title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=426 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology link: https://peerj.com/articles/16011 last-modified: 2023-09-07 description: In the literature there are numerous reports of developmental deformities in arthropods collected in their natural habitat. Since such teratogenically affected individuals are found purely by chance, the causes of their defects are unknown. Numerous potential physical, mechanical, chemical, and biological teratogens have been considered and tested in the laboratory. Thermal shocks, frequently used in teratological research on the spider Eratigena atrica, have led to deformities on both the prosoma and the opisthosoma. In the 2020/2021 breeding season, by applying alternating temperatures (14 °C and 32 °C, changed every 12 h) for the first 10 days of embryonic development, we obtained 212 postembryos (out of 3,007) with the following anomalies: oligomely, heterosymely, bicephaly, schistomely, symely, polymely, complex anomalies, and others. From these we selected six spiders with defects on the prosoma and two with short appendages on the pedicel for further consideration. The latter cases seem particularly interesting because appendages do not normally develop on this body part, viewed as the first segment of the opisthosoma, and appear to represent examples of atavism. In view of the ongoing development of molecular techniques and recent research on developmental mechanisms in spiders, we believe the observed phenotypes may result, at least in part, from the erroneous suppression or expression of segmentation or appendage patterning genes. We consider “knockdown” experiments described in the literature as a means for generating hypotheses about the sources of temperature-induced body abnormalities in E. atrica. creator: Teresa Napiórkowska creator: Julita Templin creator: Paweł Napiórkowski creator: Mark A. Townley uri: https://doi.org/10.7717/peerj.16011 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Napiórkowska et al. title: The current landscape of m6A modification in urological cancers link: https://peerj.com/articles/16023 last-modified: 2023-09-07 description: N6-methyladenosine (m6A) methylation is a dynamic and reversible procession of epigenetic modifications. It is increasingly recognized that m6A modification has been involved in the tumorigenesis, development, and progression of urological tumors. Emerging research explored the role of m6A modification in urological cancer. In this review, we will summarize the relationship between m6A modification, renal cell carcinoma, bladder cancer, and prostate cancer, and discover the biological function of m6A regulators in tumor cells. We will also discuss the possible mechanism and future application value used as a potential biomarker or therapeutic target to benefit patients with urological cancers. creator: Yaohui Zeng creator: Cai Lv creator: Bangbei Wan creator: Binghao Gong uri: https://doi.org/10.7717/peerj.16023 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zeng et al. title: Temporal variation of the relationships between rice yield and climate variables since 1925 link: https://peerj.com/articles/16045 last-modified: 2023-09-07 description: BackgroundLong-term time-series datasets of crop yield and climate variables are necessary to study the temporal variation of climate effects on crops. The aim of this study was to broadly assess assessment of the effects of climate on rice, and the associated temporal variations of the effects during the long-term period.MethodsWe conducted field experiments in Taiwan from 1925 to 2019 to collect and analyze rice yield data and evaluate the impacts of changes in average temperature, diurnal temperature range (DTR), rainfall, and sunshine duration on rice yield during cool and warm cropping seasons. We then estimated the relationships between annual grain yield and the climate variables using the time series of their first difference values. We also computed the total relative and annual actual yield changes using regression coefficients for each climate variable for the intervals 1925–1944, 1945–1983, and 1996–2019 to reveal the impacts of climate change on yields and the associated temporal variations during the overall experimental period.ResultsThe annual daily average temperature calculated from the trend of the regression lines increased by 0.94–1.03 °C during the 95-year period. The maximum temperature remained steady while the minimum temperature increased, leading to decreased DTR. The total annual rainfall decreased by 237–352 mm and the annual total sunshine duration decreased by 93.9–238.9 h during the experimental period. We observed that during the cool cropping season, yield response to temperature change decreased, while that to DTR and rainfall changes increased. During the warm cropping season, all the yield responses to temperature, DTR, and rainfall changes were negative throughout the experimental period. In recent years (1996–2019) the estimated annual actual rice yield changes during the cool cropping season were negatively affected by climate variables (except for sunshine duration), and slightly positively affected (except for temperature) during the warm cropping season. Compared to the effects of temperature and DTR, those of rainfall and sunshine duration on rice yield changes were weak. This study contributes to provide impacts of climate change on rice yield and associated long-term temporal variations over nearly a century. creator: Hungyen Chen creator: Yi-Chien Wu creator: Chih-Yung Teng uri: https://doi.org/10.7717/peerj.16045 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen et al. title: Interference with the retinoic acid signalling pathway inhibits the initiation of teeth and caudal primary scales in the small-spotted catshark Scyliorhinus canicula link: https://peerj.com/articles/15896 last-modified: 2023-09-06 description: The retinoic acid (RA) pathway was shown to be important for tooth development in mammals, and suspected to play a key role in tooth evolution in teleosts. The general modalities of development of tooth and “tooth-like” structures (collectively named odontodes) seem to be conserved among all jawed vertebrates, both with regard to histogenesis and genetic regulation. We investigated the putative function of RA signalling in tooth and scale initiation in a cartilaginous fish, the small-spotted catshark Scyliorhinus canicula. To address this issue, we identified the expression pattern of genes from the RA pathway during both tooth and scale development and performed functional experiments by exposing small-spotted catshark embryos to exogenous RA or an inhibitor of RA synthesis. Our results showed that inhibiting RA synthesis affects tooth but not caudal primary scale development while exposure to exogenous RA inhibited both. We also showed that the reduced number of teeth observed with RA exposure is probably due to a specific inhibition of tooth bud initiation while the observed effects of the RA synthesis inhibitor is related to a general delay in embryonic development that interacts with tooth development. This study provides data complementary to previous studies of bony vertebrates and support an involvement of the RA signalling pathway toolkit in odontode initiation in all jawed vertebrates. However, the modalities of RA signalling may vary depending on the target location along the body, and depending on the species lineage. creator: Isabelle Germon creator: Coralie Delachanal creator: Florence Mougel creator: Camille Martinand-Mari creator: Mélanie Debiais-Thibaud creator: Véronique Borday-Birraux uri: https://doi.org/10.7717/peerj.15896 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Germon et al. title: Site-specific length-biomass relationships of arctic arthropod families are critical for accurate ecological inferences link: https://peerj.com/articles/15943 last-modified: 2023-09-06 description: Arthropods play a crucial role in terrestrial ecosystems, for instance in mediating energy fluxes and in forming the food base for many organisms. To better understand their functional role in such ecosystem processes, monitoring of trends in arthropod biomass is essential. Obtaining direct measurements of the body mass of individual specimens is laborious. Therefore, these data are often indirectly acquired by utilizing allometric length-biomass relationships based on a correlative parameter, such as body length. Previous studies have often used such relationships with a low taxonomic resolution and/or small sample size and/or adopted regressions calibrated in different biomes. Despite the scientific interest in the ecology of arctic arthropods, no site-specific family-level length-biomass relationships have hitherto been published. Here we present 27 family-specific length-biomass relationships from two sites in the High Arctic: Zackenberg in northeast Greenland and Knipovich in north Taimyr, Russia. We show that length-biomass regressions from different sites within the same biome did not affect estimates of phenology but did result in substantially different estimates of arthropod biomass. Estimates of daily biomass at Zackenberg were on average 24% higher when calculated using regressions for Knipovich compared to using regressions for Zackenberg. In addition, calculations of daily arthropod biomass at Zackenberg based on order-level regressions from frequently cited studies in literature revealed overestimations of arthropod biomass ranging from 69.7% to 130% compared to estimates based on regressions for Zackenberg. Our results illustrate that the use of allometric relationships from different sites can significantly alter the biological interpretation of, for instance, the interaction between insectivorous birds and their arthropod prey. We conclude that length-biomass relationships should be locally established rather than being based on global relationships. creator: Tom S. L. Versluijs creator: Mikhail K. Zhemchuzhnikov creator: Dmitry Kutcherov creator: Tomas Roslin creator: Niels Martin Schmidt creator: Jan A. van Gils creator: Jeroen Reneerkens uri: https://doi.org/10.7717/peerj.15943 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Versluijs et al. title: Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences link: https://peerj.com/articles/15975 last-modified: 2023-09-06 description: The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021–2040 and 2061–2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins. creator: Shantanu Kundu creator: Tanoy Mukherjee creator: Manokaran Kamalakannan creator: Gaurav Barhadiya creator: Chirashree Ghosh creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.15975 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kundu et al. title: Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains) link: https://peerj.com/articles/15997 last-modified: 2023-09-06 description: BackgroundRhizosphere bacteria play important roles in plant growth and secondary metabolite accumulation. Moreover, only with favorable production areas and desirable germplasm can high-yield and high-quality medicinal materials be produced. However, whether origin and germplasm indirectly affect the yield and quality of Angelica dahurica var. formosana through rhizosphere bacterial effects are not known.MethodsIn this study, a high-throughput sequencing strategy was used to explore the relationship between the rhizosphere bacterial community and the cultivation of A. dahurica var. formosana from different production areas and germplasm for the first time.Results(1) Proteobacteria was the dominant bacterial phylum in the rhizosphere soil of A. dahurica var. formosana, and these bacteria were stable and conserved to a certain extent. (2) High abundance of Proteobacteria was an important rhizospheric indicator of high yield, and high abundance of Firmicutes was an important indicator of high quality. Proteobacteria and Firmicutes might have an important relationship with the yield and quality of A. dahurica var. formosana, respectively. (3) PCoA cluster analysis demonstrated that both production area and germplasm affected the bacterial community structure in the rhizosphere of A. dahurica var. formosana to a certain extent, and production area had the greatest effect. In addition to available potassium, the rhizosphere soil nutrient levels of different production areas strongly affected the bacterial diversity and community. These findings provide a theoretical basis for the exploitation and utilization of rhizosphere microbial resources of A. dahurica var. formosana and offer a novel approach for increasing the yield and quality of this crop. creator: Meiyan Jiang creator: Fei Yao creator: Yunshu Yang creator: Yang Zhou creator: Kai Hou creator: Yinyin Chen creator: Dongju Feng creator: Wei Wu uri: https://doi.org/10.7717/peerj.15997 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jiang et al. title: D-DI/PLT can be a prognostic indicator for sepsis link: https://peerj.com/articles/15910 last-modified: 2023-09-05 description: AimsTo investigate the indicators affecting the early outcome of patients with sepsis and to explore its prognostic efficacy for sepsis.MethodsWe collected clinical data from 201 patients with sepsis admitted to the emergency department of Xijing Hospital between June 2019 and June 2022. The patients were categorized into groups (survival or fatality) based on their 28-day prognosis. The clinical characteristics, biochemical indexes, organ function-related indicators, and disease scores of the patients were analyzed for both groups. Risk factor analysis was conducted for the indicators with significant differences.ResultsAmong the indicators with significant differences between the deceased and survival groups, D-dimer (D-DI), Sequential Organ Failure Assessment (SOFA) score, platelet (PLT), international normalized ratio (INR), and D-DI/PLT were identified as independent risk factors affecting the prognosis of sepsis patients. Receiver operating characteristic (ROC) curves showed that D-DI/PLT (area under the curve (AUC) = 93.9), D-DI (AUC = 89.6), PLT (AUC = 81.3), and SOFA (AUC = 78.4) had good judgment efficacy. Further, Kaplan Meier (K-M) survival analysis indicated that the 28-day survival rates of sepsis patients were significantly decreased when they had high levels of D-DI/PLT, D-DI, and SOFA as well as low PLTs. The hazard ratio (HR) of D-DI/PLT between the two groups was the largest (HR = 16.19).ConclusionsD-DI/PLT may be an independent risk factor for poor prognosis in sepsis as well as a clinical predictor of patient prognosis. creator: Xiaojun Zhao creator: Xiuhua Wu creator: Yi Si creator: Jiangang Xie creator: Linxiao Wang creator: Shanshou Liu creator: Chujun Duan creator: Qianmei Wang creator: Dan Wu creator: Yifan Wang creator: Jijun Chen creator: Jing Yang creator: Shanbo Hu creator: Wen Yin creator: Junjie Li uri: https://doi.org/10.7717/peerj.15910 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhao et al. title: Genetic structure of Trifolium pratense populations in a cityscape link: https://peerj.com/articles/15927 last-modified: 2023-09-05 description: Urban grasslands provide numerous ecosystem services, and their maintenance should be based on naturally regenerating plant populations. However, the urban environment is challenging for preserving viable populations, mostly because of their high fragmentation and small size, which can lead to genetic drift. We examined red clover (Trifolium pratense) in a medium-size city in Central Europe to test the cityscape effect on within- and among-population genetic diversity. We used eight inter-simple sequence repeat markers to examine the genetic structure of 16 populations, each represented by eight individuals. The isolation by resistance was analysed using a least cost patch approach, focusing on gene flow via pollinators. We found great variation among T. pratense populations, with no discernible geographic pattern in genetic diversity. We linked the diversity to the long history of the city and high stochasticity of land use changes that occurred with city development. In particular, we did not find that the Odra River (ca. 100 m wide) was a strong barrier to gene transfer. However, notable isolation was present due to resistance and distance, indicating that the populations are threatened by genetic drift. Therefore, gene movement between populations should be increased by appropriate management of urban green areas. We also found that small urban grassland (UG) patches with small populations can still hold rare alleles which significantly contribute to the overall genetic variation of T. pratense in the city. creator: Hassanali Mollashahi creator: Jacek Urbaniak creator: Tomasz H. Szymura creator: Magdalena Szymura uri: https://doi.org/10.7717/peerj.15927 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mollashahi et al. title: Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland link: https://peerj.com/articles/15985 last-modified: 2023-09-05 description: BackgroundLake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn.MethodsWe sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers.ResultsOverall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respectively). No signals of recent population bottlenecks were detected in the brown trout of Lake Þingvallavatn.DiscussionThis is the first time that the genetic structure and diversity of brown trout in the watershed of River Ölfusá have been assessed. Our results point towards the presence of a metapopulation in the watershed of Lake Þingvallavatn, which has been influenced by restoration efforts and is now dominated by a genetic component originated in River Öxará. Many of the locations studied represent different populations. Those that are isolated in headwater streams and lakes are genetically distinct presenting low genetic diversity, yet they can be important in increasing the genetic variation in downstream populations. These populations should be considered for conservation and direct management. creator: Marcos Lagunas creator: Arnar Pálsson creator: Benóný Jónsson creator: Magnús Jóhannsson creator: Zophonías O. Jónsson creator: Sigurður S. Snorrason uri: https://doi.org/10.7717/peerj.15985 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lagunas et al.