PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer
items: A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast
items: Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau
items: https://peerj.com/articles/7688
items: LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population
items: Phylogeny of Microphthalminae Hartmann-Schröder, 1971, and revision of Hesionella Hartman, 1939, and Struwela Hartmann-Schröder, 1959 (Annelida, Errantia)
items: The secret life of deep-sea shrimps: ecological and evolutionary clues from the larval description of Systellaspis debilis (Caridea: Oplophoridae)
items: Open ocean nocturnal insect migration in the Brazilian South Atlantic with comments on flight endurance
items: Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs
items: 13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish

Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer
type: item
type: AcademicArticle
description: Background Recent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC). Methods Here we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs. Results In this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found. Conclusions Our findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
format: application/pdf
format: text/html
creator: Wenliang Yuan
creator: Sihua Peng
creator: Jingyu Wang
creator: Cai Wei
creator: Zhen Ye
creator: Ye Wang
creator: Meiliang Wang
creator: Hao Xu
creator: Shouwen Jiang
creator: Dan Sun
creator: Chaoxu Dai
creator: Linhua Jiang
creator: Xiaobo Li
subject: Bioinformatics
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.7602
publisher: PeerJ Inc.
rights: © 2019 Yuan et al.
abstract: Background Recent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC). Methods Here we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs. Results In this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found. Conclusions Our findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
bibliographic citation: Yuan et al. (2019) Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer. PeerJ 7:e7602 https://doi.org/10.7717/peerj.7602
date submitted: 2019-05-09
date accepted: 2019-08-01
issued: 2019-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Wenliang
author list: Agent
  family name: Peng
  given name: Sihua
author list: Agent
  family name: Wang
  given name: Jingyu
author list: Agent
  family name: Wei
  given name: Cai
author list: Agent
  family name: Ye
  given name: Zhen
author list: Agent
  family name: Wang
  given name: Ye
author list: Agent
  family name: Wang
  given name: Meiliang
author list: Agent
  family name: Xu
  given name: Hao
author list: Agent
  family name: Jiang
  given name: Shouwen
author list: Agent
  family name: Sun
  given name: Dan
author list: Agent
  family name: Dai
  given name: Chaoxu
author list: Agent
  family name: Jiang
  given name: Linhua
author list: Agent
  family name: Li
  given name: Xiaobo
doi: 10.7717/peerj.7602
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-19
copyright: ©2019 Yuan et al.
attribution name: Yuan et al.

A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast
type: item
type: AcademicArticle
description: The Katalalixar National Reserve (KNR) lies in an isolated marine protected area of Magellan Sub-Antarctic channels, which represent an important area for marine biodiversity and macroalgal conservation. The present study is the first report of the species Lessonia spicata, “huiro negro”, in the Magellan Sub-Antarctic channels. This finding has implications for macroalgal biogeography and conservation concerns in the Chilean coast. In the ecological assessments of the KNR in 2018 we found populations of L. spicata, specifically on rocky shores of Torpedo Island and Castillo Channel. The morphological identification and molecular phylogeny based on nuclear (ITS1) sequences revealed that these populations of Lessonia are within the lineage of L. spicata of central Chile. This report increases the species richness of kelps for the Magellan Sub-Antarctic Channels from two to three confirmed species (L. flavicans, L. searlesiana and L. spicata), and it also extends the southern distribution range of L. spicata. This species has high harvest demand and is moving towards southern Chile; thus, these populations should be considered as essential for macroalgal conservation in high latitudes of South America.
format: application/pdf
format: text/html
creator: Sebastián Rosenfeld
creator: Fabio Mendez
creator: Martha S. Calderon
creator: Francisco Bahamonde
creator: Juan Pablo Rodríguez
creator: Jaime Ojeda
creator: Johanna Marambio
creator: Matthias Gorny
creator: Andrés Mansilla
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.7610
publisher: PeerJ Inc.
rights: © 2019 Rosenfeld et al.
abstract: The Katalalixar National Reserve (KNR) lies in an isolated marine protected area of Magellan Sub-Antarctic channels, which represent an important area for marine biodiversity and macroalgal conservation. The present study is the first report of the species Lessonia spicata, “huiro negro”, in the Magellan Sub-Antarctic channels. This finding has implications for macroalgal biogeography and conservation concerns in the Chilean coast. In the ecological assessments of the KNR in 2018 we found populations of L. spicata, specifically on rocky shores of Torpedo Island and Castillo Channel. The morphological identification and molecular phylogeny based on nuclear (ITS1) sequences revealed that these populations of Lessonia are within the lineage of L. spicata of central Chile. This report increases the species richness of kelps for the Magellan Sub-Antarctic Channels from two to three confirmed species (L. flavicans, L. searlesiana and L. spicata), and it also extends the southern distribution range of L. spicata. This species has high harvest demand and is moving towards southern Chile; thus, these populations should be considered as essential for macroalgal conservation in high latitudes of South America.
bibliographic citation: Rosenfeld et al. (2019) A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast. PeerJ 7:e7610 https://doi.org/10.7717/peerj.7610
date submitted: 2019-06-18
date accepted: 2019-08-05
issued: 2019-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rosenfeld
  given name: Sebastián
author list: Agent
  family name: Mendez
  given name: Fabio
author list: Agent
  family name: Calderon
  given name: Martha S.
author list: Agent
  family name: Bahamonde
  given name: Francisco
author list: Agent
  family name: Rodríguez
  given name: Juan Pablo
author list: Agent
  family name: Ojeda
  given name: Jaime
author list: Agent
  family name: Marambio
  given name: Johanna
author list: Agent
  family name: Gorny
  given name: Matthias
author list: Agent
  family name: Mansilla
  given name: Andrés
doi: 10.7717/peerj.7610
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-19
copyright: © 2019 Rosenfeld et al.
attribution name: Rosenfeld et al.

Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau
type: item
type: AcademicArticle
description: The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different…
format: application/pdf
format: text/html
creator: Li Ma
creator: Shixiao Xu
creator: Hongjin Liu
creator: Tianwei Xu
creator: Linyong Hu
creator: Na Zhao
creator: Xueping Han
creator: Xiaoling Zhang
subject: Agricultural Science
subject: Biochemistry
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.7645
publisher: PeerJ Inc.
rights: © 2019 Ma et al.
abstract: The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different…
bibliographic citation: Ma et al. (2019) Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau. PeerJ 7:e7645 https://doi.org/10.7717/peerj.7645
date submitted: 2018-11-29
date accepted: 2019-08-08
issued: 2019-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Li
author list: Agent
  family name: Xu
  given name: Shixiao
author list: Agent
  family name: Liu
  given name: Hongjin
author list: Agent
  family name: Xu
  given name: Tianwei
author list: Agent
  family name: Hu
  given name: Linyong
author list: Agent
  family name: Zhao
  given name: Na
author list: Agent
  family name: Han
  given name: Xueping
author list: Agent
  family name: Zhang
  given name: Xiaoling
doi: 10.7717/peerj.7645
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-19
copyright: ©2019 Ma et al.
attribution name: Ma et al.

https://peerj.com/articles/7688
type: item
type: AcademicArticle
title: Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae
description: A new istiodactylid pterosaur, Nurhachius luei sp. nov., is here reported based on a complete skull with mandible and some cervical vertebrae from the lower part of the Jiufotang Formation of western Liaoning (China). This is the second species of Nurhachius, the type-species being N. ignaciobritoi from the upper part of the Jiufotang Formation. A revised diagnosis of the genus Nurhachius is provided, being this taxon characterized by the presence of a slight dorsal deflection of the palatal anterior tip, which is homoplastic with the Anhangueria and Cimoliopterus. N. luei sp. nov. shows an unusual pattern of tooth replacement, with respect to other pterodactyloid species. The relationships within the Istiodactylidae and with their closest taxa are investigated through a phylogenetic analysis by parsimony.
format: application/pdf
format: text/html
creator: Xuanyu Zhou
creator: Rodrigo V. Pêgas
creator: Maria E.C. Leal
creator: Niels Bonde
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7688
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: A new istiodactylid pterosaur, Nurhachius luei sp. nov., is here reported based on a complete skull with mandible and some cervical vertebrae from the lower part of the Jiufotang Formation of western Liaoning (China). This is the second species of Nurhachius, the type-species being N. ignaciobritoi from the upper part of the Jiufotang Formation. A revised diagnosis of the genus Nurhachius is provided, being this taxon characterized by the presence of a slight dorsal deflection of the palatal anterior tip, which is homoplastic with the Anhangueria and Cimoliopterus. N. luei sp. nov. shows an unusual pattern of tooth replacement, with respect to other pterodactyloid species. The relationships within the Istiodactylidae and with their closest taxa are investigated through a phylogenetic analysis by parsimony.
bibliographic citation: Zhou et al. (2019) Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae. PeerJ 7:e7688 https://doi.org/10.7717/peerj.7688
date submitted: 2019-05-15
date accepted: 2019-08-19
issued: 2019-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Xuanyu
author list: Agent
  family name: Pêgas
  given name: Rodrigo V.
author list: Agent
  family name: Leal
  given name: Maria E.C.
author list: Agent
  family name: Bonde
  given name: Niels
doi: 10.7717/peerj.7688
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-19
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population
type: item
type: AcademicArticle
description: A novel application of the liquid chromatography method combined with the triple quadrupole tandem mass spectrometry method was developed for the quantification of vitamin K1 and two forms of vitamin K2 (menaquinone-4, menaquinone-7) in human serum. Total chromatography time for each run was 9 min. Time required for the sample pretreatment procedures was approximately 4 h. The coefficients of variation (CVs) of intra-assay were 10.4%, 3.2 % and 2.3% for vitamin K1 in three levels of quality control samples; were 14.3%, 3.2% and 6.7% for menaquinone-4; and were 11.1%, 6.0% and 7.0% for menaquinone-7. The inter-assay CVs were 12.8%, 11.3% and 7.4% for vitamin K1; were 15.2%, 9.2% and 8.7% for menaquinone-4; and were 13.2%,11.1% and 7.2% for menaquinone-7. No interference was found between K1, menaquinone-4 and menaquinone-7, nor any deuterated internal standards. This method was then used to determine reference values for Caucasian populations of central European origin. Samples were measured from 191 healthy volunteers (51.2 ± 16.2 years (mean ± SD)) and the values concerning K1 were 0.044–1.357 ng/mL for women and 0.030–1.214 ng/mL for men. The values for menaquinone-4 and menaquinone-7 did not exhibit any differences between women and men, and were 0.050–1.598 and 0.074–0.759 ng/mL, respectively.
format: application/pdf
format: text/html
creator: Katerina Dunovska
creator: Eva Klapkova
creator: Bruno Sopko
creator: Jana Cepova
creator: Richard Prusa
subject: Biochemistry
subject: Nutrition
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.7695
publisher: PeerJ Inc.
rights: © 2019 Dunovska et al.
abstract: A novel application of the liquid chromatography method combined with the triple quadrupole tandem mass spectrometry method was developed for the quantification of vitamin K1 and two forms of vitamin K2 (menaquinone-4, menaquinone-7) in human serum. Total chromatography time for each run was 9 min. Time required for the sample pretreatment procedures was approximately 4 h. The coefficients of variation (CVs) of intra-assay were 10.4%, 3.2 % and 2.3% for vitamin K1 in three levels of quality control samples; were 14.3%, 3.2% and 6.7% for menaquinone-4; and were 11.1%, 6.0% and 7.0% for menaquinone-7. The inter-assay CVs were 12.8%, 11.3% and 7.4% for vitamin K1; were 15.2%, 9.2% and 8.7% for menaquinone-4; and were 13.2%,11.1% and 7.2% for menaquinone-7. No interference was found between K1, menaquinone-4 and menaquinone-7, nor any deuterated internal standards. This method was then used to determine reference values for Caucasian populations of central European origin. Samples were measured from 191 healthy volunteers (51.2 ± 16.2 years (mean ± SD)) and the values concerning K1 were 0.044–1.357 ng/mL for women and 0.030–1.214 ng/mL for men. The values for menaquinone-4 and menaquinone-7 did not exhibit any differences between women and men, and were 0.050–1.598 and 0.074–0.759 ng/mL, respectively.
bibliographic citation: Dunovska et al. (2019) LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population. PeerJ 7:e7695 https://doi.org/10.7717/peerj.7695
date submitted: 2019-03-07
date accepted: 2019-08-19
issued: 2019-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dunovska
  given name: Katerina
author list: Agent
  family name: Klapkova
  given name: Eva
author list: Agent
  family name: Sopko
  given name: Bruno
author list: Agent
  family name: Cepova
  given name: Jana
author list: Agent
  family name: Prusa
  given name: Richard
doi: 10.7717/peerj.7695
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-19
copyright: © 2019 Dunovska et al.
attribution name: Dunovska et al.

Phylogeny of Microphthalminae Hartmann-Schröder, 1971, and revision of Hesionella Hartman, 1939, and Struwela Hartmann-Schröder, 1959 (Annelida, Errantia)
type: item
type: AcademicArticle
description: Microphthalminae Hartmann-Schröder, 1971 was proposed in Hesionidae to include Microphthalmus and Hesionides; however, the affinities of these genera to other members of Hesionidae have been debated, and some authors have concluded they do not belong in Hesionidae. Herein, based on morphological characters, a phylogenetic analysis of the subfamily and some other similar poorly-known genera, with an uncertain position in Hesionidae was performed to clarify their affinities. Our results indicate that Microphthalminae, as currently delimited, is paraphyletic. The inclusion of Struwela, Uncopodarke, and Westheideius, a new genus, as well as the recognition of Fridericiella are proposed to meet the requirement of monophyly; and as result of this, the elevation in rank to the family level is herein presented. Furthermore, the type species for Hesionella and Struwela are redescribed, and a new species in the latter is described. A key to identify microphthalmid genera is also included.
format: application/pdf
format: text/html
creator: Sergio I. Salazar-Vallejo
creator: Jesús Angel de León-González
creator: Luis F. Carrera-Parra
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7723
publisher: PeerJ Inc.
rights: © 2019 Salazar-Vallejo et al.
abstract: Microphthalminae Hartmann-Schröder, 1971 was proposed in Hesionidae to include Microphthalmus and Hesionides; however, the affinities of these genera to other members of Hesionidae have been debated, and some authors have concluded they do not belong in Hesionidae. Herein, based on morphological characters, a phylogenetic analysis of the subfamily and some other similar poorly-known genera, with an uncertain position in Hesionidae was performed to clarify their affinities. Our results indicate that Microphthalminae, as currently delimited, is paraphyletic. The inclusion of Struwela, Uncopodarke, and Westheideius, a new genus, as well as the recognition of Fridericiella are proposed to meet the requirement of monophyly; and as result of this, the elevation in rank to the family level is herein presented. Furthermore, the type species for Hesionella and Struwela are redescribed, and a new species in the latter is described. A key to identify microphthalmid genera is also included.
bibliographic citation: Salazar-Vallejo et al. (2019) Phylogeny of Microphthalminae Hartmann-Schröder, 1971, and revision of Hesionella Hartman, 1939, and Struwela Hartmann-Schröder, 1959 (Annelida, Errantia). PeerJ 7:e7723 https://doi.org/10.7717/peerj.7723
date submitted: 2019-06-24
date accepted: 2019-08-22
issued: 2019-09-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salazar-Vallejo
  given name: Sergio I.
author list: Agent
  family name: de León-González
  given name: Jesús Angel
author list: Agent
  family name: Carrera-Parra
  given name: Luis F.
doi: 10.7717/peerj.7723
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-19
copyright: ©2019 Salazar-Vallejo et al.
attribution name: Salazar-Vallejo et al.

The secret life of deep-sea shrimps: ecological and evolutionary clues from the larval description of Systellaspis debilis (Caridea: Oplophoridae)
type: item
type: AcademicArticle
description: Currently there are 21 shrimp species in the northeastern Atlantic and Mediterranean Sea which are considered to belong to the superfamily Oplophoroidea, but the larval development is unknown for most of them. The complete larval development of Systellaspis debilis (Milne-Edwards, 1881), here described and illustrated, is the first one to have been successfully reared in the laboratory, consisting of four zoeal and one decapodid stages. The zoeae were found to be fully lecithotrophic, which together with the females’ lower fecundity, are probably evolutionary consequences of the species mesopelagic habitat.
format: application/pdf
format: text/html
creator: Cátia Bartilotti
creator: Antonina Dos Santos
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.7334
publisher: PeerJ Inc.
rights: © 2019 Bartilotti and Dos Santos
abstract: Currently there are 21 shrimp species in the northeastern Atlantic and Mediterranean Sea which are considered to belong to the superfamily Oplophoroidea, but the larval development is unknown for most of them. The complete larval development of Systellaspis debilis (Milne-Edwards, 1881), here described and illustrated, is the first one to have been successfully reared in the laboratory, consisting of four zoeal and one decapodid stages. The zoeae were found to be fully lecithotrophic, which together with the females’ lower fecundity, are probably evolutionary consequences of the species mesopelagic habitat.
bibliographic citation: Bartilotti et al. (2019) The secret life of deep-sea shrimps: ecological and evolutionary clues from the larval description of Systellaspis debilis (Caridea: Oplophoridae). PeerJ 7:e7334 https://doi.org/10.7717/peerj.7334
date submitted: 2018-10-24
date accepted: 2019-06-21
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartilotti
  given name: Cátia
author list: Agent
  family name: Dos Santos
  given name: Antonina
doi: 10.7717/peerj.7334
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: © 2019 Bartilotti and Dos Santos
attribution name: Bartilotti and Dos Santos

Open ocean nocturnal insect migration in the Brazilian South Atlantic with comments on flight endurance
type: item
type: AcademicArticle
description: We observed a nocturnal insect swarm aboard the oceanographic ship Cruzeiro do Sul of the Brazilian Navy, while conducting a survey of the Montague guyot (seamount), 389 km distant from the nearest land in the South Atlantic. The insects came from open sea toward the ship from all directions, attracted by the powerful light of the deck. Most insects collided with the hull and fell into the ocean, but we managed to capture and determine 17 (13 Hemiptera of a single species, three Lepidoptera of three species and one Odonata). With one exception, we are certain that none of the specimens caught originated from the ship. The geographic origin, most likely the coast of Brazil, and flight endurance of these insects were inferred using data on wind speed and direction, provided by the crew of the ship, and were reconstructed using Hysplit modeling of air current trajectories.
format: application/pdf
format: text/html
creator: Ruy J.V. Alves
creator: Luíz A.A. Costa
creator: Alexandre Soares
creator: Nílber G. Silva
creator: Ângelo P. Pinto
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.7583
publisher: PeerJ Inc.
rights: © 2019 Alves et al.
abstract: We observed a nocturnal insect swarm aboard the oceanographic ship Cruzeiro do Sul of the Brazilian Navy, while conducting a survey of the Montague guyot (seamount), 389 km distant from the nearest land in the South Atlantic. The insects came from open sea toward the ship from all directions, attracted by the powerful light of the deck. Most insects collided with the hull and fell into the ocean, but we managed to capture and determine 17 (13 Hemiptera of a single species, three Lepidoptera of three species and one Odonata). With one exception, we are certain that none of the specimens caught originated from the ship. The geographic origin, most likely the coast of Brazil, and flight endurance of these insects were inferred using data on wind speed and direction, provided by the crew of the ship, and were reconstructed using Hysplit modeling of air current trajectories.
bibliographic citation: Alves et al. (2019) Open ocean nocturnal insect migration in the Brazilian South Atlantic with comments on flight endurance. PeerJ 7:e7583 https://doi.org/10.7717/peerj.7583
date submitted: 2019-02-25
date accepted: 2019-07-29
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alves
  given name: Ruy J.V.
author list: Agent
  family name: Costa
  given name: Luíz A.A.
author list: Agent
  family name: Soares
  given name: Alexandre
author list: Agent
  family name: Silva
  given name: Nílber G.
author list: Agent
  family name: Pinto
  given name: Ângelo P.
doi: 10.7717/peerj.7583
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: © 2019 Alves et al.
attribution name: Alves et al.

Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs
type: item
type: AcademicArticle
description: Measurement of body dimensions of carnivores usually requires the chemical immobilization of subjects. This process can be dangerous, costly and potentially harmful to the target individuals. Development of an alternative, inexpensive, and non-invasive method therefore warrants attention. The objective of this study was to test whether it is possible to obtain accurate measurements of body dimensions of leopards from camera trap photographs. A total of 10 leopards (Panthera pardus) were captured and collared at Malilangwe Wildlife Reserve, Zimbabwe from May 7 to June 20, 2017 and four body measurements namely shoulder height, head-to-tail, body, and tail length were recorded. The same measurements were taken from 101 scaled photographs of the leopards recorded during a baited-camera trapping (BCT) survey conducted from July 1 to October 22, 2017 and differences from the actual measurements calculated. Generalized Linear Mixed Effects Models were used to determine the effect of type of body measurement, photographic scale, posture, and sex on the accuracy of the photograph-based measurements. Type of body measurement and posture had a significant influence on accuracy. Least squares means of absolute differences between actual and photographic measurements showed that body length in the level back-straight forelimb-parallel tail posture was measured most accurately from photographs (2.0 cm, 95% CI [1.5–2.7 cm]), while head-to-tail dimensions in the arched back-bent forelimb-parallel tail posture were least accurate (8.3 cm, 95% CI [6.1–11.2 cm]). Using the BCT design, we conclude that it is possible to collect accurate morphometric data of leopards from camera trap photographs. Repeat measurements over time can provide researchers with vital body size and growth rate information which may help improve the monitoring and management of species of conservation concern, such as leopards.
format: application/pdf
format: text/html
creator: Allan Tarugara
creator: Bruce W. Clegg
creator: Edson Gandiwa
creator: Victor K. Muposhi
creator: Colin M. Wenham
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.7630
publisher: PeerJ Inc.
rights: © 2019 Tarugara et al.
abstract: Measurement of body dimensions of carnivores usually requires the chemical immobilization of subjects. This process can be dangerous, costly and potentially harmful to the target individuals. Development of an alternative, inexpensive, and non-invasive method therefore warrants attention. The objective of this study was to test whether it is possible to obtain accurate measurements of body dimensions of leopards from camera trap photographs. A total of 10 leopards (Panthera pardus) were captured and collared at Malilangwe Wildlife Reserve, Zimbabwe from May 7 to June 20, 2017 and four body measurements namely shoulder height, head-to-tail, body, and tail length were recorded. The same measurements were taken from 101 scaled photographs of the leopards recorded during a baited-camera trapping (BCT) survey conducted from July 1 to October 22, 2017 and differences from the actual measurements calculated. Generalized Linear Mixed Effects Models were used to determine the effect of type of body measurement, photographic scale, posture, and sex on the accuracy of the photograph-based measurements. Type of body measurement and posture had a significant influence on accuracy. Least squares means of absolute differences between actual and photographic measurements showed that body length in the level back-straight forelimb-parallel tail posture was measured most accurately from photographs (2.0 cm, 95% CI [1.5–2.7 cm]), while head-to-tail dimensions in the arched back-bent forelimb-parallel tail posture were least accurate (8.3 cm, 95% CI [6.1–11.2 cm]). Using the BCT design, we conclude that it is possible to collect accurate morphometric data of leopards from camera trap photographs. Repeat measurements over time can provide researchers with vital body size and growth rate information which may help improve the monitoring and management of species of conservation concern, such as leopards.
bibliographic citation: Tarugara et al. (2019) Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs. PeerJ 7:e7630 https://doi.org/10.7717/peerj.7630
date submitted: 2019-05-16
date accepted: 2019-08-06
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tarugara
  given name: Allan
author list: Agent
  family name: Clegg
  given name: Bruce W.
author list: Agent
  family name: Gandiwa
  given name: Edson
author list: Agent
  family name: Muposhi
  given name: Victor K.
author list: Agent
  family name: Wenham
  given name: Colin M.
doi: 10.7717/peerj.7630
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: © 2019 Tarugara et al.
attribution name: Tarugara et al.

13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish
type: item
type: AcademicArticle
description: Background Stable isotope analysis of single amino acids (AA) is usually applied in food web studies for tracing biosynthetic origins of AA carbon backbones and establishing trophic positions of consumers, but the method is also showing promise for characterizing quantity and quality of dietary lipids and carbohydrates. Methods To investigate whether changes in high- and low-digestible carbohydrates affect δ13C values of glycolytic AA, i.e., AA carbon backbones sourced from the glycolytic pathway, we compared Atlantic salmon (Salmo salar) from a feeding experiment with and without dietary inclusion of the red macroalga Palmaria palmata. The Control and experimental diets had similar relative proportions of macronutrients, but their ingredients differed; in the experimental treatment, 15% Palmaria inclusion substituted proteins from fishmeal and carbohydrates from corn starch. Results We found that 13C values of the glycolytic AA were highly sensitive to substitution of corn starch with Palmaria. The δ13C offsets of glycolytic AA between salmon and their diets were significantly greater in the Palmaria inclusion than Control treatment. This greater offset can be attributed to the different utilization of high- vs. low-digestible carbohydrate sources, i.e., corn starch vs. Palmaria, in the two treatments, and metabolic routing of dietary lipids. In addition, similar δ13C values of essential AA between treatments indicate similar nutrient assimilation efficiency for all terrestrial (pea protein concentrate and wheat gluten meal) and marine (fishmeal and red alga) derived protein sources. These results show that δ13CAA analysis is a promising tool for improving our understanding of how carnivorous fish utilize macronutrient and route metabolic intermediates to tissue.
format: application/pdf
format: text/html
creator: Yiming V. Wang
creator: Alex H.L. Wan
creator: Åshild Krogdahl
creator: Mark Johnson
creator: Thomas Larsen
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Ecology
description: doi:10.7717/peerj.7701
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Stable isotope analysis of single amino acids (AA) is usually applied in food web studies for tracing biosynthetic origins of AA carbon backbones and establishing trophic positions of consumers, but the method is also showing promise for characterizing quantity and quality of dietary lipids and carbohydrates. Methods To investigate whether changes in high- and low-digestible carbohydrates affect δ13C values of glycolytic AA, i.e., AA carbon backbones sourced from the glycolytic pathway, we compared Atlantic salmon (Salmo salar) from a feeding experiment with and without dietary inclusion of the red macroalga Palmaria palmata. The Control and experimental diets had similar relative proportions of macronutrients, but their ingredients differed; in the experimental treatment, 15% Palmaria inclusion substituted proteins from fishmeal and carbohydrates from corn starch. Results We found that 13C values of the glycolytic AA were highly sensitive to substitution of corn starch with Palmaria. The δ13C offsets of glycolytic AA between salmon and their diets were significantly greater in the Palmaria inclusion than Control treatment. This greater offset can be attributed to the different utilization of high- vs. low-digestible carbohydrate sources, i.e., corn starch vs. Palmaria, in the two treatments, and metabolic routing of dietary lipids. In addition, similar δ13C values of essential AA between treatments indicate similar nutrient assimilation efficiency for all terrestrial (pea protein concentrate and wheat gluten meal) and marine (fishmeal and red alga) derived protein sources. These results show that δ13CAA analysis is a promising tool for improving our understanding of how carnivorous fish utilize macronutrient and route metabolic intermediates to tissue.
bibliographic citation: Wang et al. (2019) 13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish. PeerJ 7:e7701 https://doi.org/10.7717/peerj.7701
date submitted: 2019-06-15
date accepted: 2019-08-19
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yiming V.
author list: Agent
  family name: Wan
  given name: Alex H.L.
author list: Agent
  family name: Krogdahl
  given name: Åshild
author list: Agent
  family name: Johnson
  given name: Mark
author list: Agent
  family name: Larsen
  given name: Thomas
doi: 10.7717/peerj.7701
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: ©2019 Wang et al.
attribution name: Wang et al.

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