PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Estuarine microbial networks and relationships vary between environmentally distinct communities
items: Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats
items: Melanoleuca subgriseoflava and M. substridula—two new Melanoleuca species (Agaricales, Basidiomycota) described from China
items: The antioxidant system response to drought-stressed Diospyros lotus treated with exogenous melatonin
items: The effect of enhanced variability after performance stabilization through constant practice
items: Molecular and behavioral studies reveal differences in olfaction between winter and summer morphs of Drosophila suzukii
items: Ontogenetic, dietary, and environmental shifts in Mesosauridae
items: Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes
items: Effects of L-carnitine supplementation for women with polycystic ovary syndrome: a systematic review and meta-analysis
items: Understanding the distribution and fine-scale habitat selection of mesocarnivores along a habitat quality gradient in western Himalaya

Estuarine microbial networks and relationships vary between environmentally distinct communities
type: item
type: AcademicArticle
description: Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. …
format: application/pdf
format: text/html
creator: Sean R. Anderson
creator: Elizabeth L. Harvey
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.14005
publisher: PeerJ Inc.
rights: © 2022 Anderson and Harvey
abstract: Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. …
bibliographic citation: Anderson et al. (2022) Estuarine microbial networks and relationships vary between environmentally distinct communities. PeerJ 10:e14005 https://doi.org/10.7717/peerj.14005
date submitted: 2022-01-07
date accepted: 2022-08-14
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Sean R.
author list: Agent
  family name: Harvey
  given name: Elizabeth L.
doi: 10.7717/peerj.14005
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Anderson and Harvey
attribution name: Anderson and Harvey

Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats
type: item
type: AcademicArticle
description: Background Fasting has been widely used to improve various metabolic diseases in humans. Adaptive fasting is necessary for metabolic adaptation during prolonged fasting, which could overcome the great advantages of short-term fasting. The liver is the main organ responsible for energy metabolism and metabolic homeostasis. To date, we lack literature that describes the physiologically relevant adaptations of the liver during prolonged fasting and refeeding. For that reason, this study aims to evaluate the response of the liver of Sprague-Dawley (SD) rats to prolonged fasting and refeeding. Methods Sixty-six male SD rats were divided into the fasting groups, which were fasted for 0, 4, 8, 12, 24, 48, 72, or 96 h, and the refeeding groups, which were refed for 1, 3, or 6 days after 96 h of fasting. Serum glucose, TG, FFA, β-hydroxybutyrate, insulin, glucagon, leptin, adiponectin and FGF21 levels were assessed. The glucose content, PEPCK activity, TG concentration and FFA content were measured in liver tissue, and the expression of genes involved in gluconeogenesis (PEPCK and G6Pase), ketogenesis (PPARα, CPT-1a and HMGCS2) and the protein expression of nutrient-sensing signaling molecules (AMPK, mTOR and SIRT1) were determined by RT-qPCR and western blotting, respectively. Results Fasting significantly decreased the body weight, which was totally recovered to baseline after 3 days of refeeding. A 4-day fast triggered an energy metabolic substrate shift from glucose to ketones and caused serum hormone changes and changes in the protein expression levels of nutrient-sensing signaling molecules. Glycogenolysis served as the primary fuel source during the first 24 h of fasting, while gluconeogenesis supplied the most glucose thereafter. Serum FFA concentrations increased significantly with 48 h of fasting. Serum FFAs partly caused high serum β-hydroxybutyrate levels, which became an important energy source with the prolongation of the fasting duration. One day of refeeding …
format: application/pdf
format: text/html
creator: Xiukun Sui
creator: Hailong Wang
creator: Feng Wu
creator: Chao Yang
creator: Hongyu Zhang
creator: Zihan Xu
creator: Yaxiu Guo
creator: ZhiFeng Guo
creator: Bingmu Xin
creator: Ting Ma
creator: Yinghui Li
creator: Zhongquan Dai
subject: Biochemistry
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.14009
publisher: PeerJ Inc.
rights: © 2022 Sui et al.
abstract: Background Fasting has been widely used to improve various metabolic diseases in humans. Adaptive fasting is necessary for metabolic adaptation during prolonged fasting, which could overcome the great advantages of short-term fasting. The liver is the main organ responsible for energy metabolism and metabolic homeostasis. To date, we lack literature that describes the physiologically relevant adaptations of the liver during prolonged fasting and refeeding. For that reason, this study aims to evaluate the response of the liver of Sprague-Dawley (SD) rats to prolonged fasting and refeeding. Methods Sixty-six male SD rats were divided into the fasting groups, which were fasted for 0, 4, 8, 12, 24, 48, 72, or 96 h, and the refeeding groups, which were refed for 1, 3, or 6 days after 96 h of fasting. Serum glucose, TG, FFA, β-hydroxybutyrate, insulin, glucagon, leptin, adiponectin and FGF21 levels were assessed. The glucose content, PEPCK activity, TG concentration and FFA content were measured in liver tissue, and the expression of genes involved in gluconeogenesis (PEPCK and G6Pase), ketogenesis (PPARα, CPT-1a and HMGCS2) and the protein expression of nutrient-sensing signaling molecules (AMPK, mTOR and SIRT1) were determined by RT-qPCR and western blotting, respectively. Results Fasting significantly decreased the body weight, which was totally recovered to baseline after 3 days of refeeding. A 4-day fast triggered an energy metabolic substrate shift from glucose to ketones and caused serum hormone changes and changes in the protein expression levels of nutrient-sensing signaling molecules. Glycogenolysis served as the primary fuel source during the first 24 h of fasting, while gluconeogenesis supplied the most glucose thereafter. Serum FFA concentrations increased significantly with 48 h of fasting. Serum FFAs partly caused high serum β-hydroxybutyrate levels, which became an important energy source with the prolongation of the fasting duration. One day of refeeding …
bibliographic citation: Sui et al. (2022) Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats. PeerJ 10:e14009 https://doi.org/10.7717/peerj.14009
date submitted: 2022-02-08
date accepted: 2022-08-15
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sui
  given name: Xiukun
author list: Agent
  family name: Wang
  given name: Hailong
author list: Agent
  family name: Wu
  given name: Feng
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Zhang
  given name: Hongyu
author list: Agent
  family name: Xu
  given name: Zihan
author list: Agent
  family name: Guo
  given name: Yaxiu
author list: Agent
  family name: Guo
  given name: ZhiFeng
author list: Agent
  family name: Xin
  given name: Bingmu
author list: Agent
  family name: Ma
  given name: Ting
author list: Agent
  family name: Li
  given name: Yinghui
author list: Agent
  family name: Dai
  given name: Zhongquan
doi: 10.7717/peerj.14009
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Sui et al.
attribution name: Sui et al.

Melanoleuca subgriseoflava and M. substridula—two new Melanoleuca species (Agaricales, Basidiomycota) described from China
type: item
type: AcademicArticle
description: Two new Melanoleuca species, Melanoleuca subgriseoflava and M. substridula, are originally reported and described in China based on both morphological and molecular methods. Melanoleuca subgriseoflava, collected in Liaoning province, is mainly characterized by its greyish-brown to yellowish-grey pileus, creamy to light orange lamellae, greyish-yellow context, round and warted basidiospores and fusiform hymenial cystidia. Melanoleuca substridula, discovered in Sichuan province, is mainly characterized by its light brown to dark brown pileus, whitish lamellae, light brown to greyish-brown stipe, round and warted basidiospores and lack of any forms of cystidia. The phylogenetic relationships as well as divergence-time estimation were analyzed using the combined data set (ITS-nrLSU-RPB2), and the results showed that the two Melanoleuca species formed two distinct lineages. Based on the combination of morphological and molecular data, M. subgriseoflava and M. substridula are confirmed as two new species to science. A theoretical basis is provided for the species diversity of Melanoleuca.
format: application/pdf
format: text/html
creator: Yue Qi
creator: Cai-Hong Li
creator: Yu-Meng Song
creator: Ming Zhang
creator: Hong-Bo Guo
creator: Xiao-Dan Yu
subject: Biodiversity
subject: Molecular Biology
subject: Mycology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.13807
publisher: PeerJ Inc.
rights: © 2022 Qi et al.
abstract: Two new Melanoleuca species, Melanoleuca subgriseoflava and M. substridula, are originally reported and described in China based on both morphological and molecular methods. Melanoleuca subgriseoflava, collected in Liaoning province, is mainly characterized by its greyish-brown to yellowish-grey pileus, creamy to light orange lamellae, greyish-yellow context, round and warted basidiospores and fusiform hymenial cystidia. Melanoleuca substridula, discovered in Sichuan province, is mainly characterized by its light brown to dark brown pileus, whitish lamellae, light brown to greyish-brown stipe, round and warted basidiospores and lack of any forms of cystidia. The phylogenetic relationships as well as divergence-time estimation were analyzed using the combined data set (ITS-nrLSU-RPB2), and the results showed that the two Melanoleuca species formed two distinct lineages. Based on the combination of morphological and molecular data, M. subgriseoflava and M. substridula are confirmed as two new species to science. A theoretical basis is provided for the species diversity of Melanoleuca.
bibliographic citation: Qi et al. (2022) Melanoleuca subgriseoflava and M. substridula—two new Melanoleuca species (Agaricales, Basidiomycota) described from China. PeerJ 10:e13807 https://doi.org/10.7717/peerj.13807
date submitted: 2022-04-28
date accepted: 2022-07-07
issued: 2022-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Yue
author list: Agent
  family name: Li
  given name: Cai-Hong
author list: Agent
  family name: Song
  given name: Yu-Meng
author list: Agent
  family name: Zhang
  given name: Ming
author list: Agent
  family name: Guo
  given name: Hong-Bo
author list: Agent
  family name: Yu
  given name: Xiao-Dan
doi: 10.7717/peerj.13807
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-19
copyright: ©2022 Qi et al.
attribution name: Qi et al.

The antioxidant system response to drought-stressed Diospyros lotus treated with exogenous melatonin
type: item
type: AcademicArticle
description: Drought is one of the major abiotic stresses adversely impacting the growth of persimmon, which is a widely cultivated traditional fruit tree in North China. Melatonin is a bio-stimulator involved in mediating plant responses to drought. The role of exogenous melatonin application in the drought tolerance of Diospyros lotus was examined under drought stress with different doses of melatonin (0, 10, 50, and 100 µM). Exogenous melatonin application significantly mitigated the adverse effects of drought stress on chlorophyll fluorescence, lipid peroxidation, reactive oxygen species (ROS) accumulation and nitric oxide (NO) content. The 100-µM melatonin application produced the most beneficial impacts against drought stress. The melatonin-enhanced tolerance could be attributed to improved antioxidant enzymes, reduced drought-induced ROS accumulation, and lipid peroxidation. Melatonin application activated major antioxidant enzymes such as superoxide dismutase, catalase, peroxidase, glutathione reductase, and ascorbate peroxidase. Interestingly, NO concentration was significantly higher in 10 and 50 µM melatonin treatments and lower in 100 µM melatonin treatment compared to the control. Moreover, exogenous melatonin application affected the mRNA transcript levels of several genes involved in ROS metabolism, including DlRBOHA, DlSOD, DlCAT, and DlPOD. Hence, the responses of Diospyros lotus to drought varied with different doses of melatonin. Our results provide a concrete insight into the effects of melatonin with varying doses in alleviating drought as well as a platform for its potential application in the related fields.
format: application/pdf
format: text/html
creator: Peng Zhang
creator: Yi Hu
creator: Ruijin Zhou
creator: Xiaona Zhang
creator: Huiling Hu
creator: Dongmei Lang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.13936
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Drought is one of the major abiotic stresses adversely impacting the growth of persimmon, which is a widely cultivated traditional fruit tree in North China. Melatonin is a bio-stimulator involved in mediating plant responses to drought. The role of exogenous melatonin application in the drought tolerance of Diospyros lotus was examined under drought stress with different doses of melatonin (0, 10, 50, and 100 µM). Exogenous melatonin application significantly mitigated the adverse effects of drought stress on chlorophyll fluorescence, lipid peroxidation, reactive oxygen species (ROS) accumulation and nitric oxide (NO) content. The 100-µM melatonin application produced the most beneficial impacts against drought stress. The melatonin-enhanced tolerance could be attributed to improved antioxidant enzymes, reduced drought-induced ROS accumulation, and lipid peroxidation. Melatonin application activated major antioxidant enzymes such as superoxide dismutase, catalase, peroxidase, glutathione reductase, and ascorbate peroxidase. Interestingly, NO concentration was significantly higher in 10 and 50 µM melatonin treatments and lower in 100 µM melatonin treatment compared to the control. Moreover, exogenous melatonin application affected the mRNA transcript levels of several genes involved in ROS metabolism, including DlRBOHA, DlSOD, DlCAT, and DlPOD. Hence, the responses of Diospyros lotus to drought varied with different doses of melatonin. Our results provide a concrete insight into the effects of melatonin with varying doses in alleviating drought as well as a platform for its potential application in the related fields.
bibliographic citation: Zhang et al. (2022) The antioxidant system response to drought-stressed Diospyros lotus treated with exogenous melatonin. PeerJ 10:e13936 https://doi.org/10.7717/peerj.13936
date submitted: 2022-05-07
date accepted: 2022-08-02
issued: 2022-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Peng
author list: Agent
  family name: Hu
  given name: Yi
author list: Agent
  family name: Zhou
  given name: Ruijin
author list: Agent
  family name: Zhang
  given name: Xiaona
author list: Agent
  family name: Hu
  given name: Huiling
author list: Agent
  family name: Lang
  given name: Dongmei
doi: 10.7717/peerj.13936
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-19
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

The effect of enhanced variability after performance stabilization through constant practice
type: item
type: AcademicArticle
description: There is a controversy about the benefits of variable practice on motor learning. This study aimed to analyze the effect of variable practice after the learner stabilized their performance. Thirty-two healthy adults performed a computer-simulated discrete accuracy task in which they had to release a virtual ball to try to hit a target. After a pre-test, the participants were distributed into three training groups: constant practice, variable practice and a group that started practicing in constant conditions, and when their performance stabilized, changed to variable practice. The participants performed 44 sets of 10 repetitions of the task. A post-test and two retention tests were carried out. Variable practice did not show a significant improvement compared to constant practice. Variable practice did not show higher benefits even when performance was stabilized through constant practice, but its effects seem to be modulated by the initial variability of the learners.
format: application/pdf
format: text/html
creator: Carmen Ruano
creator: Carla Caballero
creator: Francisco J. Moreno
subject: Neuroscience
subject: Kinesiology
description: doi:10.7717/peerj.13733
publisher: PeerJ Inc.
rights: © 2022 Ruano et al.
abstract: There is a controversy about the benefits of variable practice on motor learning. This study aimed to analyze the effect of variable practice after the learner stabilized their performance. Thirty-two healthy adults performed a computer-simulated discrete accuracy task in which they had to release a virtual ball to try to hit a target. After a pre-test, the participants were distributed into three training groups: constant practice, variable practice and a group that started practicing in constant conditions, and when their performance stabilized, changed to variable practice. The participants performed 44 sets of 10 repetitions of the task. A post-test and two retention tests were carried out. Variable practice did not show a significant improvement compared to constant practice. Variable practice did not show higher benefits even when performance was stabilized through constant practice, but its effects seem to be modulated by the initial variability of the learners.
bibliographic citation: Ruano et al. (2022) The effect of enhanced variability after performance stabilization through constant practice. PeerJ 10:e13733 https://doi.org/10.7717/peerj.13733
date submitted: 2021-08-24
date accepted: 2022-06-24
issued: 2022-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruano
  given name: Carmen
author list: Agent
  family name: Caballero
  given name: Carla
author list: Agent
  family name: Moreno
  given name: Francisco J.
doi: 10.7717/peerj.13733
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-16
copyright: © 2022 Ruano et al.
attribution name: Ruano et al.

Molecular and behavioral studies reveal differences in olfaction between winter and summer morphs of Drosophila suzukii
type: item
type: AcademicArticle
description: Spotted-wing drosophila, Drosophila suzukii (Matsumura), is a major economic pest of several fruit crops in Europe, North and South America, and other parts of the world because it oviposits in ripening thin-skinned fruits. This vinegar fly exhibits two distinct morphotypes: a summer and a winter morph. Although adaptations associated with the winter morph enhance this invasive pest’s capacity to survive in cold climates, winter is still a natural population bottleneck. Since monitoring early spring populations is important for accurate population forecasts, understanding the winter morph’s response to olfactory cues may improve current D. suzukii management programs. In this study, a comparative transcriptome analysis was conducted to assess gene expression differences between the female heads of the two D. suzukii morphs, which showed significant differences in 738 genes (p ≤ 0.0001). Out of twelve genes related to olfaction determined to be differentially expressed in the transcriptome, i.e., those related to location of food sources, chemosensory abilities, and mating behavior, nine genes were upregulated in the winter morph while three were downregulated. Three candidate olfactory-related genes that were most upregulated or downregulated in the winter morph were further validated using RT-qPCR. In addition, behavioral assays were performed at a range of temperatures to confirm a differing behavioral response of the two morphs to food odors. Our behavioral assays showed that, although winter morphs were more active at lower temperatures, the summer morphs were generally more attracted to food odors. This study provides new insights into the molecular and behavioral differences in response to olfactory cues between the two D. suzukii morphs that will assist in formulating more effective monitoring and physiological-based control tools.
format: application/pdf
format: text/html
creator: Timothy W. Schwanitz
creator: James J. Polashock
creator: Dara G. Stockton
creator: Cesar Rodriguez-Saona
creator: Diego Sotomayor
creator: Greg Loeb
creator: Chloe Hawkings
subject: Animal Behavior
subject: Entomology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13825
publisher: PeerJ Inc.
rights: © 2022 Schwanitz et al.
abstract: Spotted-wing drosophila, Drosophila suzukii (Matsumura), is a major economic pest of several fruit crops in Europe, North and South America, and other parts of the world because it oviposits in ripening thin-skinned fruits. This vinegar fly exhibits two distinct morphotypes: a summer and a winter morph. Although adaptations associated with the winter morph enhance this invasive pest’s capacity to survive in cold climates, winter is still a natural population bottleneck. Since monitoring early spring populations is important for accurate population forecasts, understanding the winter morph’s response to olfactory cues may improve current D. suzukii management programs. In this study, a comparative transcriptome analysis was conducted to assess gene expression differences between the female heads of the two D. suzukii morphs, which showed significant differences in 738 genes (p ≤ 0.0001). Out of twelve genes related to olfaction determined to be differentially expressed in the transcriptome, i.e., those related to location of food sources, chemosensory abilities, and mating behavior, nine genes were upregulated in the winter morph while three were downregulated. Three candidate olfactory-related genes that were most upregulated or downregulated in the winter morph were further validated using RT-qPCR. In addition, behavioral assays were performed at a range of temperatures to confirm a differing behavioral response of the two morphs to food odors. Our behavioral assays showed that, although winter morphs were more active at lower temperatures, the summer morphs were generally more attracted to food odors. This study provides new insights into the molecular and behavioral differences in response to olfactory cues between the two D. suzukii morphs that will assist in formulating more effective monitoring and physiological-based control tools.
bibliographic citation: Schwanitz et al. (2022) Molecular and behavioral studies reveal differences in olfaction between winter and summer morphs of Drosophila suzukii. PeerJ 10:e13825 https://doi.org/10.7717/peerj.13825
date submitted: 2022-03-23
date accepted: 2022-07-10
issued: 2022-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schwanitz
  given name: Timothy W.
author list: Agent
  family name: Polashock
  given name: James J.
author list: Agent
  family name: Stockton
  given name: Dara G.
author list: Agent
  family name: Rodriguez-Saona
  given name: Cesar
author list: Agent
  family name: Sotomayor
  given name: Diego
author list: Agent
  family name: Loeb
  given name: Greg
author list: Agent
  family name: Hawkings
  given name: Chloe
doi: 10.7717/peerj.13825
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-16
copyright: ©2022 Schwanitz et al.
attribution name: Schwanitz et al.

Ontogenetic, dietary, and environmental shifts in Mesosauridae
type: item
type: AcademicArticle
description: Mesosaurs are the first secondarily aquatic amniotes and one of the most enigmatic clades of reptiles from the early Permian. They have long puzzled paleontologists with their unique morphologies: possessing an elongated skull with thin needle-like teeth, a long neck, large webbed hindlimbs, banana-shaped pachyosteosclerotic ribs, and a long tail. Here, we look at a large dataset of morphometric measurements from 270 mesosaur specimens in collections around the world. These measurements characterize skull, tooth, and limb proportions and their variation with size. This data presents evidence of surprising ontogenetic changes in these animals as well as new insights into their taxonomy. Our results support the recent hypothesis that Mesosaurus tenuidens is the only valid species within Mesosauridae and suggest that “Stereosternum tumidum” and “Brazilosaurus sanpauloensis” represent immature stages or incomplete specimens of Mesosaurus by showing that all three species occupy an incomplete portion of the overall size range of mesosaurs. Under the single-species hypothesis, we highlight a number of ontogenetic trends: (1) a reduction in skull length accompanied by an elongation of the snout within the skull, (2) an elongation of teeth, (3) a reduction in hind limb length, and (4) a reduction in manus length. Concurrent with these changes, we hypothesize that mesosaurs went through a progressive ecological shift during their growth, with juveniles being more common in shallow water deposits, whereas large adults are more frequent in pelagic sediments. These parallel changes suggest that mesosaurs underwent a diet and lifestyle transition during ontogeny, from an active predatory lifestyle as juveniles to a more filter-feeding diet as adults. We propose that this change in lifestyle and environments may have been driven by the pursuit of different food sources, but a better understanding of the Irati Sea fauna will be necessary to obtain a more definitive answer to the q…
format: application/pdf
format: text/html
creator: Antoine Verrière
creator: Jörg Fröbisch
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.13866
publisher: PeerJ Inc.
rights: © 2022 Verrière and Fröbisch
abstract: Mesosaurs are the first secondarily aquatic amniotes and one of the most enigmatic clades of reptiles from the early Permian. They have long puzzled paleontologists with their unique morphologies: possessing an elongated skull with thin needle-like teeth, a long neck, large webbed hindlimbs, banana-shaped pachyosteosclerotic ribs, and a long tail. Here, we look at a large dataset of morphometric measurements from 270 mesosaur specimens in collections around the world. These measurements characterize skull, tooth, and limb proportions and their variation with size. This data presents evidence of surprising ontogenetic changes in these animals as well as new insights into their taxonomy. Our results support the recent hypothesis that Mesosaurus tenuidens is the only valid species within Mesosauridae and suggest that “Stereosternum tumidum” and “Brazilosaurus sanpauloensis” represent immature stages or incomplete specimens of Mesosaurus by showing that all three species occupy an incomplete portion of the overall size range of mesosaurs. Under the single-species hypothesis, we highlight a number of ontogenetic trends: (1) a reduction in skull length accompanied by an elongation of the snout within the skull, (2) an elongation of teeth, (3) a reduction in hind limb length, and (4) a reduction in manus length. Concurrent with these changes, we hypothesize that mesosaurs went through a progressive ecological shift during their growth, with juveniles being more common in shallow water deposits, whereas large adults are more frequent in pelagic sediments. These parallel changes suggest that mesosaurs underwent a diet and lifestyle transition during ontogeny, from an active predatory lifestyle as juveniles to a more filter-feeding diet as adults. We propose that this change in lifestyle and environments may have been driven by the pursuit of different food sources, but a better understanding of the Irati Sea fauna will be necessary to obtain a more definitive answer to the q…
bibliographic citation: Verrière et al. (2022) Ontogenetic, dietary, and environmental shifts in Mesosauridae. PeerJ 10:e13866 https://doi.org/10.7717/peerj.13866
date submitted: 2022-01-27
date accepted: 2022-07-18
issued: 2022-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Verrière
  given name: Antoine
author list: Agent
  family name: Fröbisch
  given name: Jörg
doi: 10.7717/peerj.13866
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-16
copyright: ©2022 Verrière and Fröbisch
attribution name: Verrière and Fröbisch

Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes
type: item
type: AcademicArticle
description: Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat.
format: application/pdf
format: text/html
creator: Sonia Ahluwalia
creator: Iris Holmes
creator: Rudolf von May
creator: Daniel L. Rabosky
creator: Alison R. Davis Rabosky
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13958
publisher: PeerJ Inc.
rights: © 2022 Ahluwalia et al.
abstract: Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat.
bibliographic citation: Ahluwalia et al. (2022) Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes. PeerJ 10:e13958 https://doi.org/10.7717/peerj.13958
date submitted: 2022-04-21
date accepted: 2022-08-06
issued: 2022-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahluwalia
  given name: Sonia
author list: Agent
  family name: Holmes
  given name: Iris
author list: Agent
  family name: von May
  given name: Rudolf
author list: Agent
  family name: Rabosky
  given name: Daniel L.
author list: Agent
  family name: Davis Rabosky
  given name: Alison R.
doi: 10.7717/peerj.13958
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-16
copyright: © 2022 Ahluwalia et al.
attribution name: Ahluwalia et al.

Effects of L-carnitine supplementation for women with polycystic ovary syndrome: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Polycystic ovary syndrome (PCOS) is a disorder in reproductive age women and is characterized by hyperandrogenic anovulation and oligo-amenorrhea, which leads to infertility. Anovulation in PCOS is associated with low follicle-stimulating hormone levels and the arrest of antral follicle development in the final stages of maturation. L-carnitine (LC) plays a role in fatty acid metabolism, which is found to be lacking in PCOS patients. This systematic review and meta-analysis aimed to determine the effectiveness of LC supplementation for patients with PCOS. Methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Psychological Information Database (PsycINFO), and the World Health Organization International Clinical Trials Registry Platform for all randomized control trials, comparing LC alone or in combination with other standard treatments for the treatment of PCOS from inception till June 2021. We independently screened titles and abstracts to identify available trials, and complete texts of the trials were checked for eligibility. Data on the methods, interventions, outcomes, and risk of bias from the included trials were independently extracted by the authors. The estimation of risk ratios and mean differences with a 95 percent confidence interval (CI) was performed using a random-effects model. Results Nine studies with 995 participants were included in this review. Five comparison groups were involved. In one comparison group, LC reduced the fasting plasma glucose (FPG) (mean differences (MD) −5.10, 95% CI [−6.25 to −3.95]; P = 0.00001), serum low-density lipoprotein (LDL) (MD −25.00, 95% CI [−27.93 to −22.07]; P = 0.00001), serum total cholesterol (MD −21.00, 95% CI [−24.14 to −17.86]; P = 0.00001), and serum triglyceride (TG) (MD −9.00, 95% CI [−11.46 to −6.54]; P = 0.00001) with moderate certainty of evidence. Another comparison group demons…
format: application/pdf
format: text/html
creator: Mohd Falihin Mohd Shukri
creator: Mohd Noor Norhayati
creator: Salziyan Badrin
creator: Azidah Abdul Kadir
subject: Drugs and Devices
subject: Nutrition
subject: Women’s Health
description: doi:10.7717/peerj.13992
publisher: PeerJ Inc.
rights: © 2022 Mohd Shukri et al.
abstract: Background Polycystic ovary syndrome (PCOS) is a disorder in reproductive age women and is characterized by hyperandrogenic anovulation and oligo-amenorrhea, which leads to infertility. Anovulation in PCOS is associated with low follicle-stimulating hormone levels and the arrest of antral follicle development in the final stages of maturation. L-carnitine (LC) plays a role in fatty acid metabolism, which is found to be lacking in PCOS patients. This systematic review and meta-analysis aimed to determine the effectiveness of LC supplementation for patients with PCOS. Methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Psychological Information Database (PsycINFO), and the World Health Organization International Clinical Trials Registry Platform for all randomized control trials, comparing LC alone or in combination with other standard treatments for the treatment of PCOS from inception till June 2021. We independently screened titles and abstracts to identify available trials, and complete texts of the trials were checked for eligibility. Data on the methods, interventions, outcomes, and risk of bias from the included trials were independently extracted by the authors. The estimation of risk ratios and mean differences with a 95 percent confidence interval (CI) was performed using a random-effects model. Results Nine studies with 995 participants were included in this review. Five comparison groups were involved. In one comparison group, LC reduced the fasting plasma glucose (FPG) (mean differences (MD) −5.10, 95% CI [−6.25 to −3.95]; P = 0.00001), serum low-density lipoprotein (LDL) (MD −25.00, 95% CI [−27.93 to −22.07]; P = 0.00001), serum total cholesterol (MD −21.00, 95% CI [−24.14 to −17.86]; P = 0.00001), and serum triglyceride (TG) (MD −9.00, 95% CI [−11.46 to −6.54]; P = 0.00001) with moderate certainty of evidence. Another comparison group demons…
bibliographic citation: Mohd Shukri et al. (2022) Effects of L-carnitine supplementation for women with polycystic ovary syndrome: a systematic review and meta-analysis. PeerJ 10:e13992 https://doi.org/10.7717/peerj.13992
date submitted: 2022-03-28
date accepted: 2022-08-11
issued: 2022-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohd Shukri
  given name: Mohd Falihin
author list: Agent
  family name: Norhayati
  given name: Mohd Noor
author list: Agent
  family name: Badrin
  given name: Salziyan
author list: Agent
  family name: Abdul Kadir
  given name: Azidah
doi: 10.7717/peerj.13992
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-16
copyright: ©2022 Mohd Shukri et al.
attribution name: Mohd Shukri et al.

Understanding the distribution and fine-scale habitat selection of mesocarnivores along a habitat quality gradient in western Himalaya
type: item
type: AcademicArticle
description: Background: Human activities have resulted in a rapid increase of modified habitats in proximity to wildlife habitats in the Himalaya. However, it is crucial to understand the extent to which human habitat modification affects wildlife. Mesocarnivores generally possess broader niches than large carnivores and adapt quickly to human activities. Here, we use a case study in the western Himalaya to test the hypothesis that human disturbance influenced mesocarnivore habitat use. Methods: We used camera trapping and mitochondrial DNA-based species identification from faecal samples to obtain mesocarnivore detections. We then compared the responses of mesocarnivores between an anthropogenic site and a less disturbed park along a contiguous gradient in habitat quality. The non-linear pattern in species-specific habitat selection and factors responsible for space usage around villages was captured using hierarchical generalized additive modelling (HGAM) and non-metric multidimensional scaling (NMDS) ordination. Results: Wildlife occurrences along the gradient varied by species. Leopard cat and red fox were the only terrestrial mesocarnivores that occurred in both anthropogenic site and park. We found a shift in habitat selection from less disturbed habitat in the park to disturbed habitat in anthropogenic site for the species detected in both the habitat types. For instance, red fox showed habitat selection towards high terrain ruggedness (0.5 to 0.7 TRI) and low NDVI (−0.05 to 0.2) in the park but no such specific selection in anthropogenic site. Further, leopard cat showed habitat selection towards moderate slope (20°) and medium NDVI (0.5) in park but no prominent habitat selections in anthropogenic site. The results revealed their constrained behaviour which was further supported by the intensive site usage close to houses, agricultural fields and human trails in villages. Conclusions: Our results indicate shifts in habitat selection and intensive site usage by mesocarn…
format: application/pdf
format: text/html
creator: Meghna Bandyopadhyay
creator: A. Cole Burton
creator: Sandeep Kumar Gupta
creator: Ramesh Krishnamurthy
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.13993
publisher: PeerJ Inc.
rights: © 2022 Bandyopadhyay et al.
abstract: Background: Human activities have resulted in a rapid increase of modified habitats in proximity to wildlife habitats in the Himalaya. However, it is crucial to understand the extent to which human habitat modification affects wildlife. Mesocarnivores generally possess broader niches than large carnivores and adapt quickly to human activities. Here, we use a case study in the western Himalaya to test the hypothesis that human disturbance influenced mesocarnivore habitat use. Methods: We used camera trapping and mitochondrial DNA-based species identification from faecal samples to obtain mesocarnivore detections. We then compared the responses of mesocarnivores between an anthropogenic site and a less disturbed park along a contiguous gradient in habitat quality. The non-linear pattern in species-specific habitat selection and factors responsible for space usage around villages was captured using hierarchical generalized additive modelling (HGAM) and non-metric multidimensional scaling (NMDS) ordination. Results: Wildlife occurrences along the gradient varied by species. Leopard cat and red fox were the only terrestrial mesocarnivores that occurred in both anthropogenic site and park. We found a shift in habitat selection from less disturbed habitat in the park to disturbed habitat in anthropogenic site for the species detected in both the habitat types. For instance, red fox showed habitat selection towards high terrain ruggedness (0.5 to 0.7 TRI) and low NDVI (−0.05 to 0.2) in the park but no such specific selection in anthropogenic site. Further, leopard cat showed habitat selection towards moderate slope (20°) and medium NDVI (0.5) in park but no prominent habitat selections in anthropogenic site. The results revealed their constrained behaviour which was further supported by the intensive site usage close to houses, agricultural fields and human trails in villages. Conclusions: Our results indicate shifts in habitat selection and intensive site usage by mesocarn…
bibliographic citation: Bandyopadhyay et al. (2022) Understanding the distribution and fine-scale habitat selection of mesocarnivores along a habitat quality gradient in western Himalaya. PeerJ 10:e13993 https://doi.org/10.7717/peerj.13993
date submitted: 2022-04-06
date accepted: 2022-08-11
issued: 2022-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bandyopadhyay
  given name: Meghna
author list: Agent
  family name: Burton
  given name: A. Cole
author list: Agent
  family name: Gupta
  given name: Sandeep Kumar
author list: Agent
  family name: Krishnamurthy
  given name: Ramesh
doi: 10.7717/peerj.13993
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-16
copyright: © 2022 Bandyopadhyay et al.
attribution name: Bandyopadhyay et al.

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