PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Track cycling sprint sex differences using power data
items: Optimization of a tri-drug treatment against lung cancer using orthogonal design in preclinical studies
items: First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome
items: The postcranial anatomy of Gorgonops torvus (Synapsida, Gorgonopsia) from the late Permian of South Africa
items: Characterizing the blood microbiota of omnivorous and frugivorous bats (Chiroptera: Phyllostomidae) in Casanare, eastern Colombia
items: CircRNA: a rising star in leukemia
items: Some structural features of the peptide profile of myelin basic protein-hydrolyzing antibodies in schizophrenic patients
items: Village dogs match pet dogs in reading human facial expressions
items: Development of a circHIPK3-based ceRNA network and identification of mRNA signature in breast cancer patients harboring BRCA mutation
items: Chemical weathering rates and controlling mechanisms of glacial catchments within different climate regimes in the Tibetan Plateau

Track cycling sprint sex differences using power data
type: item
type: AcademicArticle
description: Objectives Currently, there are no data on sex differences in the power profiles in sprint track cycling. This cross-section study analyses retrospective data of female and male track sprint cyclists for sex differences. We hypothesized that women would exhibit lower peak power to weight than men, as well as demonstrate a different distribution of power durations related to sprint cycling performance. Design We used training, testing, and racing data from a publicly available online depository (www.strava.com), for 29 track sprint cyclists (eight women providing 18 datasets, and 21 men providing 54 datasets) to create sex-specific profiles. R2 was used to describe model quality, and regression indices are used to compare watts per kilogram (W/kg) for each duration for both sexes against a 1:1 relationship expected for 15-s:15-s W/kg. Results We confirmed our sample were sprint cyclists, displaying higher peak and competition power than track endurance cyclists. All power profiles showed a high model quality (R2 ≥ 0.77). Regression indices for both sexes were similar for all durations, suggesting similar peak power and similar relationship between peak power and endurance level for both men and women (rejecting our hypothesis). The value of R2 for the female sprinters showed greater variation suggesting greater differences within female sprint cyclists. Conclusion The main finding shows female sprint cyclists in this study have very similar relationships between peak power and endurance power as men. Higher variation in W/kg for women in this study than men, within these strong relationships, indicates women in this study, had greater inter-athlete variability, and may thus require more personalised training. Future work needs to be performed with larger samples, and at different levels to optimize these recommendations.
format: application/pdf
format: text/html
creator: Hamish Ferguson
creator: Chris Harnish
creator: Sebastian Klich
creator: Kamil Michalik
creator: Anna Katharina Dunst
creator: Tony Zhou
creator: J Geoffrey Chase
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.15671
publisher: PeerJ Inc.
rights: © 2023 Ferguson et al.
abstract: Objectives Currently, there are no data on sex differences in the power profiles in sprint track cycling. This cross-section study analyses retrospective data of female and male track sprint cyclists for sex differences. We hypothesized that women would exhibit lower peak power to weight than men, as well as demonstrate a different distribution of power durations related to sprint cycling performance. Design We used training, testing, and racing data from a publicly available online depository (www.strava.com), for 29 track sprint cyclists (eight women providing 18 datasets, and 21 men providing 54 datasets) to create sex-specific profiles. R2 was used to describe model quality, and regression indices are used to compare watts per kilogram (W/kg) for each duration for both sexes against a 1:1 relationship expected for 15-s:15-s W/kg. Results We confirmed our sample were sprint cyclists, displaying higher peak and competition power than track endurance cyclists. All power profiles showed a high model quality (R2 ≥ 0.77). Regression indices for both sexes were similar for all durations, suggesting similar peak power and similar relationship between peak power and endurance level for both men and women (rejecting our hypothesis). The value of R2 for the female sprinters showed greater variation suggesting greater differences within female sprint cyclists. Conclusion The main finding shows female sprint cyclists in this study have very similar relationships between peak power and endurance power as men. Higher variation in W/kg for women in this study than men, within these strong relationships, indicates women in this study, had greater inter-athlete variability, and may thus require more personalised training. Future work needs to be performed with larger samples, and at different levels to optimize these recommendations.
bibliographic citation: Ferguson et al. (2023) Track cycling sprint sex differences using power data. PeerJ 11:e15671 https://doi.org/10.7717/peerj.15671
date submitted: 2023-01-09
date accepted: 2023-06-09
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferguson
  given name: Hamish
author list: Agent
  family name: Harnish
  given name: Chris
author list: Agent
  family name: Klich
  given name: Sebastian
author list: Agent
  family name: Michalik
  given name: Kamil
author list: Agent
  family name: Dunst
  given name: Anna Katharina
author list: Agent
  family name: Zhou
  given name: Tony
author list: Agent
  family name: Chase
  given name: J Geoffrey
doi: 10.7717/peerj.15671
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: © 2023 Ferguson et al.
attribution name: Ferguson et al.

Optimization of a tri-drug treatment against lung cancer using orthogonal design in preclinical studies
type: item
type: AcademicArticle
description: A growing body of evidence suggests that anesthetics impact the outcome of patients with cancer after surgical intervention. However, the optimal dose and underlying mechanisms of co-administered anesthetics in lung tumor therapy have been poorly studied. Here, we aimed to investigate the role of combined anesthetics propofol, sufentanil, and rocuronium in treating lung cancer using an orthogonal experimental design and to explore the optimal combination of anesthetics. First, we evaluated the effects of the three anesthetics on the proliferation and invasion of A-549 cells using Cell Counting Kit 8 and Transwell migration and invasion assays. Subsequently, we applied the orthogonal experimental design (OED) method to screen the appropriate concentrations of the combined anesthetics with the most effective antitumor activity. We found that all three agents inhibited the proliferation of A-549 cells in a dose- and time-dependent manner when applied individually or in combination, with the highest differences in the magnitude of inhibition occurring 24 h after combined drug exposure. The optimal combination of the three anesthetics that achieved the strongest reduction in cell viability was 1.4 µmol/L propofol, 2 nmol/L sufentanil, and 7.83 µmol/L rocuronium. This optimal 3-drug combination produced a more beneficial result at 24 h than either single drug. Our results provide a theoretical basis for improving the efficacy of lung tumor treatment and optimizing anesthetic strategies.
format: application/pdf
format: text/html
creator: Jing Tan
creator: Lijun Wang
creator: Xuming Song
creator: Yijian Zhang
creator: Zhenghuan Song
creator: Manlin Duan
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15672
publisher: PeerJ Inc.
rights: © 2023 Tan et al.
abstract: A growing body of evidence suggests that anesthetics impact the outcome of patients with cancer after surgical intervention. However, the optimal dose and underlying mechanisms of co-administered anesthetics in lung tumor therapy have been poorly studied. Here, we aimed to investigate the role of combined anesthetics propofol, sufentanil, and rocuronium in treating lung cancer using an orthogonal experimental design and to explore the optimal combination of anesthetics. First, we evaluated the effects of the three anesthetics on the proliferation and invasion of A-549 cells using Cell Counting Kit 8 and Transwell migration and invasion assays. Subsequently, we applied the orthogonal experimental design (OED) method to screen the appropriate concentrations of the combined anesthetics with the most effective antitumor activity. We found that all three agents inhibited the proliferation of A-549 cells in a dose- and time-dependent manner when applied individually or in combination, with the highest differences in the magnitude of inhibition occurring 24 h after combined drug exposure. The optimal combination of the three anesthetics that achieved the strongest reduction in cell viability was 1.4 µmol/L propofol, 2 nmol/L sufentanil, and 7.83 µmol/L rocuronium. This optimal 3-drug combination produced a more beneficial result at 24 h than either single drug. Our results provide a theoretical basis for improving the efficacy of lung tumor treatment and optimizing anesthetic strategies.
bibliographic citation: Tan et al. (2023) Optimization of a tri-drug treatment against lung cancer using orthogonal design in preclinical studies. PeerJ 11:e15672 https://doi.org/10.7717/peerj.15672
date submitted: 2023-04-05
date accepted: 2023-06-11
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Jing
author list: Agent
  family name: Wang
  given name: Lijun
author list: Agent
  family name: Song
  given name: Xuming
author list: Agent
  family name: Zhang
  given name: Yijian
author list: Agent
  family name: Song
  given name: Zhenghuan
author list: Agent
  family name: Duan
  given name: Manlin
doi: 10.7717/peerj.15672
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Tan et al.
attribution name: Tan et al.

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome
type: item
type: AcademicArticle
description: Background The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome. Methods This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways. Results Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
format: application/pdf
format: text/html
creator: J. Eduardo Martinez-Hernandez
creator: Pablo Berrios
creator: Rodrigo Santibáñez
creator: Yesid Cuesta Astroz
creator: Carolina Sanchez
creator: Alberto J. M. Martin
creator: Annette N. Trombert
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.15235
publisher: PeerJ Inc.
rights: © 2023 Martinez-Hernandez et al.
abstract: Background The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome. Methods This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways. Results Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
bibliographic citation: Martinez-Hernandez et al. (2023) First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome. PeerJ 11:e15235 https://doi.org/10.7717/peerj.15235
date submitted: 2022-08-23
date accepted: 2023-03-28
issued: 2023-07-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Hernandez
  given name: J. Eduardo
author list: Agent
  family name: Berrios
  given name: Pablo
author list: Agent
  family name: Santibáñez
  given name: Rodrigo
author list: Agent
  family name: Cuesta Astroz
  given name: Yesid
author list: Agent
  family name: Sanchez
  given name: Carolina
author list: Agent
  family name: Martin
  given name: Alberto J. M.
author list: Agent
  family name: Trombert
  given name: Annette N.
doi: 10.7717/peerj.15235
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-07
copyright: © 2023 Martinez-Hernandez et al.
attribution name: Martinez-Hernandez et al.

The postcranial anatomy of Gorgonops torvus (Synapsida, Gorgonopsia) from the late Permian of South Africa
type: item
type: AcademicArticle
description: Gorgonopsians are among the most recognizable groups of synapsids from the Permian period and have an extensive but mostly cranial fossil record. By contrast, relatively little is known about their postcranial anatomy. Here, we describe a nearly complete, semi-articulated skeleton of a gorgonopsian (identified as Gorgonops torvus) from the late Permian Endothiodon Assemblage Zone of the South African Karoo Basin and discuss its paleobiological implications. Known gorgonopsian postcrania indicate morphological conservatism in the group, but the skeletal anatomy of Gorgonops does differ from that of other gorgonopsians in some respects, such as in the triangular radiale and short terminal phalanges in the manus, and a weakly developed distinction between pubis and ischium in ventral aspect of the pelvic girdle. Similarities between the specimen described herein and a historically problematic specimen originally referred to “Scymnognathus cf. whaitsi” confirm referral of the latter specimen to Gorgonops. Since descriptions of gorgonopsian postcrania are rare, new interpretations of the lifestyle and ecology of Gorgonopsia can be drawn from our contribution. We conclude that gorgonopsians were likely ambush predators, able to chase their prey over short distances and pin them down with strong forelimbs before using their canines for the kill. This is evidenced by their different fore- and hindlimb morphology; the former stouter and more robust in comparison to the longer, more gracile, back legs. Furthermore, the completeness of the study specimen facilitates calculation of an estimated body mass of approximately 98 kg, similar to that of a modern lioness.
format: application/pdf
format: text/html
creator: Eva-Maria Bendel
creator: Christian F. Kammerer
creator: Roger M. H. Smith
creator: Jörg Fröbisch
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15378
publisher: PeerJ Inc.
rights: © 2023 Bendel et al.
abstract: Gorgonopsians are among the most recognizable groups of synapsids from the Permian period and have an extensive but mostly cranial fossil record. By contrast, relatively little is known about their postcranial anatomy. Here, we describe a nearly complete, semi-articulated skeleton of a gorgonopsian (identified as Gorgonops torvus) from the late Permian Endothiodon Assemblage Zone of the South African Karoo Basin and discuss its paleobiological implications. Known gorgonopsian postcrania indicate morphological conservatism in the group, but the skeletal anatomy of Gorgonops does differ from that of other gorgonopsians in some respects, such as in the triangular radiale and short terminal phalanges in the manus, and a weakly developed distinction between pubis and ischium in ventral aspect of the pelvic girdle. Similarities between the specimen described herein and a historically problematic specimen originally referred to “Scymnognathus cf. whaitsi” confirm referral of the latter specimen to Gorgonops. Since descriptions of gorgonopsian postcrania are rare, new interpretations of the lifestyle and ecology of Gorgonopsia can be drawn from our contribution. We conclude that gorgonopsians were likely ambush predators, able to chase their prey over short distances and pin them down with strong forelimbs before using their canines for the kill. This is evidenced by their different fore- and hindlimb morphology; the former stouter and more robust in comparison to the longer, more gracile, back legs. Furthermore, the completeness of the study specimen facilitates calculation of an estimated body mass of approximately 98 kg, similar to that of a modern lioness.
bibliographic citation: Bendel et al. (2023) The postcranial anatomy of Gorgonops torvus (Synapsida, Gorgonopsia) from the late Permian of South Africa. PeerJ 11:e15378 https://doi.org/10.7717/peerj.15378
date submitted: 2022-11-23
date accepted: 2023-04-18
issued: 2023-07-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bendel
  given name: Eva-Maria
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Smith
  given name: Roger M. H.
author list: Agent
  family name: Fröbisch
  given name: Jörg
doi: 10.7717/peerj.15378
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-07
copyright: © 2023 Bendel et al.
attribution name: Bendel et al.

Characterizing the blood microbiota of omnivorous and frugivorous bats (Chiroptera: Phyllostomidae) in Casanare, eastern Colombia
type: item
type: AcademicArticle
description: Bats are known reservoirs of seemingly-innocuous pathogenic microorganisms (including viruses, bacteria, fungi, and protozoa), which are associated with triggering disease in other zoonotic groups. The taxonomic diversity of the bats’ microbiome is likely associated with species-specific phenotypic, metabolic, and immunogenic capacities. To date, few studies have described the diversity of bat blood microbial communities. Then, this study used amplicon-based next generation sequencing of the V4 hypervariable region of the 16S-rRNA gene in blood samples from omnivorous (n = 16) and frugivorous (n = 9) bats from the department of Casanare in eastern Colombia. We found the blood microbiota in bats to be composed of, among others, Bartonella and Mycoplasma bacterial genera which are associated with various disease phenotypes in other mammals. Furthermore, our results suggest that the bats’ dietary habits might determine the composition and the persistence of some pathogens over others in their bloodstream. This study is among the first to describe the blood microbiota in bats, to reflect on co-infection rates of multiple pathogens in the same individual, and to consider the influence of diet as a factor affecting the animal’s endogenous microbial community.
format: application/pdf
format: text/html
creator: Nicolas Luna
creator: Marina Muñoz
creator: Adriana Castillo-Castañeda
creator: Carolina Hernandez
creator: Plutarco Urbano
creator: Maryia Shaban
creator: Alberto Paniz-Mondolfi
creator: Juan David Ramírez
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.15169
publisher: PeerJ Inc.
rights: © 2023 Luna et al.
abstract: Bats are known reservoirs of seemingly-innocuous pathogenic microorganisms (including viruses, bacteria, fungi, and protozoa), which are associated with triggering disease in other zoonotic groups. The taxonomic diversity of the bats’ microbiome is likely associated with species-specific phenotypic, metabolic, and immunogenic capacities. To date, few studies have described the diversity of bat blood microbial communities. Then, this study used amplicon-based next generation sequencing of the V4 hypervariable region of the 16S-rRNA gene in blood samples from omnivorous (n = 16) and frugivorous (n = 9) bats from the department of Casanare in eastern Colombia. We found the blood microbiota in bats to be composed of, among others, Bartonella and Mycoplasma bacterial genera which are associated with various disease phenotypes in other mammals. Furthermore, our results suggest that the bats’ dietary habits might determine the composition and the persistence of some pathogens over others in their bloodstream. This study is among the first to describe the blood microbiota in bats, to reflect on co-infection rates of multiple pathogens in the same individual, and to consider the influence of diet as a factor affecting the animal’s endogenous microbial community.
bibliographic citation: Luna et al. (2023) Characterizing the blood microbiota of omnivorous and frugivorous bats (Chiroptera: Phyllostomidae) in Casanare, eastern Colombia. PeerJ 11:e15169 https://doi.org/10.7717/peerj.15169
date submitted: 2022-10-17
date accepted: 2023-03-13
issued: 2023-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luna
  given name: Nicolas
author list: Agent
  family name: Muñoz
  given name: Marina
author list: Agent
  family name: Castillo-Castañeda
  given name: Adriana
author list: Agent
  family name: Hernandez
  given name: Carolina
author list: Agent
  family name: Urbano
  given name: Plutarco
author list: Agent
  family name: Shaban
  given name: Maryia
author list: Agent
  family name: Paniz-Mondolfi
  given name: Alberto
author list: Agent
  family name: Ramírez
  given name: Juan David
doi: 10.7717/peerj.15169
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-06
copyright: © 2023 Luna et al.
attribution name: Luna et al.

CircRNA: a rising star in leukemia
type: item
type: AcademicArticle
description: Non-coding RNA are a class of RNA that lack the potential to encode proteins. CircRNAs, generated by a post-splicing mechanism, are a newly discovered type of non-coding RNA with multi-functional covalent loop structures. CircRNAs may play an important role in the occurrence and progression of tumors. Research has shown that circRNAs are aberrantly expressed in various types of human cancers, including leukemia. In this review, we summarize the expression and function of circRNAs and their impact on different types of leukemia. We also illustrate the function of circRNAs on immune modulation and chemoresistance in leukemia and their impact on its diagnosis and prognosis. Herein, we provide an understanding of recent advances in research that highlight the importance of circRNAs in proliferation, apoptosis, migration, and autophagy in different types of leukemia. Furthermore, circRNAs make an indispensable difference in the modulation of the immunity and chemoresistance of leukemia. Increasing evidence suggests that circRNAs may play a vital role in the diagnostic and prognostic markers of leukemia because of their prominent properties. More detailed preclinical studies on circRNAs are needed to explore effective ways in which they can serve as biomarkers for the diagnosis and prognosis of leukemia in vivo.
format: application/pdf
format: text/html
creator: Qianan Li
creator: Xinxin Ren
creator: Ying Wang
creator: Xiaoru Xin
subject: Molecular Biology
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.15577
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Non-coding RNA are a class of RNA that lack the potential to encode proteins. CircRNAs, generated by a post-splicing mechanism, are a newly discovered type of non-coding RNA with multi-functional covalent loop structures. CircRNAs may play an important role in the occurrence and progression of tumors. Research has shown that circRNAs are aberrantly expressed in various types of human cancers, including leukemia. In this review, we summarize the expression and function of circRNAs and their impact on different types of leukemia. We also illustrate the function of circRNAs on immune modulation and chemoresistance in leukemia and their impact on its diagnosis and prognosis. Herein, we provide an understanding of recent advances in research that highlight the importance of circRNAs in proliferation, apoptosis, migration, and autophagy in different types of leukemia. Furthermore, circRNAs make an indispensable difference in the modulation of the immunity and chemoresistance of leukemia. Increasing evidence suggests that circRNAs may play a vital role in the diagnostic and prognostic markers of leukemia because of their prominent properties. More detailed preclinical studies on circRNAs are needed to explore effective ways in which they can serve as biomarkers for the diagnosis and prognosis of leukemia in vivo.
bibliographic citation: Li et al. (2023) CircRNA: a rising star in leukemia. PeerJ 11:e15577 https://doi.org/10.7717/peerj.15577
date submitted: 2023-01-13
date accepted: 2023-05-25
issued: 2023-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qianan
author list: Agent
  family name: Ren
  given name: Xinxin
author list: Agent
  family name: Wang
  given name: Ying
author list: Agent
  family name: Xin
  given name: Xiaoru
doi: 10.7717/peerj.15577
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-06
copyright: ©2023 Li et al.
attribution name: Li et al.

Some structural features of the peptide profile of myelin basic protein-hydrolyzing antibodies in schizophrenic patients
type: item
type: AcademicArticle
description: The antibodies of schizophrenic patients that hydrolyze myelin basic protein (MBP) have been actively studied recently, but the mechanism of the catalytic properties of immunoglobulin molecules remains unknown. Determination of specific immunoglobulin sequences associated with the high activity of MBP proteolysis will help to understand the mechanisms of abzyme catalysis. In the course of comparative mass spectrometric analysis of IgG peptides from the blood serum of patients with acute schizophrenia and healthy people, 12 sequences were identified, which were found only in antibodies that hydrolyze MBP. These sequences belong to IgG heavy chains and κ- and λ-type light chains, with eight of them belonging to variable domains. The content of peptides from the variable regions of the light chains does not correlate with the proteolytic activity of IgG to MBP in patients with schizophrenia, whereas for two sequences from the variable regions of the heavy chains (FQ(+0.98)GWVTMTR and *LYLQMN(+0.98)SLR), an increase in activity with increasing their concentration. The results suggest that these sequences may be involved in one way or another in MBP hydrolysis.
format: application/pdf
format: text/html
creator: Maria Zavialova
creator: Daria Kamaeva
creator: Laura Kazieva
creator: Vladlen S. Skvortsov
creator: Liudmila Smirnova
subject: Biochemistry
subject: Bioinformatics
subject: Cognitive Disorders
subject: Immunology
subject: Psychiatry
description: doi:10.7717/peerj.15584
publisher: PeerJ Inc.
rights: © 2023 Zavialova et al.
abstract: The antibodies of schizophrenic patients that hydrolyze myelin basic protein (MBP) have been actively studied recently, but the mechanism of the catalytic properties of immunoglobulin molecules remains unknown. Determination of specific immunoglobulin sequences associated with the high activity of MBP proteolysis will help to understand the mechanisms of abzyme catalysis. In the course of comparative mass spectrometric analysis of IgG peptides from the blood serum of patients with acute schizophrenia and healthy people, 12 sequences were identified, which were found only in antibodies that hydrolyze MBP. These sequences belong to IgG heavy chains and κ- and λ-type light chains, with eight of them belonging to variable domains. The content of peptides from the variable regions of the light chains does not correlate with the proteolytic activity of IgG to MBP in patients with schizophrenia, whereas for two sequences from the variable regions of the heavy chains (FQ(+0.98)GWVTMTR and *LYLQMN(+0.98)SLR), an increase in activity with increasing their concentration. The results suggest that these sequences may be involved in one way or another in MBP hydrolysis.
bibliographic citation: Zavialova et al. (2023) Some structural features of the peptide profile of myelin basic protein-hydrolyzing antibodies in schizophrenic patients. PeerJ 11:e15584 https://doi.org/10.7717/peerj.15584
date submitted: 2023-03-20
date accepted: 2023-05-26
issued: 2023-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zavialova
  given name: Maria
author list: Agent
  family name: Kamaeva
  given name: Daria
author list: Agent
  family name: Kazieva
  given name: Laura
author list: Agent
  family name: Skvortsov
  given name: Vladlen S.
author list: Agent
  family name: Smirnova
  given name: Liudmila
doi: 10.7717/peerj.15584
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-06
copyright: ©2023 Zavialova et al.
attribution name: Zavialova et al.

Village dogs match pet dogs in reading human facial expressions
type: item
type: AcademicArticle
description: Most studies on dogs’ cognitive skills in understanding human communication have been conducted on pet dogs, making them a role model for the species. However, pet dogs are just a minor and particular sample of the total dog world population, which would instead be better represented by free-ranging dogs. Since free-ranging dogs are still facing the selective forces of the domestication process, they indeed represent an important study subject to investigate the effect that such a process has had on dogs’ behavior and cognition. Despite only a few studies on free-ranging dogs (specifically village dogs) having been conducted so far, the results are intriguing. In fact, village dogs seem to place a high value on social contact with humans and understand some aspects of humans’ communication. In this study we aimed to investigate village dogs’ ability in understanding a subtle human communicative cue: human facial expressions, and compared them with pet dogs, who have already provided evidence of this social skill. We tested whether subjects were able to distinguish between neutral, happy, and angry human facial expressions in a test mimicking a potential real-life situation, where the experimenter repeatedly performed one facial expression while eating some food, and ultimately dropped it on the ground. We found evidence that village dogs, as well as pet dogs, could distinguish between subtle human communicative cues, since they performed a higher frequency of aversive gazes (looking away) in the angry condition than in the happy condition. However, we did not find other behavioral effects of the different conditions, likely due to the low intensity of the emotional expression performed. We suggest that village dogs’ ability in distinguishing between human facial expressions could provide them with an advantage in surviving in a human-dominated environment.
format: application/pdf
format: text/html
creator: Martina Lazzaroni
creator: Joana Schär
creator: Elizabeth Baxter
creator: Juliette Gratalon
creator: Friederike Range
creator: Sarah Marshall-Pescini
creator: Rachel Dale
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.15601
publisher: PeerJ Inc.
rights: © 2023 Lazzaroni et al.
abstract: Most studies on dogs’ cognitive skills in understanding human communication have been conducted on pet dogs, making them a role model for the species. However, pet dogs are just a minor and particular sample of the total dog world population, which would instead be better represented by free-ranging dogs. Since free-ranging dogs are still facing the selective forces of the domestication process, they indeed represent an important study subject to investigate the effect that such a process has had on dogs’ behavior and cognition. Despite only a few studies on free-ranging dogs (specifically village dogs) having been conducted so far, the results are intriguing. In fact, village dogs seem to place a high value on social contact with humans and understand some aspects of humans’ communication. In this study we aimed to investigate village dogs’ ability in understanding a subtle human communicative cue: human facial expressions, and compared them with pet dogs, who have already provided evidence of this social skill. We tested whether subjects were able to distinguish between neutral, happy, and angry human facial expressions in a test mimicking a potential real-life situation, where the experimenter repeatedly performed one facial expression while eating some food, and ultimately dropped it on the ground. We found evidence that village dogs, as well as pet dogs, could distinguish between subtle human communicative cues, since they performed a higher frequency of aversive gazes (looking away) in the angry condition than in the happy condition. However, we did not find other behavioral effects of the different conditions, likely due to the low intensity of the emotional expression performed. We suggest that village dogs’ ability in distinguishing between human facial expressions could provide them with an advantage in surviving in a human-dominated environment.
bibliographic citation: Lazzaroni et al. (2023) Village dogs match pet dogs in reading human facial expressions. PeerJ 11:e15601 https://doi.org/10.7717/peerj.15601
date submitted: 2022-12-20
date accepted: 2023-05-30
issued: 2023-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lazzaroni
  given name: Martina
author list: Agent
  family name: Schär
  given name: Joana
author list: Agent
  family name: Baxter
  given name: Elizabeth
author list: Agent
  family name: Gratalon
  given name: Juliette
author list: Agent
  family name: Range
  given name: Friederike
author list: Agent
  family name: Marshall-Pescini
  given name: Sarah
author list: Agent
  family name: Dale
  given name: Rachel
doi: 10.7717/peerj.15601
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-06
copyright: ©2023 Lazzaroni et al.
attribution name: Lazzaroni et al.

Development of a circHIPK3-based ceRNA network and identification of mRNA signature in breast cancer patients harboring BRCA mutation
type: item
type: AcademicArticle
description: Background Exploring the regulatory network of competing endogenous RNAs (ceRNAs) as hallmarks for breast cancer development has great significance and could provide therapeutic targets. An mRNA signature predictive of prognosis and therapy response in BRCA carriers was developed according to circular RNA homeodomain-interacting protein kinase 3 (circHIPK3)-based ceRNA network. Method We constructed a circHIPK3-based ceRNA network based on GSE173766 dataset and identified potential mRNAs that were associated with BRCA mutation patients within this ceRNA network. A total of 11 prognostic mRNAs and a risk model were identified and developed by univariate Cox regression analysis and the LASSO regression analysis as well as stepAIC method. Genomic landscape was treated by mutect2 and fisher. Immune characteristics was analyzed by ESTIMATE, MCP-counter. TIDE analysis was conducted to predict immunotherapy. The clinical treatment outcomes of BRCA mutation patients were assessed using a nomogram. The proliferation, migration and invasion in breast cancer cell lines were examined using CCK8 assay and transwell assay. Result We found 241 mRNAs within the circHIPK3-based ceRNA network. An 11 mRNA-based signature was identified for prognostic model construction. High risk patients exhibited dismal prognosis, low response to immunotherapy, less immune cell infiltration and tumor mutation burden (TMB). High-risk patients were sensitive to six anti-tumor drugs, while low-risk patient were sensitive to 47 drugs. The risk score was the most effective on evaluating patients’ survival. The robustness and good prediction performance were validated in The Cancer Genome Atlas (TCGA) dataset and immunotherapy datasets, respectively. In addition, circHIPK3 mRNA level was upregulated, and promoted cell viability, migration and invasion in breast cancer cell lines. Conclusion The current study could improve the understanding of mRNAs in relation to BRCA mutation and pave the way to develop …
format: application/pdf
format: text/html
creator: Qi-xin Lian
creator: Yang Song
creator: Lili Han
creator: Zunxian Wang
creator: Yinhui Song
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Immunology
description: doi:10.7717/peerj.15572
publisher: PeerJ Inc.
rights: © 2023 Lian et al.
abstract: Background Exploring the regulatory network of competing endogenous RNAs (ceRNAs) as hallmarks for breast cancer development has great significance and could provide therapeutic targets. An mRNA signature predictive of prognosis and therapy response in BRCA carriers was developed according to circular RNA homeodomain-interacting protein kinase 3 (circHIPK3)-based ceRNA network. Method We constructed a circHIPK3-based ceRNA network based on GSE173766 dataset and identified potential mRNAs that were associated with BRCA mutation patients within this ceRNA network. A total of 11 prognostic mRNAs and a risk model were identified and developed by univariate Cox regression analysis and the LASSO regression analysis as well as stepAIC method. Genomic landscape was treated by mutect2 and fisher. Immune characteristics was analyzed by ESTIMATE, MCP-counter. TIDE analysis was conducted to predict immunotherapy. The clinical treatment outcomes of BRCA mutation patients were assessed using a nomogram. The proliferation, migration and invasion in breast cancer cell lines were examined using CCK8 assay and transwell assay. Result We found 241 mRNAs within the circHIPK3-based ceRNA network. An 11 mRNA-based signature was identified for prognostic model construction. High risk patients exhibited dismal prognosis, low response to immunotherapy, less immune cell infiltration and tumor mutation burden (TMB). High-risk patients were sensitive to six anti-tumor drugs, while low-risk patient were sensitive to 47 drugs. The risk score was the most effective on evaluating patients’ survival. The robustness and good prediction performance were validated in The Cancer Genome Atlas (TCGA) dataset and immunotherapy datasets, respectively. In addition, circHIPK3 mRNA level was upregulated, and promoted cell viability, migration and invasion in breast cancer cell lines. Conclusion The current study could improve the understanding of mRNAs in relation to BRCA mutation and pave the way to develop …
bibliographic citation: Lian et al. (2023) Development of a circHIPK3-based ceRNA network and identification of mRNA signature in breast cancer patients harboring BRCA mutation. PeerJ 11:e15572 https://doi.org/10.7717/peerj.15572
date submitted: 2023-04-25
date accepted: 2023-05-25
issued: 2023-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lian
  given name: Qi-xin
author list: Agent
  family name: Song
  given name: Yang
author list: Agent
  family name: Han
  given name: Lili
author list: Agent
  family name: Wang
  given name: Zunxian
author list: Agent
  family name: Song
  given name: Yinhui
doi: 10.7717/peerj.15572
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-05
copyright: ©2023 Lian et al.
attribution name: Lian et al.

Chemical weathering rates and controlling mechanisms of glacial catchments within different climate regimes in the Tibetan Plateau
type: item
type: AcademicArticle
description: Background Continental weathering plays an important role in regulating atmospheric CO2 levels. Chemical weathering in glacial areas has become an intensely focused topic in the background of global change compared with other terrestrial weathering systems. However, research on the weathering of the glacial areas in the Yarlung Tsangpo River Basin (YTRB) is still limited. Methods In this article, the major ions of the Chaiqu and Niangqu catchments in the YTRB have been investigated to illustrate the chemical weathering rates and mechanisms of the glacier areas in the YTRB. Results Ca2+ and HCO ${}_{3}^{-}$ 3 − dominate the major ions of the Chaiqu and Niangqu rivers, accounting for about 71.3% and 69.2% of the TZ+ of the Chaiqu (the total cations, TZ+ = Na+ + K+ + Ca2 + + Mg2+, in µeq/L), and about 64.2% and 62.6% of the TZ+ of the Niangqu. A Monte Carlo model with six end-members is applied to quantitatively partition the dissolved load sources of the catchments. The results show that the dissolved loads of the Chaiqu and Niangqu rivers are mainly derived from carbonate weathering (accounting for about 62.9% and 79.7% of the TZ+, respectively), followed by silicate weathering (about 25.8% and 7.9% of the TZ+, respectively). The contributions of precipitation and evaporite to the Chaiqu rivers are about 5.0% and 6.2%, and those to the Niangqu rivers are about 6.3% and 6.2%. The model also calculated the proportion of sulfuric acid weathering in the Chaiqu and Niangqu catchments, which account for about 21.1% and 32.3% of the TZ+, respectively. Based on the results calculated by the model, the carbonate and silicate weathering rates in the Chaiqu catchment are about 7.9 and 1.8 ton km−2 a−1, and in the Niangqu catchment, the rates are about 13.7 and 1.5 ton km−2 a−1. The associated CO2 consumption in the Chaiqu catchment is about 4.3 and 4.4 × 104 mol km−2 a−1, and about 4.3 and 1.3 × 104 mol km−2 a−1 in the Niangqu catchment. The chemical weathering rates of the gla…
format: application/pdf
format: text/html
creator: Xiao Guo
creator: Zimiao Zhao
creator: Wenjing Liu
creator: Huiguo Sun
creator: Zhifang Xu
subject: Ecosystem Science
subject: Aquatic and Marine Chemistry
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.15594
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: Background Continental weathering plays an important role in regulating atmospheric CO2 levels. Chemical weathering in glacial areas has become an intensely focused topic in the background of global change compared with other terrestrial weathering systems. However, research on the weathering of the glacial areas in the Yarlung Tsangpo River Basin (YTRB) is still limited. Methods In this article, the major ions of the Chaiqu and Niangqu catchments in the YTRB have been investigated to illustrate the chemical weathering rates and mechanisms of the glacier areas in the YTRB. Results Ca2+ and HCO ${}_{3}^{-}$ 3 − dominate the major ions of the Chaiqu and Niangqu rivers, accounting for about 71.3% and 69.2% of the TZ+ of the Chaiqu (the total cations, TZ+ = Na+ + K+ + Ca2 + + Mg2+, in µeq/L), and about 64.2% and 62.6% of the TZ+ of the Niangqu. A Monte Carlo model with six end-members is applied to quantitatively partition the dissolved load sources of the catchments. The results show that the dissolved loads of the Chaiqu and Niangqu rivers are mainly derived from carbonate weathering (accounting for about 62.9% and 79.7% of the TZ+, respectively), followed by silicate weathering (about 25.8% and 7.9% of the TZ+, respectively). The contributions of precipitation and evaporite to the Chaiqu rivers are about 5.0% and 6.2%, and those to the Niangqu rivers are about 6.3% and 6.2%. The model also calculated the proportion of sulfuric acid weathering in the Chaiqu and Niangqu catchments, which account for about 21.1% and 32.3% of the TZ+, respectively. Based on the results calculated by the model, the carbonate and silicate weathering rates in the Chaiqu catchment are about 7.9 and 1.8 ton km−2 a−1, and in the Niangqu catchment, the rates are about 13.7 and 1.5 ton km−2 a−1. The associated CO2 consumption in the Chaiqu catchment is about 4.3 and 4.4 × 104 mol km−2 a−1, and about 4.3 and 1.3 × 104 mol km−2 a−1 in the Niangqu catchment. The chemical weathering rates of the gla…
bibliographic citation: Guo et al. (2023) Chemical weathering rates and controlling mechanisms of glacial catchments within different climate regimes in the Tibetan Plateau. PeerJ 11:e15594 https://doi.org/10.7717/peerj.15594
date submitted: 2023-02-07
date accepted: 2023-05-29
issued: 2023-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Xiao
author list: Agent
  family name: Zhao
  given name: Zimiao
author list: Agent
  family name: Liu
  given name: Wenjing
author list: Agent
  family name: Sun
  given name: Huiguo
author list: Agent
  family name: Xu
  given name: Zhifang
doi: 10.7717/peerj.15594
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-05
copyright: ©2023 Guo et al.
attribution name: Guo et al.

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