Interference with the retinoic acid signalling pathway inhibits the initiation of teeth and caudal primary scales in the small-spotted catshark Scyliorhinus canicula
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.
Germon et al. (2023) Interference with the retinoic acid signalling pathway inhibits the initiation of teeth and caudal primary scales in the small-spotted catshark Scyliorhinus canicula. PeerJ 11:e15896 https://doi.org/10.7717/peerj.15896
Site-specific length-biomass relationships of arctic arthropod families are critical for accurate ecological inferences
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.
Versluijs et al. (2023) Site-specific length-biomass relationships of arctic arthropod families are critical for accurate ecological inferences. PeerJ 11:e15943 https://doi.org/10.7717/peerj.15943
Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences
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.
Kundu et al. (2023) Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences. PeerJ 11:e15975 https://doi.org/10.7717/peerj.15975
Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)
Background Rhizosphere 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. Methods In 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.
Jiang et al. (2023) Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains). PeerJ 11:e15997 https://doi.org/10.7717/peerj.15997
D-DI/PLT can be a prognostic indicator for sepsis
Aims To investigate the indicators affecting the early outcome of patients with sepsis and to explore its prognostic efficacy for sepsis. Methods We 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. Results Among 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). Conclusions D-DI/PLT may be an independent risk factor for poor prognosis in sepsis as well as a clinical predictor of patient prognosis.
Zhao et al. (2023) D-DI/PLT can be a prognostic indicator for sepsis. PeerJ 11:e15910 https://doi.org/10.7717/peerj.15910
Genetic structure of Trifolium pratense populations in a cityscape
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.
Mollashahi et al. (2023) Genetic structure of Trifolium pratense populations in a cityscape. PeerJ 11:e15927 https://doi.org/10.7717/peerj.15927
Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland
Background Lake 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. Methods We 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. Results Overall, 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. Discussion This 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.
Lagunas et al. (2023) Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland. PeerJ 11:e15985 https://doi.org/10.7717/peerj.15985
Relationship between vertical facial morphology and dental arch measurements in class II malocclusion: a retrospective study
Background To evaluate the relationship between dental arch measurements and the vertical facial pattern determined in skeletal Class II untreated patients. Methods Lateral cephalograms and plaster models were obtained from 124 untreated female adults (average age: 17.6 ± 3.8 years). Class I (CI), Class II Division 1 (CII/1) and Class II Division 2 (CII/2) malocclusions were divided into three subgroups according to their vertical morphology as hypodivergent, normodivergent and hyperdivergent. The multivariate variance analysis (MANOVA) method was used in the comparison of measurement values according to vertical and sagittal morphology. The relationship between both A point-Nasion-B point (ANB) and Frankfurt-mandibular plane (FMA) angles and dental arch measurements was examined by Pearson correlation analysis. The significance level was received as p < 0.05. Results While vertical morphology has a statistically significant effect on mandibular arch length, sagittal morphology affects maxillary arch depth. The parameters influenced by both morphologies are maxillary and mandibular arch length, as well as maxillary intermolar width. The mandibular arch length was significantly shorter in hyperdivergent-CII-2 malocclusion (50.5 ± 7.4 mm). Larger values were obtained in both mandibular arch length and maxillary arch depth measurements in CII-1 malocclusion compared to CII-2 malocclusion. The maxillary intermolar width was significantly shorter in hypodivergent-CII-1 malocclusion (46.8 ± 3.4 mm), while it was higher in hypodivergent-CI malocclusion (51.1 ± 3.4 mm). The maxillary arch length was the lowest in hyperdivergent-CI malocclusion (63.1 ± 13.3 mm) and the highest in hypodivergent-CI malocclusion (72.8 ± 7.6 mm). Additionally, a positive but weak correlation was found between ANB and FMA angles. Conclusion Dental arch measurements have been found to be affected by both vertical facial morphology and skeletal sagittal relationship. A positive correlation was found between ANB and FMA angles.
Ocak et al. (2023) Relationship between vertical facial morphology and dental arch measurements in class II malocclusion: a retrospective study. PeerJ 11:e16031 https://doi.org/10.7717/peerj.16031
Interaction of Val66Met BDNF and 5-HTTLPR polymorphisms with prevalence of post-earthquake 27-F PTSD in Chilean population
Post-traumatic stress (PTSD) disorder is a mental health condition that can occur after experiencing or witnessing a traumatic event. The 27-F earthquake that struck Chile in 2010 was one such event that had a significant impact on the mental health of the population. A study was conducted to investigate the prevalence of PTSD and its associated factors among survivors of this earthquake. The study was a longitudinal design, involving a sample of 913 patients aged 18 to 75 years who attended 10 Primary Care Centers in Concepción, Chile. The Composite International Diagnostic Interview (CIDI) was used to assess both depressive episodes (DE) and PTSD before and after the earthquake. The study also involved genotyping studies using saliva samples from the participants, specifically focusing on the Val66Met and 5-HTTLPR polymorphisms. Statistical analysis was performed to examine the association between different variables and the presence of PTSD. These variables included demographic factors, family history of psychiatric disorders, DE, childhood maltreatment experiences, and critical traumatic events related to the earthquake. The results showed that the incidence of post-earthquake PTSD was 11.06%. No significant differences were found between the groups of participants who developed post-earthquake PTSD regarding the Val66Met or 5-HTTLPR polymorphisms. However, a significant association was found between the concomitant diagnosis of DE and the development of post-earthquake PTSD. The presence of DE doubled the risk of developing post-earthquake PTSD. The number of traumatic events experienced also had a statistically significant association with an increased risk of developing post-earthquake PTSD. The study’s limitations include the potential interference of different DE subtypes, the complexity of quantifying the degree of earthquake exposure experienced by each individual, and events entailing social disruption, such as looting, that can profoundly influence distress. In conclusion, the study found that PTSD following the 27-F earthquake in Chile was associated with a concomitant diagnosis of DE and the number of traumatic events experienced. The study did not find a significant association between PTSD and the Val66Met or 5-HTTLPR polymorphisms. The researchers recommend that mental health professionals should prioritize the detection and treatment of concomitant depressive episodes and exposure to critical traumatic events in survivors of disasters. They also suggest that further research is needed to better understand the relationship between genetic factors and post-disaster PTSD.
Castillo-Navarrete et al. (2023) Interaction of Val66Met BDNF and 5-HTTLPR polymorphisms with prevalence of post-earthquake 27-F PTSD in Chilean population. PeerJ 11:e15870 https://doi.org/10.7717/peerj.15870
A novel signaling transduction pathway of melatonin on lactose synthesis in cows via melatonin receptor 1 (MT1) and prolactin receptor (PRLR)
In the current study, we explored the relationship between melatonin and lactose synthesis in in vivo and in vitro conditions. We found that long-term melatonin feeding to the dairy cows significantly reduced the milk lactose content in a dose dependent manner. This lactose reduction was not associated with a negative energy balance, since melatonin treatment did not alter the fat, glucose, or protein metabolisms of the cows. To identify the potential molecular mechanisms, the cow’s mammary epithelial cells were cultured for gene expression analysis. The results showed that the effect of melatonin on lactose reduction was mediated by its receptor MT1. MT1 activation downregulated the mRNA expression of the prolactin receptor gene (PRLR), which then suppressed the gene expression of SLC35B1. SLC35B1 is a galactose transporter and is responsible for the transportation of galactose to Golgi apparatus for lactose synthesis. Its suppression reduced the lactose synthesis and the milk lactose content. The discovery of this signal transduction pathway of melatonin on lactose synthesis provides a novel aspect of melatonin’s effect on carbohydrate metabolism in cows and maybe also in other mammals, including humans.
Liu et al. (2023) A novel signaling transduction pathway of melatonin on lactose synthesis in cows via melatonin receptor 1 (MT1) and prolactin receptor (PRLR). PeerJ 11:e15932 https://doi.org/10.7717/peerj.15932