PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca)
items: The characteristics and roles of antimicrobial peptides as potential treatment for antibiotic-resistant pathogens: a review
items: No relevant differences in conditioned pain modulation effects between parallel and sequential test design. A cross-sectional observational study
items: Identification of quantitative trait loci underlying five major agronomic traits of soybean in three biparental populations by specific length amplified fragment sequencing (SLAF-seq)
items: Occupancy of wild southern pig-tailed macaques in intact and degraded forests in Peninsular Malaysia
items: The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain
items: Local ancestry prediction with PyLAE
items: Growth and feeding ecology of coniform conodonts
items: A longitudinal study of the impact of COVID-19 restrictions on students’ health behavior, mental health and emotional well-being
items: Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca)
type: item
type: AcademicArticle
description: The first cave-dwelling Solenogastres—marine shell-less worm-like mollusks—were sampled from Mediterranean marine caves floor silt in the Marseille area. The mollusks were 1.5 mm in length, had a transparent body with shiny spicules and appear to represent a new Tegulaherpia species. Electron microscopy revealed a high number of microbial cells, located on the surface of the spicules as well as in the cuticle of Tegulaherpia sp. The observed microbial cells varied in morphology and were unequally distributed through the cuticle, reaching a highest density on the dorsal and lateral sides and being practically absent on the ventral side. Next Generation Sequencing (NGS) of V4 region of 16S rRNA gene amplicons, obtained from the DNA samples of whole bodies of Tegulaherpia sp. revealed three dominating microorganisms, two of which were bacteria of Bacteroidetes and Nitrospirae phyla, while the third one represented archaea of Thaumarchaeota phylum. The Operational Taxonomic Unit (OTU), affiliated with Bacteroidetes was an uncultured bacteria of the family Saprospiraceae (93–95% of Bacteroidetes and 25–44% of the total community, depending on sample), OTU, affiliated with Nitrospirae belonged to the genus Nitrospira (8–30% of the community), while the thaumarchaeal OTU was classified as Candidatus Nitrosopumilus (11–15% of the community). Members of these three microbial taxa are known to form associations with various marine animals such as sponges or snails where they contribute to nitrogen metabolism or the decomposition of biopolymers. A similar role is assumed to be played by the microorganisms associated with Tegulaherpia sp.
format: application/pdf
format: text/html
creator: Elena Vortsepneva
creator: Pierre Chevaldonné
creator: Alexandra Klyukina
creator: Elizaveta Naduvaeva
creator: Christiane Todt
creator: Anna Zhadan
creator: Alexander Tzetlin
creator: Ilya Kublanov
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12655
publisher: PeerJ Inc.
rights: © 2021 Vortsepneva et al.
abstract: The first cave-dwelling Solenogastres—marine shell-less worm-like mollusks—were sampled from Mediterranean marine caves floor silt in the Marseille area. The mollusks were 1.5 mm in length, had a transparent body with shiny spicules and appear to represent a new Tegulaherpia species. Electron microscopy revealed a high number of microbial cells, located on the surface of the spicules as well as in the cuticle of Tegulaherpia sp. The observed microbial cells varied in morphology and were unequally distributed through the cuticle, reaching a highest density on the dorsal and lateral sides and being practically absent on the ventral side. Next Generation Sequencing (NGS) of V4 region of 16S rRNA gene amplicons, obtained from the DNA samples of whole bodies of Tegulaherpia sp. revealed three dominating microorganisms, two of which were bacteria of Bacteroidetes and Nitrospirae phyla, while the third one represented archaea of Thaumarchaeota phylum. The Operational Taxonomic Unit (OTU), affiliated with Bacteroidetes was an uncultured bacteria of the family Saprospiraceae (93–95% of Bacteroidetes and 25–44% of the total community, depending on sample), OTU, affiliated with Nitrospirae belonged to the genus Nitrospira (8–30% of the community), while the thaumarchaeal OTU was classified as Candidatus Nitrosopumilus (11–15% of the community). Members of these three microbial taxa are known to form associations with various marine animals such as sponges or snails where they contribute to nitrogen metabolism or the decomposition of biopolymers. A similar role is assumed to be played by the microorganisms associated with Tegulaherpia sp.
bibliographic citation: Vortsepneva et al. (2021) Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca). PeerJ 9:e12655 https://doi.org/10.7717/peerj.12655
date submitted: 2021-09-20
date accepted: 2021-11-29
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vortsepneva
  given name: Elena
author list: Agent
  family name: Chevaldonné
  given name: Pierre
author list: Agent
  family name: Klyukina
  given name: Alexandra
author list: Agent
  family name: Naduvaeva
  given name: Elizaveta
author list: Agent
  family name: Todt
  given name: Christiane
author list: Agent
  family name: Zhadan
  given name: Anna
author list: Agent
  family name: Tzetlin
  given name: Alexander
author list: Agent
  family name: Kublanov
  given name: Ilya
doi: 10.7717/peerj.12655
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: ©2021 Vortsepneva et al.
attribution name: Vortsepneva et al.

The characteristics and roles of antimicrobial peptides as potential treatment for antibiotic-resistant pathogens: a review
type: item
type: AcademicArticle
description: The emergence of antibiotic-resistant bacteria has become a significant and ever-increasing threat to global public health, increasing both morbidity and mortality rates, and the financial burden on health services. Infection by drug-resistant bacteria is anticipated to contribute to the demise of almost 10 million people by the year 2050 unless a competent and effective response is devised to engage with this issue. The emergence and spread of resistance are commonly caused by the excessive or inappropriate use of antibiotics and substandard pharmaceuticals. It arises when pathogens adapt to different conditions and develop self-defence mechanisms. Currently, novel antimicrobial peptides (AMPs) have been reported to be the sole cure for some clinical cases of infectious diseases such as sepsis and skin infections, although these agents may, on occasion, require administration together with an adjunctive low-dose antibiotic. Although AMPs are a promising alternative form of anti-microbial therapy and easily applied in the medical sector, they still have limitations that should not be taken lightly. Hence, this review explores the characteristics, advantages and disadvantages of AMPs for their potential in treating antibiotic-resistant pathogens.
format: application/pdf
format: text/html
creator: Nurul Hana Zainal Baharin
creator: Nur Fadhilah Khairil Mokhtar
creator: Mohd Nasir Mohd Desa
creator: Banulata Gopalsamy
creator: Nor Nadiha Mohd Zaki
creator: Mohd Hafis Yuswan
creator: AbdulRahman Muthanna
creator: Nurul Diana Dzaraly
creator: Sahar Abbasiliasi
creator: Amalia Mohd Hashim
creator: Muhamad Shirwan Abdullah Sani
creator: Shuhaimi Mustafa
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.12193
publisher: PeerJ Inc.
rights: © 2021 Zainal Baharin et al.
abstract: The emergence of antibiotic-resistant bacteria has become a significant and ever-increasing threat to global public health, increasing both morbidity and mortality rates, and the financial burden on health services. Infection by drug-resistant bacteria is anticipated to contribute to the demise of almost 10 million people by the year 2050 unless a competent and effective response is devised to engage with this issue. The emergence and spread of resistance are commonly caused by the excessive or inappropriate use of antibiotics and substandard pharmaceuticals. It arises when pathogens adapt to different conditions and develop self-defence mechanisms. Currently, novel antimicrobial peptides (AMPs) have been reported to be the sole cure for some clinical cases of infectious diseases such as sepsis and skin infections, although these agents may, on occasion, require administration together with an adjunctive low-dose antibiotic. Although AMPs are a promising alternative form of anti-microbial therapy and easily applied in the medical sector, they still have limitations that should not be taken lightly. Hence, this review explores the characteristics, advantages and disadvantages of AMPs for their potential in treating antibiotic-resistant pathogens.
bibliographic citation: Zainal Baharin et al. (2021) The characteristics and roles of antimicrobial peptides as potential treatment for antibiotic-resistant pathogens: a review. PeerJ 9:e12193 https://doi.org/10.7717/peerj.12193
date submitted: 2021-03-12
date accepted: 2021-08-31
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zainal Baharin
  given name: Nurul Hana
author list: Agent
  family name: Khairil Mokhtar
  given name: Nur Fadhilah
author list: Agent
  family name: Mohd Desa
  given name: Mohd Nasir
author list: Agent
  family name: Gopalsamy
  given name: Banulata
author list: Agent
  family name: Mohd Zaki
  given name: Nor Nadiha
author list: Agent
  family name: Yuswan
  given name: Mohd Hafis
author list: Agent
  family name: Muthanna
  given name: AbdulRahman
author list: Agent
  family name: Dzaraly
  given name: Nurul Diana
author list: Agent
  family name: Abbasiliasi
  given name: Sahar
author list: Agent
  family name: Mohd Hashim
  given name: Amalia
author list: Agent
  family name: Abdullah Sani
  given name: Muhamad Shirwan
author list: Agent
  family name: Mustafa
  given name: Shuhaimi
doi: 10.7717/peerj.12193
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: ©2021 Zainal Baharin et al.
attribution name: Zainal Baharin et al.

No relevant differences in conditioned pain modulation effects between parallel and sequential test design. A cross-sectional observational study
type: item
type: AcademicArticle
description: Background Conditioned pain modulation (CPM) is measured by comparing pain induced by a test stimulus with pain induced by the same test stimulus, either during (parallel design) or after (sequential design) the conditioning stimulus. Whether design, conditioning stimulus intensity and test stimulus selection affect CPM remains unclear. Methods CPM effects were evaluated in healthy participants (N = 89) at the neck, forearm and lower leg using the cold pressor test as the conditioning stimulus. In three separate experiments, we compared the impact of (1) design (sequential versus parallel), (2) conditioning stimulus intensity (VAS 40/100 versus VAS 60/100), and (3) test stimulus selection (single versus dual, i.e., mechanical and thermal). Statistical analyses of the main effect of design (adjusted for order) and experiment were conducted using linear mixed models with random intercepts. Results No significant differences were identified in absolute CPM data. In relative CPM data, a sequential design resulted in a slightly lower CPM effect compared to a parallel design, and only with a mechanical test stimulus at the neck (−6.1%; 95% CI [−10.1 to −2.1]) and lower leg (−5.9%; 95% CI [−11.7 to −0.1]) but not forearm (−4.5%; 95% CI [−9.0 to 0.1]). Conditioning stimulus intensity and test stimulus selection did not influence the CPM effect nor the difference in CPM effects derived from parallel versus sequential designs. Conclusions Differences in CPM effects between protocols were minimal or absent. A parallel design may lead to a minimally higher relative CPM effect when using a mechanical test stimulus. The conditioning stimulus intensities assessed in this study and performing two test stimuli did not substantially influence the differences between designs nor the magnitude of the CPM effect.
format: application/pdf
format: text/html
creator: Roland R. Reezigt
creator: Sjoerd C. Kielstra
creator: Michel W. Coppieters
creator: Gwendolyne G.M. Scholten-Peeters
subject: Anesthesiology and Pain Management
subject: Kinesiology
subject: Neurology
subject: Translational Medicine
description: doi:10.7717/peerj.12330
publisher: PeerJ Inc.
rights: © 2021 Reezigt et al.
abstract: Background Conditioned pain modulation (CPM) is measured by comparing pain induced by a test stimulus with pain induced by the same test stimulus, either during (parallel design) or after (sequential design) the conditioning stimulus. Whether design, conditioning stimulus intensity and test stimulus selection affect CPM remains unclear. Methods CPM effects were evaluated in healthy participants (N = 89) at the neck, forearm and lower leg using the cold pressor test as the conditioning stimulus. In three separate experiments, we compared the impact of (1) design (sequential versus parallel), (2) conditioning stimulus intensity (VAS 40/100 versus VAS 60/100), and (3) test stimulus selection (single versus dual, i.e., mechanical and thermal). Statistical analyses of the main effect of design (adjusted for order) and experiment were conducted using linear mixed models with random intercepts. Results No significant differences were identified in absolute CPM data. In relative CPM data, a sequential design resulted in a slightly lower CPM effect compared to a parallel design, and only with a mechanical test stimulus at the neck (−6.1%; 95% CI [−10.1 to −2.1]) and lower leg (−5.9%; 95% CI [−11.7 to −0.1]) but not forearm (−4.5%; 95% CI [−9.0 to 0.1]). Conditioning stimulus intensity and test stimulus selection did not influence the CPM effect nor the difference in CPM effects derived from parallel versus sequential designs. Conclusions Differences in CPM effects between protocols were minimal or absent. A parallel design may lead to a minimally higher relative CPM effect when using a mechanical test stimulus. The conditioning stimulus intensities assessed in this study and performing two test stimuli did not substantially influence the differences between designs nor the magnitude of the CPM effect.
bibliographic citation: Reezigt et al. (2021) No relevant differences in conditioned pain modulation effects between parallel and sequential test design. A cross-sectional observational study. PeerJ 9:e12330 https://doi.org/10.7717/peerj.12330
date submitted: 2021-06-01
date accepted: 2021-09-27
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reezigt
  given name: Roland R.
author list: Agent
  family name: Kielstra
  given name: Sjoerd C.
author list: Agent
  family name: Coppieters
  given name: Michel W.
author list: Agent
  family name: Scholten-Peeters
  given name: Gwendolyne G.M.
doi: 10.7717/peerj.12330
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: ©2021 Reezigt et al.
attribution name: Reezigt et al.

Identification of quantitative trait loci underlying five major agronomic traits of soybean in three biparental populations by specific length amplified fragment sequencing (SLAF-seq)
type: item
type: AcademicArticle
description: Flowering time, plant height, branch number, node numbers of main stem and pods per plant are important agronomic traits related to photoperiodic sensitivity, plant type and yield of soybean, which are controlled by multiple genes or quantitative trait loci (QTL). The main purpose of this study is to identify new QTL for five major agronomic traits, especially for flowering time. Three biparental populations were developed by crossing cultivars from northern and central China. Specific loci amplified fragment sequencing (SLAF-seq) was used to construct linkage map and QTL mapping was carried out. A total of 10 QTL for flowering time were identified in three populations, some of which were related to E1 and E2 genes or the other reported QTL listed in Soybase. In the Y159 population (Xudou No.9 × Kenfeng No.16), QTL for flowering time on chromosome 4, qFT4_1 and qFT4_2 were new. Compared with the QTL reported in Soybase, 1 QTL for plant height (PH), 3 QTL for branch number (BR), 5 QTL for node numbers of main stem, and 3 QTL for pods per plant were new QTL. Major E genes were frequently detected in different populations indicating that major the E loci had a great effect on flowering time and adaptation of soybean. Therefore, in order to further clone minor genes or QTL, it may be of great significance to carefully select the genotypes of known loci. These results may lay a foundation for fine mapping and clone of QTL/genes related to plant-type, provided a basis for high yield breeding of soybean.
format: application/pdf
format: text/html
creator: Bo Hu
creator: Yuqiu Li
creator: Hongyan Wu
creator: Hong Zhai
creator: Kun Xu
creator: Yi Gao
creator: Jinlong Zhu
creator: Yuzhuo Li
creator: Zhengjun Xia
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.12416
publisher: PeerJ Inc.
rights: © 2021 Hu et al.
abstract: Flowering time, plant height, branch number, node numbers of main stem and pods per plant are important agronomic traits related to photoperiodic sensitivity, plant type and yield of soybean, which are controlled by multiple genes or quantitative trait loci (QTL). The main purpose of this study is to identify new QTL for five major agronomic traits, especially for flowering time. Three biparental populations were developed by crossing cultivars from northern and central China. Specific loci amplified fragment sequencing (SLAF-seq) was used to construct linkage map and QTL mapping was carried out. A total of 10 QTL for flowering time were identified in three populations, some of which were related to E1 and E2 genes or the other reported QTL listed in Soybase. In the Y159 population (Xudou No.9 × Kenfeng No.16), QTL for flowering time on chromosome 4, qFT4_1 and qFT4_2 were new. Compared with the QTL reported in Soybase, 1 QTL for plant height (PH), 3 QTL for branch number (BR), 5 QTL for node numbers of main stem, and 3 QTL for pods per plant were new QTL. Major E genes were frequently detected in different populations indicating that major the E loci had a great effect on flowering time and adaptation of soybean. Therefore, in order to further clone minor genes or QTL, it may be of great significance to carefully select the genotypes of known loci. These results may lay a foundation for fine mapping and clone of QTL/genes related to plant-type, provided a basis for high yield breeding of soybean.
bibliographic citation: Hu et al. (2021) Identification of quantitative trait loci underlying five major agronomic traits of soybean in three biparental populations by specific length amplified fragment sequencing (SLAF-seq). PeerJ 9:e12416 https://doi.org/10.7717/peerj.12416
date submitted: 2020-07-09
date accepted: 2021-10-10
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Bo
author list: Agent
  family name: Li
  given name: Yuqiu
author list: Agent
  family name: Wu
  given name: Hongyan
author list: Agent
  family name: Zhai
  given name: Hong
author list: Agent
  family name: Xu
  given name: Kun
author list: Agent
  family name: Gao
  given name: Yi
author list: Agent
  family name: Zhu
  given name: Jinlong
author list: Agent
  family name: Li
  given name: Yuzhuo
author list: Agent
  family name: Xia
  given name: Zhengjun
doi: 10.7717/peerj.12416
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: © 2021 Hu et al.
attribution name: Hu et al.

Occupancy of wild southern pig-tailed macaques in intact and degraded forests in Peninsular Malaysia
type: item
type: AcademicArticle
description: Deforestation is a major threat to terrestrial tropical ecosystems, particularly in Southeast Asia where human activities have dramatic consequences for the survival of many species. However, responses of species to anthropogenic impact are highly variable. In order to establish effective conservation strategies, it is critical to determine a species’ ability to persist in degraded habitats. Here, we used camera trapping data to provide the first insights into the temporal and spatial distribution of southern pig-tailed macaques (Macaca nemestrina, listed as ‘Vulnerable’ by the IUCN) across intact and degraded forest habitats in Peninsular Malaysia, with a particular focus on the effects of clear-cutting and selective logging on macaque occupancy. Specifically, we found a 10% decline in macaque site occupancy in the highly degraded Pasoh Forest Reserve from 2013 to 2017. This may be strongly linked to the macaques’ sensitivity to intensive disturbance through clear-cutting, which significantly increased the probability that M. nemestrina became locally extinct at a previously occupied site. However, we found no clear relationship between moderate disturbance, i.e., selective logging, and the macaques’ local extinction probability or site occupancy in the Pasoh Forest Reserve and Belum-Temengor Forest Complex. Further, an identical age and sex structure of macaques in selectively logged and completely undisturbed habitat types within the Belum-Temengor Forest Complex indicated that the macaques did not show increased mortality or declining birth rates when exposed to selective logging. Overall, this suggests that low to moderately disturbed forests may still constitute valuable habitats that support viable populations of M. nemestrina, and thus need to be protected against further degradation. Our results emphasize the significance of population monitoring through camera trapping for understanding the ability of threatened species to cope with anthropogenic disturban…
format: application/pdf
format: text/html
creator: Anna Holzner
creator: D. Mark Rayan
creator: Jonathan Moore
creator: Cedric Kai Wei Tan
creator: Laura Clart
creator: Lars Kulik
creator: Hjalmar Kühl
creator: Nadine Ruppert
creator: Anja Widdig
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12462
publisher: PeerJ Inc.
rights: © 2021 Holzner et al.
abstract: Deforestation is a major threat to terrestrial tropical ecosystems, particularly in Southeast Asia where human activities have dramatic consequences for the survival of many species. However, responses of species to anthropogenic impact are highly variable. In order to establish effective conservation strategies, it is critical to determine a species’ ability to persist in degraded habitats. Here, we used camera trapping data to provide the first insights into the temporal and spatial distribution of southern pig-tailed macaques (Macaca nemestrina, listed as ‘Vulnerable’ by the IUCN) across intact and degraded forest habitats in Peninsular Malaysia, with a particular focus on the effects of clear-cutting and selective logging on macaque occupancy. Specifically, we found a 10% decline in macaque site occupancy in the highly degraded Pasoh Forest Reserve from 2013 to 2017. This may be strongly linked to the macaques’ sensitivity to intensive disturbance through clear-cutting, which significantly increased the probability that M. nemestrina became locally extinct at a previously occupied site. However, we found no clear relationship between moderate disturbance, i.e., selective logging, and the macaques’ local extinction probability or site occupancy in the Pasoh Forest Reserve and Belum-Temengor Forest Complex. Further, an identical age and sex structure of macaques in selectively logged and completely undisturbed habitat types within the Belum-Temengor Forest Complex indicated that the macaques did not show increased mortality or declining birth rates when exposed to selective logging. Overall, this suggests that low to moderately disturbed forests may still constitute valuable habitats that support viable populations of M. nemestrina, and thus need to be protected against further degradation. Our results emphasize the significance of population monitoring through camera trapping for understanding the ability of threatened species to cope with anthropogenic disturban…
bibliographic citation: Holzner et al. (2021) Occupancy of wild southern pig-tailed macaques in intact and degraded forests in Peninsular Malaysia. PeerJ 9:e12462 https://doi.org/10.7717/peerj.12462
date submitted: 2021-04-15
date accepted: 2021-10-18
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holzner
  given name: Anna
author list: Agent
  family name: Rayan
  given name: D. Mark
author list: Agent
  family name: Moore
  given name: Jonathan
author list: Agent
  family name: Tan
  given name: Cedric Kai Wei
author list: Agent
  family name: Clart
  given name: Laura
author list: Agent
  family name: Kulik
  given name: Lars
author list: Agent
  family name: Kühl
  given name: Hjalmar
author list: Agent
  family name: Ruppert
  given name: Nadine
author list: Agent
  family name: Widdig
  given name: Anja
doi: 10.7717/peerj.12462
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: © 2021 Holzner et al.
attribution name: Holzner et al.

The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain
type: item
type: AcademicArticle
description: Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.
format: application/pdf
format: text/html
creator: Mónica Torres-Beltrán
creator: Lluvia Vargas-Gastélum
creator: Dante Magdaleno-Moncayo
creator: Meritxell Riquelme
creator: Juan Carlos Herguera-García
creator: Alejandra Prieto-Davó
creator: Asunción Lago-Lestón
subject: Bioinformatics
subject: Marine Biology
subject: Microbiology
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.12474
publisher: PeerJ Inc.
rights: © 2021 Torres-Beltrán et al.
abstract: Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.
bibliographic citation: Torres-Beltrán et al. (2021) The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PeerJ 9:e12474 https://doi.org/10.7717/peerj.12474
date submitted: 2021-07-15
date accepted: 2021-10-20
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Torres-Beltrán
  given name: Mónica
author list: Agent
  family name: Vargas-Gastélum
  given name: Lluvia
author list: Agent
  family name: Magdaleno-Moncayo
  given name: Dante
author list: Agent
  family name: Riquelme
  given name: Meritxell
author list: Agent
  family name: Herguera-García
  given name: Juan Carlos
author list: Agent
  family name: Prieto-Davó
  given name: Alejandra
author list: Agent
  family name: Lago-Lestón
  given name: Asunción
doi: 10.7717/peerj.12474
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: ©2021 Torres-Beltrán et al.
attribution name: Torres-Beltrán et al.

Local ancestry prediction with PyLAE
type: item
type: AcademicArticle
description: Summary We developed PyLAE, a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimating many parameters, it can process thousands of genomes within a day. PyLAE can run on phased or unphased genomic data. We have shown how PyLAE can be applied to the identification of differentially enriched pathways between populations. The local ancestry approach results in higher enrichment scores compared to whole-genome approaches. We benchmarked PyLAE using the 1000 Genomes dataset, comparing the aggregated predictions with the global admixture results and the current gold standard program RFMix. Computational efficiency, minimal requirements for data pre-processing, straightforward presentation of results, and ease of installation make PyLAE a valuable tool to study admixed populations. Availability and implementation The source code and installation manual are available at https://github.com/smetam/pylae.
format: application/pdf
format: text/html
creator: Nikita Moshkov
creator: Aleksandr Smetanin
creator: Tatiana V. Tatarinova
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.12502
publisher: PeerJ Inc.
rights: © 2021 Moshkov et al.
abstract: Summary We developed PyLAE, a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimating many parameters, it can process thousands of genomes within a day. PyLAE can run on phased or unphased genomic data. We have shown how PyLAE can be applied to the identification of differentially enriched pathways between populations. The local ancestry approach results in higher enrichment scores compared to whole-genome approaches. We benchmarked PyLAE using the 1000 Genomes dataset, comparing the aggregated predictions with the global admixture results and the current gold standard program RFMix. Computational efficiency, minimal requirements for data pre-processing, straightforward presentation of results, and ease of installation make PyLAE a valuable tool to study admixed populations. Availability and implementation The source code and installation manual are available at https://github.com/smetam/pylae.
bibliographic citation: Moshkov et al. (2021) Local ancestry prediction with PyLAE. PeerJ 9:e12502 https://doi.org/10.7717/peerj.12502
date submitted: 2020-12-10
date accepted: 2021-10-26
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moshkov
  given name: Nikita
author list: Agent
  family name: Smetanin
  given name: Aleksandr
author list: Agent
  family name: Tatarinova
  given name: Tatiana V.
doi: 10.7717/peerj.12502
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: © 2021 Moshkov et al.
attribution name: Moshkov et al.

Growth and feeding ecology of coniform conodonts
type: item
type: AcademicArticle
description: Conodonts were the first vertebrates to develop mineralized dental tools, known as elements. Recent research suggests that conodonts were macrophagous predators and/or scavengers but we do not know how this feeding habit emerged in the earliest coniform conodonts, since most studies focus on the derived, ‘complex’ conodonts. Previous modelling of element position and mechanical properties indicate they were capable of food processing. A direct test would be provided through evidence of in vivo element crown tissue damage or through in vivo incorporated chemical proxies for a shift in their trophic position during ontogeny. Here we focus on coniform elements from two conodont taxa, the phylogenetically primitive Proconodontus muelleri Miller, 1969 from the late Cambrian and the more derived Panderodus equicostatus Rhodes, 1954 from the Silurian. Proposing that this extremely small sample is, however, representative for these taxa, we aim to describe in detail the growth of an element from each of these taxa in order to the test the following hypotheses: (1) Panderodus and Proconodontus processed hard food, which led to damage of their elements consistent with prey capture function; and (2) both genera shifted towards higher trophic levels during ontogeny. We employed backscatter electron (BSE) imaging, energy-dispersive X-ray spectroscopy (EDX) and synchrotron radiation X-ray tomographic microscopy (SRXTM) to identify growth increments, wear and damage surfaces, and the Sr/Ca ratio in bioapatite as a proxy for the trophic position. Using these data, we can identify whether they exhibit determinate or indeterminate growth and whether both species followed linear or allometric growth dynamics. Growth increments (27 in Pa. equicostatus and 58 in Pr. muelleri) were formed in bundles of 4–7 increments in Pa. equicostatus and 7–9 in Pr. muelleri. We interpret the bundles as analogous to Retzius periodicity in vertebrate teeth. Based on applied optimal resource allocation m…
format: application/pdf
format: text/html
creator: Isabella Leonhard
creator: Bryan Shirley
creator: Duncan J. E. Murdock
creator: John Repetski
creator: Emilia Jarochowska
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.12505
publisher: PeerJ Inc.
rights: © 2021 Leonhard et al.
abstract: Conodonts were the first vertebrates to develop mineralized dental tools, known as elements. Recent research suggests that conodonts were macrophagous predators and/or scavengers but we do not know how this feeding habit emerged in the earliest coniform conodonts, since most studies focus on the derived, ‘complex’ conodonts. Previous modelling of element position and mechanical properties indicate they were capable of food processing. A direct test would be provided through evidence of in vivo element crown tissue damage or through in vivo incorporated chemical proxies for a shift in their trophic position during ontogeny. Here we focus on coniform elements from two conodont taxa, the phylogenetically primitive Proconodontus muelleri Miller, 1969 from the late Cambrian and the more derived Panderodus equicostatus Rhodes, 1954 from the Silurian. Proposing that this extremely small sample is, however, representative for these taxa, we aim to describe in detail the growth of an element from each of these taxa in order to the test the following hypotheses: (1) Panderodus and Proconodontus processed hard food, which led to damage of their elements consistent with prey capture function; and (2) both genera shifted towards higher trophic levels during ontogeny. We employed backscatter electron (BSE) imaging, energy-dispersive X-ray spectroscopy (EDX) and synchrotron radiation X-ray tomographic microscopy (SRXTM) to identify growth increments, wear and damage surfaces, and the Sr/Ca ratio in bioapatite as a proxy for the trophic position. Using these data, we can identify whether they exhibit determinate or indeterminate growth and whether both species followed linear or allometric growth dynamics. Growth increments (27 in Pa. equicostatus and 58 in Pr. muelleri) were formed in bundles of 4–7 increments in Pa. equicostatus and 7–9 in Pr. muelleri. We interpret the bundles as analogous to Retzius periodicity in vertebrate teeth. Based on applied optimal resource allocation m…
bibliographic citation: Leonhard et al. (2021) Growth and feeding ecology of coniform conodonts. PeerJ 9:e12505 https://doi.org/10.7717/peerj.12505
date submitted: 2021-08-04
date accepted: 2021-10-26
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leonhard
  given name: Isabella
author list: Agent
  family name: Shirley
  given name: Bryan
author list: Agent
  family name: Murdock
  given name: Duncan J. E.
author list: Agent
  family name: Repetski
  given name: John
author list: Agent
  family name: Jarochowska
  given name: Emilia
doi: 10.7717/peerj.12505
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: © 2021 Leonhard et al.
attribution name: Leonhard et al.

A longitudinal study of the impact of COVID-19 restrictions on students’ health behavior, mental health and emotional well-being
type: item
type: AcademicArticle
description: Background COVID-related restrictions impacted the lives of students on and off campus during Academic Year 2020/2021. Methods Our study collected data on student health behavior and habits as well as their mental and emotional health using anonymous surveys. We compared these data with data collected prior to COVID in the longitudinal part of our study (n = 721) and analyzed them for the cross-sectional part of the study (n = 506). Results The longitudinal data show a significant difference for some student behaviors and habits, such as sleeping habits, physical activity, breakfast consumption, time spent online or playing video games, vaping, and marijuana use, during the COVID pandemic compared with pre-COVID data. Respondents also reported a significant increase in difficulty concentrating, remembering, or making decisions, as well as being impacted by feelings of sadness or hopelessness. Yet, there was no increase in the proportion of respondents considering, planning or attempting suicide during COVID. The cross-sectional data illuminate the negative effect of the overall situation and the restrictions on students’ mental and emotional well-being. Three-quarters of respondents reported having craved human interaction during the past six months, more than half felt that their mental/emotional health had been impacted by the lack of social events or the switch to virtual (online) teaching. Two-thirds or more of respondents also expressed that they felt less connected to their peers and less motivated in their studies than in previous semesters. Fifty percent or more of respondents selected anxious, stressed, overwhelmed, disconnected, tired, and fatigued as words that best described their emotional state during the pandemic. Conclusions The impact of COVID-related restrictions on students’ behaviors and habits as well as their mental and emotional health was less severe than one would have expected based on studies during the early stage of the pandemic. While s…
format: application/pdf
format: text/html
creator: Peter R. Reuter
creator: Bridget L. Forster
creator: Bethany J. Kruger
subject: Mental Health
subject: Environmental Health
subject: COVID-19
description: doi:10.7717/peerj.12528
publisher: PeerJ Inc.
rights: © 2021 Reuter et al.
abstract: Background COVID-related restrictions impacted the lives of students on and off campus during Academic Year 2020/2021. Methods Our study collected data on student health behavior and habits as well as their mental and emotional health using anonymous surveys. We compared these data with data collected prior to COVID in the longitudinal part of our study (n = 721) and analyzed them for the cross-sectional part of the study (n = 506). Results The longitudinal data show a significant difference for some student behaviors and habits, such as sleeping habits, physical activity, breakfast consumption, time spent online or playing video games, vaping, and marijuana use, during the COVID pandemic compared with pre-COVID data. Respondents also reported a significant increase in difficulty concentrating, remembering, or making decisions, as well as being impacted by feelings of sadness or hopelessness. Yet, there was no increase in the proportion of respondents considering, planning or attempting suicide during COVID. The cross-sectional data illuminate the negative effect of the overall situation and the restrictions on students’ mental and emotional well-being. Three-quarters of respondents reported having craved human interaction during the past six months, more than half felt that their mental/emotional health had been impacted by the lack of social events or the switch to virtual (online) teaching. Two-thirds or more of respondents also expressed that they felt less connected to their peers and less motivated in their studies than in previous semesters. Fifty percent or more of respondents selected anxious, stressed, overwhelmed, disconnected, tired, and fatigued as words that best described their emotional state during the pandemic. Conclusions The impact of COVID-related restrictions on students’ behaviors and habits as well as their mental and emotional health was less severe than one would have expected based on studies during the early stage of the pandemic. While s…
bibliographic citation: Reuter et al. (2021) A longitudinal study of the impact of COVID-19 restrictions on students’ health behavior, mental health and emotional well-being. PeerJ 9:e12528 https://doi.org/10.7717/peerj.12528
date submitted: 2021-07-27
date accepted: 2021-11-01
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reuter
  given name: Peter R.
author list: Agent
  family name: Forster
  given name: Bridget L.
author list: Agent
  family name: Kruger
  given name: Bethany J.
doi: 10.7717/peerj.12528
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: ©2021 Reuter et al.
attribution name: Reuter et al.

Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat
type: item
type: AcademicArticle
description: The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.
format: application/pdf
format: text/html
creator: Xiaowei Jia
creator: Xuyang Si
creator: Yangyang Jia
creator: Hongyan Zhang
creator: Shijun Tian
creator: Wenjing Li
creator: Ke Zhang
creator: Yanyun Pan
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12480
publisher: PeerJ Inc.
rights: © 2021 Jia et al.
abstract: The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.
bibliographic citation: Jia et al. (2021) Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat. PeerJ 9:e12480 https://doi.org/10.7717/peerj.12480
date submitted: 2020-12-16
date accepted: 2021-10-21
issued: 2021-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Xiaowei
author list: Agent
  family name: Si
  given name: Xuyang
author list: Agent
  family name: Jia
  given name: Yangyang
author list: Agent
  family name: Zhang
  given name: Hongyan
author list: Agent
  family name: Tian
  given name: Shijun
author list: Agent
  family name: Li
  given name: Wenjing
author list: Agent
  family name: Zhang
  given name: Ke
author list: Agent
  family name: Pan
  given name: Yanyun
doi: 10.7717/peerj.12480
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-14
copyright: ©2021 Jia et al.
attribution name: Jia et al.

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