PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of jasmonic acid in foliar spray and an humic acid amendment to saline soils on forage sorghum plants’ growth and antioxidant defense system
items: Virulence characteristics of Blumeria graminis f. sp. tritici and its genetic diversity by EST-SSR analyses
items: The correlation between illness perception, pain intensity and quality of life in elderly with low back pain in Denmark: a cross-sectional study
items: Fermentation characteristics of bedded pack barn dairy cattle manure on methane yield, carbon, and nitrogen content in solid-state anaerobic digestion
items: Exogenous melatonin treatment on post-harvest jujube fruits maintains physicochemical qualities during extended cold storage
items: Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature
items: The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage
items: Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea
items: biomonitoR: an R package for managing ecological data and calculating biomonitoring indices
items: RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes

Effects of jasmonic acid in foliar spray and an humic acid amendment to saline soils on forage sorghum plants’ growth and antioxidant defense system
type: item
type: AcademicArticle
description: Salinity is one of the primary abiotic stresses that cause negative physiological and biochemical changes due to the oxidative stress caused by the generation of reactive oxygen species (ROS). The effect of jasmonic acid (JA) as foliar spray and humic acid (HA) as soil amendment on the growth and biochemical attributes of forage sorghum plants exposed to salinity stress was investigated. Soil treated with NaCl at levels of 0, 2, and 4 g NaCl kg−1 dry soil (designated as S0, S1, and S2) and soil amendment with humic acid at 0, 3, and 6 g HA kg−1 dry soil (designated as HA0, HA1, and HA2). The plants were sprayed with three JA levels, including 0, 5, and 10 mM JA. Salinity stress increased carotenoid and soluble protein content, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content. In contrast, salinity stress reduced plant height, leaf area, relative growth rate, proline content, and the activity of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). At the S2 salinity level, HA2 rate increased plant high by 9.7%, relative growth rate by 70.8% and CAT by 45.5, while HA1 increased leaf area by 12.5%, chlorophyll content by 22.3%, carotenoid content by 38.1%, SOD activity by 20.9%, MDA content by 18.0%, POD activity by 24.6% and APX value by 21.7%. At the S2 salinity level, the highest plant height, chlorophyll content, soluble protein content and APX value were recorded at 5 mM JA, while the highest leaf area, the content of carotenoid, proline, and MDA, and the activity of POD and CAT were achieved at 10 mM JA. Generally, 10 mM JA and 3 g HA kg−1 dry soil produced the best positive effects on forage sorghum plants physiological responses. Our study suggested that jasmonic acid and humic acid at appropriate rates can successfully mitigate the adverse effects of salinity stress on forage sorghum.
format: application/pdf
format: text/html
creator: Adam Yousif Adam Ali
creator: Guisheng Zhou
creator: Aboagla Mohammed Elsiddig
creator: Guanglong Zhu
creator: Tianyao Meng
creator: Xiurong Jiao
creator: Irshad Ahmed
creator: Ebtehal Gabralla Ibrahim Salih
creator: Muhi Eldeen Hussien Ibrahim
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13793
publisher: PeerJ Inc.
rights: © 2022 Ali et al.
abstract: Salinity is one of the primary abiotic stresses that cause negative physiological and biochemical changes due to the oxidative stress caused by the generation of reactive oxygen species (ROS). The effect of jasmonic acid (JA) as foliar spray and humic acid (HA) as soil amendment on the growth and biochemical attributes of forage sorghum plants exposed to salinity stress was investigated. Soil treated with NaCl at levels of 0, 2, and 4 g NaCl kg−1 dry soil (designated as S0, S1, and S2) and soil amendment with humic acid at 0, 3, and 6 g HA kg−1 dry soil (designated as HA0, HA1, and HA2). The plants were sprayed with three JA levels, including 0, 5, and 10 mM JA. Salinity stress increased carotenoid and soluble protein content, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content. In contrast, salinity stress reduced plant height, leaf area, relative growth rate, proline content, and the activity of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). At the S2 salinity level, HA2 rate increased plant high by 9.7%, relative growth rate by 70.8% and CAT by 45.5, while HA1 increased leaf area by 12.5%, chlorophyll content by 22.3%, carotenoid content by 38.1%, SOD activity by 20.9%, MDA content by 18.0%, POD activity by 24.6% and APX value by 21.7%. At the S2 salinity level, the highest plant height, chlorophyll content, soluble protein content and APX value were recorded at 5 mM JA, while the highest leaf area, the content of carotenoid, proline, and MDA, and the activity of POD and CAT were achieved at 10 mM JA. Generally, 10 mM JA and 3 g HA kg−1 dry soil produced the best positive effects on forage sorghum plants physiological responses. Our study suggested that jasmonic acid and humic acid at appropriate rates can successfully mitigate the adverse effects of salinity stress on forage sorghum.
bibliographic citation: Ali et al. (2022) Effects of jasmonic acid in foliar spray and an humic acid amendment to saline soils on forage sorghum plants’ growth and antioxidant defense system. PeerJ 10:e13793 https://doi.org/10.7717/peerj.13793
date submitted: 2021-10-01
date accepted: 2022-07-05
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ali
  given name: Adam Yousif Adam
author list: Agent
  family name: Zhou
  given name: Guisheng
author list: Agent
  family name: Elsiddig
  given name: Aboagla Mohammed
author list: Agent
  family name: Zhu
  given name: Guanglong
author list: Agent
  family name: Meng
  given name: Tianyao
author list: Agent
  family name: Jiao
  given name: Xiurong
author list: Agent
  family name: Ahmed
  given name: Irshad
author list: Agent
  family name: Ibrahim Salih
  given name: Ebtehal Gabralla
author list: Agent
  family name: Ibrahim
  given name: Muhi Eldeen Hussien
doi: 10.7717/peerj.13793
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Ali et al.
attribution name: Ali et al.

Virulence characteristics of Blumeria graminis f. sp. tritici and its genetic diversity by EST-SSR analyses
type: item
type: AcademicArticle
description: Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (an obligate biotrophic pathogen) is a worldwide threat to wheat production that occurs over a wide geographic area in China. For monitoring genetic variation and virulence structure of Blumeria graminis f. sp. tritici in Liaoning, Heilongjiang, and Sichuan in 2015, 31 wheat lines with known Powdery mildew resistance genes and 2 EST-SSR markers were used to characterize the virulence and genetic diversity. Results indicated that 90% of all isolates were virulent on Pm3c, Pm3e, Pm3f, Pm4a, Pm5, Pm6 (Timgalen), Pm7, Pm16, Pm19, and Pm1 + 2 + 9 and 62.6% to 89.9% of isolates were virulent on Pm3a, Pm3b, Pm3d, Pm4b, Pm6 (Coker747), Pm8, Pm17, Pm20, Pm23, Pm30, Pm4 + 8, Pm5 + 6, Pm4b + mli, Pm2 + mld, Pm4 + 2X, Pm2 + 6. The Pm13 and PmXBD genes were effective against most collected isolates from Liaoning and Heilongjiang Provinces. Only Pm21 exhibited an immune infection response to all isolates. Furthermore, closely related isolates within each region were distinguished by cluster analyses using EST-SSR representing some gene exchanges and genetic relationships between the flora in Northeast China (Liaoning, Heilongjiang) and Sichuan. Only 45% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and the frequency of virulence gene data. However, the EST-SSR polymorphism of isolated genes did not correspond to the virulence diversity of isolates in the single-gene lineage identification of hosts.
format: application/pdf
format: text/html
creator: Yazhao Zhang
creator: Xianxin Wu
creator: Wanlin Wang
creator: Yiwei Xu
creator: Huiyan Sun
creator: Yuanyin Cao
creator: Tianya Li
creator: Mansoor Karimi-Jashni
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.14118
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (an obligate biotrophic pathogen) is a worldwide threat to wheat production that occurs over a wide geographic area in China. For monitoring genetic variation and virulence structure of Blumeria graminis f. sp. tritici in Liaoning, Heilongjiang, and Sichuan in 2015, 31 wheat lines with known Powdery mildew resistance genes and 2 EST-SSR markers were used to characterize the virulence and genetic diversity. Results indicated that 90% of all isolates were virulent on Pm3c, Pm3e, Pm3f, Pm4a, Pm5, Pm6 (Timgalen), Pm7, Pm16, Pm19, and Pm1 + 2 + 9 and 62.6% to 89.9% of isolates were virulent on Pm3a, Pm3b, Pm3d, Pm4b, Pm6 (Coker747), Pm8, Pm17, Pm20, Pm23, Pm30, Pm4 + 8, Pm5 + 6, Pm4b + mli, Pm2 + mld, Pm4 + 2X, Pm2 + 6. The Pm13 and PmXBD genes were effective against most collected isolates from Liaoning and Heilongjiang Provinces. Only Pm21 exhibited an immune infection response to all isolates. Furthermore, closely related isolates within each region were distinguished by cluster analyses using EST-SSR representing some gene exchanges and genetic relationships between the flora in Northeast China (Liaoning, Heilongjiang) and Sichuan. Only 45% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and the frequency of virulence gene data. However, the EST-SSR polymorphism of isolated genes did not correspond to the virulence diversity of isolates in the single-gene lineage identification of hosts.
bibliographic citation: Zhang et al. (2022) Virulence characteristics of Blumeria graminis f. sp. tritici and its genetic diversity by EST-SSR analyses. PeerJ 10:e14118 https://doi.org/10.7717/peerj.14118
date submitted: 2022-06-10
date accepted: 2022-09-04
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yazhao
author list: Agent
  family name: Wu
  given name: Xianxin
author list: Agent
  family name: Wang
  given name: Wanlin
author list: Agent
  family name: Xu
  given name: Yiwei
author list: Agent
  family name: Sun
  given name: Huiyan
author list: Agent
  family name: Cao
  given name: Yuanyin
author list: Agent
  family name: Li
  given name: Tianya
author list: Agent
  family name: Karimi-Jashni
  given name: Mansoor
doi: 10.7717/peerj.14118
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

The correlation between illness perception, pain intensity and quality of life in elderly with low back pain in Denmark: a cross-sectional study
type: item
type: AcademicArticle
description: Background Illness perception is related to management patterns and pain intensity, but among elderly with low back pain, this relation is unclear. The aims of this study were to analyse the associations between illness perception, pain intensity and health related quality of life in a group of elderly with low back pain and explore how different illness perception profiles would cluster and differ in terms of pain, quality of life and choice of management. Method This was a cross-sectional survey based on a cohort of originally 640 Danish children. Of the 311 respondents in 2019, 69% reported low back pain within last year and were included. Associations between illness perceptions (Brief illness perception questionnaire), health related quality of life (EuroQol-5 Domain-3L) and low back pain intensity were assessed, and participants were clustered based on their perceptions using hierarchical and K-means cluster analysis. Cluster differences in pain, quality of life and use of pharmacological and non-pharmacological treatments were explored. Results Among the 213 individuals with low back pain, 33% reported severe or fluctuating pain intensity. Higher pain intensity was associated with perceiving low back pain as a greater threat. Participants reporting fluctuating pain perceived their low back pain almost as threatening as participants reporting severe pain. Two clusters were identified. Cluster 1 reported lower quality of life (difference in medians: −0.176 (95% CI [−0.233–−0.119 ])) and was more likely to report severe or fluctuating pain (37.7% vs. 4.5% [P < 0.0001]) and to use pharmacological treatments than Cluster 2 (37.7% vs. 14.9% [P < 0.001]). No association was found between clusters concerning use of non-pharmacological treatments (P = 0.134). Conclusion Based on illness perceptions, two clusters differing in pain intensity, quality of life and use of pharmacological treatments were identified. Targeting illness perceptions may be beneficial during reh…
format: application/pdf
format: text/html
creator: Elisabeth Ginnerup-Nielsen
creator: Mette Harreby
creator: Robin Christensen
creator: Henning Bliddal
creator: Marius Henriksen
subject: Anesthesiology and Pain Management
subject: Geriatrics
subject: Orthopedics
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.14129
publisher: PeerJ Inc.
rights: © 2022 Ginnerup-Nielsen et al.
abstract: Background Illness perception is related to management patterns and pain intensity, but among elderly with low back pain, this relation is unclear. The aims of this study were to analyse the associations between illness perception, pain intensity and health related quality of life in a group of elderly with low back pain and explore how different illness perception profiles would cluster and differ in terms of pain, quality of life and choice of management. Method This was a cross-sectional survey based on a cohort of originally 640 Danish children. Of the 311 respondents in 2019, 69% reported low back pain within last year and were included. Associations between illness perceptions (Brief illness perception questionnaire), health related quality of life (EuroQol-5 Domain-3L) and low back pain intensity were assessed, and participants were clustered based on their perceptions using hierarchical and K-means cluster analysis. Cluster differences in pain, quality of life and use of pharmacological and non-pharmacological treatments were explored. Results Among the 213 individuals with low back pain, 33% reported severe or fluctuating pain intensity. Higher pain intensity was associated with perceiving low back pain as a greater threat. Participants reporting fluctuating pain perceived their low back pain almost as threatening as participants reporting severe pain. Two clusters were identified. Cluster 1 reported lower quality of life (difference in medians: −0.176 (95% CI [−0.233–−0.119 ])) and was more likely to report severe or fluctuating pain (37.7% vs. 4.5% [P < 0.0001]) and to use pharmacological treatments than Cluster 2 (37.7% vs. 14.9% [P < 0.001]). No association was found between clusters concerning use of non-pharmacological treatments (P = 0.134). Conclusion Based on illness perceptions, two clusters differing in pain intensity, quality of life and use of pharmacological treatments were identified. Targeting illness perceptions may be beneficial during reh…
bibliographic citation: Ginnerup-Nielsen et al. (2022) The correlation between illness perception, pain intensity and quality of life in elderly with low back pain in Denmark: a cross-sectional study. PeerJ 10:e14129 https://doi.org/10.7717/peerj.14129
date submitted: 2022-03-16
date accepted: 2022-09-06
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ginnerup-Nielsen
  given name: Elisabeth
author list: Agent
  family name: Harreby
  given name: Mette
author list: Agent
  family name: Christensen
  given name: Robin
author list: Agent
  family name: Bliddal
  given name: Henning
author list: Agent
  family name: Henriksen
  given name: Marius
doi: 10.7717/peerj.14129
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: ©2022 Ginnerup-Nielsen et al.
attribution name: Ginnerup-Nielsen et al.

Fermentation characteristics of bedded pack barn dairy cattle manure on methane yield, carbon, and nitrogen content in solid-state anaerobic digestion
type: item
type: AcademicArticle
description: This study aimed to estimate the fermentation characteristics of bedded pack barn dairy cattle manure (BDCM) in terms of methane yield, fibrous material, and nitrogen content in batch solid-state anaerobic digestion (SSAD). SSAD was performed in triplicate using a 1,400 ml polypropylene bottle at a constant temperature of 39 °C until less than 1% methane was produced. The cumulative methane content of BDCM was 142.5 N mL/g volatile solids (VSs). The methane content rapidly increased for 18 days, reaching 63.4 ± 4.6% until the end of the experiment. The ultimate biodegradability and total VS removal of BDCM were 23.1 and 19.0%, respectively. The slopes of the non-fibrous and hemicellulose carbon fractions, and acid detergent insoluble carbon by digestion time were −0.174 (p < 0.001), −0.141 (p = 0.003), and −0.051 (p < 0.001), respectively. The non-fibrous and hemicellulose nitrogen fraction contents quadratically decreased during SSAD (p = 0.001 and p = 0.008). No significant decrease was observed in the acid detergent insoluble nitrogen content (p = 0.840). The results of the present study provide basic data on the digestion characteristics of BDCM and could help determine fermentation conditions in the anaerobic digestion of BDCM.
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format: text/html
creator: Yongjun Choi
creator: Sangrak Lee
creator: Duck-Min Ha
creator: Youngjun Na
creator: Doo-Hwan Kim
subject: Agricultural Science
subject: Biochemistry
subject: Bioengineering
subject: Microbiology
subject: Biogeochemistry
description: doi:10.7717/peerj.14134
publisher: PeerJ Inc.
rights: © 2022 Choi et al.
abstract: This study aimed to estimate the fermentation characteristics of bedded pack barn dairy cattle manure (BDCM) in terms of methane yield, fibrous material, and nitrogen content in batch solid-state anaerobic digestion (SSAD). SSAD was performed in triplicate using a 1,400 ml polypropylene bottle at a constant temperature of 39 °C until less than 1% methane was produced. The cumulative methane content of BDCM was 142.5 N mL/g volatile solids (VSs). The methane content rapidly increased for 18 days, reaching 63.4 ± 4.6% until the end of the experiment. The ultimate biodegradability and total VS removal of BDCM were 23.1 and 19.0%, respectively. The slopes of the non-fibrous and hemicellulose carbon fractions, and acid detergent insoluble carbon by digestion time were −0.174 (p < 0.001), −0.141 (p = 0.003), and −0.051 (p < 0.001), respectively. The non-fibrous and hemicellulose nitrogen fraction contents quadratically decreased during SSAD (p = 0.001 and p = 0.008). No significant decrease was observed in the acid detergent insoluble nitrogen content (p = 0.840). The results of the present study provide basic data on the digestion characteristics of BDCM and could help determine fermentation conditions in the anaerobic digestion of BDCM.
bibliographic citation: Choi et al. (2022) Fermentation characteristics of bedded pack barn dairy cattle manure on methane yield, carbon, and nitrogen content in solid-state anaerobic digestion. PeerJ 10:e14134 https://doi.org/10.7717/peerj.14134
date submitted: 2022-05-12
date accepted: 2022-09-06
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Yongjun
author list: Agent
  family name: Lee
  given name: Sangrak
author list: Agent
  family name: Ha
  given name: Duck-Min
author list: Agent
  family name: Na
  given name: Youngjun
author list: Agent
  family name: Kim
  given name: Doo-Hwan
doi: 10.7717/peerj.14134
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: ©2022 Choi et al.
attribution name: Choi et al.

Exogenous melatonin treatment on post-harvest jujube fruits maintains physicochemical qualities during extended cold storage
type: item
type: AcademicArticle
description: This study was conducted to investigate the visual appearance and physicochemical changes of postharvest jujube fruits (Ziziphus jujuba Mill. cv. Shucuizao) stored under 0 °C for 15 days. The fruits were dipped in 0 (control), 50, 100, 200 and 400 µM melatonin solutions after harvest. The results showed that treatment with a suitable melatonin concentration improved the rate of crisp fine fruits, delayed weight loss and firmness decline, and suppressed changes in total soluble solids (TSS) and titratable acidity (TA) contents of jujube fruits compared with the control. In addition, jujube fruits soaked with melatonin showed improved antioxidant capacity through increased ascorbic acid (AsA) content, enhanced superoxide dismutase (SOD) activity, and decreased malonaldehyde (MDA) content. As a result, 50 µM melatonin showed the greatest improvement of visual appearance and quality maintenance, and could be used as an effective treatment to preserve postharvest jujube fruit.
format: application/pdf
format: text/html
creator: Yang Wang
creator: Jirui Zhang
creator: Qiaoli Ma
creator: Xaio’ai Zhang
creator: Xian Luo
creator: Qunxian Deng
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.14155
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: This study was conducted to investigate the visual appearance and physicochemical changes of postharvest jujube fruits (Ziziphus jujuba Mill. cv. Shucuizao) stored under 0 °C for 15 days. The fruits were dipped in 0 (control), 50, 100, 200 and 400 µM melatonin solutions after harvest. The results showed that treatment with a suitable melatonin concentration improved the rate of crisp fine fruits, delayed weight loss and firmness decline, and suppressed changes in total soluble solids (TSS) and titratable acidity (TA) contents of jujube fruits compared with the control. In addition, jujube fruits soaked with melatonin showed improved antioxidant capacity through increased ascorbic acid (AsA) content, enhanced superoxide dismutase (SOD) activity, and decreased malonaldehyde (MDA) content. As a result, 50 µM melatonin showed the greatest improvement of visual appearance and quality maintenance, and could be used as an effective treatment to preserve postharvest jujube fruit.
bibliographic citation: Wang et al. (2022) Exogenous melatonin treatment on post-harvest jujube fruits maintains physicochemical qualities during extended cold storage. PeerJ 10:e14155 https://doi.org/10.7717/peerj.14155
date submitted: 2022-06-22
date accepted: 2022-09-08
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Zhang
  given name: Jirui
author list: Agent
  family name: Ma
  given name: Qiaoli
author list: Agent
  family name: Zhang
  given name: Xaio’ai
author list: Agent
  family name: Luo
  given name: Xian
author list: Agent
  family name: Deng
  given name: Qunxian
doi: 10.7717/peerj.14155
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature
type: item
type: AcademicArticle
description: Pacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes.
format: application/pdf
format: text/html
creator: Grace Crandall
creator: Rhonda Elliott Thompson
creator: Benoit Eudeline
creator: Brent Vadopalas
creator: Emma Timmins-Schiffman
creator: Steven Roberts
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14158
publisher: PeerJ Inc.
rights: © 2022 Crandall et al.
abstract: Pacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes.
bibliographic citation: Crandall et al. (2022) Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158
date submitted: 2021-11-30
date accepted: 2022-09-08
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Crandall
  given name: Grace
author list: Agent
  family name: Elliott Thompson
  given name: Rhonda
author list: Agent
  family name: Eudeline
  given name: Benoit
author list: Agent
  family name: Vadopalas
  given name: Brent
author list: Agent
  family name: Timmins-Schiffman
  given name: Emma
author list: Agent
  family name: Roberts
  given name: Steven
doi: 10.7717/peerj.14158
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Crandall et al.
attribution name: Crandall et al.

The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage
type: item
type: AcademicArticle
description: Exogenous melatonin (MT) is widely used in fruit preservation, and can increase the storage time and delay the quality deterioration. Firstly, it was found that 150 μM MT was the optimal concentration to treat ‘Xinli No.7’ under storage at 4 °C for 60 days. MT could significantly improve oxidase activity and inhibit the reduction of physiological indexes, including pulp hardness, weight loss, titratable acid and soluble solid content. MT could also reduce ethylene release and limit the reduction of fruit aroma. The average content of fruit aroma substance increased by 43.53%. A relevant RNA-Seq database was built to further explore the regulation mechanism of MT. A total of 2,761 differentially expressed genes (DEGs) were identified. DEGs were enriched in 64 functional groups and 191 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. DEGs were mainly enriched in alpha-linolenic acid metabolism, fatty acid metabolism and plant hormone signal transduction pathway. The gene pycom09g05270 belonging to long chain acyl-CoA synthetase family and participating in fatty acid metabolism pathway was identified, and its expression level was consistent with fragments per kilobase per million mapped reads (FPKM) values, implying that pycom09g05270 might play a vital role in maintaining quality during the storage process.
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creator: Shuwei Wei
creator: Huijun Jiao
creator: Hongwei Wang
creator: Kun Ran
creator: Ran Dong
creator: Xiaochang Dong
creator: Wenjing Yan
creator: Shaomin Wang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.14166
publisher: PeerJ Inc.
rights: © 2022 Wei et al.
abstract: Exogenous melatonin (MT) is widely used in fruit preservation, and can increase the storage time and delay the quality deterioration. Firstly, it was found that 150 μM MT was the optimal concentration to treat ‘Xinli No.7’ under storage at 4 °C for 60 days. MT could significantly improve oxidase activity and inhibit the reduction of physiological indexes, including pulp hardness, weight loss, titratable acid and soluble solid content. MT could also reduce ethylene release and limit the reduction of fruit aroma. The average content of fruit aroma substance increased by 43.53%. A relevant RNA-Seq database was built to further explore the regulation mechanism of MT. A total of 2,761 differentially expressed genes (DEGs) were identified. DEGs were enriched in 64 functional groups and 191 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. DEGs were mainly enriched in alpha-linolenic acid metabolism, fatty acid metabolism and plant hormone signal transduction pathway. The gene pycom09g05270 belonging to long chain acyl-CoA synthetase family and participating in fatty acid metabolism pathway was identified, and its expression level was consistent with fragments per kilobase per million mapped reads (FPKM) values, implying that pycom09g05270 might play a vital role in maintaining quality during the storage process.
bibliographic citation: Wei et al. (2022) The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage. PeerJ 10:e14166 https://doi.org/10.7717/peerj.14166
date submitted: 2022-04-05
date accepted: 2022-09-12
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Shuwei
author list: Agent
  family name: Jiao
  given name: Huijun
author list: Agent
  family name: Wang
  given name: Hongwei
author list: Agent
  family name: Ran
  given name: Kun
author list: Agent
  family name: Dong
  given name: Ran
author list: Agent
  family name: Dong
  given name: Xiaochang
author list: Agent
  family name: Yan
  given name: Wenjing
author list: Agent
  family name: Wang
  given name: Shaomin
doi: 10.7717/peerj.14166
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Wei et al.
attribution name: Wei et al.

Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea
type: item
type: AcademicArticle
description: Many ecologically important and valuable fisheries marine species have been misidentified in terms of both the statistical data and market demand. Correct identification at the species level and the population genetic structure of the orange-spotted grouper (Epinephelus coioides), a precious fish in the Persian Gulf and the Oman Sea, was tested using mitochondrial cytochrome oxidase subunit I (DNA barcoding) and D-loop sequencing. The results revealed that the Epinephelus species found in the region, including E. coioides, E. bleekeri, E. polylepis, and E. chlorostigma were all mistakenly grouped together and identified as only E. coioides. Moreover, the analysis of molecular variance (AMOVA) of E. coioides samples using the D-loop showed a significantly unique genetic structure (ΦST = 0.068, p < 0.001) within the E. coioides population throughout the Persian Gulf and the Oman Sea, with the pairwise genetic difference between sampling locations in UAE and the Iranian coast. Moreover, D-loop sequences analysis showed two distinct haplotype groups scattered among the sampling locations, which did not correlate with the geographic distance between the sampling locations. These findings indicate that the issue of misidentification should be highlighted in the management and conservation of E. coioides. As this type of misidentification is likely to happen to other threatened marine species as well, the efficacy of using genetic markers for the correct identification, both at the species and the population level, is vital.
format: application/pdf
format: text/html
creator: Parviz Tavakoli-Kolour
creator: Ahmad Farhadi
creator: Ashkan Ajdari
creator: Dara Bagheri
creator: Sanaz Hazraty-Kari
creator: Ahmad Ghasemi
creator: Arya Vazirzadeh
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Population Biology
description: doi:10.7717/peerj.14179
publisher: PeerJ Inc.
rights: © 2022 Tavakoli-Kolour et al.
abstract: Many ecologically important and valuable fisheries marine species have been misidentified in terms of both the statistical data and market demand. Correct identification at the species level and the population genetic structure of the orange-spotted grouper (Epinephelus coioides), a precious fish in the Persian Gulf and the Oman Sea, was tested using mitochondrial cytochrome oxidase subunit I (DNA barcoding) and D-loop sequencing. The results revealed that the Epinephelus species found in the region, including E. coioides, E. bleekeri, E. polylepis, and E. chlorostigma were all mistakenly grouped together and identified as only E. coioides. Moreover, the analysis of molecular variance (AMOVA) of E. coioides samples using the D-loop showed a significantly unique genetic structure (ΦST = 0.068, p < 0.001) within the E. coioides population throughout the Persian Gulf and the Oman Sea, with the pairwise genetic difference between sampling locations in UAE and the Iranian coast. Moreover, D-loop sequences analysis showed two distinct haplotype groups scattered among the sampling locations, which did not correlate with the geographic distance between the sampling locations. These findings indicate that the issue of misidentification should be highlighted in the management and conservation of E. coioides. As this type of misidentification is likely to happen to other threatened marine species as well, the efficacy of using genetic markers for the correct identification, both at the species and the population level, is vital.
bibliographic citation: Tavakoli-Kolour et al. (2022) Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea. PeerJ 10:e14179 https://doi.org/10.7717/peerj.14179
date submitted: 2022-07-13
date accepted: 2022-09-13
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tavakoli-Kolour
  given name: Parviz
author list: Agent
  family name: Farhadi
  given name: Ahmad
author list: Agent
  family name: Ajdari
  given name: Ashkan
author list: Agent
  family name: Bagheri
  given name: Dara
author list: Agent
  family name: Hazraty-Kari
  given name: Sanaz
author list: Agent
  family name: Ghasemi
  given name: Ahmad
author list: Agent
  family name: Vazirzadeh
  given name: Arya
doi: 10.7717/peerj.14179
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Tavakoli-Kolour et al.
attribution name: Tavakoli-Kolour et al.

biomonitoR: an R package for managing ecological data and calculating biomonitoring indices
type: item
type: AcademicArticle
description: The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers.
format: application/pdf
format: text/html
creator: Alex Laini
creator: Simone Guareschi
creator: Rossano Bolpagni
creator: Gemma Burgazzi
creator: Daniel Bruno
creator: Cayetano Gutiérrez-Cánovas
creator: Rafael Miranda
creator: Cédric Mondy
creator: Gábor Várbíró
creator: Tommaso Cancellario
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Data Science
subject: Freshwater Biology
description: doi:10.7717/peerj.14183
publisher: PeerJ Inc.
rights: © 2022 Laini et al.
abstract: The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers.
bibliographic citation: Laini et al. (2022) biomonitoR: an R package for managing ecological data and calculating biomonitoring indices. PeerJ 10:e14183 https://doi.org/10.7717/peerj.14183
date submitted: 2022-07-22
date accepted: 2022-09-14
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laini
  given name: Alex
author list: Agent
  family name: Guareschi
  given name: Simone
author list: Agent
  family name: Bolpagni
  given name: Rossano
author list: Agent
  family name: Burgazzi
  given name: Gemma
author list: Agent
  family name: Bruno
  given name: Daniel
author list: Agent
  family name: Gutiérrez-Cánovas
  given name: Cayetano
author list: Agent
  family name: Miranda
  given name: Rafael
author list: Agent
  family name: Mondy
  given name: Cédric
author list: Agent
  family name: Várbíró
  given name: Gábor
author list: Agent
  family name: Cancellario
  given name: Tommaso
doi: 10.7717/peerj.14183
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: ©2022 Laini et al.
attribution name: Laini et al.

RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes
type: item
type: AcademicArticle
description: Numerous published genomes contain gaps or unknown sequences. Gap filling is a critical final step in de novo genome assembly, particularly for large genomes. While certain computational approaches partially address the problem, others have shortcomings regarding the draft genome’s dependability and correctness (high rates of mis-assembly at gap-closing sites and high error rates). While it is well established that genomic repeats result in gaps, many sequence reads originating from repeat-related gaps are typically missed by existing approaches. A fast and reliable statistical algorithm for closing gaps in a draft genome is presented in this paper. It utilizes the alignment statistics between scaffolds, contigs, and paired-end reads to generate a Markov chain that appropriately assigns contigs or long reads to scaffold gap regions (only corrects candidate regions), resulting in accurate and efficient gap closure. To reconstruct the missing component between the two ends of the same insert, the RFfiller meticulously searches for valid overlaps (in repeat regions) and generates transition tables for similar reads, allowing it to make a statistical guess at the missing sequence. Finally, in our experiments, we show that the RFfiller’s gap-closing accuracy is better than that of other publicly available tools when sequence data from various organisms are used. Assembly benchmarks were used to validate RFfiller. Our findings show that RFfiller efficiently fills gaps and that it is especially effective when the gap length is longer. We also show that the RFfiller outperforms other gap closing tools currently on the market.
format: application/pdf
format: text/html
creator: Firaol Dida Midekso
creator: Gangman Yi
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Computational Science
description: doi:10.7717/peerj.14186
publisher: PeerJ Inc.
rights: © 2022 Midekso and Yi
abstract: Numerous published genomes contain gaps or unknown sequences. Gap filling is a critical final step in de novo genome assembly, particularly for large genomes. While certain computational approaches partially address the problem, others have shortcomings regarding the draft genome’s dependability and correctness (high rates of mis-assembly at gap-closing sites and high error rates). While it is well established that genomic repeats result in gaps, many sequence reads originating from repeat-related gaps are typically missed by existing approaches. A fast and reliable statistical algorithm for closing gaps in a draft genome is presented in this paper. It utilizes the alignment statistics between scaffolds, contigs, and paired-end reads to generate a Markov chain that appropriately assigns contigs or long reads to scaffold gap regions (only corrects candidate regions), resulting in accurate and efficient gap closure. To reconstruct the missing component between the two ends of the same insert, the RFfiller meticulously searches for valid overlaps (in repeat regions) and generates transition tables for similar reads, allowing it to make a statistical guess at the missing sequence. Finally, in our experiments, we show that the RFfiller’s gap-closing accuracy is better than that of other publicly available tools when sequence data from various organisms are used. Assembly benchmarks were used to validate RFfiller. Our findings show that RFfiller efficiently fills gaps and that it is especially effective when the gap length is longer. We also show that the RFfiller outperforms other gap closing tools currently on the market.
bibliographic citation: Midekso et al. (2022) RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes. PeerJ 10:e14186 https://doi.org/10.7717/peerj.14186
date submitted: 2022-07-25
date accepted: 2022-09-14
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Midekso
  given name: Firaol Dida
author list: Agent
  family name: Yi
  given name: Gangman
doi: 10.7717/peerj.14186
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: ©2022 Midekso and Yi
attribution name: Midekso and Yi

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