PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae
items: Evaluation of knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic
items: Altered gut microbiota associated with symptom severity in schizophrenia
items: Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing
items: Assessment of productivity, nutrient uptake and economic benefits of rice under different nitrogen management strategies
items: The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach
items: Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study
items: Spermatogenesis is normal in Tex33 knockout mice
items: Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels
items: Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation

Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae
type: item
type: AcademicArticle
description: The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts.
format: application/pdf
format: text/html
creator: Zachary J. Waldrip
creator: Piroon Jenjaroenpun
creator: Oktawia DeYoung
creator: Intawat Nookaew
creator: Sean D. Taverna
creator: Kevin D. Raney
creator: Alan J. Tackett
subject: Biotechnology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.9442
publisher: PeerJ Inc.
rights: © 2020 Waldrip et al.
abstract: The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts.
bibliographic citation: Waldrip et al. (2020) Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae. PeerJ 8:e9442 https://doi.org/10.7717/peerj.9442
date submitted: 2020-02-21
date accepted: 2020-06-08
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Waldrip
  given name: Zachary J.
author list: Agent
  family name: Jenjaroenpun
  given name: Piroon
author list: Agent
  family name: DeYoung
  given name: Oktawia
author list: Agent
  family name: Nookaew
  given name: Intawat
author list: Agent
  family name: Taverna
  given name: Sean D.
author list: Agent
  family name: Raney
  given name: Kevin D.
author list: Agent
  family name: Tackett
  given name: Alan J.
doi: 10.7717/peerj.9442
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: ©2020 Waldrip et al.
attribution name: Waldrip et al.

Evaluation of knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic
type: item
type: AcademicArticle
description: Background The novel coronavirus disease (COVID-19) is a new viral respiratory illness, first identified in Wuhan province, China. Dental professionals and dental students are at an increased risk for these viruses from dental patients, as dental practice involves face-to-face communication with the patients and frequent exposure to saliva, blood, and other body fluids. Dental education can play an important role in the training of dental students, adequate knowledge and adopting attitudes regarding infection control measures. The aim of this study was to evaluate knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic. Methods A total of 355 pre-clinical and clinical dental students (242 and 113, respectively, comprising 190 females and 165 males) at Fırat University Dentistry Faculty, in Elazığ, Turkey answered an online questionnaire about the biosafety procedures for and their attitudes to and knowledge of COVID-19. The study was conducted in March 2020, Turkey. The data gained were analyzed using descriptive statistical methods and chi-square test. Results Both the clinical and preclinical students were found to be afraid of infecting themselves and their environment with COVID-19, and the difference between them was statistically significant. Three quarters (74.9%) of the participants responded yes to the question of whether they thought that experiences related to COVID-19 affected them psychologically, with the differences between gender and clinical status were statistically significant. Responses to the question of which clinical rotation worried them more were 29.9% endodontics, 25.1% oral and maxillofacial surgery, 16.3% prosthesis, 15.2% periodontology, 6.8% restorative dentistry, 3.9% oral diagnosis and radiology, 1.7% pedodontics, and 1.1% orthodontics, with a significant difference between the preclinical and clinical students. Regarding the measures applied by the clinical students in their clinical rotation, the resp…
format: application/pdf
format: text/html
creator: Osman Ataş
creator: Tuba Talo Yildirim
subject: Dentistry
subject: Public Health
description: doi:10.7717/peerj.9575
publisher: PeerJ Inc.
rights: © 2020 Ataş and Talo Yildirim
abstract: Background The novel coronavirus disease (COVID-19) is a new viral respiratory illness, first identified in Wuhan province, China. Dental professionals and dental students are at an increased risk for these viruses from dental patients, as dental practice involves face-to-face communication with the patients and frequent exposure to saliva, blood, and other body fluids. Dental education can play an important role in the training of dental students, adequate knowledge and adopting attitudes regarding infection control measures. The aim of this study was to evaluate knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic. Methods A total of 355 pre-clinical and clinical dental students (242 and 113, respectively, comprising 190 females and 165 males) at Fırat University Dentistry Faculty, in Elazığ, Turkey answered an online questionnaire about the biosafety procedures for and their attitudes to and knowledge of COVID-19. The study was conducted in March 2020, Turkey. The data gained were analyzed using descriptive statistical methods and chi-square test. Results Both the clinical and preclinical students were found to be afraid of infecting themselves and their environment with COVID-19, and the difference between them was statistically significant. Three quarters (74.9%) of the participants responded yes to the question of whether they thought that experiences related to COVID-19 affected them psychologically, with the differences between gender and clinical status were statistically significant. Responses to the question of which clinical rotation worried them more were 29.9% endodontics, 25.1% oral and maxillofacial surgery, 16.3% prosthesis, 15.2% periodontology, 6.8% restorative dentistry, 3.9% oral diagnosis and radiology, 1.7% pedodontics, and 1.1% orthodontics, with a significant difference between the preclinical and clinical students. Regarding the measures applied by the clinical students in their clinical rotation, the resp…
bibliographic citation: Ataş et al. (2020) Evaluation of knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic. PeerJ 8:e9575 https://doi.org/10.7717/peerj.9575
date submitted: 2020-05-07
date accepted: 2020-06-29
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ataş
  given name: Osman
author list: Agent
  family name: Talo Yildirim
  given name: Tuba
doi: 10.7717/peerj.9575
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: ©2020 Ataş and Talo Yildirim
attribution name: Ataş and Talo Yildirim

Altered gut microbiota associated with symptom severity in schizophrenia
type: item
type: AcademicArticle
description: Background The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible biological basis of psychiatric disorders. With the advance of next-generation sequencing technology, characterization of the gut microbiota in schizophrenia (SZ) patients can provide rich clues for the diagnosis and prevention of SZ. Methods In this study, we compared the differences in the fecal microbiota between 82 SZ patients and 80 demographically matched normal controls (NCs) by 16S rRNA sequencing and analyzed the correlations between altered gut microbiota and symptom severity. Results The alpha diversity showed no significant differences between the NC and SZ groups, but the beta diversity revealed significant community-level separation in microbiome composition between the two groups (pseudo-F =3.337, p < 0.001, uncorrected). At the phylum level, relatively more Actinobacteria and less Firmicutes (p < 0.05, FDR corrected) were found in the SZ group. At the genus level, the relative abundances of Collinsella, Lactobacillus, Succinivibrio, Mogibacterium, Corynebacterium, undefined Ruminococcus and undefined Eubacterium were significantly increased, whereas the abundances of Adlercreutzia, Anaerostipes, Ruminococcus and Faecalibacterium were decreased in the SZ group compared to the NC group (p < 0.05, FDR corrected). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between the two groups, including the Polyketide sugar unit biosynthesis, Valine, Leucine and Isoleucine biosynthesis, Pantothenate and CoA biosynthesis, C5-Branched dibasic acid metabolism, Phenylpropanoid biosynthesis, Ascorbate and aldarate metabolism, Nucleotide metabolism and Propanoate metabolism pathways (p < 0.05, FDR corrected). Among the SZ group, the abundance of Succinivibrio was positively correlated with the total Positive and Negative Syndrome Scale (PANSS) scores (r …
format: application/pdf
format: text/html
creator: Shijia Li
creator: Min Zhuo
creator: Xia Huang
creator: Yuanyuan Huang
creator: Jing Zhou
creator: Dongsheng Xiong
creator: Jiahui Li
creator: Ya Liu
creator: Zhilin Pan
creator: Hehua Li
creator: Jun Chen
creator: Xiaobo Li
creator: Zhiming Xiang
creator: Fengchun Wu
creator: Kai Wu
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9574
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible biological basis of psychiatric disorders. With the advance of next-generation sequencing technology, characterization of the gut microbiota in schizophrenia (SZ) patients can provide rich clues for the diagnosis and prevention of SZ. Methods In this study, we compared the differences in the fecal microbiota between 82 SZ patients and 80 demographically matched normal controls (NCs) by 16S rRNA sequencing and analyzed the correlations between altered gut microbiota and symptom severity. Results The alpha diversity showed no significant differences between the NC and SZ groups, but the beta diversity revealed significant community-level separation in microbiome composition between the two groups (pseudo-F =3.337, p < 0.001, uncorrected). At the phylum level, relatively more Actinobacteria and less Firmicutes (p < 0.05, FDR corrected) were found in the SZ group. At the genus level, the relative abundances of Collinsella, Lactobacillus, Succinivibrio, Mogibacterium, Corynebacterium, undefined Ruminococcus and undefined Eubacterium were significantly increased, whereas the abundances of Adlercreutzia, Anaerostipes, Ruminococcus and Faecalibacterium were decreased in the SZ group compared to the NC group (p < 0.05, FDR corrected). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between the two groups, including the Polyketide sugar unit biosynthesis, Valine, Leucine and Isoleucine biosynthesis, Pantothenate and CoA biosynthesis, C5-Branched dibasic acid metabolism, Phenylpropanoid biosynthesis, Ascorbate and aldarate metabolism, Nucleotide metabolism and Propanoate metabolism pathways (p < 0.05, FDR corrected). Among the SZ group, the abundance of Succinivibrio was positively correlated with the total Positive and Negative Syndrome Scale (PANSS) scores (r …
bibliographic citation: Li et al. (2020) Altered gut microbiota associated with symptom severity in schizophrenia. PeerJ 8:e9574 https://doi.org/10.7717/peerj.9574
date submitted: 2020-03-10
date accepted: 2020-06-29
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Shijia
author list: Agent
  family name: Zhuo
  given name: Min
author list: Agent
  family name: Huang
  given name: Xia
author list: Agent
  family name: Huang
  given name: Yuanyuan
author list: Agent
  family name: Zhou
  given name: Jing
author list: Agent
  family name: Xiong
  given name: Dongsheng
author list: Agent
  family name: Li
  given name: Jiahui
author list: Agent
  family name: Liu
  given name: Ya
author list: Agent
  family name: Pan
  given name: Zhilin
author list: Agent
  family name: Li
  given name: Hehua
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Li
  given name: Xiaobo
author list: Agent
  family name: Xiang
  given name: Zhiming
author list: Agent
  family name: Wu
  given name: Fengchun
author list: Agent
  family name: Wu
  given name: Kai
doi: 10.7717/peerj.9574
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: © 2020 Li et al.
attribution name: Li et al.

Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing
type: item
type: AcademicArticle
description: Background Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees. Methods To identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database. Results We identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses—ACLSV, PBNSPaV, and PNRSV—in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea.
format: application/pdf
format: text/html
creator: Yeonhwa Jo
creator: Hoseong Choi
creator: Sen Lian
creator: Jin Kyong Cho
creator: Hyosub Chu
creator: Won Kyong Cho
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.9588
publisher: PeerJ Inc.
rights: © 2020 Jo et al.
abstract: Background Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees. Methods To identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database. Results We identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses—ACLSV, PBNSPaV, and PNRSV—in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea.
bibliographic citation: Jo et al. (2020) Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing. PeerJ 8:e9588 https://doi.org/10.7717/peerj.9588
date submitted: 2019-08-13
date accepted: 2020-07-01
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jo
  given name: Yeonhwa
author list: Agent
  family name: Choi
  given name: Hoseong
author list: Agent
  family name: Lian
  given name: Sen
author list: Agent
  family name: Cho
  given name: Jin Kyong
author list: Agent
  family name: Chu
  given name: Hyosub
author list: Agent
  family name: Cho
  given name: Won Kyong
doi: 10.7717/peerj.9588
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: © 2020 Jo et al.
attribution name: Jo et al.

Assessment of productivity, nutrient uptake and economic benefits of rice under different nitrogen management strategies
type: item
type: AcademicArticle
description: Background Integrating a chemical nitrogen (N) fertilizer with an organic fertilizer and using slow-release mechanism are important N management strategies to increase the N utilization efficiency (NUE) and grain yield of rice. However, the performances of both N management strategies on the productivity, the nutrient absorption and utilization efficiency, and the economic benefits of rice have not yet been comprehensively evaluated. Methods A 2-year field experiment was conducted with seven N management strategies without fertilizer (control), 100% conventional N fertilizer (conventional compound fertilizer and urea) (N100), 75% conventional N fertilizer with 25% organic–inorganic compound fertilizer (N75+OICF25), 50% conventional N fertilizer with 50% organic–inorganic compound fertilizer (N50+OICF50), 100% organic–inorganic compound fertilizer (OICF100), slow-release compound fertilizer with urea (SRCF+U), compound fertilizer with sulfur-coated urea (CF+SCU). The responses of the productivity, the nutrient absorption and utilization efficiency, and the economic benefits of rice to the different N management strategies were evaluated. Results CF+SCU performed comparably or better than N100, judging by the grain yield (GY), the N, phosphate (P) and potassium (K) agronomic efficiency (NAE, PAE and KAE), and the apparent N, P and K recovery efficiency (ANRE, APRE and AKRE). SRCF+U significantly increased the GY by an average of 7.7%, the NAE and the ANRE by 23.8 and 26.7%, the PAE and the APRE by 90.6 and 109.3%, and the KAE and the AKRE by 74.2 and 57.7%. The higher GY and nutrient utilization efficiency when using SRCF+U were attributed to the higher total biomass and total nutrient absorption. N75+OICF25 and N50+OICF50 produced a comparable grain yield than N100, whereas a significant yield reduction was observed when using OICF100. Compared with N100, N75+OICF25 resulted in a comparable or higher fertilizer use efficiency (0.3 and 4.7% for NAE and ANRE, 0.3 and 3…
format: application/pdf
format: text/html
creator: Guoying Yang
creator: Hongting Ji
creator: Hongjiang Liu
creator: Yuefang Zhang
creator: Liugen Chen
creator: Jianchu Zheng
creator: Zhi Guo
creator: Jing Sheng
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9596
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Integrating a chemical nitrogen (N) fertilizer with an organic fertilizer and using slow-release mechanism are important N management strategies to increase the N utilization efficiency (NUE) and grain yield of rice. However, the performances of both N management strategies on the productivity, the nutrient absorption and utilization efficiency, and the economic benefits of rice have not yet been comprehensively evaluated. Methods A 2-year field experiment was conducted with seven N management strategies without fertilizer (control), 100% conventional N fertilizer (conventional compound fertilizer and urea) (N100), 75% conventional N fertilizer with 25% organic–inorganic compound fertilizer (N75+OICF25), 50% conventional N fertilizer with 50% organic–inorganic compound fertilizer (N50+OICF50), 100% organic–inorganic compound fertilizer (OICF100), slow-release compound fertilizer with urea (SRCF+U), compound fertilizer with sulfur-coated urea (CF+SCU). The responses of the productivity, the nutrient absorption and utilization efficiency, and the economic benefits of rice to the different N management strategies were evaluated. Results CF+SCU performed comparably or better than N100, judging by the grain yield (GY), the N, phosphate (P) and potassium (K) agronomic efficiency (NAE, PAE and KAE), and the apparent N, P and K recovery efficiency (ANRE, APRE and AKRE). SRCF+U significantly increased the GY by an average of 7.7%, the NAE and the ANRE by 23.8 and 26.7%, the PAE and the APRE by 90.6 and 109.3%, and the KAE and the AKRE by 74.2 and 57.7%. The higher GY and nutrient utilization efficiency when using SRCF+U were attributed to the higher total biomass and total nutrient absorption. N75+OICF25 and N50+OICF50 produced a comparable grain yield than N100, whereas a significant yield reduction was observed when using OICF100. Compared with N100, N75+OICF25 resulted in a comparable or higher fertilizer use efficiency (0.3 and 4.7% for NAE and ANRE, 0.3 and 3…
bibliographic citation: Yang et al. (2020) Assessment of productivity, nutrient uptake and economic benefits of rice under different nitrogen management strategies. PeerJ 8:e9596 https://doi.org/10.7717/peerj.9596
date submitted: 2020-01-08
date accepted: 2020-07-01
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Guoying
author list: Agent
  family name: Ji
  given name: Hongting
author list: Agent
  family name: Liu
  given name: Hongjiang
author list: Agent
  family name: Zhang
  given name: Yuefang
author list: Agent
  family name: Chen
  given name: Liugen
author list: Agent
  family name: Zheng
  given name: Jianchu
author list: Agent
  family name: Guo
  given name: Zhi
author list: Agent
  family name: Sheng
  given name: Jing
doi: 10.7717/peerj.9596
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: © 2020 Yang et al.
attribution name: Yang et al.

The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach
type: item
type: AcademicArticle
description: Background The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities. Methods DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians). Results Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavi…
format: application/pdf
format: text/html
creator: Maria Buglione
creator: Simona Petrelli
creator: Claudia Troiano
creator: Tommaso Notomista
creator: Eleonora Rivieccio
creator: Domenico Fulgione
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9606
publisher: PeerJ Inc.
rights: © 2020 Buglione et al.
abstract: Background The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities. Methods DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians). Results Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavi…
bibliographic citation: Buglione et al. (2020) The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach. PeerJ 8:e9606 https://doi.org/10.7717/peerj.9606
date submitted: 2020-03-26
date accepted: 2020-07-05
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buglione
  given name: Maria
author list: Agent
  family name: Petrelli
  given name: Simona
author list: Agent
  family name: Troiano
  given name: Claudia
author list: Agent
  family name: Notomista
  given name: Tommaso
author list: Agent
  family name: Rivieccio
  given name: Eleonora
author list: Agent
  family name: Fulgione
  given name: Domenico
doi: 10.7717/peerj.9606
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: ©2020 Buglione et al.
attribution name: Buglione et al.

Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study
type: item
type: AcademicArticle
description: Background Metagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 days after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and sequential organ failure assessment score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was a protective factor. The detection of mNGS can significantly shorten the ICU stay of immunosuppressed patients (P < 0.01), shorten the ventilation time (P < 0.01), and reduce the ICU hospitalization cost (P < 0.05). Conclusions Metagenome next-generation sequencing is a val…
format: application/pdf
format: text/html
creator: Peng Zhang
creator: Yan Chen
creator: Shuyun Li
creator: Chaoliang Li
creator: Shuang Zhang
creator: Weihao Zheng
creator: Yantang Chen
creator: Jie Ma
creator: Xin Zhang
creator: Yanming Huang
creator: Shengming Liu
subject: Bioinformatics
subject: Molecular Biology
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Respiratory Medicine
description: doi:10.7717/peerj.9623
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Metagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 days after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and sequential organ failure assessment score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was a protective factor. The detection of mNGS can significantly shorten the ICU stay of immunosuppressed patients (P < 0.01), shorten the ventilation time (P < 0.01), and reduce the ICU hospitalization cost (P < 0.05). Conclusions Metagenome next-generation sequencing is a val…
bibliographic citation: Zhang et al. (2020) Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. PeerJ 8:e9623 https://doi.org/10.7717/peerj.9623
date submitted: 2020-03-11
date accepted: 2020-07-07
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Peng
author list: Agent
  family name: Chen
  given name: Yan
author list: Agent
  family name: Li
  given name: Shuyun
author list: Agent
  family name: Li
  given name: Chaoliang
author list: Agent
  family name: Zhang
  given name: Shuang
author list: Agent
  family name: Zheng
  given name: Weihao
author list: Agent
  family name: Chen
  given name: Yantang
author list: Agent
  family name: Ma
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Huang
  given name: Yanming
author list: Agent
  family name: Liu
  given name: Shengming
doi: 10.7717/peerj.9623
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: © 2020 Zhang et al.
attribution name: Zhang et al.

Spermatogenesis is normal in Tex33 knockout mice
type: item
type: AcademicArticle
description: Testis expressed gene 33 (Tex33) is a recently reported testis-specific gene and it is evolutionarily conserved in vertebrates. The Tex33 expression is found in cytoplasm of round spermatids in Mus musculus. However, the in vivo function of Tex33 remains unknown. In this study, we made a 62bp in frame deletion on Exon2 of Tex33 gene by CRISPR/Cas9 in C57B/L6 mouse, which cause frame shift mutation of Tex33 gene. Tex33-/-adult male were fertile, and there is no significant change on litter size compared with male wildtype (Tex33+/+) adult. Besides, no overt differences were found in testis/body weight ratios, testicular/epididymal tissue morphology, sperm counts, sperm morphology and spermatozoa motility in adult Tex33-/-male mice (N = 3), in comparison with Tex33+/+ adult (N = 3). TUNEL assay also indicates the germ cells apoptosis ratio was not significantly changed in adult Tex33-/- adult male mouse testis (N = 3), compared with adult Tex33+/+ male (N = 3). Importantly, the first wave of elongating spermatids formation happens in 5w old mice. We find that the first wave of spermiogenesis is not disrupted in both 5-week-old Tex33+/+ and Tex33-/-male mouse testes and three hallmarks of spermatogenesis, PLZF,γ-H2AX and TNP1, are all detectable in seminiferous tubule. All results indicate that Tex33 is a redundant gene to spermatogenesis. This study can help other researchers avoid repetitive works on redundant genes.
format: application/pdf
format: text/html
creator: Zhendong Zhu
creator: Xin Zhang
creator: Wentao Zeng
creator: Shuqin Zhao
creator: Jianli Zhou
creator: Zuomin Zhou
creator: Mingxi Liu
subject: Biophysics
subject: Cell Biology
subject: Andrology
description: doi:10.7717/peerj.9629
publisher: PeerJ Inc.
rights: © 2020 Zhu et al.
abstract: Testis expressed gene 33 (Tex33) is a recently reported testis-specific gene and it is evolutionarily conserved in vertebrates. The Tex33 expression is found in cytoplasm of round spermatids in Mus musculus. However, the in vivo function of Tex33 remains unknown. In this study, we made a 62bp in frame deletion on Exon2 of Tex33 gene by CRISPR/Cas9 in C57B/L6 mouse, which cause frame shift mutation of Tex33 gene. Tex33-/-adult male were fertile, and there is no significant change on litter size compared with male wildtype (Tex33+/+) adult. Besides, no overt differences were found in testis/body weight ratios, testicular/epididymal tissue morphology, sperm counts, sperm morphology and spermatozoa motility in adult Tex33-/-male mice (N = 3), in comparison with Tex33+/+ adult (N = 3). TUNEL assay also indicates the germ cells apoptosis ratio was not significantly changed in adult Tex33-/- adult male mouse testis (N = 3), compared with adult Tex33+/+ male (N = 3). Importantly, the first wave of elongating spermatids formation happens in 5w old mice. We find that the first wave of spermiogenesis is not disrupted in both 5-week-old Tex33+/+ and Tex33-/-male mouse testes and three hallmarks of spermatogenesis, PLZF,γ-H2AX and TNP1, are all detectable in seminiferous tubule. All results indicate that Tex33 is a redundant gene to spermatogenesis. This study can help other researchers avoid repetitive works on redundant genes.
bibliographic citation: Zhu et al. (2020) Spermatogenesis is normal in Tex33 knockout mice. PeerJ 8:e9629 https://doi.org/10.7717/peerj.9629
date submitted: 2019-11-12
date accepted: 2020-07-08
issued: 2020-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Zhendong
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Zeng
  given name: Wentao
author list: Agent
  family name: Zhao
  given name: Shuqin
author list: Agent
  family name: Zhou
  given name: Jianli
author list: Agent
  family name: Zhou
  given name: Zuomin
author list: Agent
  family name: Liu
  given name: Mingxi
doi: 10.7717/peerj.9629
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-29
copyright: ©2020 Zhu et al.
attribution name: Zhu et al.

Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels
type: item
type: AcademicArticle
description: Previous studies indicate that obesity is an important contributor to the proceeding of thyroid cancer (TC) with limited knowledge of the underlying mechanism. Here, we hypothesize that molecules affected by obesity may play roles in the development of TC. To test the hypothesis above, we first conducted a large-scale literature-based data mining to identify genes influenced by obesity and genes related to TC. Then, a mega-analysis was conducted to study the expression changes of the obesity-specific genes in the case of TC, using 16 independent TC array-expression datasets (783 TC cases and 439 healthy controls). After that, pathway analysis was performed to explore the functional profile of the selected target genes and their potential connections with TC. We identified 1,036 genes associated with TC and 534 regulated by obesity, demonstrating a significant overlap (N = 176, p-value = 4.07e−112). Five out of the 358 obesity-specific genes, FABP4, CFD, GHR, TNFRSF11B, and LTF, presented significantly decreased expression in TC patients (LFC<−1.44; and p-value < 1e−7). Multiple literature-based pathways were identified where obesity could promote the pathologic development of TC through the regulation of these five genes and INS levels. The five obesity genes uncovered could be novel genes that play roles in the etiology of TC through the modulation of INS levels.
format: application/pdf
format: text/html
creator: Jiaming Chen
creator: Hongbao Cao
creator: Meng Lian
creator: Jugao Fang
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.9302
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Previous studies indicate that obesity is an important contributor to the proceeding of thyroid cancer (TC) with limited knowledge of the underlying mechanism. Here, we hypothesize that molecules affected by obesity may play roles in the development of TC. To test the hypothesis above, we first conducted a large-scale literature-based data mining to identify genes influenced by obesity and genes related to TC. Then, a mega-analysis was conducted to study the expression changes of the obesity-specific genes in the case of TC, using 16 independent TC array-expression datasets (783 TC cases and 439 healthy controls). After that, pathway analysis was performed to explore the functional profile of the selected target genes and their potential connections with TC. We identified 1,036 genes associated with TC and 534 regulated by obesity, demonstrating a significant overlap (N = 176, p-value = 4.07e−112). Five out of the 358 obesity-specific genes, FABP4, CFD, GHR, TNFRSF11B, and LTF, presented significantly decreased expression in TC patients (LFC<−1.44; and p-value < 1e−7). Multiple literature-based pathways were identified where obesity could promote the pathologic development of TC through the regulation of these five genes and INS levels. The five obesity genes uncovered could be novel genes that play roles in the etiology of TC through the modulation of INS levels.
bibliographic citation: Chen et al. (2020) Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels. PeerJ 8:e9302 https://doi.org/10.7717/peerj.9302
date submitted: 2020-02-11
date accepted: 2020-05-15
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jiaming
author list: Agent
  family name: Cao
  given name: Hongbao
author list: Agent
  family name: Lian
  given name: Meng
author list: Agent
  family name: Fang
  given name: Jugao
doi: 10.7717/peerj.9302
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation
type: item
type: AcademicArticle
description: Background The awareness of environmental and socio-economic impacts caused by greenhouse gas emissions from the livestock sector leverages the adoption of strategies to counteract it. Feed supplements can play an important role in the reduction of the main greenhouse gas produced by ruminants—methane (CH4). In this context, this study aims to assess the effect of two biochar sources and inclusion levels on rumen fermentation parameters in vitro. Methods Two sources of biochar (agro-forestry residues, AFB, and potato peel, PPB) were added at two levels (5 and 10%, dry matter (DM) basis) to two basal substrates (haylage and corn silage) and incubated 24-h with rumen inocula to assess the effects on CH4 production and main rumen fermentation parameters in vitro. Results AFB and PPB were obtained at different carbonization conditions resulting in different apparent surface areas, ash content, pH at the point of zero charge (pHpzc), and elemental analysis. Relative to control (0% biochar), biochar supplementation kept unaffected total gas production and yield (mL and mL/g DM, p = 0.140 and p = 0.240, respectively) and fermentation pH (p = 0.666), increased CH4production and yield (mL and mL/g DM, respectively, p = 0.001) and ammonia-N (NH3-N, p = 0.040), and decreased total volatile fatty acids (VFA) production (p < 0.001) and H2 generated and consumed (p ≤ 0.001). Biochar sources and inclusion levels had no negative effect on most of the fermentation parameters and efficiency. Acetic:propionic acid ratio (p = 0.048) and H2 consumed (p = 0.019) were lower with AFB inclusion when compared to PPB. Biochar inclusion at 10% reduced H2 consumed (p < 0.001) and tended to reduce total gas production (p = 0.055). Total VFA production (p = 0.019), acetic acid proportion (p = 0.011) and H2 generated (p = 0.048) were the lowest with AFB supplemented at 10%, no differences being observed among the other treatments. The basal substrate affected most fermentation parameters independe…
format: application/pdf
format: text/html
creator: Ana R.F. Rodrigues
creator: Margarida R.G. Maia
creator: Ana R.J. Cabrita
creator: Hugo M. Oliveira
creator: Maria Bernardo
creator: Nuno Lapa
creator: Isabel Fonseca
creator: Henrique Trindade
creator: José L. Pereira
creator: António J.M. Fonseca
subject: Agricultural Science
subject: Bioengineering
subject: Veterinary Medicine
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.9488
publisher: PeerJ Inc.
rights: © 2020 Rodrigues et al.
abstract: Background The awareness of environmental and socio-economic impacts caused by greenhouse gas emissions from the livestock sector leverages the adoption of strategies to counteract it. Feed supplements can play an important role in the reduction of the main greenhouse gas produced by ruminants—methane (CH4). In this context, this study aims to assess the effect of two biochar sources and inclusion levels on rumen fermentation parameters in vitro. Methods Two sources of biochar (agro-forestry residues, AFB, and potato peel, PPB) were added at two levels (5 and 10%, dry matter (DM) basis) to two basal substrates (haylage and corn silage) and incubated 24-h with rumen inocula to assess the effects on CH4 production and main rumen fermentation parameters in vitro. Results AFB and PPB were obtained at different carbonization conditions resulting in different apparent surface areas, ash content, pH at the point of zero charge (pHpzc), and elemental analysis. Relative to control (0% biochar), biochar supplementation kept unaffected total gas production and yield (mL and mL/g DM, p = 0.140 and p = 0.240, respectively) and fermentation pH (p = 0.666), increased CH4production and yield (mL and mL/g DM, respectively, p = 0.001) and ammonia-N (NH3-N, p = 0.040), and decreased total volatile fatty acids (VFA) production (p < 0.001) and H2 generated and consumed (p ≤ 0.001). Biochar sources and inclusion levels had no negative effect on most of the fermentation parameters and efficiency. Acetic:propionic acid ratio (p = 0.048) and H2 consumed (p = 0.019) were lower with AFB inclusion when compared to PPB. Biochar inclusion at 10% reduced H2 consumed (p < 0.001) and tended to reduce total gas production (p = 0.055). Total VFA production (p = 0.019), acetic acid proportion (p = 0.011) and H2 generated (p = 0.048) were the lowest with AFB supplemented at 10%, no differences being observed among the other treatments. The basal substrate affected most fermentation parameters independe…
bibliographic citation: Rodrigues et al. (2020) Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation. PeerJ 8:e9488 https://doi.org/10.7717/peerj.9488
date submitted: 2020-01-13
date accepted: 2020-06-15
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodrigues
  given name: Ana R.F.
author list: Agent
  family name: Maia
  given name: Margarida R.G.
author list: Agent
  family name: Cabrita
  given name: Ana R.J.
author list: Agent
  family name: Oliveira
  given name: Hugo M.
author list: Agent
  family name: Bernardo
  given name: Maria
author list: Agent
  family name: Lapa
  given name: Nuno
author list: Agent
  family name: Fonseca
  given name: Isabel
author list: Agent
  family name: Trindade
  given name: Henrique
author list: Agent
  family name: Pereira
  given name: José L.
author list: Agent
  family name: Fonseca
  given name: António J.M.
doi: 10.7717/peerj.9488
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Rodrigues et al.
attribution name: Rodrigues et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359