PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Virgin and UV-weathered polyamide microplastics posed no effect on the survival and reproduction of Daphnia magna
items: Automatic detection of the parasite Trypanosoma cruzi in blood smears using a machine learning approach applied to mobile phone images
items: Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L.
items: Ability of functional performance assessments to discriminate athletes with and without chronic ankle instability : a case-control study
items: Challenges of sperm cryopreservation in transferring heat adaptation of corals across ocean basins
items: Influence of DNA extraction kits on freshwater fungal DNA metabarcoding
items: Sexual dimorphism in shell size of the land snail Leptopoma perlucidum (Caenogastropoda: Cyclophoridae)
items: Anticancer mechanism of 7-α-hydroxyfrullanolide on microtubules and computational prediction of its target binding in triple-negative breast cancer cells
items: Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic
items: Animal reactivity to camera traps and its effects on abundance estimate using distance sampling in the Taï National Park, Côte d’Ivoire

Virgin and UV-weathered polyamide microplastics posed no effect on the survival and reproduction of Daphnia magna
type: item
type: AcademicArticle
description: Although evidence suggests that microplastic (MP) particles pose a risk to organisms, the effects of virgin and weathered MP should be evaluated separately as their effects may be different. In this work, we provide new information on the toxic potential of virgin and UV-weathered polyamide, one of the commonly used plastics worldwide. Polyamide MP particles were subjected to UV-weathering in wet conditions over 26 days in a customized irradiation chamber equipped with UV-C light tubes (15 W each, max. wavelength 254 nm). The toxicity of virgin and UV-weathered polyamide MP (< 180 µm in one dimension, 100 and 300 mg L−1) was evaluated by studying Daphnia magna reproduction in natural lake water spiked with MP, following the 21-day OECD 211 test guideline. In parallel, a nonionic surfactant Tween 20 (7 mg L−1) was added to the test medium to improve the suspendability of the MP. The results of the tests showed no adverse effects of either virgin or UV-weathered polyamide MP on the reproduction of D. magna. In addition, presence of Tween 20 in the test medium had no effects on the test results. These results bring a new perspective on the potential long-term impact of polyamide particles on aquatic organisms, especially considering that the polyamide has received marginal attention in the ecotoxicological research. However, standard test endpoints (survival and reproduction) may still miss long-term adverse effects of insoluble e.g., plastic particles and additional studies may be necessary.
format: application/pdf
format: text/html
creator: Alla Khosrovyan
creator: Anne Kahru
subject: Zoology
subject: Ecotoxicology
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13533
publisher: PeerJ Inc.
rights: © 2022 Khosrovyan and Kahru
abstract: Although evidence suggests that microplastic (MP) particles pose a risk to organisms, the effects of virgin and weathered MP should be evaluated separately as their effects may be different. In this work, we provide new information on the toxic potential of virgin and UV-weathered polyamide, one of the commonly used plastics worldwide. Polyamide MP particles were subjected to UV-weathering in wet conditions over 26 days in a customized irradiation chamber equipped with UV-C light tubes (15 W each, max. wavelength 254 nm). The toxicity of virgin and UV-weathered polyamide MP (< 180 µm in one dimension, 100 and 300 mg L−1) was evaluated by studying Daphnia magna reproduction in natural lake water spiked with MP, following the 21-day OECD 211 test guideline. In parallel, a nonionic surfactant Tween 20 (7 mg L−1) was added to the test medium to improve the suspendability of the MP. The results of the tests showed no adverse effects of either virgin or UV-weathered polyamide MP on the reproduction of D. magna. In addition, presence of Tween 20 in the test medium had no effects on the test results. These results bring a new perspective on the potential long-term impact of polyamide particles on aquatic organisms, especially considering that the polyamide has received marginal attention in the ecotoxicological research. However, standard test endpoints (survival and reproduction) may still miss long-term adverse effects of insoluble e.g., plastic particles and additional studies may be necessary.
bibliographic citation: Khosrovyan et al. (2022) Virgin and UV-weathered polyamide microplastics posed no effect on the survival and reproduction of Daphnia magna. PeerJ 10:e13533 https://doi.org/10.7717/peerj.13533
date submitted: 2022-03-16
date accepted: 2022-05-12
issued: 2022-05-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khosrovyan
  given name: Alla
author list: Agent
  family name: Kahru
  given name: Anne
doi: 10.7717/peerj.13533
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-30
copyright: ©2022 Khosrovyan and Kahru
attribution name: Khosrovyan and Kahru

Automatic detection of the parasite Trypanosoma cruzi in blood smears using a machine learning approach applied to mobile phone images
type: item
type: AcademicArticle
description: Chagas disease is a life-threatening illness caused by the parasite Trypanosoma cruzi. The diagnosis of the acute form of the disease is performed by trained microscopists who detect parasites in blood smear samples. Since this method requires a dedicated high-resolution camera system attached to the microscope, the diagnostic method is more expensive and often prohibitive for low-income settings. Here, we present a machine learning approach based on a random forest (RF) algorithm for the detection and counting of T. cruzi trypomastigotes in mobile phone images. We analyzed micrographs of blood smear samples that were acquired using a mobile device camera capable of capturing images in a resolution of 12 megapixels. We extracted a set of features that describe morphometric parameters (geometry and curvature), as well as color, and texture measurements of 1,314 parasites. The features were divided into train and test sets (4:1) and classified using the RF algorithm. The values of precision, sensitivity, and area under the receiver operating characteristic (ROC) curve of the proposed method were 87.6%, 90.5%, and 0.942, respectively. Automating image analysis acquired with a mobile device is a viable alternative for reducing costs and gaining efficiency in the use of the optical microscope.
format: application/pdf
format: text/html
creator: Mauro César Cafundó Morais
creator: Diogo Silva
creator: Matheus Marques Milagre
creator: Maykon Tavares de Oliveira
creator: Thaís Pereira
creator: João Santana Silva
creator: Luciano da F. Costa
creator: Paola Minoprio
creator: Roberto Marcondes Cesar Junior
creator: Ricardo Gazzinelli
creator: Marta de Lana
creator: Helder I. Nakaya
subject: Bioinformatics
subject: Computational Biology
subject: Parasitology
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.13470
publisher: PeerJ Inc.
rights: © 2022 Morais et al.
abstract: Chagas disease is a life-threatening illness caused by the parasite Trypanosoma cruzi. The diagnosis of the acute form of the disease is performed by trained microscopists who detect parasites in blood smear samples. Since this method requires a dedicated high-resolution camera system attached to the microscope, the diagnostic method is more expensive and often prohibitive for low-income settings. Here, we present a machine learning approach based on a random forest (RF) algorithm for the detection and counting of T. cruzi trypomastigotes in mobile phone images. We analyzed micrographs of blood smear samples that were acquired using a mobile device camera capable of capturing images in a resolution of 12 megapixels. We extracted a set of features that describe morphometric parameters (geometry and curvature), as well as color, and texture measurements of 1,314 parasites. The features were divided into train and test sets (4:1) and classified using the RF algorithm. The values of precision, sensitivity, and area under the receiver operating characteristic (ROC) curve of the proposed method were 87.6%, 90.5%, and 0.942, respectively. Automating image analysis acquired with a mobile device is a viable alternative for reducing costs and gaining efficiency in the use of the optical microscope.
bibliographic citation: Morais et al. (2022) Automatic detection of the parasite Trypanosoma cruzi in blood smears using a machine learning approach applied to mobile phone images. PeerJ 10:e13470 https://doi.org/10.7717/peerj.13470
date submitted: 2021-08-04
date accepted: 2022-04-29
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morais
  given name: Mauro César Cafundó
author list: Agent
  family name: Silva
  given name: Diogo
author list: Agent
  family name: Milagre
  given name: Matheus Marques
author list: Agent
  family name: Oliveira
  given name: Maykon Tavares de
author list: Agent
  family name: Pereira
  given name: Thaís
author list: Agent
  family name: Silva
  given name: João Santana
author list: Agent
  family name: Costa
  given name: Luciano da F.
author list: Agent
  family name: Minoprio
  given name: Paola
author list: Agent
  family name: Junior
  given name: Roberto Marcondes Cesar
author list: Agent
  family name: Gazzinelli
  given name: Ricardo
author list: Agent
  family name: de Lana
  given name: Marta
author list: Agent
  family name: Nakaya
  given name: Helder I.
doi: 10.7717/peerj.13470
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: ©2022 Morais et al.
attribution name: Morais et al.

Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L.
type: item
type: AcademicArticle
description: Background Pepper (Capsicum annuum L.) is a major cash crop throughout the world. Male sterility is an important characteristic in crop species that leads to a failure to produce functional pollen, and it has crucial roles in agricultural breeding and the utilization of heterosis. Objectives In this study, we identified many crucial factors and important components in metabolic pathways in anther and pollen development, and elucidated the molecular mechanism related to pollen abortion in pepper. Methods Pepper pollen was observed at different stages to detect the characteristics associated with male sterility and fertility. The phytohormone and oxidoreductase activities were detected in spectrophotometric and redox reaction assays, respectively. Proteins were extracted from male sterile and fertile pepper lines, and identified by TMT/iTRAQ (tandem mass tags/isobaric tags for relative and absolute quantitation) and LC-MS/MS (liquid chromatograph-mass spectrometer) analysis. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes database according to |fold change)| > 1.3 and P value < 0.05. DAPs were quantified in the meiosis, tetrad, and binucleate stages by parallel reaction monitoring (PRM). Results In this study, we screened and identified one male sterile pepper line with abnormal cytological characteristics in terms of pollen development. The peroxidase and catalase enzyme activities were significantly reduced and increased, respectively, in the male sterile line compared with the male fertile line. Phytohormone analysis demonstrated that the gibberellin, jasmonic acid, and auxin contents changed by different extents in the male sterile pepper line. Proteome analysis screened 1,645 DAPs in six clusters, which were mainly associated with the chloroplast and cytoplasm based on their similar expression levels. According to proteome analysis, 45 DAPs were quantitatively identified in t…
format: application/pdf
format: text/html
creator: Hongxia Pei
creator: Hua Xie
creator: Xuemei Wang
creator: Xiujuan Yan
creator: Baike Wang
creator: Haiping Feng
creator: Yunxia Zhao
creator: Jingxia Gao
creator: Jie Gao
subject: Agricultural Science
subject: Biotechnology
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13168
publisher: PeerJ Inc.
rights: © 2022 Pei et al.
abstract: Background Pepper (Capsicum annuum L.) is a major cash crop throughout the world. Male sterility is an important characteristic in crop species that leads to a failure to produce functional pollen, and it has crucial roles in agricultural breeding and the utilization of heterosis. Objectives In this study, we identified many crucial factors and important components in metabolic pathways in anther and pollen development, and elucidated the molecular mechanism related to pollen abortion in pepper. Methods Pepper pollen was observed at different stages to detect the characteristics associated with male sterility and fertility. The phytohormone and oxidoreductase activities were detected in spectrophotometric and redox reaction assays, respectively. Proteins were extracted from male sterile and fertile pepper lines, and identified by TMT/iTRAQ (tandem mass tags/isobaric tags for relative and absolute quantitation) and LC-MS/MS (liquid chromatograph-mass spectrometer) analysis. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes database according to |fold change)| > 1.3 and P value < 0.05. DAPs were quantified in the meiosis, tetrad, and binucleate stages by parallel reaction monitoring (PRM). Results In this study, we screened and identified one male sterile pepper line with abnormal cytological characteristics in terms of pollen development. The peroxidase and catalase enzyme activities were significantly reduced and increased, respectively, in the male sterile line compared with the male fertile line. Phytohormone analysis demonstrated that the gibberellin, jasmonic acid, and auxin contents changed by different extents in the male sterile pepper line. Proteome analysis screened 1,645 DAPs in six clusters, which were mainly associated with the chloroplast and cytoplasm based on their similar expression levels. According to proteome analysis, 45 DAPs were quantitatively identified in t…
bibliographic citation: Pei et al. (2022) Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L.. PeerJ 10:e13168 https://doi.org/10.7717/peerj.13168
date submitted: 2021-08-30
date accepted: 2022-03-04
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pei
  given name: Hongxia
author list: Agent
  family name: Xie
  given name: Hua
author list: Agent
  family name: Wang
  given name: Xuemei
author list: Agent
  family name: Yan
  given name: Xiujuan
author list: Agent
  family name: Wang
  given name: Baike
author list: Agent
  family name: Feng
  given name: Haiping
author list: Agent
  family name: Zhao
  given name: Yunxia
author list: Agent
  family name: Gao
  given name: Jingxia
author list: Agent
  family name: Gao
  given name: Jie
doi: 10.7717/peerj.13168
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: © 2022 Pei et al.
attribution name: Pei et al.

Ability of functional performance assessments to discriminate athletes with and without chronic ankle instability : a case-control study
type: item
type: AcademicArticle
description: Background The decline in motor function associated with chronic ankle instability (CAI) can be assessed using Functional Performance tests. Ankle muscular strength, endurance and range of motion (ROM) has been assessed in previous studies but functional activities such as sprinting and change of direction are less well studied in athletes with CAI. Hence the aim of this study was to determine how sprint, change of direction, ankle isometric strength, endurance and ROM measures may be associated with discriminate athletes with and without CAI. Methods One hundred and six participants (CAI: n = 53 or no CAI: n = 53) provided informed consent to participate in this study. Participants performed three functional performance tests, (30-m sprint test, Modified Illinois change of direction test (MICODT)) and change of direction test. Range of motion for dorsiflexion was measured using weight bearing lunge test and inversion, eversion and plantarflexion using Saunders® digital inclinometer. Strength was assessed using Baseline® hand-held dynamometer for plantarflexors, dorsiflexors, invertors and evertors. Muscular endurance was assessed by single heel raise test and Modified single heel raise test. Between-group comparisons utilised Student’s t-test and Mann-Whitney U-tests, with a number of unique variable and multivariable binomial logistic regression performed to determine which performance measures may discriminate participants with CAI. Results The CAI participants performed significantly worse in the three functional performance tests as well as multiple measures of ankle ROM, isometric strength and muscular endurance (p < 0.008). While several measures of ROM (plantarflexion and dorsiflexion), strength (inversion and eversion) and both muscular endurance tests were significantly associated with CAI in the univariable analysis, the strongest association was the functional performance tests, especially MICDOT time (odds ratio (95% CI): 0.06 [0.02–0.17], sensitivity 9…
format: application/pdf
format: text/html
creator: Madhura S. Jamsandekar
creator: Vivek Dineshbhai Patel
creator: Ashish J. Prabhakar
creator: Charu Eapen
creator: Justin W.L. Keogh
subject: Orthopedics
subject: Rheumatology
subject: Biomechanics
subject: Sports Injury
subject: Rehabilitation
description: doi:10.7717/peerj.13390
publisher: PeerJ Inc.
rights: © 2022 S Jamsandekar et al.
abstract: Background The decline in motor function associated with chronic ankle instability (CAI) can be assessed using Functional Performance tests. Ankle muscular strength, endurance and range of motion (ROM) has been assessed in previous studies but functional activities such as sprinting and change of direction are less well studied in athletes with CAI. Hence the aim of this study was to determine how sprint, change of direction, ankle isometric strength, endurance and ROM measures may be associated with discriminate athletes with and without CAI. Methods One hundred and six participants (CAI: n = 53 or no CAI: n = 53) provided informed consent to participate in this study. Participants performed three functional performance tests, (30-m sprint test, Modified Illinois change of direction test (MICODT)) and change of direction test. Range of motion for dorsiflexion was measured using weight bearing lunge test and inversion, eversion and plantarflexion using Saunders® digital inclinometer. Strength was assessed using Baseline® hand-held dynamometer for plantarflexors, dorsiflexors, invertors and evertors. Muscular endurance was assessed by single heel raise test and Modified single heel raise test. Between-group comparisons utilised Student’s t-test and Mann-Whitney U-tests, with a number of unique variable and multivariable binomial logistic regression performed to determine which performance measures may discriminate participants with CAI. Results The CAI participants performed significantly worse in the three functional performance tests as well as multiple measures of ankle ROM, isometric strength and muscular endurance (p < 0.008). While several measures of ROM (plantarflexion and dorsiflexion), strength (inversion and eversion) and both muscular endurance tests were significantly associated with CAI in the univariable analysis, the strongest association was the functional performance tests, especially MICDOT time (odds ratio (95% CI): 0.06 [0.02–0.17], sensitivity 9…
bibliographic citation: S. Jamsandekar et al. (2022) Ability of functional performance assessments to discriminate athletes with and without chronic ankle instability : a case-control study. PeerJ 10:e13390 https://doi.org/10.7717/peerj.13390
date submitted: 2021-10-06
date accepted: 2022-04-15
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: S. Jamsandekar
  given name: Madhura
author list: Agent
  family name: Patel
  given name: Vivek Dineshbhai
author list: Agent
  family name: J. Prabhakar
  given name: Ashish
author list: Agent
  family name: Eapen
  given name: Charu
author list: Agent
  family name: Keogh
  given name: Justin W.L.
doi: 10.7717/peerj.13390
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: © 2022 S. Jamsandekar et al.
attribution name: S Jamsandekar et al.

Challenges of sperm cryopreservation in transferring heat adaptation of corals across ocean basins
type: item
type: AcademicArticle
description: Reef-building corals live very close to their upper thermal limits and their persistence is imperiled by a rapidly warming climate. Human interventions may be used to increase the thermal limits of sensitive corals by cross-breeding with heat-adapted populations. However, the scope of breeding interventions is constrained by regional variation in the annual reproductive cycle of corals. Here we use cryopreservation technology to overcome this barrier and cross-breed conspecific coral populations across ocean basins for the first time. During regional spawning events, sperm samples were cryopreserved from populations of the widespread Indo-Pacific coral, Platygyra daedalea, from the southern Persian Gulf (maximum daily sea surface temperature of 36 °C), the Oman Sea (33 °C), and the central Great Barrier Reef (30 °C). These sperm samples were thawed during a later spawning event to test their ability to fertilize freshly spawned eggs of P. daedalea colonies from the central Great Barrier Reef. Average fertilization success for the Persian Gulf (9%) and Oman Sea (6%) sperm were 1.4–2.5 times lower than those for the native cryopreserved sperm from Great Barrier Reef (13–15%), potentially due to lower sperm quality of the Middle Eastern sperm and/or reproductive incompatibility between these distant populations. Overall, fertilization success with cryopreserved sperm was low compared with fresh sperm (>80%), likely due to the low motility of thawed sperm (≤5%, reduced from 50% to >90% in fresh sperm). To evaluate whether cross-bred offspring had enhanced thermal tolerance, the survival of larvae sired by Persian Gulf cryopreserved sperm, Great Barrier Reef cryopreserved sperm, and Great Barrier Reef fresh sperm was monitored for six days at ambient (27 °C) and elevated (33 °C) temperature. Against expectations of thermal tolerance enhancement, survival of larvae sired by Persian Gulf cryopreserved sperm was 2.6 times lower than larvae sired by Great Barrier Reef fresh …
format: application/pdf
format: text/html
creator: Emily J. Howells
creator: Mary Hagedorn
creator: Madeleine J.H. Van Oppen
creator: John A. Burt
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.13395
publisher: PeerJ Inc.
rights: © 2022 Howells et al.
abstract: Reef-building corals live very close to their upper thermal limits and their persistence is imperiled by a rapidly warming climate. Human interventions may be used to increase the thermal limits of sensitive corals by cross-breeding with heat-adapted populations. However, the scope of breeding interventions is constrained by regional variation in the annual reproductive cycle of corals. Here we use cryopreservation technology to overcome this barrier and cross-breed conspecific coral populations across ocean basins for the first time. During regional spawning events, sperm samples were cryopreserved from populations of the widespread Indo-Pacific coral, Platygyra daedalea, from the southern Persian Gulf (maximum daily sea surface temperature of 36 °C), the Oman Sea (33 °C), and the central Great Barrier Reef (30 °C). These sperm samples were thawed during a later spawning event to test their ability to fertilize freshly spawned eggs of P. daedalea colonies from the central Great Barrier Reef. Average fertilization success for the Persian Gulf (9%) and Oman Sea (6%) sperm were 1.4–2.5 times lower than those for the native cryopreserved sperm from Great Barrier Reef (13–15%), potentially due to lower sperm quality of the Middle Eastern sperm and/or reproductive incompatibility between these distant populations. Overall, fertilization success with cryopreserved sperm was low compared with fresh sperm (>80%), likely due to the low motility of thawed sperm (≤5%, reduced from 50% to >90% in fresh sperm). To evaluate whether cross-bred offspring had enhanced thermal tolerance, the survival of larvae sired by Persian Gulf cryopreserved sperm, Great Barrier Reef cryopreserved sperm, and Great Barrier Reef fresh sperm was monitored for six days at ambient (27 °C) and elevated (33 °C) temperature. Against expectations of thermal tolerance enhancement, survival of larvae sired by Persian Gulf cryopreserved sperm was 2.6 times lower than larvae sired by Great Barrier Reef fresh …
bibliographic citation: Howells et al. (2022) Challenges of sperm cryopreservation in transferring heat adaptation of corals across ocean basins. PeerJ 10:e13395 https://doi.org/10.7717/peerj.13395
date submitted: 2022-01-14
date accepted: 2022-04-16
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Howells
  given name: Emily J.
author list: Agent
  family name: Hagedorn
  given name: Mary
author list: Agent
  family name: Van Oppen
  given name: Madeleine J.H.
author list: Agent
  family name: Burt
  given name: John A.
doi: 10.7717/peerj.13395
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: ©2022 Howells et al.
attribution name: Howells et al.

Influence of DNA extraction kits on freshwater fungal DNA metabarcoding
type: item
type: AcademicArticle
description: Background Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. Results No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.
format: application/pdf
format: text/html
creator: Shunsuke Matsuoka
creator: Yoriko Sugiyama
creator: Mariko Nagano
creator: Hideyuki Doi
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.13477
publisher: PeerJ Inc.
rights: © 2022 Matsuoka et al.
abstract: Background Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. Results No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.
bibliographic citation: Matsuoka et al. (2022) Influence of DNA extraction kits on freshwater fungal DNA metabarcoding. PeerJ 10:e13477 https://doi.org/10.7717/peerj.13477
date submitted: 2021-11-02
date accepted: 2022-05-01
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsuoka
  given name: Shunsuke
author list: Agent
  family name: Sugiyama
  given name: Yoriko
author list: Agent
  family name: Nagano
  given name: Mariko
author list: Agent
  family name: Doi
  given name: Hideyuki
doi: 10.7717/peerj.13477
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: ©2022 Matsuoka et al.
attribution name: Matsuoka et al.

Sexual dimorphism in shell size of the land snail Leptopoma perlucidum (Caenogastropoda: Cyclophoridae)
type: item
type: AcademicArticle
description: Sexual dimorphism in the shell size and shape of land snails has been less explored compared to that of other marine and freshwater snail taxa. This study examined the differences in shell size and shape across both sexes of Leptopoma perlucidum land snails. We collected 84 land snails of both sexes from two isolated populations on two islands off Borneo. A total of five shell size variables were measured: (1) shell height, (2) shell width, (3) shell spire height, (4) aperture height, and (5) aperture width. We performed frequentist and Bayesian t-tests to determine if there was a significant difference between the two sexes of L. perlucidum on each of the five shell measurements. Additionally, the shell shape was quantified based on nine landmark points using the geometric morphometric approach. We used generalised Procrustes and principal component analyses to test the effects of sex and location on shell shape. The results showed that female shells were larger than male shells across all five measurements (all with p-values < 0.05), but particularly in regards to shell height and shell width. Future taxonomic studies looking to resolve the Leptopoma species’ status should consider the variability of shell size caused by sexual dimorphism.
format: application/pdf
format: text/html
creator: Chee-Chean Phung
creator: Ming-Huei Choo
creator: Thor-Seng Liew
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.13501
publisher: PeerJ Inc.
rights: © 2022 Phung et al.
abstract: Sexual dimorphism in the shell size and shape of land snails has been less explored compared to that of other marine and freshwater snail taxa. This study examined the differences in shell size and shape across both sexes of Leptopoma perlucidum land snails. We collected 84 land snails of both sexes from two isolated populations on two islands off Borneo. A total of five shell size variables were measured: (1) shell height, (2) shell width, (3) shell spire height, (4) aperture height, and (5) aperture width. We performed frequentist and Bayesian t-tests to determine if there was a significant difference between the two sexes of L. perlucidum on each of the five shell measurements. Additionally, the shell shape was quantified based on nine landmark points using the geometric morphometric approach. We used generalised Procrustes and principal component analyses to test the effects of sex and location on shell shape. The results showed that female shells were larger than male shells across all five measurements (all with p-values < 0.05), but particularly in regards to shell height and shell width. Future taxonomic studies looking to resolve the Leptopoma species’ status should consider the variability of shell size caused by sexual dimorphism.
bibliographic citation: Phung et al. (2022) Sexual dimorphism in shell size of the land snail Leptopoma perlucidum (Caenogastropoda: Cyclophoridae). PeerJ 10:e13501 https://doi.org/10.7717/peerj.13501
date submitted: 2021-07-15
date accepted: 2022-05-05
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Phung
  given name: Chee-Chean
author list: Agent
  family name: Choo
  given name: Ming-Huei
author list: Agent
  family name: Liew
  given name: Thor-Seng
doi: 10.7717/peerj.13501
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: ©2022 Phung et al.
attribution name: Phung et al.

Anticancer mechanism of 7-α-hydroxyfrullanolide on microtubules and computational prediction of its target binding in triple-negative breast cancer cells
type: item
type: AcademicArticle
description: Background Triple-negative breast cancer (TNBC) responds poorly to the available drugs; thus, the mortality rate associated with TNBC remains high. 7-α-Hydroxyfrullanolide (7HF) possesses anticancer properties and arrests cells in the G2/M-phase via modulation of several proteins involved in the G2/M-phase transition, as well as the mitotic checkpoint in MDA-MB-468 (TNBC) cells. Microtubules (MTs) dynamically regulate cell division in the G2/M phase and are related to cancer cell stress response. However, antimitotic drug cytotoxicity to multiple cancer resistance developed in response to drugs are obstacles faced to date. Here, the activity and mechanism via which 7HF controls MTs dynamics was investigated in MDA-MB-468 cells. Methods 7HF uptake by MDA-MB-468 cells was assessed using spectrophotometry. The drug-like properties of 7HF were predicted using the Swiss-absorption, distribution, metabolism, and excretion (ADME) webtool. Then, the effect of 7HF treatment (6, 12, and 24 µM) on the dynamic arrangement of MTs was assessed for 1, 12, and 24 h using indirect immunofluorescence. Polymerization of α- and β-tubulin was assessed using different 7HF concentrations in a cell-free system for 1 h. Cell proliferation assay with bromodeoxyuridine plus propidium iodide staining and flow cytometry was performed at different 7HF concentrations and time points. The mechanism of action was assessed by detecting the expression of proteins, including Bub3, cyclin B1, p-Cdk1 (Tyr15), Rb, p-Rb (Ser780), Chk1, p-Chk1 (Ser345), Chk2, p-Chk2 (Ser516), and p-H2AX (Ser139), using western blotting. Molecular docking was used to predict the molecular interactions between 7HF and tubulins in MTs. Results We observed that 7HF was able to enter the MDA-MB-468 cells. The ADME webtool analysis predicted that it possesses the high passive permeation and gastrointestinal absorption properties of drugs. Various concentrations of 7HF disrupted the dynamic arrangement of spindle MTs by causing r…
format: application/pdf
format: text/html
creator: Siriphorn Chimplee
creator: Carl Smythe
creator: Varomyalin Tipmanee
creator: Suchada Sukrong
creator: Kanyanatt Kanokwiroon
subject: Biochemistry
subject: Cell Biology
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13508
publisher: PeerJ Inc.
rights: © 2022 Chimplee et al.
abstract: Background Triple-negative breast cancer (TNBC) responds poorly to the available drugs; thus, the mortality rate associated with TNBC remains high. 7-α-Hydroxyfrullanolide (7HF) possesses anticancer properties and arrests cells in the G2/M-phase via modulation of several proteins involved in the G2/M-phase transition, as well as the mitotic checkpoint in MDA-MB-468 (TNBC) cells. Microtubules (MTs) dynamically regulate cell division in the G2/M phase and are related to cancer cell stress response. However, antimitotic drug cytotoxicity to multiple cancer resistance developed in response to drugs are obstacles faced to date. Here, the activity and mechanism via which 7HF controls MTs dynamics was investigated in MDA-MB-468 cells. Methods 7HF uptake by MDA-MB-468 cells was assessed using spectrophotometry. The drug-like properties of 7HF were predicted using the Swiss-absorption, distribution, metabolism, and excretion (ADME) webtool. Then, the effect of 7HF treatment (6, 12, and 24 µM) on the dynamic arrangement of MTs was assessed for 1, 12, and 24 h using indirect immunofluorescence. Polymerization of α- and β-tubulin was assessed using different 7HF concentrations in a cell-free system for 1 h. Cell proliferation assay with bromodeoxyuridine plus propidium iodide staining and flow cytometry was performed at different 7HF concentrations and time points. The mechanism of action was assessed by detecting the expression of proteins, including Bub3, cyclin B1, p-Cdk1 (Tyr15), Rb, p-Rb (Ser780), Chk1, p-Chk1 (Ser345), Chk2, p-Chk2 (Ser516), and p-H2AX (Ser139), using western blotting. Molecular docking was used to predict the molecular interactions between 7HF and tubulins in MTs. Results We observed that 7HF was able to enter the MDA-MB-468 cells. The ADME webtool analysis predicted that it possesses the high passive permeation and gastrointestinal absorption properties of drugs. Various concentrations of 7HF disrupted the dynamic arrangement of spindle MTs by causing r…
bibliographic citation: Chimplee et al. (2022) Anticancer mechanism of 7-α-hydroxyfrullanolide on microtubules and computational prediction of its target binding in triple-negative breast cancer cells. PeerJ 10:e13508 https://doi.org/10.7717/peerj.13508
date submitted: 2022-02-17
date accepted: 2022-05-06
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chimplee
  given name: Siriphorn
author list: Agent
  family name: Smythe
  given name: Carl
author list: Agent
  family name: Tipmanee
  given name: Varomyalin
author list: Agent
  family name: Sukrong
  given name: Suchada
author list: Agent
  family name: Kanokwiroon
  given name: Kanyanatt
doi: 10.7717/peerj.13508
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: ©2022 Chimplee et al.
attribution name: Chimplee et al.

Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic
type: item
type: AcademicArticle
description: Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man’s fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951–2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081–2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region.
format: application/pdf
format: text/html
creator: Tom L. Jenkins
creator: Jamie R. Stevens
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.13509
publisher: PeerJ Inc.
rights: © 2022 Jenkins and Stevens
abstract: Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man’s fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951–2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081–2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region.
bibliographic citation: Jenkins et al. (2022) Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic. PeerJ 10:e13509 https://doi.org/10.7717/peerj.13509
date submitted: 2021-09-14
date accepted: 2022-05-06
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jenkins
  given name: Tom L.
author list: Agent
  family name: Stevens
  given name: Jamie R.
doi: 10.7717/peerj.13509
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: © 2022 Jenkins and Stevens
attribution name: Jenkins and Stevens

Animal reactivity to camera traps and its effects on abundance estimate using distance sampling in the Taï National Park, Côte d’Ivoire
type: item
type: AcademicArticle
description: The use of camera traps (CTs) has become an increasingly popular method of studying wildlife, as CTs are able to detect rare, nocturnal, and elusive species in remote and difficult-to-access areas. It thus makes them suited to estimate animal density and abundance, identify activity patterns and new behaviours of animals. However, animals can react when they see the CTs and this can lead to bias in the animal population estimates. While CTs may provide many advantages, an improved understanding of their impacts on individual’s behaviour is necessary to avoid erroneous density estimates. Yet, the impact of CTs on detected individuals, such as human odour near the device and the environment, or the infrared illumination, has received relatively little attention. To date, there is no clear procedure to remove this potential bias. Here, we use camera trap distance sampling (CTDS) to (1) quantify the bias resulting from the different animal responses to the CTs when determining animal density and abundance, and (2) test if olfactory, visual and auditory signals have an influence on the animals’ reaction to CTs. Between March 2019 and March 2020, we deployed CTs at 267 locations distributed systematically over the entire Taï National Park. We obtained 58,947 videos from which we analysed four medium- to-large-bodied species (Maxwell’s duiker (Philantomba maxwellii), Jentink’s duiker (Cephalophus jentinki), pygmy hippopotamus (Choeropsis liberiensis) and Western chimpanzee (Pan troglodytes verus)) displaying different behaviours towards the CTs. We then established species-specific ethograms describing the behavioural responses to the CTs. Using these species-specific responses, we observed that the Maxwell’s duiker reacted weakly to CTs (about 0.11% of the distance data), contrary to Jentink’s duiker, pygmy hippopotamus and Western chimpanzee which reacted with relatively high frequencies, representing 32.82%, 52.96% and 16.14% of the distance data, respectively. Not taki…
format: application/pdf
format: text/html
creator: Noël Adiko Houa
creator: Noémie Cappelle
creator: Eloi Anderson Bitty
creator: Emmanuelle Normand
creator: Yves Aka Kablan
creator: Christophe Boesch
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13510
publisher: PeerJ Inc.
rights: © 2022 Houa et al.
abstract: The use of camera traps (CTs) has become an increasingly popular method of studying wildlife, as CTs are able to detect rare, nocturnal, and elusive species in remote and difficult-to-access areas. It thus makes them suited to estimate animal density and abundance, identify activity patterns and new behaviours of animals. However, animals can react when they see the CTs and this can lead to bias in the animal population estimates. While CTs may provide many advantages, an improved understanding of their impacts on individual’s behaviour is necessary to avoid erroneous density estimates. Yet, the impact of CTs on detected individuals, such as human odour near the device and the environment, or the infrared illumination, has received relatively little attention. To date, there is no clear procedure to remove this potential bias. Here, we use camera trap distance sampling (CTDS) to (1) quantify the bias resulting from the different animal responses to the CTs when determining animal density and abundance, and (2) test if olfactory, visual and auditory signals have an influence on the animals’ reaction to CTs. Between March 2019 and March 2020, we deployed CTs at 267 locations distributed systematically over the entire Taï National Park. We obtained 58,947 videos from which we analysed four medium- to-large-bodied species (Maxwell’s duiker (Philantomba maxwellii), Jentink’s duiker (Cephalophus jentinki), pygmy hippopotamus (Choeropsis liberiensis) and Western chimpanzee (Pan troglodytes verus)) displaying different behaviours towards the CTs. We then established species-specific ethograms describing the behavioural responses to the CTs. Using these species-specific responses, we observed that the Maxwell’s duiker reacted weakly to CTs (about 0.11% of the distance data), contrary to Jentink’s duiker, pygmy hippopotamus and Western chimpanzee which reacted with relatively high frequencies, representing 32.82%, 52.96% and 16.14% of the distance data, respectively. Not taki…
bibliographic citation: Houa et al. (2022) Animal reactivity to camera traps and its effects on abundance estimate using distance sampling in the Taï National Park, Côte d’Ivoire. PeerJ 10:e13510 https://doi.org/10.7717/peerj.13510
date submitted: 2022-02-02
date accepted: 2022-05-06
issued: 2022-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Houa
  given name: Noël Adiko
author list: Agent
  family name: Cappelle
  given name: Noémie
author list: Agent
  family name: Bitty
  given name: Eloi Anderson
author list: Agent
  family name: Normand
  given name: Emmanuelle
author list: Agent
  family name: Kablan
  given name: Yves Aka
author list: Agent
  family name: Boesch
  given name: Christophe
doi: 10.7717/peerj.13510
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-27
copyright: ©2022 Houa et al.
attribution name: Houa et al.

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