PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish
items: Empirical analysis and modeling of Argos Doppler location errors in Romania
items: Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway
items: Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)
items: High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases
items: Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
items: Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?
items: Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China
items: Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine
items: Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei

Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish
type: item
type: AcademicArticle
description: Fish are sensitive to temperature, but the intergenerational consequences of maternal exposure to high temperature on offspring behavioural plasticity and underlying mechanisms are unknown. Here we show that a thermal maternal stress induces impaired emotional and cognitive responses in offspring rainbow trout (Oncorhynchus mykiss). Thermal stress in mothers triggered the inhibition of locomotor fear-related responses upon exposure to a novel environment and decreased spatial learning abilities in progeny. Impaired behavioural phenotypes were associated with the dysregulation of several genes known to play major roles in neurodevelopment, including auts2 (autism susceptibility candidate 2), a key gene for neurodevelopment, more specifically neuronal migration and neurite extension, and critical for the acquisition of neurocognitive function. In addition, our analysis revealed the dysregulation of another neurodevelopment gene (dpysl5) as well as genes associated with human cognitive disorders (arv1, plp2). We observed major differences in maternal mRNA abundance in the eggs following maternal exposure to high temperature indicating that some of the observed intergenerational effects are mediated by maternally-inherited mRNAs accumulated in the egg. Together, our observations shed new light on the intergenerational determinism of fish behaviour and associated underlying mechanisms. They also stress the importance of maternal history on fish behavioural plasticity.
format: application/pdf
format: text/html
creator: Violaine Colson
creator: Morgane Cousture
creator: Danielle Damasceno
creator: Claudiane Valotaire
creator: Thaovi Nguyen
creator: Aurélie Le Cam
creator: Julien Bobe
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Genomics
subject: Neuroscience
description: doi:10.7717/peerj.6338
publisher: PeerJ Inc.
rights: © 2019 Colson et al.
abstract: Fish are sensitive to temperature, but the intergenerational consequences of maternal exposure to high temperature on offspring behavioural plasticity and underlying mechanisms are unknown. Here we show that a thermal maternal stress induces impaired emotional and cognitive responses in offspring rainbow trout (Oncorhynchus mykiss). Thermal stress in mothers triggered the inhibition of locomotor fear-related responses upon exposure to a novel environment and decreased spatial learning abilities in progeny. Impaired behavioural phenotypes were associated with the dysregulation of several genes known to play major roles in neurodevelopment, including auts2 (autism susceptibility candidate 2), a key gene for neurodevelopment, more specifically neuronal migration and neurite extension, and critical for the acquisition of neurocognitive function. In addition, our analysis revealed the dysregulation of another neurodevelopment gene (dpysl5) as well as genes associated with human cognitive disorders (arv1, plp2). We observed major differences in maternal mRNA abundance in the eggs following maternal exposure to high temperature indicating that some of the observed intergenerational effects are mediated by maternally-inherited mRNAs accumulated in the egg. Together, our observations shed new light on the intergenerational determinism of fish behaviour and associated underlying mechanisms. They also stress the importance of maternal history on fish behavioural plasticity.
bibliographic citation: Colson et al. (2019) Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish. PeerJ 7:e6338 https://doi.org/10.7717/peerj.6338
date submitted: 2018-05-02
date accepted: 2018-12-21
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Colson
  given name: Violaine
author list: Agent
  family name: Cousture
  given name: Morgane
author list: Agent
  family name: Damasceno
  given name: Danielle
author list: Agent
  family name: Valotaire
  given name: Claudiane
author list: Agent
  family name: Nguyen
  given name: Thaovi
author list: Agent
  family name: Le Cam
  given name: Aurélie
author list: Agent
  family name: Bobe
  given name: Julien
doi: 10.7717/peerj.6338
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 Colson et al.
attribution name: Colson et al.

Empirical analysis and modeling of Argos Doppler location errors in Romania
type: item
type: AcademicArticle
description: Background Advances in wildlife tracking technology have allowed researchers to understand the spatial ecology of many terrestrial and aquatic animal species. Argos Doppler is a technology that is widely used for wildlife tracking owing to the small size and low weight of the Argos transmitters. This allows them to be fitted to small-bodied species. The longer lifespan of the Argos units in comparison to units outfitted with miniaturized global positioning system (GPS) technology has also recommended their use. In practice, large Argos location errors often occur due to communication conditions such as transmitter settings, local environment, and the behavior of the tracked individual. Methods Considering the geographic specificity of errors and the lack of benchmark studies in Eastern Europe, the research objectives were: (1) to evaluate the accuracy of Argos Doppler technology under various environmental conditions in Romania, (2) to investigate the effectiveness of straightforward destructive filters for improving Argos Doppler data quality, and (3) to provide guidelines for processing Argos Doppler wildlife monitoring data. The errors associated with Argos locations in four geographic locations in Romania were assessed during static, low-speed and high-speed tests. The effectiveness of the Douglas Argos distance angle filter algorithm was then evaluated to ascertain its effect on the minimization of localization errors. Results Argos locations received in the tests had larger associated horizontal errors than those indicated by the operator of the Argos system, including under ideal reception conditions. Positional errors were similar to those obtained in other studies outside of Europe. The errors were anisotropic, with larger longitudinal errors for the vast majority of the data. Errors were mostly related to speed of the Argos transmitter at the time of reception, but other factors such as topographical conditions and orientation of antenna at the time of the…
format: application/pdf
format: text/html
creator: Laurentiu Rozylowicz
creator: Florian P. Bodescu
creator: Cristiana M. Ciocanea
creator: Athanasios A. Gavrilidis
creator: Steluta Manolache
creator: Marius L. Matache
creator: Iulia V. Miu
creator: Ionut C. Moale
creator: Andreea Nita
creator: Viorel D. Popescu
subject: Biogeography
subject: Ecology
subject: Spatial and Geographic Information Science
subject: Population Biology
description: doi:10.7717/peerj.6362
publisher: PeerJ Inc.
rights: © 2019 Rozylowicz et al.
abstract: Background Advances in wildlife tracking technology have allowed researchers to understand the spatial ecology of many terrestrial and aquatic animal species. Argos Doppler is a technology that is widely used for wildlife tracking owing to the small size and low weight of the Argos transmitters. This allows them to be fitted to small-bodied species. The longer lifespan of the Argos units in comparison to units outfitted with miniaturized global positioning system (GPS) technology has also recommended their use. In practice, large Argos location errors often occur due to communication conditions such as transmitter settings, local environment, and the behavior of the tracked individual. Methods Considering the geographic specificity of errors and the lack of benchmark studies in Eastern Europe, the research objectives were: (1) to evaluate the accuracy of Argos Doppler technology under various environmental conditions in Romania, (2) to investigate the effectiveness of straightforward destructive filters for improving Argos Doppler data quality, and (3) to provide guidelines for processing Argos Doppler wildlife monitoring data. The errors associated with Argos locations in four geographic locations in Romania were assessed during static, low-speed and high-speed tests. The effectiveness of the Douglas Argos distance angle filter algorithm was then evaluated to ascertain its effect on the minimization of localization errors. Results Argos locations received in the tests had larger associated horizontal errors than those indicated by the operator of the Argos system, including under ideal reception conditions. Positional errors were similar to those obtained in other studies outside of Europe. The errors were anisotropic, with larger longitudinal errors for the vast majority of the data. Errors were mostly related to speed of the Argos transmitter at the time of reception, but other factors such as topographical conditions and orientation of antenna at the time of the…
bibliographic citation: Rozylowicz et al. (2019) Empirical analysis and modeling of Argos Doppler location errors in Romania. PeerJ 7:e6362 https://doi.org/10.7717/peerj.6362
date submitted: 2018-09-13
date accepted: 2018-12-30
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rozylowicz
  given name: Laurentiu
author list: Agent
  family name: Bodescu
  given name: Florian P.
author list: Agent
  family name: Ciocanea
  given name: Cristiana M.
author list: Agent
  family name: Gavrilidis
  given name: Athanasios A.
author list: Agent
  family name: Manolache
  given name: Steluta
author list: Agent
  family name: Matache
  given name: Marius L.
author list: Agent
  family name: Miu
  given name: Iulia V.
author list: Agent
  family name: Moale
  given name: Ionut C.
author list: Agent
  family name: Nita
  given name: Andreea
author list: Agent
  family name: Popescu
  given name: Viorel D.
doi: 10.7717/peerj.6362
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Rozylowicz et al.
attribution name: Rozylowicz et al.

Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway
type: item
type: AcademicArticle
description: Background Taxifolin (TAX), is an active flavonoid, that plays an underlying protective role on the cardiovascular system. This study aimed to evaluate its effect and potential mechanisms on myocardial ischemia/reperfusion (I/R) injury. Methods Healthy rat heart was subjected to I/R using the Langendorff apparatus. Hemodynamic parameters, including heart rate, left ventricular developed pressure (LVDP), maximum/minimum rate of the left ventricular pressure rise (+dp/dtmax and −dp/dtmin) and rate pressure product (RPP) were recorded during the perfusion. Histopathological examination of left ventricular was measured by hematoxylin-eosin (H&E) staining. Creatine kinase-MB (CK-MB) and lactate dehydrogenase (LDH) activities in the effluent perfusion, and the levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) in the tissue were assayed. Apoptosis related proteins, such as B-cell lymphoma-2 (Bcl-2), Bcl2-associated X (Bax), and cytochrome c (Cyt-c) were also assayed by ELISA. Western blot was employed to determine apoptosis-executive proteins, including caspase 3 and 9. Transferase-mediated dUTP-X nick end labeling assay was performed to evaluate the effect TAX on myocardial apoptosis. Results Taxifolin significantly improved the ventricular functional recovery, as evident by the increase in LVDP, +dp/dtmax, −dp/dtmin and RPP, the levels of SOD, GSH-PX were also increased, but those of LDH, CK-MB, and MDA were decreased. Furthermore, TAX up-regulated the Bcl-2 protein level but down-regulated the levels of Bax, Cyt-c, caspase 3 and 9 protein, thereby inhibits the myocardial apoptosis. Discussion Taxifolin treatment remarkably improved the cardiac function, regulated oxidative stress and attenuated apoptosis. Hence, TAX has a cardioprotective effect against I/R injury by modulating mitochondrial apoptosis pathway.
format: application/pdf
format: text/html
creator: Zhenqiu Tang
creator: Chunjuan Yang
creator: Baoyan Zuo
creator: Yanan Zhang
creator: Gaosong Wu
creator: Yudi Wang
creator: Zhibin Wang
subject: Biochemistry
subject: Cardiology
subject: Pharmacology
description: doi:10.7717/peerj.6383
publisher: PeerJ Inc.
rights: © 2019 Tang et al.
abstract: Background Taxifolin (TAX), is an active flavonoid, that plays an underlying protective role on the cardiovascular system. This study aimed to evaluate its effect and potential mechanisms on myocardial ischemia/reperfusion (I/R) injury. Methods Healthy rat heart was subjected to I/R using the Langendorff apparatus. Hemodynamic parameters, including heart rate, left ventricular developed pressure (LVDP), maximum/minimum rate of the left ventricular pressure rise (+dp/dtmax and −dp/dtmin) and rate pressure product (RPP) were recorded during the perfusion. Histopathological examination of left ventricular was measured by hematoxylin-eosin (H&E) staining. Creatine kinase-MB (CK-MB) and lactate dehydrogenase (LDH) activities in the effluent perfusion, and the levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) in the tissue were assayed. Apoptosis related proteins, such as B-cell lymphoma-2 (Bcl-2), Bcl2-associated X (Bax), and cytochrome c (Cyt-c) were also assayed by ELISA. Western blot was employed to determine apoptosis-executive proteins, including caspase 3 and 9. Transferase-mediated dUTP-X nick end labeling assay was performed to evaluate the effect TAX on myocardial apoptosis. Results Taxifolin significantly improved the ventricular functional recovery, as evident by the increase in LVDP, +dp/dtmax, −dp/dtmin and RPP, the levels of SOD, GSH-PX were also increased, but those of LDH, CK-MB, and MDA were decreased. Furthermore, TAX up-regulated the Bcl-2 protein level but down-regulated the levels of Bax, Cyt-c, caspase 3 and 9 protein, thereby inhibits the myocardial apoptosis. Discussion Taxifolin treatment remarkably improved the cardiac function, regulated oxidative stress and attenuated apoptosis. Hence, TAX has a cardioprotective effect against I/R injury by modulating mitochondrial apoptosis pathway.
bibliographic citation: Tang et al. (2019) Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway. PeerJ 7:e6383 https://doi.org/10.7717/peerj.6383
date submitted: 2018-09-21
date accepted: 2019-01-03
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Zhenqiu
author list: Agent
  family name: Yang
  given name: Chunjuan
author list: Agent
  family name: Zuo
  given name: Baoyan
author list: Agent
  family name: Zhang
  given name: Yanan
author list: Agent
  family name: Wu
  given name: Gaosong
author list: Agent
  family name: Wang
  given name: Yudi
author list: Agent
  family name: Wang
  given name: Zhibin
doi: 10.7717/peerj.6383
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Tang et al.
attribution name: Tang et al.

Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)
type: item
type: AcademicArticle
description: Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.
format: application/pdf
format: text/html
creator: Zi-wei Zhou
creator: Hui-li Deng
creator: Qing-yang Wu
creator: Bin-bin Liu
creator: Chuan Yue
creator: Ting-ting Deng
creator: Zhong-xiong Lai
creator: Yun Sun
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6385
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.
bibliographic citation: Zhou et al. (2019) Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis). PeerJ 7:e6385 https://doi.org/10.7717/peerj.6385
date submitted: 2018-10-13
date accepted: 2018-12-28
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zi-wei
author list: Agent
  family name: Deng
  given name: Hui-li
author list: Agent
  family name: Wu
  given name: Qing-yang
author list: Agent
  family name: Liu
  given name: Bin-bin
author list: Agent
  family name: Yue
  given name: Chuan
author list: Agent
  family name: Deng
  given name: Ting-ting
author list: Agent
  family name: Lai
  given name: Zhong-xiong
author list: Agent
  family name: Sun
  given name: Yun
doi: 10.7717/peerj.6385
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases
type: item
type: AcademicArticle
description: Honey bees directly affect and are influenced by their local environment, in terms of food sources, pollinator densities, pathogen and toxin exposure and climate. Currently, there is a lack of studies analyzing these data with Geographic Information Systems (GIS) to investigate spatial relationships with the environment. Particularly for inter-colonial pathogen transmission, it is known that the likelihood of a healthy colony to become infested (e.g., Varroosis) or infected (e.g., American foulbrood—AFB, European foulbrood—EFB) increases with higher colony density. Whether these transmission paths can actually be asserted at apiary level is largely unknown. Here, we unraveled spatial distribution and high-resolution density of apiaries and bacterial honey bee brood diseases in Switzerland based on available GIS data. Switzerland as ‘model country’ offers the unique opportunity to get apiary data since 2010 owing to compulsory registration for every beekeeper. Further, both destructive bee brood diseases (AFB and EFB) are legally notifiable in Switzerland, and EFB has an epizootic character for the last decades. As governmental data sets have to be ameliorated, raw data from the cantonal agricultural or veterinary offices have been included. We found a mean density of 0.56 apiaries per km2, and high resolution spatial analyzes showed strong correlation between density of apiaries and human population density as well as agricultural landscape type. Concerning two bacterial bee brood diseases (AFB, EFB), no significant correlation was detectable with density of apiaries on cantonal level, though a high correlation of EFB cases and apiary density became obvious on higher resolution (district level). Hence, Swiss EFB epizootics seem to have benefited from high apiary densities, promoting the transmission of pathogens by adult bees. The GIS-based method presented here, might also be useful for other bee diseases, anthropogenic or environmental factors affecting bee coloni…
format: application/pdf
format: text/html
creator: Raphael S. von Büren
creator: Bernadette Oehen
creator: Nikolaus J. Kuhn
creator: Silvio Erler
subject: Agricultural Science
subject: Ecology
subject: Zoology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6393
publisher: PeerJ Inc.
rights: © 2019 von Büren et al.
abstract: Honey bees directly affect and are influenced by their local environment, in terms of food sources, pollinator densities, pathogen and toxin exposure and climate. Currently, there is a lack of studies analyzing these data with Geographic Information Systems (GIS) to investigate spatial relationships with the environment. Particularly for inter-colonial pathogen transmission, it is known that the likelihood of a healthy colony to become infested (e.g., Varroosis) or infected (e.g., American foulbrood—AFB, European foulbrood—EFB) increases with higher colony density. Whether these transmission paths can actually be asserted at apiary level is largely unknown. Here, we unraveled spatial distribution and high-resolution density of apiaries and bacterial honey bee brood diseases in Switzerland based on available GIS data. Switzerland as ‘model country’ offers the unique opportunity to get apiary data since 2010 owing to compulsory registration for every beekeeper. Further, both destructive bee brood diseases (AFB and EFB) are legally notifiable in Switzerland, and EFB has an epizootic character for the last decades. As governmental data sets have to be ameliorated, raw data from the cantonal agricultural or veterinary offices have been included. We found a mean density of 0.56 apiaries per km2, and high resolution spatial analyzes showed strong correlation between density of apiaries and human population density as well as agricultural landscape type. Concerning two bacterial bee brood diseases (AFB, EFB), no significant correlation was detectable with density of apiaries on cantonal level, though a high correlation of EFB cases and apiary density became obvious on higher resolution (district level). Hence, Swiss EFB epizootics seem to have benefited from high apiary densities, promoting the transmission of pathogens by adult bees. The GIS-based method presented here, might also be useful for other bee diseases, anthropogenic or environmental factors affecting bee coloni…
bibliographic citation: von Büren et al. (2019) High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases. PeerJ 7:e6393 https://doi.org/10.7717/peerj.6393
date submitted: 2018-10-11
date accepted: 2019-01-03
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: von Büren
  given name: Raphael S.
author list: Agent
  family name: Oehen
  given name: Bernadette
author list: Agent
  family name: Kuhn
  given name: Nikolaus J.
author list: Agent
  family name: Erler
  given name: Silvio
doi: 10.7717/peerj.6393
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 von Büren et al.
attribution name: von Büren et al.

Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
type: item
type: AcademicArticle
description: Introduction Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets. Methods Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall. Conclusions Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting ‘amplicons’ from a whole-metagenome dataset. Marker regions from the 16…
format: application/pdf
format: text/html
creator: Paul Greenfield
creator: Nai Tran-Dinh
creator: David Midgley
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6174
publisher: PeerJ Inc.
rights: © 2019 Greenfield et al.
abstract: Introduction Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets. Methods Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall. Conclusions Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting ‘amplicons’ from a whole-metagenome dataset. Marker regions from the 16…
bibliographic citation: Greenfield et al. (2019) Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets. PeerJ 6:e6174 https://doi.org/10.7717/peerj.6174
date submitted: 2018-09-18
date accepted: 2018-11-24
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greenfield
  given name: Paul
author list: Agent
  family name: Tran-Dinh
  given name: Nai
author list: Agent
  family name: Midgley
  given name: David
doi: 10.7717/peerj.6174
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: ©2019 Greenfield et al.
attribution name: Greenfield et al.

Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?
type: item
type: AcademicArticle
description: Background The main aim of the study was to analyse the influence of fleshy fruits (plums) on the post-metamorphic growth and feeding behaviour of the green toad Bufotes viridis. We tested the following two hypotheses: (1) juveniles of the green toad are characterised by faster growth in conditions involving fallen plums Prunus cerasifera due to the associated presence of more varied food such as invertebrates; (2) green toads exhibit more active feeding behaviour in the presence of fleshy fruits. Methods A total of 120 fresh metamorphs of the green toad were randomly assigned to one of four groups: two experimental groups with fleshy plums and two other groups as controls (without fruits). Each group was kept in an enclosure to which wild invertebrates had free access. Each individual toad was measured for snout-vent length (mm) and body mass (g) every other day for 30 days. In order to determine whether fallen plums influence the feeding behaviour of toads, the number of active and hidden (under an artificial shelter) individuals was also noted. Results The results showed that green toads from both enclosures with plums were characterised by more rapid growth than individuals from the control treatments. Simultaneously, in the enclosure with fleshy fruits, greater species richness of wild invertebrates was observed. No differences in active feeding behaviour were noted between control groups and groups with plums. Discussion Fleshy fruits, upon falling, attract many types of invertebrates; thus they may represent good dietary supplements for fresh amphibian metamorphs. Therefore, the presence of fruit trees close to a breeding site might influences the post-metamorphic growth of amphibians, but not their feeding behaviour. The presence of insects associated with fallen fruit seems to favour the occurrence of amphibian populations, which is particularly important, since, due to political and social pressure, numbers of fruit trees are currently being reduced. To ou…
format: application/pdf
format: text/html
creator: Mikołaj Kaczmarski
creator: Piotr Tryjanowski
creator: Anna Maria Kubicka
subject: Ecology
subject: Ecosystem Science
subject: Zoology
description: doi:10.7717/peerj.6337
publisher: PeerJ Inc.
rights: © 2019 Kaczmarski et al.
abstract: Background The main aim of the study was to analyse the influence of fleshy fruits (plums) on the post-metamorphic growth and feeding behaviour of the green toad Bufotes viridis. We tested the following two hypotheses: (1) juveniles of the green toad are characterised by faster growth in conditions involving fallen plums Prunus cerasifera due to the associated presence of more varied food such as invertebrates; (2) green toads exhibit more active feeding behaviour in the presence of fleshy fruits. Methods A total of 120 fresh metamorphs of the green toad were randomly assigned to one of four groups: two experimental groups with fleshy plums and two other groups as controls (without fruits). Each group was kept in an enclosure to which wild invertebrates had free access. Each individual toad was measured for snout-vent length (mm) and body mass (g) every other day for 30 days. In order to determine whether fallen plums influence the feeding behaviour of toads, the number of active and hidden (under an artificial shelter) individuals was also noted. Results The results showed that green toads from both enclosures with plums were characterised by more rapid growth than individuals from the control treatments. Simultaneously, in the enclosure with fleshy fruits, greater species richness of wild invertebrates was observed. No differences in active feeding behaviour were noted between control groups and groups with plums. Discussion Fleshy fruits, upon falling, attract many types of invertebrates; thus they may represent good dietary supplements for fresh amphibian metamorphs. Therefore, the presence of fruit trees close to a breeding site might influences the post-metamorphic growth of amphibians, but not their feeding behaviour. The presence of insects associated with fallen fruit seems to favour the occurrence of amphibian populations, which is particularly important, since, due to political and social pressure, numbers of fruit trees are currently being reduced. To ou…
bibliographic citation: Kaczmarski et al. (2019) Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?. PeerJ 7:e6337 https://doi.org/10.7717/peerj.6337
date submitted: 2018-09-11
date accepted: 2018-12-21
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaczmarski
  given name: Mikołaj
author list: Agent
  family name: Tryjanowski
  given name: Piotr
author list: Agent
  family name: Kubicka
  given name: Anna Maria
doi: 10.7717/peerj.6337
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: © 2019 Kaczmarski et al.
attribution name: Kaczmarski et al.

Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China
type: item
type: AcademicArticle
description: Soil pH is the main factor affecting soil nutrient availability and chemical substances in soil. It is of great significance to study the spatial variability of soil pH for the management of soil nutrients and the prediction of soil pollution. In order to explore the causes of spatial variability in soil pH in red-bed areas, the Nanxiong Basin in south China was selected as an example, and soil pH was measured in the topsoil by nested sampling (0–20 cm depth). The spatial variability characteristics of soil pH were analyzed by geostatistics and classical statistical methods, and the main factors influencing spatial variability in soil pH are discussed. The coefficient of variation in the red-bed areas of Nanxiong Basin was 17.18%, indicating moderate variability. Geostatistical analysis showed that the spherical model is the optimal theoretical model for explaining variability in soil pH, which is influenced by both structural and random factors. Analysis of the spatial distribution and pattern showed that soil pH is relatively high in the northeast and southwest, and is lower in the northwest. These results indicate that land use patterns and topographic factors are the main and secondary influencing factors, respectively.
format: application/pdf
format: text/html
creator: Ping Yan
creator: Hua Peng
creator: Luobin Yan
creator: Shaoyun Zhang
creator: Aimin Chen
creator: Kairong Lin
subject: Agricultural Science
subject: Soil Science
description: doi:10.7717/peerj.6342
publisher: PeerJ Inc.
rights: © 2019 Yan et al.
abstract: Soil pH is the main factor affecting soil nutrient availability and chemical substances in soil. It is of great significance to study the spatial variability of soil pH for the management of soil nutrients and the prediction of soil pollution. In order to explore the causes of spatial variability in soil pH in red-bed areas, the Nanxiong Basin in south China was selected as an example, and soil pH was measured in the topsoil by nested sampling (0–20 cm depth). The spatial variability characteristics of soil pH were analyzed by geostatistics and classical statistical methods, and the main factors influencing spatial variability in soil pH are discussed. The coefficient of variation in the red-bed areas of Nanxiong Basin was 17.18%, indicating moderate variability. Geostatistical analysis showed that the spherical model is the optimal theoretical model for explaining variability in soil pH, which is influenced by both structural and random factors. Analysis of the spatial distribution and pattern showed that soil pH is relatively high in the northeast and southwest, and is lower in the northwest. These results indicate that land use patterns and topographic factors are the main and secondary influencing factors, respectively.
bibliographic citation: Yan et al. (2019) Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China. PeerJ 7:e6342 https://doi.org/10.7717/peerj.6342
date submitted: 2018-08-27
date accepted: 2018-12-24
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Ping
author list: Agent
  family name: Peng
  given name: Hua
author list: Agent
  family name: Yan
  given name: Luobin
author list: Agent
  family name: Zhang
  given name: Shaoyun
author list: Agent
  family name: Chen
  given name: Aimin
author list: Agent
  family name: Lin
  given name: Kairong
doi: 10.7717/peerj.6342
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: ©2019 Yan et al.
attribution name: Yan et al.

Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine
type: item
type: AcademicArticle
description: Here we investigated the expressions of apoptosis-associated genes known to induce programed cell death through mRNA expressions of two matrix metalloproteinases (MMPs) that are involved in the degradation of collagen and basal membrane in luteal cells cultured in the treatment media. Our results show that the activity of MMP-2 gelatinase was higher in the CL2 and CL1 of luteal phase, was gradually decreased in the CH2 and CH3 of luteal phase. In particular, the expressions of P4-r and survival-associated genes (IGFr, PI3K, AKT, and mTOR) were strongly induced during CL3 stage, whereas the levels of these genes in corpus luteum (CL) were lower during CL2 and CL1 stages. In the cultured lutein cells analyzed, we found that as MMPs increase, genes related to apoptosis (20α-hydroxy steroid dehydrogenase and caspase-3) also increase. In other words, the results for P4-r and survival-related gene expression patterns in the luteal cells were contrary to the MMPs activation results. These results indicate that active MMPs are differentially expressed to induce the expression of genes associated with programed cell death from the degrading luteal cells. Therefore, our results suggest that the MMPs activation may lead to luteal cell development or death.
format: application/pdf
format: text/html
creator: Sang Hwan Kim
creator: Ji Hye Lee
creator: Jong Taek Yoon
subject: Agricultural Science
subject: Developmental Biology
description: doi:10.7717/peerj.6344
publisher: PeerJ Inc.
rights: © 2019 Kim et al.
abstract: Here we investigated the expressions of apoptosis-associated genes known to induce programed cell death through mRNA expressions of two matrix metalloproteinases (MMPs) that are involved in the degradation of collagen and basal membrane in luteal cells cultured in the treatment media. Our results show that the activity of MMP-2 gelatinase was higher in the CL2 and CL1 of luteal phase, was gradually decreased in the CH2 and CH3 of luteal phase. In particular, the expressions of P4-r and survival-associated genes (IGFr, PI3K, AKT, and mTOR) were strongly induced during CL3 stage, whereas the levels of these genes in corpus luteum (CL) were lower during CL2 and CL1 stages. In the cultured lutein cells analyzed, we found that as MMPs increase, genes related to apoptosis (20α-hydroxy steroid dehydrogenase and caspase-3) also increase. In other words, the results for P4-r and survival-related gene expression patterns in the luteal cells were contrary to the MMPs activation results. These results indicate that active MMPs are differentially expressed to induce the expression of genes associated with programed cell death from the degrading luteal cells. Therefore, our results suggest that the MMPs activation may lead to luteal cell development or death.
bibliographic citation: Kim et al. (2019) Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine. PeerJ 7:e6344 https://doi.org/10.7717/peerj.6344
date submitted: 2018-06-20
date accepted: 2018-12-22
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Sang Hwan
author list: Agent
  family name: Lee
  given name: Ji Hye
author list: Agent
  family name: Yoon
  given name: Jong Taek
doi: 10.7717/peerj.6344
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: © 2019 Kim et al.
attribution name: Kim et al.

Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei
type: item
type: AcademicArticle
description: According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.
format: application/pdf
format: text/html
creator: Victor Spangenberg
creator: Marine Arakelyan
creator: Eduard Galoyan
creator: Mark Pankin
creator: Ruzanna Petrosyan
creator: Ilona Stepanyan
creator: Tatiana Grishaeva
creator: Felix Danielyan
creator: Oxana Kolomiets
subject: Cell Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.6360
publisher: PeerJ Inc.
rights: © 2019 Spangenberg et al.
abstract: According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.
bibliographic citation: Spangenberg et al. (2019) Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei. PeerJ 7:e6360 https://doi.org/10.7717/peerj.6360
date submitted: 2018-09-11
date accepted: 2018-12-28
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spangenberg
  given name: Victor
author list: Agent
  family name: Arakelyan
  given name: Marine
author list: Agent
  family name: Galoyan
  given name: Eduard
author list: Agent
  family name: Pankin
  given name: Mark
author list: Agent
  family name: Petrosyan
  given name: Ruzanna
author list: Agent
  family name: Stepanyan
  given name: Ilona
author list: Agent
  family name: Grishaeva
  given name: Tatiana
author list: Agent
  family name: Danielyan
  given name: Felix
author list: Agent
  family name: Kolomiets
  given name: Oxana
doi: 10.7717/peerj.6360
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: © 2019 Spangenberg et al.
attribution name: Spangenberg et al.

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