title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=842
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Dendrobaena veneta avoids ethyl pentanoate and ethyl hexanoate, two compounds produced by the soil fungus Geotrichum candidum
link: https://peerj.com/articles/12148
last-modified: 2021-09-08
description: Earthworms shape the biological and physicochemical qualities of the soil they choose to reside in, but our understanding of the specific chemicals that attract or repel a particular species of earthworm remains incomplete. Current research indicates that some species feed on and are attracted to fungi, such as Geotrichum candidum. In the present study, as part of our continuing effort to characterize mechanisms of earthworm chemosensation, we tested whether ethyl hexanoate and ethyl pentanoate, two compounds produced by G. candidum, are appetitive to the European nightcrawler (Dendrobaena veneta). In a soil T-maze, both of these compounds significantly repelled individual earthworms in a dosage-dependent manner, this result ran counter to our initial hypothesis. D. veneta also avoided ethyl hexanoate and ethyl pentanoate in an assay we specifically developed to test an earthworms aversion to chemical stimuli in soil. In both of these assays, ethyl hexanoate was aversive at lower concentrations than ethyl pentanoate. These findings further clarify our understanding of the chemical cues that trigger the decision of D. veneta to select a particular soil-environment, and emphasize that different earthworm species may react very differently to commonly encountered chemical stimuli.
creator: Eileen M.S. Reed
creator: Mariel O. O’Connor
creator: Ione C. Johnson
creator: Wayne L. Silver
creator: Cecil J. Saunders
uri: https://doi.org/10.7717/peerj.12148
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Reed et al.

title: Probabilistically sampled and spectrally clustered plant species using phenotypic characteristics
link: https://peerj.com/articles/11927
last-modified: 2021-09-07
description: Phenotypic characteristics of a plant species refers to its physical properties as cataloged by plant biologists at different research centers around the world. Clustering species based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of phenotypic data. This algorithm suffers from low accuracy and high computational complexity issues. To address the accuracy challenge, we propose the use of Spectral Clustering (SC) algorithm. To make the algorithm computationally cheap, we propose using sampling, specifically, Pivotal Sampling that is probability based. Since application of samplings to phenotypic data has not been explored much, for effective comparison, another sampling technique called Vector Quantization (VQ) is adapted for this data as well. VQ has recently generated promising results for genotypic data. The novelty of our SC with Pivotal Sampling algorithm is in constructing the crucial similarity matrix for the clustering algorithm and defining probabilities for the sampling technique. Although our algorithm can be applied to any plant species, we tested it on the phenotypic data obtained from about 2,400 Soybean species. SC with Pivotal Sampling achieves substantially more accuracy (in terms of Silhouette Values) than all the other proposed competitive clustering with sampling algorithms (i.e. SC with VQ, HC with Pivotal Sampling, and HC with VQ). The complexities of our SC with Pivotal Sampling algorithm and these three variants are almost the same because of the involved sampling. In addition to this, SC with Pivotal Sampling outperforms the standard HC algorithm in both accuracy and computational complexity. We experimentally show that we are up to 45% more accurate than HC in terms of clustering accuracy. The computational complexity of our algorithm is more than a magnitude less than that of HC.
creator: Aditya A. Shastri
creator: Kapil Ahuja
creator: Milind B. Ratnaparkhe
creator: Yann Busnel
uri: https://doi.org/10.7717/peerj.11927
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Shastri et al.

title: Potential applications of personality assessments to the management of non-human primates: a review of 10 years of study
link: https://peerj.com/articles/12044
last-modified: 2021-09-07
description: Studies of primate personality have become increasingly common over the past three decades. Recently, studies have begun to focus on the health, welfare and conservation implications of personality, and the potential applications of incorporating quantitative personality assessments into animal management programmes. However, this literature is dispersed across a multitude of settings and scientific disciplines. We conducted a review of nonhuman primate personality studies relevant to these issues published since 2010, following on from an earlier review. The databases ScienceDirect, PubMed and Web of Science were used to identify relevant articles. After eliminating irrelevant or duplicate papers, 69 studies were selected. Our review reveals that, while primate personality research is carried out on a range of species, there is strong taxonomic bias. While 28 species appeared within the reviewed literature, 52% of studies were carried out on just five species. Further, the most common research focus (43%) was validating new assessment methods or describing personality in different species, rather than exploring the links between personality and animal welfare using existing validated methods. However, among the remaining studies that did explore the role of animal personality in husbandry, health, and welfare, we identified progression towards integrating personality data into various aspects of animal management. Evidence suggests the assessment of personality may benefit social group management, enrichment practices, training protocols, health and welfare monitoring, and conservation planning for endangered species. We argue that further research which develops our understanding of primate personality and its influence in these areas will provide a valuable tool to inform animal management practices.
creator: Max Norman
creator: Lewis J. Rowden
creator: Guy Cowlishaw
uri: https://doi.org/10.7717/peerj.12044
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Norman et al.

title: Interaction of interregional O3 pollution using complex network analysis
link: https://peerj.com/articles/12095
last-modified: 2021-09-07
description: In order to improve the accuracy of air pollution management and promote the efficiency of coordinated inter-regional prevention and control, this study analyzes the interaction of O3 in Qilihe District, Lanzhou City, China. Data used for analysis was obtained from 63 air quality monitoring stations between November 2017 and October 2018. This paper uses complex network theory to describe the network structure characteristics of O3 pollution spatial correlation. On this basis, the node importance method is used to mine the sub-network with the highest spatial correlation in the O3 network, and use transfer entropy theory to analyse the interaction of pollutants between regions. The results show that the O3 area of Qilihe District, Lanzhou City can be divided into three parts: the urban street community type areas in urban areas, the township and village type areas in mountain areas and the scattered areas represented by isolated nodes. An analysis of the mutual influence of O3 between each area revealed that the impact of O3 on each monitoring station in adjacent areas will vary considerably. Therefore these areas cannot be governed as a whole, and the traditional extensive management measures based on administrative divisions cannot be used to replace all other regional governance measures. There is the need to develop a joint prevention and control mechanism tailored to local conditions in order to improve the accuracy and efficiency of O3 governance.
creator: Qiang Zhang
creator: Yunan Zhu
creator: Dianxiang Xu
creator: Jiaqiong Yuan
creator: Zhihe Wang
creator: Yong Li
creator: Xueyan Liu
uri: https://doi.org/10.7717/peerj.12095
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Zhang et al.

title: Identification of immune related cells and crucial genes in the peripheral blood of ankylosing spondylitis by integrated bioinformatics analysis
link: https://peerj.com/articles/12125
last-modified: 2021-09-07
description: BackgroundAnkylosing spondylitis (AS) is a progressive rheumatic disease and studies reveal that the immune system is critical for the pathogenesis of AS. In the present study, various bioinformatics analysis methods were comprehensively applied, designed to identify potential key genes and inflammation states of AS.MethodsThe transcriptome profiles of GSE25101 and GSE73754 obtained from the Gene Expression Omnibus (GEO) database were merged for subsequent analyses. The differentially expressed genes (DEGs) were identified using the Bioconductor package Limma and threshold values. Functional enrichment and pathway enrichment analyses were performed using the clusterProfiler package and Gene Set Enrichment Analysis (GSEA). Next, protein–protein interaction (PPI) network of the identified DEGs was constructed by the online database, the Search Tool for the Retrieval of Interacting Genes (STRING), visualization and analysis were performed through Cytoscape software. Subsequently, we applied CIBERSORT algorithm to identify subpopulation proportions of immune cells in peripheral blood samples. Finally, we validated the hub genes with the GSE18781 dataset. Samples were collected from patients to validate gene and protein expression using qRT-PCR and ELISA.ResultsA total of 334 DEGs were identified, including 182 upregulated and 152 downregulated DEGs, between AS patients and normal human controls, which were primarily involved in immune response, autophagy, and natural killer cell-mediated cytotoxicity. The most prominent module and candidate biomarkers were identified from the PPI network. Biomarkers were selected for validation and their expressions were significantly decreased in peripheral blood samples which was consistent with transcriptome sequencing results. Nine genes with AUC > 0.70 were considered to be AS hub genes for ROC curve analysis, including GZMA, GZMK, PRF1, GNLY, NKG7, KLRB1, KLRD1, IL2RB and CD247. Furthermore, CIBERSORT results suggest that AS contained a higher proportion of CD8+ T cells, naive CD4+ T cells, neutrophils, and lower levels of gamma delta T cells compared with the normal controls.ConclusionIn this study, we identified DEGs combined with their closely related biological functions and propose that granule-associated proteins and immune infiltration maybe involved in the progression of ankylosing spondylitis. These validated hub genes may provide new perspectives for understanding the molecular mechanisms of ankylosing spondylitis.
creator: Yang Zheng
creator: Bingbing Cai
creator: Conglin Ren
creator: Haipeng Xu
creator: Weibin Du
creator: Yijiang Wu
creator: Fu Lin
creator: Helou Zhang
creator: Renfu Quan
uri: https://doi.org/10.7717/peerj.12125
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Zheng et al.

title: Investigation of multiple sclerosis-related pathways through the integration of genomic and proteomic data
link: https://peerj.com/articles/11922
last-modified: 2021-09-06
description: BackgroundMultiple sclerosis (MS) has a complex pathophysiology, variable clinical presentation, and unpredictable prognosis; understanding the underlying mechanisms requires combinatorial approaches that warrant the integration of diverse molecular omics data.MethodsHere, we combined genomic and proteomic data of the same individuals among a Turkish MS patient group to search for biologically important networks. We previously identified differentially-expressed proteins by cerebrospinal fluid proteome analysis of 179 MS patients and 42 non-MS controls. Among this study group, 11 unrelated MS patients and 60 independent, healthy controls were subjected to whole-genome SNP genotyping, and genome-wide associations were assessed. Pathway enrichment analyses of MS-associated SNPs and differentially-expressed proteins were conducted using the functional enrichment tool, PANOGA.ResultsNine shared pathways were detected between the genomic and proteomic datasets after merging and clustering the enriched pathways. Complement and coagulation cascade was the most significantly associated pathway (hsa04610, P = 6.96 × 10−30). Other pathways involved in neurological or immunological mechanisms included adherens junctions (hsa04520, P = 6.64 × 10−25), pathogenic Escherichia coli infection (hsa05130, P = 9.03 × 10−14), prion diseases (hsa05020, P = 5.13 × 10−13).ConclusionWe conclude that integrating multiple datasets of the same patients helps reducing false negative and positive results of genome-wide SNP associations and highlights the most prominent cellular players among the complex pathophysiological mechanisms.
creator: Elif Everest
creator: Ege Ülgen
creator: Ugur Uygunoglu
creator: Melih Tutuncu
creator: Sabahattin Saip
creator: Osman Uğur Sezerman
creator: Aksel Siva
creator: Eda Tahir Turanli
uri: https://doi.org/10.7717/peerj.11922
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Everest et al.

title: A highly effective and self-transmissible CRISPR antimicrobial for elimination of target plasmids without antibiotic selection
link: https://peerj.com/articles/11996
last-modified: 2021-09-06
description: The use of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) for sequence-specific elimination of bacteria or resistance genes is a powerful tool for combating antibiotic resistance. However, this approach requires efficient delivery of CRISPR/Cas DNA cassette(s) into the targeted bacterial population. Compared to phage transduction, plasmid conjugation can deliver DNA to a broader host range but often suffers from low delivery efficiency. Here, we developed multi-plasmid conjugation systems for efficient CRISPR/Cas delivery, target DNA elimination and plasmid replacement. The CRISPR/Cas system, delivered via a broad-host-range R1162 mobilizable plasmid, specifically eliminated the targeted plasmid in recipient cells. A self-transmissible RK2 helper plasmid facilitated the spread of mobilizable CRISPR/Cas. The replacement of the target plasmid with another plasmid from the same compatibility group helped speed up target plasmid elimination especially when the target plasmid was also mobilizable. Together, we showed that up to 100% of target plasmid from the entire recipient population could be replaced even at a low (1:180) donor-to-recipient ratio and in the absence of transconjugant selection. Such an ability to modify genetic content of microbiota efficiently in the absence of selection will be critical for future development of CRISPR antimicrobials as well as genetic tools for in situ microbiome engineering.
creator: Panjaporn Wongpayak
creator: Orapan Meesungnoen
creator: Somchai Saejang
creator: Pakpoom Subsoontorn
uri: https://doi.org/10.7717/peerj.11996
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Wongpayak et al.

title: Impact of umbilical cord arterial pH, gestational age, and birth weight on neurodevelopmental outcomes for preterm neonates
link: https://peerj.com/articles/12043
last-modified: 2021-09-06
description: BackgroundThe aim of this study was to determine the impact of umbilical cord arterial pH, gestational age, and birth weight on neurodevelopmental outcomes for preterm neonates.MethodsWe examined 112 neonates. Inclusion criteria were: Saturations greater than 88%, and heart rates between 100–205 beats per minute.MeasurementsWe assessed several neurodevelopmental factors as part of the Brazelton Neonatal Behavioral Assessment Scale (NBAS), 4th edition, such as asymmetric tonic neck reflex (ATNR), motor maturity, response to sensory stimuli, habituation, and state regulation. Initial assessment parameters such as APGAR score and umbilical cord arterial pH were used to assess neonates.ResultsWe found a strong correlation between the presence of the sucking reflex and umbilical cord arterial pH (r = 0.32; p = 0.018981). Umbilical cord arterial pH was also correlated with the presence of asymmetric tonic neck reflex (r = 0.27; p = 0.047124), cost of attention (r = 0.31; p = 0.025381) and general motor maturity (r = 0.34; p = 0.011741).ConclusionsWe found that the sucking reflex may be affected in infants with low umbilical cord arterial pH values. Practitioners and parents can use the NBAS to help determine neurodevelopmental factors and outcomes in preterm infants, possibly leading to safer and more effective feeding practices and interventions.
creator: Roksana Malak
creator: Dorota Sikorska
creator: Marta Rosołek
creator: Ewa Baum
creator: Ewa Mojs
creator: Przemysław Daroszewski
creator: Monika Matecka
creator: Brittany Fechner
creator: Włodzimierz Samborski
uri: https://doi.org/10.7717/peerj.12043
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Malak et al.

title: Downregulation of PPA2 expression correlates with poor prognosis of kidney renal clear cell carcinoma
link: https://peerj.com/articles/12086
last-modified: 2021-09-06
description: BackgroundKidney renal clear cell carcinoma (KIRC) is the most common subtype of kidney cancer. Inorganic pyrophosphatase (PPA2) is an enzyme that catalyzes the hydrolysis of pyrophosphate to inorganic phosphate; few studies have reported its significance in cancers. Therefore, we aimed to explore the prognostic value of PPA2 in KIRC.MethodsPPA2 expression was detected via immunohistochemistry in a tissue chip containing specimens from 150 patients with KIRC. We evaluated the correlation between PPA2 expression, clinicopathological characteristics, and survival. Data from online databases and another cohort (paraffin-embedded specimens from 10 patients with KIRC) were used for external validation.ResultsPPA2 expression was significantly lower in KIRC tissues than in normal renal tissues (p < 0.0001). Low expression of PPA2 was significantly associated with a high histologic grade and poor prognosis. The differential expression of PPA2 was validated at the gene and protein levels. Multivariate Cox regression analysis showed that PPA2 expression was an independent prognostic factor in patients with KIRC. Gene set enrichment analysis suggested that decreased expression of PPA2 might be related to the epithelial-mesenchymal transition in KIRC.ConclusionsOur study demonstrated that PPA2 is an important energy metabolism-associated biomarker correlated with a favorable prognosis in KIRC.
creator: Wenbiao Zhu
creator: Huiming Jiang
creator: Shoucheng Xie
creator: Huanqin Xiao
creator: Qinghua Liu
creator: Nanhui Chen
creator: Pei Wan
creator: Shanming Lu
uri: https://doi.org/10.7717/peerj.12086
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Zhu et al.

title: Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem
link: https://peerj.com/articles/12094
last-modified: 2021-09-06
description: First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids (‘thoracosaurs’) are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a ‘basal’ alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous–early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.
creator: Jonathan P. Rio
creator: Philip D. Mannion
uri: https://doi.org/10.7717/peerj.12094
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Rio and Mannion