PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation
items: Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period
items: Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer
items: Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand
items: Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
items: Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas
items: Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery
items: Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153
items: A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides
items: Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas

Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation
type: item
type: AcademicArticle
description: Background Soil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation. Methods A 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha). Results Our results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon–Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of cr…
format: application/pdf
format: text/html
creator: Qian Lyu
creator: Yi Shen
creator: Xianwei Li
creator: Gang Chen
creator: Dehui Li
creator: Chuan Fan
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.11852
publisher: PeerJ Inc.
rights: © 2021 Lyu et al.
abstract: Background Soil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation. Methods A 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha). Results Our results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon–Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of cr…
bibliographic citation: Lyu et al. (2021) Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation. PeerJ 9:e11852 https://doi.org/10.7717/peerj.11852
date submitted: 2021-03-12
date accepted: 2021-07-04
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lyu
  given name: Qian
author list: Agent
  family name: Shen
  given name: Yi
author list: Agent
  family name: Li
  given name: Xianwei
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: Li
  given name: Dehui
author list: Agent
  family name: Fan
  given name: Chuan
doi: 10.7717/peerj.11852
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Lyu et al.
attribution name: Lyu et al.

Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period
type: item
type: AcademicArticle
description: Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary …
format: application/pdf
format: text/html
creator: Ruochen Yang
creator: Chunhui Duan
creator: Yunxia Guo
creator: Yujing Ma
creator: Nazi Niu
creator: Yingjie Zhang
creator: Yueqin Liu
subject: Agricultural Science
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.11868
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary …
bibliographic citation: Yang et al. (2021) Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period. PeerJ 9:e11868 https://doi.org/10.7717/peerj.11868
date submitted: 2021-03-05
date accepted: 2021-07-05
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Ruochen
author list: Agent
  family name: Duan
  given name: Chunhui
author list: Agent
  family name: Guo
  given name: Yunxia
author list: Agent
  family name: Ma
  given name: Yujing
author list: Agent
  family name: Niu
  given name: Nazi
author list: Agent
  family name: Zhang
  given name: Yingjie
author list: Agent
  family name: Liu
  given name: Yueqin
doi: 10.7717/peerj.11868
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer
type: item
type: AcademicArticle
description: Background We investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis. Methods We obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan–Meier (K–M) curve and receiver operating characteristic (ROC) curves to explore the signature’s efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network. Results We found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1. Conclusion Our study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis.
format: application/pdf
format: text/html
creator: Lili Li
creator: Rongrong Xie
creator: Qichun Wei
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11893
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background We investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis. Methods We obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan–Meier (K–M) curve and receiver operating characteristic (ROC) curves to explore the signature’s efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network. Results We found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1. Conclusion Our study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis.
bibliographic citation: Li et al. (2021) Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer. PeerJ 9:e11893 https://doi.org/10.7717/peerj.11893
date submitted: 2021-01-28
date accepted: 2021-07-29
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Lili
author list: Agent
  family name: Xie
  given name: Rongrong
author list: Agent
  family name: Wei
  given name: Qichun
doi: 10.7717/peerj.11893
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: © 2021 Li et al.
attribution name: Li et al.

Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand
type: item
type: AcademicArticle
description: Background The populations of wild Asian elephants (Elephas maximus) have increased recently after a period of worldwide decline in protected areas. It is important to understand the dynamics and distribution of the remaining populations to ensure their conservation and prevent human-elephant conflicts. Methods We monitored the population distribution of elephants between 2016 and 2019 in the Phu Khieo Wildlife Sanctuary, Thailand. We set one hundred forty-nine camera trap locations; cameras recorded 38,834 photos over 6,896 trap nights. Elephants were captured in 4,319 photographs. The maximum entropy modeling software MaxEntwas used to identify elephants’ habitat preferences within 49 of the 149 total camera trap locations according to five environmental factors. Results One hundred fourteen elephants were identified. We identified 30 adult males, 43 adult females, 14 sub-adult males, nine sub-adult females, 11 juveniles, and seven calves. The age structure ratio based on adult femaleswas 0.7:1:0.3:0.2:0.3:0.2, and the ratio of reproductive ability between adult females, juveniles, and calves was 1:0.2:0.1. A suitable elephant habitat was determined to be 1,288.9 km2 using Area Under the Curve (AUC). An AUC = 0.061 indicated good performance. Our model classified habitat preferences associated with elevation, forests, salt licks, human activity, and slope. Conclusions According to our probability map this sanctuary can provide a suitable habitat for elephants. Our results indicate that effective management practices can protect wild Asian elephants in the region and reduce conflict between humans and elephants.
format: application/pdf
format: text/html
creator: Nyi Nyi Phyo Htet
creator: Rattanawat Chaiyarat
creator: Nikorn Thongthip
creator: Panat Anuracpreeda
creator: Namphung Youngpoy
creator: Phonlugsamee Chompoopong
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.11896
publisher: PeerJ Inc.
rights: © 2021 Htet et al.
abstract: Background The populations of wild Asian elephants (Elephas maximus) have increased recently after a period of worldwide decline in protected areas. It is important to understand the dynamics and distribution of the remaining populations to ensure their conservation and prevent human-elephant conflicts. Methods We monitored the population distribution of elephants between 2016 and 2019 in the Phu Khieo Wildlife Sanctuary, Thailand. We set one hundred forty-nine camera trap locations; cameras recorded 38,834 photos over 6,896 trap nights. Elephants were captured in 4,319 photographs. The maximum entropy modeling software MaxEntwas used to identify elephants’ habitat preferences within 49 of the 149 total camera trap locations according to five environmental factors. Results One hundred fourteen elephants were identified. We identified 30 adult males, 43 adult females, 14 sub-adult males, nine sub-adult females, 11 juveniles, and seven calves. The age structure ratio based on adult femaleswas 0.7:1:0.3:0.2:0.3:0.2, and the ratio of reproductive ability between adult females, juveniles, and calves was 1:0.2:0.1. A suitable elephant habitat was determined to be 1,288.9 km2 using Area Under the Curve (AUC). An AUC = 0.061 indicated good performance. Our model classified habitat preferences associated with elevation, forests, salt licks, human activity, and slope. Conclusions According to our probability map this sanctuary can provide a suitable habitat for elephants. Our results indicate that effective management practices can protect wild Asian elephants in the region and reduce conflict between humans and elephants.
bibliographic citation: Htet et al. (2021) Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand. PeerJ 9:e11896 https://doi.org/10.7717/peerj.11896
date submitted: 2021-01-26
date accepted: 2021-07-12
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Htet
  given name: Nyi Nyi Phyo
author list: Agent
  family name: Chaiyarat
  given name: Rattanawat
author list: Agent
  family name: Thongthip
  given name: Nikorn
author list: Agent
  family name: Anuracpreeda
  given name: Panat
author list: Agent
  family name: Youngpoy
  given name: Namphung
author list: Agent
  family name: Chompoopong
  given name: Phonlugsamee
doi: 10.7717/peerj.11896
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Htet et al.
attribution name: Htet et al.

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
type: item
type: AcademicArticle
description: Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic dist…
format: application/pdf
format: text/html
creator: Patricia Sarcinelli Stelzer
creator: Ana Carolina A. Mazzuco
creator: Luiz Eduardo Gomes
creator: João Martins
creator: Sergio Netto
creator: Angelo F. Bernardino
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.11903
publisher: PeerJ Inc.
rights: © 2021 Stelzer et al.
abstract: Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic dist…
bibliographic citation: Stelzer et al. (2021) Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil. PeerJ 9:e11903 https://doi.org/10.7717/peerj.11903
date submitted: 2021-03-26
date accepted: 2021-07-13
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stelzer
  given name: Patricia Sarcinelli
author list: Agent
  family name: Mazzuco
  given name: Ana Carolina A.
author list: Agent
  family name: Gomes
  given name: Luiz Eduardo
author list: Agent
  family name: Martins
  given name: João
author list: Agent
  family name: Netto
  given name: Sergio
author list: Agent
  family name: Bernardino
  given name: Angelo F.
doi: 10.7717/peerj.11903
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: © 2021 Stelzer et al.
attribution name: Stelzer et al.

Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas
type: item
type: AcademicArticle
description: Protected areas are one of the primary conservation tools used worldwide. However, they are often embedded in a landscape that is intensely used by people, such as for agriculture or urban development. The proximity of these land-use types to protected areas can potentially affect the ecological effectiveness (or conservation effectiveness) of protected areas. In this article, we examine to what degree adjacent agricultural and urban land uses affect the ecological effectiveness of protected areas over the greater Gauteng region of South Africa. We selected 198 common, resident bird species, and analysed detection/non-detection data for these species collected over regular grid cells (approximately 61 km2 in area). For each species, we estimated abundance per grid cell with the Royle-Nichols model in relation to the proportion of protected area as a covariate. Our study focused on how this relationship between proportion of protected area and abundance (which we term the ‘protection–abundance relationship’) changed as a function of other land-use types in the grid cell. Specifically, we examined the interaction effects between protected area and both urban and agricultural land-use type per grid cell on bird abundance. We assigned each species to one of seven guilds, namely: frugivores, gleaners, granivores, ground-feeders, hawkers, predators and vegivores, and examined how the protection–abundance relationship varied across guilds in relation to agriculture and urban area. As urban area within a grid cell increased, the protection–abundance relationship became more positive for 58% of all species. At the level of guilds, the protection–abundance relationship became more positive for two guilds (granivores and ground-feeders), more negative for frugivores, and remained unchanged for the other four guilds (gleaners, hawkers, predators and vegivores). As agricultural area within a grid cell increased, the protection–abundance relationship became more positive for 49% …
format: application/pdf
format: text/html
creator: Gregory Duncan Duckworth
creator: Res Altwegg
subject: Ecology
subject: Zoology
subject: Statistics
subject: Environmental Impacts
subject: Population Biology
description: doi:10.7717/peerj.10719
publisher: PeerJ Inc.
rights: © 2021 Duckworth and Altwegg
abstract: Protected areas are one of the primary conservation tools used worldwide. However, they are often embedded in a landscape that is intensely used by people, such as for agriculture or urban development. The proximity of these land-use types to protected areas can potentially affect the ecological effectiveness (or conservation effectiveness) of protected areas. In this article, we examine to what degree adjacent agricultural and urban land uses affect the ecological effectiveness of protected areas over the greater Gauteng region of South Africa. We selected 198 common, resident bird species, and analysed detection/non-detection data for these species collected over regular grid cells (approximately 61 km2 in area). For each species, we estimated abundance per grid cell with the Royle-Nichols model in relation to the proportion of protected area as a covariate. Our study focused on how this relationship between proportion of protected area and abundance (which we term the ‘protection–abundance relationship’) changed as a function of other land-use types in the grid cell. Specifically, we examined the interaction effects between protected area and both urban and agricultural land-use type per grid cell on bird abundance. We assigned each species to one of seven guilds, namely: frugivores, gleaners, granivores, ground-feeders, hawkers, predators and vegivores, and examined how the protection–abundance relationship varied across guilds in relation to agriculture and urban area. As urban area within a grid cell increased, the protection–abundance relationship became more positive for 58% of all species. At the level of guilds, the protection–abundance relationship became more positive for two guilds (granivores and ground-feeders), more negative for frugivores, and remained unchanged for the other four guilds (gleaners, hawkers, predators and vegivores). As agricultural area within a grid cell increased, the protection–abundance relationship became more positive for 49% …
bibliographic citation: Duckworth et al. (2021) Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas. PeerJ 9:e10719 https://doi.org/10.7717/peerj.10719
date submitted: 2018-03-20
date accepted: 2020-12-15
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duckworth
  given name: Gregory Duncan
author list: Agent
  family name: Altwegg
  given name: Res
doi: 10.7717/peerj.10719
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: © 2021 Duckworth and Altwegg
attribution name: Duckworth and Altwegg

Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery
type: item
type: AcademicArticle
description: Marine life has provided mankind with unique and extraordinary chemical structures and scaffolds with potent biological activities. Many organisms and secondary metabolites derived from fungi and symbionts are found to be more environmentally friendly to study than the marine corals per se. Marine symbionts such as Aspergillus sp., a fungus, which can be isolated and grown in the lab would be a potential and continuous source of bioactive natural compounds without affecting the marine environment. The Red Sea is known for its biodiversity and is well-studied in terms of its marine-derived bioactive metabolites. The harsh environmental conditions lead to the development of unique metabolic pathways. This, in turn, results in enhanced synthesis and release of toxic and bioactive chemicals. Interestingly, the Persian Gulf and the Gulf of Oman carry a variety of environmental stresses, some of which are similar to the Red Sea. When compared to the Red Sea, the Persian Gulf has been shown to be rich in marine fungi as well, and is, therefore, expected to contain elaborate and interesting bioactive compounds. Such compounds may or may not be similar to the ones isolated from the Red Sea environment. Astoundingly, there are a very limited number of studies on the bioactive portfolio of marine-derived metabolites from the Persian Gulf and the Gulf of Oman. In this perspective, we are looking at the Red Sea as a comparator marine environment and bioactive materials repertoire to provide a futuristic perspective on the potential of the understudied and possibly overlooked bioactive metabolites derived from the marine life of the Persian Gulf and the Gulf of Oman despite its proven biodiversity and harsher environmental stress.
format: application/pdf
format: text/html
creator: Reham K. Abuhijjleh
creator: Samiullah Shabbir
creator: Ahmed M. Al-Abd
creator: Nada H. Jiaan
creator: Shahad Alshamil
creator: Eman M. El-labbad
creator: Sherief I. Khalifa
subject: Biochemistry
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.11778
publisher: PeerJ Inc.
rights: © 2021 Abuhijjleh et al.
abstract: Marine life has provided mankind with unique and extraordinary chemical structures and scaffolds with potent biological activities. Many organisms and secondary metabolites derived from fungi and symbionts are found to be more environmentally friendly to study than the marine corals per se. Marine symbionts such as Aspergillus sp., a fungus, which can be isolated and grown in the lab would be a potential and continuous source of bioactive natural compounds without affecting the marine environment. The Red Sea is known for its biodiversity and is well-studied in terms of its marine-derived bioactive metabolites. The harsh environmental conditions lead to the development of unique metabolic pathways. This, in turn, results in enhanced synthesis and release of toxic and bioactive chemicals. Interestingly, the Persian Gulf and the Gulf of Oman carry a variety of environmental stresses, some of which are similar to the Red Sea. When compared to the Red Sea, the Persian Gulf has been shown to be rich in marine fungi as well, and is, therefore, expected to contain elaborate and interesting bioactive compounds. Such compounds may or may not be similar to the ones isolated from the Red Sea environment. Astoundingly, there are a very limited number of studies on the bioactive portfolio of marine-derived metabolites from the Persian Gulf and the Gulf of Oman. In this perspective, we are looking at the Red Sea as a comparator marine environment and bioactive materials repertoire to provide a futuristic perspective on the potential of the understudied and possibly overlooked bioactive metabolites derived from the marine life of the Persian Gulf and the Gulf of Oman despite its proven biodiversity and harsher environmental stress.
bibliographic citation: Abuhijjleh et al. (2021) Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery. PeerJ 9:e11778 https://doi.org/10.7717/peerj.11778
date submitted: 2021-03-08
date accepted: 2021-06-24
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abuhijjleh
  given name: Reham K.
author list: Agent
  family name: Shabbir
  given name: Samiullah
author list: Agent
  family name: Al-Abd
  given name: Ahmed M.
author list: Agent
  family name: Jiaan
  given name: Nada H.
author list: Agent
  family name: Alshamil
  given name: Shahad
author list: Agent
  family name: El-labbad
  given name: Eman M.
author list: Agent
  family name: Khalifa
  given name: Sherief I.
doi: 10.7717/peerj.11778
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: © 2021 Abuhijjleh et al.
attribution name: Abuhijjleh et al.

Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153
type: item
type: AcademicArticle
description: Background Polychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood. Methods Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR). Results The results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing. Conclusion This study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation.
format: application/pdf
format: text/html
creator: Jiaci Li
creator: Yaqing Jing
creator: Yi Liu
creator: Yawei Ru
creator: Mingyan Ju
creator: Yuxia Zhao
creator: Guang Li
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.11816
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Polychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood. Methods Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR). Results The results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing. Conclusion This study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation.
bibliographic citation: Li et al. (2021) Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153. PeerJ 9:e11816 https://doi.org/10.7717/peerj.11816
date submitted: 2021-04-01
date accepted: 2021-06-29
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiaci
author list: Agent
  family name: Jing
  given name: Yaqing
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Ru
  given name: Yawei
author list: Agent
  family name: Ju
  given name: Mingyan
author list: Agent
  family name: Zhao
  given name: Yuxia
author list: Agent
  family name: Li
  given name: Guang
doi: 10.7717/peerj.11816
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Li et al.
attribution name: Li et al.

A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides
type: item
type: AcademicArticle
description: Background Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date. Methods The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities. Results Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in…
format: application/pdf
format: text/html
creator: Nguyen Thi-Hanh Vu
creator: Tung Ngoc Quach
creator: Xuan Thi-Thanh Dao
creator: Ha Thanh Le
creator: Chi Phuong Le
creator: Lam Tung Nguyen
creator: Lam Tung Le
creator: Cuong Cao Ngo
creator: Ha Hoang
creator: Ha Hoang Chu
creator: Quyet-Tien Phi
subject: Biochemistry
subject: Biotechnology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.11839
publisher: PeerJ Inc.
rights: © 2021 Vu et al.
abstract: Background Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date. Methods The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities. Results Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in…
bibliographic citation: Vu et al. (2021) A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides. PeerJ 9:e11839 https://doi.org/10.7717/peerj.11839
date submitted: 2021-03-11
date accepted: 2021-07-01
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vu
  given name: Nguyen Thi-Hanh
author list: Agent
  family name: Quach
  given name: Tung Ngoc
author list: Agent
  family name: Dao
  given name: Xuan Thi-Thanh
author list: Agent
  family name: Le
  given name: Ha Thanh
author list: Agent
  family name: Le
  given name: Chi Phuong
author list: Agent
  family name: Nguyen
  given name: Lam Tung
author list: Agent
  family name: Le
  given name: Lam Tung
author list: Agent
  family name: Ngo
  given name: Cuong Cao
author list: Agent
  family name: Hoang
  given name: Ha
author list: Agent
  family name: Chu
  given name: Ha Hoang
author list: Agent
  family name: Phi
  given name: Quyet-Tien
doi: 10.7717/peerj.11839
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Vu et al.
attribution name: Vu et al.

Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas
type: item
type: AcademicArticle
description: The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of a…
format: application/pdf
format: text/html
creator: Ruben U. Tovar
creator: Valentin Cantu
creator: Brian Fremaux
creator: Pedro Gonzalez Jr
creator: Amanda Spikes
creator: Dana M. García
subject: Developmental Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.11840
publisher: PeerJ Inc.
rights: © 2021 Tovar et al.
abstract: The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of a…
bibliographic citation: Tovar et al. (2021) Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas. PeerJ 9:e11840 https://doi.org/10.7717/peerj.11840
date submitted: 2018-10-20
date accepted: 2021-07-01
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tovar
  given name: Ruben U.
author list: Agent
  family name: Cantu
  given name: Valentin
author list: Agent
  family name: Fremaux
  given name: Brian
author list: Agent
  family name: Gonzalez Jr
  given name: Pedro
author list: Agent
  family name: Spikes
  given name: Amanda
author list: Agent
  family name: García
  given name: Dana M.
doi: 10.7717/peerj.11840
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Tovar et al.
attribution name: Tovar et al.

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