title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=841 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The expansion and diversity of the CYP75 gene family in Vitaceae link: https://peerj.com/articles/12174 last-modified: 2021-09-15 description: The CYP75 gene family plays an important role in flavonoid biosynthesis in plants. Little is known about the evolution of the gene family within the grape family. Here, we extracted the CYP75 genes from transcriptome data of 15 grape species and 36 representative genomes from other plants to explore the evolutionary history of the CYP75 gene family in Vitaceae. The structure of the CYP75 protein sequences is highly conserved with the variation mainly occurring in the N terminal and the middle region. The evolutionary analyses suggested classifying the CYP75 gene family into three groups in Vitaceae, namely Vitaceae A1, Vitaceae A2 and Vitaceae B. The Vitaceae A1 and A2 belong to the CYP75A subfamily and the Vitaceae B belongs to the CYP75B subfamily. Within the Vitaceae A1, most Vitaceae taxa present only one copy of the CYP75A protein sequence except for Vitis vinifera with a high number of sequences, which might have originated through recent gene duplications after its split from the other species. Vitaceae A2 contain only CYP75A sequences from Vitaceae sister to one from Camellia sinensis, probably representing a relict lineage. The CYP75B proteins were found to be dominated in Vitaceae and other angiosperms. Our results provide important insights into understanding the evolutionary history of the CYP75 gene family in Vitaceae and other angiosperms. creator: Yang Xiao creator: Jun Wen creator: Ran Meng creator: Ying Meng creator: Qiang Zhou creator: Ze-Long Nie uri: https://doi.org/10.7717/peerj.12174 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xiao et al. title: Identification and characterization of expression profiles of neuropeptides and their GPCRs in the swimming crab, Portunus trituberculatus link: https://peerj.com/articles/12179 last-modified: 2021-09-15 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. creator: Shisheng Tu creator: Rui Xu creator: Mengen Wang creator: Xi Xie creator: Chenchang Bao creator: Dongfa Zhu uri: https://doi.org/10.7717/peerj.12179 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tu et al. title: High-resolution prediction of American red squirrel in Interior Alaska: a role model for conservation using open access data, machine learning, GIS and LIDAR link: https://peerj.com/articles/11830 last-modified: 2021-09-14 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 layer data was used to train a predictive distribution model for red squirrel middens with machine learning. The model showed the relative index of occurrence (RIO) in a map and identified canopy height, distance to trails, canopy density and the distance to a lake, together, as the strongest predictors for squirrel midden distribution whereas open landscape and disturbed areas are avoided. It is concluded that squirrels select for high and dense forests for middens while avoiding human disturbance. This study is able to present a machine learning template to easily and rapidly produce an accurate abundance prediction which can be used for management implications. creator: Richard B. Robold creator: Falk Huettmann uri: https://doi.org/10.7717/peerj.11830 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Robold and Huettmann title: Glucosylceramide synthase regulates hepatocyte repair after concanavalin A-induced immune-mediated liver injury link: https://peerj.com/articles/12138 last-modified: 2021-09-14 description: BackgroundSphingolipids 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.MethodsAll 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.ResultsCon 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, AST, IL-4, IL-6, and IL-10 expression results. However, unlike this, hepatocyte apoptosis has been further increased on the basis of the Con A group. Moreover, our qRT-PCR and WB results indicated that the expression of MMP-1 in the Con A group was significantly lower than that in the control group, whereas TIMP-1 exhibited the opposite trend. Conversely, MMP-1 expression in the GCS siRNA and Genz-123346 groups was higher than that in the Con A group, whereas TIMP-1 expression was lower.ConclusionsGCS inhibition reduces Con A-induced immune-mediated liver injury in mice, which may be due to the involvement of GCS in the hepatocyte repair process after injury. 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 uri: https://doi.org/10.7717/peerj.12138 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gan et al. title: Phylogenetic relationships of sucrose transporters (SUTs) in plants and genome-wide characterization of SUT genes in Orchidaceae reveal roles in floral organ development link: https://peerj.com/articles/11961 last-modified: 2021-09-13 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 of floral organs. Our findings provide valuable information on sucrose partitioning and the evolution and functions of SUT genes in Orchidaceae and other species. creator: Yunzhu Wang creator: Yue Chen creator: Qingzhen Wei creator: Hongjian Wan creator: Chongbo Sun uri: https://doi.org/10.7717/peerj.11961 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Active behaviour of terrestrial caterpillars on the water surface link: https://peerj.com/articles/11971 last-modified: 2021-09-13 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 to avoid drowning or aquatic predators. We further suggested potential factors related to morphology, host plant habitat, and defensive behaviour that may have led to the acquisition of aquatic behaviour in terrestrial caterpillars. creator: Masakazu Hayashi creator: Shinji Sugiura uri: https://doi.org/10.7717/peerj.11971 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hayashi and Sugiura title: Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed link: https://peerj.com/articles/12007 last-modified: 2021-09-13 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. creator: Ying Liu creator: Ying-peng Hua creator: Huan Chen creator: Ting Zhou creator: Cai-peng Yue creator: Jin-yong Huang uri: https://doi.org/10.7717/peerj.12007 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2021 Liu et al. title: Substrate type and palaeodepth do not affect the Middle Jurassic taxonomic diversity of crinoids link: https://peerj.com/articles/12017 last-modified: 2021-09-13 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. creator: Mariusz A. Salamon creator: Anna Feldman-Olszewska creator: Sreepat Jain creator: Bruno B.M. Ferré creator: Karolina Paszcza creator: Bartosz J. Płachno uri: https://doi.org/10.7717/peerj.12017 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Salamon et al. title: Catostylus tagi (Class: Scyphozoa, Order: Discomedusae, Suborder: Rhizostomida, Family: Catostylidae) life cycle and first insight into its ecology link: https://peerj.com/articles/12056 last-modified: 2021-09-13 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 essential to understand its life cycle. creator: Sonia K.M. Gueroun creator: Tatiana M. Torres creator: Antonina Dos Santos creator: Nuno Vasco-Rodrigues creator: João Canning-Clode creator: Carlos Andrade uri: https://doi.org/10.7717/peerj.12056 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gueroun et al. title: Identification and validation of hub genes for diabetic retinopathy link: https://peerj.com/articles/12126 last-modified: 2021-09-13 description: BackgroundDiabetic 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.MethodsThe 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.ResultsTwo 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.ConclusionGene 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. creator: Li Peng creator: Wei Ma creator: Qing Xie creator: Baihua Chen uri: https://doi.org/10.7717/peerj.12126 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Peng et al.