PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean
items: Genetic effects of long-term captive breeding on the endangered pygmy hog
items: Event-related potentials evoked by skin puncture reflect activation of Aβ fibers: comparison with intraepidermal and transcutaneous electrical stimulations
items: WIN 55,212-2 shows anti-inflammatory and survival properties in human iPSC-derived cardiomyocytes infected with SARS-CoV-2
items: Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar ‘Qiannan Guifei’
items: Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma
items: Improving size selectivity of round pot for Charybdis japonica by configuring escape vents in the Yellow Sea, China
items: Analysis of how the spatial and temporal patterns of fire and their bioclimatic and anthropogenic drivers vary across the Amazon rainforest in El Niño and non-El Niño years
items: Heronry distribution and site preference dynamics of tree-nesting colonial waterbirds in Tamil Nadu
items: The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)

Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean
type: item
type: AcademicArticle
description: Phosphorus (P) is one of the major constraints for crop growth and development, owing to low availability and least mobility in many tropical soil conditions. Categorization of existing germplasm under P deficient conditions is a prerequisite for the selection and development of P efficient genotypes in the mungbean. In the present investigation, 36 diverse genotypes were categorized for phosphorus use efficiency traits using four different techniques for identification of phosphorus use efficient mungbean genotypes. The studied genotypes were categorized for P efficiency based on efficiency, responsiveness, and stress tolerance score of genotypes under normal and low P conditions. The mean values of traits, root dry mass, root to shoot ratio, and P utilization efficiency are significantly higher under low P conditions indicating the high responsiveness of traits to P deficiency. The presence of significant interaction between genotypes and P treatment indicates the evaluated genotypes were significantly affected by P treatment for studied traits. The total P uptake showed significant and positive correlations with root dry mass, shoot dry mass, total dry mass,and P concentration under both P regimes. Out of the four techniques used for the categorization of genotypes for P efficiency, three techniques revealed that the genotype PUSA 1333, followed by Pusa Vishal, PUSA 1031, and Pusa Ratna is efficient. The categorization based on stress tolerance score is the finest way to study variation and for the selection of contrasting genotypes for P efficiency. The identified P efficient genotypes would be valuable resources for genetic enhancement of P use efficiency in mungbean breeding.
format: application/pdf
format: text/html
creator: Venkata Ravi Prakash Reddy
creator: Harsh Kumar Dikshit
creator: Gyan Prakash Mishra
creator: Muraleedhar Aski
creator: Akanksha Singh
creator: Ruchi Bansal
creator: Renu Pandey
creator: Ramakrishnan Madhavan Nair
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12156
publisher: PeerJ Inc.
rights: © 2021 Reddy et al.
abstract: Phosphorus (P) is one of the major constraints for crop growth and development, owing to low availability and least mobility in many tropical soil conditions. Categorization of existing germplasm under P deficient conditions is a prerequisite for the selection and development of P efficient genotypes in the mungbean. In the present investigation, 36 diverse genotypes were categorized for phosphorus use efficiency traits using four different techniques for identification of phosphorus use efficient mungbean genotypes. The studied genotypes were categorized for P efficiency based on efficiency, responsiveness, and stress tolerance score of genotypes under normal and low P conditions. The mean values of traits, root dry mass, root to shoot ratio, and P utilization efficiency are significantly higher under low P conditions indicating the high responsiveness of traits to P deficiency. The presence of significant interaction between genotypes and P treatment indicates the evaluated genotypes were significantly affected by P treatment for studied traits. The total P uptake showed significant and positive correlations with root dry mass, shoot dry mass, total dry mass,and P concentration under both P regimes. Out of the four techniques used for the categorization of genotypes for P efficiency, three techniques revealed that the genotype PUSA 1333, followed by Pusa Vishal, PUSA 1031, and Pusa Ratna is efficient. The categorization based on stress tolerance score is the finest way to study variation and for the selection of contrasting genotypes for P efficiency. The identified P efficient genotypes would be valuable resources for genetic enhancement of P use efficiency in mungbean breeding.
bibliographic citation: Reddy et al. (2021) Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean. PeerJ 9:e12156 https://doi.org/10.7717/peerj.12156
date submitted: 2021-03-29
date accepted: 2021-08-24
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reddy
  given name: Venkata Ravi Prakash
author list: Agent
  family name: Dikshit
  given name: Harsh Kumar
author list: Agent
  family name: Mishra
  given name: Gyan Prakash
author list: Agent
  family name: Aski
  given name: Muraleedhar
author list: Agent
  family name: Singh
  given name: Akanksha
author list: Agent
  family name: Bansal
  given name: Ruchi
author list: Agent
  family name: Pandey
  given name: Renu
author list: Agent
  family name: Nair
  given name: Ramakrishnan Madhavan
doi: 10.7717/peerj.12156
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: ©2021 Reddy et al.
attribution name: Reddy et al.

Genetic effects of long-term captive breeding on the endangered pygmy hog
type: item
type: AcademicArticle
description: Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding manage…
format: application/pdf
format: text/html
creator: Deepanwita Purohit
creator: Shivakumara Manu
creator: Muthuvarmadam Subramanian Ram
creator: Shradha Sharma
creator: Harika Chinchilam Patnaik
creator: Parag Jyoti Deka
creator: Goutam Narayan
creator: Govindhaswamy Umapathy
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12212
publisher: PeerJ Inc.
rights: © 2021 Purohit et al.
abstract: Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding manage…
bibliographic citation: Purohit et al. (2021) Genetic effects of long-term captive breeding on the endangered pygmy hog. PeerJ 9:e12212 https://doi.org/10.7717/peerj.12212
date submitted: 2021-05-17
date accepted: 2021-09-05
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Purohit
  given name: Deepanwita
author list: Agent
  family name: Manu
  given name: Shivakumara
author list: Agent
  family name: Ram
  given name: Muthuvarmadam Subramanian
author list: Agent
  family name: Sharma
  given name: Shradha
author list: Agent
  family name: Patnaik
  given name: Harika Chinchilam
author list: Agent
  family name: Deka
  given name: Parag Jyoti
author list: Agent
  family name: Narayan
  given name: Goutam
author list: Agent
  family name: Umapathy
  given name: Govindhaswamy
doi: 10.7717/peerj.12212
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: ©2021 Purohit et al.
attribution name: Purohit et al.

Event-related potentials evoked by skin puncture reflect activation of Aβ fibers: comparison with intraepidermal and transcutaneous electrical stimulations
type: item
type: AcademicArticle
description: Background Recently, event-related potentials (ERPs) evoked by skin puncture, commonly used for blood sampling, have received attention as a pain assessment tool in neonates. However, their latency appears to be far shorter than the latency of ERPs evoked by intraepidermal electrical stimulation (IES), which selectively activates nociceptive Aδ and C fibers. To clarify this important issue, we examined whether ERPs evoked by skin puncture appropriately reflect central nociceptive processing, as is the case with IES. Methods In Experiment 1, we recorded evoked potentials to the click sound produced by a lance device (click-only), lance stimulation with the click sound (click+lance), or lance stimulation with white noise (WN+lance) in eight healthy adults to investigate the effect of the click sound on the ERP evoked by skin puncture. In Experiment 2, we tested 18 heathy adults and recorded evoked potentials to shallow lance stimulation (SL) with a blade that did not reach the dermis (0.1 mm insertion depth); normal lance stimulation (CL) (1 mm depth); transcutaneous electrical stimulation (ES), which mainly activates Aβ fibers; and IES, which selectively activates Aδ fibers when low stimulation current intensities are applied. White noise was continuously presented during the experiments. The stimulations were applied to the hand dorsum. In the SL, the lance device did not touch the skin and the blade was inserted to a depth of 0.1 mm into the epidermis, where the free nerve endings of Aδ fibers are located, which minimized the tactile sensation caused by the device touching the skin and the activation of Aβ fibers by the blade reaching the dermis. In the CL, as in clinical use, the lance device touched the skin and the blade reached a depth of 1 mm from the skin surface, i.e., the depth of the dermis at which the Aβ fibers are located. Results The ERP N2 latencies for click-only (122 ± 2.9 ms) and click+lance (121 ± 6.5 ms) were significantly shorter than that for W…
format: application/pdf
format: text/html
creator: Yui Shiroshita
creator: Hikari Kirimoto
creator: Tatsunori Watanabe
creator: Keisuke Yunoki
creator: Ikuko Sobue
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Pediatrics
description: doi:10.7717/peerj.12250
publisher: PeerJ Inc.
rights: © 2021 Shiroshita et al.
abstract: Background Recently, event-related potentials (ERPs) evoked by skin puncture, commonly used for blood sampling, have received attention as a pain assessment tool in neonates. However, their latency appears to be far shorter than the latency of ERPs evoked by intraepidermal electrical stimulation (IES), which selectively activates nociceptive Aδ and C fibers. To clarify this important issue, we examined whether ERPs evoked by skin puncture appropriately reflect central nociceptive processing, as is the case with IES. Methods In Experiment 1, we recorded evoked potentials to the click sound produced by a lance device (click-only), lance stimulation with the click sound (click+lance), or lance stimulation with white noise (WN+lance) in eight healthy adults to investigate the effect of the click sound on the ERP evoked by skin puncture. In Experiment 2, we tested 18 heathy adults and recorded evoked potentials to shallow lance stimulation (SL) with a blade that did not reach the dermis (0.1 mm insertion depth); normal lance stimulation (CL) (1 mm depth); transcutaneous electrical stimulation (ES), which mainly activates Aβ fibers; and IES, which selectively activates Aδ fibers when low stimulation current intensities are applied. White noise was continuously presented during the experiments. The stimulations were applied to the hand dorsum. In the SL, the lance device did not touch the skin and the blade was inserted to a depth of 0.1 mm into the epidermis, where the free nerve endings of Aδ fibers are located, which minimized the tactile sensation caused by the device touching the skin and the activation of Aβ fibers by the blade reaching the dermis. In the CL, as in clinical use, the lance device touched the skin and the blade reached a depth of 1 mm from the skin surface, i.e., the depth of the dermis at which the Aβ fibers are located. Results The ERP N2 latencies for click-only (122 ± 2.9 ms) and click+lance (121 ± 6.5 ms) were significantly shorter than that for W…
bibliographic citation: Shiroshita et al. (2021) Event-related potentials evoked by skin puncture reflect activation of Aβ fibers: comparison with intraepidermal and transcutaneous electrical stimulations. PeerJ 9:e12250 https://doi.org/10.7717/peerj.12250
date submitted: 2021-02-26
date accepted: 2021-09-13
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiroshita
  given name: Yui
author list: Agent
  family name: Kirimoto
  given name: Hikari
author list: Agent
  family name: Watanabe
  given name: Tatsunori
author list: Agent
  family name: Yunoki
  given name: Keisuke
author list: Agent
  family name: Sobue
  given name: Ikuko
doi: 10.7717/peerj.12250
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: ©2021 Shiroshita et al.
attribution name: Shiroshita et al.

WIN 55,212-2 shows anti-inflammatory and survival properties in human iPSC-derived cardiomyocytes infected with SARS-CoV-2
type: item
type: AcademicArticle
description: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can infect several organs, especially impacting respiratory capacity. Among the extrapulmonary manifestations of COVID-19 is myocardial injury, which is associated with a high risk of mortality. Myocardial injury, caused directly or indirectly by SARS-CoV-2 infection, can be triggered by inflammatory processes that lead to damage to the heart tissue. Since one of the hallmarks of severe COVID-19 is the “cytokine storm”, strategies to control inflammation caused by SARS-CoV-2 infection have been considered. Cannabinoids are known to have anti-inflammatory properties by negatively modulating the release of pro-inflammatory cytokines. Herein, we investigated the effects of the cannabinoid agonist WIN 55,212-2 (WIN) in human iPSC-derived cardiomyocytes (hiPSC-CMs) infected with SARS-CoV-2. WIN did not modify angiotensin-converting enzyme II protein levels, nor reduced viral infection and replication in hiPSC-CMs. On the other hand, WIN reduced the levels of interleukins six, eight, 18 and tumor necrosis factor-alpha (TNF-α) released by infected cells, and attenuated cytotoxic damage measured by the release of lactate dehydrogenase (LDH). Our findings suggest that cannabinoids should be further explored as a complementary therapeutic tool for reducing inflammation in COVID-19 patients.
format: application/pdf
format: text/html
creator: Luiz Guilherme H. S. Aragão
creator: Júlia T. Oliveira
creator: Jairo R. Temerozo
creator: Mayara A. Mendes
creator: José Alexandre Salerno
creator: Carolina S. G. Pedrosa
creator: Teresa Puig-Pijuan
creator: Carla P. Veríssimo
creator: Isis M. Ornelas
creator: Thayana Torquato
creator: Gabriela Vitória
creator: Carolina Q. Sacramento
creator: Natalia Fintelman-Rodrigues
creator: Suelen da Silva Gomes Dias
creator: Vinicius Cardoso Soares
creator: Letícia R. Q. Souza
creator: Karina Karmirian
creator: Livia Goto-Silva
creator: Diogo Biagi
creator: Estela M. Cruvinel
creator: Rafael Dariolli
creator: Daniel R. Furtado
creator: Patrícia T. Bozza
creator: Helena L. Borges
creator: Thiago M. L. Souza
creator: Marília Zaluar P. Guimarães
creator: Stevens K. Rehen
subject: Cell Biology
subject: Molecular Biology
subject: Virology
subject: Cardiology
subject: Pharmacology
description: doi:10.7717/peerj.12262
publisher: PeerJ Inc.
rights: © 2021 Aragão et al.
abstract: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can infect several organs, especially impacting respiratory capacity. Among the extrapulmonary manifestations of COVID-19 is myocardial injury, which is associated with a high risk of mortality. Myocardial injury, caused directly or indirectly by SARS-CoV-2 infection, can be triggered by inflammatory processes that lead to damage to the heart tissue. Since one of the hallmarks of severe COVID-19 is the “cytokine storm”, strategies to control inflammation caused by SARS-CoV-2 infection have been considered. Cannabinoids are known to have anti-inflammatory properties by negatively modulating the release of pro-inflammatory cytokines. Herein, we investigated the effects of the cannabinoid agonist WIN 55,212-2 (WIN) in human iPSC-derived cardiomyocytes (hiPSC-CMs) infected with SARS-CoV-2. WIN did not modify angiotensin-converting enzyme II protein levels, nor reduced viral infection and replication in hiPSC-CMs. On the other hand, WIN reduced the levels of interleukins six, eight, 18 and tumor necrosis factor-alpha (TNF-α) released by infected cells, and attenuated cytotoxic damage measured by the release of lactate dehydrogenase (LDH). Our findings suggest that cannabinoids should be further explored as a complementary therapeutic tool for reducing inflammation in COVID-19 patients.
bibliographic citation: Aragão et al. (2021) WIN 55,212-2 shows anti-inflammatory and survival properties in human iPSC-derived cardiomyocytes infected with SARS-CoV-2. PeerJ 9:e12262 https://doi.org/10.7717/peerj.12262
date submitted: 2021-06-15
date accepted: 2021-09-16
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aragão
  given name: Luiz Guilherme H. S.
author list: Agent
  family name: Oliveira
  given name: Júlia T.
author list: Agent
  family name: Temerozo
  given name: Jairo R.
author list: Agent
  family name: Mendes
  given name: Mayara A.
author list: Agent
  family name: Salerno
  given name: José Alexandre
author list: Agent
  family name: Pedrosa
  given name: Carolina S. G.
author list: Agent
  family name: Puig-Pijuan
  given name: Teresa
author list: Agent
  family name: Veríssimo
  given name: Carla P.
author list: Agent
  family name: Ornelas
  given name: Isis M.
author list: Agent
  family name: Torquato
  given name: Thayana
author list: Agent
  family name: Vitória
  given name: Gabriela
author list: Agent
  family name: Sacramento
  given name: Carolina Q.
author list: Agent
  family name: Fintelman-Rodrigues
  given name: Natalia
author list: Agent
  family name: da Silva Gomes Dias
  given name: Suelen
author list: Agent
  family name: Cardoso Soares
  given name: Vinicius
author list: Agent
  family name: Souza
  given name: Letícia R. Q.
author list: Agent
  family name: Karmirian
  given name: Karina
author list: Agent
  family name: Goto-Silva
  given name: Livia
author list: Agent
  family name: Biagi
  given name: Diogo
author list: Agent
  family name: Cruvinel
  given name: Estela M.
author list: Agent
  family name: Dariolli
  given name: Rafael
author list: Agent
  family name: Furtado
  given name: Daniel R.
author list: Agent
  family name: Bozza
  given name: Patrícia T.
author list: Agent
  family name: Borges
  given name: Helena L.
author list: Agent
  family name: Souza
  given name: Thiago M. L.
author list: Agent
  family name: Guimarães
  given name: Marília Zaluar P.
doi: 10.7717/peerj.12262
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: © 2021 Aragão et al.
attribution name: Aragão et al.

Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar ‘Qiannan Guifei’
type: item
type: AcademicArticle
description: Background Osmanthus fragrans (Oleaceae) is one of the most important ornamental plant species in China. Many cultivars with different leaf color phenotypes and good ornamental value have recently been developed. For example, a new cultivar ‘Qiannan Guifei’, presents a rich variety of leaf colors, which change from red to yellow-green and ultimately to green as leaves develop, making this cultivar valuable for landscaping. However, the biochemical characteristics and molecular mechanisms underlying leaf color changes of these phenotypes have not been elucidated. It has been hypothesized that the biosynthesis of different pigments in O. fragrans might change during leaf coloration. Here, we analyzed transcriptional changes in genes involved in chlorophyll (Chl), flavonoid, and carotenoid metabolic pathways and identified candidate genes responsible for leaf coloration in the new cultivar ‘Qiannan Guifei’. Methods Leaf samples were collected from ‘Qiannan Guifei’ plants at the red (R), yellow-green (YG) and green (G) leaf stages. We compared the different-colored leaves via leaf pigment concentrations, chloroplast ultrastructure, and transcriptomic data. We further analyzed differentially expressed genes (DEGs) involved in the Chl, flavonoid, and carotenoid metabolic pathways. In addition, we used qRT-PCR to validate expression patterns of the DEGs at the three stages. Results We found that, compared with those at the G stage, chloroplasts at the R and YG stages were less abundant and presented abnormal morphologies. Pigment analyses revealed that the leaves had higher flavonoid and anthocyanin levels at the R stage but lower Chl and carotenoid concentrations. Similarly, Chl and carotenoid concentrations were lower at the YG stage than at the G stage. By using transcriptomic sequencing, we further identified 61 DEGs involved in the three pigment metabolic pathways. Among these DEGs, seven structural genes (OfCHS, OfCHI, OfF3H, OfDFR, OfANS, OfUGT andOf3AT) involved in…
format: application/pdf
format: text/html
creator: Qi Cui
creator: Junhua Huang
creator: Fan Wu
creator: Dong-ze Li
creator: Liqun Zheng
creator: Guang Hu
creator: Shaoqing Hu
creator: Lu Zhang
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12265
publisher: PeerJ Inc.
rights: © 2021 Cui et al.
abstract: Background Osmanthus fragrans (Oleaceae) is one of the most important ornamental plant species in China. Many cultivars with different leaf color phenotypes and good ornamental value have recently been developed. For example, a new cultivar ‘Qiannan Guifei’, presents a rich variety of leaf colors, which change from red to yellow-green and ultimately to green as leaves develop, making this cultivar valuable for landscaping. However, the biochemical characteristics and molecular mechanisms underlying leaf color changes of these phenotypes have not been elucidated. It has been hypothesized that the biosynthesis of different pigments in O. fragrans might change during leaf coloration. Here, we analyzed transcriptional changes in genes involved in chlorophyll (Chl), flavonoid, and carotenoid metabolic pathways and identified candidate genes responsible for leaf coloration in the new cultivar ‘Qiannan Guifei’. Methods Leaf samples were collected from ‘Qiannan Guifei’ plants at the red (R), yellow-green (YG) and green (G) leaf stages. We compared the different-colored leaves via leaf pigment concentrations, chloroplast ultrastructure, and transcriptomic data. We further analyzed differentially expressed genes (DEGs) involved in the Chl, flavonoid, and carotenoid metabolic pathways. In addition, we used qRT-PCR to validate expression patterns of the DEGs at the three stages. Results We found that, compared with those at the G stage, chloroplasts at the R and YG stages were less abundant and presented abnormal morphologies. Pigment analyses revealed that the leaves had higher flavonoid and anthocyanin levels at the R stage but lower Chl and carotenoid concentrations. Similarly, Chl and carotenoid concentrations were lower at the YG stage than at the G stage. By using transcriptomic sequencing, we further identified 61 DEGs involved in the three pigment metabolic pathways. Among these DEGs, seven structural genes (OfCHS, OfCHI, OfF3H, OfDFR, OfANS, OfUGT andOf3AT) involved in…
bibliographic citation: Cui et al. (2021) Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar ‘Qiannan Guifei’. PeerJ 9:e12265 https://doi.org/10.7717/peerj.12265
date submitted: 2020-05-21
date accepted: 2021-09-16
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Qi
author list: Agent
  family name: Huang
  given name: Junhua
author list: Agent
  family name: Wu
  given name: Fan
author list: Agent
  family name: Li
  given name: Dong-ze
author list: Agent
  family name: Zheng
  given name: Liqun
author list: Agent
  family name: Hu
  given name: Guang
author list: Agent
  family name: Hu
  given name: Shaoqing
author list: Agent
  family name: Zhang
  given name: Lu
doi: 10.7717/peerj.12265
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: ©2021 Cui et al.
attribution name: Cui et al.

Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background AU-rich elements (ARE) are vital cis-acting short sequences in the 3’UTR affecting mRNA stability and translation. The deregulation of ARE-mediated pathways can contribute to tumorigenesis and development. Consequently, ARE-genes are promising to predict prognosis of lung adenocarcinoma (LUAD) patients. Methods Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature. The genetic signature was combined with clinicopathological features to establish a prognostic model. LUAD patients were divided into high- and low-risk groups by the model. Kaplan–Meier curve, Harrell’s concordance index (C-index), calibration curves and decision curve analyses (DCA) were used to assess the model. Function enrichment analysis, immunity and tumor mutation analyses were performed to further explore the underlying molecular mechanisms. GEO data were used for external validation. Results Twelve prognostic genes were identified. The gene riskScore, age and stage were independent prognostic factors. The high-risk group had worse overall survival and was less sensitive to chemotherapy and radiotherapy (P < 0.01). C-index and calibration curves showed good performance on survival prediction in both TCGA (1, 3, 5-year ROC: 0.788, 0.776, 0.766) and the GSE13213 validation cohort (1, 3, 5-year ROC: 0.781, 0.811, 0.734). DCA showed the model had notable clinical net benefit. Furthermore, the high-risk group were enriched in cell cycle, DNA damage response, multiple oncological pathways and associated with higher PD-L1 expression, M1 macrophage infiltration. There was no significant difference in tumor mutation burden (TMB) between high- and low-risk groups. Conclusion ARE-genes can reliably predict prognosis of LUAD and may become new therapeutic targets for LUAD.
format: application/pdf
format: text/html
creator: Yong Liu
creator: Zhaofei Pang
creator: Xiaogang Zhao
creator: Yukai Zeng
creator: Hongchang Shen
creator: Jiajun Du
subject: Bioinformatics
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12275
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background AU-rich elements (ARE) are vital cis-acting short sequences in the 3’UTR affecting mRNA stability and translation. The deregulation of ARE-mediated pathways can contribute to tumorigenesis and development. Consequently, ARE-genes are promising to predict prognosis of lung adenocarcinoma (LUAD) patients. Methods Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature. The genetic signature was combined with clinicopathological features to establish a prognostic model. LUAD patients were divided into high- and low-risk groups by the model. Kaplan–Meier curve, Harrell’s concordance index (C-index), calibration curves and decision curve analyses (DCA) were used to assess the model. Function enrichment analysis, immunity and tumor mutation analyses were performed to further explore the underlying molecular mechanisms. GEO data were used for external validation. Results Twelve prognostic genes were identified. The gene riskScore, age and stage were independent prognostic factors. The high-risk group had worse overall survival and was less sensitive to chemotherapy and radiotherapy (P < 0.01). C-index and calibration curves showed good performance on survival prediction in both TCGA (1, 3, 5-year ROC: 0.788, 0.776, 0.766) and the GSE13213 validation cohort (1, 3, 5-year ROC: 0.781, 0.811, 0.734). DCA showed the model had notable clinical net benefit. Furthermore, the high-risk group were enriched in cell cycle, DNA damage response, multiple oncological pathways and associated with higher PD-L1 expression, M1 macrophage infiltration. There was no significant difference in tumor mutation burden (TMB) between high- and low-risk groups. Conclusion ARE-genes can reliably predict prognosis of LUAD and may become new therapeutic targets for LUAD.
bibliographic citation: Liu et al. (2021) Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma. PeerJ 9:e12275 https://doi.org/10.7717/peerj.12275
date submitted: 2021-06-10
date accepted: 2021-09-19
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yong
author list: Agent
  family name: Pang
  given name: Zhaofei
author list: Agent
  family name: Zhao
  given name: Xiaogang
author list: Agent
  family name: Zeng
  given name: Yukai
author list: Agent
  family name: Shen
  given name: Hongchang
author list: Agent
  family name: Du
  given name: Jiajun
doi: 10.7717/peerj.12275
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Improving size selectivity of round pot for Charybdis japonica by configuring escape vents in the Yellow Sea, China
type: item
type: AcademicArticle
description: Sustainable development of the important economic species, Asian paddle crab (Charybdis japonica), has attracted attention in the coastal waters of the Yellow Sea, China. The commonly used round pots are almost nonselective, resulting in severe bycatch of juveniles. In this study, we explored a method to improve the size selectivity for C. japonica by mounting escape vents on the side panels of each pot. The selectivity of pots with escape vent sizes of 70 mm × 20 mm, 70 mm × 25 mm, 70 mm × 30 mm, and 70 mm × 35 mm was tested using a catch comparison method. The estimated minimum landing size (MLS) of carapace height (27 mm), according to the regulated MLS of carapace length (50 mm), was used as a reference point to explain the results. Significant increases in the size of crabs caught by pots were found with the enlargement of escape vent size (Kruskal–Wallis test, P < 0.01). The pots with 70 mm × 20 mm, 70 mm × 25 mm and 70 mm × 30 mm escape vents released nearly 50%, 75% and 95% of undersized individuals, respectively, and these three types of pots retained approximately 90% of legal-sized individuals compared with the control pots without escape vents. The pots with 70 mm × 35 mm escape vents released nearly all undersized individuals, but they also released most legal-sized individuals. Pots with an escape vent size of 70 mm × 30 mm were recommended for the sustainable development of C. japonica in the Yellow Sea of China. The results of this study reiterate the importance of carapace height for determining the size selectivity, which can serve as a reference to formulate management regulations in the coastal waters of the Yellow Sea, China.
format: application/pdf
format: text/html
creator: Mengjie Yu
creator: Liyou Zhang
creator: Changdong Liu
creator: Yanli Tang
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12282
publisher: PeerJ Inc.
rights: © 2021 Yu et al.
abstract: Sustainable development of the important economic species, Asian paddle crab (Charybdis japonica), has attracted attention in the coastal waters of the Yellow Sea, China. The commonly used round pots are almost nonselective, resulting in severe bycatch of juveniles. In this study, we explored a method to improve the size selectivity for C. japonica by mounting escape vents on the side panels of each pot. The selectivity of pots with escape vent sizes of 70 mm × 20 mm, 70 mm × 25 mm, 70 mm × 30 mm, and 70 mm × 35 mm was tested using a catch comparison method. The estimated minimum landing size (MLS) of carapace height (27 mm), according to the regulated MLS of carapace length (50 mm), was used as a reference point to explain the results. Significant increases in the size of crabs caught by pots were found with the enlargement of escape vent size (Kruskal–Wallis test, P < 0.01). The pots with 70 mm × 20 mm, 70 mm × 25 mm and 70 mm × 30 mm escape vents released nearly 50%, 75% and 95% of undersized individuals, respectively, and these three types of pots retained approximately 90% of legal-sized individuals compared with the control pots without escape vents. The pots with 70 mm × 35 mm escape vents released nearly all undersized individuals, but they also released most legal-sized individuals. Pots with an escape vent size of 70 mm × 30 mm were recommended for the sustainable development of C. japonica in the Yellow Sea of China. The results of this study reiterate the importance of carapace height for determining the size selectivity, which can serve as a reference to formulate management regulations in the coastal waters of the Yellow Sea, China.
bibliographic citation: Yu et al. (2021) Improving size selectivity of round pot for Charybdis japonica by configuring escape vents in the Yellow Sea, China. PeerJ 9:e12282 https://doi.org/10.7717/peerj.12282
date submitted: 2021-07-19
date accepted: 2021-09-20
issued: 2021-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Mengjie
author list: Agent
  family name: Zhang
  given name: Liyou
author list: Agent
  family name: Liu
  given name: Changdong
author list: Agent
  family name: Tang
  given name: Yanli
doi: 10.7717/peerj.12282
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-08
copyright: © 2021 Yu et al.
attribution name: Yu et al.

Analysis of how the spatial and temporal patterns of fire and their bioclimatic and anthropogenic drivers vary across the Amazon rainforest in El Niño and non-El Niño years
type: item
type: AcademicArticle
description: In the past two decades, Amazon rainforest countries (Brazil, Bolivia, Colombia, Ecuador, Guyana, Peru and Venezuela) have experienced a substantial increase in fire frequency due to the changes in the patterns of different anthropogenic and climatic drivers. This study examines how both fire dynamics and bioclimatic factors varied based on the season (wet season and dry season) El Niño years across the different countries and ecosystems within the Amazon rainforest. Data from publicly available databases on forest fires (Global Fire Atlas) and bioclimatic, topographic and anthropogenic variables were employed in the analysis. Linear mixed-effect models discovered that year type (El Niño vs. non-El Niño), seasonality (dry vs. wet), land cover and forest strata (in terms of canopy cover and intactness) and their interactions varied across the Amazonian countries (and the different ecosystems) under consideration. A machine learning model, Multivariate Adaptive Regression Spline (MARS), was utilized to determine the relative importance of climatic, topographic, forest structure and human modification variables on fire dynamics across wet and dry seasons, both in El Niño and non-El Niño years. The findings of this study make clear that declining precipitation and increased temperatures have strong impact on fire dynamics (size, duration, expansion and speed) for El Niño years. El Niño years also saw greater fire sizes and speeds as compared to non-El Niño years. Dense and relatively undisturbed forests were found to have the lowest fire activity and increased human impact on a landscape was associated with exacerbated fire dynamics, especially in the El Niño years. Additionally, the presence of grass-dominated ecosystems such as grasslands also acted as a driver of fire in both El Niño and non-El Niño years. Hence, from a conservation perspective, increased interventions during the El Niño periods should be considered.
format: application/pdf
format: text/html
creator: Minerva Singh
creator: Xiaoxiang Zhu
subject: Ecosystem Science
subject: Data Science
subject: Environmental Impacts
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12029
publisher: PeerJ Inc.
rights: © 2021 Singh and Zhu
abstract: In the past two decades, Amazon rainforest countries (Brazil, Bolivia, Colombia, Ecuador, Guyana, Peru and Venezuela) have experienced a substantial increase in fire frequency due to the changes in the patterns of different anthropogenic and climatic drivers. This study examines how both fire dynamics and bioclimatic factors varied based on the season (wet season and dry season) El Niño years across the different countries and ecosystems within the Amazon rainforest. Data from publicly available databases on forest fires (Global Fire Atlas) and bioclimatic, topographic and anthropogenic variables were employed in the analysis. Linear mixed-effect models discovered that year type (El Niño vs. non-El Niño), seasonality (dry vs. wet), land cover and forest strata (in terms of canopy cover and intactness) and their interactions varied across the Amazonian countries (and the different ecosystems) under consideration. A machine learning model, Multivariate Adaptive Regression Spline (MARS), was utilized to determine the relative importance of climatic, topographic, forest structure and human modification variables on fire dynamics across wet and dry seasons, both in El Niño and non-El Niño years. The findings of this study make clear that declining precipitation and increased temperatures have strong impact on fire dynamics (size, duration, expansion and speed) for El Niño years. El Niño years also saw greater fire sizes and speeds as compared to non-El Niño years. Dense and relatively undisturbed forests were found to have the lowest fire activity and increased human impact on a landscape was associated with exacerbated fire dynamics, especially in the El Niño years. Additionally, the presence of grass-dominated ecosystems such as grasslands also acted as a driver of fire in both El Niño and non-El Niño years. Hence, from a conservation perspective, increased interventions during the El Niño periods should be considered.
bibliographic citation: Singh et al. (2021) Analysis of how the spatial and temporal patterns of fire and their bioclimatic and anthropogenic drivers vary across the Amazon rainforest in El Niño and non-El Niño years. PeerJ 9:e12029 https://doi.org/10.7717/peerj.12029
date submitted: 2021-02-11
date accepted: 2021-07-30
issued: 2021-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Singh
  given name: Minerva
author list: Agent
  family name: Zhu
  given name: Xiaoxiang
doi: 10.7717/peerj.12029
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-07
copyright: © 2021 Singh and Zhu
attribution name: Singh and Zhu

Heronry distribution and site preference dynamics of tree-nesting colonial waterbirds in Tamil Nadu
type: item
type: AcademicArticle
description: Anthropogenic disturbance and climate change have significantly affected the distribution of wetlands globally and particularly in Asian countries. Various types of wetlands are harboured across all the biogeographic zones in India. These wetlands provide vital ecological services and are rich in biodiversity. However, anthropogenic pressures continue to be a threat to these wetlands by affecting the flora and fauna that depend on them. Tree-nesting colonial waterbirds are vulnerable to these pressures as their colonies are typically located in wetlands and associated areas. Disturbances to these areas have resulted in the loss or shifting of many heronries. The present study was conducted in the Indian state of Tamil Nadu during the period of 2017–2019 to document the existing and previously unknown heronries of the landscape. A total of 101 heronries were documented in 22 districts. The Little Cormorant was the most dominant species, occurring in 79% of the sites, with relative abundances of 24% and 26% during 2017–2018 and 2018–2019, respectively. A total of 23 tree species were utilized by the birds for nesting and Vachellia nilotica trees were used for nesting in about 25% of the heronries. 19% of the heronries were situated inside protected areas and 81% were located outside protected areas. Out of the 58 active nesting sites reported in 2005, 43 have been lost or are no longer active. Species distribution modelling with presence only data indicated that the sites with a high probability of occurrence were confined to the major waterbodies and rivers. Spatial correlation showed that the heronries were dispersed randomly across the landscape. The population dynamics within heronries and colonial nesting waterbirds’ response to various environmental factors must be monitored continuously to conserve these heronries.
format: application/pdf
format: text/html
creator: Sadrack Jabaraj Dhanaraj Frank
creator: Govindan Veeraswami Gopi
creator: Bivash Pandav
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12256
publisher: PeerJ Inc.
rights: © 2021 Frank et al.
abstract: Anthropogenic disturbance and climate change have significantly affected the distribution of wetlands globally and particularly in Asian countries. Various types of wetlands are harboured across all the biogeographic zones in India. These wetlands provide vital ecological services and are rich in biodiversity. However, anthropogenic pressures continue to be a threat to these wetlands by affecting the flora and fauna that depend on them. Tree-nesting colonial waterbirds are vulnerable to these pressures as their colonies are typically located in wetlands and associated areas. Disturbances to these areas have resulted in the loss or shifting of many heronries. The present study was conducted in the Indian state of Tamil Nadu during the period of 2017–2019 to document the existing and previously unknown heronries of the landscape. A total of 101 heronries were documented in 22 districts. The Little Cormorant was the most dominant species, occurring in 79% of the sites, with relative abundances of 24% and 26% during 2017–2018 and 2018–2019, respectively. A total of 23 tree species were utilized by the birds for nesting and Vachellia nilotica trees were used for nesting in about 25% of the heronries. 19% of the heronries were situated inside protected areas and 81% were located outside protected areas. Out of the 58 active nesting sites reported in 2005, 43 have been lost or are no longer active. Species distribution modelling with presence only data indicated that the sites with a high probability of occurrence were confined to the major waterbodies and rivers. Spatial correlation showed that the heronries were dispersed randomly across the landscape. The population dynamics within heronries and colonial nesting waterbirds’ response to various environmental factors must be monitored continuously to conserve these heronries.
bibliographic citation: Frank et al. (2021) Heronry distribution and site preference dynamics of tree-nesting colonial waterbirds in Tamil Nadu. PeerJ 9:e12256 https://doi.org/10.7717/peerj.12256
date submitted: 2021-03-30
date accepted: 2021-09-14
issued: 2021-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frank
  given name: Sadrack Jabaraj Dhanaraj
author list: Agent
  family name: Gopi
  given name: Govindan Veeraswami
author list: Agent
  family name: Pandav
  given name: Bivash
doi: 10.7717/peerj.12256
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-07
copyright: © 2021 Frank et al.
attribution name: Frank et al.

The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)
type: item
type: AcademicArticle
description: This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.
format: application/pdf
format: text/html
creator: Micaela Schagen
creator: Jason Bosch
creator: Jenny Johnson
creator: Robbert Duker
creator: Pedro Lebre
creator: Alastair J. Potts
creator: Don A. Cowan
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.12176
publisher: PeerJ Inc.
rights: © 2021 Schagen et al.
abstract: This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.
bibliographic citation: Schagen et al. (2021) The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket). PeerJ 9:e12176 https://doi.org/10.7717/peerj.12176
date submitted: 2021-06-11
date accepted: 2021-08-29
issued: 2021-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schagen
  given name: Micaela
author list: Agent
  family name: Bosch
  given name: Jason
author list: Agent
  family name: Johnson
  given name: Jenny
author list: Agent
  family name: Duker
  given name: Robbert
author list: Agent
  family name: Lebre
  given name: Pedro
author list: Agent
  family name: Potts
  given name: Alastair J.
author list: Agent
  family name: Cowan
  given name: Don A.
doi: 10.7717/peerj.12176
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-06
copyright: © 2021 Schagen et al.
attribution name: Schagen et al.

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

Agent
family name: Rehen
given name: Stevens K.