PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: A within-subject comparison of different relaxation therapies in eliciting physiological and psychological changes in young women
items: Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes
items: VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo

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.

A within-subject comparison of different relaxation therapies in eliciting physiological and psychological changes in young women
type: item
type: AcademicArticle
description: Background Stress reactivity can be different in women compared to men, which might consequently influence disease risk.Stress in women may also generate adverse physiological effects on their offspring during pregnancy or lactation. The objective of this study was to compare the effects of different relaxation interventions on physiological outcomes and perceived relaxation in healthy young women, to assist in identifying the most appropriate intervention(s) for use in a subsequent trial for mothers who deliver prematurely. Methods A within-subject study was conducted in 17 women of reproductive age comparing five different relaxation interventions (guided-imagery meditation audio (GIM), music listening (ML), relaxation lighting (RL), GIM+RL, ML+RL), with control (silence/sitting), assigned in random order over a 3–6 week period. Subjective feelings of relaxation (10-point scale), heart rate (HR), systolic and diastolic blood pressure (SBP, DBP), and fingertip temperature (FT) were measured before and after each technique Results All interventions significantly increased perceived relaxation and FT, while music also significantly reduced SBP (p < 0.05). Compared to control, HR significantly decreased following GIM (mean difference = 3.2 bpm, p < 0.05), and FT increased (mean difference = 2.2 °C, p < 0.05) and SBP decreased (mean difference = 3.3 mmHg, p < 0.01) following ML. GIM + RL followed by GIM were the most preferred interventions. Conclusions Based on preference, simplicity, and the physiological and psychological effects, GIM and ML were identified as the most effective tools for reducing stress and improving relaxation. These techniques warrant further research in larger samples and other populations.
format: application/pdf
format: text/html
creator: Sarah Dib
creator: Jonathan C.K. Wells
creator: Mary Fewtrell
subject: Clinical Trials
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.9217
publisher: PeerJ Inc.
rights: © 2020 Dib et al.
abstract: Background Stress reactivity can be different in women compared to men, which might consequently influence disease risk.Stress in women may also generate adverse physiological effects on their offspring during pregnancy or lactation. The objective of this study was to compare the effects of different relaxation interventions on physiological outcomes and perceived relaxation in healthy young women, to assist in identifying the most appropriate intervention(s) for use in a subsequent trial for mothers who deliver prematurely. Methods A within-subject study was conducted in 17 women of reproductive age comparing five different relaxation interventions (guided-imagery meditation audio (GIM), music listening (ML), relaxation lighting (RL), GIM+RL, ML+RL), with control (silence/sitting), assigned in random order over a 3–6 week period. Subjective feelings of relaxation (10-point scale), heart rate (HR), systolic and diastolic blood pressure (SBP, DBP), and fingertip temperature (FT) were measured before and after each technique Results All interventions significantly increased perceived relaxation and FT, while music also significantly reduced SBP (p < 0.05). Compared to control, HR significantly decreased following GIM (mean difference = 3.2 bpm, p < 0.05), and FT increased (mean difference = 2.2 °C, p < 0.05) and SBP decreased (mean difference = 3.3 mmHg, p < 0.01) following ML. GIM + RL followed by GIM were the most preferred interventions. Conclusions Based on preference, simplicity, and the physiological and psychological effects, GIM and ML were identified as the most effective tools for reducing stress and improving relaxation. These techniques warrant further research in larger samples and other populations.
bibliographic citation: Dib et al. (2020) A within-subject comparison of different relaxation therapies in eliciting physiological and psychological changes in young women. PeerJ 8:e9217 https://doi.org/10.7717/peerj.9217
date submitted: 2019-09-18
date accepted: 2020-04-28
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dib
  given name: Sarah
author list: Agent
  family name: Wells
  given name: Jonathan C.K.
author list: Agent
  family name: Fewtrell
  given name: Mary
doi: 10.7717/peerj.9217
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Dib et al.
attribution name: Dib et al.

Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes
type: item
type: AcademicArticle
description: Introduction Retinoblastoma (RB) is one common pediatric malignant tumor with dismal outcomes. Heterogeneity of RB and subtypes of RB were identified but the association between the subtypes of RB and RB progression have not been fully investigated. Methods Four public datasets were downloaded from Gene expression omnibus and normalization was performed to remove batch effect. Two public datasets were explored to obtain the RB progression gene signatures by differentially expression analysis while another two datasets were iterated for RB subtypes identification using consensus clustering. After the RB progressive subtype gene signatures were identified, we tested the diagnostic capacity of these gene signatures by receiver operation curve. Results Three hundreds and forty six genes that were enriched in cell cycle were identified as the progression signature in RB from two independent datasets. Four subtypes of RB were stratified by consensus clustering. A total of 21 genes from RB progression signature were differentially expressed between RB subtypes. One subtype with low expression cell division genes have less progression of all four subtypes. A panel of five RB subtype genes (CLUL1, CNGB1, ROM1, LRRC39 and RDH12) predict progression of RB. Conclusion Retinoblastoma is a highly heterogeneous tumor and the level of cell cycle related gene expression is associated with RB progression. A subpopulation of RB with high expression of visual perception has less progressive features. LRRC39 is potentially the RB progression subtype biomarker.
format: application/pdf
format: text/html
creator: Manjing Cao
creator: Sha Wang
creator: Jing Zou
creator: Wanpeng Wang
subject: Bioinformatics
subject: Ophthalmology
description: doi:10.7717/peerj.8873
publisher: PeerJ Inc.
rights: © 2020 Cao et al.
abstract: Introduction Retinoblastoma (RB) is one common pediatric malignant tumor with dismal outcomes. Heterogeneity of RB and subtypes of RB were identified but the association between the subtypes of RB and RB progression have not been fully investigated. Methods Four public datasets were downloaded from Gene expression omnibus and normalization was performed to remove batch effect. Two public datasets were explored to obtain the RB progression gene signatures by differentially expression analysis while another two datasets were iterated for RB subtypes identification using consensus clustering. After the RB progressive subtype gene signatures were identified, we tested the diagnostic capacity of these gene signatures by receiver operation curve. Results Three hundreds and forty six genes that were enriched in cell cycle were identified as the progression signature in RB from two independent datasets. Four subtypes of RB were stratified by consensus clustering. A total of 21 genes from RB progression signature were differentially expressed between RB subtypes. One subtype with low expression cell division genes have less progression of all four subtypes. A panel of five RB subtype genes (CLUL1, CNGB1, ROM1, LRRC39 and RDH12) predict progression of RB. Conclusion Retinoblastoma is a highly heterogeneous tumor and the level of cell cycle related gene expression is associated with RB progression. A subpopulation of RB with high expression of visual perception has less progressive features. LRRC39 is potentially the RB progression subtype biomarker.
bibliographic citation: Cao et al. (2020) Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes. PeerJ 8:e8873 https://doi.org/10.7717/peerj.8873
date submitted: 2019-08-05
date accepted: 2020-03-09
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Manjing
author list: Agent
  family name: Wang
  given name: Sha
author list: Agent
  family name: Zou
  given name: Jing
author list: Agent
  family name: Wang
  given name: Wanpeng
doi: 10.7717/peerj.8873
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Cao et al.
attribution name: Cao et al.

VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
type: item
type: AcademicArticle
description: Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”.
format: application/pdf
format: text/html
creator: Priyansh Srivastava
creator: Alakto Choudhury
creator: Mehak Talwar
creator: Sabyasachi Mohanty
creator: Priyanka Narad
creator: Abhishek Sengupta
subject: Bioinformatics
subject: Computational Biology
subject: Dermatology
subject: Computational Science
description: doi:10.7717/peerj.9119
publisher: PeerJ Inc.
rights: © 2020 Srivastava et al.
abstract: Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”.
bibliographic citation: Srivastava et al. (2020) VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo. PeerJ 8:e9119 https://doi.org/10.7717/peerj.9119
date submitted: 2020-01-02
date accepted: 2020-04-13
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Srivastava
  given name: Priyansh
author list: Agent
  family name: Choudhury
  given name: Alakto
author list: Agent
  family name: Talwar
  given name: Mehak
author list: Agent
  family name: Mohanty
  given name: Sabyasachi
author list: Agent
  family name: Narad
  given name: Priyanka
author list: Agent
  family name: Sengupta
  given name: Abhishek
doi: 10.7717/peerj.9119
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Srivastava et al.
attribution name: Srivastava et al.

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