Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes
Background Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation. Results In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily. Conclusions With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
Calero-Layana et al. (2022) Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes. PeerJ 10:e14431 https://doi.org/10.7717/peerj.14431
Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study
Background The aim of this study is to identify echocardiographic predictors of transient left ventricle dysfunction after pulmonary valve balloon dilatation (PVBD), in neonates with pulmonary valve stenosis (PVS) and atresia with intact septum (PAIVS) at birth. Methods The study includes patients admitted at the Bambino Gesù Children Hospital from January 2012 to January 2017. Clinical, echocardiographic and cardiac catheterization data before and after PVBD were retrospectively analyzed. Results Twenty-nine infants were included in the study (21 male and eight female). The median age was 5.8 ± 7.1 days. Eight patients developed transient LV dysfunction (three PAIVS and five PVS) and comparing data before and after the procedure, there was no difference in right ventricle geometrical and functional parameters except for evidence of at least moderate pulmonary valve regurgitation after PVBD. Conclusion Moderate to severe degree pulmonary valve regurgitation was significant associated to LV dysfunction (p < 0.05) in PVS and PAIVS patients.
D’Anna et al. (2022) Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study. PeerJ 10:e14056 https://doi.org/10.7717/peerj.14056
Modeling the response of Japanese quail to arginine intake
Background Understanding how Japanese quails respond to arginine intake has been an objective that previous studies have not fulfilled. The main responses to be quantified include the arginine requirement for maintenance (mg/kg0.67) and egg mass production (mg/g). Quantifying maintenance and production relationships are essential steps for predicting animal response. The current study aimed to describe how quails respond to arginine intake and determine arginine requirements for maintenance and egg production in Japanese quails. Methods The experiment was carried out in a completely randomized design, with seven treatments and seven replicates with individual birds as experimental units. The arginine levels were: 2.43, 3.64, 4.85, 6.07, 9.07, 12.13, and 14.56 g/kg. The experiment lasted for eight weeks. The variables analyzed were daily arginine intake, daily arginine deposition in eggs, and body weight. The data were analyzed using a mixed model, with the experimental unit being the random effect and the experimental levels of arginine as a fixed effect. When the effect of arginine levels was detected (P ≤ 0.05), saturation kinetics and an exponential model with four parameters (monomolecular) were adopted. ANOVA results indicated that dietary arginine levels significantly affected (P < 0.01) the analyzed variables. The formulation strategy of the experimental diets allowed amplitude in the dietary arginine levels, and according to bird responses, arginine was the limiting nutrient. Results The arginine requirement for body weight maintenance (BW0.67) was estimated to be 90 mg/kg BW0.67 by the monomolecular function. The requirement for egg mass (EM) production was estimated to be 25 mg/g per egg. A factorial model was parameterized as follows: daily arginine intake mg/bird = 90 × BW0.67 + 25 × EM ± 12 mg. The model was applied to data obtained from literature, and the resultant error was within the expected limit of 12 mg. The recommended daily arginine intake for the daily production of 11 g of egg and 180 g of BW was determined to be 304 mg/bird. The current study provides procedures that researchers can easily adopt.
Sousa et al. (2022) Modeling the response of Japanese quail to arginine intake. PeerJ 10:e14337 https://doi.org/10.7717/peerj.14337
A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace
Fossil chondrichthyan remains are mostly known from their teeth, scales or fin spines only, whereas their cartilaginous endoskeletons require exceptional preservational conditions to become fossilized. While most cartilaginous remains of Famennian (Late Devonian) chondrichthyans were found in older layers of the eastern Anti-Atlas, such fossils were unknown from the Hangenberg black shale (HBS) and only a few chondrichthyan teeth had been found therein previously. Here, we describe a Meckel’s cartilage from the Hangenberg black shale in Morocco, which is the first fossil cartilage from these strata. Since no teeth or other skeletal elements have been found in articulation, we used elliptical Fourier (EFA), principal component (PCA), and hierarchical cluster (HCA) analyses to morphologically compare it with 41 chondrichthyan taxa of different size and age and to evaluate its possible systematic affiliation. PCA and HCA position the new specimen closest to some acanthodian and elasmobranch jaws. Accordingly, a holocephalan origin was excluded. The jaw shape as well as the presence of a polygonal pattern, typical for tessellated calcified cartilage, suggest a ctenacanth origin and we assigned the new HBS Meckel’s cartilage to the order Ctenacanthiformes with reservations.
Greif et al. (2022) A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace. PeerJ 10:e14418 https://doi.org/10.7717/peerj.14418
Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis
Background and Aims A microscopic image has been used in cell analysis for cell type identification and classification, cell counting and cell size measurement. Most previous research works are tedious, including detailed understanding and time-consuming. The scientists and researchers are seeking modern and automatic cell analysis approaches in line with the current in-demand technology. Objectives This article provides a brief overview of a general cell and specific stem cell analysis approaches from the history of cell discovery up to the state-of-the-art approaches. Methodology A content description of the literature study has been surveyed from specific manuscript databases using three review methods: manuscript identification, screening, and inclusion. This review methodology is based on Prism guidelines in searching for originality and novelty in studies concerning cell analysis. Results By analysing generic cell and specific stem cell analysis approaches, current technology offers tremendous potential in assisting medical experts in performing cell analysis using a method that is less laborious, cost-effective, and reduces error rates. Conclusion This review uncovers potential research gaps concerning generic cell and specific stem cell analysis. Thus, it could be a reference for developing automated cells analysis approaches using current technology such as artificial intelligence and deep learning.
Mohamad Zamani et al. (2022) Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis. PeerJ 10:e14513 https://doi.org/10.7717/peerj.14513
OPA1 supports mitochondrial dynamics and immune evasion to CD8+ T cell in lung adenocarcinoma
Background Mitochondrial fusion and fission were identified to play key roles during multiple biology process. Thus, we aim to investigate the roles of OPA1 in mitochondria fusion and immune evasion of non-small cell lung cancer cells. Methods The transcriptional activation of genes related to mitochondrial dynamics was determined by using multi-omics data in lung adenocarcinoma (LUAD). We elucidated the molecular mechanism and roles of OPA1 promoting lung cancer through single-cell sequencing and molecular biological experiments. Results Here, we found that copy number amplification of OPA1 and MFN1 were co-occurring and synergistically activated in tumor epithelial cells in lung cancer tissues. Both of OPA1 and MFN1 were highly expressed in LUAD tumor tissues and OPA1 high expression was associated with poor prognosis. In terms of mechanism, the damaged mitochondria activated the apoptotic signaling pathways, inducing cell cycle arrest and cell apoptosis. More interestingly, OPA1 deficiency damaged mitochondrial dynamics and further blocked the respiratory function to increase the sensitivity of tumor epithelial to CD8+ T cells in non-small cell lung cancer. Conclusions Our study demonstrated the high co-occurrence of copy number amplification and co-expression of OPA1 and MFN1 in LUAD tissue, and further revealed the contribution of OPA1 in maintaining the mitochondria respiratory function and the ability of immune evasion to CD8+ T cells of LUAD.
Wang et al. (2022) OPA1 supports mitochondrial dynamics and immune evasion to CD8+ T cell in lung adenocarcinoma. PeerJ 10:e14543 https://doi.org/10.7717/peerj.14543
The diversity, evolution, and development of setal morphologies in bumble bees (Hymenoptera: Apidae: Bombus spp.)
Bumble bees are characterized by their thick setal pile that imparts aposematic color patterns often used for species-level identification. Like all bees, the single-celled setae of bumble bees are branched, an innovation thought important for pollen collection. To date no studies have quantified the types of setal morphologies and their distribution on these bees, information that can facilitate understanding of their adaptive ecological function. This study defines several major setal morphotypes in the common eastern bumble bee Bombus impatiens Cresson, revealing these setal types differ by location across the body. The positions of these types of setae are similar across individuals, castes, and sexes within species. We analyzed the distribution of the two most common setal types (plumose and spinulate) across the body dorsum of half of the described bumble bee species. This revealed consistently high density of plumose (long-branched) setae across bumble bees on the head and mesosoma, but considerable variation in the amount of metasomal plumosity. Variation on the metasoma shows strong phylogenetic signal at subgeneric and smaller group levels, making it a useful trait for species delimitation research, and plumosity has increased from early Bombus ancestors. The distribution of these setal types suggests these setae may serve several functions, including pollen-collecting and thermoregulatory roles, and probable mechanosensory functions. This study further examines how and when setae of the pile develop, evidence for mechanosensory function, and the timing of pigmentation as a foundation for future genetic and developmental research in these bees.
Hines et al. (2022) The diversity, evolution, and development of setal morphologies in bumble bees (Hymenoptera: Apidae: Bombus spp.). PeerJ 10:e14555 https://doi.org/10.7717/peerj.14555
Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing
Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.
Moll et al. (2022) Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing. PeerJ 10:e14567 https://doi.org/10.7717/peerj.14567
Physiological changes and gene responses during Ganoderma lucidum growth with selenium supplementation
Ganoderma lucidum basidiomycota is highly appreciated for its health and nutrition value. In the present study, Ganoderma lucidum was cultivated as selenium transformation carrier, and the physiological changes and gene responses by selenium supplementation were revealed through high-throughput RNA-Seq technology. As a result, selenium supplementation increased the stipe length and the cap size, but decreased the cap thickness of G. lucidum. Mineral salt supplementation could greatly promote the formation of triterpene acids and selenium in G. lucidum. The highest yield was gained in the treatment with selenium content of 200 µg/g. Subsequently, the tissues of G. lucidum at budding and mature stages in this treatment group were sampled for transcriptome analysis and compared to those of a control group without selenium supplementation. A total of 16,113 expressed genes were obtained from the transcriptome of G. lucidum, and GO-annotated unigenes were mainly involved in molecular functions and KEGG-annotated ones were highly expressed in ribosomal pathway. Furthermore, genes involved in carbon metabolism pathway were most promoted by selenium at budding stage of G. lucidum, while gene expression was the highest in the pathway of amino acid biosynthesis at mature stage of G. lucidum. Specially, selenium-related genes in G. lucidum, such as GL23172-G, GL29881-G and GL28298-G, played a regulatory role in oxidoreductase, antioxidant activity and tryptophan synthesis. The results provide a theoretical basis for further study of selenium-enriched mushrooms and aid to development of Se-enriched foodstuff and health products made from fungi.
Zhang et al. (2022) Physiological changes and gene responses during Ganoderma lucidum growth with selenium supplementation. PeerJ 10:e14488 https://doi.org/10.7717/peerj.14488
Influence of long-term participation in amateur sports on physical posture of teenagers
Aim The aim of this cross-sectional study was to explore the influence of long-term participating in amateur sports on body posture of school students. Methods A survey on sport participation was conducted on 1,658 volunteer students aged from 6 to 17 years in two primary schools and one meddle school in Tianjin city. The PA200LE body posture evaluation system and a SpineScanSH-115 electronic spine measuring instrument were used to assess the participants’ body posture. According to the survey results and against the inclusion and exclusion criteria, 1,124 eligible participants were divided into seven sport participation groups and seven age-matched control groups for statistical comparisons. Results Compared with the age-matched controls, the natural standing thoracic kyphosis angle of the swimming group (35.0 ± 9.5 VS 31.2 ± 8.5; t = − 2.560; p = 0.011) and the football group (34.6 ± 7.2 VS 31.9 ± 7.5; t = − 2.754; p = 0.006) were found to be significantly larger; the natural standing lumbar lordosis angle (−23.0 ± 11.0 VS −27.0 ± 11.1; t = 0.344; p = 0.024) and the upright sitting lumbar lordosis angle (−11.7 ± 8.4 VS −15.2 ± 12.3; t = 5.738; p = 0.030) of the swimming group was significantly smaller; the upright sitting thoracic kyphosis angle of the running group (25.1 ± 9.3 VS 22.6 ± 9.9; t = − 1.970; p = 0.050) was significantly larger; the upright sitting thoracic kyphosis angle (23.9 ± 8.9 VS 27.0 ± 7.6; t = 2.096; p = 0.038), the learning position thoracic kyphosis angle (31.0 ± 8.6 VS 37.1 ± 8.9; t = 3.076; p = 0.003), the shoulder level (−1.3 ± 2.1 VS 0.0 ± 2.5; t = 2.389; p = 0.019) and waist level (−1.2 ± 1.7 VS −0.3 ± 1.7; t = 2.511; p = 0.013) of the table tennis group were significantly smaller. Conclusions The results showed that long-term participation in recreational sports training had an impact on the physical posture of adolescents.
Huang et al. (2022) Influence of long-term participation in amateur sports on physical posture of teenagers. PeerJ 10:e14520 https://doi.org/10.7717/peerj.14520
The effect of conventional and sustainable agricultural management practices on carbon and water fluxes in a Mexican semi-arid region
Background Agriculture is essential for food security. However, conventional agriculture alters the water and carbon cycle and soil properties. We investigated the effect of conventional management (CM) and sustainable management (SM) on the carbon and water cycle in crops of nopal (Np) and wheat (Wh). Methods A micrometeorological eddy covariance tower was installed to measure water use through evapotranspiration (ET) and the net exchange of CO2 during the crop’s development. Gross primary productivity (GPP), water use efficiency (WUE), and soil properties were obtained. Results The results showed that both agricultural managements influenced the carbon flux of the ecosystem, with a lower GPP and Reco in the nopal field (1.85 and 0.99 mmol C m−2 s−1, respectively), compared to the wheat field (6.34 and 1.8 mmol C m−2 s−1, respectively). It was mainly attributed to the metabolic plant differences, phenological stages, and wheat biomass developed during the winter. On the other hand, the accumulated ET in the SM-Wh plots was lower than SM-Np. Therefore, the crops subjected to sustainable practices use water more efficiently with 1.42 and 1.03 g C m−3 H2O for nopal and wheat, respectively. In regard to soil properties, it was observed that tillage alters microbial activity affecting organic matter and carbon. It can be concluded that the differences in agricultural management for both crops altered the carbon and water cycle and soil quality. In addition, implementing good agricultural practices allows more efficient use of water by the plant, higher retention of water in the soil, and less ET.
Guillen-Cruz et al. (2022) The effect of conventional and sustainable agricultural management practices on carbon and water fluxes in a Mexican semi-arid region. PeerJ 10:e14542 https://doi.org/10.7717/peerj.14542
Knockdown of hsa_circ_0008922 inhibits the progression of glioma
Background A glioma is a tumor originating from glial cells in the central nervous system. Although significant progress has been made in diagnosis and treatment, most high-grade glioma patients are prone to recurrence. Therefore, molecular targeted therapy may become a new direction for adjuvant therapy in glioma. In recent years, many studies have revealed that circular RNA (circRNA) may play an important role in the occurrence and development of many tumors including gliomas. Our previous study found that the expression of hsa_circ_0008922 was up-regulated in glioma tissues upon RNA sequencing. The biological mechanism of circ_0008922 is still unreported in gliomas. Therefore, in this study, we preliminarily outlined the expression of hsa_circ_0008922 in glioma and explored its biological functions. Methods The expression of hsa_circ_0008922 in forty glioma tissues and four glioma cell lines (A172, U251, SF763 and U87) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). The correlation between hsa_circ_0008922 expression and clinicopathological features of glioma patients was evaluated by Fisher’s exact test. To understand the potential function of hsa_circ_0008922 in glioma, we constructed small interfering RNA (siRNA) to hsa_circ_0008922 to downregulate its expression in glioma cell lines A172 and U251. With these hsa_circ_0008922 downregulated cells, a series of assays were carried out as follows. Cell proliferation was detected by CCK8 assay, migration and invasion were determined by wound healing assay and transwell assay, respectively. Colony formation ability was evaluated by plate clonogenic assay. Moreover, flow cytometry combined with Western blot was performed to analyze apoptosis status and the expression of apoptotic related proteins (caspase 3 and caspase 9). Finally, the possible biological pathways and potential miRNA targets of hsa_circ_0008922 were predicted by bioinformatics. Results We found that the expression of hsa_circ_0008922 in glioma tissues was 3.4 times higher than that in normal tissues. The expression of has_circ_0008922 was correlated with WHO tumor grade. After down-regulating the expression of hsa_circ_0008922, malignant biological behavior of glioma cells was inhibited, such as cell proliferation, colony formation, migration, and invasion. At the same time, it also induced apoptosis of glioma cells. Predicted analysis by bioinformatics demonstrated that hsa_circ_0008922 may be involved in tumor-related pathways by acting as a molecular sponge for multiple miRNAs (hsa-let-7e-5p, hsa-miR-506-5p, hsa-let-7b-5p, hsa-let-7c-5p and hsa-let-7a-5p). Finally, we integrated our observation to build a circRNA-miRNA-mRNA predictive network.
Xue et al. (2022) Knockdown of hsa_circ_0008922 inhibits the progression of glioma. PeerJ 10:e14552 https://doi.org/10.7717/peerj.14552
Effects of calcium on cell wall metabolism enzymes and expression of related genes associated with peel creasing in Citrus fruits
Fruit peel creasing is a serious pre-harvest physiological disorder in citrus, influencing fruit quality, storage, and yield. Four- and eight-year-old ‘Hongjiang’ oranges grafted onto Canton lemon rootstocks were treated with calcium and calcium inhibitors, respectively, to study the effects of different treatments on fruit creasing rate, mechanical properties of the peel, cell wall metabolism enzyme activities, and the expression of related genes. Foliar application of 0.5% calcium nitrate significantly reduced the fruit creasing rate, while treatment with EGTA and LaCl3, inhibitors of calcium uptake, increased the fruit creasing rate; But the effect of calcium nitrate treatment on changing the mechanical properties of pericarp and inhibiting the activity of hydrolase (PG, Cx and PE) was not very significant. Furthermore, it was observed that the expression levels of genes (PG, Cx, and PE) encoding cell wall-degrading enzymes were significantly lower in the normal fruit peel than in the creased fruit peel. Meanwhile, the expression levels of PG, Cx, and PE were higher in the peel of shaded fruit than in the peel of exposed fruit. During the high incidence period of fruit creasing, calcium nitrate treatment down-regulated the expression of PG, Cx, and PE, while EGTA treatment up-regulated the expression of these genes. In conclusion, foliar spraying of calcium nitrate at the fruit rapid enlargement stage can increase the Ca content in the peel of ‘Hongjiang’ orange and significantly suppress the expression of cell wall degrading enzymes genes (PG, PE and Cx) in ‘Hongjiang’ orange peel during the high occurrence period of fruit creasing, resulting in reducing the occurrence of fruit creasing and cracking.
Huai et al. (2022) Effects of calcium on cell wall metabolism enzymes and expression of related genes associated with peel creasing in Citrus fruits. PeerJ 10:e14574 https://doi.org/10.7717/peerj.14574
Opening the black box of bird-window collisions: passive video recordings in a residential backyard
Collisions with windows on buildings are a major source of bird mortality. The current understanding of daytime collisions is limited by a lack of empirical data on how collisions occur in the real world because most data are collected by recording evidence of mortality rather than pre-collision behaviour. Based on published literature suggesting a causal relationship between bird collision risk and the appearance of reflections on glass, the fact that reflections vary in appearance depending on viewing angle, and general principles of object collision kinematics, we hypothesized that the risk and lethality of window collisions may be related to the angle and velocity of birds’ flight. We deployed a home security camera system to passively record interactions between common North American bird species and residential windows in a backyard setting over spring, summer and fall seasons over 2 years. We captured 38 events including 29 collisions and nine near-misses in which birds approached the glass but avoided impact. Only two of the collisions resulted in immediate fatality, while 23 birds flew away immediately following impact. Birds approached the glass at variable flight speeds and from a wide range of angles, suggesting that the dynamic appearance of reflections on glass at different times of day may play a causal role in collision risk. Birds that approached the window at higher velocity were more likely to be immediately killed or stunned. Most collisions were not detected by the building occupants and, given that most birds flew away immediately, carcass surveys would only document a small fraction of window collisions. We discuss the implications of characterizing pre-collision behaviour for designing effective collision prevention methods.
Samuels et al. (2022) Opening the black box of bird-window collisions: passive video recordings in a residential backyard. PeerJ 10:e14604 https://doi.org/10.7717/peerj.14604
Palaeoecology of the Hiraiso Formation (Miyagi Prefecture, Japan) and implications for the recovery following the end-Permian mass extinction
The Hiraiso Formation of northeast Japan represents an important and under-explored archive of Early Triassic marine ecosystems. Here, we present a palaeoecological analysis of its benthic faunas in order to explore the temporal and spatial variations of diversity, ecological structure and taxonomic composition. In addition, we utilise redox proxies to make inferences about the redox state of the depositional environments. We then use this data to explore the pace of recovery in the Early Triassic, and the habitable zone hypothesis, where wave aerated marine environments are thought to represent an oxygenated refuge. The age of the Hiraiso Formation is equivocal due to the lack of key biostratigraphical index fossils, but new ammonoid finds in this study support an early Spathian age. The ichnofossils from the Hiraiso Formation show an onshore-offshore trend with high diversity and relatively large faunas in offshore transition settings and a low diversity of small ichnofossils in basinal settings. The body fossils do not, however, record either spatial or temporal changes, because the shell beds represent allochthonous assemblages due to wave reworking. The dominance of small burrow sizes, presence of key taxa including Thalassinoides, Rhizocorallium and Holocrinus, presence of complex trace fossils, and both erect and deep infaunal tiering organisms suggests that the benthic fauna represents an advanced stage of ecological recovery for the Early Triassic, but not full recovery. The ecological state suggests a similar level of ecological complexity to late Griesbachian and Spathian communities elsewhere, with the Spathian marking a globally important stage of recovery following the mass extinction. The onshore-offshore distribution of the benthic faunas supports the habitable zone hypothesis. This gradient is, however, also consistent with onshore-offshore ecological gradients known to be controlled by oxygen gradients in modern tropical and subtropical settings. This suggests that the habitable zone is not an oxygenated refuge that is only restricted to anoxic events. The lack of observed full recovery is likely a consequence of a persistent oxygen-limitation (dysoxic conditions), hot Early Triassic temperatures and the lack of a steep temperature/water-depth gradient within the habitable zone.
Foster et al. (2022) Palaeoecology of the Hiraiso Formation (Miyagi Prefecture, Japan) and implications for the recovery following the end-Permian mass extinction. PeerJ 10:e14357 https://doi.org/10.7717/peerj.14357
You are what you eat: fungal metabolites and host plant affect the susceptibility of diamondback moth to entomopathogenic fungi
Background Beauveria are entomopathogenic fungi of a broad range of arthropod pests. Many strains of Beauveria have been developed and marketed as biopesticides. Beauveria species are well-suited as the active ingredient within biopesticides because of their ease of mass production, ability to kill a wide range of pest species, consistency in different conditions, and safety with respect to human health. However, the efficacy of these biopesticides can be variable under field conditions. Two under-researched areas, which may limit the deployment of Beauveria-based biopesticides, are the type and amount of insecticidal compounds produced by these fungi and the influence of diet on the susceptibility of specific insect pests to these entomopathogens. Methods To understand and remedy this weakness, we investigated the effect of insect diet and Beauveria-derived toxins on the susceptibility of diamondback moth larvae to Beauveria infection. Two New Zealand-derived fungal isolates, B. pseudobassiana I12 Damo and B. bassiana CTL20, previously identified with high virulence towards diamondback moth larvae, were selected for this study. Larvae of diamondback moth were fed on four different plant diets, based on different types of Brassicaceae, namely broccoli, cabbage, cauliflower, and radish, before their susceptibility to the two isolates of Beauveria was assessed. A second experiment assessed secondary metabolites produced from three genetically diverse isolates of Beauveria for their virulence towards diamondback moth larvae. Results Diamondback moth larvae fed on broccoli were more susceptible to infection by B. pseudobassiana while larvae fed on radish were more susceptible to infection by B. bassiana. Furthermore, the supernatant from an isolate of B. pseudobassiana resulted in 55% and 65% mortality for half and full-strength culture filtrates, respectively, while the filtrates from two other Beauveria isolates, including a B. bassiana isolate, killed less than 50% of larvae. This study demonstrated different levels of susceptibility of the insects raised on different plant diets and the potential use of metabolites produced by Beauveria isolates in addition to their conidia.
Soth et al. (2022) You are what you eat: fungal metabolites and host plant affect the susceptibility of diamondback moth to entomopathogenic fungi. PeerJ 10:e14491 https://doi.org/10.7717/peerj.14491
Identification and validation of a ferroptosis-related lncRNA signature to robustly predict the prognosis, immune microenvironment, and immunotherapy efficiency in patients with clear cell renal cell carcinoma
Background Ferroptosis is a new type of iron- and reactive oxygen species-dependent cell death, studies on ferroptosis-related long noncoding RNAs (FerLncRNAs) in clear cell renal cell carcinoma (ccRCC) are limited. The purpose of this study was to investigate the potential prognostic value of FerLncRNAs and their relationship with the immune microenvironment and immunotherapy response of ccRCC. Methods RNA sequencing data of 526 patients with ccRCC were downloaded from The Cancer Genome Atlas (TCGA) database. The patients with ccRCC in TCGA were randomly divided (1:1) into a training and testing cohort. ICGC and GEO databases were used for validation. Screening for FerLncRNAs was performed using Pearson’s correlation analysis with the reported ferroptosis-related genes. A FerLncRNA signature was constructed using univariate, LASSO, and multivariate Cox regression analyses in the training cohort. Internal and external datasets were performed to verify the FRlncRNA signature. Four major FRlncRNAs were verified through in vitro experiment. Results We identified seven FerLncRNAs (LINC00894, DUXAP8, LINC01426, PVT1, PELATON, LINC02609, and MYG1-AS1), and established a risk signature and nomogram for predicting the prognosis of ccRCC. Four major FRlncRNAs were verified with the prognosis of ccRCC in the GEPIA and K-M Plotter databases, and their expressions were validated by realtime PCR. The risk signature can also effectively reflect the immune environment, immunotherapy response and drug sensitivity of ccRCC. These FRlncRNAs have great significance to the implementation of individualized treatment and disease monitoring of ccRCC patients.
Ju et al. (2022) Identification and validation of a ferroptosis-related lncRNA signature to robustly predict the prognosis, immune microenvironment, and immunotherapy efficiency in patients with clear cell renal cell carcinoma. PeerJ 10:e14506 https://doi.org/10.7717/peerj.14506
Are children and dogs best friends? A scoping review to explore the positive and negative effects of child-dog interactions
Personal wellbeing is greatly influenced by our childhood and adolescence, and the relationships formed during those phases of our development. The human-dog bond represents a significant relationship that started thousands of years ago. There is a higher prevalence of dog ownership around the world, especially in households including children. This has resulted in a growing number of researchers studying our interactions with dogs and an expanding evidence base from the exploration of child-dog interactions. We review the potential effects of child-dog interactions on the physical, mental, and social wellbeing of both species. A search of the SCOPUS database identified documents published between January 1980 and April 2022. Filtering for key inclusion criteria, duplicate removals, and inspecting the references of these documents for additional sources, we reviewed a total of 393 documents, 88% of which were scientific articles. We were able to define the numerous ways in which children and dogs interact, be it neutral (e.g., sharing a common area), positive (e.g., petting), or negative (e.g., biting). Then, we found evidence for an association between childhood interaction with dogs and an array of benefits such as increased physical activities, a reduction of stress, and the development of empathy. Nonetheless, several detrimental outcomes have also been identified for both humans and dogs. Children are the most at-risk population regarding dog bites and dog-borne zoonoses, which may lead to injuries/illness, a subsequent fear of dogs, or even death. Moreover, pet bereavement is generally inevitable when living with a canine companion and should not be trivialized. With a canine focus, children sometimes take part in caretaking behaviors toward them, such as feeding or going for walks. These represent opportunities for dogs to relieve themselves outside, but also to exercise and socialize. By contrast, a lack of physical activity can lead to the onset of obesity in both dogs and children. Dogs may present greater levels of stress when in the presence of children. Finally, the welfare of assistance, therapy, and free-roaming dogs who may interact with children remains underexplored. Overall, it appears that the benefits of child-dog interactions outweigh the risks for children but not for dogs; determination of the effects on both species, positive as well as negative, still requires further development. We call for longitudinal studies and cross-cultural research in the future to better understand the impact of child-dog interactions. Our review is important for people in and outside of the scientific community, to pediatricians, veterinarians, and current or future dog owners seeking to extend their knowledge, and to inform future research of scientists studying dogs and human-animal interactions.
Giraudet et al. (2022) Are children and dogs best friends? A scoping review to explore the positive and negative effects of child-dog interactions. PeerJ 10:e14532 https://doi.org/10.7717/peerj.14532
Belief in just deserts regarding individuals infected with COVID-19 in Japan and its associations with demographic factors and infection-related and socio-psychological characteristics: a cross-sectional study
Prejudice related to the coronavirus disease 2019 (COVID-19) is a social issue worldwide. A possible psychological factor that promotes prejudice is the belief in just deserts (BJD) regarding individuals infected with COVID-19 (i.e., the belief that the infected individual deserves to be infected). The BJD is based on the belief in immanent justice. It is reportedly higher in Japan than in other countries. Therefore, we conducted a cross-sectional study to investigate the BJD among Japanese individuals and clarify its associations with demographic factors or infection-related and socio-psychological characteristics. To this end, we conducted an online questionnaire survey in Japan from August 7–8, 2020, with 1,207 respondents aged 20–69 years. We performed screening to exclude inappropriate responses. We investigated the association between the BJD and demographic factors such as gender and age. We also investigated the association between the BJD and infection-related and socio-psychological characteristics, including risk perception of COVID-19 infection and human rights restrictions (i.e., the degree of agreement with government restrictions on individuals’ behavior during emergencies). Among the surveyed items, human rights restrictions showed a strong association with BJD, followed by risk perception of COVID-19 infection. Men had a slightly higher BJD than women. Our study is significant in that it is the first to investigate the items associated with the BJD, thereby providing foundational information for revising individual perceptions of justice related to COVID-19 and solving prejudice-related issues.
Murakami et al. (2022) Belief in just deserts regarding individuals infected with COVID-19 in Japan and its associations with demographic factors and infection-related and socio-psychological characteristics: a cross-sectional study. PeerJ 10:e14545 https://doi.org/10.7717/peerj.14545
Does plastic type matter? Insights into non-indigenous marine larvae recruitment under controlled conditions
Marine plastic debris (MPD) are a global threat to marine ecosystems. Among countless ecosystem impacts, MPD can serve as a vector for marine ‘hitchhikers’ by facilitating transport and subsequent spread of unwanted pests and pathogens. The transport and spread of these non-indigenous species (NIS) can have substantial impacts on native biodiversity, ecosystem services/functions and hence, important economic consequences. Over the past decade, increasing research interest has been directed towards the characterization of biological communities colonizing plastic debris, the so called Plastisphere. Despite remarkable advances in this field, little is known regarding the recruitment patterns of NIS larvae and propagules on MPD, and the factors influencing these patterns. To address this knowledge gap, we used custom-made bioassay chambers and ran four consecutive bioassays to compare the settlement patterns of four distinct model biofouling organisms’ larvae, including the three notorious invaders Crassostrea gigas, Ciona savignyi and Mytilus galloprovincialis, along with one sessile macro-invertebrate Spirobranchus cariniferus, on three different types of polymers, namely Low-Linear Density Polyethylene (LLDPE), Polylactic Acid (PLA), Nylon-6, and a glass control. Control bioassay chambers were included to investigate the microbial community composition colonizing the different substrates using 16S rRNA metabarcoding. We observed species-specific settlement patterns, with larvae aggregating on different locations on the substrates. Furthermore, our results revealed that C. savignyi and S. cariniferus generally favoured Nylon and PLA, whereas no specific preferences were observed for C. gigas and M. galloprovincialis. We did not detect significant differences in bacterial community composition between the tested substrates. Taken together, our results highlight the complexity of interactions between NIS larvae and plastic polymers. We conclude that several factors and their potential interactions influenced the results of this investigation, including: (i) species-specific larval biological traits and ecology; (ii) physical and chemical composition of the substrates; and (iii) biological cues emitted by bacterial biofilm and the level of chemosensitivity of the different NIS larvae. To mitigate the biosecurity risks associated with drifting plastic debris, additional research effort is critical to effectively decipher the mechanisms involved in the recruitment of NIS on MPD.
Environmental Contamination and Remediation
Audrézet et al. (2022) Does plastic type matter? Insights into non-indigenous marine larvae recruitment under controlled conditions. PeerJ 10:e14549 https://doi.org/10.7717/peerj.14549
Metabolomics study of flavonoids in Coreopsis tinctoria of different origins by UPLC–MS/MS
To analyze the flavonoids in Coreopsis tinctoria and compare the differences in flavonoids among C. tinctoria of different origins, the chemical composition of C. tinctoria capitulum was analyzed by ultra-high-performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and the flavonoid metabolites were analyzed and identified based on their retention time, mass-to-charge ratio and fragment ions in the UPLC-QTOF-MS matrix. Capitulum samples of C. tinctoria were collected from three locations in the Xinjiang region at different altitudes. A total of 204 flavonoid compounds were identified, and 31 different flavonoid metabolites were then identified from flowers of C. tinctoria of different origins. Further analysis of these 31 significantly accumulated metabolites identified seven flavonoid metabolites, namely, homoplantaginin, kaempferol, quercetin, isorhamnetin, avicularin, quercetin 3-O-(6′-galloyl)-β-D-galactopyranoside and isorhamnetin 3-O-glucoside, with high accumulation only in sample collected from Tashkurgan Tajik (TX) and low expression in sample collected from Yutian County (YT) and Shaya County (SY). Moreover, 7,4′-dihydroxyflavone and 4,4′-dimethoxychalcone showed high accumulation only in SY, and afzelin was specifically highly accumulated in YT. In addition, the identified flavonoid metabolites were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and key pathways that might regulate the biosynthesis of these flavonoid compounds were analyzed. These findings provide key information for research on flavonoids and their biosynthesis in C. tinctoria and will provide a theoretical basis for studying the herbal quality and origin of C. tinctoria.
Wang et al. (2022) Metabolomics study of flavonoids in Coreopsis tinctoria of different origins by UPLC–MS/MS. PeerJ 10:e14580 https://doi.org/10.7717/peerj.14580
Genetic analysis of DNA methylation in dyslipidemia: a case-control study
Background Coronary heart disease has become the leading cause of death in developed countries, and dyslipidemia is closely associated with the risk of cardiovascular disease. Dyslipidemia is caused by the abnormal regulation of several genes and signaling pathways, and dyslipidemia is influenced mainly by genetic variation. AMFR, FBXW7, INSIG1, INSIG2, and MBTPS1 genes are associated with lipid metabolism. In a recent GWAS study, the GRINA gene has been reported to be associated with dyslipidemia, but its molecular mechanism has not been thoroughly investigated. The correlation between the DNA methylation of these genes and lipid metabolism has not been studied. This study aimed to examine the relationship between the DNA methylation of these genes and the risk of dyslipidemia by comparing the methylation levels of dyslipidemia and control samples. Methods A case-control research method was used in this study. The patient’s blood samples were collected at the Heart Center of the First Affiliated Hospital of Xinjiang Medical University. In the Xinjiang Han population, 100 cases of hyperlipidemia and 80 cases of the control group were selected. The two groups were age and gender-matched. Quantitative methylation analysis of CpG sites in the gene promoter regions of six genes was performed by Solexa high-throughput sequencing. Results The DNA methylation levels of 23 CpG sites in six genes were shown to be associated with hyperlipidemia, and a total of 20 DNA methylation haplotypes showed statistically significant differences between the two groups. When compared with the control group, the dyslipidemia group had significantly higher levels of methylation in the GRINA gene (2.68 vs 2.36, P = 0.04). Additionally, we also discovered a significant methylation haplotype of GRINA (P = 0.017). Conclusion The findings of this study reveal that the DNA methylation of GRINA increases the risk for dyslipidemia in humans.
Liu et al. (2022) Genetic analysis of DNA methylation in dyslipidemia: a case-control study. PeerJ 10:e14590 https://doi.org/10.7717/peerj.14590
On the improvement of heart rate prediction using the combination of singular spectrum analysis and copula-based analysis approach
In recent years, many people have been working from home due to the exceptional circumstances concerning the coronavirus disease 2019 (COVID-19) pandemic. It has also negatively influenced general health and quality of life. Therefore, physical activity has been gaining much attention in preventing the spread of Severe Acute Respiratory Syndrome Coronavirus. For planning an effective physical activity for different clients, physical activity intensity and load degree needs to be appropriately adjusted depending on the individual’s physical/health conditions. Heart rate (HR) is one of the most critical health indicators for monitoring exercise intensity and load degree because it is closely related to the heart rate. Heart rate prediction estimates the heart rate at the next moment based on now and other influencing factors. Therefore, an accurate short-term HR prediction technique can deliver efficient early warning for human health and decrease the happening of harmful events. The work described in this article aims to introduce a novel hybrid approach to model and predict the heart rate dynamics for different exercises. The results indicate that the combination of singular spectrum analysis (SSA) and the Clayton Copula model can accurately predict HR for the short term.
Namazi (2022) On the improvement of heart rate prediction using the combination of singular spectrum analysis and copula-based analysis approach. PeerJ 10:e14601 https://doi.org/10.7717/peerj.14601
Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic
Soil salinity has been an increasing problem worldwide endangering crop production and human food security. It is an ideal strategy to excavate stress resistant genes and develop salt tolerant crops. NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors have been demonstrated to be involved in salt stress response. However, relevant studies have not been observed in garlic, an important vegetable consumed in the world. In this study, a total of 46 AsNAC genes encoding NAC proteins were identified in garlic plant by transcriptome data. Phylogenetic analysis showed that the examined AsNAC proteins were clustered into 14 subgroups. Motif discovery revealed that the conserved domain region was mainly composed of five conserved subdomains. Most of the genes selected could be induced by salt stress in different tissues, indicating a potential role in salt stress response. Further studies may focus on the molecular mechanisms of the AsNAC genes in salt stress response. The results of the current work provided valuable resources for researchers aimed at developing salt tolerant crops.
Wang et al. (2022) Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic. PeerJ 10:e14602 https://doi.org/10.7717/peerj.14602
Using Peromyscus leucopus as a biomonitor to determine the impact of heavy metal exposure on the kidney and bone mineral density: results from the Tar Creek Superfund Site
Background Human population growth and industrialization contribute to increased pollution of wildlife habitats. Heavy metal exposure from industrial and environmental sources is still a threat to public health, increasing disease susceptibility. In this study, I investigated the effects of heavy metals (cadmium (Cd), lead (Pb), and zinc (Zn)) on kidney and bone density. Objective This study aims to determine the concentrations of Cd, Pb, and Zn in soil and compare them to the levels of the same metals in Peromyscus leucopus kidney tissue. Furthermore, the study seeks to investigate the impact of heavy metals on bone density and fragility using the fourth lumbar vertebra (L4) of P. leucopus. Methods Cd, Pb, and Zn concentrations in soil specimens collected from Tar Creek Superfund Site (TCSFS), Beaver Creek (BC), and two reference sites (Oologah Wildlife Management Area (OWMA) and Sequoyah National Wildlife Refuge (SNWR)). Heavy metal concentrations were analyzed using inductively coupled plasma-mass spectroscopy (ICP-MS). Micro-computed tomography (µCT) was used to assess the influence of heavy metals on bone fragility and density. Results On the one hand, soil samples revealed that Pb is the most common pollutant in the sediment at all of the investigated sites (the highest contaminated site with Pb was TCSFS). Pb levels in the soil of TCSFS, BC, OWMA, and SNWR were found to be 1,132 ± 278, 6.4 ± 1.1, and 2.3 ± 0.3 mg/kg in the soil of TCSFS, BC and OWMA and SNWR, respectively. This is consistent with the fact that Pb is one of the less mobile heavy metals, causing its compounds to persist in soils and sediments and being barely influenced by microbial decomposition. On the other hand, the kidney samples revealed greater Cd levels, even higher than those found in the soil samples from the OWMA and SNWR sites. Cd concentrations in the kidney specimens were found to be 4.62 ± 0.71, 0.53 ± 0.08, and 0.53 ± 0.06 µg/kg, respectively. In addition, micro-CT analysis of L4 from TCSFS showed significant Pearson’s correlation coefficients between Cd concentrations and trabecular bone number (−0.67, P ≤ 0.05) and trabecular separation (0.72, P ≤ 0.05). The results showed no correlation between bone parameters and metal concentrations at reference sites. This study is one of the few that aims to employ bone architecture as an endpoint in the field of biomonitoring. Furthermore, this study confirmed some earlier research by demonstrating substantial levels of heavy metal contamination in soil samples, kidney samples, and P. leucopus L4 trabecular bone separations from TCSFS. Moreover, this is the first study to record information regarding bone microarchitecture parameters in P. leucopus in North America.
Elturki (2022) Using Peromyscus leucopus as a biomonitor to determine the impact of heavy metal exposure on the kidney and bone mineral density: results from the Tar Creek Superfund Site. PeerJ 10:e14605 https://doi.org/10.7717/peerj.14605
Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds
Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur–bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most complete morphological assessment of the postcranial skeleton of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.
Benito et al. (2022) Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds. PeerJ 10:e13919 https://doi.org/10.7717/peerj.13919
Guttigomphus avilionis gen. et sp. nov., a trirachodontid cynodont from the upper Cynognathus Assemblage Zone, Burgersdorp Formation of South Africa
The Burgersdorp Formation of South Africa is a richly fossiliferous rock sequence at the top of the Permian–Triassic Beaufort Group and is known for its abundance of Early–Middle Triassic vertebrate remains, particularly cynodonts. Fossils from the Burgersdorp Formation are referred biostratigraphically to the Cynognathus Assemblage Zone (CAZ), which is further divided into three subzones: Langbergia-Garjainia, Trirachodon-Kannemeyeria, and Cricodon-Ufudocyclops. Each subzone is characterised by the presence of a distinct species of trirachodontid, a group of gomphodont cynodonts found relatively abundantly throughout the CAZ, with the lower two subzones characterised by the medium-sized trirachodontids Langbergia and Trirachodon. The uppermost part of the formation, the Cricodon-Ufudocyclops subzone, yields trirachodontids of larger size. The majority of these trirachodontid specimens have previously been referred to Cricodon metabolus, a taxon also known from the Manda Beds of Tanzania and the Ntawere Formation of Zambia. Here we identify one of the specimens (BP/1/5538) previously referred to Cricodon as a new taxon, Guttigomphus avilionis. Guttigomphus can be distinguished from other gomphodont cynodonts by features of the upper postcanine teeth, such as an asymmetric crown in occlusal view (crown narrower along the lingual margin than the labial). Our phylogenetic analysis recovers Guttigomphus as a basal member of Trirachodontidae, outside of the clade including Cricodon, Langbergia and Trirachodon.
Rayner et al. (2022) Guttigomphus avilionis gen. et sp. nov., a trirachodontid cynodont from the upper Cynognathus Assemblage Zone, Burgersdorp Formation of South Africa. PeerJ 10:e14355 https://doi.org/10.7717/peerj.14355
Physical fitness changes in adolescents due to social distancing during the coronavirus disease pandemic in Korea
Background At least 60 min of moderate-intensity physical activity per day is recommended for physical and mental health of adolescents. Schools are one of the most suitable places for promoting students’ health as it is a place where vigorous physical activity occurs. However, the physical activity of students is threatened because schools are closed worldwide owing to the coronavirus disease (COVID-19) outbreak in 2019. Therefore, this study aimed to analyze the physical fitness changes in 27,782 Korean adolescents during the pandemic and present alternative education and health policies to the school. Methods We included 29,882 middle school students (age: 13–15 years; males: 14,941, females: 12,841) in Korea from 2019 to 2021 . Participants’ physical fitness at school was measured using the physical activity promotion system (PAPS) manual developed to measure students’ physical fitness. Physical fitness variables included body mass index (BMI), 20 m shuttle run, handgrip strength, sit-and-reach, and 50 m run. Results The COVID-19 pandemic has had a negative impact on the BMI and cardiorespiratory endurance of Korean middle school students. Specifically, male students’ BMI increased, while body composition, cardiorespiratory endurance, and grip strength decreased significantly. Female students showed significant decreases in BMI and sit-and-reach test scores. It is clear that the physical fitness level of adolescents decreased by a greater degree after the COVID-19 pandemic than before, and the decrease in the physical fitness level of male students was noticeable. Therefore, a lesson strategy should be prepared that considers the contents and methods of physical education classes to improve the physical fitness level of male and female adolescents. Conclusions Fitness-based classes suitable for online methods should be urgently added as alternative physical education classes to prepare for the second COVID-19 outbreak. In addition, it is necessary to create an environment in which physical activity is a possibility in physical education classes, in any situation using artificial intelligence and virtual reality.
Lee et al. (2022) Physical fitness changes in adolescents due to social distancing during the coronavirus disease pandemic in Korea. PeerJ 10:e14494 https://doi.org/10.7717/peerj.14494
Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers
Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types.
Lü et al. (2022) Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers. PeerJ 10:e14512 https://doi.org/10.7717/peerj.14512
Metal tolerance capacity and antioxidant responses of new Salix spp. clones in a combined Cd-Pb polluted system
To investigate the physiochemical characteristics of two new clones, Salix matsudana ‘J172’ (A7) and Salix matsudana ‘Yankang1’ (A64) in combined Cd-Pb contaminated systems, a hydroponic experiment was designed. The plant biomass, photosynthesis, antioxidant responses and the accumulation of metals in different plant parts (leaf, stem, and root) were measured after 35-day treatments with Cd (15, 30 µM) and Pb (250, 500 µM). The results showed that exposure to Cd-Pb decreased the biomass but increased the net photosynthetic rate for both A7 and A64, demonstrating that photosynthesis may be one of the metabolic processes used to resist Cd-Pb stress. Compared with control, roots exposed to Cd-Pb had higher activity of superoxide dismutase and more malondialdehyde concentrations, which indicated the roots of both clones were apt to be damaged. The concentrations of soluble protein were obviously higher in the roots of A64 than A7, indicating the roles of the antioxidative substance were different between two willow clones. Soluble protein also had significant relationship with translocation factors from accumulation in roots of A64, which illustrated it played important roles in the tolerance of A64 roots to heavy metals. The roots could accumulate more Pb rather than transport to the shoots compared with Cd. The tolerance index was more than 85% on average for both clones under all the treatments, indicating their tolerance capacities to the combined stress of Cd and Pb are strong under the tested metal levels. Both clones are the good candidates for phytoremediation of Cd and Pb by the root filtration in the combined contamination environment.
Zhang et al. (2022) Metal tolerance capacity and antioxidant responses of new Salix spp. clones in a combined Cd-Pb polluted system. PeerJ 10:e14521 https://doi.org/10.7717/peerj.14521
Effect of hyperglycemia on the immune function of COVID-19 patients with type 2 diabetes mellitus: a retrospective study
Purpose To analyze the clinical characteristics and immune function parameters and to explore the effect of hyperglycemia on the immune function in patients with Corona Virus Disease 2019 (COVID-19) with type 2 diabetes mellitus (T2DM). Methods This retrospective study included patients with COVID-19 with T2DM hospitalized in Renmin Hospital of Wuhan University between January 31, 2020, and February 10, 2020. The clinical data were collected and patients were divided into a well-controlled group (blood glucose 3.9–10.0 mmol/L) and a poorly-controlled group (blood glucose >10.0 mmol/L). The differences in routine blood tests, peripheral lymphocyte subsets, humoral immune components, C-reactive protein (CRP) level, and cytokines were compared, and the correlation between blood glucose and immune parameters as well as the severity of the disease was analyzed. Results A total of 65 patients with COVID-19 and T2DM were included in the final analysis. Compared with the well-controlled group, patients in the poorly-controlled group had decreased lymphocytes, CD16+ 56+ NK cells, CD3+ T cells, CD8+ T cells and increased neutrophil percentage, IL-6 levels, CRP levels and serum concentration of IgA. Blood glucose was inversely correlated with CD16+ 56+ NK cells, CD3+ T cells, CD4+ T cells, and CD8+ T cells and positively correlated with IL-6 and CRP levels. There was a positive correlation between blood glucose and the severity of the COVID-19. Conclusion Hyperglycemia will aggravate the immune dysfunction of COVID-19 patients with T2DM and affect the severity of COVID-19.
Wang et al. (2022) Effect of hyperglycemia on the immune function of COVID-19 patients with type 2 diabetes mellitus: a retrospective study. PeerJ 10:e14570 https://doi.org/10.7717/peerj.14570
Mitochondria and chloroplasts function in microalgae energy production
Microalgae are organisms that have the ability to perform photosynthesis, capturing CO2 from the atmosphere to produce different metabolites such as vitamins, sugars, lipids, among others, many of them with different biotechnological applications. Recently, these microorganisms have been widely studied due to their possible use to obtain clean energy. It has been postulated that the growth of microalgae and the production of high-energy metabolites depend on the correct function of cellular organelles such as mitochondria and chloroplasts. Thus, the development of different genetic tools to improve the function of these organelles is of high scientific and technological interest. In this paper we review the recent advances in microalgae engineering and the role of cellular organelles in order to increase cell productivity and biomass.
Gomez-Casati et al. (2022) Mitochondria and chloroplasts function in microalgae energy production. PeerJ 10:e14576 https://doi.org/10.7717/peerj.14576
Functional groups of Afrotropical EPT (Ephemeroptera, Plecoptera and Trichoptera) as bioindicators of semi-urban pollution in the Tsitsa River Catchment, Eastern Cape, South Africa
We examined the distribution patterns of Ephemeroptera, Plecoptera, and Trichoptera functional feeding groups (EPT FFGs) in five streams that drain semi-urban landscapes in the Tsitsa River catchment, Eastern Cape Province of South Africa. We undertook macroinvertebrate and physicochemical analysis over four seasons between 2016 and 2017 at eight sites in three land-use categories (Sites 1, 2 and 3), representing an increasing gradient of semi-urban pollution. Five EPT FFGs (shredders, grazers/scrapers, predators, collector-gatherers and collector-filterers) were fuzzy coded and analyzed using RLQ-R (environmental characteristics of samples), L (taxa distribution across samples) and Q (species traits) and fourth-corner analyses. Physicochemical variables, including phosphate-phosphorus, total inorganic nitrogen and temperature, were the most influential variables that significantly influenced the distribution patterns of EPT FFGs in the Tsitsa River. RLQ and the fourth-corner model revealed varying responses of FFGs to semi-urban pollution. Of the five FFGs, collectors were the most abundant EPT FFGs in the study area, exhibiting disparate responses to disturbances, with collector-gatherers associated with impacted sites and significantly associated with phosphate-phosphorus. On the other hand, collector-filterers decreased with increasing semi-urban disturbance and exhibited a significant negative association with phosphate-phosphorus, total inorganic nitrogen and temperature. Overall, this study provides further insights into the environmental factors that influence the distribution patterns of FFGs in Afrotropical streams and the potential use of FFGs as indicators of anthropogenic pollution in tropical streams and rivers.
Akamagwuna et al. (2022) Functional groups of Afrotropical EPT (Ephemeroptera, Plecoptera and Trichoptera) as bioindicators of semi-urban pollution in the Tsitsa River Catchment, Eastern Cape, South Africa. PeerJ 10:e13970 https://doi.org/10.7717/peerj.13970
Impacts of river fragmentation on limiting individual dietary specialization of Amazonian predatory fish
Individual dietary specialization is one of the factors that promotes variation in resource use at the individual level. Here we used stable isotope analysis of multiple tissues with different turnover rates to examine the degree of individual specialization in two sub-populations of the predator Cichla temensis inhabiting both fragmented and undammed rivers within the Uatumã River basin of the Amazon. Our results showed that the undammed river provides better conditions to promote individual dietary specialization than the fragmented river. This study contributes to the understanding of how specific life history characteristics of populations of generalist predators are impacted by fragmentation within megadiverse environments such as the Amazon basin.
Aguiar-Santos et al. (2022) Impacts of river fragmentation on limiting individual dietary specialization of Amazonian predatory fish. PeerJ 10:e14266 https://doi.org/10.7717/peerj.14266
Neospongodes atlantica, a potential case of an early biological introduction in the Southwestern Atlantic
Soft corals (Anthozoa: Octocorallia) are discreet components in the Southwestern Atlantic reef communities. In Brazil, the native octocoral shallow-reef fauna is mostly represented by gorgonians. Consequently, except for the nephtheid Neospongodes atlantica, most of the known soft corals from this region are considered non-indigenous. Hitherto, the monotypic genus Neospongodes, which was proposed in the early 1900s, has been considered to be endemic to the Northeastern Brazilian coast. Herein, based on in situ records, we show that N. atlantica is a substrate generalist that has been probably expanding its distribution by dominating extensive shallow and mesophotic sandy and reef bottoms, generally outcompeting other reef benthic organisms, including Brazilian endemic species. Based on previously unidentified museum specimens, new records, and a broad literature review, we provide the most comprehensive modelling of the potential distribution of this species in the Southwestern Atlantic. Based on molecular inference supported by in-depth morphological analysis, the probable non-indigenous and, therefore, ancient introduction of N. atlantica in Brazilian waters is discussed. Finally, these results support that Neospongodes and the Indo-Pacific Stereonephthya are synonyms, which led us to propose the latter as taxonomically invalid.
Cordeiro et al. (2022) Neospongodes atlantica, a potential case of an early biological introduction in the Southwestern Atlantic. PeerJ 10:e14347 https://doi.org/10.7717/peerj.14347
Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics
Background Human behaviour, economic activity, vaccination, and social distancing are inseparably entangled in epidemic management. This study aims to investigate the effects of various parameters such as stay-at-home restrictions, work hours, vaccination, and social distance on the containment of pandemics such as COVID-19. Methods To achieve this, we have developed an agent based model based on a time-dynamic graph with stochastic transmission events. The graph is constructed from a real-world social network. The edges of graph have been categorized into three categories: home, workplaces, and social environment. The conditions needed to mitigate the spread of wild-type COVID-19 and the delta variant have been analyzed. Our purposeful agent based model has carefully executed tens of thousands of individual-based simulations. We propose simple relationships for the trade-offs between effective reproduction number (Re), transmission rate, working hours, vaccination, and stay-at-home restrictions. Results We have found that the effect of a 13.6% increase in vaccination for wild-type (WT) COVID-19 is equivalent to reducing four hours of work or a one-day stay-at-home restriction. For the delta, 20.2% vaccination has the same effect. Also, since we can keep track of household and non-household infections, we observed that the change in household transmission rate does not significantly alter the Re. Household infections are not limited by transmission rate due to the high frequency of connections. For the specifications of COVID-19, the Re depends on the non-household transmissions rate. Conclusions Our findings highlight that decreasing working hours is the least effective among the non-pharmaceutical interventions. Our results suggest that policymakers decrease work-related activities as a last resort and should probably not do so when the effects are minimal, as shown. Furthermore, the enforcement of stay-at-home restrictions is moderately effective and can be used in conjunction with other measures if absolutely necessary.
Nashebi et al. (2022) Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics. PeerJ 10:e14353 https://doi.org/10.7717/peerj.14353
Prevalence of text neck posture, smartphone addiction, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic
The smartphone emerges as an inevitable gadget in modern society and its increased usage results in neck disorders among its users. However, the factors associated with neck disorders among smartphone users are ambiguous and less explored in the literature. The purpose of this research was to determine the prevalence of text neck posture, smartphone addiction/overuse, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic. A total of 313 university students who were aged 18 years and older, owned a smartphone, and used it during the preceding 12 months participated in this cross-sectional study. A self-administered questionnaire was used to collect data regarding the prevalence of text neck posture, smartphone addiction/overuse, neck disorders, and the level of physical activity. Binary logistic regression was used to determine the association between the prevalence of neck disorders and text neck posture, smartphone addiction/overuse, and level of physical activity. The 12 months prevalence of neck disorders due to smartphone use among the participants was found to be 46%. The neck disorders were more prevalent among participants who reported text neck posture (P < 0.001) and categorized as smartphone-addicted/overuse (P < 0.001). Measures to promote the awareness of healthy use of smartphones including postural education and to decrease its screen time are warranted to reduce neck disorders.
Sirajudeen et al. (2022) Prevalence of text neck posture, smartphone addiction, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic. PeerJ 10:e14443 https://doi.org/10.7717/peerj.14443
Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population
Background Breast cancer (BC) poses a serious threat to women worldwide. This research was designed to explore the association between the rs4784227 polymorphism of cancer susceptibility candidate gene 16 (CASC16) and BC susceptibility and prognosis, aiming to provide further information for the early detection of BC and to accelerate comprehensive cancer management. Methods A total of 1,733 subjects were recruited for this case-control study, of which 828 are BC patients and 905 are healthy individuals. The relevance between SNP rs4784227 and BC risk in diverse genetic models was analyzed by using the SNPStats analysis program and was assessed by odds ratios (ORs) and 95% confidence intervals (CIs) using the binary logistic regression model. Pearson’s χ2 test was used to determine the correlation between the polymorphism and clinical characteristics of BC patients. Additionally, univariate survival analysis was performed by the Kaplan-Meier method and log-rank test, and multivariate survival analysis was performed by Cox regression. Results SNP rs4784227 was significantly associated with susceptibility to BC in the dominant model (CT/TT versus CC, OR = 1.237, 95% CI = 1.012–1.513, P = 0.038). The minor allele of SNP rs4784227 was significantly linked to an increased risk of BC (OR = 1.197, 95% CI = 1.022–1.401, P = 0.026). In addition, the rs4784227 polymorphism of CASC16 was associated with perineural invasion (P = 0.030), menstrual status (P = 0.016) and histological grade (P = 0.001, P = 0.003, P = 0.025; respectively) of BC patients. There was no significant association between the genotypes of rs4784227 and disease-free survival (DFS) or overall survival (OS) of breast cancer patients (P > 0.05). Conclusions The rs4784227 polymorphism of CASC16 may affect susceptibility to breast cancer and is associated with perineural invasion, menstrual status and histological grade in BC patients. Additionally, our results could not confirm that this polymorphism was related to breast cancer prognosis.
Zhang et al. (2022) Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population. PeerJ 10:e14462 https://doi.org/10.7717/peerj.14462
Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network
Dynamic modelling has considerably improved our understanding of complex molecular mechanisms. Ordinary differential equations (ODEs) are the most detailed and popular approach to modelling the dynamics of molecular systems. However, their application in signalling networks, characterised by multi-state molecular complexes, can be prohibitive. Contemporary modelling methods, such as rule- based (RB) modelling, have addressed these issues. The advantages of RB modelling over ODEs have been presented and discussed in numerous reviews. In this study, we conduct a direct comparison of the time courses of a molecular system founded on the same reaction network but encoded in the two frameworks. To make such a comparison, a set of reactions that underlie an ODE model was manually encoded in the Kappa language, one of the RB implementations. A comparison of the models was performed at the level of model specification and dynamics, acquired through model simulations. In line with previous reports, we confirm that the Kappa model recapitulates the general dynamics of its ODE counterpart with minor differences. These occur when molecules have multiple sites binding the same interactor. Furthermore, activation of these molecules in the RB model is slower than in the ODE one. As reported for other molecular systems, we find that, also for the DARPP-32 reaction network, the RB representation offers a more expressive and flexible syntax that facilitates access to fine details of the model, easing model reuse. In parallel with these analyses, we report a refactored model of the DARPP-32 interaction network that can serve as a canvas for the development of more complex dynamic models to study this important molecular system.
Wysocka et al. (2022) Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 10:e14516 https://doi.org/10.7717/peerj.14516
Ethanolic extract of Ya-nang (Tiliacora triandra) leaf powder induces apoptosis in cholangiocarcinoma cell lines via induction of hyperacetylation and inhibition of growth signaling
Objective To develop alternative medicine for reducing undesired side effects of chemotherapy in CCA patients, the anticancer activity of Tiliacora triandra leaf powder ethanolic (TLPE) extract against cholangiocarcinoma cell lines was investigated. Methods Antiproliferation was studied using the MTT assay while apoptosis induction and cell cycle arrest were analyzed by flow cytometry. The levels of key proteins and phenolic acid content were analyzed by western blotting and reversed-phase HPLC, respectively. Results TLPE extract inhibited CCA cell growth in a dose- and time-dependent manner, with IC50 values of 7.86 ± 0.05 µg/ml for KKU-M213B cells and 8.59 ± 0.36 µg/ml for KKU-100 cells at an exposure time of 72 h. TLPE extract inhibited the growth of CCA cell lines by inducing apoptosis of both cell lines and causing an increased population of KKU-100 cells at G0/G1 phase. TLPE extract up-regulated Ac-H3 but down-regulated p-ERK, p53, Bax, CDK4 and Bcl2 expressions in KKU-M213B cells. TLPE extract up-regulated Ac-H3, p21 and Bax but down-regulated p-ERK, p53, CDK4 and Bcl2 expressions in KKU-100 cells. Additionally, phenolic acids including p-hydroxybenzoic, vanillic, syringic, p-coumaric, ferulic and sinapinic acids were identified. Conclusion These results suggest the possibility of developing T. triandra leaf powder ethanolic extract as a chemotherapeutic or chemoprevention agent for cholangiocarcinoma.
Samankul et al. (2022) Ethanolic extract of Ya-nang (Tiliacora triandra) leaf powder induces apoptosis in cholangiocarcinoma cell lines via induction of hyperacetylation and inhibition of growth signaling. PeerJ 10:e14518 https://doi.org/10.7717/peerj.14518
Embryonic exposure to fentanyl induces behavioral changes and neurotoxicity in zebrafish larvae
The use of fentanyl during pregnancy, whether by prescription or illicit use, may result in high blood levels that pose an early risk to fetal development. However, little is known regarding the neurotoxicity that might arise from excessive fentanyl exposure in growing organisms, particularly drug-related withdrawal symptoms. In this study, zebrafish embryos were exposed to fentanyl solutions (0.1, 1, and 5 mg/L) for 5 days post fertilization (dpf), followed by a 5-day recovery period, and then the larvae were evaluated for photomotor response, anxiety behavior, shoaling behavior, aggression, social preference, and sensitization behavior. Fentanyl solutions at 1 and 5 mg/L induced elevated anxiety, decreased social preference and aggressiveness, and behavioral sensitization in zebrafish larvae. The expression of genes revealed that embryonic exposure to fentanyl caused substantial alterations in neural activity (bdnf, c-fos) and neuronal development and plasticity (npas4a, egr1, btg2, ier2a, vgf). These results suggest that fentanyl exposure during embryonic development is neurotoxic, highlighting the importance of zebrafish as an aquatic species in research on the neurobehavioral effects of opioids in vertebrates.
Wang et al. (2022) Embryonic exposure to fentanyl induces behavioral changes and neurotoxicity in zebrafish larvae. PeerJ 10:e14524 https://doi.org/10.7717/peerj.14524
Non-random host tree infestation by the Neotropical liana Marcgravia longifolia
The question whether or not tropical lianas infest host trees randomly or they exert host selection has implications for the structure and dynamics of tropical rainforests, particularly if colonization by lianas impacts host fitness. In this study, we present evidence that the Neotropical liana Marcgravia longifolia (Marcgraviaceae) infests host trees non-randomly. We identified host trees to species or genus level for 87 of the 100 M. longifolia individuals found in the study area of the Estación Biológica Quebrada Blanco (EBQB) in north-eastern Peruvian Amazonia. Data on host availability were taken from two 1-ha plots sampled at EBQB as part of a large-scale tree inventory in western Amazonia. Of the total of 88 tree genera with two or more individuals present in the inventory, 18 were represented amongst hosts. Host genera with a probability of colonization higher than expected by chance were Eschweilera (Lecythidaceae), Pouteria (Sapotaceae), Brosimum (Moraceae), and Hymenaea (Fabaceae). These findings suggest that M. longifolia exerts some level of host selectivity, but the mechanisms for this are completely unknown. Given the large number of animal species (41 bird species, three primate species) that are dispersing the seeds of M. longifolia and that have diverse ecological strategies, directed seed dispersal is unlikely to account for the observed patterns of host infestation.
Heymann et al. (2022) Non-random host tree infestation by the Neotropical liana Marcgravia longifolia. PeerJ 10:e14535 https://doi.org/10.7717/peerj.14535
The long-term dynamics of serum antibodies against SARS-CoV-2
Objective To analyze the long-term dynamics of antibodies against SARS-CoV-2 and understand the impact of age, gender, and viral load on patients’ immunological response. Methods Serum samples were obtained from 231 COVID-19 positive patients from Macaé, in Rio de Janeiro state, in Brazil, from June 2020 until January 2021. The production of IgA, IgM, IgG, and IgE against S glycoprotein was analyzed using the S-UFRJ assay, taking into account the age, gender, and viral load. Results Analysis of antibody production over 7 months revealed that IgA positivity gradually decreased after the first month. Additionally, the highest percentage of IgM positivity occurred in the first month (97% of patients), and declined after this period, while IgG positivity remained homogeneous for all 7 months. The same analysis for IgE revealed that almost all samples were negative. The comparison of antibody production between genders showed no significant difference. Regarding the age factor and antibody production, patients aged ≥60 years produced almost twice more IgA than younger ones (17–39 years old). Finally, a relationship between viral load and antibody production was observed only for older patients. Conclusions Our work provides an overview of long-term production of antibodies against SARS-CoV-2, suggesting prolonged production of IgA and IgM antibodies for 3 months and continued IgG production for over 7 months. In addition, it identified a correlation between viral load and IgM titers in the older group and, finally, different IgA production between the age groups.
de Sousa et al. (2022) The long-term dynamics of serum antibodies against SARS-CoV-2. PeerJ 10:e14547 https://doi.org/10.7717/peerj.14547
Identification of prognostic factors and nomogram model for patients with advanced lung cancer receiving immune checkpoint inhibitors
Background and aim Some patients with lung cancer can benefit from immunotherapy, but the biomarkers that predict immunotherapy response were not well defined. Baseline characteristic of patients may be the most convenient and effective markers. Therefore, our study was designed to explore the association between baseline characteristics of patients with lung cancer and the efficacy of immunotherapy. Methods A total of 216 lung cancer patients from Tianjin Medical University Cancer Institute & Hospital who received immunotherapy between 2017 and 2021 were included in the retrospective analysis. All baseline characteristic data were collected and then univariate log-rank analysis and multivariate COX regression analysis were performed. Kaplan–Meier analysis was used to evaluate patients’ progression-free survival (PFS). A nomogram based on significant biomarkers was constructed to predict PFS rate of patients receiving immunotherapy. We evaluated the prediction accuracy of nomogram using C-indices and calibration curves. Results Univariate analysis of all collected baseline factors showed that age, clinical stage, white blood cell (WBC), lymphocyte (LYM), monocyte (MON), eosinophils (AEC), hemoglobin (HB), lactate dehydrogenase (LDH), albumin (ALB) and treatment line were significantly associated with PFS after immunotherapy. Then these 10 risk factors were included in a multivariate regression analysis, which indicated that age (HR: 1.95, 95% CI [1.01–3.78], P = 0.048), MON (HR: 1.74, 95% CI [1.07–2.81], P = 0.025), LDH (HR: 0.59, 95% CI [0.36–0.95], P = 0.030), and line (HR: 0.57, 95% CI [0.35–0.94], P = 0.026) were significantly associated with PFS in patients with lung cancer receiving immunotherapy. Patients with higher ALB showed a greater trend of benefit compared with patients with lower ALB (HR: 1.58, 95% CI [0.94–2.66], P = 0.084). Patients aged ≥51 years, with high ALB, low LDH, first-line immunotherapy, and high MON had better response rates and clinical benefits. The nomogram based on age, ALB, MON, LDH, line was established to predict the prognosis of patients treated with immune checkpoint inhibitor (ICI). The C-index of training cohort and validation cohort were close, 0.71 and 0.75, respectively. The fitting degree of calibration curve was high, which confirmed the high prediction value of our nomogram. Conclusion Age, ALB, MON, LDH, line can be used as reliable predictive biomarkers for PFS, response rate and cancer control in patients with lung cancer receiving immunotherapy. The nomogram based on age, ALB, MON, LDH, line was of great significance for predicting 1-year-PFS, 2-year-PFS and 3-year-PFS in patients with advanced lung cancer treated with immunotherapy.
Chen et al. (2022) Identification of prognostic factors and nomogram model for patients with advanced lung cancer receiving immune checkpoint inhibitors. PeerJ 10:e14566 https://doi.org/10.7717/peerj.14566
Seroprevalence of Toxoplasma gondii infection in women with a gynecological tumor living in eastern China
The association between Toxoplasma gondii (T. gondii) infection and malignancy has attracted increased attention in recent years, but little is known of T. gondii infection among women diagnosed with a gynecological tumor (GT) in China. We conducted a case-control study involving 460 women diagnosed with a GT and 460 age-matched healthy controls (HCs) to estimate the infection process of T. gondii and understand the risk factors of T. gondii infection in patients with a GT. Levels of anti-T. gondii IgG and IgM were measured by enzyme-linked immunoassays every 12 months. After a median follow-up time of 4.3 years (range 4 to 5 years), 55/460 (11.96%) patients with a GT and 15/460 (3.26%) HCs were seroprevalence for T. gondii antibodies, respectively (P = 0.001). IgG antibodies against T. gondii were found in 54 GT patients (11.74%) and 15 HCs (3.26%), respectively (P = 0.001). The seroprevalence of T. gondii IgM antibodies was similar in patients with a GT and with HCs (2.83% vs 1.3%, P = 0.105). Multivariate stepwise logistic regression analysis revealed contact with cats (OR, 6.67; 95% CI [2.89–10.75]; P = 0.001), exposure to soil (OR, 2.16; 95% CI [1.14–4.10]; P = 0.019), being a farm-worker (OR, 4.17; 95% CI [1.20–11.49]; P = 0.006) and history of chemotherapy (OR, 3.16; 95% CI [1.56–6.45]; P = 0.001) to be independent risk factors for T. gondii infection. Women with an ovarian cancer or endometrial cancer had higher T. gondii seroprevalence than that of HCs. Moreover, T. gondii infection in patients with a GT mostly acquired within two years of diagnosis, but the infection in healthy controls had no obvious time characteristics. Here, we demonstrated that T. gondii infection is significantly higher in patients with a GT (especially in women with an ovarian tumor) compared to HCs. Thus, infection with this parasite should be avoided in patients with a GT, and the causal relationship between T. gondii and GTs should be studied in detail.
Wang et al. (2022) Seroprevalence of Toxoplasma gondii infection in women with a gynecological tumor living in eastern China. PeerJ 10:e14569 https://doi.org/10.7717/peerj.14569
Patch and matrix characteristics determine the outcome of ecosystem engineering by mole rats in dry grasslands
Background Burrowing mammals are important ecosystem engineers, especially in open ecosystems where they create patches that differ from the surrounding matrix in their structure or ecosystem functions. Methods We evaluated the fine-scale effects of a subterranean ecosystem engineer, the Lesser blind mole rat on the vegetation composition of sandy dry grasslands in Hungary. In this model system we tested whether the characteristics of the patch (mound size) and the matrix (total vegetation cover in the undisturbed grassland) influence the structural and functional contrasts between the mounds and the undisturbed grasslands. We sampled the vegetation of 80 mounds and 80 undisturbed grassland plots in four sites, where we recorded the total vegetation cover, and the occurrence and cover of each vascular plant species. We used two proxies to characterise the patches (mounds) and the matrix (undisturbed grassland): we measured the perimeter of the mounds and estimated the total vegetation cover of the undisturbed grasslands. First, we compared the vegetation characteristics of the mounds and the surrounding grasslands with general linear models. Second, we characterised the contrasts between the mounds and the undisturbed grassland by relative response indices (RRIs) of the vegetation characteristics studied in the first step. Results Species composition of the vegetation of the mounds and undisturbed grasslands was well separated in three out of the four study sites. Mounds were characterised by lower vegetation cover, lower cover of perennial graminoids, and higher diversity, and evenness compared to undisturbed grasslands. The contrast in vegetation cover between mounds and undisturbed grasslands increased with decreasing patch size. Increasing vegetation cover in the matrix grasslands increased the contrasts between the mounds and undisturbed grasslands in terms of total cover, perennial graminoid cover, diversity, and evenness. Our results suggest that mole rat mounds provide improved establishment conditions for subordinate species, because they are larger than other types of natural gaps and are characterised by less intense belowground competition. The ecosystem engineering effect, i.e., the contrast between the patches and the matrix was the largest in the more closed grasslands.
Valkó et al. (2022) Patch and matrix characteristics determine the outcome of ecosystem engineering by mole rats in dry grasslands. PeerJ 10:e14582 https://doi.org/10.7717/peerj.14582
Genome-wide investigation and expression pattern of PHR family genes in cotton under low phosphorus stress
Phosphorus starvation response (PHR) protein is an important transcription factor in phosphorus regulatory network, which plays a vital role in regulating the effective utilization of phosphorus. So far, the PHR genes have not been systematically investigated in cotton. In the present study, we have identified 22, 23, 41 and 42 PHR genes in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. Phylogenetic analysis showed that cotton PHR genes were classified into five distinct subfamilies. The gene structure, protein motifs and gene expression were further investigated. The PHR genes of G. hirsutum from the same subfamily had similar gene structures, all containing Myb_DNA-binding and Myb_CC_LHEQLE conserved domain. The structures of paralogous genes were considerably conserved in exons number and introns length. The cis-element prediction in their promoters showed that genes were not only regulated by light induction, but also were related to auxin, MeJA, abscisic acid-responsive elements, of which might be regulated by miRNA. The expression analysis showed that the GhPHR genes were differentially expressed in different tissues under various stresses. Furthermore, GhPHR6, GhPHR11, GhPHR18 and GhPHR38 were significantly changed under low phosphorus stress. The results of this study provide a basis for further cloning and functional verification of genes related to regulatory network of low phosphorus tolerance in cotton.
Zhao et al. (2022) Genome-wide investigation and expression pattern of PHR family genes in cotton under low phosphorus stress. PeerJ 10:e14584 https://doi.org/10.7717/peerj.14584
Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo
Mulberry flavonoids can modulate the composition of rumen microbiota in ruminants to improve nutrient digestibility, owing to their strong biological activities. This study aimed to explore the effect of mulberry leaf flavonoids (MLF) on rumen bacteria, fermentation kinetics, and metagenomic functional profile in water buffalo. Forty buffaloes (4 ± 1 lactations) with almost same body weight (av. 600 ± 50 Kg) and days in milk (90 ± 20 d) were randomly allocated to four treatments having different levels of MLF: 0 g/d (control), 15 g/d (MLF15), 30 g/d (MLF30), and 45 g/d (MLF45) supplemented in a basal diet. After 35 days of supplementation, rumen contents were collected to determine rumen fermentation parameters. The 16S rRNA gene sequencing was performed to elucidate rumen bacteria composition. The obtained taxonomic data were analyzed to explore the rumen bacteriome and predict the associated gene functions and metabolic pathways. Results demonstrated a linear increase (p < 0.01) in rumen acetate, propionate, and total VFAs in the MLF45 group as compared to control. No effect of treatment was observed on rumen pH and butyrate contents. Acetate to propionate ratio in the MLF45 group linearly and quadratically decreased (p = 0.001) as compared to MLF15 and control groups. Similarly, MLF45 linearly increased (p < 0.05) the microbial protein (MCP) and NH3-N as compared to other treatments. Treatment adversely affected (p < 0.01) almost all alpha diversity parameters of rumen bacteria except Simpson index. MLF promoted the abundance of Proteobacteria while reducing the relative abundances of Actinobacteria, Acidobacteria, Chloroflexi, and Patescibacteria. The MLF supplementation tended to substantially reduce (0.05 < p < 0.1) the abundance of Actinobacteria, and Patescibacteria while completely eliminating Acidobacteria (p = 0.029), Chloroflexi (p = 0.059), and Gemmatimonadetes (p = 0.03) indicating the negative effect of flavonoids on the growth of these bacteria. However, MLF45 tended to substantially increase (p = 0.07) the abundance (~21.5%) of Acetobacter. The MLF treatment exhibited negative effect on five genera by significantly reducing (Sphingomonas) or eliminating (Arthobactor, unclassified_c__Actinobacteria, norank_c__Subgroup_6, norank_o__Saccharimonadales, and Nocardioides) them from the rumen microbiota. Pearson correlation analysis revealed 3, 5 and 23 positive correlations of rumen bacteria with milk yield, rumen fermentation and serum antioxidant parameters, respectively. A positive correlation of MCP was observed with three bacterial genera (Acetobacter, Enterobacter, and Klebsiella). The relative abundance of Pseudobutyrivibrio and Empedobacter also showed a positive correlation with the ruminal acetate and propionate. The present study indicated 45 g/d as an appropriate dose of MLF which modulated rumen bacteria and its functional profile in water buffalo.
Li et al. (2022) Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo. PeerJ 10:e14309 https://doi.org/10.7717/peerj.14309
The use of audio self-hypnosis to promote weight loss using the transtheoretical model of change: a randomized clinical pilot trial
Background Few studies suggest the use of hypnosis in weight loss may be beneficial, especially when in conjunction with other lifestyle modifications or cognitive behavioral therapy. The primary aim of this study was to determine the ability of self-hypnosis audiotape to promote weight loss by measuring its effects on the Transtheoretical Model (TTM) of change stages and processes. Methods This study is a 3-week randomized double-blinded parallel controlled trial among adults who have overweight or obesity. The intervention group listened to a self-hypnosis audio file while the control group listened to a placebo audio file. Results Forty-six participants completed the 3-week follow-up visit. There was no association between progression across stages of change and self-hypnosis (X2(2, 46) = 1.909, p-value = 0.580). Gender, baseline BMD, and baseline S-weight had no effect on the association between stage change progression and self-hypnosis. The mean difference in weight at 3 weeks was −0.63 ± 0.43 kg in the hypnosis group and 0.0 ± 1.5 kg in the control group, independent t-test, p = 0.148. Conclusion Self-hypnosis was not associated with a progression in the TTM’s stages of change or with weight loss after 3 weeks. As this pilot study was underpowered, further research with larger sample size and an examination of the effect of various self-hypnosis content and duration is recommended.
Antoun et al. (2022) The use of audio self-hypnosis to promote weight loss using the transtheoretical model of change: a randomized clinical pilot trial. PeerJ 10:e14422 https://doi.org/10.7717/peerj.14422
The rhythm of chemotherapy and cancer patients’ time perspectives
Background While it is well known that illnesses such as cancer modify the experience of time, the impact of the rhythm and length of treatment on patients’ time perspectives remains unknown. Methods A short version of Zimbardo Time Perspective Inventory and Transcendental Future Perspective Questionnaire as well as a demographic questionnaire on a convenience sample of 259 patients (66.8% female, mean age 52.36) with various cancers and undergoing chemotherapy with different frequencies (1, 2, 3 weeks) and mean time in treatment 23.4 months. Results The temporal perspectives mean scores of cancer patients are: positive past 3.69, negative past 3.13, present hedonism 3.08, future 3.77, transcendental future 3.40. Patients tend only slightly to lose faith alongside the course of oncological treatment regardless of their age (ρ = − 0.210, p < 0.01). The frequency of chemotherapy mildly differentiates temporal perspectives of patients regarding present hedonism and transcendental future: a weekly treatment is more disturbing than the triweekly one and no treatment in terms of hedonism, while patients not in chemo score significantly higher in transcendental future than patients in biweekly and triweekly chemo. Conclusions The variations of treatment rhythm are less significant than predicted, although still relevant. Since most sociodemographic variables are of no relevance, cancer experience likely unifies temporal perspectives among people of different backgrounds.
Moskalewicz et al. (2022) The rhythm of chemotherapy and cancer patients’ time perspectives. PeerJ 10:e14486 https://doi.org/10.7717/peerj.14486
Bird diversity-environment relationships in urban parks and cemeteries of the Neotropics during breeding and non-breeding seasons
Background Urbanization will increase in the next decades, causing the loss of green areas and bird diversity within cities. There is a lack of studies at a continental scale analyzing the relationship between urban green areas, such as parks and cemeteries, and bird species richness in the Neotropical region. Bird diversity-environment relationships in urban parks and cemeteries may be influenced by latitudinal gradients or species-area relationships. However, the seasonal variation of species diversity- environment has not been analyzed at a continental scale in the Neotropics. Methods Bird surveys were conducted in 36 cemeteries and 37 parks within 18 Neotropical cities during non-breeding and breeding seasons. Bird diversity was assessed through Hill numbers, focusing on species richness, the effective number of species derived from Shannon index and the Simpson index. Environmental variables included latitude, altitude, and local scale variables such as area size, habitat diversity and pedestrian traffic. Results Species richness and Shannon diversity were higher during the breeding season, whereas Simpson diversity did not vary between seasons. During both seasons, species richness increased with area size, was negatively related to altitude, and was the highest at 20° latitude. Species richness was also positively related to habitat diversity, pedestrian traffic, and was highest in suburban areas during the non-breeding season. Shannon and Simpson diversity showed significant relationships with habitat diversity and area size during the breeding season. Bird diversity was similar between parks and cemeteries. Discussion Our results showed that urban parks and cemeteries have similar roles in conserving urban bird diversity in Neotropical cities. However, species diversity-environment relations at the continental scale varied between seasons, highlighting the importance of conducting annual studies.
Leveau et al. (2022) Bird diversity-environment relationships in urban parks and cemeteries of the Neotropics during breeding and non-breeding seasons. PeerJ 10:e14496 https://doi.org/10.7717/peerj.14496
EcoCountHelper: an R package and analytical pipeline for the analysis of ecological count data using GLMMs, and a case study of bats in Grand Teton National Park
Here we detail the use of an R package, ‘EcoCountHelper’, and an associated analytical pipeline aimed at making generalized linear mixed-effects model (GLMM)-based analysis of ecological count data more accessible. We recommend a GLMM-based analysis workflow that allows the user to (1) employ selection of distributional forms (Poisson vs negative binomial) and zero-inflation (ZIP and ZINB, respectively) using AIC and variance-mean plots, (2) examine models for goodness-of-fit using simulated residual diagnostics, (3) interpret model results via easy to understand outputs of changes in predicted responses, and (4) compare the magnitude of predictor variable effects via effects plots. Our package uses a series of easy-to-use functions that can accept both wide- and long-form multi-taxa count data without the need for programming experience. To demonstrate the utility of this approach, we use our package to model acoustic bat activity data relative to multiple landscape characteristics in a protected area (Grand Teton National Park), which is threatened by encroaching disease—white nose syndrome. Global threats to bat conservation such as disease and deforestation have prompted extensive research to better understand bat ecology. Notwithstanding these efforts, managers operating on lands crucial to the persistence of bat populations are often equipped with too little information regarding local bat activity to make informed land-management decisions. In our case study in the Tetons, we found that an increased prevalence of porous buildings increases activity levels of Eptesicus fuscus and Myotis volans; Myotis lucifugus activity decreases as distance to water increases; and Myotis volans activity increases with the amount of forested area. By using GLMMs in tandem with ‘EcoCountHelper’, managers without advanced programmatic or statistical expertise can assess the effects of landscape characteristics on wildlife in a statistically-robust framework.
Cole et al. (2022) EcoCountHelper: an R package and analytical pipeline for the analysis of ecological count data using GLMMs, and a case study of bats in Grand Teton National Park. PeerJ 10:e14509 https://doi.org/10.7717/peerj.14509
Transcriptomic analyses provide new insights into green and purple color pigmentation in Rheum tanguticum medicinal plants
Background Rheum tanguticum Maxim. ex Balf is a traditional Chinese medicinal plant that is commonly used to treat many ailments. It belongs to the Polygonacae family and grows in northwest and southwest China. At high elevations, the color of the plant’s young leaves is purple, which gradually changes to green during the growth cycle. Anthraquinone, which is known for various biological activities, is the main bioactive compound in R. tanguticum. Although a significant amount of research has been done on R. tanguticum in the past, the lack of transcriptome data limits our knowledge of the gene regulatory networks involved in pigmentation and in the metabolism of bioactive compounds in Rheum species. Methods To fill this knowledge gap, we generated high-quality RNA-seq data and performed multi-tissue transcriptomic analyses of R. tanguticum. Results We found that three chlorophyll degradation enzymes (RtPPH, RtPao and RtRCCR) were highly expressed in purple samples, which suggests that the purple pigmentation is mainly due to the effects of chlorophyll degradation. Overall, these data may aid in drafting the transcriptional network in the regulation and biosynthesis of medicinally active compounds in the future.
Chen et al. (2022) Transcriptomic analyses provide new insights into green and purple color pigmentation in Rheum tanguticum medicinal plants. PeerJ 10:e14265 https://doi.org/10.7717/peerj.14265
Determination of PaO2/FiO2 after 24 h of invasive mechanical ventilation and ΔPaO2/FiO2 at 24 h as predictors of survival in patients diagnosed with ARDS due to COVID-19
Introduction Acute respiratory distress syndrome (ARDS) due to Coronavirus Disease 2019 (COVID-19) causes high mortality. The objective of this study is to determine whether the arterial pressure of oxygen/inspiratory fraction of oxygen (PaO2/FiO2) 24 h after invasive mechanical ventilation (IMV) and the difference between PaO2/FiO2 at 24 h after IMV and PaO2/FiO2 before admission to IMV (ΔPaO2/FiO2 24 h) are predictors of survival in patients with ARDS due to COVID-19. Methods A retrospective cohort study was conducted that included patients with ARDS due to COVID-19 in IMV admitted to the intensive care unit (ICU) of a hospital in southern Peru from April 2020 to April 2021. The ROC curves and the Youden index were used to establish the cut-off point for PaO2/FiO2 at 24 h of IMV and ΔPaO2/FiO2 at 24 h associated with mortality. The association with mortality was determined by Cox regression, calculating the crude (cHR) and adjusted (aHR) risk ratios, with their respective 95% confidence intervals (95% CI). Results Two hundred patients were analyzed. The average age was 54.29 years, 79% were men, and 25.5% (n = 51) died. The cut-off point calculated for PaO2/FiO2 24 h after IMV and ΔPaO2/FiO2 24 h was 222.5 and 109.5, respectively. Those participants with a value below the cut-off point of ΔPaO2/FiO2 24 h and PaO2/FiO2 24 h after IMV had higher mortality, aHR = 3.32 (CI 95% [1.82–6.07]) and aHR = 2.87 (CI 95% [1.48–5.57]) respectively. Conclusion PaO2/FiO2 24 h after IMV and ΔPaO2/FiO2 24 h in patients diagnosed with ARDS due to COVID-19 on IMV were associated with higher hospital mortality. These findings are helpful to identify those patients with a higher risk of dying on admission to the ICU.
Hueda-Zavaleta et al. (2022) Determination of PaO2/FiO2 after 24 h of invasive mechanical ventilation and ΔPaO2/FiO2 at 24 h as predictors of survival in patients diagnosed with ARDS due to COVID-19. PeerJ 10:e14290 https://doi.org/10.7717/peerj.14290
Predicting RNA secondary structure by a neural network: what features may be learned?
Deep learning is a class of machine learning techniques capable of creating internal representation of data without explicit preprogramming. Hence, in addition to practical applications, it is of interest to analyze what features of biological data may be learned by such models. Here, we describe PredPair, a deep learning neural network trained to predict base pairs in RNA structure from sequence alone, without any incorporated prior knowledge, such as the stacking energies or possible spatial structures. PredPair learned the Watson-Crick and wobble base-pairing rules and created an internal representation of the stacking energies and helices. Application to independent experimental (DMS-Seq) data on nucleotide accessibility in mRNA showed that the nucleotides predicted as paired indeed tend to be involved in the RNA structure. The performance of the constructed model was comparable with the state-of-the-art method based on the thermodynamic approach, but with a higher false positives rate. On the other hand, it successfully predicted pseudoknots. t-SNE clusters of embeddings of RNA sequences created by PredPair tend to contain embeddings from particular Rfam families, supporting the predictions of PredPair being in line with biological classification.
Grigorashvili et al. (2022) Predicting RNA secondary structure by a neural network: what features may be learned?. PeerJ 10:e14335 https://doi.org/10.7717/peerj.14335
Experience of COVID-19 disease and fear of the SARS-CoV-2 virus among Polish students
Background The SARS-CoV-2 virus pandemic has significantly affected individuals and entire societies. It has caused a number of adverse consequences for public health. It has contributed to lower average life expectancy and significantly reduced the sense of health security. It has affected not only physical but also mental health. COVID-19 infections have become so common in many countries, including Poland, that almost every member of society has either experienced it themselves or has a family member or friend who have been affected by the disease. The investigations undertaken in the article concern the fear of COVID-19 infection among Polish university students, determined by the experience of the disease –whether direct or among loved ones. Methods An online survey was conducted with 851 students. It took place between 1 and 15 March 2021, a year after detection of the first case of infection with the virus in Poland. The aim of the study was to find out about the relationship between the experience of COVID-19 disease (whether direct or among people close to the respondent) and fear of this disease among university students in Poland. The analysis used intergroup comparison tests (Mann–Whitney U Test and t-test). Results The results indicate that the level of fear of COVID-19 among Polish university students was low (M = 1.98; SD = .49), with women (M = 2.04; SD = .75) presenting statistically higher (t (620.46) = 3.05; p = .002) fear than men (M = 1.87; SD = .74). The situation of the respondent having had a close person fall ill with COVID-19 or die as a result of coronavirus infection was found to be significant for the level of experienced fear of COVID-19 in the studied group (t (469.46) = −2.98; p = .003). Conclusions The significantly higher level of fear in the group of young people who knew someone close with severe (fatal) COVID-19 disease indicates that psychological support may be more significant for such people than for individuals who have not experienced such a situation. A similar conclusion can be formulated taking into account the gender criterion, as the results make it possible to predict that women expect more support in a pandemic situation.
Turska et al. (2022) Experience of COVID-19 disease and fear of the SARS-CoV-2 virus among Polish students. PeerJ 10:e14356 https://doi.org/10.7717/peerj.14356
Animal movement ecology in India: insights from 2011–2021 and prospective for the future
The field of animal movement ecology has advanced by leaps and bounds in the past few decades with the advent of sophisticated technology, advanced analytical tools, and multiple frameworks and paradigms to address key ecological problems. Unlike the longer history and faster growth of the field in North America, Europe, and Africa, movement ecology in Asia has only recently been gaining momentum. Here, we provide a review of the field from studies based in India over the last 11 years (2011–2021) curated from the database, Scopus, and search engine, Google Scholar. We identify current directions in the research objectives, taxa studied, tracking technology and the biogeographic regions in which animals were tracked, considering the years since the last systematic review of movement ecology research in the country. As an indication of the growing interest in this field, there has been a rapid increase in the number of publications over the last decade. Class Mammalia continues to dominate the taxa tracked, with tiger and leopard being the most common species studied across publications. Invertebrates and other small and medium-sized animals, as well as aquatic animals, in comparison, are understudied and remain among the important target taxa for tracking in future studies. As in the previous three decades, researchers have focussed on characterising home ranges and habitat use of animals. There is, however, a notable shift to examine the movement decision of animals in human-modified landscapes, although efforts to use movement ecology to understand impacts of climate change remain missing. Given the biogeographic and taxonomic diversity of India, and the fact that the interface between anthropogenic activity and wildlife interactions is increasing, we suggest ways in which the field of movement ecology can be expanded to facilitate ecological insights and conservation efforts. With the advancement of affordable technologies and the availability of analytical tools, the potential to expand the field of movement ecology, shift research foci, and gain new insights is now prime.
Spatial and Geographic Information Science
Prakash et al. (2022) Animal movement ecology in India: insights from 2011–2021 and prospective for the future. PeerJ 10:e14401 https://doi.org/10.7717/peerj.14401
Hygiene of housing conditions and proinflammatory signals alter gene expressions in porcine adipose tissues and blood cells
Adipose tissue is an organ with metabolic, endocrine and immune functions. In this tissue, the expressions of genes associated with several metabolic pathways, including lipid metabolism, have been shown to be affected by genetic selection for feed efficiency, an important trait to consider in livestock. We hypothesized that the stimulation of immune system caused by poor hygiene conditions of housing impacts the molecular and cellular features of adipose tissue and that the impact may differ between pigs that diverge in feed efficiency. At the age of 12 weeks, Large White pigs from two genetic lines divergent for residual feed intake (RFI) were housed in two contrasting hygiene conditions (good vs poor). After six weeks of exposure, pigs were slaughtered (n = 36). Samples of blood, subcutaneous (SCAT) and perirenal (PRAT) adipose tissues were collected for cell response and gene expression investigations. The decrease in the relative weight of PRAT was associated with a decline in mRNA levels of FASN, ME, LCN2 and TLR4 (P < 0.05) in pigs housed in poor conditions compared with pigs housed in good conditions for both RFI lines. In SCAT, the expressions of only two key genes (PPARG and TLR4) were significantly affected by the hygiene of housing conditions. Besides, the mRNA levels of both LCN2 and GPX3 were influenced by the RFI line (P < 0.05). Because we suspected an effect of poor hygiene at the cellular levels, we investigated the differentiation of stromal vascular cells isolated from SCAT in vitro in the absence or presence of a pro-inflammatory cytokine, Tumor Necrosis Factor-α (TNF-α). The ability of these cells to differentiate in the absence or presence of TNF-α did not differ among the four groups of animals (P > 0.05). We also investigated the expressions of genes involved in the immune response and lipid metabolism in whole blood cells cultured in the absence and presence of LPS. The hygiene conditions had no effect but, the relative expression of the GPX3 gene was higher (P < 0.001) in high RFI than in low RFI pigs while the expressions of IL-10 (P = 0.027), TGFβ1 (P = 0.023) and ADIPOR2 (P = 0.05) genes were lower in high RFI than in low RFI pigs. Overall, the current study indicates that the hygiene of housing had similar effects on both RFI lines on the expression of genes in adipose tissues and on the features of SCAT adipose cells and whole blood cells in response to TNF-α and LPS. It further demonstrates that the number of genes with expression impacted by housing conditions was higher in PRAT than in SCAT. It suggests a depot-specific response of adipose tissue to the current challenge.
Quéméner et al. (2022) Hygiene of housing conditions and proinflammatory signals alter gene expressions in porcine adipose tissues and blood cells. PeerJ 10:e14405 https://doi.org/10.7717/peerj.14405
Transcriptome and metabolome analyses reveal anthocyanins pathways associated with fruit color changes in plum (Prunus salicina Lindl.)
Plum (Prunus salicina Lindl.) is one of the most widely cultivated and important fruit trees in temperate and cold regions. Fruit color is a significant trait relating to fruit quality in plum. However, its development mechanism has not been studied from the aspects of transcriptional regulation and metabolomic progress. To reveal the mechanism of fruit color developments in plums, we selected the fruits of two plum cultivars, ‘Changli84’ (Ch84, red fruit) and ‘Dahuangganhe’ (D, yellow fruit) as plant materials for transcriptome sequencing and metabolomic analysis were performed. Based on the data of transcriptome and metabolome at three fruit developmental stages, young fruit stage, color-change stage, and maturation stage, we identified 2,492 differentially expressed genes (DEGs) and 54 differential metabolites (DMs). The KEGG analysis indicated that “Flavonoid biosynthesis” was significantly enriched during three fruit development stages. Some DEGs in the “Flavonoid biosynthesis” pathway, had opposite trends between Ch84 and D, including chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR) and flavonol synthase (FLS). Also, the genes encoding MYB–bHLH–WD (MBW) protein complexes, especially MYBs and bHLHs, showed a close relationship with plum fruit color. In the current study, DMs like procyanidin B1, cyanidin 3-glucoside, and cyanidin-3-O-alpha-arabinopyranoside were key pigments (or precursors), while the carotene and carotenoids did not show key relationships with fruit color. In conclusion, the anthocyanins dominate the color change of plum fruit. Carotenes and carotenoids might be related to the color of plum fruit, but do not play a dominate role.
Chen et al. (2022) Transcriptome and metabolome analyses reveal anthocyanins pathways associated with fruit color changes in plum (Prunus salicina Lindl.). PeerJ 10:e14413 https://doi.org/10.7717/peerj.14413
Diversification and historical demography of Haloxylon ammodendron in relation to Pleistocene climatic oscillations in northwestern China
The influence of aridification and climatic oscillations on the genetic diversity and evolutionary processes of organisms during the Quaternary in northwestern China is examined using Haloxylon ammodendron. Based on the variation of two cpDNA regions (trnS-trnG and trnV) and one nDNA sequence (ITS1-ITS4) in 420 individuals from 36 populations, the spatial genetic structure and demographic history of H. ammodendron in arid China is examined. Median-joining network and Bayesian inference trees enabled the identification of three diverged lineages within H. ammodendron from 24 different haplotypes and 16 ribotypes, distributed across western (Xinjiang), eastern (Gansu and Inner Mongolia) and southern (Qinghai) regions. AMOVA analysis demonstrated that more than 80% of observed genetic variation related to lineage split was based on cpDNA and nDNA variation. Allopatric divergence among the three groups was mainly triggered by geographical isolation due to Xingxingxia rock and uplift of the Qilian Mountains during the Quaternary. Local adaptive differentiation among western, eastern and southern groups occurred due to gene flow obstruction resulting from arid landscape fragmentation accompanied by local environmental heterogeneity of different geographical populations. The southern margin of the Junggar Basin and the Tengger Desert possibly served as two independent glacial refugia for H. ammodendron. The distribution of genetic variation, coupled with SDMs and LCP results, indicated that H. ammodendron probably moved northward along the Junggar Basin and westward along Tengger Desert at the end of the last glacial maximum; postglacial re-colonization was probably westward and southward along the Hexi Corridor.
Chen et al. (2022) Diversification and historical demography of Haloxylon ammodendron in relation to Pleistocene climatic oscillations in northwestern China. PeerJ 10:e14476 https://doi.org/10.7717/peerj.14476
Population development and landscape preference of reintroduced wild ungulates: successful rewilding in Southern Italy
Background In the past decades, the abandonment of traditional land use practices has determined landscape changes inducing reforestation dynamics. This phenomenon can be contrasted with rewilding practices, i.e., the reintroduction of animals that may promote the recovery of landscape diversity. In this study, we explore the dynamics of expansion of two reintroduced populations of wild ungulates, Italian roe deer (Capreolus capreolus italicus) and red deer (Cervus elaphus), assessing their contribution in the recovery of landscape diversity. Methods By using direct and indirect information on the two species, collected by nocturnal and diurnal surveys and camera trapping, we modelled a habitat suitability map, and estimated the density and distribution of the populations. We also performed a land use changes analysis, combining the presence of wild ungulates and livestock. Results and Discussion We demonstrated that deer dispersed gradually from their release location, increasing in population size, and this occurred in the entire study area. Moreover, we show that areas with lower grazing density are significantly affected by forest encroachment. A possible interpretation of this result could be that wild grazers (roe deer and red deer) prefer semi-open areas surrounded by the forest. This, in association with other factors, such as domestic grazing, could be one of the main responsible in maintaining landscape mosaic typical of the Apennine mountain, confirming the value of grazers as a landscape management tool. Moreover, we show the possibility to conserve through reintroduction the vulnerable C.c. italicus.
Rivieccio et al. (2022) Population development and landscape preference of reintroduced wild ungulates: successful rewilding in Southern Italy. PeerJ 10:e14492 https://doi.org/10.7717/peerj.14492
Stigmatization towards healthcare personnel during the first COVID-19 wave in Central and Northern Mexico
The evidence all over the world shows an alarming increase in the stigmatization of health personnel during the COVID-19 pandemic. We sought to explore possible psychological factors that help explain the disposition to stigmatize health personnel in the central and northern regions of Mexico. Two studies explore possible psychological factors to explain the disposition to stigmatize healthcare personnel (HP) in Mexico during the COVID-19 pandemic. In study one, 520 participants responded to three instruments that measure the disposition to stigmatize, the perceived contagion risk, and the positive beliefs towards HP. Results showed a generalized low disposition to stigmatization, where only a small percentage obtained high scores. A regression analysis identified that stigmatization towards HP can derive mainly from the perception of risk of contagion, although positive beliefs of HP decrease this disposition. The second study extends this finding by analyzing responses of 286 participants to seven instruments measuring factors hypothesized as predictors towards stigmatization: uncertainty generated by the pandemic, selfish strategies to face off the pandemic, social capital, trust in institutions, perceived vulnerability of contagion, perceived risk of contagion, and positive beliefs towards HP. A path analysis reveals that the main predictor of stigmatization is the perceived risk of contagion, increased by the strategy of selfishness, and the uncertainty generated by the pandemic. These results are discussed emphasizing the importance of cooperation and community ties to prevent the stigmatization of HP in the context of sanitary emergencies generated by contagious diseases.
Cruz-Torres et al. (2022) Stigmatization towards healthcare personnel during the first COVID-19 wave in Central and Northern Mexico. PeerJ 10:e14503 https://doi.org/10.7717/peerj.14503
New estimators for estimating population total: an application to water demand in Thailand under unequal probability sampling without replacement for missing data
Water shortage could play an imperative role in the future due to an influx of water demand when compared to water supplies. Inadequate water could damage human life and other aspects related to living. This serious issue can be prevented by estimating the demand for water to bridge the small gap between demand and supplies for water. Some water consumption data recorded daily may be missing and could affect the estimated value of water demand. In this article, new ratio estimators for estimating population total are proposed under unequal probability sampling without replacement when data are missing. Two situations are considered: known or unknown mean of an auxiliary variable and missing data are missing at random for both study and auxiliary variables. The variance and associated estimators of the proposed estimators are investigated under a reverse framework. The proposed estimators are applied to data from simulation studies and empirical data on water demand in Thailand which contain some missing values, to assess the efficacies of the estimators.
Ponkaew et al. (2022) New estimators for estimating population total: an application to water demand in Thailand under unequal probability sampling without replacement for missing data. PeerJ 10:e14551 https://doi.org/10.7717/peerj.14551
DNA barcoding unveils a high diversity of caddisflies (Trichoptera) in the Mount Halimun Salak National Park (West Java; Indonesia)
Background Trichoptera are one of the most diverse groups of freshwater insects worldwide and one of the main bioindicators for freshwater quality. However, in many areas, caddisflies remain understudied due to lack of taxonomic expertise. Meanwhile, globally increasing anthropogenic stress on freshwater streams also threatens Trichoptera diversity. Methods To assess the Trichoptera diversity of the area within and around the Mount Halimun Salak National Park (MHSNP or Taman Nasional Gunung Halimun Salak) in West Java (Indonesia), we conducted a molecular-morphological study on Trichoptera diversity using larvae from a benthic survey and adults from hand-netting. In addition to morphological identification, we applied four different molecular taxon delimitation approaches (Generalized Mixed Yule Coalescent, Bayesian Poisson Tree Processes, Automatic Barcode Gap Discovery and Assemble Species by Automatic Partitioning) based on DNA barcoding of Cytochrome-C-Oxidase I (COI). Results The molecular delimitation detected 72 to 81 Operational Taxonomic Units (OTU). Only five OTUs could be identified to species level by comparing sequences against the BOLD database using BLAST, and four more to the genus level. Adults and larvae could be successfully associated in 18 cases across six families. The high diversity of Trichoptera in this area highlights their potential as bioindicators for water quality assessment. Conclusions This study provides an example of how molecular approaches can benefit the exploration of hidden diversity in unexplored areas and can be a valuable tool to link life stages. However, our study also highlights the need to improve DNA barcode reference libraries of Trichoptera for the Oriental region.
Kilian et al. (2022) DNA barcoding unveils a high diversity of caddisflies (Trichoptera) in the Mount Halimun Salak National Park (West Java; Indonesia). PeerJ 10:e14182 https://doi.org/10.7717/peerj.14182
Miocene Cupressinoxylon from Gökçeada (Imbros), Turkey with Protophytobia cambium mining and the study of ecological signals of wood anatomy
Premise The recognition of the Miocene Climate Optimum (MCO) in terrestrial palaeoenvironments of the Eastern Mediterranean is restricted to Lesbos and Lemnos Islands, Greece. This area is significant for its wood microfossils. A recently-discovered fossil wood assemblage from Gökçeada (Imbros) Island, Turkey, including tree species similar to the Greek findings, is thought to have an early Miocene age. Here, we revise the age of the latter plant fossiliferous locality, re-evaluate the area for the study of MCO for the terrestrial palaeoecosystems of the Eastern Mediterranean and the nomenclature errors referring to the occurrence of fossil wood. We present the plant–insect–environment interactions using detailed anatomical descriptions, of an extinct conifer and its extinct cambium miner feeding traces observed in its secondary xylem. Methods Three thin sections were prepared with standard palaeoxylotomical techniques from a small section of the silicified wood; the sections were observed under a light microscope. The anatomy of the conifer and its damage patterns were compared with those of extant and fossil Cupressaceae and Agromyzidae, respectively. Pivotal results The common anatomical features of the studied wood specimen and Hesperocyparis macrocarpa (Hartw.) Bartel and a shared characteristic (the number of the cross-field pits – a feature we consider of diagnostic value) with Xanthocyparis vietnamensis Farjon & T.H. Nguyên led to its assignment to the Hesperocyparis–Xanthocyparis–Callitropsis clade. The detailed study of the wound scars and anatomical abnormalities, the anatomical–environmental associations, and structural–functional reactions follow the identification of the wood’s anatomy sensu Carlquist providing decisive results. Conclusions Based on the distinctive characteristics presented, we identify our macrofossil as Cupressinoxylon matromnense Grambast, a stem or an extinct lineage of the Hesperocyparis–Xanthocyparis vietnamensis–Callitropsis nootkatensis clade with feeding traces of the fossil cambium miner of the genus Protophytobia Süss (Diptera: Agromyzidae), and anatomical damage and reaction tissue on adventitious shoots. The use of Protopinaceae and Pinoxylon F. H. Knowlton from the eastern Mediterranean are re–evaluated and corrections are provided. The age of the studied plant fossiliferous locality in Gökçeada is revised as middle Miocene, allowing the proposal of an eastern Mediterranean MCO hotspot, including Lesbos, Lemnos, and Gökçeada (Imbros) Islands.
Mantzouka et al. (2022) Miocene Cupressinoxylon from Gökçeada (Imbros), Turkey with Protophytobia cambium mining and the study of ecological signals of wood anatomy. PeerJ 10:e14212 https://doi.org/10.7717/peerj.14212
A manikin or human simulator—development of a tool for measuring students’ perception
Background Education with the use of medical simulation may involve the use of two modalities: manikins or standardized patients (SPs) to meet specific learning objectives. We have collected students’ opinions about the two modalities which can be helpful in planning and evaluating the curriculum process. Although reviews or comparisons of student opinions appear in the literature, it is difficult to find a scale that would be based on a comparison of specific effects that can be obtained in the educational process. In order to fill this gap, an attempt was made to construct a questionnaire. Methods An experimental version of a questionnaire measuring the final-year students’ (273) opinions about the effectiveness of both simulation techniques has been designed on the basis of semi-structured interviews. They were conducted with 14 final-year students excluded from the subsequently analyzed cohort. The scale has been completed, tested and validated. Results The authors developed a 33-statement questionnaire which contain two scales: teaching medicine with the manikins and with the SPs. Two factors were identified for each scale: Doctor-patient relationship and practical aspects. The scales can be used complementary or separately, as the article reports independent statistics for each scale. The Cronbach’s alpha coefficient for the manikin scale is 0.721 and for the SP scale is 0.758. Conclusions The questionnaire may be applied to medical students to identify their opinions about using manikins and SPs in teaching. It may have an important impact for planning curriculum and implementing particular modalities in accordance with the intended learning objectives.
Torres et al. (2022) A manikin or human simulator—development of a tool for measuring students’ perception. PeerJ 10:e14214 https://doi.org/10.7717/peerj.14214
Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework
Terrestrial mammals face a severe crisis of habitat loss worldwide. Therefore, assessing information on habitat loss throughout different time periods is crucial for assessing species’ conservation statuses based on the IUCN Red List system. To support the national extinction risk assessment in Brazil (2016–2022), we developed a script that uses the MapBiomas Project 6.0 data source of land cover and land use (annual maps at 30 m scale) within the Google Earth Engine (GEE) platform to calculate habitat loss. We defined suitable habitats from the MapBiomas Project land cover classification for 190 mammalian taxa, according to each species range map and ecological characteristics. We considered a period of three generation lengths to assess habitat loss in accordance with the Red List assessment criteria. We used the script to estimate changes in available habitat throughout the analyzed period within the species’ known ranges. The results indicated that habitat loss occurred within 94.3% of the analyzed taxa range, with the Carnivora order suffering the greatest habitat loss, followed by the Cingulata order. These analyses may be decisive for applying criteria, defining categories during the assessment of at least 17 species (9%), enriching discussions, and raising new questions for several other species. We considered the outcome of estimating habitat loss for various taxa when applying criterion A, which refers to population reduction, thus supporting more accurate inferences about past population declines.
Butti et al. (2022) Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework. PeerJ 10:e14289 https://doi.org/10.7717/peerj.14289
Wildlife overpass structure size, distribution, effectiveness, and adherence to expert design recommendations
It is now well evidenced that wildlife crossing structures paired with exclusion fencing reduce wildlife vehicles collisions while facilitating wildlife connectivity across roadways. Managing animal mortality and subpopulation connectivity is crucial to successful species and landscape stewardship. Highway mitigation projects are large economic investments that remain on the landscape for many decades. Governments and planning agents thus strive to balance cost and benefit to build cost-effective structures with the greatest positive impact on local wildlife and motorists. Ideal dimensions of overpasses and underpasses vary by species, but scientists generally suggest that overpasses for large mammals should be approximately 50 m wide. Optimal width also depends on structure length, with longer structures requiring additional width. Accordingly, experts have suggested a width to length ratio of 0.8. We sought to assess how these recommendations manifested in practice—where agencies use this information to design and build structures while also balancing cost and logistical challenges—and the degree to which built structures conform to current recommendations. We identified 120 wildlife overpasses across the world that were constructed to reduce the negative impacts of roads. Using a novel measurement technique, we analyzed the dimensions of these 120 overpasses located in North America, Europe, Asia, and Oceania. The average width of the wildlife overpasses was 34 m. Most wildlife overpasses located in North America and Europe did not meet their respective dimensional expert guidelines. We investigate reasons explaining the non-compliance and provide recommendations for future overpass designs. Building on previous evidence showing that wider overpasses have increased crossing rates, we examined crossing rates for multiple large mammal species across 12 overpasses located in western North America. We qualitatively observed that wider North American overpasses (40–60 m), in or near compliance with expert guidelines, were associated with a more diverse set of species use and had nearly twice the average crossing rates when compared to non-compliant, narrow North American overpasses. In reviewing various studies from around the world, we conclude that wide overpasses (~50 m) continue to present ecologically sound and cost-effective solutions for decreasing the barrier of roadways, especially when targeting width-sensitive species and large assemblages of mammals. Future studies, however, are encouraged to further explore the specific instances when underpasses and narrower overpasses present more cost-effective ecological solutions, or how these structures can complement wide overpasses in successful wildlife crossing systems.
Brennan et al. (2022) Wildlife overpass structure size, distribution, effectiveness, and adherence to expert design recommendations. PeerJ 10:e14371 https://doi.org/10.7717/peerj.14371
Composition of terrestrial mammal assemblages and their habitat use in unflooded and flooded blackwater forests in the Central Amazon
Several forest types compose the apparently homogenous forest landscape of the lowland Amazon. The seasonally flooded forests (igapós) of the narrow floodplains of the blackwater rivers of the Amazon basin support their community of animals; however, these animals are required to adapt to survive in this environment. Furthermore, several taxa are an important source of seasonal resources for the animals in the adjacent unflooded forest (terra firme). During the low-water phase, the igapó becomes available to terrestrial species that make use of terra firme and igapó forests. Nonetheless, these lateral movements of terrestrial mammals between hydrologically distinct forest types remain poorly understood. This study tested the hypothesis that the attributes of the assemblages (abundance, richness, evenness, and functional groups) of the terrestrial mammals in both these forest types of the Cuieiras River basin, which is located in the Central Amazon, are distinct and arise from the ecological heterogeneity induced by seasonal floods. After a sampling effort of 10,743 camera trap days over four campaigns, two for the terra firme (6,013 trap days) and two for the igapó forests (4,730 trap days), a total of 31 mammal species (five were considered eventual) were recorded in both forest types. The species richness was similar in the igapó and terra firme forests, and the species abundance and biomass were greater in the terra firme forest, which were probably due to its higher primary productivity; whereas the evenness was increased in the igapós when compared to the terra firme forest. Although both forest types shared 84% of the species, generally a marked difference was observed in the composition of the terrestrial mammal species. These differences were associated with abundances of some specific functional groups, i.e., frugivores/granivores. Within-group variation was explained by balanced variation in abundance and turnover, which the individuals of a given species at one site were substituted by an equivalent number of individuals of a different species at another site. However, the occupancy was similar between both forest types for some groups such as carnivores. These findings indicate that seasonal flooding is a relevant factor in structuring the composition of terrestrial mammal assemblages between terra firme and floodplain forests, even in nutrient-poor habitats such as igapós. The results also highlight the importance of maintaining the mosaic of natural habitats on the scale of the entire landscape, with major drainage basins representing management units that provide sufficiently large areas to support a range of ecological processes (e.g., nutrient transport, lateral movements and the persistence of apex predators).
Gonçalves et al. (2022) Composition of terrestrial mammal assemblages and their habitat use in unflooded and flooded blackwater forests in the Central Amazon. PeerJ 10:e14374 https://doi.org/10.7717/peerj.14374
Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest
The influence of nutrient availability on transpiration is not well understood, in spite of the importance of transpiration to forest water budgets. Soil nutrients have the potential to affect tree water use through indirect effects on leaf area or stomatal conductance. For example, following addition of calcium silicate to a watershed at Hubbard Brook, in New Hampshire, streamflow was reduced for 3 years, which was attributed to a 25% increase in evapotranspiration associated with increased foliar production. The first objective of this study was to quantify the effect of nutrient availability on sap flux density in a nitrogen, phosphorus, and calcium addition experiment in New Hampshire in which tree diameter growth, foliar chemistry, and soil nutrient availability had responded to treatments. We measured sap flux density in American beech (Fagus grandifolia, Ehr.), red maple (Acer rubrum L.), sugar maple (Acer saccharum Marsh.), white birch (Betula papyrifera Marsh.), or yellow birch (Betula alleghaniensis Britton.) trees, over five years of experiments in five stands distributed across three sites. In 2018, 3 years after a calcium silicate addition, sap flux density averaged 36% higher in trees in the treatment than the control plot, but this effect was not very significant (p = 0.07). Our second objective was to determine whether this failure to detect effects with greater statistical confidence was due to small effect sizes or high variability among trees. We found that tree-to-tree variability was high, with coefficients of variation averaging 39% within treatment plots. Depending on the species and year of the study, the minimum difference in sap flux density detectable with our observed variability ranged from 46% to 352%, for a simple ANOVA. We analyzed other studies reported in the literature that compared tree water use among species or treatments and found detectable differences ranging from 16% to 78%. Future sap flux density studies could benefit from power analyses to guide sampling intensity. Including pretreatment data, in the case of manipulative studies, would also increase statistical power.
Rice et al. (2022) Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest. PeerJ 10:e14410 https://doi.org/10.7717/peerj.14410
Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics
Docynia delavayi (Franch.) Schneid is an evergreen tree with multiple benefits and high development and utilization value. The fruit is consumed as fresh and dry fruit, juices, and other products. However, it is unknown the chemical changes that occur upon fruit maturation. The metabolite content of unripe and ripe fruit was examined using UPLC-MS/MS technology based on a broadly targeted metabolome. We identified 477 metabolites, of which 130 differed between ripe and unripe fruit. These compounds are primarily involved in the biosynthesis of secondary metabolites, such as pantothenic acid, flavonoids, and amino acids. Moreover, in ripe fruit, there are 94 metabolites that are upregulated, particularly flavonoids and terpenoids. In comparison, compounds associated with sour flavors (amino acids, phenolic acids, organic acids) are down-regulated. Remarkably, these metabolites have a strong relationship with the medicinal properties of D. delavayi. This study provides a global perspective of the D. delavayi fruit metabolome and a comprehensive analysis of metabolomic variations during fruit development, thereby increasing the knowledge of the metabolic basis of important fruit quality traits in D. delavayi fruit.
Chen et al. (2022) Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics. PeerJ 10:e14441 https://doi.org/10.7717/peerj.14441
Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi)
The establishment of new symbiotic interactions between introduced species may facilitate invasion success. For instance, tawny crazy ant (Nylanderia fulva Mayr) is known to be an opportunistic tender of honeydew producing insects and this ants’ symbiotic interactions have exacerbated agricultural damage in some invaded regions of the world. The invasive sorghum aphid (Melanaphis sorghi Theobald) was first reported as a pest in the continental United States–in Texas and Louisiana–as recent as 2013, and tawny crazy ant (TCA) was reported in Texas in the early 2000s. Although these introductions are relatively recent, TCA workers tend sorghum aphids in field and greenhouse settings. This study quantified the tending duration of TCA workers to sorghum aphids and the impact of TCA tending on aphid biomass. For this study aphids were collected from three different host plant species (i.e., sugarcane, Johnson grass, and sorghum) and clone colonies were established. Sorghum is the main economic crop in which these aphids occur, hence we focused our study on the potential impacts of interactions on sorghum. Quantification of invasive ant-aphid interactions, on either stems or leaves of sorghum plants, were conducted in greenhouse conditions. Our results show that although these two invasive insect species do not have a long coevolutionary history, TCA developed a tending interaction with sorghum aphid, and aphids were observed excreting honeydew after being antennated by TCA workers. Interestingly, this relatively recent symbiotic interaction significantly increased overall aphid biomass for aphids that were positioned on stems and collected from Johnson grass. It is recommended to continue monitoring the interaction between TCA and sorghum aphid in field conditions due to its potential to increase aphid populations and sorghum plant damage.
Holt et al. (2022) Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi). PeerJ 10:e14448 https://doi.org/10.7717/peerj.14448
Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole
Background Insufficient low temperatures in winter and soil residues caused by paclobutrazol (PBZ) application pose a considerable challenge for mango floral induction (FI). Gibberellin inhibitors SPD (compound of mepiquat chloride, prohexadione-calcium and uniconazole) had a significant influence on enhancing the flowering rate and yield of mango for two consecutive years (2020–2021). Researchers have indicated that FI is regulated at the metabolic level; however, little is known about the metabolic changes during FI in response to SPD treatment. Methods Here, ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based widely targeted metabolomic analysis was carried out to assess the metabolic differences in the mango stem apex during different stage of mango FI (30, 80, 100 days after SPD/water treatment). Results A total of 582 compounds were annotated and 372 metabolites showed two-fold differences in abundance (variable importance in projection, VIP ≥ 1 and fold change, FC≥ 2 or≤ 0.5) between buds at 30, 80, 100 days after SPD/water treatment or between buds under different treatment. Lipids, phenolic acids, amino acids, carbohydrates, and vitamins were among metabolites showing significant differences over time after SPD treatment. Here, 18 out of 20 lipids, including the lysophosphatidylethanolamine (12, LPE), lysophosphatidylcholine (7, LPC), and free fatty acids (1, FA), were significantly upregulated from 80 to 100 days after SPD treatment comared to water treatment. Meanwhile, the dormancy release of mango buds from 80 to 100 days after SPD treatment was accompanied by the accumulation of proline, ascorbic acid, carbohydrates, and tannins. In addition, metabolites, such as L-homocysteine, L-histidine, and L-homomethionine, showed more than a ten-fold difference in relative abundance from 30 to 100 days after SPD treatment, however, there were no significant changes after water treatment. The present study reveals novel metabolites involved in mango FI in response to SPD, which would provide a theoretical basis for utilizing SPD to induce mango flowering.
Liang et al. (2022) Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole. PeerJ 10:e14458 https://doi.org/10.7717/peerj.14458
An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients
Background The severe form of COVID-19 can cause a dysregulated host immune syndrome that might lead patients to death. To understand the underlying immune mechanisms that contribute to COVID-19 disease we have examined 28 different biomarkers in two cohorts of COVID-19 patients, aiming to systematically capture, quantify, and algorithmize how immune signals might be associated to the clinical outcome of COVID-19 patients. Methods The longitudinal concentration of 28 biomarkers of 95 COVID-19 patients was measured. We performed a dimensionality reduction analysis to determine meaningful biomarkers for explaining the data variability. The biomarkers were used as input of artificial neural network, random forest, classification and regression trees, k-nearest neighbors and support vector machines. Two different clinical cohorts were used to grant validity to the findings. Results We benchmarked the classification capacity of two COVID-19 clinicals studies with different models and found that artificial neural networks was the best classifier. From it, we could employ different sets of biomarkers to predict the clinical outcome of COVID-19 patients. First, all the biomarkers available yielded a satisfactory classification. Next, we assessed the prediction capacity of each protein separated. With a reduced set of biomarkers, our model presented 94% accuracy, 96.6% precision, 91.6% recall, and 95% of specificity upon the testing data. We used the same model to predict 83% and 87% (recovered and deceased) of unseen data, granting validity to the results obtained. Conclusions In this work, using state-of-the-art computational techniques, we systematically identified an optimal set of biomarkers that are related to a prediction capacity of COVID-19 patients. The screening of such biomarkers might assist in understanding the underlying immune response towards inflammatory diseases.
Martinez et al. (2022) An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients. PeerJ 10:e14487 https://doi.org/10.7717/peerj.14487
A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture
Cell density signaling drives tendon morphogenesis by regulating both procollagen production and cell proliferation. The signal is composed of a small, highly conserved protein (SNZR P) tightly bound to a tissue-specific, unique lipid (SNZR L). This allows the complex (SNZR PL) to bind to the membrane of the cell and locally diffuse over a radius of ~1 mm. The cell produces low levels of this signal but the binding to the membrane increases with the number of tendon cells in the local environment. In this article SNZR P was produced in E.coli and SNZR L was chemically synthesized. The two bind together when heated to 60 °C in the presence of Ca++ and Mg++ and the synthesized SNZR PL at ng/ml levels can replace serum. Adding SNZR PL to the medium was also tested on primary tendon cells from adult roosters. The older cells were in a maintenance state in vivo and in cell culture they proliferate more slowly than embryonic cells. Nevertheless, after reaching a moderately high cell density, they produced high levels of procollagen similar to the embryonic cells. This data was not expected from older cells but suggests that adult tendon cells can regenerate the tissue after injury when given the correct signals.
Schwarz (2022) A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture. PeerJ 10:e14533 https://doi.org/10.7717/peerj.14533
Treatment outcome of class II malocclusion therapy including extraction of maxillary first molars: a cephalometric comparison between normodivergent and hyperdivergent facial types
Background The dentoalveolar component of a Class II division 1 malocclusion can be orthodontically treated either with extractions or by distalization of the molars. This study aimed to compare skeletal, dentoalveolar and profile changes in normodivergent and hyperdivergent Class II Division I growing patients orthodontically treated with fixed appliances including maxillary first molar extraction. Methods Sixty-four patients treated orthodontically with full fixed appliances including maxillary first molar extractions were retrospectively analyzed. Patients were divided into a normodivergent group (Group N; 30° ≤ SN^GoGn < 36°) consisting of 38 patients (17M, 21F; mean age 13.2 ± 1.3 years) and a hyperdivergent (Group H; SN^GoGn ≥ 36°) including 26 patients (12M, 14F; mean age 13.7 ± 1.1 years). Lateral cephalograms were available before (T0) and after treatment (T1) and cephalometric changes were calculated for 10 linear and 13 angular variables. The Shapiro–Wilk test confirmed a normal distribution of data, hence parametric tests were employed. The Student t-test was used to compare groups at baseline. The paired t-test was used to analyze intragroup changes between timepoints, and the Student t-test for intergroup comparisons. The level of significance was set at 0.05. Results The Class II division 1 malocclusion was successfully corrected, and the facial profile improved both in normodivergent and hyperdivergent patients. Divergency increased by 0.76 ± 1.99° in Group N (p = 0.02) while it decreased −0.23 ± 2.25° (p = 0.60); These changes were not significant between groups after treatment (p = 0.680). Most dentoskeletal measurements changed significantly within groups but none of them showed statistically significant differences between groups after treatment. Dental and soft tissue changes were in accordance with the biomechanics used for this Class II orthodontic therapy. Discussion The effect of orthodontic treatment of Class II division 1 malocclusion including extraction of the maxillary first molars in growing patients can be considered clinically equivalent in normodivergent and hyperdivergent patients. For this reason, this orthodontic treatment can be considered a viable option in the armamentarium of the Class II Division I therapy for both facial types.
Booij et al. (2022) Treatment outcome of class II malocclusion therapy including extraction of maxillary first molars: a cephalometric comparison between normodivergent and hyperdivergent facial types. PeerJ 10:e14537 https://doi.org/10.7717/peerj.14537
Association between type 2 diabetes and 5-year overall survival in early-stage pancreatic cancer: a retrospective cohort study
Background This study examined the association between type 2 diabetes mellitus (T2DM) and 5-year overall survival (OS) in patients with pancreatic cancer (PC). Methods This retrospective cohort study included patients diagnosed with stage I/II PC at Shengjing Hospital of China Medical University from January 2012 to December 2017. All patients had pancreatic ductal adenocarcinoma or its subtypes. The outcome was the 5-year OS rate based on data from the patient charts. Data analysis was performed using SPSS 22.0 Results A total of 238 patients were included: 72 with T2DM and 166 without T2DM. There were significant differences in blood glucose levels and OS between the two groups (all P < 0.05). The median OS was 11.4 (95% confidence interval CI [8.49–14.31]) months in the T2DM group and 16.3 (95% CI [12.44–20.16], P = 0.023) months in the non-T2DM group. After adjustment for confounders, T2DM was an independent factor affecting 5-year OS (P = 0.010). Compared with non-T2DM patients, T2DM patients had a higher risk of death (HR = 1.475, 95% CI [1.096–1.985]). Conclusions T2DM is associated with 5-year OS in patients with PC.
Tang et al. (2022) Association between type 2 diabetes and 5-year overall survival in early-stage pancreatic cancer: a retrospective cohort study. PeerJ 10:e14538 https://doi.org/10.7717/peerj.14538
Using solar radiation data in soil moisture diagnostic equation for estimating root-zone soil moisture
The soil moisture daily diagnostic equation (SMDE) evaluates the relationship between the loss function coefficient and the summation of the weighted average of precipitation. The loss function coefficient uses the day of the year (DOY) to approximate the seasonal changes in soil moisture loss for a given location. Solar radiation is the source of the energy that drives the complex and intricates of the earth-atmospheric processes and biogeochemical cycles in the environment. Previous research assumed DOY is the approximation of other environmental factors (e.g., temperature, wind speed, solar radiation). In this article, two solar radiation parameters were introduced, i.e., the actual solar radiation and the clear sky solar radiation and were incorporated into the loss function coefficient to improve its estimation. This was applied to 2 years of continuous rainfall, soil moisture data from USDA soil climate network (SCAN) sites AL2053, GA2027 MS2025, and TN2076. It was observed that the correlation coefficient between the observed soil moisture and B values (which is the cumulated average of rainfall to soil moisture loss) increased on average by 2.3% and the root mean square errors (RMSEs) for estimating volumetric soil moisture at columns 0–5, 0–10, 0–20, 0–50, 0–100 cm reduced on average by 8.6% for all the study sites. The study has confirmed that using actual solar radiation data in the soil moisture daily diagnostic equation can improve its accuracy.
Omotere et al. (2022) Using solar radiation data in soil moisture diagnostic equation for estimating root-zone soil moisture. PeerJ 10:e14561 https://doi.org/10.7717/peerj.14561
Autumnal migration patterns of hoverflies (Diptera: Syrphidae): interannual variability in timing and sex ratio
Background The migration of hoverflies (Diptera: Syrphidae) is a well-known phenomenon, with growing interest due to the ecosystem services provided by migrants. However, we still lack fundamental data on species composition, timing of migration, or sex ratio of migrants. To address this gap, we focused on the southward autumnal migration of hoverflies through central Europe. Methods To recognize migrating individuals from resident ones, we used a pair of one-side-blocked Malaise traps, exposed in a mountain pass in the Jeseníky mountains, Czech Republic, where a mass migration of hoverflies takes place annually. Traps were set for 4 years, from August to October. Results In total, we recorded 31 species of migrating hoverflies. The timing of migration differed between the years, taking place from the beginning of September to the end of October. Differences in phenology were observed in the four most common migrant species, where larger species seemed to migrate earlier or at the same time compared to the smaller ones. The sex ratio was strongly asymmetrical in most common species Episyrphus balteatus, Eupeodes corollae, and Sphaerophoria scripta, and varied between years for each species. Weather conditions strongly influenced the migration intensity at ground-level: hoverflies migrate mainly during days with south wind, high temperature, high atmospheric pressure, and low precipitation.
Hlaváček et al. (2022) Autumnal migration patterns of hoverflies (Diptera: Syrphidae): interannual variability in timing and sex ratio. PeerJ 10:e14393 https://doi.org/10.7717/peerj.14393
Anti-Acanthamoeba activity of a semi-synthetic mangostin derivative and its ability in removal of Acanthamoeba triangularis WU19001 on contact lens
Garcinia mangostana L., also known as the mangosteen tree, is a native medicinal plant in Southeast Asia having a wide variety of pharmacologically active compounds, including xanthonoid mangostin. In this study, we examined the pharmacological activities of the selected semi-synthetic mangostin derivative, namely, amoebicidal activity, encystation inhibition, excystation activity, and removal capacity of adhesive Acanthamoeba from the surface of contact lens (CL). Among the three derivatives, C1 exhibited promising anti-Acanthamoeba activity against Acanthamoeba triangularis WU19001 trophozoites and cysts. SEM images displayed morphological changes in Acanthamoeba trophozoites, including the loss of acanthopodia, pore formation in the cell membrane, and membrane damage. In addition, the treated cyst was shrunken and adopted an irregular flat cyst shape. Under a fluorescence microscope, acridine orange and propidium iodide (AO/PI) staining revealed C1 induced condensation of cytoplasm and chromatin with the loss of cell volume in the treated trophozoites, while calcofluor white staining demonstrated the leakage of cell wall in treated cysts, leading to cell death. Interestingly, at the concentration ranges in which C1 showed the anti-Acanthamoeba effects (IC50 values ranging from 0.035–0.056 mg/mL), they were not toxic to Vero cells. C1 displayed the highest inhibitory effect on A. triangularis encystation at 1/16×MIC value (0.004 mg/mL). While C1 demonstrated the excystation activity at 1/128×MIC value with a high rate of 89.47%. Furthermore, C1 exhibited the removal capacity of adhesive Acanthamoeba from the surface of CL comparable with commercial multipurpose solutions (MPSs). Based on the results obtained, C1 may be a promising lead agent to develop a therapeutic for the treatment of Acanthamoeba infections and disinfectant solutions for CL.
Chuprom et al. (2022) Anti-Acanthamoeba activity of a semi-synthetic mangostin derivative and its ability in removal of Acanthamoeba triangularis WU19001 on contact lens. PeerJ 10:e14468 https://doi.org/10.7717/peerj.14468
Analysis of influencing factors of serum total protein and serum calcium content in plasma donors
Background and objectives The adverse effects of plasma donation on the body has lowered the odds of donation. The aim of this study was to investigate the prevalence of abnormal serum calcium and total serum protein related to plasma donation, identify the influencing factors, and come up with suggestions to make plasma donation safer. Methods Donors from 10 plasmapheresis centers in five provinces of China participated in this study. Serum samples were collected before donation. Serum calcium was measured by arsenazo III colorimetry, and the biuret method was used for total serum protein assay. An automatic biochemical analyzer was used to conduct serum calcium and total serum protein tests. Results The mean serum calcium was 2.3 ± 0.15 mmol/L and total serum protein was 67.75 ± 6.02 g/L. The proportions of plasma donors whose serum calcium and total serum protein were lower than normal were 20.55% (815/3,966) and 27.99% (1,111/3,969), respectively. There were significant differences in mean serum calcium and total serum protein of plasma donors with different plasma donation frequencies, gender, age, regions, and body mass index (BMI), (all p < 0.05). Logistic regression analysis revealed that donation frequencies, age, BMI and regions were significantly associated with a higher risk of low serum calcium level, and donation frequencies, gender, age and regions were significant determinants factors of odds of abnormal total serum protein. Conclusions Donation frequencies, gender, age, regions, and BMI showed different effects on serum calcium and total serum protein. More attention should be paid to the age, donation frequency and region of plasma donors to reduce the probability of low serum calcium and low total serum protein.
Liu et al. (2022) Analysis of influencing factors of serum total protein and serum calcium content in plasma donors. PeerJ 10:e14474 https://doi.org/10.7717/peerj.14474
The influence of parenting style and coping behavior on nonsuicidal self-injury behavior in different genders based on path analysis
Background Nonsuicidal self-injury (NSSI) behaviors—an important factor that profoundly affects the physical and mental health of young people—are induced by complex and diverse factors, while showing significant differences at the gender level. We examined mediating behaviors among parenting styles, students’ coping styles, and endogenous and exogenous influencing variables of adolescents’ NSSI behaviors. Methods In this cross-sectional study, Secondary school students in Ningbo, Zhejiang Province, China (n = 2,689; F/M:1532/1157) were surveyed for basic attributes, parenting styles, coping styles, and NSSI behaviors. After the initial screening of the sample data, several external derivatives were screened based on the single factor analysis method. On this basis, the construction of path analysis models under multivariate multiple elicitations was carried out. Results The overall prevalence of NSSI was 15.16%, and the incidence of NSSI in boys was lower than that in girls (OR = 0.334, 95% CI [0.235–0.474]). The path analysis model data fit well; the indicators of female and male part are: CFI = 0.913/0.923, GFI = 0.964/0.977, SRMR = 0.055/0.047, RMSEA = 0.097/0.069 with 90% confidence interval (CI) [0.084–0.111]/[0.054–0.084]. For female, when negative coping style and extreme education affect NSSI respectively, the standardized path coefficient values are 0.478 (z = 20.636, P = 0.000 < 0.01) and 0.151 (z = 6.524, P = 0.000 < 0.01) respectively, while for male, the corresponding values become 0.225 (z = 7.057, P < 0.001) and 0.104 (z = 3.262, P < 0.001). Conclusion In particular, we investigated the mediating effects of gender-specific NSSI influences and found that NSSI behaviors were strongly associated with environmental variables and individual factors, especially family parenting style and adolescent coping style, which influenced NSSI in a gender-specific manner. The results showed that males were the target of both positive and negative parenting styles, whereas females were more likely to choose negative coping styles directed towards emotions in response to external stimuli, and instead showed a more significant predisposition towards NSSI behaviors. This phenomenon seems to be influenced by multilevel factors such as sociocultural, individual value identity, and physiological structure differences. In the path analysis model with the introduction of mediating effects, the influence of gender differences on NSSI behavior becomes more pronounced under the interaction of multiple factors: women seem to be more significantly influenced by the external derivatives in the internal derivatives than male subjects, and are more likely to trigger NSSI behavior under the interaction of multiple factors. These findings effectively reveal the significant role of different end-influencing factors in NSSI behaviors at the level of gender differences, which can provide effective theoretical support to prevent and treat NSSI behaviors in adolescents.
Cheng et al. (2022) The influence of parenting style and coping behavior on nonsuicidal self-injury behavior in different genders based on path analysis. PeerJ 10:e14507 https://doi.org/10.7717/peerj.14507
Biomechanical analyses of pterygotid sea scorpion chelicerae uncover predatory specialisation within eurypterids
Eurypterids (sea scorpions) are extinct aquatic chelicerates. Within this group, members of Pterygotidae represent some of the largest known marine arthropods. Representatives of this family all have hypertrophied, anteriorly-directed chelicerae and are commonly considered Silurian and Devonian apex predators. Despite a long history of research interest in these appendages, pterygotids have been subject to limited biomechanical investigation. Here, we present finite element analysis (FEA) models of four different pterygotid chelicerae—those of Acutiramus bohemicus, Erettopterus bilobus, Jaekelopterus rhenaniae, and Pterygotus anglicus—informed through muscle data and finite element models (FEMs) of chelae from 16 extant scorpion taxa. We find that Er. bilobus and Pt. anglicus have comparable stress patterns to modern scorpions, suggesting a generalised diet that probably included other eurypterids and, in the Devonian species, armoured fishes, as indicated by co-occurring fauna. Acutiramus bohemicus is markedly different, with the stress being concentrated in the proximal free ramus and the serrated denticles. This indicates a morphology better suited for targeting softer prey. Jaekelopterus rhenaniae exhibits much lower stress across the entire model. This, combined with an extremely large body size, suggests that the species likely fed on larger and harder prey, including heavily armoured fishes. The range of cheliceral morphologies and stress patterns within Pterygotidae demonstrate that members of this family had variable diets, with only the most derived species likely to feed on armoured prey, such as placoderms. Indeed, increased sizes of these forms throughout the mid-Palaeozoic may represent an ‘arms race’ between eurypterids and armoured fishes, with Devonian pterygotids adapting to the rapid diversification of placoderms.
Bicknell et al. (2022) Biomechanical analyses of pterygotid sea scorpion chelicerae uncover predatory specialisation within eurypterids. PeerJ 10:e14515 https://doi.org/10.7717/peerj.14515
Generation of raptor diversity in Europe: linking speciation with climate changes and the ability to migrate
Europe holds a rich community of diurnal birds of prey, and the highest proportion of transcontinental migratory raptorial species of any landmass. This study will test the hypotheses that the high diversification of the raptor assemblage in Europe is a recent event, that closely related species sharing the same trophic niches can only coexist in sympatry during the breeding period, when food availability is higher, and finally that migration is a function of size, with the smaller species in every trophic group moving further. A consensus molecular phylogeny for the 38 regular breeding species of raptors in Europe was obtained from BirdTree (www.birdtree.org). For the same species, a trophic niche cluster dendrogram was constructed. Size and migratory strategy were introduced in the resulting phylogeny, where trophic groups were also identified. Multispecific trophic groups tended to be composed of reciprocal sister species of different sizes, while monospecific groups (n = 3) were composed of highly specialized species. Many speciation events took place recently, during the glacial cycles of the Quaternary, and size divergence among competing species may be due to character displacement. Nowadays, the smaller species in every trophic group migrate to sub-Saharan Africa. This investigation illustrates how the rich assemblage of diurnal birds of prey in Europe, more diverse and more migratory than, for instance, the North American assemblage at equivalent latitudes, has emerged recently due to the multiplication of look-alike species with similar trophic ecologies, possibly in climate refugia during cold periods.
Negro et al. (2022) Generation of raptor diversity in Europe: linking speciation with climate changes and the ability to migrate. PeerJ 10:e14505 https://doi.org/10.7717/peerj.14505
Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost
Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.
Chang et al. (2022) Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost. PeerJ 10:e14426 https://doi.org/10.7717/peerj.14426
Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults
Background Adequate trunk muscle endurance is considered to be an important indicator of good low back stability; therefore, its assessment is needed when determining an individual’s risk for back pain. Optimal tests to assess each trunk muscle group separately are difficult to find. The objective of this study was to verify if two groups of trunk muscle endurance tests (standard and alternative) show comparable results in terms of muscle endurance ratios, holding times and rated perceived effort to perform each test. Methods The study was designed as a quasi-experimental repeated-measures design. There was a single group of participants who took part in two different trunk muscle endurance testing. Sixty-eight healthy adult volunteers, aged 20–45 years (31.9 ± 7.2 years), without recent musculoskeletal injury or disorder participated in the study. All participants finished the study. Trunk muscle endurance tests as tested on the Roman chair (B tests) were compared with standard tests as suggested by McGill (A tests). Each group of tests consisted of an endurance test for trunk extensors, trunk flexors, and lateral trunk muscles for left and right side. The order of tests’ performances was randomly assigned to each participant, whereby a participant did perform A and B tests in the same order. In each test of A and B the holding time was recorded and a perceived effort in each test performance was also assessed by participants. Post testing performance the four ratios of trunk muscles endurance comparison were calculated for each group of tests to determine if there is a good or poor ratio between muscles. Results of each participant were compared for trunk muscle endurance ratio calculations, holding times and rated perceived effort for A and B tests. Results Results showed comparable trunk muscle endurance ratios in the three ratios observed, except for the flexors:extensors ratio (AFL:EX: 1.2 (IQR: 0.7–1.6) vs. BFL:EX: 0.6 (IQR: 0.3–0.8); p < 0.001). As compared to A tests, holding times were significantly longer in B tests for the extensors (AEX: 125.5 s (IQR: 104.8–182.8 s) vs. BEX: 284.0 s (IQR: 213.0–342.3 s); p < 0.001) and lateral trunk muscles (AL-LM: 61.0 s (IQR: 48.3–80.8 s) vs. BL-LM: 131.5 s (IQR: 95.5–158.5 s); AR-LM: 63.5 s (IQR: 45.8–77.3 s) vs. BR-LM: 113.0 s (IQR: 86.3–148.8 s); p < 0.001), both were also rated as slightly easier to perform in the extensors (ARPE-EX: 13 (IQR: 12.0–14.0) vs BRPE-EX: 11 (IQR: 10.0–13.0); pRPE-EX < 0.001) and lateral muscles testing (ARPE-LM: 14.0 (IQR: 12.3–15.8) vs. BRPE-LM: 13.0 (IQR: 12.0–15.0); pRPE-LM = 0.001). Conclusions A and B tests are comparable in three of four trunk muscle endurance ratios, while longer holding times and lower perceived effort to perform were observed in most of the B tests. The Roman chair tests could be used as an alternative to standard tests.
Petrič et al. (2022) Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults. PeerJ 10:e14469 https://doi.org/10.7717/peerj.14469
Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia
Background Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013–2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn’t demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.
Davidović et al. (2022) Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia. PeerJ 10:e14477 https://doi.org/10.7717/peerj.14477
Catalases in the pathogenesis of Sporothrix schenckii research
Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants.
Vargas-Maya et al. (2022) Catalases in the pathogenesis of Sporothrix schenckii research. PeerJ 10:e14478 https://doi.org/10.7717/peerj.14478
Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions
Weighted percentiles in many areas can be used to investigate the overall trend in a particular context. In this article, the confidence intervals for the common percentile are constructed to estimate rainfall in Thailand. The confidence interval for the common percentile help to indicate intensity of rainfall. Herein, four new approaches for estimating confidence intervals for the common percentile of several delta-lognormal distributions are presented: the fiducial generalized confidence interval, the adjusted method of variance estimates recovery, and two Bayesian approaches using fiducial quantity and approximate fiducial distribution. The Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths via the R statistical program. The proposed confidence intervals are compared in terms of their coverage probabilities and average lengths, and the results of a comparative study based on these metrics indicate that one of the Bayesian confidence intervals is better than the others. The efficacies of the approaches are also illustrated by applying them to daily rainfall datasets from various regions in Thailand.
Thangjai et al. (2022) Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions. PeerJ 10:e14498 https://doi.org/10.7717/peerj.14498
Symbiotic association of microalgae and plants in a deep water culture system
In this study, microalgae culture (Chlorella vulgaris) and mint seedlings (Mentha spp.) were combined in a hydroponic system to improve plant growth. Mint seedlings were grown both in microalgae-containing and in microalgae-free trial groups, and both groups were subjected to aerated and non-aerated conditions to show the effect of aeration and microalgae co-cultivation on the mint weight and height. The plant quality was also determined with color measurements of the mint leaves. The increase in the weight of the plants was the highest in microalgae-containing and aerated group (0.47 g) and the lowest in microalgae-free and non-aerated group (0.22 g). On the other hand, the variation in the plant height was not significant between the groups, the growth was lateral. The best quality mint leaves were also produced in microalgae-containing and aerated group. Our results have revealed the symbiotic life of the mint plant placed in the hydroponic system with microalgae and demonstrated improved mint growth and quality. This co-cultivation system is also potentially more environmentally friendly compared to growing microalgae and mint independently because of lower cost of aeration and mixing for microalgae cultivation, higher nutrient consumption efficiency, and reduced nutrient outflow.
Özer Uyar et al. (2022) Symbiotic association of microalgae and plants in a deep water culture system. PeerJ 10:e14536 https://doi.org/10.7717/peerj.14536
N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India
Reliable estimation of abundance is a prerequisite for a species’ conservation planning in human-dominated landscapes, especially if the species is elusive and involved in conflicts. As a means of population estimation, the importance of camera traps has been recognized globally, although estimating the abundance of unmarked, cryptic species has always been a challenge to conservation biologists. This study explores the use of the N-mixture model with three probability distributions, i.e., Poisson, negative binomial (NB) and zero-inflated Poisson (ZIP), to estimate the relative abundance of sloth bears (Melursus ursinus) based on a camera trapping exercise in Sanjay Tiger Reserve, Madhya Pradesh from December 2016 to April 2017. We used environmental and anthropogenic covariates to model the variation in the abundance of sloth bears. We also compared null model estimates (mean site abundance) obtained from the N-mixture model to those of the Royle-Nichols abundance-induced heterogeneity model (RN model) to assess the application of similar site-structured models. Models with Poisson distributions produced ecologically realistic and more precise estimates of mean site abundance (λ = 2.60 ± 0.64) compared with other distributions, despite the relatively high Akaike Information Criterion value. Area of mixed and sal forest, the photographic capture rate of humans and distance to the nearest village predicted a higher relative abundance of sloth bears. Mean site abundance estimates of sloth bears obtained from the N-mixture model (Poisson distribution) and the RN model were comparable, indicating the overall utility of these models in this field. However, density estimates of sloth bears based on spatially explicit methods are essential for evaluating the efficacy of the relatively more cost-effective N-mixture model. Compared to commonly used index/encounter-based methods, the N-mixture model equipped with knowledge on governing biotic and abiotic factors provides better relative abundance estimates for a species like the sloth bear. In the absence of absolute abundance estimates, the present study could be insightful for the long-term conservation and management of sloth bears.
Chaudhuri et al. (2022) N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India. PeerJ 10:e13649 https://doi.org/10.7717/peerj.13649
Hypoxia-induced factor and its role in liver fibrosis
Liver fibrosis develops as a result of severe liver damage and is considered a major clinical concern throughout the world. Many factors are crucial for liver fibrosis progression. While advancements have been made to understand this disease, no effective pharmacological drug and treatment strategies have been established that can effectively prevent liver fibrosis or even could halt the fibrotic process. Most of those advances in curing liver fibrosis have been aimed towards mitigating the causes of fibrosis, including the development of potent antivirals to inhibit the hepatitis virus. It is not practicable for many individuals; however, a liver transplant becomes the only suitable alternative. A liver transplant is an expensive procedure. Thus, there is a significant need to identify potential targets of liver fibrosis and the development of such agents that can effectively treat or reverse liver fibrosis by targeting them. Researchers have identified hypoxia-inducible factors (HIFs) in the last 16 years as important transcription factors driving several facets of liver fibrosis, making them possible therapeutic targets. The latest knowledge on HIFs and their possible role in liver fibrosis, along with the cell-specific activities of such transcription factors that how they play role in liver fibrosis progression, is discussed in this review.
Mohammad Omar et al. (2022) Hypoxia-induced factor and its role in liver fibrosis. PeerJ 10:e14299 https://doi.org/10.7717/peerj.14299
Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers
Background Indoor climbing involves overloading the shoulder girdle, including the rotator cuff and upper trapezius muscles. This on the field study aimed to investigate the effects of repeated climbing bouts on morphological and mechanical measures of the upper trapezius muscle. Materials and Methods Fifteen experienced male climbers participated in the study. Rate of perceived exertion (RPE), blood lactate concentration ([La−]b), and stiffness and thickness over four points of the upper trapezius were assessed before and after a repeated climbing exercise. The procedure for the climbing exercise consisted of five climbs for a total time of 5-minutes per climb, followed by a 5-minute rest. Results The analysis showed an increase from baseline to after the 3rd climb (p ≤ 0.01) for RPE and after the 5th climb for [La−]b (p ≤ 0.001). Muscle stiffness and thickness increased at all points (1–2–3–4) after the 5th climb (p ≤ 0.01). We found spatial heterogeneity in muscle stiffness and thickness; muscle stiffness was the highest at Point 4 (p ≤ 0.01), while muscle thickness reached the highest values at points 1–2 (both p ≤ 0.01). Moreover, the analysis between the dominant and non-dominant shoulder showed greater stiffness after the 1st climb at Point 1 (p = 0.004) and after the 5th climb at Point 4 (p ≤ 0.001). Conclusions For muscle thickness, the analysis showed significant changes in time and location between the dominant and the non-dominant shoulder. Bilateral increases in upper trapezius muscle stiffness and thickness, with simultaneous increases in RPE and blood lactate in response to consecutive climbs eliciting fatigue.
Klich et al. (2022) Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers. PeerJ 10:e14409 https://doi.org/10.7717/peerj.14409
Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction
Ubiquitination is an important post-translational modification of proteins that regulates many cellular activities. Traditional experimental methods for identification are costly and time-consuming, so many researchers have proposed computational methods for ubiquitination site prediction in recent years. However, traditional machine learning methods focus on feature engineering and are not suitable for large-scale proteomic data. In addition, deep learning methods are mostly based on convolutional neural networks and fuse multiple coding approaches to achieve classification prediction. This cannot effectively identify potential fine-grained features of the input data and has limitations in the representation of dependencies between low-level features and high-level features. A multi-dimensional feature recognition model based on a capsule network (MDCapsUbi) was proposed to predict protein ubiquitination sites. The proposed module consisting of convolution operations and channel attention was used to recognize coarse-grained features in the sequence dimension and the feature map dimension. The capsule network module consisting of capsule vectors was used to identify fine-grained features and classify ubiquitinated sites. With ten-fold cross-validation, the MDCapsUbi achieved 91.82% accuracy, 91.39% sensitivity, 92.24% specificity, 0.837 MCC, 0.918 F-Score and 0.97 AUC. Experimental results indicated that the proposed method outperformed other ubiquitination site prediction technologies.
Li et al. (2022) Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction. PeerJ 10:e14427 https://doi.org/10.7717/peerj.14427
Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica
The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered ‘endangered’ by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.
Baeza (2022) Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica. PeerJ 10:e14428 https://doi.org/10.7717/peerj.14428
Prediction of individual mortality risk among patients with chronic obstructive pulmonary disease: a convenient, online, individualized, predictive mortality risk tool based on a retrospective cohort study
Background Chronic obstructive pulmonary disease (COPD) is a serious condition with a poor prognosis. No clinical study has reported an individual-level mortality risk curve for patients with COPD. As such, the present study aimed to construct a prognostic model for predicting individual mortality risk among patients with COPD, and to provide an online predictive tool to more easily predict individual mortality risk in this patient population. Patients and methods The current study retrospectively included data from 1,255 patients with COPD. Random survival forest plots and Cox proportional hazards regression were used to screen for independent risk factors in patients with COPD. A prognostic model for predicting mortality risk was constructed using eight risk factors. Results Cox proportional hazards regression analysis identified eight independent risk factors among COPD patients: B-type natriuretic peptide (hazard ratio [HR] 1.248 [95% confidence interval (CI) 1.155–1.348]); albumin (HR 0.952 [95% CI 0.931–0.974); age (HR 1.033 [95% CI 1.022–1.044]); globulin (HR 1.057 [95% CI 1.038–1.077]); smoking years (HR 1.011 [95% CI 1.006–1.015]); partial pressure of arterial carbon dioxide (HR 1.012 [95% CI 1.007–1.017]); granulocyte ratio (HR 1.018 [95% CI 1.010–1.026]); and blood urea nitrogen (HR 1.041 [95% CI 1.017–1.066]). A prognostic model for predicting risk for death was constructed using these eight risk factors. The areas under the time-dependent receiver operating characteristic curves for 1, 3, and 5 years were 0.784, 0.801, and 0.806 in the model cohort, respectively. Furthermore, an online predictive tool, the “Survival Curve Prediction System for COPD patients”, was developed, providing an individual mortality risk predictive curve, and predicted mortality rate and 95% CI at a specific time. Conclusion The current study constructed a prognostic model for predicting an individual mortality risk curve for COPD patients after discharge and provides a convenient online predictive tool for this patient population. This predictive tool may provide valuable prognostic information for clinical treatment decision making during hospitalization and health management after discharge (https://zhangzhiqiao15.shinyapps.io/Smart_survival_predictive_system_for_COPD/).
Lu et al. (2022) Prediction of individual mortality risk among patients with chronic obstructive pulmonary disease: a convenient, online, individualized, predictive mortality risk tool based on a retrospective cohort study. PeerJ 10:e14457 https://doi.org/10.7717/peerj.14457
LncRNA RP11-551L14.4 suppresses breast cancer development by inhibiting the expression of miR-4472
Background Previous studies have been reported that long non-coding RNA (lncRNA) can regulate the expression of genes which are involved in many important cellular processes The potential role of lncRNA RP11-551L14.4 in the development of breast cancer and the possible regulatory mechanisms was investigated. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze RP11-551L14.4 expression in 36 paired breast cancer tissues and adjacent tissues. The expression of RP11-551L14.4 in multiple breast cancer cell lines was detected by qRT-PCR. Meanwhile, overexpression of RP11-551L14.4 models was established using lentivirus in BT474 and T47D breast cancer cells. Cell counting kit-8 (CCK-8), cell colony formation and cell cycle assays were performed to detect the effects of RP11-551L14.4 on the biological function of breast cancer cells. Besides, bioinformatics techniques, dual luciferase reporter gene assay and rescue experiments were used to investigate the potential mechanisms. Results RP11-551L14.4 expression was negatively associated with the advanced tumor stage. Breast cancer patients with low RP11-551L14.4 expression manifested a poorer prognosis. The results of qRT-PCR showed that RP11-551L14.4 expression in breast cancer tissues was significantly lower than in adjacent tissues. Meanwhile, overexpression of RP11-551L14.4 significantly decreased the cell proliferation and cell cycle. Bioinformatics technology showed that RP11-551L14.4 could complementarily bind to miR-4472. qRT-PCR results indicated that the expression levels of miR-4472 and RP11-551L14.4 in breast cancer were negatively correlated. Luciferase reporter gene assay showed that miR-4472 remarkably decreased the relative luciferase activity of the wild-type RP11-551L14.4 vector. miR-4472 is a direct target gene of RP11-551L14.4. miR-4472 levels were reduced, and repulsive guidance molecule A (RGMA) mRNA or protein levels were increased after overexpression of RP11-551L14.4 in the breast cancer cells. miR-4472 reversed the effects caused by RP11-551L14.4 in breast cancer cells. Conclusion RP11-551L14.4 expression was remarkably decreased in breast cancer tissues and cells. RP11-551L14.4 may inhibit the malignant progression of breast cancer by regulating miR-4472 expression.
Wang et al. (2022) LncRNA RP11-551L14.4 suppresses breast cancer development by inhibiting the expression of miR-4472. PeerJ 10:e14482 https://doi.org/10.7717/peerj.14482
A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use
Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling. Methods A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented. Results A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries). Discussion Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.
Reginato (2022) A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 10:e14525 https://doi.org/10.7717/peerj.14525
Cryptic population structure at the northern range margin of the service tree Sorbus domestica
Climate change has aroused interest in planting warm- and drought-adapted trees in managed forests and urban areas. An option is to focus on tree species that occur naturally, but have centers of distribution in warmer and drier areas. However, in order to protect the species pool of genetic diversity, efforts of planting and promotion should be informed by knowledge on the local genetic diversity. Here, we studied the macro- and micro-scale population genetic structure of the rare European fruit tree Sorbus domestica at its northern range margin, in western Switzerland. New microsatellite data were combined with published data from across the European distribution of the species. Analyses revealed the presence of mainly one of two species-wide ancestral clusters, i.e., the western European cluster, with evidence that it consists of two cryptic sub-clusters. Average pairwise FST of 0.118 was low across the range, and only allelic richness was reduced in the northern margin compared to more southern and southeastern areas of Europe. Based on our finding of considerable genetic diversity of the species in western and northern Switzerland, we suggest that a national propagation program should focus on collecting seeds from natural, high-density tree stands and propagate locally. More generally, our study shows that rare tree species in marginal areas of their distributions do not necessarily have low genetic diversity or heightened levels of inbreeding, and in those cases probably need no assisted migration in efforts to propagate them.
Armbruster et al. (2022) Cryptic population structure at the northern range margin of the service tree Sorbus domestica. PeerJ 10:e14397 https://doi.org/10.7717/peerj.14397
Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis
Background Karyotyping and genome copy number variation sequencing (CNV-seq) are two techniques frequently used in prenatal diagnosis. This study aimed to explore the diagnostic potential of using a combination of these two methods in order to provide a more accurate clinical basis for prenatal diagnosis. Methods We selected 822 pregnant women undergoing amniocentesis and separated them into six groups according to different risk indicators. Karyotyping and CNV-seq were performed simultaneously to compare the diagnostic performance of the two methods. Results Among the different amniocentesis indicators, abnormal fetal ultrasounds accounted for 39.29% of the total number of examinees and made up the largest group. The abnormal detection rate of non-invasive prenatal testing (NIPT) high risk was 37.93% and significantly higher than the other five groups (P < 0.05). The abnormal detection rate of mixed indicators was significantly higher than the history of the adverse reproductive outcomes group (P = 0.0151). The two methods combined found a total of 119 abnormal cases (14.48%). Karyotyping detected 57 cases (6.93%) of abnormal karyotypes, 30 numerical aberrations, and 27 structural aberrations. CNV-seq identified 99 cases (12.04%) with altered CNVs, 30 cases of chromosome aneuploidies, and 69 structural aberrations (28 pathogenic, eight that were likely pathogenic, and 33 microdeletion/duplication variants of uncertain significance (VUS)). Thirty-seven cases were found abnormal by both methods, 20 cases were detected abnormally by karyotyping (mainly mutual translocation and mostly balanced), and 62 cases of microdeletion/duplication were detected by CNV-seq. Steroid sulfatase gene (STS) deletion was identified at chromosome Xp22.31 in three cases. Postnatal follow-up confirmed that babies manifested skin abnormalities one week after birth. Six fetuses had Xp22.31 duplications ranging from 1.5 Kb to 1.7 Mb that were detected by CNV-seq. Follow-up showed that five babies presented no abnormalities during follow-up, except for one terminated pregnancy due to a history of adverse reproductive outcomes. Conclusion The combination of using CNV-seq and karyotyping significantly improved the detection rate of fetal pathogenic chromosomal abnormalities. CNV-seq is an effective complement to karyotyping and improves the accuracy of prenatal diagnosis.
Zhang et al. (2022) Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis. PeerJ 10:e14400 https://doi.org/10.7717/peerj.14400
Upregulated TUBG1 expression is correlated with poor prognosis in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) development is a complex pathological process. Tubulin gamma 1 (TUBG1) plays an oncogenic role in several human cancers; however, its functional role in HCC tumorigenesis remains unknown. Methods Herein we first evaluated the gene expression levels of TUBG1 in HCC using data from The Cancer Genome Atlas and Gene Expression Profiling Interactive Analysis databases. We then elucidated the association between TUBG1 gene expression levels and survival rates of patients with HCC. Cell cycle, proliferation, transwell migration, and matrigel invasion assays were used to study the effects of TUBG1 on the malignant phenotypes of HCC cells. Results Based on the data obtained from the aforementioned databases and our in vitro experiments, TUBG1 was found to be overexpressed in HCC and patients with high TUBG1 expression levels showed a remarkably poor overall survival rate. In addition, the expression of TUBG1 significantly promoted the malignant phenotypes of HCC cells in vitro. Gene ontology term enrichment analysis revealed that co-regulated genes were enriched in biological processes mainly involved in chromosome segregation, chromosomal region, and chromatin binding; moreover, Kyoto Encyclopedia of Genes and Genome pathway analysis showed that they were mainly involved in cell cycle, oocyte meiosis, platinum drug resistance, and the p53 signaling pathway. Conclusions We report that TUBG1 is an important oncogene in HCC. It promotes HCC progression and may serve as a potential prognostic biomarker for HCC. Future studies are warranted to unveil molecular biological mechanisms underlying TUBG1 carcinogenesis.
Zhang et al. (2022) Upregulated TUBG1 expression is correlated with poor prognosis in hepatocellular carcinoma. PeerJ 10:e14415 https://doi.org/10.7717/peerj.14415
Effects of saddle tilt and stirrup length on the kinetics of horseback riders
Background How the modification of saddle fitting parameters in horse riding affects rider’s kinetics is very uncertain. The aim of this study is to describe how manipulating the two main adjustments that an end-user is likely to perform (saddle tilt and stirrup length) affects the biomechanics of a horse rider on a living horse. Methods Eleven showjumpers volunteered to take part in this study. Each participant performed a 120-strides standardization trial at trot and canter, with 0° saddle tilt and stirrup length that would position the rider’s knee at 90°. Following the standardization trial, four interventions were performed, which consisted of 60 strides with 60 mm shorter stirrups, 60 mm longer stirrups, 4° forward tilted saddle and 4° backward tilted saddle. Stirrup and rein tension forces were measured with tension loadcells. A symmetry index was calculated. Acceleration was measured with inertial measuring units at the helmet and back of the rider and shock attenuation was calculated. Results Shortening the stirrups and adjusting saddle tilt significantly enhanced shock attenuation at canter and increased force on the stirrups at trot and canter (p < 0.05). Lowering the stirrups reduced rein tension forces (p = 0.01). At trot, adjusting saddle tilt and stirrup length enhanced symmetry index on the bit (p < 0.05). These results allowed for general guidelines to be proposed, although individualization became an evident part of any saddle setup design due to a high inter-subject variability.
Elmeua González et al. (2022) Effects of saddle tilt and stirrup length on the kinetics of horseback riders. PeerJ 10:e14438 https://doi.org/10.7717/peerj.14438
Prevalence, classification and dental treatment requirements of dens invaginatus by cone-beam computed tomography
Background This study aimed the evaluation of the prevalence, characteristics, types of dens invaginatus (DI) and co-observed dental anomalies to understand dental treatment requirements in anterior teeth that are susceptible to developmental anomalies by using cone-beam computed tomography (CBCT). Methods In this retrospective study, the anterior teeth of 958 patients were evaluated by using CBCT for the presence of DI. The demographic features, types of DI and treatment requirements were also recorded. The association between sex and the presence of DI was evaluated using chi-squared test. Results Seventy-three DI anomalies were detected in the anterior teeth of 49 patients (18 females, 31 males). The frequency of DI was 5.11% and the most frequently involved teeth were lateral (57.53%). Forty-six teeth were classified as Type I (63.01%), 24 as Type II (32.87%), and three as Type III (4.10%). Apical pathosis was found to be 20.54% in all DIs detected and accounted for all Type III and one-third of Type II. Conclusions CBCT imaging can be effective in the detection of dental anomalies such as DI and planning for root canal therapy and surgical treatments. Prophylactic interventions might be possible to prevent apical pathosis with the data obtained from CBCT images.
Yalcin et al. (2022) Prevalence, classification and dental treatment requirements of dens invaginatus by cone-beam computed tomography. PeerJ 10:e14450 https://doi.org/10.7717/peerj.14450
Genome-wide identification and expression pattern analysis of quinoa BBX family
BBX is a transcription factor encoding zinc finger protein that plays a key role in plant growth and development as well as in responding to abiotic stresses. However, in quinoa, which is known as a “super grain” and has extremely high nutritional value, this gene family has not yet been thoroughly studied. In this study, in order to fully understand the family function of the BBX in quinoa, a total of 31 BBX members were identified by bioinformatics methods. These BBX members were mainly acidic proteins, and most of their secondary structures were random coil s, 31 CqBBX members were unevenly distributed on 17 chromosomes, and the analysis of replication events found that quinoa BBX genes produced a total of 14 pairs of gene replication. The BBX genes were divided into five subfamilies according to phylogenetics, and its gene structure and conserved motif were basically consistent with the classification of its phylogenetic tree. In addition, a total of 43 light response elements, hormone response elements, tissue-specific expression response elements, and abiotic stress response elements were found in the promoter region, involving stress elements such as drought and low temperature. Finally, the expression patterns of CqBBX genes in different tissues and abiotic stresses were studied by combining transcriptome data and qRT-PCR , and all 13 genes responded to drought, salt, and low-temperature stress to varying degrees. This study is the first comprehensive study of the BBX family of quinoa, and its results provide important clues for further analysis of the function of the abiotic stress response.
Xuefen et al. (2022) Genome-wide identification and expression pattern analysis of quinoa BBX family. PeerJ 10:e14463 https://doi.org/10.7717/peerj.14463
Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza
In response to abiotic stresses, transcription factors are essential. Heat shock transcription factors (HSFs), which control gene expression, serve as essential regulators of plant growth, development, and stress response. As a model medicinal plant, Salvia miltiorrhiza is a crucial component in the treatment of cardiovascular illnesses. But throughout its growth cycle, S.miltiorrhiza is exposed to a series of abiotic challenges, including heat and drought. In this study, 35 HSF genes were identified based on genome sequencing of Salvia miltiorrhiza utilizing bioinformatics techniques. Additionally, 35 genes were classified into three groups by phylogeny and gene structural analysis, comprising 22 HSFA, 11 HSFB, and two HSFC. The distribution and sequence analysis of motif showed that SmHSFs were relatively conservative. In SmHSF genes, analysis of the promoter region revealed the presence of many cis-acting elements linked to stress, hormones, and growth and development, suggesting that these factors have regulatory roles. The majority of SmHSFs were expressed in response to heat and drought stress, according to combined transcriptome and real-time quantitative PCR (qRT-PCR) analyses. In conclusion, this study looked at the SmHSF gene family using genome-wide identification, evolutionary analysis, sequence characterization, and expression analysis. This research serves as a foundation for further investigations into the role of HSF genes and their molecular mechanisms in plant stress responses.
Liu et al. (2022) Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza. PeerJ 10:e14464 https://doi.org/10.7717/peerj.14464
Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast
Background An enhanced understanding of larval ecology is fundamental to improve the management of locally depleted horseshoe crab populations in Asia. Recent studies in the northern Beibu Gulf, China demonstrated that nesting sites of Asian horseshoe crabs are typically close to their nursery beaches with high-density juveniles distributed around mangrove, seagrass and other structured habitats. Methods A laboratory Y-maze chamber was used to test whether the dispersal of early-stage juvenile tri-spine horseshoe crab Tachypleus tridentatus is facilitated by chemical cues to approach suitable nursery habitats. The juvenile orientation to either side of the chamber containing controlled seawater or another with various vegetation cues, as well as their movement time, the largest distance and displacement were recorded. Results The juveniles preferred to orient toward seagrass Halophila beccarii cues when the concentration reached 0.5 g l−1, but ceased at 2 g l−1. The results can be interpreted as a shelter-seeking process to get closer to the preferred settlement habitats. However, the juveniles exhibited avoidance behaviors in the presence of mangrove Avicennia marina and invasive saltmarsh cordgrass Spartina alterniflora at 2 g l−1. The juveniles also spent less time moving in the presence of the A. marina cue, as well as reduced displacement in water containing the S. alterniflora cue at 1 and 2 g l−1. These results may explain the absence of juvenile T. tridentatus within densely vegetated areas, which have generally higher organic matter and hydrogen sulfide. Conclusion Early-stage juvenile T. tridentatus are capable of detecting and responding to habitat chemical cues, which can help guide them to high-quality settlement habitats. Preserving and restoring seagrass beds in the intertidal areas should be prioritized when formulating habitat conservation and management initiatives for the declining horseshoe crab populations.
Kwan et al. (2022) Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast. PeerJ 10:e14465 https://doi.org/10.7717/peerj.14465
Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria
Background Sports mouthguards, worn in the oral cavity to prevent sports injuries, are constantly exposed to various microorganisms that cause oral infections. Hence, the optimal cleaning methods for sports mouthguards have been thoroughly examined. In this study, we evaluated the efficiency of cleaning effects with a mouthguard cleaner (MC) on microbial biofilm formation in sports mouthguards in vitro and in vivo. Methods We evaluated the cleaning effects of the discs produced by ethylene-vinyl acetate (EVA) on bacterial biofilms formed by the commensal bacterium Streptococcus oralis, the cariogenic bacterium Streptococcus mutans, and the opportunistic pathogen Staphylococcus aureus in vitro. EVA discs with biofilm were subjected to sterile distilled water (CTRL) and ultrasonic washing (UW), followed by treatment with MC and sodium hypochlorite (NaClO) as positive controls. Thereafter, the viable bacterial cell counts were determined. The bacteria adhering to the sheets before and after the treatment were observed under an electron microscope. The degree of cleanliness and measurement of viable microbial cell counts for total bacteria, Streptococci and Candida, opportunistic fungi, were evaluated on the used experimental sports mouthguards with and without UW and MC treatment in vivo. Results The number of bacterial cells significantly decreased against all the tested biofilm bacteria upon treatment with MC, compared with CTRL and UW. Electron microscopy analysis revealed the biofilm formation by all bacteria on the EVA discs before cleaning. We observed fewer bacteria on the EVA discs treated with MC than those treated with CTRL and UW. Furthermore, the degree of cleanliness of the used experimental sports mouthguards cleaned using MC was significantly higher than that of the CTRL-treated mouthguards. Moreover, the viable microbial cell counts on the used experimental sports mouthguard were considerably lower than those on the CTRL ones. Conclusion The cleaning effect of MC against oral bacteria was more effective than that of UW. MC treatment might have a potential future application as a cleaning method for sports mouthguards to protect athletes from oral infection.
Hayashi et al. (2022) Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria. PeerJ 10:e14480 https://doi.org/10.7717/peerj.14480
Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study
Background The efficacy and indications of tonsillectomy in IgA nephropathy (IgAN) remain uncertain. Methods We performed a retrospective cohort study of 452 patients with primary IgAN, including 226 patients who received tonsillectomy and 226 controls selected by propensity score matching who had never undergone tonsillectomy. Study outcomes were clinical remission defined as negative hematuria and proteinuria on three consecutive visits over a 6-month period, the endpoint defined as end-stage renal disease or an irreversible 100% increase in serum creatinine from the baseline value. In addition, we further analyzed the critical level of proteinuria in the efficacy of tonsillectomy and the correlation between MEST-C score and tonsillectomy. Results Up to December 2019, the follow-up period lasted 46 ± 23 months (12–106 months). Kaplan–Meier and multivariate Cox regression analysis revealed that tonsillectomy was beneficial for clinical remission and renal survival. Whether proteinuria was ≤ 1 g/24h or >1 g/24h, the clinical remission and renal survival rates were greater in patients treated with tonsillectomy than without. When the pathological damage was mild or relatively severe, tonsillectomy may be beneficial to clinical remission or renal survival. Conclusions Tonsillectomy had a favorable effect on clinical remission and delayed renal deterioration in IgAN. In addition to patients with early stage IgAN, it may also be beneficial to IgAN patients with higher levels of proteinuria and relatively severe pathological damage.
Li et al. (2022) Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study. PeerJ 10:e14481 https://doi.org/10.7717/peerj.14481
Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory
Background When the moisture content of a fuel bed is higher than the fiber saturation moisture content (0.35 g g−1), the drying process is controlled by evaporation (>0.35 g g−1) and diffusion (>0.35 g g−1). Packing ratio has a significant effect on the drying process. Ignoring the impacts of packing ratio or the separate phases of the drying process is one main reason for inaccurate moisture content predictions. Method This study simulated the drying process in five Masson pine (Pinus massoniana Lamb.) needle beds with different packing ratios. Using the fiber saturation moisture content as the cut-off point, we divided the drying process into two phases. The drying mechanism of each phase was different and had its own drying equation. Using a model that does not distinguish the two phases of the drying process as a comparison, the prediction effect of the two-phase model was analyzed. The influence of the fuel bed packing ratio on the drying process was also analyzed. Results We found that, regardless of any changes in packing ratio, the two-phase model could better simulate the drying process, with a mean absolute error (MAE) and mean relative error (MRE) of the two-phase model 18.4% and 25.6% less than the one-phase model, respectively. The time-lag prediction model was established with the packing ratio, and the errors were all within the allowable range, but the prediction effect of the time-lag prediction model based on the two-phase model was larger. Conclusion It was further demonstrated that considering the packing ratio of the fuel bed and distinguishing the two separate phases of the drying process could both effectively improve the prediction accuracy of the moisture content of fuel beds based on the semi-physical method.
Zhang (2022) Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory. PeerJ 10:e14484 https://doi.org/10.7717/peerj.14484
Knowledge, attitudes, and practices towards mosquito control and used vehicle tire dumping by median household income, in metropolitan New Orleans, Louisiana
Background Discarded vehicle tires are an important artificial habitat for the larvae of many container-breeding mosquito species worldwide, including in the United States. Unmanaged discarded vehicle tires create health, environmental and social costs, and with budget and staffing constraints, effective management of discarded used vehicle tires a mosquito larval habitat depends in part on the knowledge, attitude, and practices (KAP) of community residents. Objectives This study aims to examine the knowledge, attitude and practices of New Orleans, Louisiana residents toward illegally discarded vehicle tires, and larval mosquito control. Methods A descriptive cross-sectional design study was used where 422 households were selected using a two-stage cluster random sampling procedure in New Orleans, Louisiana. Heads of households or a person aged 18 years or older self-administered the survey. The questionnaire comprised five parts: screening, tire sightings, preferred communication method, knowledge, attitude and precautionary measures against mosquito control, disease risk and illegal discarding. We then statistically compared above and below median income household responses to identify likely causes of detected differences. The data were analyzed using ordinal regression models via IBM SPSS statistics V.26.0. Statistical significance was set at p < 0.05. Results Out of 290 responding households, 95.5% strongly agree or agree that mosquitoes can spread serious diseases like West Nile, Zika or Dengue. Only 2.3% of the sample had high knowledge of illegally discarded tires dumping and mosquito larval control. Those employed were 1.0 times more likely to possess good knowledge than the unemployed (p < 0.001). Despite low knowledge levels regarding mosquito breeding and polluted water in discarded tires, 29.9% of respondents had positive attitude and 20.5% reported sufficient practices. Among the socio-demographic variables, only home ownership and being employed were predictors of knowledge and attitude towards mosquito breeding in illegally discarded tires (p < 0.05). Conclusions Despite the observed increasing number of illegally discarded vehicle tires in New Orleans, the knowledge of people about illegal tire dumping and their associated risk factors as suitable larval habitants was low. Therefore, there is a need for developing community-based and place-based tailored sensitization campaigns to prevent illegal used tire dumping, and larval control.
Moise et al. (2022) Knowledge, attitudes, and practices towards mosquito control and used vehicle tire dumping by median household income, in metropolitan New Orleans, Louisiana. PeerJ 10:e14188 https://doi.org/10.7717/peerj.14188
M1 macrophage-derived extracellular vesicle containing tsRNA-5006c promotes osteogenic differentiation of aortic valve interstitial cells through regulating mitophagy
Background Osteogenic differentiation of aortic valve interstitial cells (AVICs) plays a key role in the calcific aortic valve disease progression. Extracellular vesicles (EVs)-derived from M1-polarized macrophages (M1-EVs) orchestrated intercellular communication by delivering non-coding RNAs such as tRNA-derived small RNAs (tsRNAs) is crucial for cardiovascular disease. However, the role and mechanism of M1-EVs tsRNAs in osteogenic differentiation of AVICs remains largely unclear. Methods M1-EVs and PBS treated-RAW 264.7 cell-derived EVs (NC-EVs) were incubated with AVICs and subjected to small RNA sequencing. Candidate tsRNA in M1-EVs was silenced to explore their effects on AVIC osteogenic differentiation and mitophagy. Results DiI-labeled M1-EVs were internalized by AVICs, resulting in significantly increased calcium nodule formation and expression of osteogenesis-related genes in AVICs, including RUNX2, BMP2, osteopontin, and SPP1, compared with NC-EVs. Small RNA sequencing revealed that 17 tsRNAs were significantly up-regulated such as tsRNA-5006c, while 28 tsRNAs were significantly down-regulated in M1-EVs compared with NC-EVs. Intriguingly, tsRNA-5006c-deleted M1-EVs treatment significantly reduced calcium nodule formation and expression of osteogenesis-related genes in AVICs relative to control group. Moreover, target genes of tsRNA-5006c were mainly involved in autophagy-related signaling pathways, such as MAPK, Ras, Wnt, and Hippo signaling pathway. Hallmarks of mitophagy activation in AVICs including mitophagosome formation, TMRM fluorescence, expression of LC3-II, BINP3, and PGC1α, were significantly elevated in the M1-EVs group compared with NC-EVs group, whereas M1-EVs tsRNA-5006c inhibitor led to a significant reduction in these indicators. Conclusion M1-EVs carried tsRNA-5006c regulates AVIC osteogenic differentiation from the perspective of mitophagy, and we provide a new target for the prevention and treatment of aortic valve calcification.
Xia et al. (2022) M1 macrophage-derived extracellular vesicle containing tsRNA-5006c promotes osteogenic differentiation of aortic valve interstitial cells through regulating mitophagy. PeerJ 10:e14307 https://doi.org/10.7717/peerj.14307
Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic
Estuarine environments are suggested to be the final receivers of human pollution and are impacted by surrounding urbanization and compounds carried by the river waters that flow from the continent. Polycyclic aromatic hydrocarbons (PAHs) are among the contaminants that can reach estuaries and can directly affect marine conservation, being considered highly deleterious to organisms living in these environments. This research investigated the meiofauna of three estuaries exposed to different levels of urbanization and consequently different levels of PAH concentrations, in order to assess how these compounds and environmental factors affect the distribution, structure and diversity of these interstitial invertebrates. A total of 15 major meiofauna groups were identified, with Nematoda being the dominant taxon (74.64%), followed by Copepoda (9.55%) and Polychaeta (8.56%). It was possible to observe significant differences in all diversity indices studied in the estuaries. With the exception of average density, the diversity indices (richness, Shannon index and evenness) were higher in the reference estuary, Goiana estuarine system (GES). On the other hand, the Timbó estuarine system (TES) had the lowest Shannon index value and richness, while the Capibaribe estuarine system (CES) had the lowest evenness value. The latter two estuaries (TES and CES) presented intermediate and high levels of urbanization, respectively. The ecological quality assessment (EcoQ) in the studied estuaries was classified from Poor to Moderate and the estuary with the lowest demographic density in its surroundings, GES, showed a better ecological quality (Moderate EcoQ). A significant distance-based multivariate linear modelling regression (DistLM) was observed between the environmental variables and the density of the meiobenthic community, where PAHs and pH were the main contributors to organism variation. The sediments were characterized by predominance of very fine sand and silt-clay in the most polluted environments, while the control site environment (GES) was dominated by medium grains. The highest concentrations of PAHs were found in the most urbanized estuaries, and directly affected the structure of the interstitial benthic community. The metrics used in the present study proved to be adequate for assessing the environmental quality of the investigated estuaries.
da Silva et al. (2022) Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic. PeerJ 10:e14407 https://doi.org/10.7717/peerj.14407
Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides
Cynanchum thesioides (Freyn) K. Schum. is an important economic and medicinal plant widely distributed in northern China. WRKY transcription factors (TFs) play important roles in plant growth, development and regulating responses. However, there is no report on the WRKY genes in Cynanchum thesioides. A total of 19 WRKY transcriptome sequences with complete ORFs were identified as WRKY transcriptome sequences by searching for WRKYs in RNA sequencing data. Then, the WRKY genes were classified by phylogenetic and conserved motif analysis of the WRKY family in Cynanchum thesioides and Arabidopsis thaliana. qRT–PCR was used to determine the expression patterns of 19 CtWRKY genes in different tissues and seedlings of Cynanchum thesioides under plant hormone (ABA and ETH) and abiotic stresses (cold and salt). The results showed that 19 CtWRKY genes could be divided into groups I-III according to their structure and phylogenetic characteristics, and group II could be divided into five subgroups. The prediction of CtWRKY gene protein interactions indicates that CtWRKY is involved in many biological processes. In addition, the CtWRKY gene was differentially expressed in different tissues and positively responded to abiotic stress and phytohormone treatment, among which CtWRKY9, CtWRKY18, and CtWRKY19 were significantly induced under various stresses. This study is the first to identify the WRKY gene family in Cynanchum thesioides, and the systematic analysis lays a foundation for further identification of the function of WRKY genes in Cynanchum thesioides.
Chang et al. (2022) Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides. PeerJ 10:e14436 https://doi.org/10.7717/peerj.14436
Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows
Background Yak cows produce higher quality milk with higher concentrations of milk fat than dairy cows. Recently, studies have found the yak milk yield and milk fat percentage have decreased significantly over the past decade, highlighting the urgency for yak milk improvement. Therefore, we aimed to analyze how the gut microbiome impacts milk fat synthesis in Zhongdian yak cows. Methods We collected milk samples from Zhongdian yak cows and analyzed the milk fat percentage, selecting five Zhongdian yak cows with a very high milk fat percentage (>7%, 8.70 ± 1.89%, H group) and five Zhongdian yak cows with a very low milk fat percentage (<5%, 4.12 ± 0.43%, L group), and then obtained gut samples of these ten Zhongdian yak cows through rectal palpation. Gut metagenomics, metabolomics, and conjoint metagenomics and metabolomics analyses were performed on these samples, identifying taxonomic changes, functional changes, and changes in gut microbes-metabolite interactions within the milk fat synthesis-associated Zhongdian yak cows gut microbiome, to identify potential regulatory mechanisms of milk fat at the gut microbiome level in Zhongdian yak cows. Results The metagenomics analysis revealed Firmicutes and Proteobacteria were significantly more abundant in the gut of the high-milk fat Zhongdian yak cows. These bacteria are involved in the biosynthesis of unsaturated fatty acids and amino acids, leading to greater efficiency in converting energy to milk fat. The metabolomics analysis showed that the elevated gut metabolites in high milk fat percentage Zhongdian yak cows were mainly enriched in lipid and amino acid metabolism. Using a combined metagenomic and metabolomics analysis, positive correlations between Firmicutes (Desulfocucumis, Anaerotignum, Dolosiccus) and myristic acid, and Proteobacteria (Catenovulum, Comamonas, Rubrivivax, Marivita, Succinimouas) and choline were found in the gut of Zhongdian yak cows. These interactions may be the main contributors to methanogen inhibition, producing less methane leading to higher-efficient milk fat production. Conclusions A study of the gut microbe, gut metabolites, and milk fat percentage of Zhongdian yak cows revealed that the variations in milk fat percentage between yak cows may be caused by the gut microbes and their metabolites, especially Firmicutes-myristic acid and Proteobacteria-choline interactions, which are important to milk fat synthesis. Our study provides new insights into the functional roles of the gut microbiome in producing small molecule metabolites and contributing to milk performance traits in yak cows.
Liu et al. (2022) Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows. PeerJ 10:e14444 https://doi.org/10.7717/peerj.14444
Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja)
Background NDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress. Methods We identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR. Results In this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.
Zhang et al. (2022) Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja). PeerJ 10:e14451 https://doi.org/10.7717/peerj.14451
The effects of a set amount of regular maternal exercise during pregnancy on gut microbiota are diet-dependent in mice and do not cause significant diversity changes
Background Diet and exercise can affect the gut microbiota (GM); however, the effects of the same amount of exercise on gut microbiota changes in people on a low-fat diet (LFD) and high-fat diet (HFD) during pregnancy are unknown. Do different nutritional conditions respond equally to exercise intervention? This study aimed to investigate the effects of regular maternal exercise during pregnancy on the GM in mice fed different diets during pregnancy. Methods Six-week-old nulliparous female KunMing mice were fed either a HFD or LFD before and during pregnancy. Each group of mice were then randomly divided into two groups upon confirmation of pregnancy: sedentary (HFD or LFD; n = 4 and 5, respectively) and exercised (HFDex or LFDex, n = 5 and 6, respectively). Mice were sacrificed on day 19 of gestation and their colon contents were collected. We then performed 16S rDNA gene sequencing of the V3 and V4 regions of the GM. Results The pregnancy success rate was 60% for LFDex and 100% for HFDex. Both Chao1 and Simpson indices were not significantly different for either LFD vs. LFDex or HFD vs. HFDex. Desulfobacterota, Desulfovibrionia Desulfovibrionales, Desulfovibrionaceae, Desulfovibrio, Coriobacteriia, Coriobacteriales, and Eggerthellaceae were markedly decreased after exercise intervention in LFDex vs. LFD, whereas Actinobacteria, Bifidobacteriales, Bifidobacteriaceae, Bifidobacterium, and Bifidobacterium pseudolongum were significantly increased in LFDex vs. LFD. Furthermore, decreased Peptostreptococcales-Tissierellales and Peptostreptococcaceae and increased Bacteroides dorei were identified in the HFDex vs. HFD group. p_Desulfobacterota, c_Desulfovibrionia, o_Desulfovibrionales, f_Desulfovibrionaceae and g_Desulfovibrio were markedly decreased in the LFDex group vs. HFDex group. Conclusions Our data suggested that quantitative maternal exercise during pregnancy resulted in alterations in GM composition, but did not significantly change the diversity of the GM. These findings may have important implications when considering an individual’s overall diet when recommending exercise during pregnancy.
Duan et al. (2022) The effects of a set amount of regular maternal exercise during pregnancy on gut microbiota are diet-dependent in mice and do not cause significant diversity changes. PeerJ 10:e14459 https://doi.org/10.7717/peerj.14459
Cathepsin B plays a role in spermatogenesis and sperm maturation through regulating autophagy and apoptosis in mice
Spermatogenesis and sperm maturation are complex and highly ordered biological processes. Any failure or disorder in these processes can cause defects in sperm morphology, motility, and fertilization ability. Cathepsin B (CTSB) is involved in the regulation of a variety of pathological processes. In the present study, we found that CTSB was abundantly expressed in the male reproductive system, however, the specific role of CTSB in regulating spermatogenesis and sperm maturation remained elusive. Hence, we generated Ctsb-/- mice using CRISPR/Cas9 technology. In Ctsb-/- mice, sperm count was significantly decreased while the level of morphologically abnormal sperm was markedly increased. Additionally, these mice had significantly lower levels of progressive motility sperm and elevated levels of immobilized sperm. Histological analysis showed slight vacuolization in the testis epithelium, as well as the loss of epididymal epithelium cells. Further investigation showed that autophagic activity was inhibited and apoptotic activity was increased in both the testis and epididymis of Ctsb-/- mice. Together, our findings demonstrate that CTSB plays an important role in spermatogenesis and sperm maturation in mice.
Wen et al. (2022) Cathepsin B plays a role in spermatogenesis and sperm maturation through regulating autophagy and apoptosis in mice. PeerJ 10:e14472 https://doi.org/10.7717/peerj.14472
Litter inputs and standing stocks in riparian zones and streams under secondary forest and managed and abandoned cocoa agroforestry systems
Background Cocoa is an important tropical tree crop that is mainly cultivated in agroforestry systems (AFS). This system, known as cabruca in northeastern Brazil, holds promise to reconcile biodiversity conservation and economic development. However, since cocoa AFS alters forest structure composition, it can affect litter dynamics in riparian zones and streams. Thus, our objective was to determine litter inputs and standing stocks in riparian zones and streams under three types of forest: managed cocoa AFS, abandoned cocoa AFS, and secondary forest. Methods We determined terrestrial litter fall (TI), vertical (VI) and lateral (LI) litter inputs to streams, and litter standing stocks on streambeds (BS) in the Atlantic Forest of northeastern Brazil. Litter was collected every 30 days from August 2018 to July 2019 using custom-made traps. The litter was dried, separated into four fractions (leaves, branches, reproductive organs, and miscellaneous material) and weighed. Results Terrestrial litter fall was similar in all forests, ranging from 89 g m−2 month−1 in secondary forest (SF) to 96 g m−2 month−1 in abandoned cocoa AFS (AC). Vertical input were higher in AC (82 g m−2 month−1) and MC (69 g m−2 month−1) than in SF (40 g m−2 month−1), whereas lateral input were higher in MC (43 g m−2 month−1) than in AC (15 g m−2 month−1) and SF (24 g m−2 month−1). Standing stocks followed the order SF > AC > MC, corresponding to 425, 299 and 152 g m−2. Leaves contributed most to all litter fractions in all forests. Reproductive plant parts accounted for a larger proportion in managed AFS. Branches and miscellaneous litter were also similar in all forests, except for higher benthic standing stocks of miscellaneous litter in the SF. Despite differences in the amounts of litter inputs and standing stocks among the forests, seasonal patterns in the abandoned AFS (AC) were more similar to those of the secondary forest (SF) than the managed AFS, suggesting potential of abandoned AFS to restore litter dynamics resembling those of secondary forests.
Rialli Santos Brandão et al. (2022) Litter inputs and standing stocks in riparian zones and streams under secondary forest and managed and abandoned cocoa agroforestry systems. PeerJ 10:e13787 https://doi.org/10.7717/peerj.13787
Establishment of the non-native horned-face bee Osmia cornifrons and the taurus mason bee Osmia taurus (Hymenoptera: Megachilidae) in Canada
Established populations of the non-native horned-face bee, Osmia cornifrons (Radoszkowski, 1887), and the taurus mason bee, Osmia taurus Smith, 1873 (Hymenoptera: Megachilidae), have been identified from Canada for the first time. In the US, the importation of O. cornifrons, beginning in the 1970s, led to its release for agricultural crop pollination and spread across the country. In this article, we report on O. cornifrons captured while sampling wild bees in Toronto, Ontario using hand nets, bug vacuums, and vane traps, as well as established populations in trap nests, from 2017–2020. The morphologically similar O. taurus, which was accidentally introduced to the US with shipments of imported O. cornifrons, was also recorded in our samples. Recently, a few individual O. taurus specimens have been identified from Ontario and Quebec; however, the extent of our sampling included nests, indicating it is also established in Canada. Others have shown its population growth to have been associated with concordant declines in abundances of native mason bee species in the US, and similar impacts are possible in Canada if action is not taken. We propose three non-mutually exclusive possible pathways for the arrival of O. cornifrons, as well as O. taurus, in Canada: (1) natural migration northward from non-native populations in the US, (2) international importation in the 1980s–2000s to support agricultural research programs, and (3) unintentional release of mason bee cocoons purchased from non-local vendors. We argue that a focus on enhancing populations of locally occurring native bees and stronger policy on the importation and sale of non-native bees are needed.
MacIvor et al. (2022) Establishment of the non-native horned-face bee Osmia cornifrons and the taurus mason bee Osmia taurus (Hymenoptera: Megachilidae) in Canada. PeerJ 10:e14216 https://doi.org/10.7717/peerj.14216
Level of anxiety and depression among healthcare workers in Saudi Arabia during the COVID-19 pandemic
Background The coronavirus disease 2019 (COVID-19) pandemic places a high demand on frontline healthcare workers. Healthcare workers are at high-risk of contracting the virus and are subjected to its consequential emotional and psychological effects. This study aimed to measure the level of depression and anxiety among healthcare workers in Saudi Arabia during the early stages of the COVID-19 pandemic. Methods This was a cross-sectional study; data were collected from healthcare workers in Saudi Arabia using a survey that included the Zung Self-Rating Depression Scale and the Generalized Anxiety Disorder Scale-7. A total of 326 participants took part in the study by completing and submitting the survey. Results The vast majority of the participating healthcare workers were Saudi nationals (98.8%) working in a public healthcare facility (89.9%). The results indicated that most of the participants had mild levels of anxiety and depression. A total of 72.5% of the respondents had anxiety, ranging from mild (44.1%) to moderate (16.2%) and severe (12.2%). Moreover, 24.4% of the respondents had depression ranging from mild (21.7%) to moderate (2.1%) and severe (0.6%). The generalized linear models showed that the <30 age group (Beta = 0.556, p = 0.037) and the 30–39-year age group (Beta = 0.623, p = 0.019) were predicted to have anxiety. The analysis revealed that females were more anxious (Beta = 0.241, p = 0.005) than males. Healthcare providers working in primary healthcare centers (Beta = −0.315, p = 0.008) and labs (Beta = −0.845. p = 0.0001 were predicted to be less anxious than those working in other healthcare facilities. The data analysis showed that participants with good economic status had more depression than the participants in the other economic status groups (Beta = 0.067, p = 0.003). Conclusion This study found that the level of anxiety and depression in healthcare workers was mild. The factors that may contribute to anxiety in healthcare workers included being female, being younger than 30 or between the ages of 31 and 39, working in a specialized hospital facility, and the number of COVID-19 cases the workers dealt with. Economic status was associated with depression. A longitudinal study design is needed to understand the pattern of anxiety levels among healthcare workers over time during the COVID-19 pandemic.
Shamsan et al. (2022) Level of anxiety and depression among healthcare workers in Saudi Arabia during the COVID-19 pandemic. PeerJ 10:e14246 https://doi.org/10.7717/peerj.14246
Spatial and temporal trends in western polecat road mortality in Wales
Roads have considerable ecological effects that threaten the survival of some species, including many terrestrial carnivores. The western polecat is a small-medium sized mustelid native to Asia and Europe, including Britain where its historical stronghold is in Wales. Polecats are frequently killed on roads and road casualties represent the most common source of data on the species in the UK. However, little is known about the factors that increase the risk of collision. We used Generalized Additive Models to explore seasonal patterns in collisions as well as using Principal Component Analysis and regression modelling to identify landscape characteristics associated with polecat road casualties in Wales. Polecat road casualties had a bimodal distribution, occurring most frequently in March and October. Casualties were more frequently associated with road density, traffic volume, presence of rabbits, habitat patchiness and the abundance of proximal improved grassland habitat. Casualties were negatively associated with elevation and the abundance of semi-natural grassland habitat. The results of this study provide a framework for understanding and mitigating the impacts of roads on polecats in their historic stronghold, hence has considerable value to polecat conservation as well as broader applicability to ecologically similar species.
Barg et al. (2022) Spatial and temporal trends in western polecat road mortality in Wales. PeerJ 10:e14291 https://doi.org/10.7717/peerj.14291
Adherence to the Mediterranean diet, kinanthropometric characteristics and physical performance of young male handball players
Introduction Handball is a team sport whose performance depends on a large number of factors. The objectives of the present study were to analyze the differences in physical performance, kinanthropometric variables, and adherence to the Mediterranean diet (MD), in handball players according to sports category, as well as the possible relationships between these variables. Methods One hundred and thirty-three male handball players (35 infant; 46 cadets; 26 juniors and 26 seniors players) underwent a kinanthropometric analysis following the ISAK protocol, self-completed the KIDMED questionnaire, and their physical condition was evaluated with different physical tests. Results Significant differences (p < 0.001–0.007) were found between the sports categories in most of the physical condition variables and anthropometric characteristics, but not in the degree of adherence to the MD. The predominant level of adherence to the MD was medium (47.4%), followed by good (42.1%), and correlated with the body mass, the height, the BMI, the muscle mass and the ∑3-girths sum corrected, but not with physical test results. A multiple linear regression analysis showed that the fat mass and muscle mass variables had a more specific weight in the results of the physical fitness tests. Conclusions There are differences according to sports category in kinanthropometric characteristics and physical fitness tests in adolescent handball players. The predominant degrees of adherence to the MD were medium and good. A relationship was found between anthropometric characteristics and physical performance in handball players.
Romero-García et al. (2022) Adherence to the Mediterranean diet, kinanthropometric characteristics and physical performance of young male handball players. PeerJ 10:e14329 https://doi.org/10.7717/peerj.14329
METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner
Background As the most prevalent chemical modifications on eukaryotic mRNAs, N6-methyladenosine (m6A) methylation was reported to participate in the regulation of various metabolic diseases. This study aimed to investigate the roles of m6A methylation and methyltransferase-like16 (METTL16) in non-alcoholic fatty liver disease (NAFLD). Methods In this study, we used a model of diet-induced NAFLD, maintaining six male C57BL/6J mice on high-fat diet (HFD) to generate hepatic steatosis. The high-throughput sequencing and RNA sequencing were performed to identify the m6A methylation patterns and differentially expressed mRNAs in HFD mice livers. Furthermore, we detected the expression levels of m6A modify enzymes by qRT-PCR in liver tissues, and further investigated the potential role of METTL16 in NAFLD through constructing overexpression and a knockdown model of METTL16 in HepG2 cells. Results In total, we confirmed 15,999 m6A recurrent peaks in HFD mice and 12,322 in the control. Genes with differentially methylated m6A peaks were significantly associated with the dysregulated glucolipid metabolism and aggravated hepatic inflammatory response. In addition, we identified five genes (CIDEA, THRSP, OSBPL3, GDF15 and LGALS1) that played important roles in NAFLD progression after analyzing the differentially expressed genes containing differentially methylated m6A peaks. Intriguingly, we found that the expression levels of METTL16 were substantially increased in the NAFLD model in vivo and in vitro, and further confirmed that METTL16 upregulated the expression level of lipogenic genes CIDEA in HepG2 cells. Conclusions These results indicate the critical roles of m6A methylation and METTL16 in HFD-induced mice and cell NAFLD models, which broaden people’s perspectives on potential m6A-related treatments and biomarkers for NAFLD.
Tang et al. (2022) METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner. PeerJ 10:e14379 https://doi.org/10.7717/peerj.14379
Effects of land use types on soil erodibility in a small karst watershed in western Hubei
Background Soil erosion is a severe problem in the karst watershed, and analysis of soil erosion at the watershed scale is urgently needed. Methods This study tried to estimate the soil erodibility factor (K-factor) using the Erosion Productivity Impact Calculator (EPIC) nomograph and evaluate the spatial distribution of the predicted K-factor in a karst watershed. Soil properties and K-factors of five land use types (NF: natural mixed forest, CF: cypress forest, EF: economic forest, ST: stone dike terrace, VF: vegetable land) in the Xialaoxi small watershed were compared and key factors affecting erodibility were analyzed. Results Results showed that (1) The erodibility K-factor was unevenly distributed within different site types and strongly influenced by anthropogenic activities. The soil K-factors of sample sites subjected to frequent human disturbance (ST, VF) were high, ranging from 0.0480-0.0520 t hm2 h/(MJ mm hm2), while the soil K-factors of natural site types (NF, CF, and EF) were low, ranging from 0.0436-0.0448 t hm2 h/(MJ mm hm2). (2) The soil texture in the Xialaoxi watershed was mostly loamy, and that of the agricultural areas frequently disturbed by agricultural practices (ST, VF) was silty loam. (3) Soil carbon fractions were affected by land use types. Soil organic carbon storage of NF and CF had strong spatial heterogeneity. The soil organic carbon (SOC) and labile organic carbon (LOC) of the two were significantly higher than those of the disturbed EF and cultivated land soil. (4) There was a synergistic effect between the soil properties and the K-factor. K was significantly negatively related to sand fractions (2-0.05 mm) and non-capillary porosity, while positively related to silt content (0.05–0.002 mm). Overall, changes in bulk density (BD), total porosity (TP), non-capillary porosity (NCP), texture, and organic matter content caused by natural restoration or anthropogenic disturbance were the main reasons for soil erodibility. Natural care (sealing) and construction of stone dike planting practices were effective ways to reduce soil erosion in small karst watershed areas of western Hubei.
Luo et al. (2022) Effects of land use types on soil erodibility in a small karst watershed in western Hubei. PeerJ 10:e14423 https://doi.org/10.7717/peerj.14423
Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L
Foxtail millet is commonly used as a food and forage grass. ERECTA (ER) is a receptor-like kinase that can improve plant biomass and stress resistance. The sorghum SbER10_X1 gene was used as a probe to identify ER family genes on the Setaria italica genomes (SiERs), and determine the characteristics of the SiERs family. Herein, the structural features, expression patterns, and thermotolerance of SiERs function were identified by bioinformatics analysis, real-time PCR and transgenesis estimation. Results showed that SiERs had four members: two members were located on chromosome 1 with a total of six copies (SiER1_X1, SiER1_X2, SiER1_X3, SiER1_X4, SiER1_X5, and SiER1_X6), and two were on chromosome 4, namely, SiER4 (SiER4_X1 and SiER4_X2) and SiERL1. Among them, SiER1_X4 and SiER4_X1 were expressed highest in above-ground organs of foxtail millet, and actively responded to treatments with abscisic acid, brassinolide, gibberellin, and indole acetic acid. After overexpression of SiER1_X4 and SiER4_X1 in Arabidopsis, the plant height and biomass of the transgenic Arabidopsis significantly increased. Following high-temperature treatment, transgenic seedlings survived better compared to wild type. Transgenic lines showed higher SOD and POD activities, and expression level of AtHSF1 and AtBl1 genes significantly increased. These results indicated that SiER1_X4 and SiER4_X1 played important regulatory roles in plant growth and thermotolerance. The two genes provide potential targets for conventional breeding or biotechnological intervention to improve the biomass of forage grass and thermotolerance of field crops.
Zheng et al. (2022) Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L. PeerJ 10:e14452 https://doi.org/10.7717/peerj.14452
A systematic review of effects of daytime napping strategies on sports performance in physically active individuals with and without partial-sleep deprivation
Background Sleep is the body’s natural recovery process, restoring routine metabolic and regulatory functions. Various sleep interventions have been developed to facilitate recovery, and athletic performance, and daytime napping are among them. However, due to inconsistencies in studies, it remains unclear whether daytime napping affects sports performance. This article aims to review the effects of daytime napping on various variables of sports performance in physically active individuals with and without partial-sleep deprivation. Methods A systematic search in three clinical databases, namely Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and Web of Science, was conducted. To be included in the current review, the study should be a randomized controlled trial that evaluated the influence of daytime napping on one or more components of sports performance in healthy adults, 18 years old or older. Results In the accessible data available until December 2021, 1,094 records were found, of which 12 relevant randomized controlled trials were selected for qualitative synthesis. The majority of studies reported favourable effects of daytime napping on sports performance. However, only one study reported no significant impact, possibly due to a different methodological approach and a shorter nap duration. Conclusion Napping strategies optimize sports performance in physically active, athletic populations, benefitting partially sleep-deprived and well-slept individuals, with longer nap durations (~90 min) having more significant advantages. Daytime naps can be considered as cost-efficient, self-administered methods promoting recovery of body functions.
Sirohi et al. (2022) A systematic review of effects of daytime napping strategies on sports performance in physically active individuals with and without partial-sleep deprivation. PeerJ 10:e14460 https://doi.org/10.7717/peerj.14460
Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication
Humans and other mammalian species communicate emotions in ways that reflect evolutionary conservation and continuity, an observation first made by Darwin. One approach to testing this hypothesis has been to assess the capacity to perceive the emotional content of the vocalizations of other species. Using a binary forced choice task, we tested perception of the emotional intensity represented in coos and screams of infant and juvenile female rhesus macaques (Macaca mulatta) by 113 human listeners without, and 12 listeners with, experience (as researchers or care technicians) with this species. Each stimulus pair contained one high- and one low-arousal vocalization, as measured at the time of recording by stress hormone levels for coos and the degree of intensity of aggression for screams. For coos as well as screams, both inexperienced and experienced participants accurately identified the high-arousal vocalization at significantly above-chance rates. Experience was associated with significantly greater accuracy with scream stimuli but not coo stimuli, and with a tendency to indicate screams as reflecting greater emotional intensity than coos. Neither measures of empathy, human emotion recognition, nor attitudes toward animal welfare showed any relationship with responses. Participants were sensitive to the fundamental frequency, noisiness, and duration of vocalizations; some of these tendencies likely facilitated accurate perceptions, perhaps due to evolutionary homologies in the physiology of arousal and vocal production between humans and macaques. Overall, our findings support a view of evolutionary continuity in emotional vocal communication. We discuss hypotheses about how distinctive dimensions of human nonverbal communication, like the expansion of scream usage across a range of contexts, might influence perceptions of other species’ vocalizations.
Schwartz et al. (2022) Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication. PeerJ 10:e14471 https://doi.org/10.7717/peerj.14471
Differential responses of the seed germination of three functional groups to low temperature and darkness in a typical steppe, Northern China
Seed germination is a key stage in the life history of plants, which has a crucial effect on plant community structure. Climate change has substantially altered the surface soil temperature and light availability, which can affect seed germination. However, whether the seed germination of different functional groups is affected by the interactions of light and temperature remains unclear. Under laboratory conditions, we examined the effects of low temperature and darkness, as well as their interaction, on the seed germination of 16 species belonging to three plant functional groups (annual and biennials, perennial grasses, and perennial forbs) in a typical steppe, Northern China. We found that low temperature had a significant negative effect on seed germination of all species. Low temperature significantly decreased the final germination percentage and germinative force of the three plant functional groups, and the germination duration of perennial grasses. Darkness significantly decreased the germinative force of perennial forbs and total seeds, and the germination duration of perennial grasses. The interactive effects of light and temperature on the seed final germination percentage and germinative force of perennial grass indicated that darkness strengthened the inhibitory effect of low temperature on the seed germination of the grass functional group. Our study indicate that the seed germination of different plant functional groups varied greatly in response to changing environmental conditions. Our results suggest that future climate change could alter the regeneration and species composition of plant communities through changing seed germination.
Liu et al. (2022) Differential responses of the seed germination of three functional groups to low temperature and darkness in a typical steppe, Northern China. PeerJ 10:e14485 https://doi.org/10.7717/peerj.14485