Complete mitochondrial DNA and phylogenetic study of qionglai native black chicken

The complete mitochondrial genome sequence of the qionglai black chicken was measured by PCR-based methods, the molecular characterization and phyletic evolution analyzed in detail. Our result showed that the entire mitochondrial genome of the qionglai black chicken is a circular molecule consisting of 16,785 bp (GenBank accession number: KT958484). The contents of A, T, C, and G were 30.25%, 23.74%, 32.54% and 13.48%in the mitochondrial genome, respectively. The complete mitochondrial genome of the qionglai blackchicken contains a typical structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (D-loop region). The phyletic evolution analysis shown that this chicken was evolution between the red jungle fowl and the special egg chicken white loghorn chicken.This complete mitochondrial genome sequence provides essential information in understanding phylogenetic relationships among Gallusgallus domesticus mitochondrial genomes and the breeding of native chic

Complete mitochondrial DNA and phylogenetic study of qionglai native black chicken

The complete mitochondrial genome sequence of the qionglai black chicken was measured by PCR-based methods, the molecular characterization and phyletic evolution analyzed in detail. Our result showed that the entire mitochondrial genome of the qionglai black chicken is a circular molecule consisting of 16,785 bp (GenBank accession number: KT958484). The contents of A, T, C, and G were 30.25%, 23.74%, 32.54% and 13.48%in the mitochondrial genome, respectively. The complete mitochondrial genome of the qionglai blackchicken contains a typical structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (D-loop region). The phyletic evolution analysis shown that this chicken was evolution between the red jungle fowl and the special egg chicken white loghorn chicken.This complete mitochondrial genome sequence provides essential information in understanding phylogenetic relationships among Gallusgallus domesticus mitochondrial genomes and the breeding of native chic

Complete mitochondrial DNA and phylogenetic study of qionglai native black chicken

The complete mitochondrial genome sequence of the qionglai black chicken was measured by PCR-based methods, the molecular characterization and phyletic evolution analyzed in detail. Our result showed that the entire mitochondrial genome of the qionglai black chicken is a circular molecule consisting of 16,785 bp (GenBank accession number: KT958484). The contents of A, T, C, and G were 30.25%, 23.74%, 32.54% and 13.48%in the mitochondrial genome, respectively. The complete mitochondrial genome of the qionglai blackchicken contains a typical structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (D-loop region). The phyletic evolution analysis shown that this chicken was evolution between the red jungle fowl and the special egg chicken white loghorn chicken.This complete mitochondrial genome sequence provides essential information in understanding phylogenetic relationships among Gallusgallus domesticus mitochondrial genomes and the breeding of native chic

To explore the causal association between the serum lipid profile and inflammatory bowel disease using bidirectional Mendelian randomisation analysis

Background Despite studies confirming that patients with inflammatory bowel disease (IBD) present with dyslipidaemia, the associations between IBD and the serum lipid profile have not been determined. The present study aimed to investigate the causal relationship between the serum lipid profile and IBD risk and elucidate the nature of the interactions between them.Methods Two-sample Mendelian randomisation (MR) analysis was performed to investigate the causal links between total cholesterol (TC), total triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apolipoprotein A (Apo A), apolipoprotein B (Apo B) and lipoprotein (a) (Lp(a)) and IBD. The study was carried out using the R TwoSampleMR and Mendelian randomisation packages.Results All MR methods, including the weighted median, weighted mode, inverse-variance weighted model, MR-PRESSO, contamination mixture and MR Egger, supported a null causal relationship between TG, TC, HDL-C, LDL-C, Apo A, Apo B and Lp(a) and between IBD, Crohn’s disease and ulcerative colitis. Null causal effects of lipid indices on IBD were validated through independent genome-wide association studies (GWAS), indicating that the findings are robust.Conclusion Our findings suggest that none of the seven lipid indices may be a potential risk factor for the onset of IBD. However, additional research is needed since our MR analyses cannot assess the potential non-linear causal relationship between serum lipids and IBD

The Morphological Differentiation and Evolutionary Origins of <i>Artemia</i> in China

Artemia is a genus of halophilic zooplanktons comprising bisexual and parthenogenetic forms, which is an important model for investigating adaption to hypersaline ecosystems. The genus Artemia in China comprises four species: A. sinica, A. tibetiana, A. franciscana and A. parthenogenetica. To investigate the evolutionary relationship of bisexual and parthenogenetic Artemia in China, we analyzed the morphometrics and phylogenetics among twenty-two geographical populations in China. We found significant morphological differentiation across different species and strains of Artemia in China, which exhibited a high level of intra-population variation. We also found overlaps in morphological characteristics between populations, which may raise challenges for the classification of Artemia species using traditional morphological methods. A. franciscana, which originated from various regions in America, was generally distributed along the Chinese coastlines through multiple human introductions. Additionally, native Asian clades split into Western and Eastern Lineages during the late Miocene due to the Himalayan orogeny. Within the Western Lineage, A. tibetiana can be grouped into three taxon units: A. tibeitiana, A. sorgeloosi and A. urmiana. We also found that the distribution and genetic structure of A. sinica were influenced by climate oscillations during the Pleistocene, which might play a pivotal role in driving the formation of parthenogenetic strains in the Eastern Lineage. Overall, our study provides new insight into invertebrate evolution under geographical and climatic impacts in hypersaline environments

Cefotaxime Exposure-Caused Oxidative Stress, Intestinal Damage and Gut Microbial Disruption in <i>Artemia sinica</i>

Cefotaxime (CTX) is an easily detectable antibiotic pollutant in the water environment, but little is known about its toxic effects on aquatic invertebrates, especially on the intestine. Here, we determined the oxidative stress conditions of A. sinica under CTX exposure with five concentrations (0, 0.001, 0.01, 0.1 and 1 mg/L) for 14 days. After that, we focused on changes in intestinal tissue morphology and gut microbiota in A. sinica caused by CTX exposure at 0.01 mg/L. We found malondialdehyde (MDA) was elevated in CTX treatment groups, suggesting the obvious antibiotic-induced oxidative stress. We also found CTX exposure at 0.01 mg/L decreased the villus height and muscularis thickness in gut tissue. The 16S rRNA gene analysis indicated that CTX exposure reshaped the gut microbiota diversity and community composition. Proteobacteria, Actinobacteriota and Bacteroidota were the most widely represented phyla in A. sinica gut. The exposure to CTX led to the absence of Verrucomicrobia in dominant phyla and an increase in Bacteroidota abundance. At the genus level, eleven genera with an abundance greater than 0.1% exhibited statistically significant differences among groups. Furthermore, changes in gut microbiota composition were accompanied by modifications in gut microbiota functions, with an up-regulation in amino acid and drug metabolism functions and a down-regulation in xenobiotic biodegradation and lipid metabolism-related functions under CTX exposure. Overall, our study enhances our understanding of the intestinal damage and microbiota disorder caused by the cefotaxime pollutant in aquatic invertebrates, which would provide guidance for healthy aquaculture

BDS-3/GPS/Galileo OSB Estimation and PPP-AR Positioning Analysis of Different Positioning Models

With the completion of the BeiDou Global Navigation Satellite System (BDS-3), the multi-system precise point positioning ambiguity resolution (PPP-AR) has been realized. The satellite phase fractional cycle bias (FCB) is a key to the PPP-AR. Compared to the combined ionosphere-free (IF) model, the undifferenced and uncombined (UDUC) model retains all the information from the observations and can be easily extended to arbitrary frequencies. However, the FCB is difficult to apply directly to the UDUC model. An observable-specific signal bias (OSB) can interact directly with the original observations, providing complete flexibility for PPP-AR for multi-frequency multi-GNSS. In this study, the OSB product generation for the GPS (G), Galileo (E), and BDS-3 (C) systems is performed using 117 globally distributed multi-GNSS experiment (MGEX) stations, and their performances are evaluated. Then, the PPP-AR comparison and analysis of the two positioning models of the UDUC and IF are conducted. The results show that the stability of OSB products of the three systems is better than 0.05 ns. For the precise point positioning (PPP) ambiguity fixed solution, with comparable positioning accuracy and convergence time to the products of both the Wuhan University (WUM) and the Centre National d&rsquo;Etudes Spatials (CNES) institutions, an average fixed-ambiguity rate is over 90%. Compared to the PPP float solution, the PPP-AR has the most significant improvement in positioning accuracy in the E-direction. The average improvements in the positioning accuracy under the IF and UDUC models in the static and kinematic modes are higher than 45% and 40%, respectively. The convergence times of the IF and UDUC models are improved on average by 48% and 60% in the static mode and by 40% and 55% in the kinematic mode, respectively. Among the IF and UDUC positioning models, the former has slightly better positioning accuracy and convergence time than the latter for the PPP float solution. However, both models have comparable positioning accuracy and convergence time after the PPP-AR. The GCE multi-system combination is superior to other system combinations. The average convergence time for the static PPP fixed solution is 8.5 min, and the average convergence time for the kinematic PPP fixed solution is 16.4 min

Plastic waste discharge to the global ocean constrained by seawater observations

Marine plastic pollution poses a potential threat to the ecosystem, but the sources and their magnitudes remain largely unclear. Existing bottom-up emission inventories vary among studies for two to three orders of magnitudes (OMs). Here, we adopt a top-down approach that uses observed dataset of sea surface plastic concentrations and an ensemble of ocean transport models to reduce the uncertainty of global plastic discharge. The optimal estimation of plastic emissions in this study varies about 1.5 OMs: 0.70 (0.13-3.8 as a 95% confidence interval) million metric tons yr-1 at the present day. We find that the variability of surface plastic abundance caused by different emission inventories is higher than that caused by model parameters. We suggest that more accurate emission inventories, more data for the abundance in the seawater and other compartments, and more accurate model parameters are required to further reduce the uncertainty of our estimate