PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology
items: Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
items: Oxidative stress and antioxidants in the trabecular meshwork
items: Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
items: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
items: Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
items: Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
items: Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
items: Familiarity with visual stimuli boosts recency bias in macaques
items: Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry

Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology
type: item
type: AcademicArticle
description: Background There are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep. Methods Indigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis. Results We identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (G…
format: application/pdf
format: text/html
creator: Haiyu Ma
creator: Chao Fang
creator: Lingling Liu
creator: Qiong Wang
creator: Jueken Aniwashi
creator: Yiming Sulaiman
creator: Kezierkailedi Abudilaheman
creator: Wujun Liu
subject: Developmental Biology
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.8079
publisher: PeerJ Inc.
rights: © 2019 Ma et al.
abstract: Background There are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep. Methods Indigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis. Results We identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (G…
bibliographic citation: Ma et al. (2019) Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology. PeerJ 7:e8079 https://doi.org/10.7717/peerj.8079
date submitted: 2019-05-21
date accepted: 2019-10-21
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Haiyu
author list: Agent
  family name: Fang
  given name: Chao
author list: Agent
  family name: Liu
  given name: Lingling
author list: Agent
  family name: Wang
  given name: Qiong
author list: Agent
  family name: Aniwashi
  given name: Jueken
author list: Agent
  family name: Sulaiman
  given name: Yiming
author list: Agent
  family name: Abudilaheman
  given name: Kezierkailedi
author list: Agent
  family name: Liu
  given name: Wujun
doi: 10.7717/peerj.8079
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Ma et al.
attribution name: Ma et al.

Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
type: item
type: AcademicArticle
description: Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us un…
format: application/pdf
format: text/html
creator: Haiping Zhang
creator: Jian Zou
creator: Ying Yin
creator: Bo Zhang
creator: Yaling Hu
creator: Jingjing Wang
creator: Huijun Mu
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.8096
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us un…
bibliographic citation: Zhang et al. (2019) Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma. PeerJ 7:e8096 https://doi.org/10.7717/peerj.8096
date submitted: 2019-08-23
date accepted: 2019-10-24
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haiping
author list: Agent
  family name: Zou
  given name: Jian
author list: Agent
  family name: Yin
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Hu
  given name: Yaling
author list: Agent
  family name: Wang
  given name: Jingjing
author list: Agent
  family name: Mu
  given name: Huijun
doi: 10.7717/peerj.8096
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Oxidative stress and antioxidants in the trabecular meshwork
type: item
type: AcademicArticle
description: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention.
format: application/pdf
format: text/html
creator: Mingxuan Wang
creator: Yajuan Zheng
subject: Geriatrics
subject: Ophthalmology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.8121
publisher: PeerJ Inc.
rights: © 2019 Wang and Zheng
abstract: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention.
bibliographic citation: Wang et al. (2019) Oxidative stress and antioxidants in the trabecular meshwork. PeerJ 7:e8121 https://doi.org/10.7717/peerj.8121
date submitted: 2019-06-14
date accepted: 2019-10-30
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mingxuan
author list: Agent
  family name: Zheng
  given name: Yajuan
doi: 10.7717/peerj.8121
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Wang and Zheng
attribution name: Wang and Zheng

Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
type: item
type: AcademicArticle
description: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
format: application/pdf
format: text/html
creator: Kyle K. Biggar
creator: Jing Zhang
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8144
publisher: PeerJ Inc.
rights: © 2019 Biggar et al.
abstract: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
bibliographic citation: Biggar et al. (2019) Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia. PeerJ 7:e8144 https://doi.org/10.7717/peerj.8144
date submitted: 2019-05-21
date accepted: 2019-11-01
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biggar
  given name: Kyle K.
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.8144
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Biggar et al.
attribution name: Biggar et al.

Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
type: item
type: AcademicArticle
description: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
format: application/pdf
format: text/html
creator: Xin Hu
creator: Lili Zhu
creator: Yi Zhang
creator: Li Xu
creator: Na Li
creator: Xingguo Zhang
creator: Yu Pan
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7929
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
bibliographic citation: Hu et al. (2019) Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.). PeerJ 7:e7929 https://doi.org/10.7717/peerj.7929
date submitted: 2019-05-09
date accepted: 2019-09-20
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Xin
author list: Agent
  family name: Zhu
  given name: Lili
author list: Agent
  family name: Zhang
  given name: Yi
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Zhang
  given name: Xingguo
author list: Agent
  family name: Pan
  given name: Yu
doi: 10.7717/peerj.7929
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Hu et al.
attribution name: Hu et al.

Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
type: item
type: AcademicArticle
description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
format: application/pdf
format: text/html
creator: Siuli Mitra
creator: Vaishnavi Kunteepuram
creator: Klaus-Peter Koepfli
creator: Neha Mehra
creator: Wajeeda Tabasum
creator: Ara Sreenivas
creator: Ajay Gaur
subject: Conservation Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.8033
publisher: PeerJ Inc.
rights: © 2019 Mitra et al.
abstract: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
bibliographic citation: Mitra et al. (2019) Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications. PeerJ 7:e8033 https://doi.org/10.7717/peerj.8033
date submitted: 2019-02-07
date accepted: 2019-10-14
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitra
  given name: Siuli
author list: Agent
  family name: Kunteepuram
  given name: Vaishnavi
author list: Agent
  family name: Koepfli
  given name: Klaus-Peter
author list: Agent
  family name: Mehra
  given name: Neha
author list: Agent
  family name: Tabasum
  given name: Wajeeda
author list: Agent
  family name: Sreenivas
  given name: Ara
author list: Agent
  family name: Gaur
  given name: Ajay
doi: 10.7717/peerj.8033
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Mitra et al.
attribution name: Mitra et al.

Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
type: item
type: AcademicArticle
description: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number o…
format: application/pdf
format: text/html
creator: Neil S. Cobb
creator: Lawrence F. Gall
creator: Jennifer M. Zaspel
creator: Nicolas J. Dowdy
creator: Lindsie M. McCabe
creator: Akito Y. Kawahara
subject: Biodiversity
subject: Entomology
description: doi:10.7717/peerj.8086
publisher: PeerJ Inc.
rights: © 2019 Cobb et al.
abstract: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number o…
bibliographic citation: Cobb et al. (2019) Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 7:e8086 https://doi.org/10.7717/peerj.8086
date submitted: 2019-08-02
date accepted: 2019-10-23
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cobb
  given name: Neil S.
author list: Agent
  family name: Gall
  given name: Lawrence F.
author list: Agent
  family name: Zaspel
  given name: Jennifer M.
author list: Agent
  family name: Dowdy
  given name: Nicolas J.
author list: Agent
  family name: McCabe
  given name: Lindsie M.
author list: Agent
  family name: Kawahara
  given name: Akito Y.
doi: 10.7717/peerj.8086
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Cobb et al.
attribution name: Cobb et al.

Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
type: item
type: AcademicArticle
description: Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to susp…
format: application/pdf
format: text/html
creator: Eva Cuesta
creator: Jorge M. Lobo
subject: Biophysics
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.8104
publisher: PeerJ Inc.
rights: © 2019 Cuesta and Lobo
abstract: Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to susp…
bibliographic citation: Cuesta et al. (2019) Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference. PeerJ 7:e8104 https://doi.org/10.7717/peerj.8104
date submitted: 2019-06-14
date accepted: 2019-10-25
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuesta
  given name: Eva
author list: Agent
  family name: Lobo
  given name: Jorge M.
doi: 10.7717/peerj.8104
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: © 2019 Cuesta and Lobo
attribution name: Cuesta and Lobo

Familiarity with visual stimuli boosts recency bias in macaques
type: item
type: AcademicArticle
description: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
format: application/pdf
format: text/html
creator: Nicolas Brunet
creator: Bharathi Jagadeesh
subject: Animal Behavior
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8105
publisher: PeerJ Inc.
rights: © 2019 Brunet and Jagadeesh
abstract: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
bibliographic citation: Brunet et al. (2019) Familiarity with visual stimuli boosts recency bias in macaques. PeerJ 7:e8105 https://doi.org/10.7717/peerj.8105
date submitted: 2019-06-11
date accepted: 2019-10-26
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brunet
  given name: Nicolas
author list: Agent
  family name: Jagadeesh
  given name: Bharathi
doi: 10.7717/peerj.8105
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Brunet and Jagadeesh
attribution name: Brunet and Jagadeesh

Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry
type: item
type: AcademicArticle
description: Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
format: application/pdf
format: text/html
creator: Samir Meramo-Hurtado
creator: Kariana Moreno-Sader
creator: Ángel D. González-Delgado
subject: Green Chemistry
description: doi:10.7717/peerj.8113
publisher: PeerJ Inc.
rights: © 2019 Meramo-Hurtado et al.
abstract: Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
bibliographic citation: Meramo-Hurtado et al. (2019) Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry. PeerJ 7:e8113 https://doi.org/10.7717/peerj.8113
date submitted: 2019-05-21
date accepted: 2019-10-28
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meramo-Hurtado
  given name: Samir
author list: Agent
  family name: Moreno-Sader
  given name: Kariana
author list: Agent
  family name: González-Delgado
  given name: Ángel D.
doi: 10.7717/peerj.8113
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Meramo-Hurtado et al.
attribution name: Meramo-Hurtado et al.

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