PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels
items: Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage
items: A bright idea—metabarcoding arthropods from light fixtures
items: Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis
items: ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
items: How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China
items: Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population
items: Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments
items: Impacts of heat stress and storm events on the benthic communities of Kenting National Park (Taiwan)
items: Furongian (Jiangshanian) occurrences of radiodonts in Poland and South China and the fossil record of the Hurdiidae

Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels
type: item
type: AcademicArticle
description: Backgroud This study’s objectives were to compare the clinical, perinatal, and obstetrical outcomes of patients with different estradiol (E2) levels in fresh single-blastocyst-transfer (SBT) cycles under an early follicular phase prolonged regimen on the day of trigger. Methods We recruited patients in fresh SBT cycles (n = 771) undergoing early follicular phase prolonged protocols with β-hCG values above 10 IU/L between June 2016 and December 2018. Patients who met the inclusion and exclusion criteria were divided into four groups according to their serum E2 level percentages on the day of trigger: <25th, 25th–50th, 51st–75th, and >75th percentile groups. Results Although the rates of clinical pregnancy (85.57% (166/194)), embryo implantation 86.60% (168/194), ongoing pregnancy (71.13% (138/194)), and live birth (71.13% (138/194)) were lowest in the >75th percentile group, we did not observe any significant differences (all P > 0.05). We used this information to predict the rate of severe ovarian hyperstimulation syndrome (OHSS) area under the curve (AUC) = 72.39%, P = 0.029, cut off value of E2 = 2,893 pg/ml with the 75% sensitivity and 70% specificity. The 51st–75th percentile group had the highest rates of low birth weight infants (11.73% (19/162), P = 0.0408), premature delivery (11.43% (20/175), P = 0.0269), admission to the neonatal intensive care unit (NICU) (10.49% (17/162), P = 0.0029), twin pregnancies (8.57% (15/175), P = 0.0047), and monochorionic diamniotic pregnancies (8.57% (15/175); P = 0.001). We did not observe statistical differences in obstetrics complications, including gestational diabetes mellitus (GDM), gestational hypertension, placenta previa, premature rupture of membranes (PROM), and preterm premature rupture of membranes (PPROM). Conclusion We concluded that serum E2 levels on the day of trigger were not good predictors of live birth rate or perinatal and obstetrical outcomes. However, we found that high E2 levels may not be conducive t…
format: application/pdf
format: text/html
creator: Yingfen Ying
creator: Xiaosheng Lu
creator: Huina Zhang
creator: Samuel Kofi Arhin
creator: Xiaohong Hou
creator: Zefan Wang
creator: Han Wu
creator: Jieqiang Lu
creator: Yunbing Tang
subject: Evidence Based Medicine
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.11785
publisher: PeerJ Inc.
rights: © 2021 Ying et al.
abstract: Backgroud This study’s objectives were to compare the clinical, perinatal, and obstetrical outcomes of patients with different estradiol (E2) levels in fresh single-blastocyst-transfer (SBT) cycles under an early follicular phase prolonged regimen on the day of trigger. Methods We recruited patients in fresh SBT cycles (n = 771) undergoing early follicular phase prolonged protocols with β-hCG values above 10 IU/L between June 2016 and December 2018. Patients who met the inclusion and exclusion criteria were divided into four groups according to their serum E2 level percentages on the day of trigger: <25th, 25th–50th, 51st–75th, and >75th percentile groups. Results Although the rates of clinical pregnancy (85.57% (166/194)), embryo implantation 86.60% (168/194), ongoing pregnancy (71.13% (138/194)), and live birth (71.13% (138/194)) were lowest in the >75th percentile group, we did not observe any significant differences (all P > 0.05). We used this information to predict the rate of severe ovarian hyperstimulation syndrome (OHSS) area under the curve (AUC) = 72.39%, P = 0.029, cut off value of E2 = 2,893 pg/ml with the 75% sensitivity and 70% specificity. The 51st–75th percentile group had the highest rates of low birth weight infants (11.73% (19/162), P = 0.0408), premature delivery (11.43% (20/175), P = 0.0269), admission to the neonatal intensive care unit (NICU) (10.49% (17/162), P = 0.0029), twin pregnancies (8.57% (15/175), P = 0.0047), and monochorionic diamniotic pregnancies (8.57% (15/175); P = 0.001). We did not observe statistical differences in obstetrics complications, including gestational diabetes mellitus (GDM), gestational hypertension, placenta previa, premature rupture of membranes (PROM), and preterm premature rupture of membranes (PPROM). Conclusion We concluded that serum E2 levels on the day of trigger were not good predictors of live birth rate or perinatal and obstetrical outcomes. However, we found that high E2 levels may not be conducive t…
bibliographic citation: Ying et al. (2021) Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels. PeerJ 9:e11785 https://doi.org/10.7717/peerj.11785
date submitted: 2020-09-25
date accepted: 2021-06-24
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ying
  given name: Yingfen
author list: Agent
  family name: Lu
  given name: Xiaosheng
author list: Agent
  family name: Zhang
  given name: Huina
author list: Agent
  family name: Arhin
  given name: Samuel Kofi
author list: Agent
  family name: Hou
  given name: Xiaohong
author list: Agent
  family name: Wang
  given name: Zefan
author list: Agent
  family name: Wu
  given name: Han
author list: Agent
  family name: Lu
  given name: Jieqiang
author list: Agent
  family name: Tang
  given name: Yunbing
doi: 10.7717/peerj.11785
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Ying et al.
attribution name: Ying et al.

Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage
type: item
type: AcademicArticle
description: Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize.
format: application/pdf
format: text/html
creator: Baizhao Ren
creator: Juan Hu
creator: Peng Liu
creator: Bin Zhao
creator: Jiwang Zhang
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11834
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize.
bibliographic citation: Ren et al. (2021) Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage. PeerJ 9:e11834 https://doi.org/10.7717/peerj.11834
date submitted: 2021-03-30
date accepted: 2021-06-30
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Baizhao
author list: Agent
  family name: Hu
  given name: Juan
author list: Agent
  family name: Liu
  given name: Peng
author list: Agent
  family name: Zhao
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Jiwang
doi: 10.7717/peerj.11834
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Ren et al.
attribution name: Ren et al.

A bright idea—metabarcoding arthropods from light fixtures
type: item
type: AcademicArticle
description: Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
format: application/pdf
format: text/html
creator: Vasco Elbrecht
creator: Angie Lindner
creator: Laura Manerus
creator: Dirk Steinke
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11841
publisher: PeerJ Inc.
rights: © 2021 Elbrecht et al.
abstract: Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
bibliographic citation: Elbrecht et al. (2021) A bright idea—metabarcoding arthropods from light fixtures. PeerJ 9:e11841 https://doi.org/10.7717/peerj.11841
date submitted: 2021-05-25
date accepted: 2021-07-01
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elbrecht
  given name: Vasco
author list: Agent
  family name: Lindner
  given name: Angie
author list: Agent
  family name: Manerus
  given name: Laura
author list: Agent
  family name: Steinke
  given name: Dirk
doi: 10.7717/peerj.11841
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Elbrecht et al.
attribution name: Elbrecht et al.

Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis
type: item
type: AcademicArticle
description: Background Nurses’ knowledge regarding palliative and end-of-life (EOL) care has been documented, but the competence of nurses in Taiwan has not been deeply analyzed and may affect the use of EOL care. Purpose We aimed to (1) assess the palliative care knowledge, competence and attitude of nurses in a general hospital and (2) examine the paths connecting nurses’ demographic characteristics, previous experiences, knowledge, competence, and attitude. Method A correlational, cross-sectional survey design was implemented to recruit 682 eligible nurses. The questionnaires included demographic information and palliative and EOL care knowledge, attitude, and competence scales. Path analysis was employed for statistical analysis using structural equation modeling. Results Overall, 76% of the questions assessing palliative and hospice knowledge were answered correctly. Nurses’ palliative attitudes were divided into “positive perception” and “negative perception”. “Positive perception” was highly correlated with competence (r = 0.48, p < 0.001), but “negative perception” was not significantly correlated with competence (r = −0.07, p = 0.25). “Positive perception” (β = −0.01, p = 0.84) and competence (β = 0.02, p = 0.80) were not related to palliative knowledge. “Negative perception”, however, was negatively associated with palliative knowledge (β = −0.20, p < 0.01). Conclusions This study suggests continuing education to decrease nurses’ “negative perception” attitude regarding the provision of information to patients and families to provide better palliative and EOL care. Implications for Practice Nurses’ attitudes and competences with respect to palliative care and EOL care are critical. Areas for further research and advanced palliative and EOL care-related education and training are suggested and may be applied in future clinical interventions.
format: application/pdf
format: text/html
creator: Hung-Yu Lin
creator: Chun-I Chen
creator: Chu-Yun Lu
creator: Shu-Chuan Lin
creator: Chiung-Yu Huang
subject: Geriatrics
subject: Nursing
subject: Science and Medical Education
subject: Palliative Care
description: doi:10.7717/peerj.11864
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Background Nurses’ knowledge regarding palliative and end-of-life (EOL) care has been documented, but the competence of nurses in Taiwan has not been deeply analyzed and may affect the use of EOL care. Purpose We aimed to (1) assess the palliative care knowledge, competence and attitude of nurses in a general hospital and (2) examine the paths connecting nurses’ demographic characteristics, previous experiences, knowledge, competence, and attitude. Method A correlational, cross-sectional survey design was implemented to recruit 682 eligible nurses. The questionnaires included demographic information and palliative and EOL care knowledge, attitude, and competence scales. Path analysis was employed for statistical analysis using structural equation modeling. Results Overall, 76% of the questions assessing palliative and hospice knowledge were answered correctly. Nurses’ palliative attitudes were divided into “positive perception” and “negative perception”. “Positive perception” was highly correlated with competence (r = 0.48, p < 0.001), but “negative perception” was not significantly correlated with competence (r = −0.07, p = 0.25). “Positive perception” (β = −0.01, p = 0.84) and competence (β = 0.02, p = 0.80) were not related to palliative knowledge. “Negative perception”, however, was negatively associated with palliative knowledge (β = −0.20, p < 0.01). Conclusions This study suggests continuing education to decrease nurses’ “negative perception” attitude regarding the provision of information to patients and families to provide better palliative and EOL care. Implications for Practice Nurses’ attitudes and competences with respect to palliative care and EOL care are critical. Areas for further research and advanced palliative and EOL care-related education and training are suggested and may be applied in future clinical interventions.
bibliographic citation: Lin et al. (2021) Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis. PeerJ 9:e11864 https://doi.org/10.7717/peerj.11864
date submitted: 2020-12-03
date accepted: 2021-07-05
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Hung-Yu
author list: Agent
  family name: Chen
  given name: Chun-I
author list: Agent
  family name: Lu
  given name: Chu-Yun
author list: Agent
  family name: Lin
  given name: Shu-Chuan
author list: Agent
  family name: Huang
  given name: Chiung-Yu
doi: 10.7717/peerj.11864
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: ©2021 Lin et al.
attribution name: Lin et al.

ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
type: item
type: AcademicArticle
description: Background High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs. Methods The ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments. Results The ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimi…
format: application/pdf
format: text/html
creator: Dylan Catlett
creator: Kevin Son
creator: Connie Liang
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.11865
publisher: PeerJ Inc.
rights: © 2021 Catlett et al.
abstract: Background High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs. Methods The ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments. Results The ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimi…
bibliographic citation: Catlett et al. (2021) ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences. PeerJ 9:e11865 https://doi.org/10.7717/peerj.11865
date submitted: 2021-03-31
date accepted: 2021-07-05
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Catlett
  given name: Dylan
author list: Agent
  family name: Son
  given name: Kevin
author list: Agent
  family name: Liang
  given name: Connie
doi: 10.7717/peerj.11865
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: ©2021 Catlett et al.
attribution name: Catlett et al.

How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China
type: item
type: AcademicArticle
description: Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots.
format: application/pdf
format: text/html
creator: Lijiao Wang
creator: Xin Jing
creator: Jincheng Han
creator: Lei Yu
creator: Yutao Wang
creator: Ping Liu
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.11873
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots.
bibliographic citation: Wang et al. (2021) How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China. PeerJ 9:e11873 https://doi.org/10.7717/peerj.11873
date submitted: 2021-02-08
date accepted: 2021-07-06
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lijiao
author list: Agent
  family name: Jing
  given name: Xin
author list: Agent
  family name: Han
  given name: Jincheng
author list: Agent
  family name: Yu
  given name: Lei
author list: Agent
  family name: Wang
  given name: Yutao
author list: Agent
  family name: Liu
  given name: Ping
doi: 10.7717/peerj.11873
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population
type: item
type: AcademicArticle
description: Background Some single nucleotide polymorphisms (SNPs) in the cytochrome P450 (CYP)2B6 gene lead to decreased enzyme activity and have an impact on drug metabolism. The present study was designed to investigate the patterns of genetic distinction across a hypervariable region of the CYP2B6 gene, known to contain important SNPs, i.e. rs4803419 and rs3745274, among five major ethnic groups of the Pakistani population. Methods Arlequin v3.5.DnaSPv6.12. and network 5 resources were used to analyze population genetic variance in the partial CYP2B6 gene sequences obtained from 104 human samples belonging to Punjabi, Pathan, Sindhi, Seraiki and Baloch ethnicities of Pakistan. The partial CYP2B6 gene region analyzed in the current study is previously known to possess important SNPs. Results The data analyses revealed that genetic variance among samples mainly came from differentiation within the ethnic groups. However, significant genetic variation was also found among the various ethnic groups. The high pairwise Fst genetic distinction was observed between Seraiki and Sindhi ethnic groups (Fst = 0.13392, P-value = 0.026) as well as between Seraiki and Balochi groups (Fst = 0.04303, P-value = −0.0030). However, the degree of genetic distinction was low between Pathan and Punjabi ethnic groups. Some SNPs, including rs3745274 and rs4803419, which are previously shown in strong association with increased plasma Efavirenz level, were found in high frequency. Besides, a novel SNP, which was not found in dbSNP and Ensemble databases, was identified in the Balochi ethnicity. This novel SNP is predicted to affect the CYP2B6 splicing pattern. Conclusion These results may have significant implications in Pakistani ethnicities in the context of drugs metabolized by CYP2B6, especially in Seraiki and Balochi ethnicity. The novel heterogeneous SNP, found in the present study, might lead to altered drug-metabolizing potential of CYP2B6 and, therefore, may be implicated in non-responder ph…
format: application/pdf
format: text/html
creator: Sagheer Ahmed
creator: Hizbullah Khan
creator: Asifullah Khan
creator: Muhammad Hanif Bangash
creator: Abrar Hussain
creator: Mughal Qayum
creator: Mohammad Hamid Hamdard
subject: Drugs and Devices
subject: Pharmacology
subject: Public Health
subject: Translational Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.11149
publisher: PeerJ Inc.
rights: © 2021 Ahmed et al.
abstract: Background Some single nucleotide polymorphisms (SNPs) in the cytochrome P450 (CYP)2B6 gene lead to decreased enzyme activity and have an impact on drug metabolism. The present study was designed to investigate the patterns of genetic distinction across a hypervariable region of the CYP2B6 gene, known to contain important SNPs, i.e. rs4803419 and rs3745274, among five major ethnic groups of the Pakistani population. Methods Arlequin v3.5.DnaSPv6.12. and network 5 resources were used to analyze population genetic variance in the partial CYP2B6 gene sequences obtained from 104 human samples belonging to Punjabi, Pathan, Sindhi, Seraiki and Baloch ethnicities of Pakistan. The partial CYP2B6 gene region analyzed in the current study is previously known to possess important SNPs. Results The data analyses revealed that genetic variance among samples mainly came from differentiation within the ethnic groups. However, significant genetic variation was also found among the various ethnic groups. The high pairwise Fst genetic distinction was observed between Seraiki and Sindhi ethnic groups (Fst = 0.13392, P-value = 0.026) as well as between Seraiki and Balochi groups (Fst = 0.04303, P-value = −0.0030). However, the degree of genetic distinction was low between Pathan and Punjabi ethnic groups. Some SNPs, including rs3745274 and rs4803419, which are previously shown in strong association with increased plasma Efavirenz level, were found in high frequency. Besides, a novel SNP, which was not found in dbSNP and Ensemble databases, was identified in the Balochi ethnicity. This novel SNP is predicted to affect the CYP2B6 splicing pattern. Conclusion These results may have significant implications in Pakistani ethnicities in the context of drugs metabolized by CYP2B6, especially in Seraiki and Balochi ethnicity. The novel heterogeneous SNP, found in the present study, might lead to altered drug-metabolizing potential of CYP2B6 and, therefore, may be implicated in non-responder ph…
bibliographic citation: Ahmed et al. (2021) Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population. PeerJ 9:e11149 https://doi.org/10.7717/peerj.11149
date submitted: 2020-11-10
date accepted: 2021-03-03
issued: 2021-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmed
  given name: Sagheer
author list: Agent
  family name: Khan
  given name: Hizbullah
author list: Agent
  family name: Khan
  given name: Asifullah
author list: Agent
  family name: Bangash
  given name: Muhammad Hanif
author list: Agent
  family name: Hussain
  given name: Abrar
author list: Agent
  family name: Qayum
  given name: Mughal
author list: Agent
  family name: Hamdard
  given name: Mohammad Hamid
doi: 10.7717/peerj.11149
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-23
copyright: © 2021 Ahmed et al.
attribution name: Ahmed et al.

Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments
type: item
type: AcademicArticle
description: Phenotypic plasticity allows individuals to respond to the selective forces of a new environment, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and reaction norms to temperature of strains of two bacterial lineages, Bacillus cereus sensu lato and Bacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite the co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only in strains within the lineages, suggesting fixed phenotypic plasticity. Additionally, strains from the H environment showed only two to three degrees centigrade more heat tolerance than strains from the T environment. Their viability decreased at temperatures above their optimal for growth, particularly for the B. cereus lineage. However, sporulation occurred at all temperatures, consistent with the known cell population heterogeneity that allows the Bacillus to anticipate adversity. We suggest that these mesophilic strains survive in the hot-spring as spores and complete their life cycle of germination and growth during intermittent opportunities of moderate temperatures. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact of climate change on all biological cycles in the planet, which at its most basic level depends on microorganisms.
format: application/pdf
format: text/html
creator: Enrique Hurtado-Bautista
creator: Laura F. Pérez Sánchez
creator: Africa Islas-Robles
creator: Gustavo Santoyo
creator: Gabriela Olmedo-Alvarez
subject: Ecology
subject: Evolutionary Studies
subject: Microbiology
subject: Climate Change Biology
description: doi:10.7717/peerj.11734
publisher: PeerJ Inc.
rights: © 2021 Hurtado-Bautista et al.
abstract: Phenotypic plasticity allows individuals to respond to the selective forces of a new environment, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and reaction norms to temperature of strains of two bacterial lineages, Bacillus cereus sensu lato and Bacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite the co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only in strains within the lineages, suggesting fixed phenotypic plasticity. Additionally, strains from the H environment showed only two to three degrees centigrade more heat tolerance than strains from the T environment. Their viability decreased at temperatures above their optimal for growth, particularly for the B. cereus lineage. However, sporulation occurred at all temperatures, consistent with the known cell population heterogeneity that allows the Bacillus to anticipate adversity. We suggest that these mesophilic strains survive in the hot-spring as spores and complete their life cycle of germination and growth during intermittent opportunities of moderate temperatures. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact of climate change on all biological cycles in the planet, which at its most basic level depends on microorganisms.
bibliographic citation: Hurtado-Bautista et al. (2021) Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments. PeerJ 9:e11734 https://doi.org/10.7717/peerj.11734
date submitted: 2020-09-08
date accepted: 2021-06-16
issued: 2021-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado-Bautista
  given name: Enrique
author list: Agent
  family name: Pérez Sánchez
  given name: Laura F.
author list: Agent
  family name: Islas-Robles
  given name: Africa
author list: Agent
  family name: Santoyo
  given name: Gustavo
author list: Agent
  family name: Olmedo-Alvarez
  given name: Gabriela
doi: 10.7717/peerj.11734
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-23
copyright: ©2021 Hurtado-Bautista et al.
attribution name: Hurtado-Bautista et al.

Impacts of heat stress and storm events on the benthic communities of Kenting National Park (Taiwan)
type: item
type: AcademicArticle
description: Over the past few decades, extreme events—such as ocean warming, typhoons, and coral bleaching—have been increasing in intensity and frequency, threatening coral reefs from the physiological to ecosystem level. In the present study, the impacts of rising seawater temperatures, typhoons, and coral bleaching events on benthic communities were seasonally assessed over a 21 month-period, using photo-transects at 11 sites in Kenting National Park (KNP), Taiwan. Between August 2015 and April 2017, seven typhoon events were recorded and in situ seawater temperatures in KNP reached a maximum of 31.2 °C, as opposed to an average maximum SST of 28.8 °C (2007–2016). The state and response of benthic communities to these events were interpreted based on the environmental conditions of KNP. The repeated storms lowered the levels of thermal stress during the 2015–2016 El Niño event and may have mitigated its impact on the Taiwanese coral reefs. However, storm-induced local shifts from coral to macro-algae dominance were observed. Storms may mitigate the negative effects of heatwaves, but the mechanical damage induced by the storms may also decrease the structural complexity of reefs and their associated diversity. Eventually, despite reef persistence, the composition and function of remnant communities may profoundly diverge from those in regions with less active storms.
format: application/pdf
format: text/html
creator: Lauriane Ribas-Deulofeu
creator: Vianney Denis
creator: Pierre-Alexandre Château
creator: Chaolun Allen Chen
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.11744
publisher: PeerJ Inc.
rights: © 2021 Ribas-Deulofeu et al.
abstract: Over the past few decades, extreme events—such as ocean warming, typhoons, and coral bleaching—have been increasing in intensity and frequency, threatening coral reefs from the physiological to ecosystem level. In the present study, the impacts of rising seawater temperatures, typhoons, and coral bleaching events on benthic communities were seasonally assessed over a 21 month-period, using photo-transects at 11 sites in Kenting National Park (KNP), Taiwan. Between August 2015 and April 2017, seven typhoon events were recorded and in situ seawater temperatures in KNP reached a maximum of 31.2 °C, as opposed to an average maximum SST of 28.8 °C (2007–2016). The state and response of benthic communities to these events were interpreted based on the environmental conditions of KNP. The repeated storms lowered the levels of thermal stress during the 2015–2016 El Niño event and may have mitigated its impact on the Taiwanese coral reefs. However, storm-induced local shifts from coral to macro-algae dominance were observed. Storms may mitigate the negative effects of heatwaves, but the mechanical damage induced by the storms may also decrease the structural complexity of reefs and their associated diversity. Eventually, despite reef persistence, the composition and function of remnant communities may profoundly diverge from those in regions with less active storms.
bibliographic citation: Ribas-Deulofeu et al. (2021) Impacts of heat stress and storm events on the benthic communities of Kenting National Park (Taiwan). PeerJ 9:e11744 https://doi.org/10.7717/peerj.11744
date submitted: 2021-01-14
date accepted: 2021-06-17
issued: 2021-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ribas-Deulofeu
  given name: Lauriane
author list: Agent
  family name: Denis
  given name: Vianney
author list: Agent
  family name: Château
  given name: Pierre-Alexandre
author list: Agent
  family name: Chen
  given name: Chaolun Allen
doi: 10.7717/peerj.11744
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-23
copyright: ©2021 Ribas-Deulofeu et al.
attribution name: Ribas-Deulofeu et al.

Furongian (Jiangshanian) occurrences of radiodonts in Poland and South China and the fossil record of the Hurdiidae
type: item
type: AcademicArticle
description: The Furongian period represents an important gap in the fossil record of most groups of non-biomineralizing organisms, owing to a scarcity of Konservat-Lagerstätten of that age. The most significant of these deposits, the Jiangshanian strata of the Sandu Formation near Guole Township (Guangxi, South China), have yielded a moderately abundant, but taxonomically diverse soft-bodied fossil assemblage, which provides rare insights into the evolution of marine life at that time. In this contribution, we report the first discovery of a radiodont fossil from the Guole Konservat-Lagerstätte. The specimen is an incomplete frontal appendage of a possibly new representative of the family Hurdiidae. It is tentatively interpreted as composed of seven podomeres, six of which bearing laminiform endites. The best preserved of these endites is especially long, and it bears short auxiliary spines that greatly vary in size. This is the second occurrence of hurdiids and more generally radiodonts in the Furongian, the first being the external mould of an oral cone from Jiangshanian strata of the Wiśniówka Sandstone Formation in Poland. Restudy of this Polish specimen confirms that it belongs to a hurdiid radiodont and best compares to Peytoia. The family Hurdiidae includes the oldest (basal Cambrian Epoch 2) and youngest (Early Ordovician, possibly Early Devonian) representatives of the Radiodonta and as such, has the longest stratigraphical range of the group. Yet, hurdiids only became prominent components of marine ecosystems during the middle Cambrian (Miaolingian), and their fossil record in younger strata remains limited.
format: application/pdf
format: text/html
creator: Xuejian Zhu
creator: Rudy Lerosey-Aubril
creator: Javier Ortega-Hernández
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11800
publisher: PeerJ Inc.
rights: © 2021 Zhu et al.
abstract: The Furongian period represents an important gap in the fossil record of most groups of non-biomineralizing organisms, owing to a scarcity of Konservat-Lagerstätten of that age. The most significant of these deposits, the Jiangshanian strata of the Sandu Formation near Guole Township (Guangxi, South China), have yielded a moderately abundant, but taxonomically diverse soft-bodied fossil assemblage, which provides rare insights into the evolution of marine life at that time. In this contribution, we report the first discovery of a radiodont fossil from the Guole Konservat-Lagerstätte. The specimen is an incomplete frontal appendage of a possibly new representative of the family Hurdiidae. It is tentatively interpreted as composed of seven podomeres, six of which bearing laminiform endites. The best preserved of these endites is especially long, and it bears short auxiliary spines that greatly vary in size. This is the second occurrence of hurdiids and more generally radiodonts in the Furongian, the first being the external mould of an oral cone from Jiangshanian strata of the Wiśniówka Sandstone Formation in Poland. Restudy of this Polish specimen confirms that it belongs to a hurdiid radiodont and best compares to Peytoia. The family Hurdiidae includes the oldest (basal Cambrian Epoch 2) and youngest (Early Ordovician, possibly Early Devonian) representatives of the Radiodonta and as such, has the longest stratigraphical range of the group. Yet, hurdiids only became prominent components of marine ecosystems during the middle Cambrian (Miaolingian), and their fossil record in younger strata remains limited.
bibliographic citation: Zhu et al. (2021) Furongian (Jiangshanian) occurrences of radiodonts in Poland and South China and the fossil record of the Hurdiidae. PeerJ 9:e11800 https://doi.org/10.7717/peerj.11800
date submitted: 2021-01-19
date accepted: 2021-06-26
issued: 2021-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Xuejian
author list: Agent
  family name: Lerosey-Aubril
  given name: Rudy
author list: Agent
  family name: Ortega-Hernández
  given name: Javier
doi: 10.7717/peerj.11800
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-23
copyright: ©2021 Zhu et al.
attribution name: Zhu et al.

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