PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study
items: Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.
items: Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
items: Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma
items: The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust
items: Connectivity in Spanish metapopulation of Dupont’s lark may be maintained by dispersal over medium-distance range and stepping stones
items: Nitrous oxide, methane emissions and grain yield in rainfed wheat grown under nitrogen enriched biochar and straw in a semiarid environment
items: A new species of Phrynoglossus Peters, 1867; Dicroglossidae) from southeastern Bangladesh, with comments on the genera Occidozyga and Phrynoglossus
items: Prevalence of abnormal urinary cadmium and risk of albuminuria as a primary bioindicator for kidney problems among a healthy population
items: The relationship between characteristics of root morphology and grain filling in wheat under drought stress

Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study
type: item
type: AcademicArticle
description: Background Alzheimer’s disease (AD) is an age-related neurodegenerative disease caused by central nervous system disorders. Late-onset Alzheimer disease (LOAD) is the most common neurodegenerative disorder worldwide. Differences at the expression level of certain genes, resulting from either genetic variations or environmental interactions, might be one of the mechanisms underlying differential risks for developing AD. Peripheral blood genome transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tau for AD research. Methods This preliminary study explores molecular pathogenesis of LOAD-related inflammation through next generation sequencing, to assess RNA expression profiles in peripheral blood from five patients with LOAD and 10 healthy controls. Results The analysis of RNA expression profiles revealed 94 genes up-regulated and 147 down-regulated. Gene function analysis, including Gene Ontology (GO) and KOBAS-Kyoto Encyclopedia of DEGs and Genomes (KEGG) pathways indicated upregulation of interferon family (INF) signaling, while the down-regulated genes were mainly associated with the cell cycle process. KEGG metabolic pathways mapping showed gene expression alterations in the signaling pathways of JAK/STAT, chemokines, MAP kinases and Alzheimer disease. The results of this preliminary study provided not only a comprehensive picture of gene expression, but also the key processes associated with pathology for the regulation of neuroinflammation, to improve the current mechanisms to treat LOAD.
format: application/pdf
format: text/html
creator: Kelly Cardona
creator: Javier Medina
creator: Mary Orrego-Cardozo
creator: Francia Restrepo de Mejía
creator: Xabier Elcoroaristizabal
creator: Carlos Andrés Naranjo Galvis
subject: Bioinformatics
subject: Molecular Biology
subject: Cognitive Disorders
subject: Geriatrics
subject: Neurology
description: doi:10.7717/peerj.12016
publisher: PeerJ Inc.
rights: © 2021 Cardona et al.
abstract: Background Alzheimer’s disease (AD) is an age-related neurodegenerative disease caused by central nervous system disorders. Late-onset Alzheimer disease (LOAD) is the most common neurodegenerative disorder worldwide. Differences at the expression level of certain genes, resulting from either genetic variations or environmental interactions, might be one of the mechanisms underlying differential risks for developing AD. Peripheral blood genome transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tau for AD research. Methods This preliminary study explores molecular pathogenesis of LOAD-related inflammation through next generation sequencing, to assess RNA expression profiles in peripheral blood from five patients with LOAD and 10 healthy controls. Results The analysis of RNA expression profiles revealed 94 genes up-regulated and 147 down-regulated. Gene function analysis, including Gene Ontology (GO) and KOBAS-Kyoto Encyclopedia of DEGs and Genomes (KEGG) pathways indicated upregulation of interferon family (INF) signaling, while the down-regulated genes were mainly associated with the cell cycle process. KEGG metabolic pathways mapping showed gene expression alterations in the signaling pathways of JAK/STAT, chemokines, MAP kinases and Alzheimer disease. The results of this preliminary study provided not only a comprehensive picture of gene expression, but also the key processes associated with pathology for the regulation of neuroinflammation, to improve the current mechanisms to treat LOAD.
bibliographic citation: Cardona et al. (2021) Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PeerJ 9:e12016 https://doi.org/10.7717/peerj.12016
date submitted: 2021-03-15
date accepted: 2021-07-29
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardona
  given name: Kelly
author list: Agent
  family name: Medina
  given name: Javier
author list: Agent
  family name: Orrego-Cardozo
  given name: Mary
author list: Agent
  family name: Restrepo de Mejía
  given name: Francia
author list: Agent
  family name: Elcoroaristizabal
  given name: Xabier
author list: Agent
  family name: Naranjo Galvis
  given name: Carlos Andrés
doi: 10.7717/peerj.12016
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: ©2021 Cardona et al.
attribution name: Cardona et al.

Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.
type: item
type: AcademicArticle
description: Cryptosporidium spp. is a protozoan having the potential to cause zoonosis in humans and animals. Despite the zoonotic importance of this protozoan parasite, limited data are available about its prevalence in zoo felids in North-Eastern China. Hence, the current study was designed to determine the occurrence and molecular characterization of Cryptosporidium spp. from the fecal samples of captive zoo felids. Fecal samples (N = 244) were collected from different felids from five different zoos of North-Eastern China. 18S rRNA gene was amplified from the genomic DNA using species specific primers in nested polymerase chain reaction (nPCR) and Cryptosporidium parvum and Cryptosporidium spp. was found. The overall prevalence of Cryptosporidium was 9.43% (23/244). The 18S rRNA gene similarity analysis showed that 6 Cryptosporidium isolates were Cryptosporidium parvum and the remaining 17 Cryptosporidium isolates were resembling to a Cryptosporidium spp., which is similar to Cryptosporidium NEV10. Phylogenetic tree was constructed based on 18S rRNA of Cryptosporidium spp. The similarity of Cryptosporidium parvum was with its other isolates in China, India, Iran, Iraq, Turkey, Czech Republic, Spain and USA while Cryptosporidium NEV10 alike had a close relationship with Turkish isolates. In conclusion, Cryptosporidium was prevailing in feline animals of China zoo and zoo officials are directed to consider their control policy as it can be a cause of zoonosis.
format: application/pdf
format: text/html
creator: Shakeel Hussain
creator: Syed Mohsin Bukhari
creator: Lixin Wang
creator: Nimra Khalid
creator: Zhijun Hou
subject: Genomics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.11819
publisher: PeerJ Inc.
rights: © 2021 Hussain et al.
abstract: Cryptosporidium spp. is a protozoan having the potential to cause zoonosis in humans and animals. Despite the zoonotic importance of this protozoan parasite, limited data are available about its prevalence in zoo felids in North-Eastern China. Hence, the current study was designed to determine the occurrence and molecular characterization of Cryptosporidium spp. from the fecal samples of captive zoo felids. Fecal samples (N = 244) were collected from different felids from five different zoos of North-Eastern China. 18S rRNA gene was amplified from the genomic DNA using species specific primers in nested polymerase chain reaction (nPCR) and Cryptosporidium parvum and Cryptosporidium spp. was found. The overall prevalence of Cryptosporidium was 9.43% (23/244). The 18S rRNA gene similarity analysis showed that 6 Cryptosporidium isolates were Cryptosporidium parvum and the remaining 17 Cryptosporidium isolates were resembling to a Cryptosporidium spp., which is similar to Cryptosporidium NEV10. Phylogenetic tree was constructed based on 18S rRNA of Cryptosporidium spp. The similarity of Cryptosporidium parvum was with its other isolates in China, India, Iran, Iraq, Turkey, Czech Republic, Spain and USA while Cryptosporidium NEV10 alike had a close relationship with Turkish isolates. In conclusion, Cryptosporidium was prevailing in feline animals of China zoo and zoo officials are directed to consider their control policy as it can be a cause of zoonosis.
bibliographic citation: Hussain et al. (2021) Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.. PeerJ 9:e11819 https://doi.org/10.7717/peerj.11819
date submitted: 2020-10-15
date accepted: 2021-06-29
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hussain
  given name: Shakeel
author list: Agent
  family name: Mohsin Bukhari
  given name: Syed
author list: Agent
  family name: Wang
  given name: Lixin
author list: Agent
  family name: Khalid
  given name: Nimra
author list: Agent
  family name: Hou
  given name: Zhijun
doi: 10.7717/peerj.11819
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: © 2021 Hussain et al.
attribution name: Hussain et al.

Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
type: item
type: AcademicArticle
description: With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
format: application/pdf
format: text/html
creator: Yen-Yi Liu
creator: Bo-Han Chen
creator: Chih-Chieh Chen
creator: Chien-Shun Chiou
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.11842
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
bibliographic citation: Liu et al. (2021) Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type. PeerJ 9:e11842 https://doi.org/10.7717/peerj.11842
date submitted: 2021-04-21
date accepted: 2021-07-01
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yen-Yi
author list: Agent
  family name: Chen
  given name: Bo-Han
author list: Agent
  family name: Chen
  given name: Chih-Chieh
author list: Agent
  family name: Chiou
  given name: Chien-Shun
doi: 10.7717/peerj.11842
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung cancer is a common malignant carcinoma of respiratory system with high morbidity and mortality. Kelch-like epichlorohydrin-related protein 1 (Keap1), a member of the BTB-Kelch protein family, has been reported as an important molecule in several cancers. However, its potential role in tumor is still controversial. Here we aim to clarify the effect of Keap1 on the biological characteristics and chemotherapy resistance in lung adenocarcinoma (LUAD). Methods Immunohistochemistry was conducted to compare Keap1 expression in lung adenocarcinoma tissues and matched non-cancerous tissues, and the correlation between Keap1 expression and clinicopathological features was analyzed. Subsequently, the stable A549 and H1299 cell lines with Keap1 knockdown or overexpression were constructed using lentivirus. The roles of Keap1 on the cell proliferation, migration, invasion and drug resistance were investigated by colony formation assay, cell proliferation assay, wound scratch test, transwell invasion assay and drug sensitivity assay, respectively. Results Keap1 was lowly expressed in tumor tissues compared to matched non-cancerous tissues, and its expression was correlated with TNM stage and lymph node metastasis. Early stage (I) tumors without lymph node metastasis had higher levels of Keap1 expression compared with late-stage tumors (II, III) with the presence of lymphatic metastasis. Colony formation assays showed that Keap1 knockdown promoted the proliferation of A549 and H1299 cells, and the cell growth curves further confirmed this feature. In contrast, wound scratch and transwell invasion experiments showed that Keap1 overexpression inhibited cell migration and invasive malignancy. The IC50 for cisplatin and paclitaxel were significantly increased by Keap1 knockdown in A549 and H1299 cell lines. Conclusion Keap1 knockdown promotes tumor cell growth, proliferation, invasion, metastasis and chemotherapy resistance in LUAD. It may be a potential tumor marker t…
format: application/pdf
format: text/html
creator: Hong Gao
creator: Peipei Tang
creator: Kejie Ni
creator: Lun Zhu
creator: Song Chen
creator: Yulong Zheng
creator: Yufeng Wan
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pathology
subject: Respiratory Medicine
description: doi:10.7717/peerj.11908
publisher: PeerJ Inc.
rights: © 2021 Gao et al.
abstract: Background Lung cancer is a common malignant carcinoma of respiratory system with high morbidity and mortality. Kelch-like epichlorohydrin-related protein 1 (Keap1), a member of the BTB-Kelch protein family, has been reported as an important molecule in several cancers. However, its potential role in tumor is still controversial. Here we aim to clarify the effect of Keap1 on the biological characteristics and chemotherapy resistance in lung adenocarcinoma (LUAD). Methods Immunohistochemistry was conducted to compare Keap1 expression in lung adenocarcinoma tissues and matched non-cancerous tissues, and the correlation between Keap1 expression and clinicopathological features was analyzed. Subsequently, the stable A549 and H1299 cell lines with Keap1 knockdown or overexpression were constructed using lentivirus. The roles of Keap1 on the cell proliferation, migration, invasion and drug resistance were investigated by colony formation assay, cell proliferation assay, wound scratch test, transwell invasion assay and drug sensitivity assay, respectively. Results Keap1 was lowly expressed in tumor tissues compared to matched non-cancerous tissues, and its expression was correlated with TNM stage and lymph node metastasis. Early stage (I) tumors without lymph node metastasis had higher levels of Keap1 expression compared with late-stage tumors (II, III) with the presence of lymphatic metastasis. Colony formation assays showed that Keap1 knockdown promoted the proliferation of A549 and H1299 cells, and the cell growth curves further confirmed this feature. In contrast, wound scratch and transwell invasion experiments showed that Keap1 overexpression inhibited cell migration and invasive malignancy. The IC50 for cisplatin and paclitaxel were significantly increased by Keap1 knockdown in A549 and H1299 cell lines. Conclusion Keap1 knockdown promotes tumor cell growth, proliferation, invasion, metastasis and chemotherapy resistance in LUAD. It may be a potential tumor marker t…
bibliographic citation: Gao et al. (2021) Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma. PeerJ 9:e11908 https://doi.org/10.7717/peerj.11908
date submitted: 2021-01-12
date accepted: 2021-07-14
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Hong
author list: Agent
  family name: Tang
  given name: Peipei
author list: Agent
  family name: Ni
  given name: Kejie
author list: Agent
  family name: Zhu
  given name: Lun
author list: Agent
  family name: Chen
  given name: Song
author list: Agent
  family name: Zheng
  given name: Yulong
author list: Agent
  family name: Wan
  given name: Yufeng
doi: 10.7717/peerj.11908
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: © 2021 Gao et al.
attribution name: Gao et al.

The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust
type: item
type: AcademicArticle
description: Orchardgrass (Dactylis glomerata) is one of the top four perennial forages worldwide and, despite its large economic advantages, often threatened by various environmental stresses. WRKY transcription factors (TFs) can regulate a variety of plant processes, widely participate in plant responses to biotic and abiotic stresses, and are one of the largest gene families in plants. WRKYs can usually bind W-box elements specifically. In this study, we identified a total of 93 DgWRKY genes and 281 RGAs, including 65, 169 and 47 nucleotide-binding site-leucine-rich repeats (NBS-LRRs), leucine-rich repeats receptor-like protein kinases (LRR-RLKs), and leucine-rich repeats receptor-like proteins (LRR-RLPs), respectively. Through analyzing the expression of DgWRKY genes in orchardgrass under different environmental stresses, it was found that many DgWRKY genes were differentially expressed under heat, drought, submergence, and rust stress. In particular, it was found that the greatest number of genes were differentially expressed under rust infection. Consistently, GO and KEGG enrichment analysis of all genes showed that 78 DgWRKY TFs were identified in the plant–pathogen interaction pathway, with 59 of them differentially expressed. Through cis-acting element prediction, 154 RGAs were found to contain W-box elements. Among them, DG6C02319.1 (a member of the LRR-RLK family) was identified as likely to interact with 14 DGWRKYs. Moreover, their expression levels in susceptible plants after rust inoculation were first up-regulated and then down-regulated, while those in the resistant plants were always up-regulated. In general, DgWRKYs responded to both biotic stress and abiotic stress. DgWRKYs and RGAs may synergistically respond to the response of orchardgrass to rust. This study provides meaningful insight into the molecular mechanisms of WRKY proteins in orchardgrass.
format: application/pdf
format: text/html
creator: Juncai Ren
creator: Jialing Hu
creator: Ailing Zhang
creator: Shuping Ren
creator: Tingting Jing
creator: Xiaoshan Wang
creator: Min Sun
creator: Linkai Huang
creator: Bing Zeng
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.11919
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Orchardgrass (Dactylis glomerata) is one of the top four perennial forages worldwide and, despite its large economic advantages, often threatened by various environmental stresses. WRKY transcription factors (TFs) can regulate a variety of plant processes, widely participate in plant responses to biotic and abiotic stresses, and are one of the largest gene families in plants. WRKYs can usually bind W-box elements specifically. In this study, we identified a total of 93 DgWRKY genes and 281 RGAs, including 65, 169 and 47 nucleotide-binding site-leucine-rich repeats (NBS-LRRs), leucine-rich repeats receptor-like protein kinases (LRR-RLKs), and leucine-rich repeats receptor-like proteins (LRR-RLPs), respectively. Through analyzing the expression of DgWRKY genes in orchardgrass under different environmental stresses, it was found that many DgWRKY genes were differentially expressed under heat, drought, submergence, and rust stress. In particular, it was found that the greatest number of genes were differentially expressed under rust infection. Consistently, GO and KEGG enrichment analysis of all genes showed that 78 DgWRKY TFs were identified in the plant–pathogen interaction pathway, with 59 of them differentially expressed. Through cis-acting element prediction, 154 RGAs were found to contain W-box elements. Among them, DG6C02319.1 (a member of the LRR-RLK family) was identified as likely to interact with 14 DGWRKYs. Moreover, their expression levels in susceptible plants after rust inoculation were first up-regulated and then down-regulated, while those in the resistant plants were always up-regulated. In general, DgWRKYs responded to both biotic stress and abiotic stress. DgWRKYs and RGAs may synergistically respond to the response of orchardgrass to rust. This study provides meaningful insight into the molecular mechanisms of WRKY proteins in orchardgrass.
bibliographic citation: Ren et al. (2021) The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust. PeerJ 9:e11919 https://doi.org/10.7717/peerj.11919
date submitted: 2021-02-15
date accepted: 2021-07-16
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Juncai
author list: Agent
  family name: Hu
  given name: Jialing
author list: Agent
  family name: Zhang
  given name: Ailing
author list: Agent
  family name: Ren
  given name: Shuping
author list: Agent
  family name: Jing
  given name: Tingting
author list: Agent
  family name: Wang
  given name: Xiaoshan
author list: Agent
  family name: Sun
  given name: Min
author list: Agent
  family name: Huang
  given name: Linkai
author list: Agent
  family name: Zeng
  given name: Bing
doi: 10.7717/peerj.11919
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: © 2021 Ren et al.
attribution name: Ren et al.

Connectivity in Spanish metapopulation of Dupont’s lark may be maintained by dispersal over medium-distance range and stepping stones
type: item
type: AcademicArticle
description: Background Dupont’s Lark is an endangered bird, whose fragmented distribution in Europe is entirely restricted to Spain. This lark, suffering pronounced population decline and range contraction, inhabits steppes that have long been used for grazing sheep and are now threatened by rural abandonment and land use changes. Thus, for conservation of the lark, increasing knowledge about the connectivity of the Spanish metapopulation and identifying the most important connectivity nodes are crucial. Methods The study was carried out in Spain, using over 16,000 Dupont’s Lark georeferenced observations. We used distance buffers to define populations and subpopulations, based on the available scientific information. We identified potential stepping stones using a MaxEnt probability of presence model. Connectivity was assessed using Conefor software, using the centroid of each subpopulation and stepping stone as nodes. Each node was assigned a quantitative attribute based on total habitat area, within-node habitat quality and internal fragmentation. We evaluated different connectivity scenarios by potential movement thresholds (5–20–100 km) and presence or absence of stepping stones in the network. Results Dupont’s Lark Iberian metapopulation comprises 24 populations and 100 subpopulations, plus 294 potential stepping stones. Movement thresholds and stepping stones had a strong influence in the potential network connectivity. The most important nodes are located in the core of the metapopulation, which shows connectivity among subpopulations in the different indices and scenarios evaluated. Peripheral populations are more isolated and require stepping stones or medium (20 km) or long (100 km) potential movement thresholds to join the network. Discussion Metapopulation connectivity may be greater than expected, thanks to stepping stones and potential medium-distance movements. Connectivity is crucial for conservation and can be increased by preserving or improving adequate habi…
format: application/pdf
format: text/html
creator: Alexander García-Antón
creator: Vicente Garza
creator: Juan Traba
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.11925
publisher: PeerJ Inc.
rights: © 2021 García-Antón et al.
abstract: Background Dupont’s Lark is an endangered bird, whose fragmented distribution in Europe is entirely restricted to Spain. This lark, suffering pronounced population decline and range contraction, inhabits steppes that have long been used for grazing sheep and are now threatened by rural abandonment and land use changes. Thus, for conservation of the lark, increasing knowledge about the connectivity of the Spanish metapopulation and identifying the most important connectivity nodes are crucial. Methods The study was carried out in Spain, using over 16,000 Dupont’s Lark georeferenced observations. We used distance buffers to define populations and subpopulations, based on the available scientific information. We identified potential stepping stones using a MaxEnt probability of presence model. Connectivity was assessed using Conefor software, using the centroid of each subpopulation and stepping stone as nodes. Each node was assigned a quantitative attribute based on total habitat area, within-node habitat quality and internal fragmentation. We evaluated different connectivity scenarios by potential movement thresholds (5–20–100 km) and presence or absence of stepping stones in the network. Results Dupont’s Lark Iberian metapopulation comprises 24 populations and 100 subpopulations, plus 294 potential stepping stones. Movement thresholds and stepping stones had a strong influence in the potential network connectivity. The most important nodes are located in the core of the metapopulation, which shows connectivity among subpopulations in the different indices and scenarios evaluated. Peripheral populations are more isolated and require stepping stones or medium (20 km) or long (100 km) potential movement thresholds to join the network. Discussion Metapopulation connectivity may be greater than expected, thanks to stepping stones and potential medium-distance movements. Connectivity is crucial for conservation and can be increased by preserving or improving adequate habi…
bibliographic citation: García-Antón et al. (2021) Connectivity in Spanish metapopulation of Dupont’s lark may be maintained by dispersal over medium-distance range and stepping stones. PeerJ 9:e11925 https://doi.org/10.7717/peerj.11925
date submitted: 2021-01-13
date accepted: 2021-07-16
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Antón
  given name: Alexander
author list: Agent
  family name: Garza
  given name: Vicente
author list: Agent
  family name: Traba
  given name: Juan
doi: 10.7717/peerj.11925
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: © 2021 García-Antón et al.
attribution name: García-Antón et al.

Nitrous oxide, methane emissions and grain yield in rainfed wheat grown under nitrogen enriched biochar and straw in a semiarid environment
type: item
type: AcademicArticle
description: Background Soil application of biochar and straw alone or their combinations with nitrogen (N) fertilizer are becoming increasingly common, but little is known about their agronomic and environmental performance in semiarid environments. This study was conducted to investigate the effect(s) of these amendments on soil properties, nitrous oxide (N2O) and methane (CH4) emissions and grain and biomass yield of spring wheat (Triticum aestivum L.), and to produce background dataset that may be used to inform nutrient management guidelines for semiarid environments. Methods The experiment involved the application of biochar, straw or urea (46% nitrogen [N]) alone or their combinations. The treatments were: CN0–control (zero-amendment), CN50 –50 kg ha–1 N, CN100–100 kg ha–1 N, BN0 –15 t ha–1 biochar, BN50–15 t ha–1 biochar + 50 kg ha–1 N, BN100–15 t ha–1 biochar + 100 kg ha–1 N, SN0 –4.5 t ha–1 straw, SN50 –4.5 t ha–1 straw + 50 kg ha–1 N and SN100–4.5 t ha–1 straw + 100 kg ha–1 N. Fluxes of N2O, CH4 and grain yield were monitored over three consecutive cropping seasons between 2014 and 2016 using the static chamber-gas chromatography method. Results On average, BN100reported the highest grain yield (2054 kg ha–1), which was between 25.04% and 38.34% higher than all other treatments. In addition, biomass yield was much higher under biochar treated plots relative to the other treatments. These findings are supported by the increased in soil organic C by 17.14% and 21.65% in biochar amended soils (at 0–10 cm) compared to straw treated soils and soils without carbon respectively. The BN100treatment also improved bulk density and hydraulic properties (P < 0.05), which supported the above results. The greatest N2O emissions and CH4 sink were recorded under the highest rate of N fertilization (100 kg N ha–1). Cumulative N2O emissions were 39.02% and 48.23% lower in BN100 compared with CN0 and CN100, respectively. There was also a ≈ 37.53% reduction in CH4 uptake under BN100compa…
format: application/pdf
format: text/html
creator: Stephen Yeboah
creator: Wu Jun
creator: Cai Liqun
creator: Patricia Oteng-Darko
creator: Erasmus Narteh Tetteh
creator: Zhang Renzhi
subject: Agricultural Science
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.11937
publisher: PeerJ Inc.
rights: © 2021 Yeboah et al.
abstract: Background Soil application of biochar and straw alone or their combinations with nitrogen (N) fertilizer are becoming increasingly common, but little is known about their agronomic and environmental performance in semiarid environments. This study was conducted to investigate the effect(s) of these amendments on soil properties, nitrous oxide (N2O) and methane (CH4) emissions and grain and biomass yield of spring wheat (Triticum aestivum L.), and to produce background dataset that may be used to inform nutrient management guidelines for semiarid environments. Methods The experiment involved the application of biochar, straw or urea (46% nitrogen [N]) alone or their combinations. The treatments were: CN0–control (zero-amendment), CN50 –50 kg ha–1 N, CN100–100 kg ha–1 N, BN0 –15 t ha–1 biochar, BN50–15 t ha–1 biochar + 50 kg ha–1 N, BN100–15 t ha–1 biochar + 100 kg ha–1 N, SN0 –4.5 t ha–1 straw, SN50 –4.5 t ha–1 straw + 50 kg ha–1 N and SN100–4.5 t ha–1 straw + 100 kg ha–1 N. Fluxes of N2O, CH4 and grain yield were monitored over three consecutive cropping seasons between 2014 and 2016 using the static chamber-gas chromatography method. Results On average, BN100reported the highest grain yield (2054 kg ha–1), which was between 25.04% and 38.34% higher than all other treatments. In addition, biomass yield was much higher under biochar treated plots relative to the other treatments. These findings are supported by the increased in soil organic C by 17.14% and 21.65% in biochar amended soils (at 0–10 cm) compared to straw treated soils and soils without carbon respectively. The BN100treatment also improved bulk density and hydraulic properties (P < 0.05), which supported the above results. The greatest N2O emissions and CH4 sink were recorded under the highest rate of N fertilization (100 kg N ha–1). Cumulative N2O emissions were 39.02% and 48.23% lower in BN100 compared with CN0 and CN100, respectively. There was also a ≈ 37.53% reduction in CH4 uptake under BN100compa…
bibliographic citation: Yeboah et al. (2021) Nitrous oxide, methane emissions and grain yield in rainfed wheat grown under nitrogen enriched biochar and straw in a semiarid environment. PeerJ 9:e11937 https://doi.org/10.7717/peerj.11937
date submitted: 2021-02-04
date accepted: 2021-07-19
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeboah
  given name: Stephen
author list: Agent
  family name: Jun
  given name: Wu
author list: Agent
  family name: Liqun
  given name: Cai
author list: Agent
  family name: Oteng-Darko
  given name: Patricia
author list: Agent
  family name: Narteh Tetteh
  given name: Erasmus
author list: Agent
  family name: Renzhi
  given name: Zhang
doi: 10.7717/peerj.11937
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: ©2021 Yeboah et al.
attribution name: Yeboah et al.

A new species of Phrynoglossus Peters, 1867; Dicroglossidae) from southeastern Bangladesh, with comments on the genera Occidozyga and Phrynoglossus
type: item
type: AcademicArticle
description: We describe a new cryptic species of Phrynoglossus from Chattogram Division, Bangladesh based on an integrative taxonomic analysis based on morphology, phylogenetics, and bioacoustics which unambiguously support the placement of the species in the genus Phrynoglossus. We also present a compilation of published morphological characters for all twelve Phrynoglossus species and two species of Occidozyga as well as comments on taxonomy, morphology, and geographic distribution for the two genera. The new species is found to be most morphologically similar to P. martensii, however a provided set of character states visibly differentiates these two species. Finally, habitat for Phrynoglossus swanbornorum sp. nov. is highly fragmented and faces imminent threats from development and agriculture, and although it is confirmed to occur within government protected areas in the southeastern region of Bangladesh, few wildlife regulations are enforced within them. Thus, following IUCN criteria, we consider the new species as Endangered based on criteria B1ab(i,ii,iii,iv) + 2ab(i,ii,iii,iv).
format: application/pdf
format: text/html
creator: Scott Trageser
creator: Hassan Al-Razi
creator: Marjan Maria
creator: Fahimuzzaman Nobel
creator: Md. Asaduzzaman
creator: Shahriar Caesar Rahman
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11998
publisher: PeerJ Inc.
rights: © 2021 Trageser et al.
abstract: We describe a new cryptic species of Phrynoglossus from Chattogram Division, Bangladesh based on an integrative taxonomic analysis based on morphology, phylogenetics, and bioacoustics which unambiguously support the placement of the species in the genus Phrynoglossus. We also present a compilation of published morphological characters for all twelve Phrynoglossus species and two species of Occidozyga as well as comments on taxonomy, morphology, and geographic distribution for the two genera. The new species is found to be most morphologically similar to P. martensii, however a provided set of character states visibly differentiates these two species. Finally, habitat for Phrynoglossus swanbornorum sp. nov. is highly fragmented and faces imminent threats from development and agriculture, and although it is confirmed to occur within government protected areas in the southeastern region of Bangladesh, few wildlife regulations are enforced within them. Thus, following IUCN criteria, we consider the new species as Endangered based on criteria B1ab(i,ii,iii,iv) + 2ab(i,ii,iii,iv).
bibliographic citation: Trageser et al. (2021) A new species of Phrynoglossus Peters, 1867; Dicroglossidae) from southeastern Bangladesh, with comments on the genera Occidozyga and Phrynoglossus. PeerJ 9:e11998 https://doi.org/10.7717/peerj.11998
date submitted: 2021-01-14
date accepted: 2021-07-27
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trageser
  given name: Scott
author list: Agent
  family name: Al-Razi
  given name: Hassan
author list: Agent
  family name: Maria
  given name: Marjan
author list: Agent
  family name: Nobel
  given name: Fahimuzzaman
author list: Agent
  family name: Asaduzzaman
  given name: Md.
author list: Agent
  family name: Rahman
  given name: Shahriar Caesar
doi: 10.7717/peerj.11998
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: ©2021 Trageser et al.
attribution name: Trageser et al.

Prevalence of abnormal urinary cadmium and risk of albuminuria as a primary bioindicator for kidney problems among a healthy population
type: item
type: AcademicArticle
description: Background The prevalence of chronic kidney disease is increasing globally, ranking 27th as the cause of death in the 1990s, rising to 18th in 2010 and 10th in 2019. Non-communicable diseases such as diabetes and hypertension have been identified as the common contributing factors, while there is also evidence linking environmental pollutants, especially cadmium, to kidney disease. This study aimed at investigating the level of urinary cadmium and its relationship to albuminuria as an early indicator of kidney problems in the Kepong community. Methods Respondents were surveyed as part of several health-related programs organized by the Kepong District Health Office involving local communities in and around the district from April 2019 to December 2019. Urinalysis of two urine samples was carried out using a Mission reagent strip and an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) test to detect the presence and level of urinary cadmium. Results A total of 240 respondents were enrolled from April 2019 to December 2019. Urinalysis of two urine samples was carried out using a Mission reagent strip and an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) test to detect the level of urinary cadmium. The respondents’ average age was 41-year-old (±13.23). Among them, 49.6% were male, 85.0% Malay, 5.8% Chinese and 8.3% Indian. 55.0% had background of tertiary, 39.6% secondary and 5.4% primary level of education. 52.1% were categorized in B40, 34.6% in M40 and 13.3% in T20 based on monthly household income category. 26.7% were hypertensive, 6.7% diabetic, 4.2% had dyslipidemia, 51.7% had urinary cadmium above the alert level, and 27.1% had albuminuria. Discussion Risk factors for albuminuria that have been identified are age with adjusted odds ratio (AOR) 3.53 (1.41–8.83; p < 0.05), highest educational level with AOR 2.18 (1.14–4.17; p < 0.05), diabetes with AOR 3.36 (1.07–10.52; p < 0.05), and urinary cadmium with AOR 4.72 (2.33–9.59; p < 0.001), with future sc…
format: application/pdf
format: text/html
creator: Mohd Faizal Madrim
creator: Mohd Hasni Ja’afar
creator: Rozita Hod
subject: Toxicology
subject: Epidemiology
subject: Nephrology
subject: Public Health
subject: Urology
description: doi:10.7717/peerj.12014
publisher: PeerJ Inc.
rights: © 2021 Madrim et al.
abstract: Background The prevalence of chronic kidney disease is increasing globally, ranking 27th as the cause of death in the 1990s, rising to 18th in 2010 and 10th in 2019. Non-communicable diseases such as diabetes and hypertension have been identified as the common contributing factors, while there is also evidence linking environmental pollutants, especially cadmium, to kidney disease. This study aimed at investigating the level of urinary cadmium and its relationship to albuminuria as an early indicator of kidney problems in the Kepong community. Methods Respondents were surveyed as part of several health-related programs organized by the Kepong District Health Office involving local communities in and around the district from April 2019 to December 2019. Urinalysis of two urine samples was carried out using a Mission reagent strip and an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) test to detect the presence and level of urinary cadmium. Results A total of 240 respondents were enrolled from April 2019 to December 2019. Urinalysis of two urine samples was carried out using a Mission reagent strip and an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) test to detect the level of urinary cadmium. The respondents’ average age was 41-year-old (±13.23). Among them, 49.6% were male, 85.0% Malay, 5.8% Chinese and 8.3% Indian. 55.0% had background of tertiary, 39.6% secondary and 5.4% primary level of education. 52.1% were categorized in B40, 34.6% in M40 and 13.3% in T20 based on monthly household income category. 26.7% were hypertensive, 6.7% diabetic, 4.2% had dyslipidemia, 51.7% had urinary cadmium above the alert level, and 27.1% had albuminuria. Discussion Risk factors for albuminuria that have been identified are age with adjusted odds ratio (AOR) 3.53 (1.41–8.83; p < 0.05), highest educational level with AOR 2.18 (1.14–4.17; p < 0.05), diabetes with AOR 3.36 (1.07–10.52; p < 0.05), and urinary cadmium with AOR 4.72 (2.33–9.59; p < 0.001), with future sc…
bibliographic citation: Madrim et al. (2021) Prevalence of abnormal urinary cadmium and risk of albuminuria as a primary bioindicator for kidney problems among a healthy population. PeerJ 9:e12014 https://doi.org/10.7717/peerj.12014
date submitted: 2021-04-22
date accepted: 2021-07-28
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Madrim
  given name: Mohd Faizal
author list: Agent
  family name: Ja’afar
  given name: Mohd Hasni
author list: Agent
  family name: Hod
  given name: Rozita
doi: 10.7717/peerj.12014
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: ©2021 Madrim et al.
attribution name: Madrim et al.

The relationship between characteristics of root morphology and grain filling in wheat under drought stress
type: item
type: AcademicArticle
description: Drought is a common yield limiting factor in wheat production and has become a significant threat to global food security. Root system is the organ responsible for water uptake from soil and root growth is closely associated with yield and quality of wheat. However, the relationship between morphological and structural characteristics of root growth and caryopsis enrichment in wheat under drought stress is unclear. In this study, two wheat cultivars (YM13 and YN19) were treated with drought from flowering to caryopsis maturity stage. The changes in morphological structure of roots and characteristics of endosperm enrichment were investigated. Drought stress significantly reduced the root length, plant height, root dry weight and aboveground parts dry weight, whereas the root-shoot ratio of YM13 and YN19 increased by 17.65% and 8.33% under drought stress, respectively. The spike length, spike weight, grains number per spike and 1,000-grains weight of mature wheat also significantly declined under drought stress. Meanwhile, the cross section structure of roots was changed with the enlargement of vascular cylinder and dense distribution of xylem vessels under drought stress. Additionally, drought stress affected the substance enrichment in wheat caryopses, decreasing starch accumulation and increasing protein accumulation of endosperm. Correlation analysis suggested that the root length was closely correlated with the relative areas of amyloplast (0.51) and protein body (0.70), and drought stress increased the correlation coefficient (0.79 and 0.78, respectively). While the root dry weight had a significantly positive correlation with the plant height and aboveground parts dry weight. The results can provide theoretical basis for root architecture optimization, water-saving and high-yield cultivation and quality improvement in wheat.
format: application/pdf
format: text/html
creator: Xinyu Chen
creator: Yu Zhu
creator: Yuan Ding
creator: Rumo Pan
creator: Wenyuan Shen
creator: Xurun Yu
creator: Fei Xiong
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12015
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Drought is a common yield limiting factor in wheat production and has become a significant threat to global food security. Root system is the organ responsible for water uptake from soil and root growth is closely associated with yield and quality of wheat. However, the relationship between morphological and structural characteristics of root growth and caryopsis enrichment in wheat under drought stress is unclear. In this study, two wheat cultivars (YM13 and YN19) were treated with drought from flowering to caryopsis maturity stage. The changes in morphological structure of roots and characteristics of endosperm enrichment were investigated. Drought stress significantly reduced the root length, plant height, root dry weight and aboveground parts dry weight, whereas the root-shoot ratio of YM13 and YN19 increased by 17.65% and 8.33% under drought stress, respectively. The spike length, spike weight, grains number per spike and 1,000-grains weight of mature wheat also significantly declined under drought stress. Meanwhile, the cross section structure of roots was changed with the enlargement of vascular cylinder and dense distribution of xylem vessels under drought stress. Additionally, drought stress affected the substance enrichment in wheat caryopses, decreasing starch accumulation and increasing protein accumulation of endosperm. Correlation analysis suggested that the root length was closely correlated with the relative areas of amyloplast (0.51) and protein body (0.70), and drought stress increased the correlation coefficient (0.79 and 0.78, respectively). While the root dry weight had a significantly positive correlation with the plant height and aboveground parts dry weight. The results can provide theoretical basis for root architecture optimization, water-saving and high-yield cultivation and quality improvement in wheat.
bibliographic citation: Chen et al. (2021) The relationship between characteristics of root morphology and grain filling in wheat under drought stress. PeerJ 9:e12015 https://doi.org/10.7717/peerj.12015
date submitted: 2021-06-04
date accepted: 2021-07-29
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xinyu
author list: Agent
  family name: Zhu
  given name: Yu
author list: Agent
  family name: Ding
  given name: Yuan
author list: Agent
  family name: Pan
  given name: Rumo
author list: Agent
  family name: Shen
  given name: Wenyuan
author list: Agent
  family name: Yu
  given name: Xurun
author list: Agent
  family name: Xiong
  given name: Fei
doi: 10.7717/peerj.12015
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: ©2021 Chen et al.
attribution name: Chen et al.

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