PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Body mass index and the risk of basal cell carcinoma: evidence from Mendelian randomization analysis
items: Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time
items: Relationship between fruit phenotypes and domestication in hexaploid populations of biribá (Annona mucosa) in Brazilian Amazonia
items: Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment
items: Effects of prohexadione calcium spraying during the booting stage on panicle traits, yield, and related physiological characteristics of rice under salt stress
items: Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring
items: Hydrometeorological characterization and estimation of landfill leachate generation in the Eastern Amazon/Brazil
items: Musculoskeletal simulations to examine the effects of accentuated eccentric loading (AEL) on jump height
items: Genome-wide identification and expression reveal the involvement of the FCS-like zinc finger (FLZ) gene family in Gossypium hirsutum at low temperature
items: A clustering method for small scRNA-seq data based on subspace and weighted distance

Body mass index and the risk of basal cell carcinoma: evidence from Mendelian randomization analysis
type: item
type: AcademicArticle
description: Objective We aim to test whether body mass index (BMI) is causally associated with the risk of basal cell carcinoma (BCC) using Mendelian randomization (MR) analysis. Methods Single-nucleotide polymorphisms (SNPs) associated with four BMI-related traits were screened via a genome-wide association study (GWAS) with 681,275, 336,107, 454,884, and 461,460 European-descent individuals, respectively. Summary-level data for BCC (17,416 cases and 375,455 controls) were extracted from UK Biobank. An inverse variance weighted (IVW) method was employed as the primary MR analysis. Sensitivity analyses were conducted via MR-Egger regression, heterogeneity test, pleiotropy test, and leave-one-out sensitivity test. The assumption that exposure causes outcome was verified using the MR Steiger test. Meta-analysis was also used to estimate the average genetically predicted effect of BMI on BCC. Results Two-sample MR analysis showed inverse associations between genetically predicted BMI and BCC risk. Moreover, when exposure and outcome were switched to see if reverse causation was possible, there was no evidence of a cause-and-effect relationship from BCC to BMI. Finally, the meta-analysis also showed a strong negative causal relationship between BMI and BCC. Conclusion Genetical predicted higher BMI were associated with lower BCC risk. Further research is required to comprehend the mechanisms underlying this putative causative association.
format: application/pdf
format: text/html
creator: Likui Lu
creator: Bangbei Wan
creator: Hongtao Zeng
creator: Jun Guo
creator: Min Li
creator: Miao Sun
subject: Genetics
subject: Genomics
subject: Oncology
subject: Data Science
subject: Obesity
description: doi:10.7717/peerj.14781
publisher: PeerJ Inc.
rights: © 2023 Lu et al.
abstract: Objective We aim to test whether body mass index (BMI) is causally associated with the risk of basal cell carcinoma (BCC) using Mendelian randomization (MR) analysis. Methods Single-nucleotide polymorphisms (SNPs) associated with four BMI-related traits were screened via a genome-wide association study (GWAS) with 681,275, 336,107, 454,884, and 461,460 European-descent individuals, respectively. Summary-level data for BCC (17,416 cases and 375,455 controls) were extracted from UK Biobank. An inverse variance weighted (IVW) method was employed as the primary MR analysis. Sensitivity analyses were conducted via MR-Egger regression, heterogeneity test, pleiotropy test, and leave-one-out sensitivity test. The assumption that exposure causes outcome was verified using the MR Steiger test. Meta-analysis was also used to estimate the average genetically predicted effect of BMI on BCC. Results Two-sample MR analysis showed inverse associations between genetically predicted BMI and BCC risk. Moreover, when exposure and outcome were switched to see if reverse causation was possible, there was no evidence of a cause-and-effect relationship from BCC to BMI. Finally, the meta-analysis also showed a strong negative causal relationship between BMI and BCC. Conclusion Genetical predicted higher BMI were associated with lower BCC risk. Further research is required to comprehend the mechanisms underlying this putative causative association.
bibliographic citation: Lu et al. (2023) Body mass index and the risk of basal cell carcinoma: evidence from Mendelian randomization analysis. PeerJ 11:e14781 https://doi.org/10.7717/peerj.14781
date submitted: 2022-08-26
date accepted: 2023-01-03
issued: 2023-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Likui
author list: Agent
  family name: Wan
  given name: Bangbei
author list: Agent
  family name: Zeng
  given name: Hongtao
author list: Agent
  family name: Guo
  given name: Jun
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Sun
  given name: Miao
doi: 10.7717/peerj.14781
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-24
copyright: ©2023 Lu et al.
attribution name: Lu et al.

Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time
type: item
type: AcademicArticle
description: Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
format: application/pdf
format: text/html
creator: Raphael Eisenhofer
creator: Kylie L. Brice
creator: Michaela DJ Blyton
creator: Scott E. Bevins
creator: Kellie Leigh
creator: Brajesh K. Singh
creator: Kristofer M. Helgen
creator: Ian Hough
creator: Christopher B. Daniels
creator: Natasha Speight
creator: Ben D. Moore
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14598
publisher: PeerJ Inc.
rights: © 2023 Eisenhofer et al.
abstract: Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
bibliographic citation: Eisenhofer et al. (2023) Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time. PeerJ 11:e14598 https://doi.org/10.7717/peerj.14598
date submitted: 2022-07-05
date accepted: 2022-11-29
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eisenhofer
  given name: Raphael
author list: Agent
  family name: Brice
  given name: Kylie L.
author list: Agent
  family name: Blyton
  given name: Michaela DJ
author list: Agent
  family name: Bevins
  given name: Scott E.
author list: Agent
  family name: Leigh
  given name: Kellie
author list: Agent
  family name: Singh
  given name: Brajesh K.
author list: Agent
  family name: Helgen
  given name: Kristofer M.
author list: Agent
  family name: Hough
  given name: Ian
author list: Agent
  family name: Daniels
  given name: Christopher B.
author list: Agent
  family name: Speight
  given name: Natasha
author list: Agent
  family name: Moore
  given name: Ben D.
doi: 10.7717/peerj.14598
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: © 2023 Eisenhofer et al.
attribution name: Eisenhofer et al.

Relationship between fruit phenotypes and domestication in hexaploid populations of biribá (Annona mucosa) in Brazilian Amazonia
type: item
type: AcademicArticle
description: Background Biribá (Annona mucosa Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics, including weight (100–4,000 g) and differences in carpel protrusions. Two cytotypes are recorded in the literature (2n = 28, 42) and genome size records are divergent (2C = 4.77, 5.42 and 6.00 pg). To decipher the role of polyploidy in the domestication of A. mucosa, we examined the relationships among phenotypic variation, chromosome number and genome size, and which came first, polyploidization or domestication. Methodology We performed chromosome counts of A. mucosa from central and western Brazilian Amazonia, and estimated genome size by flow cytometry. We performed phylogenetic reconstruction with publicly available data using a Bayesian framework, time divergence analysis and reconstructed the ancestral chromosome number for the genus Annona and for A. mucosa. Results We observed that variation in fruit phenotypes is not associated with variation in chromosome number and genome size. The most recent common ancestor of A. mucosa is inferred to be polyploid and diverged before domestication. Conclusions We conclude that, when domesticated, A. mucosa was already polyploid and we suggest that human selection is the main evolutionary force behind fruit size and fruit morphological variation in Annona mucosa.
format: application/pdf
format: text/html
creator: Giulia Melilli Serbin
creator: Diego Sotero de Barros Pinangé
creator: Raquel Moura Machado
creator: Santelmo Vasconcelos
creator: Bruno Sampaio Amorim
creator: Charles Roland Clement
subject: Agricultural Science
subject: Genetics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.14659
publisher: PeerJ Inc.
rights: © 2023 Serbin et al.
abstract: Background Biribá (Annona mucosa Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics, including weight (100–4,000 g) and differences in carpel protrusions. Two cytotypes are recorded in the literature (2n = 28, 42) and genome size records are divergent (2C = 4.77, 5.42 and 6.00 pg). To decipher the role of polyploidy in the domestication of A. mucosa, we examined the relationships among phenotypic variation, chromosome number and genome size, and which came first, polyploidization or domestication. Methodology We performed chromosome counts of A. mucosa from central and western Brazilian Amazonia, and estimated genome size by flow cytometry. We performed phylogenetic reconstruction with publicly available data using a Bayesian framework, time divergence analysis and reconstructed the ancestral chromosome number for the genus Annona and for A. mucosa. Results We observed that variation in fruit phenotypes is not associated with variation in chromosome number and genome size. The most recent common ancestor of A. mucosa is inferred to be polyploid and diverged before domestication. Conclusions We conclude that, when domesticated, A. mucosa was already polyploid and we suggest that human selection is the main evolutionary force behind fruit size and fruit morphological variation in Annona mucosa.
bibliographic citation: Serbin et al. (2023) Relationship between fruit phenotypes and domestication in hexaploid populations of biribá (Annona mucosa) in Brazilian Amazonia. PeerJ 11:e14659 https://doi.org/10.7717/peerj.14659
date submitted: 2022-10-11
date accepted: 2022-12-08
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serbin
  given name: Giulia Melilli
author list: Agent
  family name: Pinangé
  given name: Diego Sotero de Barros
author list: Agent
  family name: Machado
  given name: Raquel Moura
author list: Agent
  family name: Vasconcelos
  given name: Santelmo
author list: Agent
  family name: Amorim
  given name: Bruno Sampaio
author list: Agent
  family name: Clement
  given name: Charles Roland
doi: 10.7717/peerj.14659
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: © 2023 Serbin et al.
attribution name: Serbin et al.

Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment
type: item
type: AcademicArticle
description: Purpose Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major healthcare threat worldwide. Since it was first identified in November 2021, the Omicron (B.1.1.529) variant of SARS-CoV-2 has evolved into several lineages, including BA.1, BA.2–BA.4, and BA.5. SARS-CoV-2 variants might increase transmissibility, pathogenicity, and resistance to vaccine-induced immunity. Thus, the epidemiological surveillance of circulating lineages using variant phenotyping is essential. The aim of the current study was to characterize the clinical outcome of Omicron BA.2 infections among hospitalized COVID-19 patients and to perform an immunological assessment of such cases against SARS-CoV-2. Patients and Methods We evaluated the analytical and clinical performance of the BioIC SARS-CoV-2 immunoglobulin (Ig)M/IgG detection kit, which was used for detecting antibodies against SARS-CoV-2 in 257 patients infected with the Omicron variant. Results Poor prognosis was noted in 38 patients, including eight deaths in patients characterized by comorbidities predisposing them to severe COVID-19. The variant-of-concern (VOC) typing and serological analysis identified time-dependent epidemic trends of BA.2 variants emerging in the outbreak of the fourth wave in Taiwan. Of the 257 specimens analyzed, 108 (42%) and 24 (9.3%) were positive for anti-N IgM and IgG respectively. Conclusion The VOC typing of these samples allowed for the identification of epidemic trends by time intervals, including the B.1.1.529 variant replacing the B.1.617.2 variant. Moreover, antibody testing might serve as a complementary method for COVID-19 diagnosis. The combination of serological testing results with the reverse transcription-polymerase chain reaction cycle threshold value has potential value in disease prognosis, thereby aiding in epidemic investigations conducted by clinicians or the healthcare department.
format: application/pdf
format: text/html
creator: Chi-Sheng Chen
creator: Ming-Jr Jian
creator: Chih-Kai Chang
creator: Hsing-Yi Chung
creator: Shih-Yi Li
creator: Jung-Chung Lin
creator: Kuo-Ming Yeh
creator: Ya-Sung Yang
creator: Chien-Wen Chen
creator: Shan-Shan Hsieh
creator: Sheng-Hui Tang
creator: Cherng-Lih Perng
creator: Feng-Yee Chang
creator: Hung-Sheng Shang
subject: Allergy and Clinical Immunology
subject: Global Health
subject: Health Policy
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.14666
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Purpose Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major healthcare threat worldwide. Since it was first identified in November 2021, the Omicron (B.1.1.529) variant of SARS-CoV-2 has evolved into several lineages, including BA.1, BA.2–BA.4, and BA.5. SARS-CoV-2 variants might increase transmissibility, pathogenicity, and resistance to vaccine-induced immunity. Thus, the epidemiological surveillance of circulating lineages using variant phenotyping is essential. The aim of the current study was to characterize the clinical outcome of Omicron BA.2 infections among hospitalized COVID-19 patients and to perform an immunological assessment of such cases against SARS-CoV-2. Patients and Methods We evaluated the analytical and clinical performance of the BioIC SARS-CoV-2 immunoglobulin (Ig)M/IgG detection kit, which was used for detecting antibodies against SARS-CoV-2 in 257 patients infected with the Omicron variant. Results Poor prognosis was noted in 38 patients, including eight deaths in patients characterized by comorbidities predisposing them to severe COVID-19. The variant-of-concern (VOC) typing and serological analysis identified time-dependent epidemic trends of BA.2 variants emerging in the outbreak of the fourth wave in Taiwan. Of the 257 specimens analyzed, 108 (42%) and 24 (9.3%) were positive for anti-N IgM and IgG respectively. Conclusion The VOC typing of these samples allowed for the identification of epidemic trends by time intervals, including the B.1.1.529 variant replacing the B.1.617.2 variant. Moreover, antibody testing might serve as a complementary method for COVID-19 diagnosis. The combination of serological testing results with the reverse transcription-polymerase chain reaction cycle threshold value has potential value in disease prognosis, thereby aiding in epidemic investigations conducted by clinicians or the healthcare department.
bibliographic citation: Chen et al. (2023) Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment. PeerJ 11:e14666 https://doi.org/10.7717/peerj.14666
date submitted: 2022-09-28
date accepted: 2022-12-09
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Chi-Sheng
author list: Agent
  family name: Jian
  given name: Ming-Jr
author list: Agent
  family name: Chang
  given name: Chih-Kai
author list: Agent
  family name: Chung
  given name: Hsing-Yi
author list: Agent
  family name: Li
  given name: Shih-Yi
author list: Agent
  family name: Lin
  given name: Jung-Chung
author list: Agent
  family name: Yeh
  given name: Kuo-Ming
author list: Agent
  family name: Yang
  given name: Ya-Sung
author list: Agent
  family name: Chen
  given name: Chien-Wen
author list: Agent
  family name: Hsieh
  given name: Shan-Shan
author list: Agent
  family name: Tang
  given name: Sheng-Hui
author list: Agent
  family name: Perng
  given name: Cherng-Lih
author list: Agent
  family name: Chang
  given name: Feng-Yee
author list: Agent
  family name: Shang
  given name: Hung-Sheng
doi: 10.7717/peerj.14666
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Effects of prohexadione calcium spraying during the booting stage on panicle traits, yield, and related physiological characteristics of rice under salt stress
type: item
type: AcademicArticle
description: Prohexadione calcium (Pro-Ca), as a growth retardant, can effectively alleviate the damage of salt stress to plants. In order to explore the effects of NaCl stress on the physiological characteristics and panicle traits of rice plants as well as the alleviating effect of Pro-Ca at the booting stage, we performed pot experiments on two rice cultivars: conventional rice ‘Huanghuazhan’ and hybrid rice ‘Xiangliangyou900’. Rice plants were treated with 0.3% NaCl 48 hours after Pro-Ca (100 mg L−1) treatment to study the effects of Pro-Ca on the physiological characteristics of the leaves and panicles, as well as the panicle and yield traits of rice under salt stress. Our analysis indicated that NaCl treatment inhibited the morphological growth parameters and photosynthetic efficiency, destroyed the antioxidant defense systems of leaves and panicles, increased soluble protein and proline in both rice cultivars. Foliar application of Pro-Ca significantly increased the leaf area, uppermost internode length, panicle length, panicle weight, number of primary branches, number of grains per panicle, seed setting rate and yield under salt stress. Pro-Ca application significantly affected chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and apparent mesophyll conductance (AMC) in NaCl-treated rice cultivars compared with NaCl treatment alone. Moreover, Pro-Ca also increased ascorbic acid (AsA) content, enhanced superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and further increased the accumulation of soluble protein and proline in leaves and panicles. These results illustrated that foliar application of Pro-Ca at the booting stage could alleviate the damage caused by NaCl stress by regulating the physiological and metabolic processes of rice plants, thereby enhancing the stress resistance of the plants, increasing total rice yield in salt stress conditions.
format: application/pdf
format: text/html
creator: XiXin Huang
creator: Dianfeng Zheng
creator: Naijie Feng
creator: Anqi Huang
creator: Rongjun Zhang
creator: Fengyan Meng
creator: Yin Jie
creator: Baomin Mu
creator: Dewei Mu
creator: Hang Zhou
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.14673
publisher: PeerJ Inc.
rights: © 2023 Huang et al.
abstract: Prohexadione calcium (Pro-Ca), as a growth retardant, can effectively alleviate the damage of salt stress to plants. In order to explore the effects of NaCl stress on the physiological characteristics and panicle traits of rice plants as well as the alleviating effect of Pro-Ca at the booting stage, we performed pot experiments on two rice cultivars: conventional rice ‘Huanghuazhan’ and hybrid rice ‘Xiangliangyou900’. Rice plants were treated with 0.3% NaCl 48 hours after Pro-Ca (100 mg L−1) treatment to study the effects of Pro-Ca on the physiological characteristics of the leaves and panicles, as well as the panicle and yield traits of rice under salt stress. Our analysis indicated that NaCl treatment inhibited the morphological growth parameters and photosynthetic efficiency, destroyed the antioxidant defense systems of leaves and panicles, increased soluble protein and proline in both rice cultivars. Foliar application of Pro-Ca significantly increased the leaf area, uppermost internode length, panicle length, panicle weight, number of primary branches, number of grains per panicle, seed setting rate and yield under salt stress. Pro-Ca application significantly affected chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and apparent mesophyll conductance (AMC) in NaCl-treated rice cultivars compared with NaCl treatment alone. Moreover, Pro-Ca also increased ascorbic acid (AsA) content, enhanced superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and further increased the accumulation of soluble protein and proline in leaves and panicles. These results illustrated that foliar application of Pro-Ca at the booting stage could alleviate the damage caused by NaCl stress by regulating the physiological and metabolic processes of rice plants, thereby enhancing the stress resistance of the plants, increasing total rice yield in salt stress conditions.
bibliographic citation: Huang et al. (2023) Effects of prohexadione calcium spraying during the booting stage on panicle traits, yield, and related physiological characteristics of rice under salt stress. PeerJ 11:e14673 https://doi.org/10.7717/peerj.14673
date submitted: 2022-07-12
date accepted: 2022-12-11
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: XiXin
author list: Agent
  family name: Zheng
  given name: Dianfeng
author list: Agent
  family name: Feng
  given name: Naijie
author list: Agent
  family name: Huang
  given name: Anqi
author list: Agent
  family name: Zhang
  given name: Rongjun
author list: Agent
  family name: Meng
  given name: Fengyan
author list: Agent
  family name: Jie
  given name: Yin
author list: Agent
  family name: Mu
  given name: Baomin
author list: Agent
  family name: Mu
  given name: Dewei
author list: Agent
  family name: Zhou
  given name: Hang
doi: 10.7717/peerj.14673
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: ©2023 Huang et al.
attribution name: Huang et al.

Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring
type: item
type: AcademicArticle
description: Background Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges. Methods In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit. Results We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification. Conclusions Altogether, our results showed that eDNA ddPCR signals lagged beh…
format: application/pdf
format: text/html
creator: Ying Chen
creator: Orianne Tournayre
creator: Haolun Tian
creator: Stephen C. Lougheed
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14679
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Background Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges. Methods In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit. Results We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification. Conclusions Altogether, our results showed that eDNA ddPCR signals lagged beh…
bibliographic citation: Chen et al. (2023) Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring. PeerJ 11:e14679 https://doi.org/10.7717/peerj.14679
date submitted: 2022-09-28
date accepted: 2022-12-13
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Tournayre
  given name: Orianne
author list: Agent
  family name: Tian
  given name: Haolun
author list: Agent
  family name: Lougheed
  given name: Stephen C.
doi: 10.7717/peerj.14679
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: © 2023 Chen et al.
attribution name: Chen et al.

Hydrometeorological characterization and estimation of landfill leachate generation in the Eastern Amazon/Brazil
type: item
type: AcademicArticle
description: The complex physical-chemical and microbiological composition of leachate in sanitary landfills sets the adequate treatment for different waste types. However, before the final disposal of wastes in receptor waterbodies, it is essential to use specific methods to quantitatively prevent internal flows to find proper treatments. The aim of the present research is to use hydrological models to estimate monthly leachate flow generation in Macapá’s Municipal Sanitary Landfill (ASMM), Amapá State, Brazil. Disregarding the temporal trend bias, the average (0.45 m3s−1), minimum (0.07 m3s−1) and maximum (0.72 m3s−1) flows were estimated based on hydrological models in the literature (Rmax = 99%, p < 0.05). The results estimated from different hydrological gauges pointed towards significant spatial variations in final discharge. Thus, estimated flows worked as reference to calculate the loads of coproducts and nutrients concerning different operational stages in ASMM. Therefore, rain intensity estimates have pointed out precipitation variability, and it has significantly affected leachate flow. In conclusion, there would be a proportional increase in leachate flow during extreme maximum precipitation events; overflow would be the effect of such flows and it would assumingly have impact on its surrounding areas. It is also possible estimating some degree of rainfall impact over ASMM’s infrastructure in the long term (>10 years), since it could influence its lifespan.
format: application/pdf
format: text/html
creator: Carlos Armando Reyes Flores
creator: Helenilza Ferreira Albuquerque Cunha
creator: Alan Cavalcanti da Cunha
subject: Ecohydrology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.14686
publisher: PeerJ Inc.
rights: © 2023 Reyes Flores et al.
abstract: The complex physical-chemical and microbiological composition of leachate in sanitary landfills sets the adequate treatment for different waste types. However, before the final disposal of wastes in receptor waterbodies, it is essential to use specific methods to quantitatively prevent internal flows to find proper treatments. The aim of the present research is to use hydrological models to estimate monthly leachate flow generation in Macapá’s Municipal Sanitary Landfill (ASMM), Amapá State, Brazil. Disregarding the temporal trend bias, the average (0.45 m3s−1), minimum (0.07 m3s−1) and maximum (0.72 m3s−1) flows were estimated based on hydrological models in the literature (Rmax = 99%, p < 0.05). The results estimated from different hydrological gauges pointed towards significant spatial variations in final discharge. Thus, estimated flows worked as reference to calculate the loads of coproducts and nutrients concerning different operational stages in ASMM. Therefore, rain intensity estimates have pointed out precipitation variability, and it has significantly affected leachate flow. In conclusion, there would be a proportional increase in leachate flow during extreme maximum precipitation events; overflow would be the effect of such flows and it would assumingly have impact on its surrounding areas. It is also possible estimating some degree of rainfall impact over ASMM’s infrastructure in the long term (>10 years), since it could influence its lifespan.
bibliographic citation: Reyes Flores et al. (2023) Hydrometeorological characterization and estimation of landfill leachate generation in the Eastern Amazon/Brazil. PeerJ 11:e14686 https://doi.org/10.7717/peerj.14686
date submitted: 2022-07-07
date accepted: 2022-12-13
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reyes Flores
  given name: Carlos Armando
author list: Agent
  family name: Ferreira Albuquerque Cunha
  given name: Helenilza
author list: Agent
  family name: Cavalcanti da Cunha
  given name: Alan
doi: 10.7717/peerj.14686
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: ©2023 Reyes Flores et al.
attribution name: Reyes Flores et al.

Musculoskeletal simulations to examine the effects of accentuated eccentric loading (AEL) on jump height
type: item
type: AcademicArticle
description: Background During counter movement jumps, adding weight in the eccentric phase and then suddenly releasing this weight during the concentric phase, known as accentuated eccentric loading (AEL), has been suggested to immediately improve jumping performance. The level of evidence for the positive effects of AEL remains weak, with conflicting evidence over the effectiveness in enhancing performance. Therefore, we proposed to theoretically explore the influence of implementing AEL during constrained vertical jumping using computer modelling and simulation and examined whether the proposed mechanism of enhanced power, increased elastic energy storage and return, could enhance work and power. Methods We used a simplified model, consisting of a ball-shaped body (head, arm, and trunk), two lower limb segments (thigh and shank), and four muscles, to simulate the mechanisms of AEL. We adjusted the key activation parameters of the muscles to influence the performance outcome of the model. Numerical optimization was applied to search the optimal solution for the model. We implemented AEL and non-AEL conditions in the model to compare the simulated data between conditions. Results Our model predicted that the optimal jumping performance was achieved when the model utilized the whole joint range. However, there was no difference in jumping performance in AEL and non-AEL conditions because the model began its push-off at the similar state (posture, fiber length, fiber velocity, fiber force, tendon length, and the same activation level). Therefore, the optimal solution predicted by the model was primarily driven by intrinsic muscle dynamics (force-length-velocity relationship), and this coupled with the similar model state at the start of the push-off, resulting in similar push-off performance across all conditions. There was also no evidence of additional tendon-loading effect in AEL conditions compared to non-AEL condition. Discussion Our simplified simulations did not show impro…
format: application/pdf
format: text/html
creator: Eric Yung-Sheng Su
creator: Timothy J. Carroll
creator: Dominic J. Farris
creator: Glen A. Lichtwark
subject: Biophysics
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.14687
publisher: PeerJ Inc.
rights: © 2023 Su et al.
abstract: Background During counter movement jumps, adding weight in the eccentric phase and then suddenly releasing this weight during the concentric phase, known as accentuated eccentric loading (AEL), has been suggested to immediately improve jumping performance. The level of evidence for the positive effects of AEL remains weak, with conflicting evidence over the effectiveness in enhancing performance. Therefore, we proposed to theoretically explore the influence of implementing AEL during constrained vertical jumping using computer modelling and simulation and examined whether the proposed mechanism of enhanced power, increased elastic energy storage and return, could enhance work and power. Methods We used a simplified model, consisting of a ball-shaped body (head, arm, and trunk), two lower limb segments (thigh and shank), and four muscles, to simulate the mechanisms of AEL. We adjusted the key activation parameters of the muscles to influence the performance outcome of the model. Numerical optimization was applied to search the optimal solution for the model. We implemented AEL and non-AEL conditions in the model to compare the simulated data between conditions. Results Our model predicted that the optimal jumping performance was achieved when the model utilized the whole joint range. However, there was no difference in jumping performance in AEL and non-AEL conditions because the model began its push-off at the similar state (posture, fiber length, fiber velocity, fiber force, tendon length, and the same activation level). Therefore, the optimal solution predicted by the model was primarily driven by intrinsic muscle dynamics (force-length-velocity relationship), and this coupled with the similar model state at the start of the push-off, resulting in similar push-off performance across all conditions. There was also no evidence of additional tendon-loading effect in AEL conditions compared to non-AEL condition. Discussion Our simplified simulations did not show impro…
bibliographic citation: Su et al. (2023) Musculoskeletal simulations to examine the effects of accentuated eccentric loading (AEL) on jump height. PeerJ 11:e14687 https://doi.org/10.7717/peerj.14687
date submitted: 2022-04-01
date accepted: 2022-12-13
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Eric Yung-Sheng
author list: Agent
  family name: Carroll
  given name: Timothy J.
author list: Agent
  family name: Farris
  given name: Dominic J.
author list: Agent
  family name: Lichtwark
  given name: Glen A.
doi: 10.7717/peerj.14687
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: ©2023 Su et al.
attribution name: Su et al.

Genome-wide identification and expression reveal the involvement of the FCS-like zinc finger (FLZ) gene family in Gossypium hirsutum at low temperature
type: item
type: AcademicArticle
description: FCS-like zinc finger (FLZ) is a plant-specific gene family that plays an important regulatory role in plant growth and development and its response to stress. However, studies on the characteristics and functions of cotton FLZ family genes are still lacking. This study systematically identified members of the cotton FLZ gene family based on cotton genome data. The cotton FLZ family genes were systematically analyzed by bioinformatics, and their expression patterns in different tissues and under low-temperature stress were analyzed by transcriptome and qRT–PCR. The G. hirsutum genome contains 56 FLZ genes distributed on 20 chromosomes, and most of them are located in the nucleus. According to the number and evolution analysis of FLZ family genes, FLZ family genes can be divided into five subgroups in cotton. The G. hirsutum FLZ gene has a wide range of tissue expression types, among which the expression is generally higher in roots, stems, leaves, receptacles and calyx. Through promoter analysis, it was found that it contained the most cis-acting elements related to methyl jasmonate (MeJA) and abscisic acid (ABA). Combined with the promoter and qRT–PCR results, it was speculated that GhFLZ11, GhFLZ25, GhFLZ44 and GhFLZ55 were involved in the response of cotton to low-temperature stress. Taken together, our findings suggest an important role for the FLZ gene family in the cotton response to cold stress. This study provides an important theoretical basis for further research on the function of the FLZ gene family and the molecular mechanism of the cotton response to low temperature.
format: application/pdf
format: text/html
creator: JunDuo Wang
creator: Zhiqiang Li
creator: Yajun Liang
creator: Juyun Zheng
creator: Zhaolong Gong
creator: Guohui Zhou
creator: Yuhui Xu
creator: Xueyuan Li
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14690
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: FCS-like zinc finger (FLZ) is a plant-specific gene family that plays an important regulatory role in plant growth and development and its response to stress. However, studies on the characteristics and functions of cotton FLZ family genes are still lacking. This study systematically identified members of the cotton FLZ gene family based on cotton genome data. The cotton FLZ family genes were systematically analyzed by bioinformatics, and their expression patterns in different tissues and under low-temperature stress were analyzed by transcriptome and qRT–PCR. The G. hirsutum genome contains 56 FLZ genes distributed on 20 chromosomes, and most of them are located in the nucleus. According to the number and evolution analysis of FLZ family genes, FLZ family genes can be divided into five subgroups in cotton. The G. hirsutum FLZ gene has a wide range of tissue expression types, among which the expression is generally higher in roots, stems, leaves, receptacles and calyx. Through promoter analysis, it was found that it contained the most cis-acting elements related to methyl jasmonate (MeJA) and abscisic acid (ABA). Combined with the promoter and qRT–PCR results, it was speculated that GhFLZ11, GhFLZ25, GhFLZ44 and GhFLZ55 were involved in the response of cotton to low-temperature stress. Taken together, our findings suggest an important role for the FLZ gene family in the cotton response to cold stress. This study provides an important theoretical basis for further research on the function of the FLZ gene family and the molecular mechanism of the cotton response to low temperature.
bibliographic citation: Wang et al. (2023) Genome-wide identification and expression reveal the involvement of the FCS-like zinc finger (FLZ) gene family in Gossypium hirsutum at low temperature. PeerJ 11:e14690 https://doi.org/10.7717/peerj.14690
date submitted: 2022-06-29
date accepted: 2022-12-14
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: JunDuo
author list: Agent
  family name: Li
  given name: Zhiqiang
author list: Agent
  family name: Liang
  given name: Yajun
author list: Agent
  family name: Zheng
  given name: Juyun
author list: Agent
  family name: Gong
  given name: Zhaolong
author list: Agent
  family name: Zhou
  given name: Guohui
author list: Agent
  family name: Xu
  given name: Yuhui
author list: Agent
  family name: Li
  given name: Xueyuan
doi: 10.7717/peerj.14690
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: © 2023 Wang et al.
attribution name: Wang et al.

A clustering method for small scRNA-seq data based on subspace and weighted distance
type: item
type: AcademicArticle
description: Background Identifying the cell types using unsupervised methods is essential for scRNA-seq research. However, conventional similarity measures introduce challenges to single-cell data clustering because of the high dimensional, high noise, and high dropout. Methods We proposed a clustering method for small ScRNA-seq data based on Subspace and Weighted Distance (SSWD), which follows the assumption that the sets of gene subspace composed of similar density-distributing genes can better distinguish cell groups. To accurately capture the intrinsic relationship among cells or genes, a new distance metric that combines Euclidean and Pearson distance through a weighting strategy was proposed. The relative Calinski-Harabasz (CH) index was used to estimate the cluster numbers instead of the CH index because it is comparable across degrees of freedom. Results We compared SSWD with seven prevailing methods on eight publicly scRNA-seq datasets. The experimental results show that the SSWD has better clustering accuracy and the partitioning ability of cell groups. SSWD can be downloaded at https://github.com/ningzilan/SSWD.
format: application/pdf
format: text/html
creator: Zilan Ning
creator: Zhijun Dai
creator: Hongyan Zhang
creator: Yuan Chen
creator: Zheming Yuan
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.14706
publisher: PeerJ Inc.
rights: © 2023 Ning et al.
abstract: Background Identifying the cell types using unsupervised methods is essential for scRNA-seq research. However, conventional similarity measures introduce challenges to single-cell data clustering because of the high dimensional, high noise, and high dropout. Methods We proposed a clustering method for small ScRNA-seq data based on Subspace and Weighted Distance (SSWD), which follows the assumption that the sets of gene subspace composed of similar density-distributing genes can better distinguish cell groups. To accurately capture the intrinsic relationship among cells or genes, a new distance metric that combines Euclidean and Pearson distance through a weighting strategy was proposed. The relative Calinski-Harabasz (CH) index was used to estimate the cluster numbers instead of the CH index because it is comparable across degrees of freedom. Results We compared SSWD with seven prevailing methods on eight publicly scRNA-seq datasets. The experimental results show that the SSWD has better clustering accuracy and the partitioning ability of cell groups. SSWD can be downloaded at https://github.com/ningzilan/SSWD.
bibliographic citation: Ning et al. (2023) A clustering method for small scRNA-seq data based on subspace and weighted distance. PeerJ 11:e14706 https://doi.org/10.7717/peerj.14706
date submitted: 2022-07-25
date accepted: 2022-12-15
issued: 2023-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ning
  given name: Zilan
author list: Agent
  family name: Dai
  given name: Zhijun
author list: Agent
  family name: Zhang
  given name: Hongyan
author list: Agent
  family name: Chen
  given name: Yuan
author list: Agent
  family name: Yuan
  given name: Zheming
doi: 10.7717/peerj.14706
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-23
copyright: ©2023 Ning et al.
attribution name: Ning et al.

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