PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Social cognition and social functioning in people with borderline personality disorder and their first-degree relatives
items: Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis
items: Construction of fibronectin conditional gene knock-out mice and the effect of fibronectin gene knockout on hematopoietic, biochemical and immune parameters in mice
items: Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility
items: On local scouring downstream small water structures
items: A review of Euryoryzomys legatus (Rodentia, Sigmodontinae): morphological redescription, cytogenetics, and molecular phylogeny
items: A 14 immune-related gene signature predicts clinical outcomes of kidney renal clear cell carcinoma
items: Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing
items: Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic
items: The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota

Social cognition and social functioning in people with borderline personality disorder and their first-degree relatives
type: item
type: AcademicArticle
description: Background A few papers studying healthy, first-degree relatives of people with borderline personality disorder (BPD) have found that this group presents attention and memory problems. However, current research has not analyzed their social cognition. Materials and Methods We designed an age-, gender- and education-level matched case-control study involving 57 people with BPD, 32 of their first-degree relatives, and 57 healthy controls in Spain in 2018–2019. All were assessed for social cognition and functioning using the Movie for Assessment of Social Cognition and the Social Functioning Scale; other potential confounders were also collected (marital status, occupation and household variables). Results There were differences in the social cognition domain of overmentalizing errors, with the BPD group scoring significantly higher than controls; however, there was no significant difference with relatives; in the social functioning domain of family relationships, with the controls showing the highest scores. Social engagement/withdrawal, interpersonal behavior, independence-competence, prosocial activities, full scale and categorization domains showed the same pattern: the BPD group had lower scores than their relatives and the controls. Relatives were significantly different from BPD patients in family relationships, social engagement/withdrawal and interpersonal behavior, as well as on the full Social Functioning Scale (both as a linear and categorical variable). However, only controls showed differences with relatives in family relationships. Conclusions All in all, relatives show similar levels of social cognition and functioning compared with controls, and people with BPD show some alterations in different domains of both social cognition and functioning.
format: application/pdf
format: text/html
creator: Esther Ortega-Díaz
creator: Jonatan García-Campos
creator: José María Rico-Gomis
creator: Carlos Cuesta-Moreno
creator: Antonio Palazón-Bru
creator: Gabriel Estañ-Cerezo
creator: José Antonio Piqueras-Rodríguez
creator: Jesús Rodríguez-Marín
subject: Cognitive Disorders
subject: Epidemiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10212
publisher: PeerJ Inc.
rights: © 2020 Ortega-Díaz et al.
abstract: Background A few papers studying healthy, first-degree relatives of people with borderline personality disorder (BPD) have found that this group presents attention and memory problems. However, current research has not analyzed their social cognition. Materials and Methods We designed an age-, gender- and education-level matched case-control study involving 57 people with BPD, 32 of their first-degree relatives, and 57 healthy controls in Spain in 2018–2019. All were assessed for social cognition and functioning using the Movie for Assessment of Social Cognition and the Social Functioning Scale; other potential confounders were also collected (marital status, occupation and household variables). Results There were differences in the social cognition domain of overmentalizing errors, with the BPD group scoring significantly higher than controls; however, there was no significant difference with relatives; in the social functioning domain of family relationships, with the controls showing the highest scores. Social engagement/withdrawal, interpersonal behavior, independence-competence, prosocial activities, full scale and categorization domains showed the same pattern: the BPD group had lower scores than their relatives and the controls. Relatives were significantly different from BPD patients in family relationships, social engagement/withdrawal and interpersonal behavior, as well as on the full Social Functioning Scale (both as a linear and categorical variable). However, only controls showed differences with relatives in family relationships. Conclusions All in all, relatives show similar levels of social cognition and functioning compared with controls, and people with BPD show some alterations in different domains of both social cognition and functioning.
bibliographic citation: Ortega-Díaz et al. (2020) Social cognition and social functioning in people with borderline personality disorder and their first-degree relatives. PeerJ 8:e10212 https://doi.org/10.7717/peerj.10212
date submitted: 2020-05-20
date accepted: 2020-09-28
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ortega-Díaz
  given name: Esther
author list: Agent
  family name: García-Campos
  given name: Jonatan
author list: Agent
  family name: Rico-Gomis
  given name: José María
author list: Agent
  family name: Cuesta-Moreno
  given name: Carlos
author list: Agent
  family name: Palazón-Bru
  given name: Antonio
author list: Agent
  family name: Estañ-Cerezo
  given name: Gabriel
author list: Agent
  family name: Piqueras-Rodríguez
  given name: José Antonio
author list: Agent
  family name: Rodríguez-Marín
  given name: Jesús
doi: 10.7717/peerj.10212
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: © 2020 Ortega-Díaz et al.
attribution name: Ortega-Díaz et al.

Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis
type: item
type: AcademicArticle
description: The identification of differing physical characteristics of dogs is an uncomplicated and straightforward way to categorize dog breeds. However, many dog owners and veterinarians still struggle to distinguish between pure breed and mixed variations in certain breeds of dogs. Presently, the absence of the tools and methods needed to confirm a pure breed dog is a significant problem since the only method available to validate pure or mongrel breeds is the official pedigree system. Inter-simple sequence repeat markers have been successfully used to assess genetic variations and differentiations. Notably, inter-simple sequence repeat markers coupled with high resolution melting analysis were effectively used for the breed identification of 43 breeds of dogs (total 463 dogs). The 10 primers chosen for analysis resulted in a range of 31–78.6% of breed discrimination when using one primer, while a combination of two primers was able to successfully discriminate between all of the 43 dog breeds (100%). Shannon’s index information (I = 2.586 ± 0.034) and expected heterozygosity (He = 0.908 ± 0.003) indicated a high level of genetic diversity among breeds. The fixation index (Fst) revealed a value of 10.4%, demonstrating that there was a high level of genetic subdivision between populations. This study showed that inter-simple sequence repeat marker analysis was effective in demonstrating high genetic diversity among varying breeds of dogs, while a combination of Inter-simple sequence repeat marker analysis and high resolution melting analysis could provide an optional technique for researchers to effectively identify breeds through genetic variations.
format: application/pdf
format: text/html
creator: Wannapimol Kriangwanich
creator: Korakot Nganvongpanit
creator: Kittisak Buddhachat
creator: Puntita Siengdee
creator: Siriwadee Chomdej
creator: Siriluck Ponsuksili
creator: Chatchote Thitaram
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10215
publisher: PeerJ Inc.
rights: © 2020 Kriangwanich et al.
abstract: The identification of differing physical characteristics of dogs is an uncomplicated and straightforward way to categorize dog breeds. However, many dog owners and veterinarians still struggle to distinguish between pure breed and mixed variations in certain breeds of dogs. Presently, the absence of the tools and methods needed to confirm a pure breed dog is a significant problem since the only method available to validate pure or mongrel breeds is the official pedigree system. Inter-simple sequence repeat markers have been successfully used to assess genetic variations and differentiations. Notably, inter-simple sequence repeat markers coupled with high resolution melting analysis were effectively used for the breed identification of 43 breeds of dogs (total 463 dogs). The 10 primers chosen for analysis resulted in a range of 31–78.6% of breed discrimination when using one primer, while a combination of two primers was able to successfully discriminate between all of the 43 dog breeds (100%). Shannon’s index information (I = 2.586 ± 0.034) and expected heterozygosity (He = 0.908 ± 0.003) indicated a high level of genetic diversity among breeds. The fixation index (Fst) revealed a value of 10.4%, demonstrating that there was a high level of genetic subdivision between populations. This study showed that inter-simple sequence repeat marker analysis was effective in demonstrating high genetic diversity among varying breeds of dogs, while a combination of Inter-simple sequence repeat marker analysis and high resolution melting analysis could provide an optional technique for researchers to effectively identify breeds through genetic variations.
bibliographic citation: Kriangwanich et al. (2020) Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis. PeerJ 8:e10215 https://doi.org/10.7717/peerj.10215
date submitted: 2020-06-11
date accepted: 2020-09-28
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kriangwanich
  given name: Wannapimol
author list: Agent
  family name: Nganvongpanit
  given name: Korakot
author list: Agent
  family name: Buddhachat
  given name: Kittisak
author list: Agent
  family name: Siengdee
  given name: Puntita
author list: Agent
  family name: Chomdej
  given name: Siriwadee
author list: Agent
  family name: Ponsuksili
  given name: Siriluck
author list: Agent
  family name: Thitaram
  given name: Chatchote
doi: 10.7717/peerj.10215
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: ©2020 Kriangwanich et al.
attribution name: Kriangwanich et al.

Construction of fibronectin conditional gene knock-out mice and the effect of fibronectin gene knockout on hematopoietic, biochemical and immune parameters in mice
type: item
type: AcademicArticle
description: Fibronectin (FN) is a multi-functional glycoprotein that primarily acts as a cell adhesion molecule and tethers cells to the extra cellular matrix. In order to clarify the effect of FN deficiency on hematopoiesis, biochemical and immune parameters in mice. We constructed a tamoxifen-induced conditional (cre-loxp system) fibronectin knock-out (FnKO) mouse model on a C57BL/6 background, and monitored their behavior, fertility, histological, hematopoietic, biochemical and immunological indices. We found that the Fn KO mice had reduced fertility, high platelet counts, smaller bone marrow megakaryocytes and looser attachment between the hepatocyte and vascular endothelial junctions compared to the wild type (WT) mice. In contrast, the behavior, hematological counts, serum biochemical indices and vital organ histology were similar in both Fn KO and WT mice. This model will greatly help in elucidating the role of FN in immune-related diseases in future.
format: application/pdf
format: text/html
creator: Xiaohong Yuan
creator: Shu Yang
creator: Wen Li
creator: Jinggang Li
creator: Jia Lin
creator: Yong Wu
creator: Yuanzhong Chen
subject: Biochemistry
subject: Genetics
subject: Zoology
subject: Hematology
subject: Immunology
description: doi:10.7717/peerj.10224
publisher: PeerJ Inc.
rights: © 2020 Yuan et al.
abstract: Fibronectin (FN) is a multi-functional glycoprotein that primarily acts as a cell adhesion molecule and tethers cells to the extra cellular matrix. In order to clarify the effect of FN deficiency on hematopoiesis, biochemical and immune parameters in mice. We constructed a tamoxifen-induced conditional (cre-loxp system) fibronectin knock-out (FnKO) mouse model on a C57BL/6 background, and monitored their behavior, fertility, histological, hematopoietic, biochemical and immunological indices. We found that the Fn KO mice had reduced fertility, high platelet counts, smaller bone marrow megakaryocytes and looser attachment between the hepatocyte and vascular endothelial junctions compared to the wild type (WT) mice. In contrast, the behavior, hematological counts, serum biochemical indices and vital organ histology were similar in both Fn KO and WT mice. This model will greatly help in elucidating the role of FN in immune-related diseases in future.
bibliographic citation: Yuan et al. (2020) Construction of fibronectin conditional gene knock-out mice and the effect of fibronectin gene knockout on hematopoietic, biochemical and immune parameters in mice. PeerJ 8:e10224 https://doi.org/10.7717/peerj.10224
date submitted: 2020-07-06
date accepted: 2020-09-29
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Xiaohong
author list: Agent
  family name: Yang
  given name: Shu
author list: Agent
  family name: Li
  given name: Wen
author list: Agent
  family name: Li
  given name: Jinggang
author list: Agent
  family name: Lin
  given name: Jia
author list: Agent
  family name: Wu
  given name: Yong
author list: Agent
  family name: Chen
  given name: Yuanzhong
doi: 10.7717/peerj.10224
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: ©2020 Yuan et al.
attribution name: Yuan et al.

Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility
type: item
type: AcademicArticle
description: A dwarf, multi-pistil and male sterile dms mutant was previously reported by us. However, the genetic changes in this dms are unclear. To examine the genetic changes, single nucleotide polymorphism (SNP) association, chromosome counting, and high-resolution chromosome fluorescence in situ hybridization (FISH) techniques were employed. By comparing tall plants (T) with dwarf plants (D) in the offspring of dms mutant plants, SNP association analysis indicated that most SNPs were on chromosome 2A. There were three types in offspring of dms plants, with 42, 41 and 40 chromosomes respectively. High-resolution chromosome painting analysis demonstrated that T plants had all 42 wheat chromosomes; the medium plants (M) had 41 chromosomes, lacking one chromosome 2A; while D plants had 40 wheat chromosomes, and lacked both 2A chromosomes. These data demonstrated that dms resulted from a loss of chromosome 2A. We identified 23 genes on chromosome 2A which might be involved in the development of stamens or pollen grains. These results lay a solid foundation for further analysis of the molecular mechanisms of wheat male sterility. Because D plants can be used as a female parent to cross with other wheat genotypes, dms is a unique germplasm for any functional study of chromosome 2A and wheat breeding specifically targeting genes on 2A.
format: application/pdf
format: text/html
creator: Zhixin Jiao
creator: Xinxin Zhu
creator: Huijuan Li
creator: Zhitao Liu
creator: Xinyi Huang
creator: Nan Wu
creator: Junhang An
creator: Junchang Li
creator: Jing Zhang
creator: Yumei Jiang
creator: Qiaoyun Li
creator: Zengjun Qi
creator: Jishan Niu
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10275
publisher: PeerJ Inc.
rights: © 2020 Jiao et al.
abstract: A dwarf, multi-pistil and male sterile dms mutant was previously reported by us. However, the genetic changes in this dms are unclear. To examine the genetic changes, single nucleotide polymorphism (SNP) association, chromosome counting, and high-resolution chromosome fluorescence in situ hybridization (FISH) techniques were employed. By comparing tall plants (T) with dwarf plants (D) in the offspring of dms mutant plants, SNP association analysis indicated that most SNPs were on chromosome 2A. There were three types in offspring of dms plants, with 42, 41 and 40 chromosomes respectively. High-resolution chromosome painting analysis demonstrated that T plants had all 42 wheat chromosomes; the medium plants (M) had 41 chromosomes, lacking one chromosome 2A; while D plants had 40 wheat chromosomes, and lacked both 2A chromosomes. These data demonstrated that dms resulted from a loss of chromosome 2A. We identified 23 genes on chromosome 2A which might be involved in the development of stamens or pollen grains. These results lay a solid foundation for further analysis of the molecular mechanisms of wheat male sterility. Because D plants can be used as a female parent to cross with other wheat genotypes, dms is a unique germplasm for any functional study of chromosome 2A and wheat breeding specifically targeting genes on 2A.
bibliographic citation: Jiao et al. (2020) Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility. PeerJ 8:e10275 https://doi.org/10.7717/peerj.10275
date submitted: 2020-06-19
date accepted: 2020-10-08
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Zhixin
author list: Agent
  family name: Zhu
  given name: Xinxin
author list: Agent
  family name: Li
  given name: Huijuan
author list: Agent
  family name: Liu
  given name: Zhitao
author list: Agent
  family name: Huang
  given name: Xinyi
author list: Agent
  family name: Wu
  given name: Nan
author list: Agent
  family name: An
  given name: Junhang
author list: Agent
  family name: Li
  given name: Junchang
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Jiang
  given name: Yumei
author list: Agent
  family name: Li
  given name: Qiaoyun
author list: Agent
  family name: Qi
  given name: Zengjun
author list: Agent
  family name: Niu
  given name: Jishan
doi: 10.7717/peerj.10275
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: ©2020 Jiao et al.
attribution name: Jiao et al.

On local scouring downstream small water structures
type: item
type: AcademicArticle
description: Background In order to regulate water flow, hydraulic structures such as weirs or checks, frequently equipped with gates, are used. Water can flow below or over the gate or, simultaneously, over and below the gate. Both diversifications of hydraulic gradient, being an effect of damming up a river by the structure and shear stresses at the bed, which exceeds the critical shear stress value, invoke the local scouring downstream the structure. This phenomenon has been studied in laboratory and field conditions for many years, however Researchers do not agree on the parameters that affect the size of the local scour and the intensity of its formation. There are no universal methods for estimating its magnitude However, solutions are sought in the form of calculation formulas typical for the method of flow through the structure, taking into account the parameters that characterize a given structure. These formulas are based on factors that affect the size of the local scours, that is, their dimensions and location. Examples of such formulas are those contained in this article: Franke (1960), Straube (1963), Tarajmovič (1966), Rossinski & Kuzmin (1969) equations. The need to study this phenomenon results from the prevalence of hydrotechnical structures equipped with gates (from small gated checks to large weirs) and from potential damage that may be associated with excessive development of local erosion downstream, including washing of foundations and, consequently, loss of stability of the structure. Methods This study verifies empirical formulas applied to estimate the geometry parameters of a scour hole on a laboratory model of a structure where water is conducted downstream the gate with bottom reinforcements of various roughness. A specially designed remote-controlled measuring device, equipped with laser scanner, was applied to determine the shape of the sandy bottom. Then the formula optimization is conducted, using Monte Carlo sampling method, followed by verifica…
format: application/pdf
format: text/html
creator: Marta Kiraga
creator: Zbigniew Popek
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.10282
publisher: PeerJ Inc.
rights: © 2020 Kiraga and Popek
abstract: Background In order to regulate water flow, hydraulic structures such as weirs or checks, frequently equipped with gates, are used. Water can flow below or over the gate or, simultaneously, over and below the gate. Both diversifications of hydraulic gradient, being an effect of damming up a river by the structure and shear stresses at the bed, which exceeds the critical shear stress value, invoke the local scouring downstream the structure. This phenomenon has been studied in laboratory and field conditions for many years, however Researchers do not agree on the parameters that affect the size of the local scour and the intensity of its formation. There are no universal methods for estimating its magnitude However, solutions are sought in the form of calculation formulas typical for the method of flow through the structure, taking into account the parameters that characterize a given structure. These formulas are based on factors that affect the size of the local scours, that is, their dimensions and location. Examples of such formulas are those contained in this article: Franke (1960), Straube (1963), Tarajmovič (1966), Rossinski & Kuzmin (1969) equations. The need to study this phenomenon results from the prevalence of hydrotechnical structures equipped with gates (from small gated checks to large weirs) and from potential damage that may be associated with excessive development of local erosion downstream, including washing of foundations and, consequently, loss of stability of the structure. Methods This study verifies empirical formulas applied to estimate the geometry parameters of a scour hole on a laboratory model of a structure where water is conducted downstream the gate with bottom reinforcements of various roughness. A specially designed remote-controlled measuring device, equipped with laser scanner, was applied to determine the shape of the sandy bottom. Then the formula optimization is conducted, using Monte Carlo sampling method, followed by verifica…
bibliographic citation: Kiraga et al. (2020) On local scouring downstream small water structures. PeerJ 8:e10282 https://doi.org/10.7717/peerj.10282
date submitted: 2020-03-12
date accepted: 2020-10-09
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kiraga
  given name: Marta
author list: Agent
  family name: Popek
  given name: Zbigniew
doi: 10.7717/peerj.10282
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: ©2020 Kiraga and Popek
attribution name: Kiraga and Popek

A review of Euryoryzomys legatus (Rodentia, Sigmodontinae): morphological redescription, cytogenetics, and molecular phylogeny
type: item
type: AcademicArticle
description: The taxonomic history of Euryoryzomys legatus has been complex and controversial, being either included in the synonymy of other oryzomyine species or considered as a valid species, as in the most recent review of the genus. Previous phylogenetic analyses segregated E. legatus from E. russatus, its putative senior synonym, but recovered it nested within E. nitidus. A general lack of authoritative evaluation of morphological attributes, details of the chromosome complement, or other data types has hampered the ability to choose among alternative taxonomic hypotheses, and thus reach a general consensus for the status of the taxon. Herein we revisit the status of E. legatus using an integrated approach that includes: (1) a morphological review, especially centered on specimens from northwestern Argentina not examined previously, (2) comparative cytogenetics, and (3) phylogenetic reconstruction, using mitochondrial genes. Euryoryzomys legatus is morphologically and phylogenetically distinct from all other species-level taxa in the genus, but its 2n=80, FN=86 karyotype is shared with E. emmonsae, E. nitidus, and E. russatus. Several morphological and morphometric characters distinguish E. legatus from other species of Euryoryzomys, and we provide an amended diagnosis for the species. Morphological characters useful in distinguishing E. legatus from E. nitidus, its sister taxon following molecular analyses, include: larger overall size, dorsal fur with a strong yellowish brown to orange brown tinge, flanks and cheeks with an orange lateral line, ventral color grayish-white with pure white hairs present only on the chin, presence of a thin blackish eye-ring, tail bicolored, presence of an alisphenoid strut and a well-developed temporal and lambdoid crests in the skull, and a labial cingulum on M3. Molecular phylogenetic analyses recovered E. legatus as a monophyletic group with high support nested within a paraphyletic E. nitidus; genetic distances segregated members of bo…
format: application/pdf
format: text/html
creator: Mariana D. Guilardi
creator: Pablo Jayat
creator: Marcelo Weksler
creator: James L. Patton
creator: Pablo Edmundo Ortiz
creator: Keila Almeida
creator: Maria José de J. Silva
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9884
publisher: PeerJ Inc.
rights: © 2020 Guilardi et al.
abstract: The taxonomic history of Euryoryzomys legatus has been complex and controversial, being either included in the synonymy of other oryzomyine species or considered as a valid species, as in the most recent review of the genus. Previous phylogenetic analyses segregated E. legatus from E. russatus, its putative senior synonym, but recovered it nested within E. nitidus. A general lack of authoritative evaluation of morphological attributes, details of the chromosome complement, or other data types has hampered the ability to choose among alternative taxonomic hypotheses, and thus reach a general consensus for the status of the taxon. Herein we revisit the status of E. legatus using an integrated approach that includes: (1) a morphological review, especially centered on specimens from northwestern Argentina not examined previously, (2) comparative cytogenetics, and (3) phylogenetic reconstruction, using mitochondrial genes. Euryoryzomys legatus is morphologically and phylogenetically distinct from all other species-level taxa in the genus, but its 2n=80, FN=86 karyotype is shared with E. emmonsae, E. nitidus, and E. russatus. Several morphological and morphometric characters distinguish E. legatus from other species of Euryoryzomys, and we provide an amended diagnosis for the species. Morphological characters useful in distinguishing E. legatus from E. nitidus, its sister taxon following molecular analyses, include: larger overall size, dorsal fur with a strong yellowish brown to orange brown tinge, flanks and cheeks with an orange lateral line, ventral color grayish-white with pure white hairs present only on the chin, presence of a thin blackish eye-ring, tail bicolored, presence of an alisphenoid strut and a well-developed temporal and lambdoid crests in the skull, and a labial cingulum on M3. Molecular phylogenetic analyses recovered E. legatus as a monophyletic group with high support nested within a paraphyletic E. nitidus; genetic distances segregated members of bo…
bibliographic citation: Guilardi et al. (2020) A review of Euryoryzomys legatus (Rodentia, Sigmodontinae): morphological redescription, cytogenetics, and molecular phylogeny. PeerJ 8:e9884 https://doi.org/10.7717/peerj.9884
date submitted: 2020-03-02
date accepted: 2020-08-16
issued: 2020-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guilardi
  given name: Mariana D.
author list: Agent
  family name: Jayat
  given name: Pablo
author list: Agent
  family name: Weksler
  given name: Marcelo
author list: Agent
  family name: Patton
  given name: James L.
author list: Agent
  family name: Ortiz
  given name: Pablo Edmundo
author list: Agent
  family name: Almeida
  given name: Keila
author list: Agent
  family name: Silva
  given name: Maria José de J.
doi: 10.7717/peerj.9884
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-29
copyright: ©2020 Guilardi et al.
attribution name: Guilardi et al.

A 14 immune-related gene signature predicts clinical outcomes of kidney renal clear cell carcinoma
type: item
type: AcademicArticle
description: Kidney renal clear cell carcinoma (KIRC) is the leading cause of kidney cancer-related deaths. Currently, there are no studies in tumor immunology investigating the use of signatures as a predictor of overall survival in KIRC patients. Our study attempts to establish an immune-related gene risk signature to predict clinical outcomes in KIRC. A total of 528 patients from The Cancer Genome Atlas (TCGA) database were included in our analysis and randomly divided into training (n = 315) and testing sets (n = 213). We collected 1,534 immune-related genes from the Immunology Database and Analysis Portal as candidates to construct our signature. LASSO-COX was used to find gene models with the highest predictive ability. We used survival and Cox analysis to test the model’s independent prognostic ability. Univariate analysis identified 650 immune-related genes with prognostic abilities. After 1,000 iterations, we choose 14 of the most frequent and stable immune-related genes as our signature. We found that the signature was associated with M stage, T stage, and pathological staging. More importantly, the signature can independently predict clinical prognosis in KIRC patients. Gene Set Enrichment Analysis (GSEA) showed an association between our signature and critical metabolism pathways. Our research established a model based upon 14 immune-related genes that predicted the prognosis of KIRC patients based on tumor immune microenvironments.
format: application/pdf
format: text/html
creator: Yong Zou
creator: Chuan Hu
subject: Bioinformatics
subject: Oncology
subject: Urology
subject: Data Science
description: doi:10.7717/peerj.10183
publisher: PeerJ Inc.
rights: © 2020 Zou and Hu
abstract: Kidney renal clear cell carcinoma (KIRC) is the leading cause of kidney cancer-related deaths. Currently, there are no studies in tumor immunology investigating the use of signatures as a predictor of overall survival in KIRC patients. Our study attempts to establish an immune-related gene risk signature to predict clinical outcomes in KIRC. A total of 528 patients from The Cancer Genome Atlas (TCGA) database were included in our analysis and randomly divided into training (n = 315) and testing sets (n = 213). We collected 1,534 immune-related genes from the Immunology Database and Analysis Portal as candidates to construct our signature. LASSO-COX was used to find gene models with the highest predictive ability. We used survival and Cox analysis to test the model’s independent prognostic ability. Univariate analysis identified 650 immune-related genes with prognostic abilities. After 1,000 iterations, we choose 14 of the most frequent and stable immune-related genes as our signature. We found that the signature was associated with M stage, T stage, and pathological staging. More importantly, the signature can independently predict clinical prognosis in KIRC patients. Gene Set Enrichment Analysis (GSEA) showed an association between our signature and critical metabolism pathways. Our research established a model based upon 14 immune-related genes that predicted the prognosis of KIRC patients based on tumor immune microenvironments.
bibliographic citation: Zou et al. (2020) A 14 immune-related gene signature predicts clinical outcomes of kidney renal clear cell carcinoma. PeerJ 8:e10183 https://doi.org/10.7717/peerj.10183
date submitted: 2019-11-27
date accepted: 2020-09-23
issued: 2020-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Yong
author list: Agent
  family name: Hu
  given name: Chuan
doi: 10.7717/peerj.10183
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-29
copyright: ©2020 Zou and Hu
attribution name: Zou and Hu

Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing
type: item
type: AcademicArticle
description: Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
format: application/pdf
format: text/html
creator: Alaa Emara Rabee
creator: Robert Forster
creator: Chijioke Elekwachi
creator: Ebrahim Sabra
creator: Mebarek Lamara
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.10184
publisher: PeerJ Inc.
rights: © 2020 Rabee et al.
abstract: Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
bibliographic citation: Rabee et al. (2020) Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 8:e10184 https://doi.org/10.7717/peerj.10184
date submitted: 2019-12-17
date accepted: 2020-09-23
issued: 2020-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rabee
  given name: Alaa Emara
author list: Agent
  family name: Forster
  given name: Robert
author list: Agent
  family name: Elekwachi
  given name: Chijioke
author list: Agent
  family name: Sabra
  given name: Ebrahim
author list: Agent
  family name: Lamara
  given name: Mebarek
doi: 10.7717/peerj.10184
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-29
copyright: © 2020 Rabee et al.
attribution name: Rabee et al.

Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic
type: item
type: AcademicArticle
description: A critical lack of personal protective equipment has occurred during the COVID-19 pandemic. Polylactic acid (PLA), a polyester made from renewable natural resources, can be exploited for 3D printing of protective face masks using the Fused Deposition Modelling technique. Since the possible high porosity of this material raised questions regarding its suitability for protection against viruses, we have investigated its microstructure using scanning electron microscopy and aerosol generator and photometer certified as the test system according to the standards EN 143 and EN 149. Moreover, the efficiency of decontaminating PLA surfaces by conventional chemical disinfectants including 96% ethanol, 70% isopropanol, and a commercial disinfectant containing 0.85% sodium hypochlorite has been determined. We confirmed that the structure of PLA protective masks is compact and can be considered a sufficient barrier protection against particles of a size corresponding to microorganisms including viruses. Complete decontamination of PLA surfaces from externally applied Staphylococcus epidermidis, Escherichia coli, Candida albicans and SARS-CoV-2 was achieved using all disinfectants tested, and human adenovirus was completely inactivated by sodium hypochlorite-containing disinfectant. Natural contamination of PLA masks worn by test persons was decontaminated easily and efficiently by ethanol. No disinfectant caused major changes to the PLA surface properties, and the pore size did not change despite severe mechanical damage of the surface. Therefore, PLA may be regarded as a suitable material for 3D printing of protective masks during the current or future pandemic crises.
format: application/pdf
format: text/html
creator: Eva Vaňková
creator: Petra Kašparová
creator: Josef Khun
creator: Anna Machková
creator: Jaroslav Julák
creator: Michal Sláma
creator: Jan Hodek
creator: Lucie Ulrychová
creator: Jan Weber
creator: Klára Obrová
creator: Karin Kosulin
creator: Thomas Lion
creator: Vladimír Scholtz
subject: Microbiology
subject: Virology
subject: Emergency and Critical Care
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.10259
publisher: PeerJ Inc.
rights: © 2020 Vaňková et al.
abstract: A critical lack of personal protective equipment has occurred during the COVID-19 pandemic. Polylactic acid (PLA), a polyester made from renewable natural resources, can be exploited for 3D printing of protective face masks using the Fused Deposition Modelling technique. Since the possible high porosity of this material raised questions regarding its suitability for protection against viruses, we have investigated its microstructure using scanning electron microscopy and aerosol generator and photometer certified as the test system according to the standards EN 143 and EN 149. Moreover, the efficiency of decontaminating PLA surfaces by conventional chemical disinfectants including 96% ethanol, 70% isopropanol, and a commercial disinfectant containing 0.85% sodium hypochlorite has been determined. We confirmed that the structure of PLA protective masks is compact and can be considered a sufficient barrier protection against particles of a size corresponding to microorganisms including viruses. Complete decontamination of PLA surfaces from externally applied Staphylococcus epidermidis, Escherichia coli, Candida albicans and SARS-CoV-2 was achieved using all disinfectants tested, and human adenovirus was completely inactivated by sodium hypochlorite-containing disinfectant. Natural contamination of PLA masks worn by test persons was decontaminated easily and efficiently by ethanol. No disinfectant caused major changes to the PLA surface properties, and the pore size did not change despite severe mechanical damage of the surface. Therefore, PLA may be regarded as a suitable material for 3D printing of protective masks during the current or future pandemic crises.
bibliographic citation: Vaňková et al. (2020) Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic. PeerJ 8:e10259 https://doi.org/10.7717/peerj.10259
date submitted: 2020-06-19
date accepted: 2020-10-06
issued: 2020-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaňková
  given name: Eva
author list: Agent
  family name: Kašparová
  given name: Petra
author list: Agent
  family name: Khun
  given name: Josef
author list: Agent
  family name: Machková
  given name: Anna
author list: Agent
  family name: Julák
  given name: Jaroslav
author list: Agent
  family name: Sláma
  given name: Michal
author list: Agent
  family name: Hodek
  given name: Jan
author list: Agent
  family name: Ulrychová
  given name: Lucie
author list: Agent
  family name: Weber
  given name: Jan
author list: Agent
  family name: Obrová
  given name: Klára
author list: Agent
  family name: Kosulin
  given name: Karin
author list: Agent
  family name: Lion
  given name: Thomas
author list: Agent
  family name: Scholtz
  given name: Vladimír
doi: 10.7717/peerj.10259
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-29
copyright: © 2020 Vaňková et al.
attribution name: Vaňková et al.

The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota
type: item
type: AcademicArticle
description: Background The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. Methods We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. Results The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.
format: application/pdf
format: text/html
creator: Yan-Fu Qu
creator: Yan-Qing Wu
creator: Yu-Tian Zhao
creator: Long-Hui Lin
creator: Yu Du
creator: Peng Li
creator: Hong Li
creator: Xiang Ji
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10271
publisher: PeerJ Inc.
rights: © 2020 Qu et al.
abstract: Background The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. Methods We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. Results The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.
bibliographic citation: Qu et al. (2020) The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota. PeerJ 8:e10271 https://doi.org/10.7717/peerj.10271
date submitted: 2020-08-04
date accepted: 2020-10-08
issued: 2020-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Yan-Fu
author list: Agent
  family name: Wu
  given name: Yan-Qing
author list: Agent
  family name: Zhao
  given name: Yu-Tian
author list: Agent
  family name: Lin
  given name: Long-Hui
author list: Agent
  family name: Du
  given name: Yu
author list: Agent
  family name: Li
  given name: Peng
author list: Agent
  family name: Li
  given name: Hong
author list: Agent
  family name: Ji
  given name: Xiang
doi: 10.7717/peerj.10271
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-29
copyright: ©2020 Qu et al.
attribution name: Qu et al.

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