PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages
items: Increasing evidence that bats actively forage at wind turbines
items: Carbohydrates digestion and metabolism in the spiny lobster (Panulirus argus): biochemical indication for limited carbohydrate utilization
items: New species of the endemic Neotropical caddisfly genus Contulma from the Andes of Ecuador (Trichoptera: Anomalopsychidae)
items: Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India
items: Revisiting the tryptophan-serotonin deficiency and the inflammatory hypotheses of major depression in a biopsychosocial approach
items: Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
items: Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry
items: Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar)
items: Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands)

Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages
type: item
type: AcademicArticle
description: Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU) was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter, Propionigenium, Synechococcus, Shewanella and Cetobacterium. Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage-specific community i…
format: application/pdf
format: text/html
creator: Shenzheng Zeng
creator: Zhijian Huang
creator: Dongwei Hou
creator: Jian Liu
creator: Shaoping Weng
creator: Jianguo He
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
description: doi:10.7717/peerj.3986
publisher: PeerJ Inc.
rights: © 2017 Zeng et al.
abstract: Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU) was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter, Propionigenium, Synechococcus, Shewanella and Cetobacterium. Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage-specific community i…
bibliographic citation: Zeng et al. (2017) Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages. PeerJ 5:e3986 https://doi.org/10.7717/peerj.3986
date submitted: 2017-06-28
date accepted: 2017-10-12
issued: 2017-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Shenzheng
author list: Agent
  family name: Huang
  given name: Zhijian
author list: Agent
  family name: Hou
  given name: Dongwei
author list: Agent
  family name: Liu
  given name: Jian
author list: Agent
  family name: Weng
  given name: Shaoping
author list: Agent
  family name: He
  given name: Jianguo
doi: 10.7717/peerj.3986
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-06
copyright: ©2017 Zeng et al.
attribution name: Zeng et al.

Increasing evidence that bats actively forage at wind turbines
type: item
type: AcademicArticle
description: Although the ultimate causes of high bat fatalities at wind farms are not well understood, several lines of evidence suggest that bats are attracted to wind turbines. One hypothesis is that bats would be attracted to turbines as a foraging resource if the insects that bats prey upon are commonly present on and around the turbine towers. To investigate the role that foraging activity may play in bat fatalities, we conducted a series of surveys at a wind farm in the southern Great Plains of the US from 2011–2016. From acoustic monitoring we recorded foraging activity, including feeding buzzes indicative of prey capture, in the immediate vicinity of turbine towers from all six bat species known to be present at this site. From insect surveys we found Lepidoptera, Coleoptera, and Orthoptera in consistently high proportions over several years suggesting that food resources for bats were consistently available at wind turbines. We used DNA barcoding techniques to assess bat diet composition of (1) stomach contents from 47 eastern red bat (Lasiurus borealis) and 24 hoary bat (Lasiurus cinereus) carcasses collected in fatality searches, and (2) fecal pellets from 23 eastern red bats that were found on turbine towers, transformers, and tower doors. We found that the majority of the eastern red bat and hoary bat stomachs, the two bat species most commonly found in fatality searches at this site, were full or partially full, indicating that the bats were likely killed while foraging. Although Lepidoptera and Orthoptera dominated the diets of these two bat species, both consumed a range of prey items with individual bats having from one to six insect species in their stomachs at the time of death. The prey items identified from eastern red bat fecal pellets showed similar results. A comparison of the turbine insect community to the diet analysis results revealed that the most abundant insects at wind turbines, including terrestrial insects such as crickets and several important…
format: application/pdf
format: text/html
creator: Cecily F. Foo
creator: Victoria J. Bennett
creator: Amanda M. Hale
creator: Jennifer M. Korstian
creator: Alison J. Schildt
creator: Dean A. Williams
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Zoology
description: doi:10.7717/peerj.3985
publisher: PeerJ Inc.
rights: © 2017 Foo et al.
abstract: Although the ultimate causes of high bat fatalities at wind farms are not well understood, several lines of evidence suggest that bats are attracted to wind turbines. One hypothesis is that bats would be attracted to turbines as a foraging resource if the insects that bats prey upon are commonly present on and around the turbine towers. To investigate the role that foraging activity may play in bat fatalities, we conducted a series of surveys at a wind farm in the southern Great Plains of the US from 2011–2016. From acoustic monitoring we recorded foraging activity, including feeding buzzes indicative of prey capture, in the immediate vicinity of turbine towers from all six bat species known to be present at this site. From insect surveys we found Lepidoptera, Coleoptera, and Orthoptera in consistently high proportions over several years suggesting that food resources for bats were consistently available at wind turbines. We used DNA barcoding techniques to assess bat diet composition of (1) stomach contents from 47 eastern red bat (Lasiurus borealis) and 24 hoary bat (Lasiurus cinereus) carcasses collected in fatality searches, and (2) fecal pellets from 23 eastern red bats that were found on turbine towers, transformers, and tower doors. We found that the majority of the eastern red bat and hoary bat stomachs, the two bat species most commonly found in fatality searches at this site, were full or partially full, indicating that the bats were likely killed while foraging. Although Lepidoptera and Orthoptera dominated the diets of these two bat species, both consumed a range of prey items with individual bats having from one to six insect species in their stomachs at the time of death. The prey items identified from eastern red bat fecal pellets showed similar results. A comparison of the turbine insect community to the diet analysis results revealed that the most abundant insects at wind turbines, including terrestrial insects such as crickets and several important…
bibliographic citation: Foo et al. (2017) Increasing evidence that bats actively forage at wind turbines. PeerJ 5:e3985 https://doi.org/10.7717/peerj.3985
date submitted: 2017-06-28
date accepted: 2017-10-12
issued: 2017-11-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Foo
  given name: Cecily F.
author list: Agent
  family name: Bennett
  given name: Victoria J.
author list: Agent
  family name: Hale
  given name: Amanda M.
author list: Agent
  family name: Korstian
  given name: Jennifer M.
author list: Agent
  family name: Schildt
  given name: Alison J.
author list: Agent
  family name: Williams
  given name: Dean A.
doi: 10.7717/peerj.3985
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-03
copyright: ©2017 Foo et al.
attribution name: Foo et al.

Carbohydrates digestion and metabolism in the spiny lobster (Panulirus argus): biochemical indication for limited carbohydrate utilization
type: item
type: AcademicArticle
description: As other spiny lobsters, Panulirus argus is supposed to use preferentially proteins and lipids in energy metabolism, while carbohydrates are well digested but poorly utilized. The aim of this study was to evaluate the effect of dietary carbohydrate level on digestion and metabolism in the spiny lobster P. argus. We used complementary methodologies such as post-feeding flux of nutrients and metabolites, as well as measurements of α-amylase expression and activity in the digestive tract. Lobsters readily digested and absorbed carbohydrates with a time-course that is dependent on their content in diet. Lobster showed higher levels of free glucose and stored glycogen in different tissues as the inclusion of wheat flour increased. Modifications in intermediary metabolism revealed a decrease in amino acids catabolism coupled with a higher use of free glucose as carbohydrates rise up to 20%. However, this effect seems to be limited by the metabolic capacity of lobsters to use more than 20% of carbohydrates in diets. Lobsters were not able to tightly regulate α-amylase expression according to dietary carbohydrate level but exhibited a marked difference in secretion of this enzyme into the gut. Results are discussed to highlight the limitations to increasing carbohydrate utilization by lobsters. Further growout trials are needed to link the presented metabolic profiles with phenotypic outcomes.
format: application/pdf
format: text/html
creator: Leandro Rodríguez-Viera
creator: Erick Perera
creator: Vivian Montero-Alejo
creator: Rolando Perdomo-Morales
creator: Tsai García-Galano
creator: Gonzalo Martínez-Rodríguez
creator: Juan M. Mancera
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.3975
publisher: PeerJ Inc.
rights: © 2017 Rodríguez-Viera et al.
abstract: As other spiny lobsters, Panulirus argus is supposed to use preferentially proteins and lipids in energy metabolism, while carbohydrates are well digested but poorly utilized. The aim of this study was to evaluate the effect of dietary carbohydrate level on digestion and metabolism in the spiny lobster P. argus. We used complementary methodologies such as post-feeding flux of nutrients and metabolites, as well as measurements of α-amylase expression and activity in the digestive tract. Lobsters readily digested and absorbed carbohydrates with a time-course that is dependent on their content in diet. Lobster showed higher levels of free glucose and stored glycogen in different tissues as the inclusion of wheat flour increased. Modifications in intermediary metabolism revealed a decrease in amino acids catabolism coupled with a higher use of free glucose as carbohydrates rise up to 20%. However, this effect seems to be limited by the metabolic capacity of lobsters to use more than 20% of carbohydrates in diets. Lobsters were not able to tightly regulate α-amylase expression according to dietary carbohydrate level but exhibited a marked difference in secretion of this enzyme into the gut. Results are discussed to highlight the limitations to increasing carbohydrate utilization by lobsters. Further growout trials are needed to link the presented metabolic profiles with phenotypic outcomes.
bibliographic citation: Rodríguez-Viera et al. (2017) Carbohydrates digestion and metabolism in the spiny lobster (Panulirus argus): biochemical indication for limited carbohydrate utilization. PeerJ 5:e3975 https://doi.org/10.7717/peerj.3975
date submitted: 2017-06-07
date accepted: 2017-10-10
issued: 2017-11-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Viera
  given name: Leandro
author list: Agent
  family name: Perera
  given name: Erick
author list: Agent
  family name: Montero-Alejo
  given name: Vivian
author list: Agent
  family name: Perdomo-Morales
  given name: Rolando
author list: Agent
  family name: García-Galano
  given name: Tsai
author list: Agent
  family name: Martínez-Rodríguez
  given name: Gonzalo
author list: Agent
  family name: Mancera
  given name: Juan M.
doi: 10.7717/peerj.3975
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-03
copyright: ©2017 Rodríguez-Viera et al.
attribution name: Rodríguez-Viera et al.

New species of the endemic Neotropical caddisfly genus Contulma from the Andes of Ecuador (Trichoptera: Anomalopsychidae)
type: item
type: AcademicArticle
description: The genus Contulma Flint (Trichoptera: Anomalopsychidae) is composed mostly of regionally endemic species occurring above 2,000 m, with a few more widespread species and some that are found at lower elevations. Adults of three new species of Contulma are described and illustrated from the Andes of Ecuador, Contulma lina, new species, Contulma quito, new species, and Contulma sangay, new species. These species are similar to previously described species from the region, including C. paluguillensis, C. nevada, and C. lancelolata. New provincial records are provided for C. bacula, C. cataracta, and C. echinata. Contulma duffi Oláh, 2016 is considered a junior, subjective synonym of C. penai, Holzenthal & Flint, 1995. Also, we provide an identification key to males of the 30 Contulma species now known.
format: application/pdf
format: text/html
creator: Ralph W. Holzenthal
creator: Blanca Ríos-Touma
creator: Ernesto Rázuri-Gonzales
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.3967
publisher: PeerJ Inc.
rights: © 2017 Holzenthal et al.
abstract: The genus Contulma Flint (Trichoptera: Anomalopsychidae) is composed mostly of regionally endemic species occurring above 2,000 m, with a few more widespread species and some that are found at lower elevations. Adults of three new species of Contulma are described and illustrated from the Andes of Ecuador, Contulma lina, new species, Contulma quito, new species, and Contulma sangay, new species. These species are similar to previously described species from the region, including C. paluguillensis, C. nevada, and C. lancelolata. New provincial records are provided for C. bacula, C. cataracta, and C. echinata. Contulma duffi Oláh, 2016 is considered a junior, subjective synonym of C. penai, Holzenthal & Flint, 1995. Also, we provide an identification key to males of the 30 Contulma species now known.
bibliographic citation: Holzenthal et al. (2017) New species of the endemic Neotropical caddisfly genus Contulma from the Andes of Ecuador (Trichoptera: Anomalopsychidae). PeerJ 5:e3967 https://doi.org/10.7717/peerj.3967
date submitted: 2017-08-29
date accepted: 2017-10-07
issued: 2017-11-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holzenthal
  given name: Ralph W.
author list: Agent
  family name: Ríos-Touma
  given name: Blanca
author list: Agent
  family name: Rázuri-Gonzales
  given name: Ernesto
doi: 10.7717/peerj.3967
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-03
copyright: ©2017 Holzenthal et al.
attribution name: Holzenthal et al.

Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India
type: item
type: AcademicArticle
description: Background Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals’ ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. Methods We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly’s selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D2 method and the Boyce index. Results There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Bas…
format: application/pdf
format: text/html
creator: Mriganka Shekhar Sarkar
creator: Ramesh Krishnamurthy
creator: Jeyaraj A. Johnson
creator: Subharanjan Sen
creator: Goutam Kumar Saha
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3920
publisher: PeerJ Inc.
rights: © 2017 Sarkar et al.
abstract: Background Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals’ ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. Methods We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly’s selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D2 method and the Boyce index. Results There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Bas…
bibliographic citation: Sarkar et al. (2017) Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India. PeerJ 5:e3920 https://doi.org/10.7717/peerj.3920
date submitted: 2017-05-16
date accepted: 2017-09-22
issued: 2017-11-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarkar
  given name: Mriganka Shekhar
author list: Agent
  family name: Krishnamurthy
  given name: Ramesh
author list: Agent
  family name: Johnson
  given name: Jeyaraj A.
author list: Agent
  family name: Sen
  given name: Subharanjan
author list: Agent
  family name: Saha
  given name: Goutam Kumar
doi: 10.7717/peerj.3920
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-03
copyright: ©2017 Sarkar et al.
attribution name: Sarkar et al.

Revisiting the tryptophan-serotonin deficiency and the inflammatory hypotheses of major depression in a biopsychosocial approach
type: item
type: AcademicArticle
description: Background The aim of this cross-sectional study was to identify important biopsychosocial correlates of major depression. Biological mechanisms, including the inflammatory and the tryptophan-serotonin deficiency hypotheses of major depression, were investigated alongside health-related quality of life, life satisfaction, and social support. Methods The concentrations of plasma tryptophan, plasma kynurenine, plasma kynurenic acid, serum quinolinic acid, and the tryptophan breakdown to kynurenine were determined alongside health-related quality of life (Medical Outcome Study Form, SF-36), life satisfaction (Life Satisfaction Questionnaire, FLZ), and social support (Social Support Survey, SSS) in 71 depressive patients at the time of their in-patient admittance and 48 healthy controls. Results Corresponding with the inflammatory hypothesis of major depression, our study results suggest a tryptophan breakdown to kynurenine in patients with major depression, and depressive patients had a lower concentration of neuroprotective kynurenic acid in comparison to the healthy controls (Mann–Whitney-U: 1315.0; p = 0.046). Contradicting the inflammatory theory, the concentrations of kynurenine (t: −0.945; df = 116; p = 0.347) and quinolinic acid (Mann-Whitney-U: 1376.5; p = 0.076) in depressive patients were not significantly different between depressed and healthy controls. Our findings tend to support the tryptophan-serotonin deficiency hypothesis of major depression, as the deficiency of the serotonin precursor tryptophan in depressive patients (t: −3.931; df = 116; p < 0.001) suggests dysfunction of serotonin neurotransmission. A two-step hierarchical linear regression model showed that low tryptophan concentrations, low social support (SSS), occupational requirements (FLZ), personality traits (FLZ), impaired physical role (SF-36), and impaired vitality (SF-36) predict higher Beck Depression Inventory (BDI-II) scores. Discussion Our study results argue for the validity of a …
format: application/pdf
format: text/html
creator: Andreas Baranyi
creator: Omid Amouzadeh-Ghadikolai
creator: Dirk von Lewinski
creator: Robert J. Breitenecker
creator: Hans-Bernd Rothenhäusler
creator: Christoph Robier
creator: Maria Baranyi
creator: Simon Theokas
creator: Andreas Meinitzer
subject: Immunology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3968
publisher: PeerJ Inc.
rights: © 2017 Baranyi et al.
abstract: Background The aim of this cross-sectional study was to identify important biopsychosocial correlates of major depression. Biological mechanisms, including the inflammatory and the tryptophan-serotonin deficiency hypotheses of major depression, were investigated alongside health-related quality of life, life satisfaction, and social support. Methods The concentrations of plasma tryptophan, plasma kynurenine, plasma kynurenic acid, serum quinolinic acid, and the tryptophan breakdown to kynurenine were determined alongside health-related quality of life (Medical Outcome Study Form, SF-36), life satisfaction (Life Satisfaction Questionnaire, FLZ), and social support (Social Support Survey, SSS) in 71 depressive patients at the time of their in-patient admittance and 48 healthy controls. Results Corresponding with the inflammatory hypothesis of major depression, our study results suggest a tryptophan breakdown to kynurenine in patients with major depression, and depressive patients had a lower concentration of neuroprotective kynurenic acid in comparison to the healthy controls (Mann–Whitney-U: 1315.0; p = 0.046). Contradicting the inflammatory theory, the concentrations of kynurenine (t: −0.945; df = 116; p = 0.347) and quinolinic acid (Mann-Whitney-U: 1376.5; p = 0.076) in depressive patients were not significantly different between depressed and healthy controls. Our findings tend to support the tryptophan-serotonin deficiency hypothesis of major depression, as the deficiency of the serotonin precursor tryptophan in depressive patients (t: −3.931; df = 116; p < 0.001) suggests dysfunction of serotonin neurotransmission. A two-step hierarchical linear regression model showed that low tryptophan concentrations, low social support (SSS), occupational requirements (FLZ), personality traits (FLZ), impaired physical role (SF-36), and impaired vitality (SF-36) predict higher Beck Depression Inventory (BDI-II) scores. Discussion Our study results argue for the validity of a …
bibliographic citation: Baranyi et al. (2017) Revisiting the tryptophan-serotonin deficiency and the inflammatory hypotheses of major depression in a biopsychosocial approach. PeerJ 5:e3968 https://doi.org/10.7717/peerj.3968
date submitted: 2017-04-13
date accepted: 2017-10-08
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baranyi
  given name: Andreas
author list: Agent
  family name: Amouzadeh-Ghadikolai
  given name: Omid
author list: Agent
  family name: von Lewinski
  given name: Dirk
author list: Agent
  family name: Breitenecker
  given name: Robert J.
author list: Agent
  family name: Rothenhäusler
  given name: Hans-Bernd
author list: Agent
  family name: Robier
  given name: Christoph
author list: Agent
  family name: Baranyi
  given name: Maria
author list: Agent
  family name: Theokas
  given name: Simon
author list: Agent
  family name: Meinitzer
  given name: Andreas
doi: 10.7717/peerj.3968
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Baranyi et al.
attribution name: Baranyi et al.

Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
type: item
type: AcademicArticle
description: Extensive and in-depth investigations of high-altitude adaptation have been carried out at the level of morphology, anatomy, physiology and genomics, but few investigations focused on the roles of microRNA (miRNA) in high-altitude adaptation. We examined the differences in the miRNA transcriptomes of two representative hypoxia-sensitive tissues (heart and lung) between yak and cattle, two closely related species that live in high and low altitudes, respectively. In this study, we identified a total of 808 mature miRNAs, which corresponded to 715 pre-miRNAs in the two species. The further analysis revealed that both tissues showed relatively high correlation coefficient between yak and cattle, but a greater differentiation was present in lung than heart between the two species. In addition, miRNAs with significantly differentiated patterns of expression in two tissues exhibited co-operation effect in high altitude adaptation based on miRNA family and cluster. Functional analysis revealed that differentially expressed miRNAs were enriched in hypoxia-related pathways, such as the HIF-1α signaling pathway, the insulin signaling pathway, the PI3K-Akt signaling pathway, nucleotide excision repair, cell cycle, apoptosis and fatty acid metabolism, which indicated the important roles of miRNAs in high altitude adaptation. These results suggested the diverse degrees of miRNA transcriptome variation in different tissues between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation.
format: application/pdf
format: text/html
creator: Jiuqiang Guan
creator: Keren Long
creator: Jideng Ma
creator: Jinwei Zhang
creator: Dafang He
creator: Long Jin
creator: Qianzi Tang
creator: Anan Jiang
creator: Xun Wang
creator: Yaodong Hu
creator: Shilin Tian
creator: Zhi Jiang
creator: Mingzhou Li
creator: Xiaolin Luo
subject: Agricultural Science
subject: Biodiversity
subject: Molecular Biology
description: doi:10.7717/peerj.3959
publisher: PeerJ Inc.
rights: © 2017 Guan et al.
abstract: Extensive and in-depth investigations of high-altitude adaptation have been carried out at the level of morphology, anatomy, physiology and genomics, but few investigations focused on the roles of microRNA (miRNA) in high-altitude adaptation. We examined the differences in the miRNA transcriptomes of two representative hypoxia-sensitive tissues (heart and lung) between yak and cattle, two closely related species that live in high and low altitudes, respectively. In this study, we identified a total of 808 mature miRNAs, which corresponded to 715 pre-miRNAs in the two species. The further analysis revealed that both tissues showed relatively high correlation coefficient between yak and cattle, but a greater differentiation was present in lung than heart between the two species. In addition, miRNAs with significantly differentiated patterns of expression in two tissues exhibited co-operation effect in high altitude adaptation based on miRNA family and cluster. Functional analysis revealed that differentially expressed miRNAs were enriched in hypoxia-related pathways, such as the HIF-1α signaling pathway, the insulin signaling pathway, the PI3K-Akt signaling pathway, nucleotide excision repair, cell cycle, apoptosis and fatty acid metabolism, which indicated the important roles of miRNAs in high altitude adaptation. These results suggested the diverse degrees of miRNA transcriptome variation in different tissues between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation.
bibliographic citation: Guan et al. (2017) Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation. PeerJ 5:e3959 https://doi.org/10.7717/peerj.3959
date submitted: 2017-04-07
date accepted: 2017-10-04
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guan
  given name: Jiuqiang
author list: Agent
  family name: Long
  given name: Keren
author list: Agent
  family name: Ma
  given name: Jideng
author list: Agent
  family name: Zhang
  given name: Jinwei
author list: Agent
  family name: He
  given name: Dafang
author list: Agent
  family name: Jin
  given name: Long
author list: Agent
  family name: Tang
  given name: Qianzi
author list: Agent
  family name: Jiang
  given name: Anan
author list: Agent
  family name: Wang
  given name: Xun
author list: Agent
  family name: Hu
  given name: Yaodong
author list: Agent
  family name: Tian
  given name: Shilin
author list: Agent
  family name: Jiang
  given name: Zhi
author list: Agent
  family name: Li
  given name: Mingzhou
author list: Agent
  family name: Luo
  given name: Xiaolin
doi: 10.7717/peerj.3959
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Guan et al.
attribution name: Guan et al.

Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry
type: item
type: AcademicArticle
description: Background Currently, there is limited knowledge about the genetics underlying pigmentary traits in East Asian populations. Here, we report the results of the first genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. Methods We obtained quantitative skin pigmentation measures (M-index) in the inner upper arm of the participants using a portable reflectometer (N = 305). Quantitative measures of iris color (expressed as L*, a* and b* CIELab coordinates) were extracted from high-resolution iris pictures (N = 342). We also measured the color differences between the pupillary and ciliary regions of the iris (e.g., iris heterochromia). DNA samples were genotyped with Illumina’s Infinium Multi-Ethnic Global Array (MEGA) and imputed using the 1000 Genomes Phase 3 samples as reference haplotypes. Results For skin pigmentation, we did not observe any genome-wide significant signal. We followed-up in three independent Chinese samples the lead SNPs of five regions showing multiple common markers (minor allele frequency ≥ 5%) with good imputation scores and suggestive evidence of association (p-values < 10−5). One of these markers, rs2373391, which is located in an intron of the ZNF804B gene on chromosome 7, was replicated in one of the Chinese samples (p = 0.003). For iris color, we observed genome-wide signals in the OCA2 region on chromosome 15. This signal is driven by the non-synonymous rs1800414 variant, which explains 11.9%, 10.4% and 6% of the variation observed in the b*, a* and L* coordinates in our sample, respectively. However, the OCA2 region was not associated with iris heterochromia. Discussion Additional genome-wide association studies in East Asian samples will be necessary to further disentangle the genetic architecture of pigmentary traits in East Asian populations.
format: application/pdf
format: text/html
creator: Lida Rawofi
creator: Melissa Edwards
creator: S Krithika
creator: Phuong Le
creator: David Cha
creator: Zhaohui Yang
creator: Yanyun Ma
creator: Jiucun Wang
creator: Bing Su
creator: Li Jin
creator: Heather L. Norton
creator: Esteban J. Parra
subject: Anthropology
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.3951
publisher: PeerJ Inc.
rights: © 2017 Rawofi et al.
abstract: Background Currently, there is limited knowledge about the genetics underlying pigmentary traits in East Asian populations. Here, we report the results of the first genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. Methods We obtained quantitative skin pigmentation measures (M-index) in the inner upper arm of the participants using a portable reflectometer (N = 305). Quantitative measures of iris color (expressed as L*, a* and b* CIELab coordinates) were extracted from high-resolution iris pictures (N = 342). We also measured the color differences between the pupillary and ciliary regions of the iris (e.g., iris heterochromia). DNA samples were genotyped with Illumina’s Infinium Multi-Ethnic Global Array (MEGA) and imputed using the 1000 Genomes Phase 3 samples as reference haplotypes. Results For skin pigmentation, we did not observe any genome-wide significant signal. We followed-up in three independent Chinese samples the lead SNPs of five regions showing multiple common markers (minor allele frequency ≥ 5%) with good imputation scores and suggestive evidence of association (p-values < 10−5). One of these markers, rs2373391, which is located in an intron of the ZNF804B gene on chromosome 7, was replicated in one of the Chinese samples (p = 0.003). For iris color, we observed genome-wide signals in the OCA2 region on chromosome 15. This signal is driven by the non-synonymous rs1800414 variant, which explains 11.9%, 10.4% and 6% of the variation observed in the b*, a* and L* coordinates in our sample, respectively. However, the OCA2 region was not associated with iris heterochromia. Discussion Additional genome-wide association studies in East Asian samples will be necessary to further disentangle the genetic architecture of pigmentary traits in East Asian populations.
bibliographic citation: Rawofi et al. (2017) Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. PeerJ 5:e3951 https://doi.org/10.7717/peerj.3951
date submitted: 2017-08-23
date accepted: 2017-10-01
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rawofi
  given name: Lida
author list: Agent
  family name: Edwards
  given name: Melissa
author list: Agent
  family name: Krithika
  given name: S
author list: Agent
  family name: Le
  given name: Phuong
author list: Agent
  family name: Cha
  given name: David
author list: Agent
  family name: Yang
  given name: Zhaohui
author list: Agent
  family name: Ma
  given name: Yanyun
author list: Agent
  family name: Wang
  given name: Jiucun
author list: Agent
  family name: Su
  given name: Bing
author list: Agent
  family name: Jin
  given name: Li
author list: Agent
  family name: Norton
  given name: Heather L.
author list: Agent
  family name: Parra
  given name: Esteban J.
doi: 10.7717/peerj.3951
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Rawofi et al.
attribution name: Rawofi et al.

Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar)
type: item
type: AcademicArticle
description: In female Atlantic salmon (Salmo salar), exposure to warm summer temperatures causes a reduction in plasma 17β-estradiol (E2), which impairs downstream vitellogenesis and zonagenesis, and reduces egg fertility and embryo survival. The aim of the present study was to determine whether E2-treatment could offset thermal impairment of endocrine function and maintain egg quality in maiden (first-time-spawning) S. salar reared at 22 °C. Treatment with E2 at 22 °C stimulated vitellogenin (vtg) gene expression and subsequent protein synthesis which promoted oocyte growth and increased egg size relative to untreated fish at 14 and 22 °C. However, E2-treatment at 22 °C was not associated with an increase in egg fertility and embryo survival relative to untreated fish at 22 °C, despite the positive effects of E2-treatment on vitellogenesis and oocyte growth. As there was no evidence to suggest that the estrogen receptor alpha expression was suppressed by high temperature, this could be due to the lack of stimulation on zonagenesis by E2-treatment observed at high temperature during oocyte development. Our results demonstrate that treatment with E2 is not able to maintain zonagenesis or egg quality in maiden S. salar at high temperature, even when vtg gene expression, protein synthesis and subsequent oocyte growth is promoted. This implies that the mechanisms regulating zonagenesis, but not vitellogenesis are impaired at elevated temperature in female S. salar broodstock, and highlights the remarkable complexity of thermally induced endocrine disruption in fish.
format: application/pdf
format: text/html
creator: Kelli Anderson
creator: Ned Pankhurst
creator: Harry King
creator: Abigail Elizur
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3897
publisher: PeerJ Inc.
rights: © 2017 Anderson et al.
abstract: In female Atlantic salmon (Salmo salar), exposure to warm summer temperatures causes a reduction in plasma 17β-estradiol (E2), which impairs downstream vitellogenesis and zonagenesis, and reduces egg fertility and embryo survival. The aim of the present study was to determine whether E2-treatment could offset thermal impairment of endocrine function and maintain egg quality in maiden (first-time-spawning) S. salar reared at 22 °C. Treatment with E2 at 22 °C stimulated vitellogenin (vtg) gene expression and subsequent protein synthesis which promoted oocyte growth and increased egg size relative to untreated fish at 14 and 22 °C. However, E2-treatment at 22 °C was not associated with an increase in egg fertility and embryo survival relative to untreated fish at 22 °C, despite the positive effects of E2-treatment on vitellogenesis and oocyte growth. As there was no evidence to suggest that the estrogen receptor alpha expression was suppressed by high temperature, this could be due to the lack of stimulation on zonagenesis by E2-treatment observed at high temperature during oocyte development. Our results demonstrate that treatment with E2 is not able to maintain zonagenesis or egg quality in maiden S. salar at high temperature, even when vtg gene expression, protein synthesis and subsequent oocyte growth is promoted. This implies that the mechanisms regulating zonagenesis, but not vitellogenesis are impaired at elevated temperature in female S. salar broodstock, and highlights the remarkable complexity of thermally induced endocrine disruption in fish.
bibliographic citation: Anderson et al. (2017) Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar). PeerJ 5:e3897 https://doi.org/10.7717/peerj.3897
date submitted: 2017-06-19
date accepted: 2017-09-16
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Kelli
author list: Agent
  family name: Pankhurst
  given name: Ned
author list: Agent
  family name: King
  given name: Harry
author list: Agent
  family name: Elizur
  given name: Abigail
doi: 10.7717/peerj.3897
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Anderson et al.
attribution name: Anderson et al.

Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands)
type: item
type: AcademicArticle
description: Background The family Pontoporiidae (Cetacea, Odontoceti, Inioidea) is currently represented in our oceans by just one species of diminutive dolphin (Pontoporia blainvillei, franciscana). Although P. blainvillei is limited to coastal waters of the South Atlantic along Brazil, Uruguay and Argentina, multiple Miocene and Pliocene fossils indicate the past presence of members of the family in the South Atlantic, South Paciifc and North Atlantic oceans. Our comprehension of the origin and diversity of this clade and of the relationships of its members with other inioids is hampered by the fact that part of the described fossil specimens, especially from the North Atlantic realm, are cranial fragments often associated to limited stratigraphic information. Methods Based on an almost complete fossil cranium of pontoporiid from the Westerschelde estuary, The Netherlands, whose preservation allows for detailed morphological observations, we describe a new genus and species. The latter is compared to other pontoporiids, as well as a few non-pontoporiid inioids. A phylogenetic analysis is performed to investigate the relationship of S. vandokkumi with the best-known extinct and extant inioids. Palynological analysis of the sediment associated to the holotype is used to assess its geological age. Results and discussion The new genus and species Scaldiporia vandokkumi is characterized among others by greatly thickened premaxillary eminences reaching the level of the antorbital notch. Palynologically dated from the late Tortonian—earliest Zanclean (7.6–5 Ma, Late Miocene—earliest Pliocene), this new pontoporiid confirms the surprising past diversity of marine inioids in the North Atlantic area. Finally the content of the pontoporiid subfamily Brachydelphininae is briefly discussed.
format: application/pdf
format: text/html
creator: Klaas Post
creator: Stephen Louwye
creator: Olivier Lambert
subject: Paleontology
description: doi:10.7717/peerj.3991
publisher: PeerJ Inc.
rights: © 2017 Post et al.
abstract: Background The family Pontoporiidae (Cetacea, Odontoceti, Inioidea) is currently represented in our oceans by just one species of diminutive dolphin (Pontoporia blainvillei, franciscana). Although P. blainvillei is limited to coastal waters of the South Atlantic along Brazil, Uruguay and Argentina, multiple Miocene and Pliocene fossils indicate the past presence of members of the family in the South Atlantic, South Paciifc and North Atlantic oceans. Our comprehension of the origin and diversity of this clade and of the relationships of its members with other inioids is hampered by the fact that part of the described fossil specimens, especially from the North Atlantic realm, are cranial fragments often associated to limited stratigraphic information. Methods Based on an almost complete fossil cranium of pontoporiid from the Westerschelde estuary, The Netherlands, whose preservation allows for detailed morphological observations, we describe a new genus and species. The latter is compared to other pontoporiids, as well as a few non-pontoporiid inioids. A phylogenetic analysis is performed to investigate the relationship of S. vandokkumi with the best-known extinct and extant inioids. Palynological analysis of the sediment associated to the holotype is used to assess its geological age. Results and discussion The new genus and species Scaldiporia vandokkumi is characterized among others by greatly thickened premaxillary eminences reaching the level of the antorbital notch. Palynologically dated from the late Tortonian—earliest Zanclean (7.6–5 Ma, Late Miocene—earliest Pliocene), this new pontoporiid confirms the surprising past diversity of marine inioids in the North Atlantic area. Finally the content of the pontoporiid subfamily Brachydelphininae is briefly discussed.
bibliographic citation: Post et al. (2017) Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands). PeerJ 5:e3991 https://doi.org/10.7717/peerj.3991
date submitted: 2017-07-17
date accepted: 2017-10-14
issued: 2017-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Post
  given name: Klaas
author list: Agent
  family name: Louwye
  given name: Stephen
author list: Agent
  family name: Lambert
  given name: Olivier
doi: 10.7717/peerj.3991
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-01
copyright: ©2017 Post et al.
attribution name: Post et al.

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