PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Maternal trauma and fear history predict BDNF methylation and gene expression in newborns
items: A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology
items: Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review
items: Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice
items: Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt
items: Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
items: Creatinine is a biochemical marker for assessing how untrained people adapt to fitness training loads
items: https://peerj.com/articles/9151
items: In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair
items: Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns

Maternal trauma and fear history predict BDNF methylation and gene expression in newborns
type: item
type: AcademicArticle
description: Trauma and related fear exert significant influence on mental and physical health throughout the lifespan and are associated with intergenerational patterns of development, health, and behavior. DNA methylation and gene expression are involved in our developmental adaptations to our experiences and can be influenced by social interventions. Patterns of DNA methylation and expression of a gene involved in neurodevelopment and psychiatric risk (BDNF) have been linked with childhood trauma. Given the intergenerational patterns of health and behavior, and previous links between childhood trauma and BDNF methylation and expression, this study investigated the potential for maternal history of traumatic experiences to influence development in her newborn, via changes in her newborn’s BDNF methylation and expression. We found that mothers’ trauma history was associated with epigenetic regulation of BDNF in their newborns. Moreover, the association between maternal trauma and BDNF methylation and expression patterns were moderated by newborn sex. Male newborns showed increased BDNF expression with maternal exposure to child abuse (p = .001), and increased BDNF methylation with greater maternal fear (p = .001). Female newborns showed reduced BDNF expression with greater maternal fear (p = .004). Practitioners strive to identify prevention and intervention avenues that will reduce the harmful effects of trauma. Future research should consider the potential for maternal historical trauma experiences to influence offspring DNA methylation and gene expression in a manner that could alter development and inform novel prevention strategies.
format: application/pdf
format: text/html
creator: Stefanie R. Pilkay
creator: Terri Combs-Orme
creator: Frances Tylavsky
creator: Nicole Bush
creator: Alicia K. Smith
subject: Genetics
subject: Neuroscience
description: doi:10.7717/peerj.8858
publisher: PeerJ Inc.
rights: © 2020 Pilkay et al.
abstract: Trauma and related fear exert significant influence on mental and physical health throughout the lifespan and are associated with intergenerational patterns of development, health, and behavior. DNA methylation and gene expression are involved in our developmental adaptations to our experiences and can be influenced by social interventions. Patterns of DNA methylation and expression of a gene involved in neurodevelopment and psychiatric risk (BDNF) have been linked with childhood trauma. Given the intergenerational patterns of health and behavior, and previous links between childhood trauma and BDNF methylation and expression, this study investigated the potential for maternal history of traumatic experiences to influence development in her newborn, via changes in her newborn’s BDNF methylation and expression. We found that mothers’ trauma history was associated with epigenetic regulation of BDNF in their newborns. Moreover, the association between maternal trauma and BDNF methylation and expression patterns were moderated by newborn sex. Male newborns showed increased BDNF expression with maternal exposure to child abuse (p = .001), and increased BDNF methylation with greater maternal fear (p = .001). Female newborns showed reduced BDNF expression with greater maternal fear (p = .004). Practitioners strive to identify prevention and intervention avenues that will reduce the harmful effects of trauma. Future research should consider the potential for maternal historical trauma experiences to influence offspring DNA methylation and gene expression in a manner that could alter development and inform novel prevention strategies.
bibliographic citation: Pilkay et al. (2020) Maternal trauma and fear history predict BDNF methylation and gene expression in newborns. PeerJ 8:e8858 https://doi.org/10.7717/peerj.8858
date submitted: 2019-11-21
date accepted: 2020-03-05
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pilkay
  given name: Stefanie R.
author list: Agent
  family name: Combs-Orme
  given name: Terri
author list: Agent
  family name: Tylavsky
  given name: Frances
author list: Agent
  family name: Bush
  given name: Nicole
author list: Agent
  family name: Smith
  given name: Alicia K.
doi: 10.7717/peerj.8858
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Pilkay et al.
attribution name: Pilkay et al.

A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology
type: item
type: AcademicArticle
description: The new ichnospecies Paleohelcura araraquarensis isp. nov. is described from the Upper Jurassic-Lower Cretaceous Botucatu Formation of Brazil. This formation records a gigantic eolian sand sea (erg), formed under an arid climate in the south-central part of Gondwana. This trackway is composed of two track rows, whose internal width is less than one-quarter of the external width, with alternating to staggered series, consisting of three elliptical tracks that can vary from slightly elongated to tapered or circular. The trackways were found in yellowish/reddish sandstone in a quarry in the Araraquara municipality, São Paulo State. Comparisons with neoichnological studies and morphological inferences indicate that the producer of Paleohelcura araraquarensis isp. nov. was most likely a pterygote insect, and so could have fulfilled one of the ecological roles that different species of this group are capable of performing in dune deserts. The producer could have had a herbivorous or carnivorous diet or been part of the fauna of omnivores, being able to adopt herbivorous, carnivorous, and saprophagous diets when necessary. In modern dune deserts, some species of pterygote insects are detritivores (like Tenebrionidae), relying on organic matter that accumulated among the sand grains of the dunes during dry periods with no plant growth. The presence of additional burrows suggests that the Botucatu paleodesert would have had a detritivorous fauna like this. Based on the interpretation of the ichnofossil producers, it was possible to reconstruct the food web of this paleodesert. All the omnivorous and herbivorous invertebrates and the herbivorous ornithopod dinosaurs made up the primary consumers. These animals were, in turn, the food source for bigger carnivorous or omnivorous animals unable to feed on detritus, like arachnids, possible predatory insects, mammaliaforms, and theropod dinosaurs. The highest trophic level was occupied by larger theropod dinosaurs and mammaliafor…
format: application/pdf
format: text/html
creator: Bernardo de C.P. e M. Peixoto
creator: M. Gabriela Mángano
creator: Nicholas J. Minter
creator: Luciana Bueno dos Reis Fernandes
creator: Marcelo Adorna Fernandes
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.8880
publisher: PeerJ Inc.
rights: © 2020 Peixoto et al.
abstract: The new ichnospecies Paleohelcura araraquarensis isp. nov. is described from the Upper Jurassic-Lower Cretaceous Botucatu Formation of Brazil. This formation records a gigantic eolian sand sea (erg), formed under an arid climate in the south-central part of Gondwana. This trackway is composed of two track rows, whose internal width is less than one-quarter of the external width, with alternating to staggered series, consisting of three elliptical tracks that can vary from slightly elongated to tapered or circular. The trackways were found in yellowish/reddish sandstone in a quarry in the Araraquara municipality, São Paulo State. Comparisons with neoichnological studies and morphological inferences indicate that the producer of Paleohelcura araraquarensis isp. nov. was most likely a pterygote insect, and so could have fulfilled one of the ecological roles that different species of this group are capable of performing in dune deserts. The producer could have had a herbivorous or carnivorous diet or been part of the fauna of omnivores, being able to adopt herbivorous, carnivorous, and saprophagous diets when necessary. In modern dune deserts, some species of pterygote insects are detritivores (like Tenebrionidae), relying on organic matter that accumulated among the sand grains of the dunes during dry periods with no plant growth. The presence of additional burrows suggests that the Botucatu paleodesert would have had a detritivorous fauna like this. Based on the interpretation of the ichnofossil producers, it was possible to reconstruct the food web of this paleodesert. All the omnivorous and herbivorous invertebrates and the herbivorous ornithopod dinosaurs made up the primary consumers. These animals were, in turn, the food source for bigger carnivorous or omnivorous animals unable to feed on detritus, like arachnids, possible predatory insects, mammaliaforms, and theropod dinosaurs. The highest trophic level was occupied by larger theropod dinosaurs and mammaliafor…
bibliographic citation: Peixoto et al. (2020) A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology. PeerJ 8:e8880 https://doi.org/10.7717/peerj.8880
date submitted: 2019-11-06
date accepted: 2020-03-10
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peixoto
  given name: Bernardo de C.P. e M.
author list: Agent
  family name: Mángano
  given name: M. Gabriela
author list: Agent
  family name: Minter
  given name: Nicholas J.
author list: Agent
  family name: dos Reis Fernandes
  given name: Luciana Bueno
author list: Agent
  family name: Fernandes
  given name: Marcelo Adorna
doi: 10.7717/peerj.8880
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Peixoto et al.
attribution name: Peixoto et al.

Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review
type: item
type: AcademicArticle
description: The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
format: application/pdf
format: text/html
creator: Sergei Yu. Zaitsev
creator: Nadezhda V. Bogolyubova
creator: Xuying Zhang
creator: Bertram Brenig
subject: Biochemistry
subject: Veterinary Medicine
description: doi:10.7717/peerj.8997
publisher: PeerJ Inc.
rights: © 2020 Zaitsev et al.
abstract: The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
bibliographic citation: Zaitsev et al. (2020) Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review. PeerJ 8:e8997 https://doi.org/10.7717/peerj.8997
date submitted: 2019-06-20
date accepted: 2020-03-26
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zaitsev
  given name: Sergei Yu.
author list: Agent
  family name: Bogolyubova
  given name: Nadezhda V.
author list: Agent
  family name: Zhang
  given name: Xuying
author list: Agent
  family name: Brenig
  given name: Bertram
doi: 10.7717/peerj.8997
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: © 2020 Zaitsev et al.
attribution name: Zaitsev et al.

Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice
type: item
type: AcademicArticle
description: Background Benzalkonium chloride (BAK), commonly used in glaucoma treatment, is an eye drop preservative with dose-dependent toxicity. Previous studies have observed the multi-functional benefits of angiogenin (ANG) against glaucoma. In our study, we evaluated ANG’s cytoprotective effect on the trabecular meshwork (TM) damage induced by BAK. Additionally, we developed a plant-derived ANG fusion protein and evaluated its effect on TM structure and function. Methods We synthesized plant-derived ANG (ANG-FcK) by fuzing immunoglobulin G’s Fc region and KDEL to conventional recombinant human ANG (Rh-ANG) purified from transgenic tobacco plants. We established a mouse model using BAK to look for degenerative changes in the TM, and to evaluate the protective effects of ANG-FcK and Rh-ANG. Intraocular pressure (IOP) was measured for 4 weeks and ultrastructural changes, deposition of fluorescent microbeads, type I and IV collagen, fibronectin, laminin and α-SMA expression were analyzed after the mice were euthanized. Results TM structural and functional degeneration were induced by 0.1% BAK instillation in mice. ANG co-treatment preserved TM outflow function, which we measured using IOP and a microbead tracer. ANG prevented phenotypic and ultrastructure changes, and that protective effect might be related to the anti-fibrosis mechanism. We observed a similar cytoprotective effect in the BAK-induced degenerative TM mouse model, suggesting that plant-derived ANG-FcK could be a promising glaucoma treatment.
format: application/pdf
format: text/html
creator: Jae Hoon Jeong
creator: Soo Jin Lee
creator: Kisung Ko
creator: Jeong Hwan Lee
creator: Jungmook Lyu
creator: Moon Hyang Park
creator: Jaeku Kang
creator: Jae Chan Kim
subject: Bioengineering
subject: Drugs and Devices
subject: Ophthalmology
subject: Pharmacology
description: doi:10.7717/peerj.9084
publisher: PeerJ Inc.
rights: © 2020 Jeong et al.
abstract: Background Benzalkonium chloride (BAK), commonly used in glaucoma treatment, is an eye drop preservative with dose-dependent toxicity. Previous studies have observed the multi-functional benefits of angiogenin (ANG) against glaucoma. In our study, we evaluated ANG’s cytoprotective effect on the trabecular meshwork (TM) damage induced by BAK. Additionally, we developed a plant-derived ANG fusion protein and evaluated its effect on TM structure and function. Methods We synthesized plant-derived ANG (ANG-FcK) by fuzing immunoglobulin G’s Fc region and KDEL to conventional recombinant human ANG (Rh-ANG) purified from transgenic tobacco plants. We established a mouse model using BAK to look for degenerative changes in the TM, and to evaluate the protective effects of ANG-FcK and Rh-ANG. Intraocular pressure (IOP) was measured for 4 weeks and ultrastructural changes, deposition of fluorescent microbeads, type I and IV collagen, fibronectin, laminin and α-SMA expression were analyzed after the mice were euthanized. Results TM structural and functional degeneration were induced by 0.1% BAK instillation in mice. ANG co-treatment preserved TM outflow function, which we measured using IOP and a microbead tracer. ANG prevented phenotypic and ultrastructure changes, and that protective effect might be related to the anti-fibrosis mechanism. We observed a similar cytoprotective effect in the BAK-induced degenerative TM mouse model, suggesting that plant-derived ANG-FcK could be a promising glaucoma treatment.
bibliographic citation: Jeong et al. (2020) Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice. PeerJ 8:e9084 https://doi.org/10.7717/peerj.9084
date submitted: 2019-11-04
date accepted: 2020-04-08
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jeong
  given name: Jae Hoon
author list: Agent
  family name: Lee
  given name: Soo Jin
author list: Agent
  family name: Ko
  given name: Kisung
author list: Agent
  family name: Lee
  given name: Jeong Hwan
author list: Agent
  family name: Lyu
  given name: Jungmook
author list: Agent
  family name: Park
  given name: Moon Hyang
author list: Agent
  family name: Kang
  given name: Jaeku
author list: Agent
  family name: Kim
  given name: Jae Chan
doi: 10.7717/peerj.9084
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: © 2020 Jeong et al.
attribution name: Jeong et al.

Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt
type: item
type: AcademicArticle
description: Lizard and snake remains from the early Miocene (Burdigalian) of the Moghra Formation, Egypt, are described herein. This material comprises the first fossil remains of squamates recovered from the otherwise rich and well known vertebrate assemblage of Moghra. The material pertains to two different genera, the varanid lizard Varanus and the pythonid snake Python and adds to the so far rather poorly known squamate fossil record from Africa. On the basis of the new remains, Moghra marks the oldest so far described co-occurrence of Varanus and Python in the African continent. The close sympatry of these two genera in the African fossil record is thoroughly analyzed and discussed, a co-existence, which is still widespread in the extant herpetofauna of the continent. Situated rather close to the so called “Levantine Corridor” and dated at the Burdigalian, practically when Afro-Arabia collided with Eurasia, the Moghra squamate assemblage offers the potential of important insights in the biogeography and dispersal events of vertebrate groups during the early Miocene.
format: application/pdf
format: text/html
creator: Georgios L. Georgalis
creator: Mohamed K. Abdel Gawad
creator: Safiya M. Hassan
creator: Ahmed N. El-Barkooky
creator: Mohamed A. Hamdan
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9092
publisher: PeerJ Inc.
rights: © 2020 Georgalis et al.
abstract: Lizard and snake remains from the early Miocene (Burdigalian) of the Moghra Formation, Egypt, are described herein. This material comprises the first fossil remains of squamates recovered from the otherwise rich and well known vertebrate assemblage of Moghra. The material pertains to two different genera, the varanid lizard Varanus and the pythonid snake Python and adds to the so far rather poorly known squamate fossil record from Africa. On the basis of the new remains, Moghra marks the oldest so far described co-occurrence of Varanus and Python in the African continent. The close sympatry of these two genera in the African fossil record is thoroughly analyzed and discussed, a co-existence, which is still widespread in the extant herpetofauna of the continent. Situated rather close to the so called “Levantine Corridor” and dated at the Burdigalian, practically when Afro-Arabia collided with Eurasia, the Moghra squamate assemblage offers the potential of important insights in the biogeography and dispersal events of vertebrate groups during the early Miocene.
bibliographic citation: Georgalis et al. (2020) Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt. PeerJ 8:e9092 https://doi.org/10.7717/peerj.9092
date submitted: 2020-01-14
date accepted: 2020-04-09
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Georgalis
  given name: Georgios L.
author list: Agent
  family name: Abdel Gawad
  given name: Mohamed K.
author list: Agent
  family name: Hassan
  given name: Safiya M.
author list: Agent
  family name: El-Barkooky
  given name: Ahmed N.
author list: Agent
  family name: Hamdan
  given name: Mohamed A.
doi: 10.7717/peerj.9092
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Georgalis et al.
attribution name: Georgalis et al.

Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
type: item
type: AcademicArticle
description: The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
format: application/pdf
format: text/html
creator: Shuilian He
creator: Yang Yang
creator: Ziwei Li
creator: Xuejiao Wang
creator: Yanbing Guo
creator: Hongzhi Wu
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9132
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
bibliographic citation: He et al. (2020) Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment. PeerJ 8:e9132 https://doi.org/10.7717/peerj.9132
date submitted: 2019-12-05
date accepted: 2020-04-14
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Shuilian
author list: Agent
  family name: Yang
  given name: Yang
author list: Agent
  family name: Li
  given name: Ziwei
author list: Agent
  family name: Wang
  given name: Xuejiao
author list: Agent
  family name: Guo
  given name: Yanbing
author list: Agent
  family name: Wu
  given name: Hongzhi
doi: 10.7717/peerj.9132
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 He et al.
attribution name: He et al.

Creatinine is a biochemical marker for assessing how untrained people adapt to fitness training loads
type: item
type: AcademicArticle
description: Background To study the peculiarities of changes in creatinine concentration in blood serum of untrained men during the prolonged usage of training loads different in volume and intensity, and to determine the value of this biochemical marker for the assessment of adaptive body changes during fitness training. Methods We examined 50 untrained men aged 18–20 years who had no contraindications for practicing fitness. Taking into account the aim of the research, we divided these people into two groups: group A and group B. The research participants used training load regimes different in volume and intensity: representatives of group Aused low intensity training load regime (Ra = 0.53) and representatives of group B used high intensity training load regime (Ra = 0.72). To assess the adaptive body changes in the examined contingent, we used the anthropometry method (circumference body size) and bioimpedansometry (body composition indicators). We also determined the features of adaptation-compensatory body reactions to different training loads by means of biochemical control of creatinine concentration in blood serum. Results The obtained results showed a significant increase in basal level of creatinine concentration in blood serum (by 17.6%) of group B representatives fixed after 3 months of practicing fitness in high intensity training load regime (Ra = 0.72). This group representative also revealed the most pronounced manifestation of adaptive body changes confirmed by the results of the maximal muscle strength growth (1RM) and circumference body size, which was almost 2.5 times higher than the results of group A representatives for the same period of time. The parameters indicating the load volume in a set (Wn) were almost 62.0 % higher in group A representatives in comparison with group B during all stages of control. Nonetheless, the highest creatinine concentration in blood serum (by 11.1 % (p < 0.05) was fixed in group A representatives in response to training l…
format: application/pdf
format: text/html
creator: Andrii Chernozub
creator: Vladimir Potop
creator: Georgiy Korobeynikov
creator: Olivia Carmen Timnea
creator: Oleg Dubachinskiy
creator: Oksana Ikkert
creator: Yuriy Briskin
creator: Yuriy Boretsky
creator: Lesia Korobeynikova
subject: Biochemistry
subject: Anatomy and Physiology
subject: Kinesiology
subject: Statistics
description: doi:10.7717/peerj.9137
publisher: PeerJ Inc.
rights: © 2020 Chernozub et al.
abstract: Background To study the peculiarities of changes in creatinine concentration in blood serum of untrained men during the prolonged usage of training loads different in volume and intensity, and to determine the value of this biochemical marker for the assessment of adaptive body changes during fitness training. Methods We examined 50 untrained men aged 18–20 years who had no contraindications for practicing fitness. Taking into account the aim of the research, we divided these people into two groups: group A and group B. The research participants used training load regimes different in volume and intensity: representatives of group Aused low intensity training load regime (Ra = 0.53) and representatives of group B used high intensity training load regime (Ra = 0.72). To assess the adaptive body changes in the examined contingent, we used the anthropometry method (circumference body size) and bioimpedansometry (body composition indicators). We also determined the features of adaptation-compensatory body reactions to different training loads by means of biochemical control of creatinine concentration in blood serum. Results The obtained results showed a significant increase in basal level of creatinine concentration in blood serum (by 17.6%) of group B representatives fixed after 3 months of practicing fitness in high intensity training load regime (Ra = 0.72). This group representative also revealed the most pronounced manifestation of adaptive body changes confirmed by the results of the maximal muscle strength growth (1RM) and circumference body size, which was almost 2.5 times higher than the results of group A representatives for the same period of time. The parameters indicating the load volume in a set (Wn) were almost 62.0 % higher in group A representatives in comparison with group B during all stages of control. Nonetheless, the highest creatinine concentration in blood serum (by 11.1 % (p < 0.05) was fixed in group A representatives in response to training l…
bibliographic citation: Chernozub et al. (2020) Creatinine is a biochemical marker for assessing how untrained people adapt to fitness training loads. PeerJ 8:e9137 https://doi.org/10.7717/peerj.9137
date submitted: 2019-12-05
date accepted: 2020-04-15
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chernozub
  given name: Andrii
author list: Agent
  family name: Potop
  given name: Vladimir
author list: Agent
  family name: Korobeynikov
  given name: Georgiy
author list: Agent
  family name: Timnea
  given name: Olivia Carmen
author list: Agent
  family name: Dubachinskiy
  given name: Oleg
author list: Agent
  family name: Ikkert
  given name: Oksana
author list: Agent
  family name: Briskin
  given name: Yuriy
author list: Agent
  family name: Boretsky
  given name: Yuriy
author list: Agent
  family name: Korobeynikova
  given name: Lesia
doi: 10.7717/peerj.9137
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Chernozub et al.
attribution name: Chernozub et al.

https://peerj.com/articles/9151
type: item
type: AcademicArticle
title: Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov
description: Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium discoideum. The new species P. agricolaris sp. nov., P. hayleyella sp. nov., and P. bonniea sp. nov. are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. discoideum. We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. discoideum amoebae and form a symbiotic relationship. All three of these new species facilitate the prolonged carriage of food bacteria by D. discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. discoideum should be fruitful for understanding the ecology and evolution of symbioses.
format: application/pdf
format: text/html
creator: Debra A. Brock
creator: Suegene Noh
creator: Alicia N.M. Hubert
creator: Tamara S. Haselkorn
creator: Susanne DiSalvo
creator: Melanie K. Suess
creator: Alexander S. Bradley
creator: Mahboubeh Tavakoli-Nezhad
creator: Katherine S. Geist
creator: David C. Queller
creator: Joan E. Strassmann
subject: Ecology
subject: Evolutionary Studies
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.9151
publisher: PeerJ Inc.
rights: © 2020 Brock et al.
abstract: Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium discoideum. The new species P. agricolaris sp. nov., P. hayleyella sp. nov., and P. bonniea sp. nov. are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. discoideum. We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. discoideum amoebae and form a symbiotic relationship. All three of these new species facilitate the prolonged carriage of food bacteria by D. discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. discoideum should be fruitful for understanding the ecology and evolution of symbioses.
bibliographic citation: Brock et al. (2020) Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov. PeerJ 8:e9151 https://doi.org/10.7717/peerj.9151
date submitted: 2019-02-20
date accepted: 2020-04-17
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brock
  given name: Debra A.
author list: Agent
  family name: Noh
  given name: Suegene
author list: Agent
  family name: Hubert
  given name: Alicia N.M.
author list: Agent
  family name: Haselkorn
  given name: Tamara S.
author list: Agent
  family name: DiSalvo
  given name: Susanne
author list: Agent
  family name: Suess
  given name: Melanie K.
author list: Agent
  family name: Bradley
  given name: Alexander S.
author list: Agent
  family name: Tavakoli-Nezhad
  given name: Mahboubeh
author list: Agent
  family name: Geist
  given name: Katherine S.
author list: Agent
  family name: Queller
  given name: David C.
author list: Agent
  family name: Strassmann
  given name: Joan E.
doi: 10.7717/peerj.9151
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Brock et al.
attribution name: Brock et al.

In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair
type: item
type: AcademicArticle
description: Background DNA double strand break repair is important to preserve the fidelity of our genetic makeup after DNA damage. Rad50 is one of the components in MRN complex important for DNA repair mechanism. Rad50 mutations can lead to microcephaly, mental retardation and growth retardation in human. However, Rad50 mutations in human and other organisms have never been gathered and heuristically compared for their deleterious effects. It is important to assess the conserved region in Rad50 and its homolog to identify vital mutations that can affect functions of the protein. Method In this study, Rad50 mutations were retrieved from SNPeffect 4.0 database and literature. Each of the mutations was analyzed using various bioinformatic analyses such as PredictSNP, MutPred, SNPeffect 4.0, I-Mutant and MuPro to identify its impact on molecular mechanism, biological function and protein stability, respectively. Results We identified 103 mostly occurred mutations in the Rad50 protein domains and motifs, which only 42 mutations were classified as most deleterious. These mutations are mainly situated at the specific motifs such as Walker A, Q-loop, Walker B, D-loop and signature motif of the Rad50 protein. Some of these mutations were predicted to negatively affect several important functional sites that play important roles in DNA repair mechanism and cell cycle signaling pathway, highlighting Rad50 crucial role in this process. Interestingly, mutations located at non-conserved regions were predicted to have neutral/non-damaging effects, in contrast with previous experimental studies that showed deleterious effects. This suggests that software used in this study may have limitations in predicting mutations in non-conserved regions, implying further improvement in their algorithm is needed. In conclusion, this study reveals the priority of acid substitution associated with the genetic disorders. This finding highlights the vital roles of certain residues such as K42E, C681A/S, CC684…
format: application/pdf
format: text/html
creator: Juwairiah Remali
creator: Wan Mohd Aizat
creator: Chyan Leong Ng
creator: Yi Chieh Lim
creator: Zeti-Azura Mohamed-Hussein
creator: Shazrul Fazry
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.9197
publisher: PeerJ Inc.
rights: © 2020 Remali et al.
abstract: Background DNA double strand break repair is important to preserve the fidelity of our genetic makeup after DNA damage. Rad50 is one of the components in MRN complex important for DNA repair mechanism. Rad50 mutations can lead to microcephaly, mental retardation and growth retardation in human. However, Rad50 mutations in human and other organisms have never been gathered and heuristically compared for their deleterious effects. It is important to assess the conserved region in Rad50 and its homolog to identify vital mutations that can affect functions of the protein. Method In this study, Rad50 mutations were retrieved from SNPeffect 4.0 database and literature. Each of the mutations was analyzed using various bioinformatic analyses such as PredictSNP, MutPred, SNPeffect 4.0, I-Mutant and MuPro to identify its impact on molecular mechanism, biological function and protein stability, respectively. Results We identified 103 mostly occurred mutations in the Rad50 protein domains and motifs, which only 42 mutations were classified as most deleterious. These mutations are mainly situated at the specific motifs such as Walker A, Q-loop, Walker B, D-loop and signature motif of the Rad50 protein. Some of these mutations were predicted to negatively affect several important functional sites that play important roles in DNA repair mechanism and cell cycle signaling pathway, highlighting Rad50 crucial role in this process. Interestingly, mutations located at non-conserved regions were predicted to have neutral/non-damaging effects, in contrast with previous experimental studies that showed deleterious effects. This suggests that software used in this study may have limitations in predicting mutations in non-conserved regions, implying further improvement in their algorithm is needed. In conclusion, this study reveals the priority of acid substitution associated with the genetic disorders. This finding highlights the vital roles of certain residues such as K42E, C681A/S, CC684…
bibliographic citation: Remali et al. (2020) In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair. PeerJ 8:e9197 https://doi.org/10.7717/peerj.9197
date submitted: 2019-04-28
date accepted: 2020-04-24
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Remali
  given name: Juwairiah
author list: Agent
  family name: Aizat
  given name: Wan Mohd
author list: Agent
  family name: Ng
  given name: Chyan Leong
author list: Agent
  family name: Lim
  given name: Yi Chieh
author list: Agent
  family name: Mohamed-Hussein
  given name: Zeti-Azura
author list: Agent
  family name: Fazry
  given name: Shazrul
doi: 10.7717/peerj.9197
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: © 2020 Remali et al.
attribution name: Remali et al.

Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns
type: item
type: AcademicArticle
description: Background Human milk microbiota plays a role in the bacterial colonization of the neonatal gut, which has important consequences in the health and development of the newborn. However, there are few studies about the vertical transfer of bacteria from mother to infant in Latin American populations. Methods We performed a cross-sectional study characterizing the bacterial diversity of 67 human milk-neonatal stool pairs by high-throughput sequencing of V3-16S rDNA libraries, to assess the effect of the human milk microbiota on the bacterial composition of the neonate’s gut at early days. Results Human milk showed higher microbial diversity as compared to the neonatal stool. Members of the Staphylococcaceae and Sphingomonadaceae families were more prevalent in human milk, whereas the Pseudomonadaceae family, Clostridium and Bifidobacterium genera were in the neonatal stool. The delivery mode showed association with the neonatal gut microbiota diversity, but not with the human milk microbiota diversity; for instance, neonates born by C-section showed greater richness and diversity in stool microbiota than those born vaginally. We found 25 bacterial taxa shared by both ecosystems and 67.7% of bacteria found in neonate stool were predicted to originate from human milk. This study contributes to the knowledge of human milk and neonatal stool microbiota in healthy Mexican population and supports the idea of vertical mother-neonate transmission through exclusive breastfeeding.
format: application/pdf
format: text/html
creator: Karina Corona-Cervantes
creator: Igrid García-González
creator: Loan Edel Villalobos-Flores
creator: Fernando Hernández-Quiroz
creator: Alberto Piña-Escobedo
creator: Carlos Hoyo-Vadillo
creator: Martín Noé Rangel-Calvillo
creator: Jaime García-Mena
subject: Bioinformatics
subject: Microbiology
subject: Pediatrics
description: doi:10.7717/peerj.9205
publisher: PeerJ Inc.
rights: © 2020 Corona-Cervantes et al.
abstract: Background Human milk microbiota plays a role in the bacterial colonization of the neonatal gut, which has important consequences in the health and development of the newborn. However, there are few studies about the vertical transfer of bacteria from mother to infant in Latin American populations. Methods We performed a cross-sectional study characterizing the bacterial diversity of 67 human milk-neonatal stool pairs by high-throughput sequencing of V3-16S rDNA libraries, to assess the effect of the human milk microbiota on the bacterial composition of the neonate’s gut at early days. Results Human milk showed higher microbial diversity as compared to the neonatal stool. Members of the Staphylococcaceae and Sphingomonadaceae families were more prevalent in human milk, whereas the Pseudomonadaceae family, Clostridium and Bifidobacterium genera were in the neonatal stool. The delivery mode showed association with the neonatal gut microbiota diversity, but not with the human milk microbiota diversity; for instance, neonates born by C-section showed greater richness and diversity in stool microbiota than those born vaginally. We found 25 bacterial taxa shared by both ecosystems and 67.7% of bacteria found in neonate stool were predicted to originate from human milk. This study contributes to the knowledge of human milk and neonatal stool microbiota in healthy Mexican population and supports the idea of vertical mother-neonate transmission through exclusive breastfeeding.
bibliographic citation: Corona-Cervantes et al. (2020) Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns. PeerJ 8:e9205 https://doi.org/10.7717/peerj.9205
date submitted: 2019-12-04
date accepted: 2020-04-25
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Corona-Cervantes
  given name: Karina
author list: Agent
  family name: García-González
  given name: Igrid
author list: Agent
  family name: Villalobos-Flores
  given name: Loan Edel
author list: Agent
  family name: Hernández-Quiroz
  given name: Fernando
author list: Agent
  family name: Piña-Escobedo
  given name: Alberto
author list: Agent
  family name: Hoyo-Vadillo
  given name: Carlos
author list: Agent
  family name: Rangel-Calvillo
  given name: Martín Noé
author list: Agent
  family name: García-Mena
  given name: Jaime
doi: 10.7717/peerj.9205
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Corona-Cervantes et al.
attribution name: Corona-Cervantes et al.

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