title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=706 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz link: https://peerj.com/articles/13429 last-modified: 2022-05-12 description: C-repeat binding factors (CBFs) are transcription factors that are known to play important roles in plant cold acclimation. They are highly conserved in most higher plants. Taraxacum kok-saghyz (TKS) is an herb native to China and Kazakhstan and is well-known for its production of rubber silk with industrial and economic value. To understand cold acclimation mechanisms, we conducted a genome-wide discovery of the CBF family genes in TKS and revealed ten CBF genes. A bioinformatic analysis of the CBF genes was carried out to analyze the phylogenetic relationship, protein conservative motifs, protein physicochemical properties, gene structure, promoter cis-acting elements, and the gene expression patterns under cold acclimation and control conditions. It was found that most of these genes were highly responsive at the late stage of cold acclimation, indicating that they play important roles in the cold acclimation processes of TKS. This study provides a theoretical basis for the study of the molecular functions of the CBF gene family in TKS, and a useful guidance for the genetic improvement of the cold tolerance traits of TKS and other plants, including crops. creator: Haifeng Zhang creator: Yongyong Gong creator: Peilin Sun creator: Sixue Chen creator: Chunquan Ma uri: https://doi.org/10.7717/peerj.13429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Dental pathologies in lamniform and carcharhiniform sharks with comments on the classification and homology of double tooth pathologies in vertebrates link: https://peerj.com/articles/12775 last-modified: 2022-05-11 description: Double tooth pathologies are important indicators of trauma, disease, diet, and feeding biomechanics, and are widely documented in mammals. However, diagnosis of double tooth pathologies in extinct non-mammalian vertebrates is complicated by several compounding factors including: a lack of shared terminology reflecting shared etiology, inconsistencies in definitions and key features within and outside of mammals (e.g., gemination, fusion, twinning, concrescence); differences in tooth morphology, heterodonty, regeneration, and implantation between mammals and non-mammalian vertebrates; and the unmet need for diagnostic criteria that can be applied to isolated teeth, which are common in the fossil record. Here we report on double tooth pathologies in the lamniform and carcharhiniform Cenozoic sharks Otodus megalodon (NCSM 33639) and Carcharhinus leucas (NCSM 33640, 33641). All three teeth bear a singular bifid crown with mirrored halves and abnormal internal microstructure—a single, bifurcating pulp cavity in C. leucas and a more than tripling of vessels in O. megalodon (from two to seven main ascending canals). We identify these abnormalities as likely examples of gemination due to their symmetry, which rules out fusion of tooth buds in one tooth file in different developmental stages in polyphyodont taxa; however, we note that incomplete forms of mesiodistal tooth fusion can be morphologically indistinguishable from gemination, and thus fusion cannot be rejected. We further compile and recategorize, when possible, the diversity of tooth pathologies in sharks. The identification of double tooth pathologies in O. megalodon and C. leucas has paleobiological implications. Such pathologies in sharks are largely hypothesized to stem from trauma to developing tooth buds. Carcharhinus leucas is known to feed on prey documented to cause feeding-related oral traumas (e.g., rays, sawfish, spiny fish, and sea urchins). However, O. megalodon, is considered to have largely fed on marine mammals, and perhaps turtles and/or fish, raising the possibility that the dietary diversity of this species is, as of yet, underappreciated. The genetic underpinnings of tooth morphogenesis and regeneration is highly conserved throughout vertebrate evolution, suggesting a homologous framework can be established. However, more research is needed to link developmental, paleobiological, and/or paleoenvironmental factors to gemination/fusion in polyphyodont taxa. We argue that the definitions and diagnostic criteria for dental pathologies in vertebrates require standardization in order to advance macroevolutionary studies of feeding trauma in deep time. creator: Harrison S. Miller creator: Haviv M. Avrahami creator: Lindsay E. Zanno uri: https://doi.org/10.7717/peerj.12775 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Miller et al. title: DeepNC: a framework for drug-target interaction prediction with graph neural networks link: https://peerj.com/articles/13163 last-modified: 2022-05-11 description: The exploration of drug-target interactions (DTI) is an essential stage in the drug development pipeline. Thanks to the assistance of computational models, notably in the deep learning approach, scientists have been able to shorten the time spent on this stage. Widely practiced deep learning algorithms such as convolutional neural networks and recurrent neural networks are commonly employed in DTI prediction projects. However, they can hardly utilize the natural graph structure of molecular inputs. For that reason, a graph neural network (GNN) is an applicable choice for learning the chemical and structural characteristics of molecules when it represents molecular compounds as graphs and learns the compound features from those graphs. In an effort to construct an advanced deep learning-based model for DTI prediction, we propose Deep Neural Computation (DeepNC), which is a framework utilizing three GNN algorithms: Generalized Aggregation Networks (GENConv), Graph Convolutional Networks (GCNConv), and Hypergraph Convolution-Hypergraph Attention (HypergraphConv). In short, our framework learns the features of drugs and targets by the layers of GNN and 1-D convolution network, respectively. Then, representations of the drugs and targets are fed into fully-connected layers to predict the binding affinity values. The models of DeepNC were evaluated on two benchmarked datasets (Davis, Kiba) and one independently proposed dataset (Allergy) to confirm that they are suitable for predicting the binding affinity of drugs and targets. Moreover, compared to the results of baseline methods that worked on the same problem, DeepNC proves to improve the performance in terms of mean square error and concordance index. creator: Huu Ngoc Tran Tran creator: J. Joshua Thomas creator: Nurul Hashimah Ahamed Hassain Malim uri: https://doi.org/10.7717/peerj.13163 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tran et al. title: Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis link: https://peerj.com/articles/13304 last-modified: 2022-05-11 description: The long dormancy period of Paris polyphylla var. yunnanensis seeds affects the supply of this scarce plant, which is used as an important traditional Chinese medicine. Mature seeds with a globular embryo and germinating seeds with developed embryo were used to explore the mechanisms of seed germination in this species. The protein profiles between the mature and germinating seeds were compared using the isobaric tags for relative and absolute quantification (iTRAQ) approach. Of the 4,488 proteins identified, a total of 1,305 differentially expressed proteins (DEPs) were detected. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEPs indicated that metabolic pathways and the biosynthesis of secondary metabolites were the two top pathways. Additionally, phytohormone quantification shows that the abscisic acid (ABA) level significantly decreased, whereas the GA3 level dramatically increased among nine endogenous gibberellins (GAs), resulting in a significant increase of the GA3/ABA ratio in germinating seeds. The biosynthesis pathways of carotenoid as a precursor for ABA production and GA were further analyzed, and showed that proteinic expressions of the candidate genes in the two pathways did not correlate with the transcriptional abundances. However, 9-cis-epoxycarotenoid dioxygenase (NCED), a rate limited enzyme for ABA biosynthesis, was significantly decreased in mRNA levels in germinating seeds. By contrast, gibberellin 20-oxidase (GA20ox), a key enzyme GA biosynthesis, exhibited the major increase in one copy and a slight decrease in three others at the protentional level in germinating seeds. Gibberellin 2-oxidase (GA2ox), an inactivate enzyme in bioactive GAs, has the tendency to down-regulate in mRNA or at the proteinic level in germinating seeds. Altogether, these results suggested that the analyses of ABA and GA levels, the GA3/ABA ratio, and the expressional patterns of their regulatory genes may provide a novel mechanistic understanding of how phytohormones regulate seed germination in P. polyphylla var. yunnanensis. creator: Li-Zhen Ling creator: Shu-Dong Zhang uri: https://doi.org/10.7717/peerj.13304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ling and Zhang title: QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study link: https://peerj.com/articles/13407 last-modified: 2022-05-11 description: Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding. creator: Feng Mao creator: Depeng Wu creator: Fangfang Lu creator: Xin Yi creator: Yujuan Gu creator: Bin Liu creator: Fuxia Liu creator: Tang Tang creator: Jianxin Shi creator: Xiangxiang Zhao creator: Lei Liu creator: Lilian Ji uri: https://doi.org/10.7717/peerj.13407 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mao et al. title: Combinations of action observation and motor imagery on golf putting’s performance link: https://peerj.com/articles/13432 last-modified: 2022-05-11 description: Motor imagery (MI) and action observation (AO) have been found to enhance motor performance, but recent research found that a combination of action observation and motor imagery (AOMI) together is even better. Despite this initial finding, the most effective way to combine them is unknown. The present study examined the effects of synchronized (i e., concurrently doing AO and MI), asynchronised (i.e., first doing AO then MI), and progressive (first asynchronised approach, then doing synchronized approach) AOMI on golf putting performance and learning. We recruited 45 university students (Mage = 20.18 + 1.32 years; males = 23, females = 22) and randomly assigned them into the following four groups: synchronized group (S-AOMI), asynchronised group (A-AOMI), progressive group (A-S-AOMI), and a control group with a pre-post research design. Participants engaged in a 6-week (three times/per-week) intervention, plus two retention tests. A two-way (group × time) mixed ANOVA statistical analysis found that the three experimental groups performed better than the control group after intervention. However, we found progressive and asynchronised had better golf putting scores than synchronized group and the control group on the retention tests. Our results advance knowledge in AOMI research, but it needs more research to reveal the best way of combining AOMI in the future. Theoretical implications, limitations, applications, and future suggestions are also discussed. creator: Chi-Hsian Lin creator: Frank J.H. Lu creator: Diane L. Gill creator: Ken Shih-Kuei Huang creator: Shu-Ching Wu creator: Yi-Hsiang Chiu uri: https://doi.org/10.7717/peerj.13432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lin et al. title: Base water potential but not hydrotime predicts seedling emergence of Medicago sativa under water stress conditions link: https://peerj.com/articles/13206 last-modified: 2022-05-10 description: We determined the hydrotime model parameters of 10 alfalfa seed lots by incubating seeds at various water potentials in the laboratory. Meanwhile, seedling emergence under drought and salinity conditions in a greenhouse pot experiment, and seedling establishment in the field were determined. Correlation analysis was utilized to detect the relationship between hydrotime model parameters and seedling emergence under water stress conditions. The germination percentage did not differ significantly among seed lots when seeds were incubated at −0.1 MPa, while it differed significantly among seed lots at water potentials of −0.3 and −0.6 MPa. Compared to control conditions, drought and salinity decreased seedling emergence to different extents, depending on seed lots. Seedling emergence in the field differed significantly among seed lots and ranged from 30% to 80%. Ψb(50) showed a significant correlation with seedling emergence under various conditions and with seedling establishment in the field, while no correlation was observed between θH, σφb and seedling emergence and establishment. These results suggest that Ψb(50) can be used to rank the vigor of alfalfa seed lots and thus predict seedling emergence and establishment under water stress conditions. creator: Xianglai Chen creator: Zhichao Wei creator: Dali Chen creator: Xiaowen Hu uri: https://doi.org/10.7717/peerj.13206 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Contrasting patterns from two invasion fronts suggest a niche shift of an invasive predator of native bees link: https://peerj.com/articles/13269 last-modified: 2022-05-10 description: BackgroundThe accuracy of predictions of invasive species ranges is dependent on niche similarity between invasive and native populations and on our ability to identify the niche characteristics. With this work we aimed to compare the niche dynamics of two genetically related invasive populations of Vespa velutina (an effective predator of honeybees and wild pollinators), in two distinct climatic regions, one in central Europe and another one in the north-western Iberian Peninsula, and hence to identify uninvaded regions susceptible to invasion.MethodsNiche dynamics and shifts of V. velutina were assessed by comparing the environmental niches of the native and of the two invasive populations, using climatic, topographic and land use variables. We also ran reciprocal distribution models using different algorithms and records from both native and invasive ranges to compare model predictions and estimate which regions are at a greater risk of being invaded.ResultsAn apparent niche shift was detected in the population of the NW of Iberian Peninsula, where the species is living under environmental conditions different from the native niche. In central Europe, large suitable areas remain unoccupied. The fact that both invasive populations are well established, despite occupying environmentally distinct regions indicates that V. velutina has a high ability to successfully invade different environmental envelopes from those existing in its native range. For example, in north-western Iberian Peninsula the species is now thriving out of its native niche limits. Moreover, the large extent of still unoccupied environmental space with similar conditions to those used by the species in its native range suggests that there is still a large area of central and eastern Europe that can be potentially invaded by the species. creator: Maria João Verdasca creator: Luisa Carvalheiro creator: Jesus Aguirre Gutierrez creator: José Pedro Granadeiro creator: Quentin Rome creator: Sebastien J. Puechmaille creator: Rui Rebelo creator: Hugo Rebelo uri: https://doi.org/10.7717/peerj.13269 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Verdasca et al. title: Effects of fire disturbance on species and functional compositions vary with tree sizes in a tropical dry forest link: https://peerj.com/articles/13270 last-modified: 2022-05-10 description: BackgroundDisturbances are crucial in determining forest biodiversity, dynamics, and ecosystem functions. Surface fire is a significant disturbance in tropical forests, but research on the effect of surface fire on structuring species and functional composition in a community through time remains scarce. Using a 20-year dataset of tree demography in a seasonal evergreen tropical forest in Thailand, we specifically addressed two essential questions: (1) What is the pattern of temporal turnover in species and functional composition in a community with frequent fire disturbance? (2) How did the temporal turnover vary with tree size?MethodsWe analyzed species compositional and functional temporal turnovers in four different tree size classes among five tree censuses. We quantified species turnover by calculating Bray-Curtis dissimilarity, and investigated its underlying mechanisms by comparing pairwise dissimilarity of functional traits with simulations from null models. If fire disturbances contribute more to a stochastic process, the functional composition would display a random pattern. However, if they contribute more towards a deterministic process, the functional composition should reveal a non-random pattern.ResultsOver 20 years (1994–2014), we observed changes in species composition, whereas functional composition remained relatively stable. The temporal turnover patterns of species and functional compositions varied with tree sizes. In particular, temporal functional turnover shifted very little for large trees, suggesting that changes in species composition of larger trees are contributed by species with similar functional traits through time. The temporal functional composition turnovers of smaller trees (DBH ≤ 5 cm) were mostly at random. We detected a higher functional turnover than expected by null models in some quadrats throughout the 50-ha study plot, and their observed turnover varied with diameter classes.ConclusionsSpecies compositional changes were caused by changes in the abundance of species with similar functional traits through time. Temporal functional turnover in small trees was random in most quadrats, suggesting that the recruits came from the equal proportions of surviving trees and new individuals of fast-growing species, which increased rapidly after fires. On the other hand, functional composition in big trees was more likely determined by surviving trees which maintained higher functional similarities than small trees through time. Fire disturbance is important for ecosystem functions, as changing forest fire frequency may alter forest turnover, particularly in functional composition in the new recruits of this forest. creator: Kanokporn Kaewsong creator: Chia-Hao Chang-Yang creator: Sarayudh Bunyavejchewin creator: Ekaphan Kraichak creator: Jie Yang creator: Zhenhua Sun creator: Caicai Zhang creator: Wenfei Li creator: Luxiang Lin creator: I-Fang Sun uri: https://doi.org/10.7717/peerj.13270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kaewsong et al. title: An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples link: https://peerj.com/articles/13277 last-modified: 2022-05-10 description: ImportanceThe rise of novel, more infectious SARS-CoV-2 variants has made clear the need to rapidly deploy large-scale testing for COVID-19 to protect public health. However, testing remains limited due to shortages of personal protective equipment (PPE), naso- and oropharyngeal swabs, and healthcare workers. Simple test methods are needed to enhance COVID-19 screening. Here, we describe a simple, and inexpensive spit-test for COVID-19 screening called Patient Self-Collection of Sample-CoV2 (PSCS-CoV2).ObjectiveTo evaluate an affordable and convenient test for COVID-19.MethodsThe collection method relies on deep throat sputum (DTS) self-collected by the subject without the use of swabs, and was hence termed the Self-Collection of Sample for SARS-CoV-2 (abbreviated PSCS-CoV2). We used a phenol-chloroform extraction method for the viral RNA. We then tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction with primers against at least two coding regions of the viral nucleocapsid protein (N1 and N2 or E) of SARS-CoV-2. We evaluted the sensitivity and specificity of our protocol. In addition we assess the limit of detection, and efficacy of our Viral Inactivating Solution. We also evaluated our protocol, and pooling strategy from volunteers on a local college campus.ResultsWe show that the PSCS-CoV2 method accurately identified 42 confirmed COVID-19 positives, which were confirmed through the nasopharyngeal swabbing method of an FDA approved testing facility. For samples negative for COVID-19, we show that the cycle threshold for N1, N2, and RP are similar between the PSCS-CoV2 and nasopharynx swab collection method (n = 30). We found a sensitivity of 100% (95% Confidence Interval [CI], 92-100) and specifity of 100% (95% CI, 89-100) for our PSCS-CoV2 method. We determined our protocol has a limit of detection of 1/10,000 for DTS from a COVID-19 patient. In addition, we show field data of the PSCS-CoV2 method on a college campus. Ten of the twelve volunteers (N1 < 30) that we tested as positive were subsequently tested positive by an independent laboratory. Finally, we show proof of concept of a pooling strategy to test for COVID-19, and recommend pool sizes of four if the positivity rate is less than 15%.Conclusion and RelevanceWe developed a DTS-based protocol for COVID-19 testing with high sensitivity and specificity. This protocol can be used by non-debilitated adults without the assistance of another adult, or by non-debilitated children with the assistance of a parent or guardian. We also discuss pooling strategies based on estimated positivity rates to help conserve resources, time, and increase throughput. The PSCS-CoV2 method can be a key component of community-wide efforts to slow the spread of COVID-19. creator: Sunny C. Huang creator: Thomas K. Pak creator: Cameron P. Graber creator: Charles C. Searby creator: Guanghao Liu creator: Jennifer Marcy creator: Alexandra K. Yaszemski creator: Kurt Bedell creator: Emily Bui creator: Stanley Perlman creator: Qihong Zhang creator: Kai Wang creator: Val C. Sheffield creator: Calvin S. Carter uri: https://doi.org/10.7717/peerj.13277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Huang et al.