Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes.

Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Methods: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of non-synonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Results: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

IL-4 modified expanded polytetrafluoroethylene (e-PTFE) surgical patch promotes angiogenesis in transplanted flap and inhibits inflammatory response.

Skin flap transplantation is one of the most common tissue transplantation methods for wound repair and organ reconstruction in plastic surgery. During the transplantation process, the inflammatory response of transplanted flap and angiogenesis are critical to the successful rate of skin flap transplantation. In recent years, to improve the biocompatibility and cell affinity of biomedical materials, the modified biomaterials have gradually become a popular subject in scientific researches. In our study, the IL-4 modified expanded polytetrafluoroethylene (e-PTFE) surgical patch IL4-e-PTFE was prepared, and the rat skin flap transplantation model was constructed. The results of cell experiment prove that IL-4 has potentiation in the angiogenesis of human umbilical vein endothelial cell (HUVEC) induced by monocyte, and IL-4 can also promote angiogenesis by inducing the M2 macrophages. According to the results of in vivo experiment, the apoptosis level of transplanted flap cells of rats in the IL4-e-PTFE group was lower than that in the e-PTFE group, and in the IL4-e-PTFE group, the expression levels of pro-inflammatory cytokines IL-1ß, IL-6 and TNF-α showed significantly decline compared to the e-PTFE group, while the expression levels of anti-inflammatory cytokines IL-1Ra, IL-10 and TGF-ß presented significant increase compared to the e-PTFE group; the immunofluorescence staining results show that the number of M2 macrophages in transplanted flap area of rats in the IL4-e-PTFE group was significantly higher than that in the e-PTFE group, and the angiogenesis level was remarkably improved. In this study, by preparing IL4-e-PTFE and carrying out the cell and in vivo experiments, a reference method is proposed, which can reduce the inflammatory response during skin transplantation process using e-PTFE and optimize the long-term effects of flap blood vessels, hoping to provide a broader space for the applications of e-PTFE in medicine.

A novel atrial fibrillation automatic detection algorithm based on ensemble learning and multi-feature discrimination.

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia disorder that necessitates long-time electrocardiogram (ECG) data for clinical diagnosis, leading to low detection efficiency. Automatic detection of AF signals within short-time ECG recordings is challenging. To address these issues, this paper proposes a novel algorithm called Ensemble Learning and Multi-Feature Discrimination (ELMD) for the identification and detection of AF signals. Firstly, a robust classifier, BSK-Model, is constructed using ensemble learning. Subsequently, the ECG R-waves are detected, and the ECG signals are segmented into consecutive RR intervals. Time domain, frequency domain, and nonlinear features are extracted from these intervals. Finally, these features are fed into the BSK-Model to discriminate AF. The proposed methodology is evaluated using the MIT-BIH AF database. The results demonstrate that when RR intervals are employed as classification units, the specificity and accuracy of AF detection in long-time ECG data exceed 99%, showcasing a significant improvement over traditional single-model classification. Additionally, the sensitivity and accuracy achieved by testing cardiac segments are both above 96%. With a minimum requirement of only four cardiac segments, AF events can be accurately identified, thereby enabling rapid discrimination of short-time single-lead ECG AF events. Consequently, this approach is suitable for real-time and accurate AF detection using low-computational-power ECG diagnostic analysis devices, such as wearable devices.

Using DNA barcoding and field surveys to guide wildlife management at Nanjing Lukou International Airport, China.

The conflicts between wildlife and aircraft have increased due to the development of the aviation industry. While many studies have quantified the relative hazards of wildlife to aircraft, few studies have combined DNA barcoding techniques with field surveys of bird communities in different habitats to reveal the exact species involved in bird strikes and how the habitat heterogeneity around airports affects bird communities and even the occurrence of bird strikes. Taking Nanjing Lukou International Airport in China as an example, based on the DNA barcoding technology and detailed field research, we establish the most commonly struck species, which can help managers identify the level of hazard and lead to meaningful reductions in hazards and costs associated with bird strike. The investigation of bird communities showed that there were 149 bird species recorded within an 8 km radius. There were 89, 88, 61, and 88 species in the woodland, wetland, farmland, and urban area, respectively. In total, 303 samples identified 82 species representing 13 orders and 32 family of birds from bird strike cases, of which 24 species were not found in the field survey. Passeriformes were the most common order of birds identified, with 43 species represented in 167 identifications. Skylark, Thrush, Shrike, Lapwing, and Swallow were most likely to cause damage or substantial damage to aircraft when strikes occurred. In addition to birds, we identified 69 bats individuals (accounting for 22.77%) using DNA barcoding. The Bray-Curtis similarity analysis revealed that species involved in bird strike had the highest similarity with urban area. Our findings suggest that policymakers should pay more attention to managing the wetlands and urban areas surrounding the airport. These findings imply that DNA barcoding can add to the environmental monitoring in airports, which can facilitate hazard management and improve air safety.

LDL receptor related protein 1 is an adverse prognostic biomarker that correlates with stromal remodeling and macrophages infiltration in bladder cancer.

Introduction: Bladder cancer (BLCA) is a highly heterogeneous disease influenced by the tumor microenvironment, which may affect patients' response to immune checkpoint blockade therapy. Therefore, identifying molecular markers and therapeutic targets to improve treatment is essential. In this study, we aimed to investigate the prognostic significance of LRP1 in BLCA. Methods: We analyzed TCGA and IMvigor210 cohorts to investigate the relationship of LRP1 with BLCA prognosis. We utilized gene mutation analysis and enrichment to identify LRP1-associated mutated genes and biological processes. Deconvolution algorithms and single-cell analysis were used to understand the tumor-infiltrated cells and biological pathways associated with LRP1 expression. Immunohistochemistry was conducted to validate the bioinformatics analysis. Results: Our study revealed that LRP1 was an independent risk factor for overall survival in BLCA patients and was associated with clinicopathological features and FGFR3 mutation frequency. Enrichment analysis demonstrated that LRP1 was involved in extracellular matrix remodeling and tumor metabolic processes. Furthermore, the ssGSEA algorithm revealed that LRP1 was positively correlated with the activities of tumor-associated pathways. Our study also found that high LRP1 expression impaired patients' responsiveness to ICB therapy in BLCA, which was predicted by TIDE prediction and validated by IMvigor210 cohort. Immunohistochemistry confirmed the expression of LRP1 in Cancer-Associated Fibroblasts (CAFs) and macrophages in the tumor microenvironment of BLCA. Discussion: Our study suggests that LRP1 may be a potential prognostic biomarker and therapeutic target in BLCA. Further research on LRP1 may improve BLCA precision medicine and enhance the efficacy of immune checkpoint blockade therapy.

Identification of key genes related to intramuscular fat deposition in Beijing-You chicken by mRNA and miRNA transcriptome analysis.

Intramuscular fat (IMF) is an important factor affecting chicken quality. However, the age-related mechanism of IMF deposition has not yet been elucidated. In this study, the IMF, phospholipids (PL), triglycerides (TG), and fatty acid (FA) content in the breast muscle of Beijing-You chicken (BJY) at 1, 56, 98, and 120 d of age was measured, and mRNA and miRNA sequencing was integrated to explore the regulatory genes of IMF deposition. The results showed that the IMF content of BJY at 1 d of age was significantly higher than that at later stage of birth (P < 0.05). The transcriptome sequencing results showed that 7, 225 differentially expressed genes (DEGs) and 243 differentially expressed miRNAs (DE-miRNAs) were identified. The cluster analysis showed that the expression of DEGs and DE-miRNAs at 1 d of age was significantly different from that at later stages of birth. Furthermore, a potential mRNA-miRNA regulatory network related to IMF deposition was established by weighted gene co-expression network analysis (WGCNA); gga-miR-29c-3p-PIK3R1, gga-miR-6701-3p-PTEN, gga-miR-363-3p-PTEN, gga-miR-1563-WWP1, gga-miR-449c/d-5p-TRAF6, and gga-miR-6701-3p-BMPR1B were identified as key mRNA-miRNA pairs for the regulation of IMF deposition. These results will help elucidate the mechanism of IMF formation mediated by miRNAs in chickens, and provide a theoretical foundation for the genetic improvement of broiler meat quality.

Identification of Key Genes Affecting Flavor Formation in Beijing-You Chicken Meat by Transcriptome and Metabolome Analyses.

The flavor of chicken meat is influenced by muscle metabolites and regulatory genes and varies with age. In this study, the metabolomic and transcriptomic data of breast muscle at four developmental stages (days 1, 56, 98, and 120) of Beijing-You chickens (BJYs) were integrated and 310 significantly changed metabolites (SCMs) and 7,225 differentially expressed genes (DEGs) were identified. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that SCMs and DEGs were enriched in amino acid, lipid, and inosine monophosphate (IMP) metabolism pathways. Furthermore, genes highly associated with flavor amino acids, lipids, and IMP were identified by a weighted gene co-expression network analysis (WGCNA), including cystathionine ß-synthase (CBS), glycine amidinotransferase (GATM), glutamate decarboxylase 2 (GAD2), patatin-like phospholipasedomain containing 6 (PNPLA6), low-specificity L-threonine aldolase (ItaE), and adenylate monophosphate deaminase 1 (AMPD1) genes. A regulatory network related to the accumulation of key flavor components was constructed. In conclusion, this study provides new perspectives regarding the regulatory mechanisms of flavor metabolites in chicken meat during development.

Identification of key genes affecting sperm motility in chicken based on whole-transcriptome sequencing.

Sperm motility is an important index for the evaluation of semen quality. Improving sperm motility is important to improve reproductive performance, promote breeding process, and reduce production cost. However, the molecular mechanisms regulating sperm motility in chickens remain unclear. In this study, histological observation and whole-transcriptome analysis were performed on testicular tissue of chickens with high and low sperm motility. Histological observations showed that roosters with high sperm motility exhibited better semen quality than those with low sperm motility. In addition, the germinal epithelial cells of roosters with low sperm motility were loosely arranged and contained many vacuoles. RNA-seq results revealed the expression of 23,033 mRNAs, 2,893 lncRNAs, and 515 miRNAs in chicken testes. Among them, there were 417 differentially expressed mRNAs (DEmRNAs), 106 differentially expressed lncRNAs (DElncRNAs), and 15 differentially expressed miRNAs (DEmiRNAs) between high and low sperm motility testes. These differentially expressed genes were involved in the G protein-coupled receptor signaling pathway, cilia structure, Wnt signaling, MAPK signaling, GnRH signaling, and mTOR signaling. By integrating the competitive relationships between DEmRNAs, DElncRNAs, and DEmiRNAs, we identified the regulatory pathway of MSTRG.3077.3/MSTRG.9085.1-gga-miR-138-5p-CADM1 and MSTRG.2290.1-gga-miR-142-3p-GNAQ/PPP3CA as crucial in the modulation of chicken sperm motility. This study provides new insights into the function and mechanism of ceRNAs in regulating sperm motility in chicken testes.

Zinc pyrithione (ZPT) -induced embryonic toxicogenomic responses reveal involvement of oxidative damage, apoptosis, endoplasmic reticulum (ER) stress and autophagy.

Zinc pyrithione (ZPT) is a frequently used organometallic biocide, carrying potentially adverse consequences to multiple species in the environment. Previously we have demonstrated its embryonic, organ developmental and liver metabolic toxicity of zebrafish. However, details of ZPT toxicity during embryogenesis are still limited. The present study was designed to evaluate the effects and possible mechanisms of ZPT-induced embryonic toxicogenomic responses by morphological investigations, transcriptome and gene quantitative analysis, as well as biochemical assays. The results revealed that treatment with ZPT caused embryogenesis toxicity, specifically in irregular cell division and rearrangement, delayed differentiations of eyes and notochords, the epiboly and germ ring formation and somite segmentation defects. In addition, ZPT exposure altered gene expression during early embryonic development, especially related with morphological abnormities and metabolic dysfunctions including reduction of oxidoreductase activity. Activities of antioxidants and caspases examinations showed inductions of oxidative stress and apoptosis by ZPT and quantitative analysis of marker genes further indicated that ZPT also triggered endoplasmic reticulum (ER) stress and autophagy. Thus, we deduce here that ZPT-induced embryonic toxicogenomic responses reveal involvement of oxidative damage, apoptosis, endoplasmic reticulum (ER) stress and autophagy.

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata).

BACKGROUND: Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress. RESULTS: We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'. CONCLUSIONS: Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.

In-memory direct processing based on nanoscale perpendicular magnetic tunnel junctions.

Perpendicular magnetic tunnel junctions (p-MTJs) provide advantages such as infinite endurance, high thermal stability, and fast and low-power switching. They are considered as a promising non-volatile memory device to build non-von Neumann computing paradigms and definitively overcome the power bottleneck. Numerous design proposals have been made for p-MTJ logic, but a few physical realizations have been reported. In this paper, we present the experimental implementation of universal stateful logic gates such as "OR", "AND", and material implication ("IMP") by connecting two nanoscale p-MTJs in parallel. Owing to the voltage dependence of switching probability for the spin transfer torque mechanism, the same structure can be reconfigured to different logic gates with only electrical signals. One single-cycle operation is thus required for all the basic Boolean functions. Such in-memory direct processing has great potential to meet some key requirements such as a high energy/areal efficiency and high speed for future computing hardware.