PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation
items: Gene drives as a new quality in GMO releases—a comparative technology characterization
items: Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids
items: Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
items: Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
items: Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task
items: Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio)
items: Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations
items: Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci
items: Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center

Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation
type: item
type: AcademicArticle
description: Ultraviolet radiation can cause many serious problems for all living organisms. With a growing population, the UV sensitivity of crop plants presents a particular problem. To evaluate the suitability of growing in areas under UV irradiance, the influence of different doses of UV-B (3.042, 6.084 and 9.126 kJm−2d−1) on the sugar beet (Beta vulgaris L) plants was studied. UV-B induced a significant decrease in growth displayed as reduced height and fresh and dry weight. This reduction is not dose dependent and was associated with diminishing photosynthetic O2 evolution, relative chlorophyll content, photosynthetic pigments and chlorophyll fluorescence. On the other hand, antioxidant enzyme activities, total protein content, compatible solutes, total free amino acids and total betalain content were increased under 9.126 kJm−2d−1 UV-B treatments, representing mechanisms by which the plants coped with the stress. The oxidative stress upon UV-B treatment was evident by increased malondialdehyde (MDA) content, however, hydrogen peroxide (H2O2) was not affected in UV-B exposed plants. Thus, the studied sugar beet variety BR1seems to be suitable particularly for areas with high doses of UV-B irradiation.
format: application/pdf
format: text/html
creator: Parisa Rahimzadeh Karvansara
creator: Seyed Mehdi Razavi
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6790
publisher: PeerJ Inc.
rights: © 2019 Rahimzadeh Karvansara and Razavi
abstract: Ultraviolet radiation can cause many serious problems for all living organisms. With a growing population, the UV sensitivity of crop plants presents a particular problem. To evaluate the suitability of growing in areas under UV irradiance, the influence of different doses of UV-B (3.042, 6.084 and 9.126 kJm−2d−1) on the sugar beet (Beta vulgaris L) plants was studied. UV-B induced a significant decrease in growth displayed as reduced height and fresh and dry weight. This reduction is not dose dependent and was associated with diminishing photosynthetic O2 evolution, relative chlorophyll content, photosynthetic pigments and chlorophyll fluorescence. On the other hand, antioxidant enzyme activities, total protein content, compatible solutes, total free amino acids and total betalain content were increased under 9.126 kJm−2d−1 UV-B treatments, representing mechanisms by which the plants coped with the stress. The oxidative stress upon UV-B treatment was evident by increased malondialdehyde (MDA) content, however, hydrogen peroxide (H2O2) was not affected in UV-B exposed plants. Thus, the studied sugar beet variety BR1seems to be suitable particularly for areas with high doses of UV-B irradiation.
bibliographic citation: Rahimzadeh Karvansara et al. (2019) Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation. PeerJ 7:e6790 https://doi.org/10.7717/peerj.6790
date submitted: 2018-12-02
date accepted: 2019-03-12
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahimzadeh Karvansara
  given name: Parisa
author list: Agent
  family name: Razavi
  given name: Seyed Mehdi
doi: 10.7717/peerj.6790
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Rahimzadeh Karvansara and Razavi
attribution name: Rahimzadeh Karvansara and Razavi

Gene drives as a new quality in GMO releases—a comparative technology characterization
type: item
type: AcademicArticle
description: Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits—the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations.
format: application/pdf
format: text/html
creator: Johannes L. Frieß
creator: Arnim von Gleich
creator: Bernd Giese
subject: Biotechnology
subject: Ecology
subject: Genetics
subject: Coupled Natural and Human Systems
subject: Population Biology
description: doi:10.7717/peerj.6793
publisher: PeerJ Inc.
rights: © 2019 Frieß et al.
abstract: Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits—the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations.
bibliographic citation: Frieß et al. (2019) Gene drives as a new quality in GMO releases—a comparative technology characterization. PeerJ 7:e6793 https://doi.org/10.7717/peerj.6793
date submitted: 2018-11-28
date accepted: 2019-03-15
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frieß
  given name: Johannes L.
author list: Agent
  family name: von Gleich
  given name: Arnim
author list: Agent
  family name: Giese
  given name: Bernd
doi: 10.7717/peerj.6793
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Frieß et al.
attribution name: Frieß et al.

Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids
type: item
type: AcademicArticle
description: Background Feeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama. Methods Our approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents. Results We find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores.
format: application/pdf
format: text/html
creator: Laurel B. Symes
creator: Nicole L. Wershoven
creator: Lars-Olaf Hoeger
creator: Jessica S. Ralston
creator: Sharon J. Martinson
creator: Hannah M. ter Hofstede
creator: Christine M. Palmer
subject: Ecology
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.6808
publisher: PeerJ Inc.
rights: © 2019 Symes et al.
abstract: Background Feeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama. Methods Our approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents. Results We find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores.
bibliographic citation: Symes et al. (2019) Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids. PeerJ 7:e6808 https://doi.org/10.7717/peerj.6808
date submitted: 2019-01-07
date accepted: 2019-03-18
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Symes
  given name: Laurel B.
author list: Agent
  family name: Wershoven
  given name: Nicole L.
author list: Agent
  family name: Hoeger
  given name: Lars-Olaf
author list: Agent
  family name: Ralston
  given name: Jessica S.
author list: Agent
  family name: Martinson
  given name: Sharon J.
author list: Agent
  family name: ter Hofstede
  given name: Hannah M.
author list: Agent
  family name: Palmer
  given name: Christine M.
doi: 10.7717/peerj.6808
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Symes et al.
attribution name: Symes et al.

Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
type: item
type: AcademicArticle
description: Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
format: application/pdf
format: text/html
creator: Eric Gonzalez-Segovia
creator: Sergio Pérez-Limon
creator: G. Carolina Cíntora-Martínez
creator: Alejandro Guerrero-Zavala
creator: Garrett M. Janzen
creator: Matthew B. Hufford
creator: Jeffrey Ross-Ibarra
creator: Ruairidh J. H. Sawers
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6815
publisher: PeerJ Inc.
rights: © 2019 Gonzalez-Segovia et al.
abstract: Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
bibliographic citation: Gonzalez-Segovia et al. (2019) Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize. PeerJ 7:e6815 https://doi.org/10.7717/peerj.6815
date submitted: 2019-01-15
date accepted: 2019-03-19
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzalez-Segovia
  given name: Eric
author list: Agent
  family name: Pérez-Limon
  given name: Sergio
author list: Agent
  family name: Cíntora-Martínez
  given name: G. Carolina
author list: Agent
  family name: Guerrero-Zavala
  given name: Alejandro
author list: Agent
  family name: Janzen
  given name: Garrett M.
author list: Agent
  family name: Hufford
  given name: Matthew B.
author list: Agent
  family name: Ross-Ibarra
  given name: Jeffrey
author list: Agent
  family name: Sawers
  given name: Ruairidh J. H.
doi: 10.7717/peerj.6815
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Gonzalez-Segovia et al.
attribution name: Gonzalez-Segovia et al.

Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
type: item
type: AcademicArticle
description: In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley.
format: application/pdf
format: text/html
creator: Jie Li
creator: Xinhao Liu
subject: Agricultural Science
subject: Bioinformatics
description: doi:10.7717/peerj.6832
publisher: PeerJ Inc.
rights: © 2019 Li and Liu
abstract: In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley.
bibliographic citation: Li et al. (2019) Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.). PeerJ 7:e6832 https://doi.org/10.7717/peerj.6832
date submitted: 2018-12-31
date accepted: 2019-03-22
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Liu
  given name: Xinhao
doi: 10.7717/peerj.6832
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Li and Liu
attribution name: Li and Liu

Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task
type: item
type: AcademicArticle
description: Background Cognitive processes are required during walking to appropriately respond to environmental and task demands. There are now many studies that have used functional Near-Infrared Spectroscopy (fNIRS) to record brain activation to investigate neural bases of cognitive contributions in gait. The aim of this systematic review was to summarize the published research regarding Prefrontal cortical (PFC) activation patterns during simple and complex walking tasks in young adults, older adults and clinical groups with balance disorders using fNIRS. Our secondary aim was to evaluate each included study based on methodological reporting criteria important for good data quality. Methods We conducted searches in June 2018 using four databases: Embase, PubMed, Scopus and PsycINFO. The strategy search used was: (((((near infrared spectroscopy) OR functional near infrared spectroscopy) OR nirs) OR fnirs) AND (((gait) OR walking) OR locomotion) AND (((((young) OR adult) OR older) OR elderly) NOT children)) AND (((Brain) OR cortex) OR cortical) for our search. The papers included met the specific review criteria: (i) used fNIRS to measure PFC activation patterns; (ii) included walking tasks (simple and complex) and; (iii) assessed young people, older people and/or clinical groups with balance disorders. Results Thirty five (describing 75 brain activation comparisons) of the 308 studies retrieved through our search met the inclusion criteria. Based on 6 methodological reporting considerations, 20 were of high quality, 10 were of medium quality and 5 were of low quality. Eleven/20 comparisons in young people, 23/37 comparisons in older people and 15/18 comparisons in clinical groups reported increased PFC activation with increased walking task complexity. The majority of comparisons that used verbal fluency, counting backwards or secondary motor tasks reported increases in PFC activation (83%, 64% and 58% of these studies, respectively). In contrast, no studies found secondary …
format: application/pdf
format: text/html
creator: Paulo H.S. Pelicioni
creator: Mylou Tijsma
creator: Stephen R. Lord
creator: Jasmine Menant
subject: Bioengineering
subject: Neuroscience
subject: Cognitive Disorders
subject: Geriatrics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.6833
publisher: PeerJ Inc.
rights: © 2019 Pelicioni et al.
abstract: Background Cognitive processes are required during walking to appropriately respond to environmental and task demands. There are now many studies that have used functional Near-Infrared Spectroscopy (fNIRS) to record brain activation to investigate neural bases of cognitive contributions in gait. The aim of this systematic review was to summarize the published research regarding Prefrontal cortical (PFC) activation patterns during simple and complex walking tasks in young adults, older adults and clinical groups with balance disorders using fNIRS. Our secondary aim was to evaluate each included study based on methodological reporting criteria important for good data quality. Methods We conducted searches in June 2018 using four databases: Embase, PubMed, Scopus and PsycINFO. The strategy search used was: (((((near infrared spectroscopy) OR functional near infrared spectroscopy) OR nirs) OR fnirs) AND (((gait) OR walking) OR locomotion) AND (((((young) OR adult) OR older) OR elderly) NOT children)) AND (((Brain) OR cortex) OR cortical) for our search. The papers included met the specific review criteria: (i) used fNIRS to measure PFC activation patterns; (ii) included walking tasks (simple and complex) and; (iii) assessed young people, older people and/or clinical groups with balance disorders. Results Thirty five (describing 75 brain activation comparisons) of the 308 studies retrieved through our search met the inclusion criteria. Based on 6 methodological reporting considerations, 20 were of high quality, 10 were of medium quality and 5 were of low quality. Eleven/20 comparisons in young people, 23/37 comparisons in older people and 15/18 comparisons in clinical groups reported increased PFC activation with increased walking task complexity. The majority of comparisons that used verbal fluency, counting backwards or secondary motor tasks reported increases in PFC activation (83%, 64% and 58% of these studies, respectively). In contrast, no studies found secondary …
bibliographic citation: Pelicioni et al. (2019) Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task. PeerJ 7:e6833 https://doi.org/10.7717/peerj.6833
date submitted: 2018-12-03
date accepted: 2019-03-22
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pelicioni
  given name: Paulo H.S.
author list: Agent
  family name: Tijsma
  given name: Mylou
author list: Agent
  family name: Lord
  given name: Stephen R.
author list: Agent
  family name: Menant
  given name: Jasmine
doi: 10.7717/peerj.6833
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Pelicioni et al.
attribution name: Pelicioni et al.

Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio)
type: item
type: AcademicArticle
description: We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca2+/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
format: application/pdf
format: text/html
creator: Matthew Tuttle
creator: Mark R. Dalman
creator: Qin Liu
creator: Richard L. Londraville
subject: Evolutionary Studies
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6848
publisher: PeerJ Inc.
rights: © 2019 Tuttle et al.
abstract: We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca2+/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
bibliographic citation: Tuttle et al. (2019) Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio). PeerJ 7:e6848 https://doi.org/10.7717/peerj.6848
date submitted: 2018-12-07
date accepted: 2019-03-26
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tuttle
  given name: Matthew
author list: Agent
  family name: Dalman
  given name: Mark R.
author list: Agent
  family name: Liu
  given name: Qin
author list: Agent
  family name: Londraville
  given name: Richard L.
doi: 10.7717/peerj.6848
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Tuttle et al.
attribution name: Tuttle et al.

Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations
type: item
type: AcademicArticle
description: Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.
format: application/pdf
format: text/html
creator: Weian Du
creator: Chunlei Feng
creator: Ting Yao
creator: Cheng Xiao
creator: Hongyan Huang
creator: Weibin Wu
creator: Linnan Zhu
creator: Honghua Qiao
creator: Chao Liu
creator: Ling Chen
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.6861
publisher: PeerJ Inc.
rights: © 2019 Du et al.
abstract: Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.
bibliographic citation: Du et al. (2019) Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations. PeerJ 7:e6861 https://doi.org/10.7717/peerj.6861
date submitted: 2018-09-14
date accepted: 2019-03-28
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Weian
author list: Agent
  family name: Feng
  given name: Chunlei
author list: Agent
  family name: Yao
  given name: Ting
author list: Agent
  family name: Xiao
  given name: Cheng
author list: Agent
  family name: Huang
  given name: Hongyan
author list: Agent
  family name: Wu
  given name: Weibin
author list: Agent
  family name: Zhu
  given name: Linnan
author list: Agent
  family name: Qiao
  given name: Honghua
author list: Agent
  family name: Liu
  given name: Chao
author list: Agent
  family name: Chen
  given name: Ling
doi: 10.7717/peerj.6861
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Du et al.
attribution name: Du et al.

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci
type: item
type: AcademicArticle
description: The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.
format: application/pdf
format: text/html
creator: Marshal Hedin
creator: Shahan Derkarabetian
creator: Adan Alfaro
creator: Martín J. Ramírez
creator: Jason E. Bond
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.6864
publisher: PeerJ Inc.
rights: © 2019 Hedin et al.
abstract: The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.
bibliographic citation: Hedin et al. (2019) Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci. PeerJ 7:e6864 https://doi.org/10.7717/peerj.6864
date submitted: 2019-02-01
date accepted: 2019-03-28
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hedin
  given name: Marshal
author list: Agent
  family name: Derkarabetian
  given name: Shahan
author list: Agent
  family name: Alfaro
  given name: Adan
author list: Agent
  family name: Ramírez
  given name: Martín J.
author list: Agent
  family name: Bond
  given name: Jason E.
doi: 10.7717/peerj.6864
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Hedin et al.
attribution name: Hedin et al.

Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center
type: item
type: AcademicArticle
description: Background The objective of this study is to investigate small cell neuroendocrine carcinoma of the cervix (SCCC), using a retrospective clinicopathological characteristic and treatment approach. Method We retrospectively analyzed cases of early-stage SCCC, identified between 2006 and 2016, in women who received radical surgery and adjuvant chemotherapy with or without radiotherapy. Kaplan–Meier and one-way ANOVA analyses were performed. Result A total of 37 cases of SCCC are presented in this study, of which 21 had stage IB1 SCCC, 12 had stage IB2, 3 had stage IIA1, and 1 had stage IIA2. All patients were treated with radical surgery and adjuvant chemotherapy, specifically, 26 with radical surgery followed by adjuvant chemotherapy plus radiation and 11 with neoadjuvant chemotherapy (NACT) followed by radical surgery. After a median follow-up time of 27 months (range, 8–115 months), the 2-year and 5-year disease-free survival rate for all patients was 51.9% and 34.1%, respectively, and the overall survival rate was 60.3% and 38.6%, respectively. Univariate analysis showed that International Federation of Gynecology and Obstetrics (FIGO) stage and tumor size may be a predictor of a poor prognosis. NACT and adjuvant radiation did not improve survival over adjuvant chemotherapy alone but should not be a significant independent prognostic factor for survival. Conclusion Even in patients with early-stage SCCC, the prognosis is poor, although FIGO stage and tumor size may act as surrogate factors prognostic of survival.
format: application/pdf
format: text/html
creator: Dandan Zhang
creator: Xiaoxin Ma
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.6868
publisher: PeerJ Inc.
rights: © 2019 Zhang and Ma
abstract: Background The objective of this study is to investigate small cell neuroendocrine carcinoma of the cervix (SCCC), using a retrospective clinicopathological characteristic and treatment approach. Method We retrospectively analyzed cases of early-stage SCCC, identified between 2006 and 2016, in women who received radical surgery and adjuvant chemotherapy with or without radiotherapy. Kaplan–Meier and one-way ANOVA analyses were performed. Result A total of 37 cases of SCCC are presented in this study, of which 21 had stage IB1 SCCC, 12 had stage IB2, 3 had stage IIA1, and 1 had stage IIA2. All patients were treated with radical surgery and adjuvant chemotherapy, specifically, 26 with radical surgery followed by adjuvant chemotherapy plus radiation and 11 with neoadjuvant chemotherapy (NACT) followed by radical surgery. After a median follow-up time of 27 months (range, 8–115 months), the 2-year and 5-year disease-free survival rate for all patients was 51.9% and 34.1%, respectively, and the overall survival rate was 60.3% and 38.6%, respectively. Univariate analysis showed that International Federation of Gynecology and Obstetrics (FIGO) stage and tumor size may be a predictor of a poor prognosis. NACT and adjuvant radiation did not improve survival over adjuvant chemotherapy alone but should not be a significant independent prognostic factor for survival. Conclusion Even in patients with early-stage SCCC, the prognosis is poor, although FIGO stage and tumor size may act as surrogate factors prognostic of survival.
bibliographic citation: Zhang et al. (2019) Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center. PeerJ 7:e6868 https://doi.org/10.7717/peerj.6868
date submitted: 2018-11-15
date accepted: 2019-03-29
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Dandan
author list: Agent
  family name: Ma
  given name: Xiaoxin
doi: 10.7717/peerj.6868
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Zhang and Ma
attribution name: Zhang and Ma

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