title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=844
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

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

title: Comparative analysis morphology, anatomical structure and transcriptional regulatory network of chlorophyll biosynthesis in Oryza longistaminata, O. sativa and their F1 generation
link: https://peerj.com/articles/12099
last-modified: 2021-09-06
description: Oryza longistaminata, a perennial wild species, is widely distributed in the African continent. It has strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. Chlorophyll biosynthesis is important for photosynthesis in rice. However, the chlorophyll biosynthesis and related gene profiles of O. longistaminata and its descendants remained unclear. Here, the F1 generation of O. sativa and O. longistaminata were obtained. Then, the comparative analysis morphology, anatomical structure, and transcriptional regulatory networks of chlorophyll biosynthesis were detected and analyzed. Results showed that the F1 generation has obvious long awn, similar with that of the male parent. The purple color of the long awn is different from that of the male parent. Microstructural results showed that the flag leaves of F1 have large mesophyll cell gaps in the upper- and lower-positions, small mesophyll cell gaps in the middle position, and more chloroplasts. Increased chlorophyll content was also observed in the F1 generation. In the lower-position flag leaves, the total chlorophyll contents of F1 were 1.55 and 1.5 times those of O. sativa and O. longistaminata, respectively. POR, MgCH and HEMA1 showed higher expression levels than the other related genes selected in the chlorophyll biosynthesis pathway. The HEMA1 expression level in the middle-position flag leaves of O. longistaminata was the highest, and it was 2.83 and 2.51 times that of O. sativa and F1, respectively. The expression level of DVR gene in lower-position flag leaves of F1 were 93.16% and 95.06% lower than those of O. sativa and O. longistaminata, respectively. This study provided a potential reference for studying the photosynthesis and heterosis utilization of O. longistaminata.
creator: Zhihang Hu
creator: Xinyu Chen
creator: Liexiang Huangfu
creator: Shaobo Shao
creator: Xiang Tao
creator: Lishuang Song
creator: Wenzhi Tong
creator: Chuan-Deng Yi
uri: https://doi.org/10.7717/peerj.12099
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Hu et al.

title: Detection of spreader nodes in human-SARS-CoV protein-protein interaction network
link: https://peerj.com/articles/12117
last-modified: 2021-09-06
description: The entire world is witnessing the coronavirus pandemic (COVID-19), caused by a novel coronavirus (n-CoV) generally distinguished as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 promotes fatal chronic respiratory disease followed by multiple organ failure, ultimately putting an end to human life. International Committee on Taxonomy of Viruses (ICTV) has reached a consensus that SARS-CoV-2 is highly genetically similar (up to 89%) to the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), which had an outbreak in 2003. With this hypothesis, current work focuses on identifying the spreader nodes in the SARS-CoV-human protein–protein interaction network (PPIN) to find possible lineage with the disease propagation pattern of the current pandemic. Various PPIN characteristics like edge ratio, neighborhood density, and node weight have been explored for defining a new feature spreadability index by which spreader proteins and protein–protein interaction (in the form of network edges) are identified. Top spreader nodes with a high spreadability index have been validated by Susceptible-Infected-Susceptible (SIS) disease model, first using a synthetic PPIN followed by a SARS-CoV-human PPIN. The ranked edges highlight the path of entire disease propagation from SARS-CoV to human PPIN (up to level-2 neighborhood). The developed network attribute, spreadability index, and the generated SIS model, compared with the other network centrality-based methodologies, perform better than the existing state-of-art.
creator: Sovan Saha
creator: Piyali Chatterjee
creator: Mita Nasipuri
creator: Subhadip Basu
uri: https://doi.org/10.7717/peerj.12117
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Saha et al.

title: VGEA: an RNA viral assembly toolkit
link: https://peerj.com/articles/12129
last-modified: 2021-09-06
description: Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user’s choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA under the GNU General Public License.
creator: Paul E. Oluniyi
creator: Fehintola Ajogbasile
creator: Judith Oguzie
creator: Jessica Uwanibe
creator: Adeyemi Kayode
creator: Anise Happi
creator: Alphonsus Ugwu
creator: Testimony Olumade
creator: Olusola Ogunsanya
creator: Philomena Ehiaghe Eromon
creator: Onikepe Folarin
creator: Simon D.W. Frost
creator: Jonathan Heeney
creator: Christian T. Happi
uri: https://doi.org/10.7717/peerj.12129
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Oluniyi et al.

title: Comprehensive analysis of abnormal expression, prognostic value and oncogenic role of the hub gene FN1 in pancreatic ductal adenocarcinoma via bioinformatic analysis and in vitro experiments
link: https://peerj.com/articles/12141
last-modified: 2021-09-06
description: BackgroundPancreatic ductal adenocarcinoma (PDAC) is one of the most commonly diagnosed cancers with a poor prognosis worldwide. Although the treatment of PDAC has made great progress in recent years, the therapeutic effects are still unsatisfactory. Methods. In this study, we identified differentially expressed genes (DEGs) between PDAC and normal pancreatic tissues based on four Gene Expression Omnibus (GEO) datasets (GSE15471, GSE16515, GSE28735 and GSE71729). A protein–protein interaction (PPI) network was established to evaluate the relationship between the DEGs and to screen hub genes. The expression levels of the hub genes were further validated through the Gene Expression Profiling Interactive Analysis (GEPIA), ONCOMINE and Human Protein Atlas (HPA) databases, as well as the validation GEO dataset GSE62452. Additionally, the prognostic values of the hub genes were evaluated by Kaplan–Meier plotter and the validation GEO dataset GSE62452. Finally, the mechanistic roles of the most remarkable hub genes in PDAC were examined through in vitro experiments.ResultsWe identified the following nine hub genes by performing an integrated bioinformatics analysis: COL1A1, COL1A2, FN1, ITGA2, KRT19, LCN2, MMP9, MUC1 and VCAN. All of the hub genes were significantly upregulated in PDAC tissues compared with normal pancreatic tissues. Two hub genes (FN1 and ITGA2) were associated with poor overall survival (OS) rates in PDAC patients. Finally, in vitro experiments indicated that FN1 plays vital roles in PDAC cell proliferation, colony formation, apoptosis and the cell cycle.ConclusionsIn summary, we identified two hub genes that are associated with the expression and prognosis of PDAC. The oncogenic role of FN1 in PDAC was first illustrated by performing an integrated bioinformatic analysis and in vitro experiments. Our results provide a fundamental contribution for further research aimed finding novel therapeutic targets for overcoming PDAC.
creator: Xiaohua Lei
creator: Guodong Chen
creator: Jiangtao Li
creator: Wu Wen
creator: Jian Gong
creator: Jie Fu
uri: https://doi.org/10.7717/peerj.12141
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Lei et al.

title: An evaluation of factors affecting pain during transrectal ultrasonographic prostate biopsy: a real-life scenario in a retrospective cohort study
link: https://peerj.com/articles/12144
last-modified: 2021-09-06
description: BackgroundPeriprostatic infiltration anesthesia (PPIA) and intrarectal topical anesthesia (IRTA) are recommended methods to control pain in transrectal ultrasonographic prostate biopsy (TRUS-Bx). This study evaluates the factors affecting pain during TRUS-Bx, considering the pathologies involved in anorectal pain etiology and comparing the effectiveness of local anesthesia techniques in providing patient comfort.Material and MethodsWe retrospectively evaluated 477 consecutive patients with TRUS-Bx for elevated Prostate Specific Antigen (PSA), abnormal rectal examination findings, or both. Patients were grouped as local anesthesia methods for pain control during TRUS-Bx. Both groups were compared in terms of age, body mass index, clinical T stage, PSA, prostate volume, number of biopsy cores, type of anesthesia, previous biopsy history, and presence of prostate cancer. We used a visual analog pain scale (VAS) to evaluate the patient’s pain status; pre-procedure (VAS-0), during probe insertion (VAS-I), administration of anesthetic (VAS-A), and simultaneous with the biopsy procedure itself (VAS-Bx). For PPIA and IRTA, 4 ml lidocaine 20 mg/ml injection and 5 g 5% prilocaine-5% lidocaine cream was used, respectively.ResultsThe PPIA was used 74.2% (n = 354) and IRTA was used for 25.8% (n = 123) patients. VAS-0, VAS-I, and VAS-A scores are similar between groups. VAS-Bx was significantly higher in the IRTA than in the PPIA (3.37 ± 0.18 vs. 2.36 ± 0.12 p > 0.001). Clinical T stage (OR: 0.59), number of biopsy cores (OR: 1.80), and type of anesthesia application (OR: 2.65) were independent variables on TRUS-Bx for pain.ConclusionThree factors play roles as independent variables associated with the pain in TRUS-Bx; abnormal rectal examination findings, collection of more than twelve core samples during the biopsy, and the type of anesthesia used. Compared with PPIA, IRTA does not improve pain related to probe insertion, and using IRTA results in higher pain scores for biopsy-related pain. Thus, we recommend a PPIA to lower biopsy-related pain.
creator: Oğuz Özden Cebeci
creator: Alp Ozkan
uri: https://doi.org/10.7717/peerj.12144
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Cebeci and Ozkan