PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels
items: Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation
items: Comparison of long-term changes in size and longevity of bee colonies in mid-west Japan and Maui with and without exposure to pesticide, cold winters, and mites
items: Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas
items: Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers
items: Predatory functional response and fitness parameters of Orius strigicollis Poppius when fed Bemisia tabaci and Trialeurodes vaporariorum as determined by age-stage, two-sex life table
items: Comparative proteome analysis reveals VPS28 regulates milk fat synthesis through ubiquitylation in bovine mammary epithelial cells
items: Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
items: Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae)
items: Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques

Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels
type: item
type: AcademicArticle
description: Previous studies indicate that obesity is an important contributor to the proceeding of thyroid cancer (TC) with limited knowledge of the underlying mechanism. Here, we hypothesize that molecules affected by obesity may play roles in the development of TC. To test the hypothesis above, we first conducted a large-scale literature-based data mining to identify genes influenced by obesity and genes related to TC. Then, a mega-analysis was conducted to study the expression changes of the obesity-specific genes in the case of TC, using 16 independent TC array-expression datasets (783 TC cases and 439 healthy controls). After that, pathway analysis was performed to explore the functional profile of the selected target genes and their potential connections with TC. We identified 1,036 genes associated with TC and 534 regulated by obesity, demonstrating a significant overlap (N = 176, p-value = 4.07e−112). Five out of the 358 obesity-specific genes, FABP4, CFD, GHR, TNFRSF11B, and LTF, presented significantly decreased expression in TC patients (LFC<−1.44; and p-value < 1e−7). Multiple literature-based pathways were identified where obesity could promote the pathologic development of TC through the regulation of these five genes and INS levels. The five obesity genes uncovered could be novel genes that play roles in the etiology of TC through the modulation of INS levels.
format: application/pdf
format: text/html
creator: Jiaming Chen
creator: Hongbao Cao
creator: Meng Lian
creator: Jugao Fang
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.9302
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Previous studies indicate that obesity is an important contributor to the proceeding of thyroid cancer (TC) with limited knowledge of the underlying mechanism. Here, we hypothesize that molecules affected by obesity may play roles in the development of TC. To test the hypothesis above, we first conducted a large-scale literature-based data mining to identify genes influenced by obesity and genes related to TC. Then, a mega-analysis was conducted to study the expression changes of the obesity-specific genes in the case of TC, using 16 independent TC array-expression datasets (783 TC cases and 439 healthy controls). After that, pathway analysis was performed to explore the functional profile of the selected target genes and their potential connections with TC. We identified 1,036 genes associated with TC and 534 regulated by obesity, demonstrating a significant overlap (N = 176, p-value = 4.07e−112). Five out of the 358 obesity-specific genes, FABP4, CFD, GHR, TNFRSF11B, and LTF, presented significantly decreased expression in TC patients (LFC<−1.44; and p-value < 1e−7). Multiple literature-based pathways were identified where obesity could promote the pathologic development of TC through the regulation of these five genes and INS levels. The five obesity genes uncovered could be novel genes that play roles in the etiology of TC through the modulation of INS levels.
bibliographic citation: Chen et al. (2020) Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels. PeerJ 8:e9302 https://doi.org/10.7717/peerj.9302
date submitted: 2020-02-11
date accepted: 2020-05-15
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jiaming
author list: Agent
  family name: Cao
  given name: Hongbao
author list: Agent
  family name: Lian
  given name: Meng
author list: Agent
  family name: Fang
  given name: Jugao
doi: 10.7717/peerj.9302
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation
type: item
type: AcademicArticle
description: Background The awareness of environmental and socio-economic impacts caused by greenhouse gas emissions from the livestock sector leverages the adoption of strategies to counteract it. Feed supplements can play an important role in the reduction of the main greenhouse gas produced by ruminants—methane (CH4). In this context, this study aims to assess the effect of two biochar sources and inclusion levels on rumen fermentation parameters in vitro. Methods Two sources of biochar (agro-forestry residues, AFB, and potato peel, PPB) were added at two levels (5 and 10%, dry matter (DM) basis) to two basal substrates (haylage and corn silage) and incubated 24-h with rumen inocula to assess the effects on CH4 production and main rumen fermentation parameters in vitro. Results AFB and PPB were obtained at different carbonization conditions resulting in different apparent surface areas, ash content, pH at the point of zero charge (pHpzc), and elemental analysis. Relative to control (0% biochar), biochar supplementation kept unaffected total gas production and yield (mL and mL/g DM, p = 0.140 and p = 0.240, respectively) and fermentation pH (p = 0.666), increased CH4production and yield (mL and mL/g DM, respectively, p = 0.001) and ammonia-N (NH3-N, p = 0.040), and decreased total volatile fatty acids (VFA) production (p < 0.001) and H2 generated and consumed (p ≤ 0.001). Biochar sources and inclusion levels had no negative effect on most of the fermentation parameters and efficiency. Acetic:propionic acid ratio (p = 0.048) and H2 consumed (p = 0.019) were lower with AFB inclusion when compared to PPB. Biochar inclusion at 10% reduced H2 consumed (p < 0.001) and tended to reduce total gas production (p = 0.055). Total VFA production (p = 0.019), acetic acid proportion (p = 0.011) and H2 generated (p = 0.048) were the lowest with AFB supplemented at 10%, no differences being observed among the other treatments. The basal substrate affected most fermentation parameters independe…
format: application/pdf
format: text/html
creator: Ana R.F. Rodrigues
creator: Margarida R.G. Maia
creator: Ana R.J. Cabrita
creator: Hugo M. Oliveira
creator: Maria Bernardo
creator: Nuno Lapa
creator: Isabel Fonseca
creator: Henrique Trindade
creator: José L. Pereira
creator: António J.M. Fonseca
subject: Agricultural Science
subject: Bioengineering
subject: Veterinary Medicine
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.9488
publisher: PeerJ Inc.
rights: © 2020 Rodrigues et al.
abstract: Background The awareness of environmental and socio-economic impacts caused by greenhouse gas emissions from the livestock sector leverages the adoption of strategies to counteract it. Feed supplements can play an important role in the reduction of the main greenhouse gas produced by ruminants—methane (CH4). In this context, this study aims to assess the effect of two biochar sources and inclusion levels on rumen fermentation parameters in vitro. Methods Two sources of biochar (agro-forestry residues, AFB, and potato peel, PPB) were added at two levels (5 and 10%, dry matter (DM) basis) to two basal substrates (haylage and corn silage) and incubated 24-h with rumen inocula to assess the effects on CH4 production and main rumen fermentation parameters in vitro. Results AFB and PPB were obtained at different carbonization conditions resulting in different apparent surface areas, ash content, pH at the point of zero charge (pHpzc), and elemental analysis. Relative to control (0% biochar), biochar supplementation kept unaffected total gas production and yield (mL and mL/g DM, p = 0.140 and p = 0.240, respectively) and fermentation pH (p = 0.666), increased CH4production and yield (mL and mL/g DM, respectively, p = 0.001) and ammonia-N (NH3-N, p = 0.040), and decreased total volatile fatty acids (VFA) production (p < 0.001) and H2 generated and consumed (p ≤ 0.001). Biochar sources and inclusion levels had no negative effect on most of the fermentation parameters and efficiency. Acetic:propionic acid ratio (p = 0.048) and H2 consumed (p = 0.019) were lower with AFB inclusion when compared to PPB. Biochar inclusion at 10% reduced H2 consumed (p < 0.001) and tended to reduce total gas production (p = 0.055). Total VFA production (p = 0.019), acetic acid proportion (p = 0.011) and H2 generated (p = 0.048) were the lowest with AFB supplemented at 10%, no differences being observed among the other treatments. The basal substrate affected most fermentation parameters independe…
bibliographic citation: Rodrigues et al. (2020) Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation. PeerJ 8:e9488 https://doi.org/10.7717/peerj.9488
date submitted: 2020-01-13
date accepted: 2020-06-15
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodrigues
  given name: Ana R.F.
author list: Agent
  family name: Maia
  given name: Margarida R.G.
author list: Agent
  family name: Cabrita
  given name: Ana R.J.
author list: Agent
  family name: Oliveira
  given name: Hugo M.
author list: Agent
  family name: Bernardo
  given name: Maria
author list: Agent
  family name: Lapa
  given name: Nuno
author list: Agent
  family name: Fonseca
  given name: Isabel
author list: Agent
  family name: Trindade
  given name: Henrique
author list: Agent
  family name: Pereira
  given name: José L.
author list: Agent
  family name: Fonseca
  given name: António J.M.
doi: 10.7717/peerj.9488
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Rodrigues et al.
attribution name: Rodrigues et al.

Comparison of long-term changes in size and longevity of bee colonies in mid-west Japan and Maui with and without exposure to pesticide, cold winters, and mites
type: item
type: AcademicArticle
description: Four long-term field experiments in mid-west Japan (Shika) made it clear that extinction of colonies exposed to neonicotinoid was much higher than for colonies exposed to organophosphates. The incidence of hive death for of organophosphate-exposed and control (pesticide-free) colonies was similar. We conducted a field experiment in Maui for 271 days using the same pesticides (dinotefuran: 0.2 ppm, clothianidin: 0.08 ppm, fenitrothion: 1 ppm) as used in Shika with the honeybee, Apis mellifera, colonies without mites. Numbers of adult bees, capped brood, mites and other hive parameters were accurately counted on photographs of combs and on the inside of the hives. All six neonicotinoid (dinotefuran & clothianidin)-exposed colonies failed during the experiment. One of three organophosphate (fenitrothion)-exposed colonies and one of the three control colonies also failed. The findings from Maui, where colonies displayed no mites, provides evidence from Shika, with mites, that neonicotinoids are more hazardous to honeybee colonies than organophosphates. The apparent longevity of honeybee colonies on Maui was estimated by numbers of adult bees and capped brood using a mathematical model previously proposed. Seasonal changes in longevity on Maui differ greatly from changes at Shika, the latter showing distinct seasonal variation. Longevity on Maui remains nearly constant throughout the year with wide variations. At Shika, it increases drastically in winter, by six- to ten fold more than the other seasons. Differences seem to depend on the existence of cold winters and the length of flowering seasons. In a perpetually hospitable environment, small changes in conditions can be sensitively reflected in apparent longevity. Examining wide variations in apparent longevity that are seemingly incoherent, we recognized several differences in apparent longevity between neonicotinoid-exposed and organophosphate-exposed colonies: The colony that failed in after organophosphate-exposur…
format: application/pdf
format: text/html
creator: Toshiro Yamada
creator: Kazuko Yamada
subject: Animal Behavior
subject: Computational Biology
description: doi:10.7717/peerj.9505
publisher: PeerJ Inc.
rights: © 2020 Yamada and Yamada
abstract: Four long-term field experiments in mid-west Japan (Shika) made it clear that extinction of colonies exposed to neonicotinoid was much higher than for colonies exposed to organophosphates. The incidence of hive death for of organophosphate-exposed and control (pesticide-free) colonies was similar. We conducted a field experiment in Maui for 271 days using the same pesticides (dinotefuran: 0.2 ppm, clothianidin: 0.08 ppm, fenitrothion: 1 ppm) as used in Shika with the honeybee, Apis mellifera, colonies without mites. Numbers of adult bees, capped brood, mites and other hive parameters were accurately counted on photographs of combs and on the inside of the hives. All six neonicotinoid (dinotefuran & clothianidin)-exposed colonies failed during the experiment. One of three organophosphate (fenitrothion)-exposed colonies and one of the three control colonies also failed. The findings from Maui, where colonies displayed no mites, provides evidence from Shika, with mites, that neonicotinoids are more hazardous to honeybee colonies than organophosphates. The apparent longevity of honeybee colonies on Maui was estimated by numbers of adult bees and capped brood using a mathematical model previously proposed. Seasonal changes in longevity on Maui differ greatly from changes at Shika, the latter showing distinct seasonal variation. Longevity on Maui remains nearly constant throughout the year with wide variations. At Shika, it increases drastically in winter, by six- to ten fold more than the other seasons. Differences seem to depend on the existence of cold winters and the length of flowering seasons. In a perpetually hospitable environment, small changes in conditions can be sensitively reflected in apparent longevity. Examining wide variations in apparent longevity that are seemingly incoherent, we recognized several differences in apparent longevity between neonicotinoid-exposed and organophosphate-exposed colonies: The colony that failed in after organophosphate-exposur…
bibliographic citation: Yamada et al. (2020) Comparison of long-term changes in size and longevity of bee colonies in mid-west Japan and Maui with and without exposure to pesticide, cold winters, and mites. PeerJ 8:e9505 https://doi.org/10.7717/peerj.9505
date submitted: 2019-03-07
date accepted: 2020-06-17
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamada
  given name: Toshiro
author list: Agent
  family name: Yamada
  given name: Kazuko
doi: 10.7717/peerj.9505
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Yamada and Yamada
attribution name: Yamada and Yamada

Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas
type: item
type: AcademicArticle
description: Background The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial. Methods A panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea. Results This study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale.
format: application/pdf
format: text/html
creator: Tommaso Righi
creator: Andrea Splendiani
creator: Tatiana Fioravanti
creator: Andrea Petetta
creator: Michela Candelma
creator: Giorgia Gioacchini
creator: Kyle Gillespie
creator: Alex Hanke
creator: Oliana Carnevali
creator: Vincenzo Caputo Barucchi
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.9518
publisher: PeerJ Inc.
rights: © 2020 Righi et al.
abstract: Background The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial. Methods A panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea. Results This study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale.
bibliographic citation: Righi et al. (2020) Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas. PeerJ 8:e9518 https://doi.org/10.7717/peerj.9518
date submitted: 2020-01-08
date accepted: 2020-06-19
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Righi
  given name: Tommaso
author list: Agent
  family name: Splendiani
  given name: Andrea
author list: Agent
  family name: Fioravanti
  given name: Tatiana
author list: Agent
  family name: Petetta
  given name: Andrea
author list: Agent
  family name: Candelma
  given name: Michela
author list: Agent
  family name: Gioacchini
  given name: Giorgia
author list: Agent
  family name: Gillespie
  given name: Kyle
author list: Agent
  family name: Hanke
  given name: Alex
author list: Agent
  family name: Carnevali
  given name: Oliana
author list: Agent
  family name: Caputo Barucchi
  given name: Vincenzo
doi: 10.7717/peerj.9518
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Righi et al.
attribution name: Righi et al.

Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers
type: item
type: AcademicArticle
description: Background Cervical cancer is the most common gynecological cancer, encompassing cervical squamous cell carcinoma, adenocarcinoma, and other epithelial tumors. There are many diagnostic methods to detect cervical cancers but no precision screening tool for cervical adenocarcinoma at present. Material and methods The cervical mucus from three normal cervices (Ctrl), three endocervical adenocarcinoma (EA), and three cervical adenocarcinoma in situ (AIS) was collected for proteomic analysis. The proteins were screened using liquid chromatography-mass spectrometry analysis (LC-MS). The biological function of the differently expressed proteins were predicted by Gene Ontology (GO). Results A total of 711 proteins were identified, including 237 differently expressed proteins identified in EA/Ctrl comparison, 256 differently expressed proteins identified in AIS/Ctrl comparison, and 242 differently expressed proteins identified in AIS/EA comparison (up-regulate ≥ 1.5 or down-regulate ≤ 0.67). Functional annotation was performed using GO analysis on 1,056 differently expressed proteins to identify those that may impact cervical cancer, such as heme protein myeloperoxidase, which is involved in the immune process, and APOA1, which is associated with lipid metabolism. Conclusion We used proteomic analysis to screen out differently expressed proteins from normal cervical mucus and cervical adenocarcinoma mucus samples. These differently expressed proteins may be potential biomarkers for the diagnosis and treatment of cervical adenocarcinoma but require additional study.
format: application/pdf
format: text/html
creator: Zhifang Ma
creator: Jie Chen
creator: Ting Luan
creator: Chengzhuo Chu
creator: Wangfei Wu
creator: Yichao Zhu
creator: Yun Gu
subject: Biochemistry
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.9527
publisher: PeerJ Inc.
rights: © 2020 Ma et al.
abstract: Background Cervical cancer is the most common gynecological cancer, encompassing cervical squamous cell carcinoma, adenocarcinoma, and other epithelial tumors. There are many diagnostic methods to detect cervical cancers but no precision screening tool for cervical adenocarcinoma at present. Material and methods The cervical mucus from three normal cervices (Ctrl), three endocervical adenocarcinoma (EA), and three cervical adenocarcinoma in situ (AIS) was collected for proteomic analysis. The proteins were screened using liquid chromatography-mass spectrometry analysis (LC-MS). The biological function of the differently expressed proteins were predicted by Gene Ontology (GO). Results A total of 711 proteins were identified, including 237 differently expressed proteins identified in EA/Ctrl comparison, 256 differently expressed proteins identified in AIS/Ctrl comparison, and 242 differently expressed proteins identified in AIS/EA comparison (up-regulate ≥ 1.5 or down-regulate ≤ 0.67). Functional annotation was performed using GO analysis on 1,056 differently expressed proteins to identify those that may impact cervical cancer, such as heme protein myeloperoxidase, which is involved in the immune process, and APOA1, which is associated with lipid metabolism. Conclusion We used proteomic analysis to screen out differently expressed proteins from normal cervical mucus and cervical adenocarcinoma mucus samples. These differently expressed proteins may be potential biomarkers for the diagnosis and treatment of cervical adenocarcinoma but require additional study.
bibliographic citation: Ma et al. (2020) Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers. PeerJ 8:e9527 https://doi.org/10.7717/peerj.9527
date submitted: 2020-02-21
date accepted: 2020-06-21
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Zhifang
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Luan
  given name: Ting
author list: Agent
  family name: Chu
  given name: Chengzhuo
author list: Agent
  family name: Wu
  given name: Wangfei
author list: Agent
  family name: Zhu
  given name: Yichao
author list: Agent
  family name: Gu
  given name: Yun
doi: 10.7717/peerj.9527
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Ma et al.
attribution name: Ma et al.

Predatory functional response and fitness parameters of Orius strigicollis Poppius when fed Bemisia tabaci and Trialeurodes vaporariorum as determined by age-stage, two-sex life table
type: item
type: AcademicArticle
description: Background The polyphagous predatory bug O. strigicollis is an active predator used to control thrips and aphids. The whitefly species Bemisia tabaci and Trialeurodes vaporariorum are voracious pests of different economic agricultural crops and vegetables. Method In this study, the Holling disc equation and the age-stage, two-sex life table technique were used to investigate the functional response and biological traits of third instar nymphs and adult female O. strigicollis when presented third instar nymphs of both whitefly species as prey. Results The results showed a type II functional response for each life stage of O. strigicollis when fed each whitefly species. The calculated prey handling time for different O. strigicollis life stages were shorter when fed T. vaporariorum than when fed B. tabaci nymphs. In contrast, the nymphal development of O. strigicollis was significantly shorter when fed B. tabaci than T. vaporariorum nymphs. Additionally, the total pre-oviposition period of adult females was statistically shorter when fed B. tabaci nymphs than T. vaporariorum nymphs. Furthermore, the survival rates and total fecundity of O. strigicollis were higher when fed B. tabaci than T. vaporariorum. There were no significant differences in any population parameters of O. strigicollis when fed either whitefly species. These results show that O. strigicollis could survive and maintain its populations on both species of whitefly and could therefore serve as a biological control agent in integrated pest management (IPM).
format: application/pdf
format: text/html
creator: Shakeel Ur Rehman
creator: Xingmiao Zhou
creator: Shahzaib Ali
creator: Muhammad Asim Rasheed
creator: Yasir Islam
creator: Muhammad Hafeez
creator: Muhammad Aamir Sohail
creator: Haris Khurram
subject: Agricultural Science
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.9540
publisher: PeerJ Inc.
rights: © 2020 Rehman et al.
abstract: Background The polyphagous predatory bug O. strigicollis is an active predator used to control thrips and aphids. The whitefly species Bemisia tabaci and Trialeurodes vaporariorum are voracious pests of different economic agricultural crops and vegetables. Method In this study, the Holling disc equation and the age-stage, two-sex life table technique were used to investigate the functional response and biological traits of third instar nymphs and adult female O. strigicollis when presented third instar nymphs of both whitefly species as prey. Results The results showed a type II functional response for each life stage of O. strigicollis when fed each whitefly species. The calculated prey handling time for different O. strigicollis life stages were shorter when fed T. vaporariorum than when fed B. tabaci nymphs. In contrast, the nymphal development of O. strigicollis was significantly shorter when fed B. tabaci than T. vaporariorum nymphs. Additionally, the total pre-oviposition period of adult females was statistically shorter when fed B. tabaci nymphs than T. vaporariorum nymphs. Furthermore, the survival rates and total fecundity of O. strigicollis were higher when fed B. tabaci than T. vaporariorum. There were no significant differences in any population parameters of O. strigicollis when fed either whitefly species. These results show that O. strigicollis could survive and maintain its populations on both species of whitefly and could therefore serve as a biological control agent in integrated pest management (IPM).
bibliographic citation: Rehman et al. (2020) Predatory functional response and fitness parameters of Orius strigicollis Poppius when fed Bemisia tabaci and Trialeurodes vaporariorum as determined by age-stage, two-sex life table. PeerJ 8:e9540 https://doi.org/10.7717/peerj.9540
date submitted: 2020-02-14
date accepted: 2020-06-23
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rehman
  given name: Shakeel Ur
author list: Agent
  family name: Zhou
  given name: Xingmiao
author list: Agent
  family name: Ali
  given name: Shahzaib
author list: Agent
  family name: Asim Rasheed
  given name: Muhammad
author list: Agent
  family name: Islam
  given name: Yasir
author list: Agent
  family name: Hafeez
  given name: Muhammad
author list: Agent
  family name: Aamir Sohail
  given name: Muhammad
author list: Agent
  family name: Khurram
  given name: Haris
doi: 10.7717/peerj.9540
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Rehman et al.
attribution name: Rehman et al.

Comparative proteome analysis reveals VPS28 regulates milk fat synthesis through ubiquitylation in bovine mammary epithelial cells
type: item
type: AcademicArticle
description: In our previous study, we found that VPS28 (vacuolar protein sorting 28 homolog) could alter ubiquitylation level to regulate milk fat synthesis in bovine primary mammary epithelial cells (BMECs). While the information on the regulation of VPS28 on proteome of milk fat synthesis is less known, we explored its effect on milk fat synthesis using isobaric tags for relative and absolute quantitation assay after knocking down VPS28 in BMECs. A total of 2,773 proteins in three biological replicates with a false discovery rate of less than 1.2% were identified and quantified. Among them, a subset of 203 proteins were screened as significantly down-(111) and up-(92) regulated in VPS28 knockdown BMECs compared with the control groups. According to Gene Ontology analysis, the differentially expressed proteins were enriched in the “proteasome,” “ubiquitylation,” “metabolism of fatty acids,” “phosphorylation,” and “ribosome.” Meanwhile, some changes occurred in the morphology of BMECs and an accumulation of TG (triglyceride) and dysfunction of proteasome were identified, and a series of genes associated with milk fat synthesis, ubiquitylation and proteasome pathways were analyzed by quantitative real-time PCR. The results of this study suggested VPS28 regulated milk fat synthesis was mediated by ubiquitylation; it could be an important new area of study for milk fat synthesis and other milk fat content traits in bovine.
format: application/pdf
format: text/html
creator: Lily Liu
creator: Qin Zhang
subject: Agricultural Science
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.9542
publisher: PeerJ Inc.
rights: © 2020 Liu and Zhang
abstract: In our previous study, we found that VPS28 (vacuolar protein sorting 28 homolog) could alter ubiquitylation level to regulate milk fat synthesis in bovine primary mammary epithelial cells (BMECs). While the information on the regulation of VPS28 on proteome of milk fat synthesis is less known, we explored its effect on milk fat synthesis using isobaric tags for relative and absolute quantitation assay after knocking down VPS28 in BMECs. A total of 2,773 proteins in three biological replicates with a false discovery rate of less than 1.2% were identified and quantified. Among them, a subset of 203 proteins were screened as significantly down-(111) and up-(92) regulated in VPS28 knockdown BMECs compared with the control groups. According to Gene Ontology analysis, the differentially expressed proteins were enriched in the “proteasome,” “ubiquitylation,” “metabolism of fatty acids,” “phosphorylation,” and “ribosome.” Meanwhile, some changes occurred in the morphology of BMECs and an accumulation of TG (triglyceride) and dysfunction of proteasome were identified, and a series of genes associated with milk fat synthesis, ubiquitylation and proteasome pathways were analyzed by quantitative real-time PCR. The results of this study suggested VPS28 regulated milk fat synthesis was mediated by ubiquitylation; it could be an important new area of study for milk fat synthesis and other milk fat content traits in bovine.
bibliographic citation: Liu et al. (2020) Comparative proteome analysis reveals VPS28 regulates milk fat synthesis through ubiquitylation in bovine mammary epithelial cells. PeerJ 8:e9542 https://doi.org/10.7717/peerj.9542
date submitted: 2020-04-13
date accepted: 2020-06-24
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lily
author list: Agent
  family name: Zhang
  given name: Qin
doi: 10.7717/peerj.9542
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Liu and Zhang
attribution name: Liu and Zhang

Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
type: item
type: AcademicArticle
description: Background Plants interact with a variety of microorganisms during their life cycle, among which beneficial bacteria deserve special attention. Gluconacetobacter diazotrophicus is a beneficial bacterium able to fix nitrogen and promote plant growth. Despite its biotechnological potential, the mechanisms regulating the interaction between G. diazotrophicus and host plants remain unclear. Methods We analyzed the response of G. diazotrophicus to cocultivation with Arabidopsis thaliana seedlings. Bacterial growth in response to cocultivation and plant exudates was analyzed. Through comparative proteomic analysis, G. diazotrophicus proteins regulated during cocultivation were investigated. Finally, the role of some up-accumulated proteins in the response G. diazotrophicus to cocultivation was analyzed by reverse genetics, using insertion mutants. Results Our results revealed the induction of bacterial growth in response to cocultivation. Comparative proteomic analysis identified 450 bacterial proteins, with 39 up-accumulated, and 12 down-accumulated in response to cocultivation. Among the up-accumulated pathways, the metabolism of pentoses and protein synthesis were highlighted. Proteins potentially relevant to bacterial growth response such as ABC-F-Etta, ClpX, Zwf, MetE, AcnA, IlvC, and AccC were also increased. Reverse genetics analysis, using insertion mutants, revealed that the lack of ABC-F-Etta and AccC proteins severely affects G. diazotrophicus response to cocultivation. Our data demonstrated that specific mechanisms are activated in the bacterial response to plant exudates, indicating the essential role of “ribosomal activity” and “fatty acid biosynthesis” in such a process. This is the first study to demonstrate the participation of EttA and AccC proteins in plant-bacteria interactions, and open new perspectives for understanding the initial steps of such associations.
format: application/pdf
format: text/html
creator: Tamires Cruz dos Santos
creator: Mariana Ramos Leandro
creator: Clara Yohana Maia
creator: Patrícia Rangel
creator: Fabiano S. Soares
creator: Ricardo Reis
creator: Lucas Passamani
creator: Vanildo Silveira
creator: Gonçalo Apolinário de Souza Filho
subject: Biotechnology
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9600
publisher: PeerJ Inc.
rights: © 2020 dos Santos et al.
abstract: Background Plants interact with a variety of microorganisms during their life cycle, among which beneficial bacteria deserve special attention. Gluconacetobacter diazotrophicus is a beneficial bacterium able to fix nitrogen and promote plant growth. Despite its biotechnological potential, the mechanisms regulating the interaction between G. diazotrophicus and host plants remain unclear. Methods We analyzed the response of G. diazotrophicus to cocultivation with Arabidopsis thaliana seedlings. Bacterial growth in response to cocultivation and plant exudates was analyzed. Through comparative proteomic analysis, G. diazotrophicus proteins regulated during cocultivation were investigated. Finally, the role of some up-accumulated proteins in the response G. diazotrophicus to cocultivation was analyzed by reverse genetics, using insertion mutants. Results Our results revealed the induction of bacterial growth in response to cocultivation. Comparative proteomic analysis identified 450 bacterial proteins, with 39 up-accumulated, and 12 down-accumulated in response to cocultivation. Among the up-accumulated pathways, the metabolism of pentoses and protein synthesis were highlighted. Proteins potentially relevant to bacterial growth response such as ABC-F-Etta, ClpX, Zwf, MetE, AcnA, IlvC, and AccC were also increased. Reverse genetics analysis, using insertion mutants, revealed that the lack of ABC-F-Etta and AccC proteins severely affects G. diazotrophicus response to cocultivation. Our data demonstrated that specific mechanisms are activated in the bacterial response to plant exudates, indicating the essential role of “ribosomal activity” and “fatty acid biosynthesis” in such a process. This is the first study to demonstrate the participation of EttA and AccC proteins in plant-bacteria interactions, and open new perspectives for understanding the initial steps of such associations.
bibliographic citation: dos Santos et al. (2020) Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus. PeerJ 8:e9600 https://doi.org/10.7717/peerj.9600
date submitted: 2020-03-17
date accepted: 2020-07-03
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: dos Santos
  given name: Tamires Cruz
author list: Agent
  family name: Leandro
  given name: Mariana Ramos
author list: Agent
  family name: Maia
  given name: Clara Yohana
author list: Agent
  family name: Rangel
  given name: Patrícia
author list: Agent
  family name: Soares
  given name: Fabiano S.
author list: Agent
  family name: Reis
  given name: Ricardo
author list: Agent
  family name: Passamani
  given name: Lucas
author list: Agent
  family name: Silveira
  given name: Vanildo
author list: Agent
  family name: de Souza Filho
  given name: Gonçalo Apolinário
doi: 10.7717/peerj.9600
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 dos Santos et al.
attribution name: dos Santos et al.

Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae)
type: item
type: AcademicArticle
description: Detritus (decaying organic matter) and phyllodes of mosses are two main components in the diet of groundhoppers (Orthoptera: Tetrigidae). We studied the energy balance of consumed food under laboratory conditions in the detrito-bryophagous groundhopper, Tetrix subulata (Linnaeus, 1758). The results indicated that the energy food budget of this detrito-bryophagous groundhopper was comparable to those of small herbivorous grasshoppers (Acrididae: Gomphocerinae, Melanoplinae), which have a similar energy food budget of approximately 800–1,100 J/g. T. subulata consumed four times more detritus than mosses, although both components provided similar amounts of energy (ca. 15–16 kJ/g). However, in contrast with detritus, moss fragments passed through the digestive tract without a distinct change in their mass or a loss in their energy value. We assume that moss may cause the longer retention of semifluid mass of partly digested food in the alimentary tract; hence, the digestion and efficiency of nutrient absorption from detritus could be more effective.
format: application/pdf
format: text/html
creator: Kateřina Kuřavová
creator: Jan Šipoš
creator: Petr Kočárek
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Food Science and Technology
subject: Zoology
description: doi:10.7717/peerj.9603
publisher: PeerJ Inc.
rights: © 2020 Kuřavová et al.
abstract: Detritus (decaying organic matter) and phyllodes of mosses are two main components in the diet of groundhoppers (Orthoptera: Tetrigidae). We studied the energy balance of consumed food under laboratory conditions in the detrito-bryophagous groundhopper, Tetrix subulata (Linnaeus, 1758). The results indicated that the energy food budget of this detrito-bryophagous groundhopper was comparable to those of small herbivorous grasshoppers (Acrididae: Gomphocerinae, Melanoplinae), which have a similar energy food budget of approximately 800–1,100 J/g. T. subulata consumed four times more detritus than mosses, although both components provided similar amounts of energy (ca. 15–16 kJ/g). However, in contrast with detritus, moss fragments passed through the digestive tract without a distinct change in their mass or a loss in their energy value. We assume that moss may cause the longer retention of semifluid mass of partly digested food in the alimentary tract; hence, the digestion and efficiency of nutrient absorption from detritus could be more effective.
bibliographic citation: Kuřavová et al. (2020) Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae). PeerJ 8:e9603 https://doi.org/10.7717/peerj.9603
date submitted: 2019-09-24
date accepted: 2020-07-03
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuřavová
  given name: Kateřina
author list: Agent
  family name: Šipoš
  given name: Jan
author list: Agent
  family name: Kočárek
  given name: Petr
doi: 10.7717/peerj.9603
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Kuřavová et al.
attribution name: Kuřavová et al.

Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques
type: item
type: AcademicArticle
description: The pterosaurs first appear in the fossil record in the middle of the Late Triassic. Their earliest representatives are known from Northern Hemisphere localities but, by the end of the Jurassic Period, this clade of flying reptiles achieved a global distribution, as well as high levels of diversity and disparity. Our understanding of early pterosaur evolution and the fundamental interrelationships within Pterosauria has improved dramatically in recent decades. However, there is still debate about how the various pterosaur subgroups relate to one another and about which taxa comprise these. Many recent phylogenetic analyses, while sampling well from among the known Triassic and Early Jurassic pterosaurs, have not included many non-pterosaurian ornithodirans or other avemetatarsalians. Given the close relationship between these groups of archosaurs, the omission of other ornithodirans and avemetatarsalians has the potential to adversely affect the results of phylogenetic analyses, in terms of character optimisation and ingroup relationships recovered. This study has addressed this issue and tests the relationships between the early diverging pterosaur taxa following the addition of avemetatarsalian taxa and anatomical characters to an existing early pterosaur dataset. This study has, for the first time, included taxa that represent the aphanosaurs, lagerpetids, silesaurids and dinosaurs, in addition to early pterosaurs. Anatomical characters used in other recent studies of archosaurs and early dinosaurs have also been incorporated. By expanding the outgroup taxa and anatomical character coverage in this pterosaur dataset, better resolution between the taxa within certain early pterosaur subclades has been achieved and stronger support for some existing clades has been found; other purported clades of early pterosaurs have not been found in this analysis—for example there is no support for a monophyletic Eopterosauria or Eudimorphodontidae. Further support has been fou…
format: application/pdf
format: text/html
creator: Matthew G. Baron
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9604
publisher: PeerJ Inc.
rights: © 2020 Baron
abstract: The pterosaurs first appear in the fossil record in the middle of the Late Triassic. Their earliest representatives are known from Northern Hemisphere localities but, by the end of the Jurassic Period, this clade of flying reptiles achieved a global distribution, as well as high levels of diversity and disparity. Our understanding of early pterosaur evolution and the fundamental interrelationships within Pterosauria has improved dramatically in recent decades. However, there is still debate about how the various pterosaur subgroups relate to one another and about which taxa comprise these. Many recent phylogenetic analyses, while sampling well from among the known Triassic and Early Jurassic pterosaurs, have not included many non-pterosaurian ornithodirans or other avemetatarsalians. Given the close relationship between these groups of archosaurs, the omission of other ornithodirans and avemetatarsalians has the potential to adversely affect the results of phylogenetic analyses, in terms of character optimisation and ingroup relationships recovered. This study has addressed this issue and tests the relationships between the early diverging pterosaur taxa following the addition of avemetatarsalian taxa and anatomical characters to an existing early pterosaur dataset. This study has, for the first time, included taxa that represent the aphanosaurs, lagerpetids, silesaurids and dinosaurs, in addition to early pterosaurs. Anatomical characters used in other recent studies of archosaurs and early dinosaurs have also been incorporated. By expanding the outgroup taxa and anatomical character coverage in this pterosaur dataset, better resolution between the taxa within certain early pterosaur subclades has been achieved and stronger support for some existing clades has been found; other purported clades of early pterosaurs have not been found in this analysis—for example there is no support for a monophyletic Eopterosauria or Eudimorphodontidae. Further support has been fou…
bibliographic citation: Baron (2020) Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques. PeerJ 8:e9604 https://doi.org/10.7717/peerj.9604
date submitted: 2020-04-08
date accepted: 2020-07-03
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baron
  given name: Matthew G.
doi: 10.7717/peerj.9604
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Baron
attribution name: Baron

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