title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1275 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Exploring the expression and preliminary function of chicken Gimap5 gene link: https://peerj.com/articles/7618 last-modified: 2019-09-26 description: GTPase immune-associated protein 5 (Gimap5) plays a key role in maintaining T cell homeostasis, immunological tolerance and inflammatory processes. However, there are no reports on the chicken Gimap5 gene. In this study, the Gimap5 gene was first cloned from chicken and characterized its tissue expression characteristics in different developmental stages. The transcriptional activities of the Gimap5 gene in immune response were identified. The results showed that full-length cDNA sequence of Gimap5 contained 771 bp and encoded a 256-amino acid protein. The Gimap5 gene was transcribed in various tissues and different development stages. The transcriptional activities of Gimap5 gene in the most tissues increased with the development of chicken, but significantly up to peak in liver and large intestine of 10-month-old chicken. The Gimap5 gene exhibited differential transcriptional activities in immune-related tissues in immune responses, with down-regulated in liver (P < 0.01), spleen (P < 0.05) and bursa of Fabricius (P < 0.05), and up-regulated in thymus (P < 0.01). The results show that Gimap5 may be a multifunctional gene involved in tissue function, development and immune response in chicken. These data can provide the foundation for further study of Gimap5. creator: Wanting Zhang creator: Sifan Xu creator: Guanxian Wu creator: Yang Liu creator: Qiuyuan Wang creator: Chaolai Man uri: https://doi.org/10.7717/peerj.7618 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers link: https://peerj.com/articles/7647 last-modified: 2019-09-26 description: Among amniotes, numerous lineages are subject to an evolutionary trend toward body mass and size increases. Large terrestrial species may face important constraints linked to weight bearing, and the limb segments are particularly affected by such constraints due to their role in body support and locomotion. Such groups showing important limb modifications related to high body mass have been called “graviportal.” Often considered graviportal, rhinoceroses are among the heaviest terrestrial mammals and are thus of particular interest to understand the limb modifications related to body mass and size increase. Here, we present a morphofunctional study of the shape variation of the limb long bones among the five living rhinos to understand how the shape may vary between these species in relation with body size, body mass and phylogeny. We used three dimensional geometric morphometrics and comparative analyses to quantify the shape variation. Our results indicate that the five species display important morphological differences depending on the considered bones. The humerus and the femur exhibit noticeable interspecific differences between African and Asiatic rhinos, associated with a significant effect of body mass. The radius and ulna are more strongly correlated with body mass. While the tibia exhibits shape variation both linked with phylogeny and body mass, the fibula displays the greatest intraspecific variation. We highlight three distinct morphotypes of bone shape, which appear in accordance with the phylogeny. The influence of body mass also appears unequally expressed on the different bones. Body mass increase among the five extant species is marked by an increase of the general robustness, more pronounced attachments for muscles and a development of medial parts of the bones. Our study underlines that the morphological features linked to body mass increase are not similar between rhinos and other heavy mammals such as elephants and hippos, suggesting that the weight bearing constraint can lead to different morphological responses. creator: Christophe Mallet creator: Raphaël Cornette creator: Guillaume Billet creator: Alexandra Houssaye uri: https://doi.org/10.7717/peerj.7647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mallet et al. title: Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy link: https://peerj.com/articles/7691 last-modified: 2019-09-26 description: Abyssal plains are among the most biodiverse yet least explored marine ecosystems on our planet, and they are increasingly threatened by human impacts, including future deep seafloor mining. Recovery of abyssal populations from the impacts of polymetallic nodule mining will be partially determined by the availability and dispersal of pelagic larvae leading to benthic recolonization of disturbed areas of the seafloor. Here we use a tree-of-life (TOL) metabarcoding approach to investigate the species richness, diversity, and spatial variability of the larval assemblage at mesoscales across the abyssal seafloor in two mining-claim areas in the eastern Clarion Clipperton Fracture Zone (CCZ; abyssal Pacific). Our approach revealed a previously unknown taxonomic richness within the meroplankton assemblage, detecting larvae from 12 phyla, 23 Classes, 46 Orders, and 65 Families, including a number of taxa not previously reported at abyssal depths or within the Pacific Ocean. A novel suite of parasitic copepods and worms were sampled, from families that are known to associate with other benthic invertebrates or demersal fishes as hosts. Larval assemblages were patchily distributed at the mesoscale, with little similarity in OTUs detected among deployments even within the same 30 × 30 km study area. Our results provide baseline observations on larval diversity prior to polymetallic nodule mining in this region, and emphasize our overwhelming lack of knowledge regarding larvae of the benthic boundary layer in abyssal plain ecosystems. creator: Oliver Kersten creator: Eric W. Vetter creator: Michelle J. Jungbluth creator: Craig R. Smith creator: Erica Goetze uri: https://doi.org/10.7717/peerj.7691 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kersten et al. title: Effect of orienteering experience on walking and running in the absence of vision and hearing link: https://peerj.com/articles/7736 last-modified: 2019-09-26 description: PurposeThis study aimed to examine differences between track and field (T&F) runners and foot-orienteers (Foot-O) in the walking and running tests in the absence of vision and hearing. We attempted to determine whether experienced foot orienteers show better ability to maintain the indicated direction compared to track and field runners.MethodsThis study examined 11 Foot-O and 11 T&F runners. The study consisted of an interview, a field experiment of walking and running in a straight line in the absence of vision and hearing, and coordination skills tests.ResultsParticipants moved straight min. 20 m and max. 40 m during the walking test and min. 20 m and max. 125 m during the running test and then they moved around in a circle. Significant differences between groups were found for the distance covered by walking. Differences between sexes were documented for the distance covered by running and angular deviations. Relationship between lateralization and tendencies to veer were not found. Differences were observed between Foot-O and T&F groups in terms of coordination abilities.ConclusionsParticipants moved in circles irrespective of the type of movement and experience in practicing the sport. Orienteers may use information about their tendencies to turning more often left or right to correct it during their races in dense forests with limited visibility or during night orienteering competition. creator: Weronika Machowska creator: Piotr Cych creator: Adam Siemieński creator: Juliusz Migasiewicz uri: https://doi.org/10.7717/peerj.7736 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Machowska et al. title: Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses link: https://peerj.com/articles/7744 last-modified: 2019-09-26 description: Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production. creator: Gian Maria Niccolò Benucci creator: Reid Longley creator: Peng Zhang creator: Qi Zhao creator: Gregory Bonito creator: Fuqiang Yu uri: https://doi.org/10.7717/peerj.7744 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Benucci et al. title: Kinematics of male Eupalaestrus weijenberghi (Araneae, Theraphosidae) locomotion on different substrates and inclines link: https://peerj.com/articles/7748 last-modified: 2019-09-26 description: BackgroundThe mechanics and energetics of spider locomotion have not been deeply investigated, despite their importance in the life of a spider. For example, the reproductive success of males of several species is dependent upon their ability to move from one area to another. The aim of this work was to describe gait patterns and analyze the gait parameters of Eupalaestrus weijenberghi (Araneae, Theraphosidae) in order to investigate the mechanics of their locomotion and the mechanisms by which they conserve energy while traversing different inclinations and surfaces.MethodsTarantulas were collected and marked for kinematic analysis. Free displacements, both level and on an incline, were recorded using glass and Teflon as experimental surfaces. Body segments of the experimental animals were measured, weighed, and their center of mass was experimentally determined. Through reconstruction of the trajectories of the body segments, we were able to estimate their internal and external mechanical work and analyze their gait patterns.ResultsSpiders mainly employed a walk-trot gait. Significant differences between the first two pairs and the second two pairs were detected. No significant differences were detected regarding the different planes or surfaces with respect to duty factor, time lags, stride frequency, and stride length. However, postural changes were observed on slippery surfaces. The mechanical work required for traversing a level plane was lower than expected. In all conditions, the external work, and within it the vertical work, accounted for almost all of the total mechanical work. The internal work was extremely low and did not rise as the gradient increased.DiscussionOur results support the idea of considering the eight limbs functionally divided into two quadrupeds in series. The anterior was composed of the first two pairs of limbs, which have an explorative and steering purpose and the posterior was more involved in supporting the weight of the body. The mechanical work to move one unit of mass a unit distance is almost constant among the different species tested. However, spiders showed lower values than expected. Minimizing the mechanical work could help to limit metabolic energy expenditure that, in small animals, is relatively very high. However, energy recovery due to inverted pendulum mechanics only accounts for only a small fraction of the energy saved. Adhesive setae present in the tarsal, scopulae, and claw tufts could contribute in different ways during different moments of the step cycle, compensating for part of the energetic cost on gradients which could also help to maintain constant gait parameters. creator: Valentina Silva-Pereyra creator: C Gabriel Fábrica creator: Carlo M. Biancardi creator: Fernando Pérez-Miles uri: https://doi.org/10.7717/peerj.7748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Silva-Pereyra et al. title: Physiological responses of hydroponically-grown Japanese mint under nutrient deficiency link: https://peerj.com/articles/7751 last-modified: 2019-09-26 description: This research aims to determine growth and deficiency patterns as well as antioxidative potentials of Japanese mint (Mentha arvensis) hydroponically grown under limited macronutrients and micronutrients. The experiment was conducted for 60 days after transplanting in an evaporative greenhouse (avg temp = 28–30 °C, 60–65 %RH), using deep water culture technique. Plants were grown in nutrient solution consisting of complete Hoagland’s solution (CTRL), and nutrient solutions lacking one of the following macronutrients and micronutrients: nitrogen (-N), phosphorus (-P), potassium (-K), iron (-Fe), manganese (-Mn), and copper (-Cu). The deficiency symptoms, growth patterns, and stress response mechanism were followed. All treatments except for the CTRL induced deficiency symptoms and physiological changes. Macronutrient deprivation reduced growth determined by the morphological parameters while micronutrient omission had no effect except for no iron treatment. The result showed that potassium and iron deficiencies had foremost adversely effect on growth of Japanese mint. Under nutrient stress conditions, plant only gave antioxidative responses to phosphorus and potassium deficiencies. However, the negative plant-stress relationship was found for no iron treatment indicating the detoxification mode of plant for lacking of micronutrient. creator: Chananchida Janpen creator: Naruemon Kanthawang creator: Chaiartid Inkham creator: Fui Ying Tsan creator: Sarana Rose Sommano uri: https://doi.org/10.7717/peerj.7751 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Janpen et al. title: Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system link: https://peerj.com/articles/7762 last-modified: 2019-09-26 description: BackgroundChanges in gut microbiome are closely related to dietary and environment variations, and diurnal circle interventions impact on human metabolism and the microbiome. Changes in human gut microbiome and serum biochemical parameters during long-term isolation in a controlled ecological life support system (CELSS) are of great significance for maintaining the health of crewmembers. The Green Star 180 project performed an integrated study involving a four-person, 180-day duration assessment in a CELSS, during which variations in gut microbiome and the concentration of serum 25-hydroxyvitamin D, α-tocopherol, retinol and folic acid from the crewmembers were determined.ResultsEnergy intake and body mass index decreased during the experiment. A trade-off between Firmicutes and Bacteroidetes during the study period was observed. Dynamic variations in the two dominant genus Bacteroides and Prevotella indicated a variation of enterotypes. Both the evenness and richness of the fecal microbiome decreased during the isolation in the CELSS. Transition of diurnal circle from Earth to Mars increased the abundance of Fusobacteria phylum and decreased alpha diversity of the fecal microbiome. The levels of serum 25-hydroxyvitamin D in the CELSS were significantly lower than those outside the CELSS.ConclusionsThe unique isolation process in the CELSS led to a loss of alpha diversity and a transition of enterotypes between Bacteroides and Prevotella. Attention should therefore be paid to the transition of the diurnal circle and its effects on the gut microbiome during manned Mars explorations. In particular, serum 25-hydroxyvitamin D levels require monitoring under artificial light environments and during long-term space flight. Large-scale studies are required to further consolidate our findings. creator: Hai-Sheng Dong creator: Pu Chen creator: Yan-Bo Yu creator: Peng Zang creator: Zhao Wei uri: https://doi.org/10.7717/peerj.7762 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dong et al. title: The relationships between bilingual learning, willingness to study abroad and convergent creativity link: https://peerj.com/articles/7776 last-modified: 2019-09-26 description: Convergent creativity is a form of creative thinking that uses existing knowledge or traditional methods to analyze available information and generate an appropriate solution. The differences in the performance of participants in convergent creativity caused by bilingual learning is a popular research area in creativity. A final sample of 68 participants was asked to complete the remote associates test (RAT). The results indicate that a moderate positive correlation exists between bilingual learning and convergent creativity. Students who want to study abroad perform better on the RAT than those who do not, and this effect is mediated by second language proficiency. These findings suggest that improving students’ English proficiency and increasing their opportunities to study abroad may be effective ways to promoting convergent creativity. creator: Yuan Zhao creator: Yuan Yuan creator: Wangbing Shen creator: Chuanlin Zhu creator: Dianzhi Liu uri: https://doi.org/10.7717/peerj.7776 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Transcriptome association studies of neuropsychiatric traits in African Americans implicate PRMT7 in schizophrenia link: https://peerj.com/articles/7778 last-modified: 2019-09-26 description: In the past 15 years, genome-wide association studies (GWAS) have provided novel insight into the genetic architecture of various complex traits; however, this insight has been primarily focused on populations of European descent. This emphasis on European populations has led to individuals of recent African descent being grossly underrepresented in the study of genetics. With African Americans making up less than 2% of participants in neuropsychiatric GWAS, this discrepancy is magnified in diseases such as schizophrenia and bipolar disorder. In this study, we performed GWAS and the gene-based association method PrediXcan for schizophrenia (n = 2,256) and bipolar disorder (n = 1,019) in African American cohorts. In our PrediXcan analyses, we identified PRMT7 (P = 5.5 × 10−6, local false sign rate = 0.12) as significantly associated with schizophrenia following an adaptive shrinkage multiple testing adjustment. This association with schizophrenia was confirmed in the much larger, predominantly European, Psychiatric Genomics Consortium. In addition to the PRMT7 association with schizophrenia, we identified rs10168049 (P = 1.0 × 10−6) as a potential candidate locus for bipolar disorder with highly divergent allele frequencies across populations, highlighting the need for diversity in genetic studies. creator: Peter N. Fiorica creator: Heather E. Wheeler uri: https://doi.org/10.7717/peerj.7778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fiorica and Wheeler