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 expression profiles of neuropeptides and their GPCRs in the swimming crab, Portunus trituberculatus
items: High-resolution prediction of American red squirrel in Interior Alaska: a role model for conservation using open access data, machine learning, GIS and LIDAR
items: Glucosylceramide synthase regulates hepatocyte repair after concanavalin A-induced immune-mediated liver injury
items: Phylogenetic relationships of sucrose transporters (SUTs) in plants and genome-wide characterization of SUT genes in Orchidaceae reveal roles in floral organ development
items: Active behaviour of terrestrial caterpillars on the water surface
items: Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed
items: Substrate type and palaeodepth do not affect the Middle Jurassic taxonomic diversity of crinoids
items: Catostylus tagi (Class: Scyphozoa, Order: Discomedusae, Suborder: Rhizostomida, Family: Catostylidae) life cycle and first insight into its ecology
items: Identification and validation of hub genes for diabetic retinopathy
items: Sex- and stage-dependent expression patterns of odorant-binding and chemosensory protein genes in Spodoptera exempta

Identification and characterization of expression profiles of neuropeptides and their GPCRs in the swimming crab, Portunus trituberculatus
type: item
type: AcademicArticle
description: Neuropeptides and their G protein-coupled receptors (GPCRs) regulate multiple physiological processes. Currently, little is known about the identity of native neuropeptides and their receptors in Portunus trituberculatus. This study employed RNA-sequencing and reverse transcription-polymerase chain reaction (RT-PCR) techniques to identify neuropeptides and their receptors that might be involved in regulation of reproductive processes of P. trituberculatus. In the central nervous system transcriptome data, 47 neuropeptide transcripts were identified. In further analyses, the tissue expression profile of 32 putative neuropeptide-encoding transcripts was estimated. Results showed that the 32 transcripts were expressed in the central nervous system and 23 of them were expressed in the ovary. A total of 47 GPCR-encoding transcripts belonging to two classes were identified, including 39 encoding GPCR-A family and eight encoding GPCR-B family. In addition, we assessed the tissue expression profile of 33 GPCRs (27 GPCR-As and six GPCR-Bs) transcripts. These GPCRs were found to be widely expressed in different tissues. Similar to the expression profiles of neuropeptides, 20 of these putative GPCR-encoding transcripts were also detected in the ovary. This is the first study to establish the identify of neuropeptides and their GPCRs in P. trituberculatus, and provide information for further investigations into the effect of neuropeptides on the physiology and behavior of decapod crustaceans.
format: application/pdf
format: text/html
creator: Shisheng Tu
creator: Rui Xu
creator: Mengen Wang
creator: Xi Xie
creator: Chenchang Bao
creator: Dongfa Zhu
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12179
publisher: PeerJ Inc.
rights: © 2021 Tu et al.
abstract: Neuropeptides and their G protein-coupled receptors (GPCRs) regulate multiple physiological processes. Currently, little is known about the identity of native neuropeptides and their receptors in Portunus trituberculatus. This study employed RNA-sequencing and reverse transcription-polymerase chain reaction (RT-PCR) techniques to identify neuropeptides and their receptors that might be involved in regulation of reproductive processes of P. trituberculatus. In the central nervous system transcriptome data, 47 neuropeptide transcripts were identified. In further analyses, the tissue expression profile of 32 putative neuropeptide-encoding transcripts was estimated. Results showed that the 32 transcripts were expressed in the central nervous system and 23 of them were expressed in the ovary. A total of 47 GPCR-encoding transcripts belonging to two classes were identified, including 39 encoding GPCR-A family and eight encoding GPCR-B family. In addition, we assessed the tissue expression profile of 33 GPCRs (27 GPCR-As and six GPCR-Bs) transcripts. These GPCRs were found to be widely expressed in different tissues. Similar to the expression profiles of neuropeptides, 20 of these putative GPCR-encoding transcripts were also detected in the ovary. This is the first study to establish the identify of neuropeptides and their GPCRs in P. trituberculatus, and provide information for further investigations into the effect of neuropeptides on the physiology and behavior of decapod crustaceans.
bibliographic citation: Tu et al. (2021) Identification and characterization of expression profiles of neuropeptides and their GPCRs in the swimming crab, Portunus trituberculatus. PeerJ 9:e12179 https://doi.org/10.7717/peerj.12179
date submitted: 2021-05-31
date accepted: 2021-08-29
issued: 2021-09-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tu
  given name: Shisheng
author list: Agent
  family name: Xu
  given name: Rui
author list: Agent
  family name: Wang
  given name: Mengen
author list: Agent
  family name: Xie
  given name: Xi
author list: Agent
  family name: Bao
  given name: Chenchang
author list: Agent
  family name: Zhu
  given name: Dongfa
doi: 10.7717/peerj.12179
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-15
copyright: ©2021 Tu et al.
attribution name: Tu et al.

High-resolution prediction of American red squirrel in Interior Alaska: a role model for conservation using open access data, machine learning, GIS and LIDAR
type: item
type: AcademicArticle
description: American red squirrels (Tamiasciurus hudsonicus) are small mammals that are abundantly distributed throughout North America. Urbanization in the Anthropocene is now a global process, and squirrels live in affected landscapes. This leads to squirrels adjusting to human developments. Not much is known about the distribution of squirrels and squirrel middens near humans, especially not in the subarctic and sub-urbanized regions. Although this species is hunted, there are no real publicly available distribution and abundance estimates nor management plans and bag limits for squirrels in Alaska or in the United States known by us, except the endangered Mt. Graham squirrel. In general, insufficient squirrel conservation research is carried out; they are underrepresented in research and its literature. To further the science-based management for such species, this study aims to generate the first digital open access workflow as a generic research template for small mammal work including the latest machine learning of open source and high-resolution LIDAR data in an Open Source Geographic Information System (QGIS) and ArcGIS. Machine learning has proven to be less modeler biased and improve accuracy of the analysis outcome, therefore it is the preferred approach. This template is designed to be rapid, simple, robust, generic and effective for being used by a global audience. As a unique showcase, here a squirrel midden survey was carried out for two years (2016 and 2017). These squirrel middens were detected in a research area of 45,5 hectares (0,455 km2) in downtown Fairbanks, interior boreal forest of Alaska, U.S. Transect distances were geo-referenced with a GPS and adjusted to the visual conditions to count all squirrel middens within the survey area. Different layers of proximity to humans and habitat characteristics were assembled using aerial imagery and LIDAR data (3D data needed for an arboreal species like the red squirrels) consisting of a 3 × 3 m resolution. The…
format: application/pdf
format: text/html
creator: Richard B. Robold
creator: Falk Huettmann
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Data Mining and Machine Learning
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.11830
publisher: PeerJ Inc.
rights: © 2021 Robold and Huettmann
abstract: American red squirrels (Tamiasciurus hudsonicus) are small mammals that are abundantly distributed throughout North America. Urbanization in the Anthropocene is now a global process, and squirrels live in affected landscapes. This leads to squirrels adjusting to human developments. Not much is known about the distribution of squirrels and squirrel middens near humans, especially not in the subarctic and sub-urbanized regions. Although this species is hunted, there are no real publicly available distribution and abundance estimates nor management plans and bag limits for squirrels in Alaska or in the United States known by us, except the endangered Mt. Graham squirrel. In general, insufficient squirrel conservation research is carried out; they are underrepresented in research and its literature. To further the science-based management for such species, this study aims to generate the first digital open access workflow as a generic research template for small mammal work including the latest machine learning of open source and high-resolution LIDAR data in an Open Source Geographic Information System (QGIS) and ArcGIS. Machine learning has proven to be less modeler biased and improve accuracy of the analysis outcome, therefore it is the preferred approach. This template is designed to be rapid, simple, robust, generic and effective for being used by a global audience. As a unique showcase, here a squirrel midden survey was carried out for two years (2016 and 2017). These squirrel middens were detected in a research area of 45,5 hectares (0,455 km2) in downtown Fairbanks, interior boreal forest of Alaska, U.S. Transect distances were geo-referenced with a GPS and adjusted to the visual conditions to count all squirrel middens within the survey area. Different layers of proximity to humans and habitat characteristics were assembled using aerial imagery and LIDAR data (3D data needed for an arboreal species like the red squirrels) consisting of a 3 × 3 m resolution. The…
bibliographic citation: Robold et al. (2021) High-resolution prediction of American red squirrel in Interior Alaska: a role model for conservation using open access data, machine learning, GIS and LIDAR. PeerJ 9:e11830 https://doi.org/10.7717/peerj.11830
date submitted: 2021-01-18
date accepted: 2021-06-30
issued: 2021-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robold
  given name: Richard B.
author list: Agent
  family name: Huettmann
  given name: Falk
doi: 10.7717/peerj.11830
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-14
copyright: © 2021 Robold and Huettmann
attribution name: Robold and Huettmann

Glucosylceramide synthase regulates hepatocyte repair after concanavalin A-induced immune-mediated liver injury
type: item
type: AcademicArticle
description: Background Sphingolipids produce pleiotropic signaling pathways, and participate in the pathological mechanism of hepatocyte apoptosis and necrosis during liver injury. However, the role of glucosylceramide synthase (GCS)–key enzyme that catalyzes the first glycosylation step, in liver injury is still vague. Methods All experiments were conducted using 7–9-week-old pathogen-free male C57BL/6 mice. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were detected in murine models of liver disease, in addition to histological characterization of liver injuries. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the relative expression of the GCS, matrix metallopeptidase-1 (MMP-1), and tissue inhibitor of metalloproteinase-1 (TIMP-1) genes. The GCS was observed through a fluorescence microscope, and the flow cytometry was used to detect hepatocyte apoptosis. The concentrations of serum IL-4, IL-6, and IL-10 were measured using enzyme-linked immune-sorbent assay (ELISA) kit. MMP-1 and TIMP-1 protein expression was measured via western blot (WB) analysis. Results Con A is often used as a mitogen to activate T lymphocytes and promote mitosis. A single dose of Con A injected intravenously will cause a rapid increase of ALT and AST, which is accompanied by the release of cytokines that cause injury and necrosis of hepatocytes. In this study, we successfully induced acute immune hepatitis in mice by Con A. Con A administration resulted in GCS upregulation in liver tissues. Moreover, the mice in the Con A group had significantly higher levels of ALT, AST, IL-4, IL-6, IL-10 and increased hepatocyte apoptosis than the control group. In contrast, all of the aforementioned genes were significantly downregulated after the administration of a GCS siRNA or Genz-123346 (i.e., a glucosylceramide synthase inhibitor) to inhibit the GCS gene. Additionally, the histopathological changes observed herein were consistent with our ALT, A…
format: application/pdf
format: text/html
creator: Jian Gan
creator: Qin Gao
creator: Li Li Wang
creator: Ai Ping Tian
creator: Long Dong Zhu
creator: Li Ting Zhang
creator: Wei Zhou
creator: Xiao Rong Mao
creator: Jun Feng Li
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Histology
description: doi:10.7717/peerj.12138
publisher: PeerJ Inc.
rights: © 2021 Gan et al.
abstract: Background Sphingolipids produce pleiotropic signaling pathways, and participate in the pathological mechanism of hepatocyte apoptosis and necrosis during liver injury. However, the role of glucosylceramide synthase (GCS)–key enzyme that catalyzes the first glycosylation step, in liver injury is still vague. Methods All experiments were conducted using 7–9-week-old pathogen-free male C57BL/6 mice. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were detected in murine models of liver disease, in addition to histological characterization of liver injuries. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the relative expression of the GCS, matrix metallopeptidase-1 (MMP-1), and tissue inhibitor of metalloproteinase-1 (TIMP-1) genes. The GCS was observed through a fluorescence microscope, and the flow cytometry was used to detect hepatocyte apoptosis. The concentrations of serum IL-4, IL-6, and IL-10 were measured using enzyme-linked immune-sorbent assay (ELISA) kit. MMP-1 and TIMP-1 protein expression was measured via western blot (WB) analysis. Results Con A is often used as a mitogen to activate T lymphocytes and promote mitosis. A single dose of Con A injected intravenously will cause a rapid increase of ALT and AST, which is accompanied by the release of cytokines that cause injury and necrosis of hepatocytes. In this study, we successfully induced acute immune hepatitis in mice by Con A. Con A administration resulted in GCS upregulation in liver tissues. Moreover, the mice in the Con A group had significantly higher levels of ALT, AST, IL-4, IL-6, IL-10 and increased hepatocyte apoptosis than the control group. In contrast, all of the aforementioned genes were significantly downregulated after the administration of a GCS siRNA or Genz-123346 (i.e., a glucosylceramide synthase inhibitor) to inhibit the GCS gene. Additionally, the histopathological changes observed herein were consistent with our ALT, A…
bibliographic citation: Gan et al. (2021) Glucosylceramide synthase regulates hepatocyte repair after concanavalin A-induced immune-mediated liver injury. PeerJ 9:e12138 https://doi.org/10.7717/peerj.12138
date submitted: 2021-05-07
date accepted: 2021-08-18
issued: 2021-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Jian
author list: Agent
  family name: Gao
  given name: Qin
author list: Agent
  family name: Wang
  given name: Li Li
author list: Agent
  family name: Tian
  given name: Ai Ping
author list: Agent
  family name: Zhu
  given name: Long Dong
author list: Agent
  family name: Zhang
  given name: Li Ting
author list: Agent
  family name: Zhou
  given name: Wei
author list: Agent
  family name: Mao
  given name: Xiao Rong
author list: Agent
  family name: Li
  given name: Jun Feng
doi: 10.7717/peerj.12138
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-14
copyright: ©2021 Gan et al.
attribution name: Gan et al.

Phylogenetic relationships of sucrose transporters (SUTs) in plants and genome-wide characterization of SUT genes in Orchidaceae reveal roles in floral organ development
type: item
type: AcademicArticle
description: Sucrose is the primary form of photosynthetically produced carbohydrates transported long distance in many plant species and substantially affects plant growth, development and physiology. Sucrose transporters (SUTs or SUCs) are a group of membrane proteins that play vital roles in mediating sucrose allocation within cells and at the whole-plant level. In this study, we investigated the relationships among SUTs in 24 representative plant species and performed an analysis of SUT genes in three sequenced Orchidaceae species: Dendrobium officinale, Phalaenopsis equestris, and Apostasia shenzhenica. All the SUTs from the 24 plant species were classified into three groups and five subgroups, subgroups A, B1, B2.1, B2.2, and C, based on their evolutionary relationships. A total of 22 SUT genes were identified among Orchidaceae species, among which D. officinale had 8 genes (DoSUT01-08), P. equestris had eight genes (PeqSUT01-08) and A. shenzhenica had 6 genes (AsSUT01-06). For the 22 OrchidaceaeSUTs, subgroups A, B2.2 and C contained three genes, whereas the SUT genes were found to have significantly expanded in the monocot-specific subgroup B2.1, which contained 12 genes. To understand sucrose partitioning and the functions of sucrose transporters in Orchidaceae species, we analyzed the water-soluble sugar content and performed RNA sequencing of different tissues of D. officinale, including leaves, stems, flowers and roots. The results showed that although the total content of water-soluble polysaccharides was highest in the stems of D. officinale, the sucrose content was highest in the flowers. Moreover, gene expression analysis showed that most of the DoSUTs were expressed in the flowers, among which DoSUT01,DoSUT07 and DoSUT06 had significantly increased expression levels. These results indicated that stems are used as the main storage sinks for photosynthetically produced sugar in D. officinale and that DoSUTs mainly function in the cellular machinery and development…
format: application/pdf
format: text/html
creator: Yunzhu Wang
creator: Yue Chen
creator: Qingzhen Wei
creator: Hongjian Wan
creator: Chongbo Sun
subject: Bioinformatics
subject: Developmental Biology
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11961
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Sucrose is the primary form of photosynthetically produced carbohydrates transported long distance in many plant species and substantially affects plant growth, development and physiology. Sucrose transporters (SUTs or SUCs) are a group of membrane proteins that play vital roles in mediating sucrose allocation within cells and at the whole-plant level. In this study, we investigated the relationships among SUTs in 24 representative plant species and performed an analysis of SUT genes in three sequenced Orchidaceae species: Dendrobium officinale, Phalaenopsis equestris, and Apostasia shenzhenica. All the SUTs from the 24 plant species were classified into three groups and five subgroups, subgroups A, B1, B2.1, B2.2, and C, based on their evolutionary relationships. A total of 22 SUT genes were identified among Orchidaceae species, among which D. officinale had 8 genes (DoSUT01-08), P. equestris had eight genes (PeqSUT01-08) and A. shenzhenica had 6 genes (AsSUT01-06). For the 22 OrchidaceaeSUTs, subgroups A, B2.2 and C contained three genes, whereas the SUT genes were found to have significantly expanded in the monocot-specific subgroup B2.1, which contained 12 genes. To understand sucrose partitioning and the functions of sucrose transporters in Orchidaceae species, we analyzed the water-soluble sugar content and performed RNA sequencing of different tissues of D. officinale, including leaves, stems, flowers and roots. The results showed that although the total content of water-soluble polysaccharides was highest in the stems of D. officinale, the sucrose content was highest in the flowers. Moreover, gene expression analysis showed that most of the DoSUTs were expressed in the flowers, among which DoSUT01,DoSUT07 and DoSUT06 had significantly increased expression levels. These results indicated that stems are used as the main storage sinks for photosynthetically produced sugar in D. officinale and that DoSUTs mainly function in the cellular machinery and development…
bibliographic citation: Wang et al. (2021) Phylogenetic relationships of sucrose transporters (SUTs) in plants and genome-wide characterization of SUT genes in Orchidaceae reveal roles in floral organ development. PeerJ 9:e11961 https://doi.org/10.7717/peerj.11961
date submitted: 2021-02-25
date accepted: 2021-07-21
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yunzhu
author list: Agent
  family name: Chen
  given name: Yue
author list: Agent
  family name: Wei
  given name: Qingzhen
author list: Agent
  family name: Wan
  given name: Hongjian
author list: Agent
  family name: Sun
  given name: Chongbo
doi: 10.7717/peerj.11961
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Active behaviour of terrestrial caterpillars on the water surface
type: item
type: AcademicArticle
description: Most butterfly and moth larvae (Lepidoptera) are terrestrial. When terrestrial caterpillars accidentally fall into water, they may drown or be preyed upon by aquatic predators before they can safely reach land. However, how terrestrial caterpillars escape aquatic environments and predators remains unclear. In July 2018, we observed a terrestrial caterpillar actively moving forward on the surface of a pond in Japan until it successfully reached the shore. To further investigate this behaviour in terrestrial caterpillars, we experimentally placed larvae of 13 moth species (four families) on a water surface under laboratory and field conditions. All caterpillars floated. Larvae of seven species moved forward on the water surface, whereas those of six species did not. A total of two types of behaviour were observed; in Dinumma deponens, Hypopyra vespertilio, Spirama retorta, Laelia coenosa, Lymantria dispar (all Erebidae), and Naranga aenescens (Noctuidae), larvae swung their bodies rapidly from side to side to propel themselves along the water surface (i.e., undulatory behaviour); in contrast, larvae of Acosmetia biguttula (Noctuidae) rapidly moved the abdomen (posterior segments) up and down for propulsion along the water surface (i.e., flick behaviour). Although thoracic legs were not used for undulatory and flick behaviour, rapid movements of the abdomen were used to propel caterpillars on the water surface. We also observed that undulatory and flick behaviour on the water surface aided caterpillars in escaping aquatic predators under field conditions. In addition, we investigated the relationship between body size and undulatory behaviour on the water surface in the erebid S. retorta under laboratory conditions. The frequency and speed of forward movement on the water surface increased with body length. Together, these results show that the rapid movement of elongated bodies results in forward propulsion on the water surface, allowing some terrestrial caterpillars …
format: application/pdf
format: text/html
creator: Masakazu Hayashi
creator: Shinji Sugiura
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.11971
publisher: PeerJ Inc.
rights: © 2021 Hayashi and Sugiura
abstract: Most butterfly and moth larvae (Lepidoptera) are terrestrial. When terrestrial caterpillars accidentally fall into water, they may drown or be preyed upon by aquatic predators before they can safely reach land. However, how terrestrial caterpillars escape aquatic environments and predators remains unclear. In July 2018, we observed a terrestrial caterpillar actively moving forward on the surface of a pond in Japan until it successfully reached the shore. To further investigate this behaviour in terrestrial caterpillars, we experimentally placed larvae of 13 moth species (four families) on a water surface under laboratory and field conditions. All caterpillars floated. Larvae of seven species moved forward on the water surface, whereas those of six species did not. A total of two types of behaviour were observed; in Dinumma deponens, Hypopyra vespertilio, Spirama retorta, Laelia coenosa, Lymantria dispar (all Erebidae), and Naranga aenescens (Noctuidae), larvae swung their bodies rapidly from side to side to propel themselves along the water surface (i.e., undulatory behaviour); in contrast, larvae of Acosmetia biguttula (Noctuidae) rapidly moved the abdomen (posterior segments) up and down for propulsion along the water surface (i.e., flick behaviour). Although thoracic legs were not used for undulatory and flick behaviour, rapid movements of the abdomen were used to propel caterpillars on the water surface. We also observed that undulatory and flick behaviour on the water surface aided caterpillars in escaping aquatic predators under field conditions. In addition, we investigated the relationship between body size and undulatory behaviour on the water surface in the erebid S. retorta under laboratory conditions. The frequency and speed of forward movement on the water surface increased with body length. Together, these results show that the rapid movement of elongated bodies results in forward propulsion on the water surface, allowing some terrestrial caterpillars …
bibliographic citation: Hayashi et al. (2021) Active behaviour of terrestrial caterpillars on the water surface. PeerJ 9:e11971 https://doi.org/10.7717/peerj.11971
date submitted: 2020-07-21
date accepted: 2021-07-23
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hayashi
  given name: Masakazu
author list: Agent
  family name: Sugiura
  given name: Shinji
doi: 10.7717/peerj.11971
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: © 2021 Hayashi and Sugiura
attribution name: Hayashi and Sugiura

Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed
type: item
type: AcademicArticle
description: Plant defensins (PDFs), short peptides with strong antibacterial activity, play important roles in plant growth, development, and stress resistance. However, there are few systematic analyses on PDFs in Brassica napus. Here, bioinformatics methods were used to identify genome-wide PDFs in Brassica napus, and systematically analyze physicochemical properties, expansion pattern, phylogeny, and expression profiling of BnaPDFs under diverse nutrient stresses. A total of 37 full-length PDF homologs, divided into two subgroups (PDF1s and PDF2s), were identified in the rapeseed genome. A total of two distinct clades were identified in the BnaPDF phylogeny. Clade specific conserved motifs were identified within each clade respectively. Most BnaPDFs were proved to undergo powerful purified selection. The PDF members had enriched cis-elements related to growth and development, hormone response, environmental stress response in their promoter regions. GO annotations indicate that the functional pathways of BnaPDFs are mainly involved in cells killing and plant defense responses. In addition, bna-miRNA164 and bna-miRNA172 respectively regulate the expression of their targets BnaA2.PDF2.5 and BnaC7.PDF2.6. The expression patterns of BnaPDFs were analyzed in different tissues. BnaPDF1.2bs was mainly expressed in the roots, whereas BnaPDF2.2s and BnaPDF2.3s were both expressed in stamen, pericarp, silique, and stem. However, the other BnaPDF members showed low expression levels in various tissues. Differential expression of BnaPDFs under nitrate limitation, ammonium excess, phosphorus starvation, potassium deficiency, cadmium toxicity, and salt stress indicated that they might participate in different nutrient stress resistance. The genome-wide identification and characterization of BnaPDFs will enrich understanding of their molecular characteristics and provide elite gene resources for genetic improvement of rapeseed resistance to nutrient stresses.
format: application/pdf
format: text/html
creator: Ying Liu
creator: Ying-peng Hua
creator: Huan Chen
creator: Ting Zhou
creator: Cai-peng Yue
creator: Jin-yong Huang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12007
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Plant defensins (PDFs), short peptides with strong antibacterial activity, play important roles in plant growth, development, and stress resistance. However, there are few systematic analyses on PDFs in Brassica napus. Here, bioinformatics methods were used to identify genome-wide PDFs in Brassica napus, and systematically analyze physicochemical properties, expansion pattern, phylogeny, and expression profiling of BnaPDFs under diverse nutrient stresses. A total of 37 full-length PDF homologs, divided into two subgroups (PDF1s and PDF2s), were identified in the rapeseed genome. A total of two distinct clades were identified in the BnaPDF phylogeny. Clade specific conserved motifs were identified within each clade respectively. Most BnaPDFs were proved to undergo powerful purified selection. The PDF members had enriched cis-elements related to growth and development, hormone response, environmental stress response in their promoter regions. GO annotations indicate that the functional pathways of BnaPDFs are mainly involved in cells killing and plant defense responses. In addition, bna-miRNA164 and bna-miRNA172 respectively regulate the expression of their targets BnaA2.PDF2.5 and BnaC7.PDF2.6. The expression patterns of BnaPDFs were analyzed in different tissues. BnaPDF1.2bs was mainly expressed in the roots, whereas BnaPDF2.2s and BnaPDF2.3s were both expressed in stamen, pericarp, silique, and stem. However, the other BnaPDF members showed low expression levels in various tissues. Differential expression of BnaPDFs under nitrate limitation, ammonium excess, phosphorus starvation, potassium deficiency, cadmium toxicity, and salt stress indicated that they might participate in different nutrient stress resistance. The genome-wide identification and characterization of BnaPDFs will enrich understanding of their molecular characteristics and provide elite gene resources for genetic improvement of rapeseed resistance to nutrient stresses.
bibliographic citation: Liu et al. (2021) Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed. PeerJ 9:e12007 https://doi.org/10.7717/peerj.12007
date submitted: 2021-01-14
date accepted: 2021-07-27
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Liu
  given name: Ying
author list: Agent
  family name: Hua
  given name: Ying-peng
author list: Agent
  family name: Chen
  given name: Huan
author list: Agent
  family name: Zhou
  given name: Ting
author list: Agent
  family name: Yue
  given name: Cai-peng
author list: Agent
  family name: Huang
  given name: Jin-yong
doi: 10.7717/peerj.12007
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: © 2021 Liu et al.
attribution name: Liu et al.

Substrate type and palaeodepth do not affect the Middle Jurassic taxonomic diversity of crinoids
type: item
type: AcademicArticle
description: Crinoids are largely considered as good indicators for determining environmental conditions. They are robust proxies for inferring changes in salinity and sedimentation rate and for inferring substrate type. Some crinoid groups (e.g., certain comatulids, cyrtocrinids, millericrinids) have a depth preference, thus, making them useful for palaeodepth estimation. The hypotheses that crinoid distribution is substrate-dependent (rock type) or palaeodepth-dependent is tested here based on (a) archival Bathonian-Callovian (Middle Jurassic) crinoid occurrences from Poland and (b) newer finds from five boreholes from eastern Poland. Qualitative data suggests that isocrinids and cyclocrinids occur in both carbonate and siliciclastic rocks. The cyrtocrinids and roveacrinids occur within carbonate rocks, whereas the comatulids are exclusive to siliciclastics. In terms of palaeodepth, most crinoid groups dominate in shallow environments with the sole exception of cyrtocrinids, that are ubiquitous and occur in both shallow (near shore and shallow marine) and slightly deeper (deeper sublittoral to open shelf) settings. The occurrences of the cosmopolitan taxa, Chariocrinus andreae and Balanocrinus subteres (isocrinids), is independent of both substrate type and palaeodepth. Quantitative analyses (Analysis Of Variance; ANOVA) based on substrate type, i.e., substrate-dependency (claystones, sandstones and limestones), and palaeodepth i.e., palaeodepth-dependency (near shore, shallow-marine, mid-ramp and offshore), corroborate qualitative results. Statistical analysis suggest that the distribution of crinoids shows a strong substrate-dependency but not for palaeodepth, although very weak significance (low p value) is noted for near shore and shallow marine settings and crinoid distribution.
format: application/pdf
format: text/html
creator: Mariusz A. Salamon
creator: Anna Feldman-Olszewska
creator: Sreepat Jain
creator: Bruno B.M. Ferré
creator: Karolina Paszcza
creator: Bartosz J. Płachno
subject: Biogeography
subject: Ecosystem Science
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.12017
publisher: PeerJ Inc.
rights: © 2021 Salamon et al.
abstract: Crinoids are largely considered as good indicators for determining environmental conditions. They are robust proxies for inferring changes in salinity and sedimentation rate and for inferring substrate type. Some crinoid groups (e.g., certain comatulids, cyrtocrinids, millericrinids) have a depth preference, thus, making them useful for palaeodepth estimation. The hypotheses that crinoid distribution is substrate-dependent (rock type) or palaeodepth-dependent is tested here based on (a) archival Bathonian-Callovian (Middle Jurassic) crinoid occurrences from Poland and (b) newer finds from five boreholes from eastern Poland. Qualitative data suggests that isocrinids and cyclocrinids occur in both carbonate and siliciclastic rocks. The cyrtocrinids and roveacrinids occur within carbonate rocks, whereas the comatulids are exclusive to siliciclastics. In terms of palaeodepth, most crinoid groups dominate in shallow environments with the sole exception of cyrtocrinids, that are ubiquitous and occur in both shallow (near shore and shallow marine) and slightly deeper (deeper sublittoral to open shelf) settings. The occurrences of the cosmopolitan taxa, Chariocrinus andreae and Balanocrinus subteres (isocrinids), is independent of both substrate type and palaeodepth. Quantitative analyses (Analysis Of Variance; ANOVA) based on substrate type, i.e., substrate-dependency (claystones, sandstones and limestones), and palaeodepth i.e., palaeodepth-dependency (near shore, shallow-marine, mid-ramp and offshore), corroborate qualitative results. Statistical analysis suggest that the distribution of crinoids shows a strong substrate-dependency but not for palaeodepth, although very weak significance (low p value) is noted for near shore and shallow marine settings and crinoid distribution.
bibliographic citation: Salamon et al. (2021) Substrate type and palaeodepth do not affect the Middle Jurassic taxonomic diversity of crinoids. PeerJ 9:e12017 https://doi.org/10.7717/peerj.12017
date submitted: 2021-04-01
date accepted: 2021-07-29
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salamon
  given name: Mariusz A.
author list: Agent
  family name: Feldman-Olszewska
  given name: Anna
author list: Agent
  family name: Jain
  given name: Sreepat
author list: Agent
  family name: Ferré
  given name: Bruno B.M.
author list: Agent
  family name: Paszcza
  given name: Karolina
author list: Agent
  family name: Płachno
  given name: Bartosz J.
doi: 10.7717/peerj.12017
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: ©2021 Salamon et al.
attribution name: Salamon et al.

Catostylus tagi (Class: Scyphozoa, Order: Discomedusae, Suborder: Rhizostomida, Family: Catostylidae) life cycle and first insight into its ecology
type: item
type: AcademicArticle
description: Jellyfish proliferations, which are conspicuous and natural events, cause blooms that may lead to severe consequences for anthropogenic activities and ecosystem structure and functioning. Although research during the last decade has focused on factors influencing the different jellyfish life stages, few species currently have their full life cycle known. In this context, we describe for the first time the developmental stages in the life cycle of Catostylus tagi, from planula to young medusa, reared in the laboratory. The species displays the typical Rhizostomida metagenetic life cycle. Mature scyphistomae display 16 tentacles and a total body length of 1.5 ± 0.2 mm. Only podocyst production and strobilation were observed. Strobilation, occurring continuously under laboratory conditions, was mainly polydisc. The eight-rayed typical ephyrae, with a total body diameter of 2.4 ± 0.4 mm at detachment, showed development typical of the Rhizostomida. As a first step in studying this species’ ecology, we also present preliminary assessments of: (i) the influence of different temperature and salinity regimes on planulae survival, settlement and metamorphosis and (ii) the effect of temperature and diet on asexual reproduction. The results showed a high tolerance of planulae to a wide range of salinities (15‰ to 25‰), while polyp development was significantly faster at higher temperature (20–25 °C). Strobilation onset was 2–3 times faster at 20 °C (10.6 ± 5.4 to 15 ± 6.6 day at various tested diet) than at 15 °C (32.2 ± 3 day). Feeding was a key factor as unfed polyps never underwent strobilation during the trial. Finally, we present the spatial and seasonal distribution of C. tagi in the Tagus estuary (Portugal) in 2019, showing its occurrence throughout the year (except in April), with most observations recorded on the northern shoreline. As C. tagi shows the ability to form blooms and a wide tolerance for temperature and salinity (for planulae and medusae stage), it is ess…
format: application/pdf
format: text/html
creator: Sonia K.M. Gueroun
creator: Tatiana M. Torres
creator: Antonina Dos Santos
creator: Nuno Vasco-Rodrigues
creator: João Canning-Clode
creator: Carlos Andrade
subject: Developmental Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12056
publisher: PeerJ Inc.
rights: © 2021 Gueroun et al.
abstract: Jellyfish proliferations, which are conspicuous and natural events, cause blooms that may lead to severe consequences for anthropogenic activities and ecosystem structure and functioning. Although research during the last decade has focused on factors influencing the different jellyfish life stages, few species currently have their full life cycle known. In this context, we describe for the first time the developmental stages in the life cycle of Catostylus tagi, from planula to young medusa, reared in the laboratory. The species displays the typical Rhizostomida metagenetic life cycle. Mature scyphistomae display 16 tentacles and a total body length of 1.5 ± 0.2 mm. Only podocyst production and strobilation were observed. Strobilation, occurring continuously under laboratory conditions, was mainly polydisc. The eight-rayed typical ephyrae, with a total body diameter of 2.4 ± 0.4 mm at detachment, showed development typical of the Rhizostomida. As a first step in studying this species’ ecology, we also present preliminary assessments of: (i) the influence of different temperature and salinity regimes on planulae survival, settlement and metamorphosis and (ii) the effect of temperature and diet on asexual reproduction. The results showed a high tolerance of planulae to a wide range of salinities (15‰ to 25‰), while polyp development was significantly faster at higher temperature (20–25 °C). Strobilation onset was 2–3 times faster at 20 °C (10.6 ± 5.4 to 15 ± 6.6 day at various tested diet) than at 15 °C (32.2 ± 3 day). Feeding was a key factor as unfed polyps never underwent strobilation during the trial. Finally, we present the spatial and seasonal distribution of C. tagi in the Tagus estuary (Portugal) in 2019, showing its occurrence throughout the year (except in April), with most observations recorded on the northern shoreline. As C. tagi shows the ability to form blooms and a wide tolerance for temperature and salinity (for planulae and medusae stage), it is ess…
bibliographic citation: Gueroun et al. (2021) Catostylus tagi (Class: Scyphozoa, Order: Discomedusae, Suborder: Rhizostomida, Family: Catostylidae) life cycle and first insight into its ecology. PeerJ 9:e12056 https://doi.org/10.7717/peerj.12056
date submitted: 2021-05-31
date accepted: 2021-08-04
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gueroun
  given name: Sonia K.M.
author list: Agent
  family name: Torres
  given name: Tatiana M.
author list: Agent
  family name: Dos Santos
  given name: Antonina
author list: Agent
  family name: Vasco-Rodrigues
  given name: Nuno
author list: Agent
  family name: Canning-Clode
  given name: João
author list: Agent
  family name: Andrade
  given name: Carlos
doi: 10.7717/peerj.12056
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: © 2021 Gueroun et al.
attribution name: Gueroun et al.

Identification and validation of hub genes for diabetic retinopathy
type: item
type: AcademicArticle
description: Background Diabetic retinopathy (DR) is characterized by a gradually progressive alteration in the retinal microvasculature that leads to middle-aged adult acquired persistent blindness. Limited research has been conducted on DR pathogenesis at the gene level. Thus, we aimed to reveal novel key genes that might be associated with DR formation via a bioinformatics analysis. Methods The GSE53257 dataset from the Gene Expression Omnibus was downloaded for gene co-expression analysis. We identified significant gene modules via the Weighted Gene Co-expression Network Analysis, which was conducted by the Protein-Protein Interaction (PPI) Network via Cytoscape and from this we screened for key genes and gene sets for particular functional and pathway-specific enrichments. The hub gene expression was verified by real-time PCR in DR rats modeling and an external database. Results Two significant gene modules were identified. Significant key genes were predominantly associated with mitochondrial function, fatty acid oxidation and oxidative stress. Among all key genes analyzed, six up-regulated genes (i.e., SLC25A33, NDUFS1, MRPS23, CYB5R1, MECR, and MRPL15) were highly and significantly relevant in the context of DR formation. The PCR results showed that SLC25A33 and NDUFS1 expression were increased in DR rats modeling group. Conclusion Gene co-expression network analysis highlights the importance of mitochondria and oxidative stress in the pathophysiology of DR. DR co-expressing gene module was constructed and key genes were identified, and both SLC25A33 and NDUFS1 may serve as potential biomarker and therapeutic target for DR.
format: application/pdf
format: text/html
creator: Li Peng
creator: Wei Ma
creator: Qing Xie
creator: Baihua Chen
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Ophthalmology
description: doi:10.7717/peerj.12126
publisher: PeerJ Inc.
rights: © 2021 Peng et al.
abstract: Background Diabetic retinopathy (DR) is characterized by a gradually progressive alteration in the retinal microvasculature that leads to middle-aged adult acquired persistent blindness. Limited research has been conducted on DR pathogenesis at the gene level. Thus, we aimed to reveal novel key genes that might be associated with DR formation via a bioinformatics analysis. Methods The GSE53257 dataset from the Gene Expression Omnibus was downloaded for gene co-expression analysis. We identified significant gene modules via the Weighted Gene Co-expression Network Analysis, which was conducted by the Protein-Protein Interaction (PPI) Network via Cytoscape and from this we screened for key genes and gene sets for particular functional and pathway-specific enrichments. The hub gene expression was verified by real-time PCR in DR rats modeling and an external database. Results Two significant gene modules were identified. Significant key genes were predominantly associated with mitochondrial function, fatty acid oxidation and oxidative stress. Among all key genes analyzed, six up-regulated genes (i.e., SLC25A33, NDUFS1, MRPS23, CYB5R1, MECR, and MRPL15) were highly and significantly relevant in the context of DR formation. The PCR results showed that SLC25A33 and NDUFS1 expression were increased in DR rats modeling group. Conclusion Gene co-expression network analysis highlights the importance of mitochondria and oxidative stress in the pathophysiology of DR. DR co-expressing gene module was constructed and key genes were identified, and both SLC25A33 and NDUFS1 may serve as potential biomarker and therapeutic target for DR.
bibliographic citation: Peng et al. (2021) Identification and validation of hub genes for diabetic retinopathy. PeerJ 9:e12126 https://doi.org/10.7717/peerj.12126
date submitted: 2021-04-29
date accepted: 2021-08-17
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Li
author list: Agent
  family name: Ma
  given name: Wei
author list: Agent
  family name: Xie
  given name: Qing
author list: Agent
  family name: Chen
  given name: Baihua
doi: 10.7717/peerj.12126
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: ©2021 Peng et al.
attribution name: Peng et al.

Sex- and stage-dependent expression patterns of odorant-binding and chemosensory protein genes in Spodoptera exempta
type: item
type: AcademicArticle
description: As potential molecular targets for developing novel pest management strategies, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) have been considered to initiate odor recognition in insects. Herein, we investigated the OBPs and CSPs in a major global crop pest (Spodoptera exempta). Using transcriptome analysis, we identified 40 OBPs and 33 CSPs in S. exempta, among which 35 OBPs and 29 CSPs had intact open reading frames. Sequence alignment indicated that 30 OBPs and 23 CSPs completely contained the conserved cysteines. OBPs of lepidopteran insects usually belonged to classical, minus-C, and plus-C groups. However, phylogenetic analyses indicated that we only identified 28 classical and seven minus-C OBPs in S. exempta, suggesting that we might have missed some typical OBPs in lepidopteran insects, probably due to their low expression levels. All of the CSPs from S. exempta clustered with the orthologs of other moths. The identification and expression of the OBPs and CSPs were well studied in insect adults by transcriptional analyses, and herein we used samples at different stages to determine the expression of OBPs and CSPs in S. exempta. Interestingly, our data indicated that several OBPs and CSPs were especially or more highly expressed in larvae or pupae than other stages, including three exclusively (SexeOBP13, SexeOBP16 and SexeCSP23) and six more highly (SexeOBP15, SexeOBP37, SexeCSP4, SexeCSP8, SexeCSP19, and SexeCSP33) expressed in larvae, two exclusively (SexeCSP6 and SexeCSP20) and three more highly (SexeOBP18, SexeCSP17, and SexeCSP26) expressed in pupae. Usually, OBPs and CSPs had both male- and female-biased expression patterns in adult antennae. However, our whole-body data indicated that all highly expressed OBPs and CSPs in adults were male-biased or did not differ, suggesting diverse OBP and CSP functions in insect adults. Besides identifying OBPs and CSPs as well as their expression patterns, these results provide a molecular basis…
format: application/pdf
format: text/html
creator: Yonghao Dong
creator: Tong Li
creator: Jin Liu
creator: Meixue Sun
creator: Xingyu Chen
creator: Yongjie Liu
creator: Pengjun Xu
subject: Agricultural Science
subject: Bioinformatics
subject: Entomology
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.12132
publisher: PeerJ Inc.
rights: © 2021 Dong et al.
abstract: As potential molecular targets for developing novel pest management strategies, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) have been considered to initiate odor recognition in insects. Herein, we investigated the OBPs and CSPs in a major global crop pest (Spodoptera exempta). Using transcriptome analysis, we identified 40 OBPs and 33 CSPs in S. exempta, among which 35 OBPs and 29 CSPs had intact open reading frames. Sequence alignment indicated that 30 OBPs and 23 CSPs completely contained the conserved cysteines. OBPs of lepidopteran insects usually belonged to classical, minus-C, and plus-C groups. However, phylogenetic analyses indicated that we only identified 28 classical and seven minus-C OBPs in S. exempta, suggesting that we might have missed some typical OBPs in lepidopteran insects, probably due to their low expression levels. All of the CSPs from S. exempta clustered with the orthologs of other moths. The identification and expression of the OBPs and CSPs were well studied in insect adults by transcriptional analyses, and herein we used samples at different stages to determine the expression of OBPs and CSPs in S. exempta. Interestingly, our data indicated that several OBPs and CSPs were especially or more highly expressed in larvae or pupae than other stages, including three exclusively (SexeOBP13, SexeOBP16 and SexeCSP23) and six more highly (SexeOBP15, SexeOBP37, SexeCSP4, SexeCSP8, SexeCSP19, and SexeCSP33) expressed in larvae, two exclusively (SexeCSP6 and SexeCSP20) and three more highly (SexeOBP18, SexeCSP17, and SexeCSP26) expressed in pupae. Usually, OBPs and CSPs had both male- and female-biased expression patterns in adult antennae. However, our whole-body data indicated that all highly expressed OBPs and CSPs in adults were male-biased or did not differ, suggesting diverse OBP and CSP functions in insect adults. Besides identifying OBPs and CSPs as well as their expression patterns, these results provide a molecular basis…
bibliographic citation: Dong et al. (2021) Sex- and stage-dependent expression patterns of odorant-binding and chemosensory protein genes in Spodoptera exempta. PeerJ 9:e12132 https://doi.org/10.7717/peerj.12132
date submitted: 2021-04-01
date accepted: 2021-08-18
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Yonghao
author list: Agent
  family name: Li
  given name: Tong
author list: Agent
  family name: Liu
  given name: Jin
author list: Agent
  family name: Sun
  given name: Meixue
author list: Agent
  family name: Chen
  given name: Xingyu
author list: Agent
  family name: Liu
  given name: Yongjie
author list: Agent
  family name: Xu
  given name: Pengjun
doi: 10.7717/peerj.12132
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: ©2021 Dong et al.
attribution name: Dong et al.

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