulates behavior and increases the applicability of EEG ISA.
Sihn et al. (2022) Differential modulation of behavior by infraslow activities of different brain regions. PeerJ 10:e12875 https://doi.org/10.7717/peerj.12875