PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication
items: MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions
items: Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan
items: Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study
items: ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review
items: The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico
items: Effect of modified pomace on copper migration via riverbank soil in southwest China
items: PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
items: Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China
items: Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan

Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication
type: item
type: AcademicArticle
description: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.
format: application/pdf
format: text/html
creator: Susana Marcela Simancas-Giraldo
creator: Nan Xiang
creator: Meghan Moger Kennedy
creator: Rassil Nafeh
creator: Edoardo Zelli
creator: Christian Wild
subject: Marine Biology
subject: Climate Change Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.11663
publisher: PeerJ Inc.
rights: © 2021 Simancas-Giraldo et al.
abstract: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.
bibliographic citation: Simancas-Giraldo et al. (2021) Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication. PeerJ 9:e11663 https://doi.org/10.7717/peerj.11663
date submitted: 2020-12-09
date accepted: 2021-06-01
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simancas-Giraldo
  given name: Susana Marcela
author list: Agent
  family name: Xiang
  given name: Nan
author list: Agent
  family name: Kennedy
  given name: Meghan Moger
author list: Agent
  family name: Nafeh
  given name: Rassil
author list: Agent
  family name: Zelli
  given name: Edoardo
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.11663
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Simancas-Giraldo et al.
attribution name: Simancas-Giraldo et al.

MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions
type: item
type: AcademicArticle
description: Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use.
format: application/pdf
format: text/html
creator: Xiaoying Wang
creator: Eva Cheng
creator: Ian S. Burnett
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Computational Science
subject: Freshwater Biology
description: doi:10.7717/peerj.11750
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use.
bibliographic citation: Wang et al. (2021) MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions. PeerJ 9:e11750 https://doi.org/10.7717/peerj.11750
date submitted: 2020-11-25
date accepted: 2021-06-19
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoying
author list: Agent
  family name: Cheng
  given name: Eva
author list: Agent
  family name: Burnett
  given name: Ian S.
doi: 10.7717/peerj.11750
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Wang et al.
attribution name: Wang et al.

Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan
type: item
type: AcademicArticle
description: Background International and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan. Methods A total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires. Results On the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months post…
format: application/pdf
format: text/html
creator: Keiko Nanishi
creator: Joseph Green
creator: Hiroko Hongo
subject: Nursing
subject: Nutrition
subject: Pediatrics
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.11779
publisher: PeerJ Inc.
rights: © 2021 Nanishi et al.
abstract: Background International and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan. Methods A total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires. Results On the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months post…
bibliographic citation: Nanishi et al. (2021) Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan. PeerJ 9:e11779 https://doi.org/10.7717/peerj.11779
date submitted: 2020-12-16
date accepted: 2021-06-24
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Nanishi
  given name: Keiko
author list: Agent
  family name: Green
  given name: Joseph
author list: Agent
  family name: Hongo
  given name: Hiroko
doi: 10.7717/peerj.11779
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Nanishi et al.
attribution name: Nanishi et al.

Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study
type: item
type: AcademicArticle
description: Background The relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly. Methods A case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected. Results Our study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001).
format: application/pdf
format: text/html
creator: Yunfang Zhou
creator: Zhenyu Ma
creator: Cun-Xian Jia
creator: Liang Zhou
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11801
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Background The relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly. Methods A case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected. Results Our study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001).
bibliographic citation: Zhou et al. (2021) Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study. PeerJ 9:e11801 https://doi.org/10.7717/peerj.11801
date submitted: 2020-07-24
date accepted: 2021-06-26
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yunfang
author list: Agent
  family name: Ma
  given name: Zhenyu
author list: Agent
  family name: Jia
  given name: Cun-Xian
author list: Agent
  family name: Zhou
  given name: Liang
doi: 10.7717/peerj.11801
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Zhou et al.
attribution name: Zhou et al.

ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review
type: item
type: AcademicArticle
description: Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker…
format: application/pdf
format: text/html
creator: Richard Dormatey
creator: Chao Sun
creator: Kazim Ali
creator: Sajid Fiaz
creator: Derong Xu
creator: Alejandro Calderón-Urrea
creator: Zhenzhen Bi
creator: Junlian Zhang
creator: Jiangping Bai
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.11809
publisher: PeerJ Inc.
rights: © 2021 Dormatey et al.
abstract: Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker…
bibliographic citation: Dormatey et al. (2021) ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review. PeerJ 9:e11809 https://doi.org/10.7717/peerj.11809
date submitted: 2020-12-15
date accepted: 2021-06-27
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dormatey
  given name: Richard
author list: Agent
  family name: Sun
  given name: Chao
author list: Agent
  family name: Ali
  given name: Kazim
author list: Agent
  family name: Fiaz
  given name: Sajid
author list: Agent
  family name: Xu
  given name: Derong
author list: Agent
  family name: Calderón-Urrea
  given name: Alejandro
author list: Agent
  family name: Bi
  given name: Zhenzhen
author list: Agent
  family name: Zhang
  given name: Junlian
author list: Agent
  family name: Bai
  given name: Jiangping
doi: 10.7717/peerj.11809
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Dormatey et al.
attribution name: Dormatey et al.

The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico
type: item
type: AcademicArticle
description: The vulnerability of a fish stock to becoming overfished is dependent upon biological traits that influence productivity and external factors that determine susceptibility or exposure to fishing effort. While a suite of life history traits are traditionally incorporated into management efforts due to their direct association with vulnerability to overfishing, spawning behavioral traits are seldom considered. We synthesized the existing biological and fisheries information of 28 fish stocks in the U.S. Gulf of Mexico to investigate relationships between life history traits, spawning behavioral traits, management regulations, and vulnerability to fishing during the spawning season. Our results showed that spawning behavioral traits were not correlated with life history traits but improved identification of species that have been historically overfished. Species varied widely in their intrinsic vulnerability to fishing during spawning in association with a broad range of behavioral strategies. Extrinsic vulnerability was high for nearly all species due to exposure to fishing during the spawning season and few management measures in place to protect spawning fish. Similarly, several species with the highest vulnerability scores were historically overfished in association with spawning aggregations. The most vulnerable species included several stocks that have not been assessed and should be prioritized for further research and monitoring. Collectively, the results of this study illustrate that spawning behavior is a distinct aspect of fish ecology that is important to consider for predictions of vulnerability and resilience to fisheries exploitation.
format: application/pdf
format: text/html
creator: Christopher R. Biggs
creator: William D. Heyman
creator: Nicholas A. Farmer
creator: Shin’ichi Kobara
creator: Derek G. Bolser
creator: Jan Robinson
creator: Susan K. Lowerre-Barbieri
creator: Brad E. Erisman
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.11814
publisher: PeerJ Inc.
rights: © 2021
abstract: The vulnerability of a fish stock to becoming overfished is dependent upon biological traits that influence productivity and external factors that determine susceptibility or exposure to fishing effort. While a suite of life history traits are traditionally incorporated into management efforts due to their direct association with vulnerability to overfishing, spawning behavioral traits are seldom considered. We synthesized the existing biological and fisheries information of 28 fish stocks in the U.S. Gulf of Mexico to investigate relationships between life history traits, spawning behavioral traits, management regulations, and vulnerability to fishing during the spawning season. Our results showed that spawning behavioral traits were not correlated with life history traits but improved identification of species that have been historically overfished. Species varied widely in their intrinsic vulnerability to fishing during spawning in association with a broad range of behavioral strategies. Extrinsic vulnerability was high for nearly all species due to exposure to fishing during the spawning season and few management measures in place to protect spawning fish. Similarly, several species with the highest vulnerability scores were historically overfished in association with spawning aggregations. The most vulnerable species included several stocks that have not been assessed and should be prioritized for further research and monitoring. Collectively, the results of this study illustrate that spawning behavior is a distinct aspect of fish ecology that is important to consider for predictions of vulnerability and resilience to fisheries exploitation.
bibliographic citation: Biggs et al. (2021) The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico. PeerJ 9:e11814 https://doi.org/10.7717/peerj.11814
date submitted: 2020-12-12
date accepted: 2021-06-28
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Biggs
  given name: Christopher R.
author list: Agent
  family name: Heyman
  given name: William D.
author list: Agent
  family name: Farmer
  given name: Nicholas A.
author list: Agent
  family name: Kobara
  given name: Shin’ichi
author list: Agent
  family name: Bolser
  given name: Derek G.
author list: Agent
  family name: Robinson
  given name: Jan
author list: Agent
  family name: Lowerre-Barbieri
  given name: Susan K.
author list: Agent
  family name: Erisman
  given name: Brad E.
doi: 10.7717/peerj.11814
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27

Effect of modified pomace on copper migration via riverbank soil in southwest China
type: item
type: AcademicArticle
description: To explore the effects of modified pomace on copper migration via the soil on the banks of the rivers in northern Sichuan and Chongqing, fruit pomace (P) and ethylene diamine tetra-acetic acid (EDTA) modified P (EP) were evenly added (1% mass ratio) to the soil samples of Guanyuan, Nanbu, Jialing, and Hechuan from the Jialing River; Mianyang and Suining from the Fu River; and Guangan and Dazhou from the Qu River. The geochemical characteristics and migration rules of copper in different amended soils were simulated by column experiment. Results showed that the permeation time of copper in each soil column was categorized as EP-amended > P-amended > original soil, and the permeation time of amended soil samples at different locations was Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guanyuan > Hechuan. Meanwhile, the average flow rate of copper in each soil column showed a reverse trend with the permeation time. Copper in exchangeable, carbonate, and iron–manganese oxide forms decreased with the increase of vertical depth in the soil column, among which the most evident decreases appeared in the carbonate-bonding form. The copper accumulation in different locations presented a trend of Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guangyuan > Hechuan, and the copper content under the same soil showed EP-amended > P-amended > original soil. The copper proportion of the carbonate form was the highest in each soil sample, followed by the exchangeable form. The proportions of iron-manganese oxide and organic matter forms were relatively small. A significant correlation was observed between the cation exchange capacity and the copper content in exchangeable and carbonate forms. Moreover, total organic carbon and copper contents were negatively correlated.
format: application/pdf
format: text/html
creator: Lingyuan Chen
creator: Touqeer Abbas
creator: Lin Yang
creator: Yao Xu
creator: Hongyan Deng
creator: Lei Hou
creator: Wenbin Li
subject: Soil Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11844
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: To explore the effects of modified pomace on copper migration via the soil on the banks of the rivers in northern Sichuan and Chongqing, fruit pomace (P) and ethylene diamine tetra-acetic acid (EDTA) modified P (EP) were evenly added (1% mass ratio) to the soil samples of Guanyuan, Nanbu, Jialing, and Hechuan from the Jialing River; Mianyang and Suining from the Fu River; and Guangan and Dazhou from the Qu River. The geochemical characteristics and migration rules of copper in different amended soils were simulated by column experiment. Results showed that the permeation time of copper in each soil column was categorized as EP-amended > P-amended > original soil, and the permeation time of amended soil samples at different locations was Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guanyuan > Hechuan. Meanwhile, the average flow rate of copper in each soil column showed a reverse trend with the permeation time. Copper in exchangeable, carbonate, and iron–manganese oxide forms decreased with the increase of vertical depth in the soil column, among which the most evident decreases appeared in the carbonate-bonding form. The copper accumulation in different locations presented a trend of Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guangyuan > Hechuan, and the copper content under the same soil showed EP-amended > P-amended > original soil. The copper proportion of the carbonate form was the highest in each soil sample, followed by the exchangeable form. The proportions of iron-manganese oxide and organic matter forms were relatively small. A significant correlation was observed between the cation exchange capacity and the copper content in exchangeable and carbonate forms. Moreover, total organic carbon and copper contents were negatively correlated.
bibliographic citation: Chen et al. (2021) Effect of modified pomace on copper migration via riverbank soil in southwest China. PeerJ 9:e11844 https://doi.org/10.7717/peerj.11844
date submitted: 2020-10-08
date accepted: 2021-07-01
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Lingyuan
author list: Agent
  family name: Abbas
  given name: Touqeer
author list: Agent
  family name: Yang
  given name: Lin
author list: Agent
  family name: Xu
  given name: Yao
author list: Agent
  family name: Deng
  given name: Hongyan
author list: Agent
  family name: Hou
  given name: Lei
author list: Agent
  family name: Li
  given name: Wenbin
doi: 10.7717/peerj.11844
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Chen et al.
attribution name: Chen et al.

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
type: item
type: AcademicArticle
description: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenom…
format: application/pdf
format: text/html
creator: Maxime Borry
creator: Alexander Hübner
creator: Adam B. Rohrlach
creator: Christina Warinner
subject: Anthropology
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Paleontology
description: doi:10.7717/peerj.11845
publisher: PeerJ Inc.
rights: © 2021 Borry et al.
abstract: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenom…
bibliographic citation: Borry et al. (2021) PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ 9:e11845 https://doi.org/10.7717/peerj.11845
date submitted: 2021-03-29
date accepted: 2021-07-01
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borry
  given name: Maxime
author list: Agent
  family name: Hübner
  given name: Alexander
author list: Agent
  family name: Rohrlach
  given name: Adam B.
author list: Agent
  family name: Warinner
  given name: Christina
doi: 10.7717/peerj.11845
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Borry et al.
attribution name: Borry et al.

Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China
type: item
type: AcademicArticle
description: Heavy metals are released into the water system through various natural processes and anthropogenic activities, thus indirectly or directly endangering human health. The distribution, source, water quality and health risk assessment of dissolved heavy metals (V, Mn, Fe, Co, Ni, Zn, As, Mo, Sb) in major rivers in Wuhan were analyzed by correlation analysis (CA), principal component analysis (PCA), heavy metal pollution index (HPI), hazard index (HI) and carcinogenic risk (CR). The results showed that the spatial variability of heavy metal contents was pronounced. PCA and CA results indicated that natural sources controlled Mn, Fe, Co, Ni and Mo, and industrial emissions were the dominant factor for V, Zn and Sb, while As was mainly from the mixed input of urban and agricultural activities. According to the heavy metal pollution index (HPI, ranging from 23.74 to 184.0) analysis, it should be noted that As and Sb contribute most of the HPI values. The health risk assessment using HI and CR showed that V and Sb might have a potential non-carcinogenic risk and As might have a potential carcinogenic risk to adults and children in the study area (CR value exceeded target risk 10−4). At the same time, it was worth noting that As might have a potential non-carcinogenic risk for children around QLR (HI value exceeded the threshold value 1). The secular variation of As and Sb should be monitor in high-risk areas. The results of this study can provide important data for improving water resources management efficiency and heavy metal pollution prevention in Wuhan.
format: application/pdf
format: text/html
creator: Xingyong Zhang
creator: Qixin Wu
creator: Shilin Gao
creator: Zhuhong Wang
creator: Shouyang He
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11853
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Heavy metals are released into the water system through various natural processes and anthropogenic activities, thus indirectly or directly endangering human health. The distribution, source, water quality and health risk assessment of dissolved heavy metals (V, Mn, Fe, Co, Ni, Zn, As, Mo, Sb) in major rivers in Wuhan were analyzed by correlation analysis (CA), principal component analysis (PCA), heavy metal pollution index (HPI), hazard index (HI) and carcinogenic risk (CR). The results showed that the spatial variability of heavy metal contents was pronounced. PCA and CA results indicated that natural sources controlled Mn, Fe, Co, Ni and Mo, and industrial emissions were the dominant factor for V, Zn and Sb, while As was mainly from the mixed input of urban and agricultural activities. According to the heavy metal pollution index (HPI, ranging from 23.74 to 184.0) analysis, it should be noted that As and Sb contribute most of the HPI values. The health risk assessment using HI and CR showed that V and Sb might have a potential non-carcinogenic risk and As might have a potential carcinogenic risk to adults and children in the study area (CR value exceeded target risk 10−4). At the same time, it was worth noting that As might have a potential non-carcinogenic risk for children around QLR (HI value exceeded the threshold value 1). The secular variation of As and Sb should be monitor in high-risk areas. The results of this study can provide important data for improving water resources management efficiency and heavy metal pollution prevention in Wuhan.
bibliographic citation: Zhang et al. (2021) Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China. PeerJ 9:e11853 https://doi.org/10.7717/peerj.11853
date submitted: 2021-04-14
date accepted: 2021-07-04
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xingyong
author list: Agent
  family name: Wu
  given name: Qixin
author list: Agent
  family name: Gao
  given name: Shilin
author list: Agent
  family name: Wang
  given name: Zhuhong
author list: Agent
  family name: He
  given name: Shouyang
doi: 10.7717/peerj.11853
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan
type: item
type: AcademicArticle
description: Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.
format: application/pdf
format: text/html
creator: Akerke Amalova
creator: Saule Abugalieva
creator: Adylkhan Babkenov
creator: Sandukash Babkenova
creator: Yerlan Turuspekov
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.11857
publisher: PeerJ Inc.
rights: © 2021 Amalova et al.
abstract: Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.
bibliographic citation: Amalova et al. (2021) Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan. PeerJ 9:e11857 https://doi.org/10.7717/peerj.11857
date submitted: 2021-04-08
date accepted: 2021-07-05
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amalova
  given name: Akerke
author list: Agent
  family name: Abugalieva
  given name: Saule
author list: Agent
  family name: Babkenov
  given name: Adylkhan
author list: Agent
  family name: Babkenova
  given name: Sandukash
author list: Agent
  family name: Turuspekov
  given name: Yerlan
doi: 10.7717/peerj.11857
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Amalova et al.
attribution name: Amalova et al.

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