农学最新文献

Short tandem repeat (STR) is a significant genetic marker for the identification of forensic DNA. DNA databases worldwide, including those in China, are established based on STR markers. Length- and sequence-based polymorphism are two features of STR markers. Sequence-based polymorphism includes polymorphisms in both repeat and flanking regions. Traditional capillary electrophoresis-based STR genotyping method can only profile length-based genotypes. However, a deep understanding of the sequence polymorphism of core STR loci is crucial for primer design and DNA identification. Firstly, single nucleotide polymorphisms and insertions/deletions in STR primer binding regions may reduce the affinity between primers and DNA templates, leading to allele dropout or poor interlocus balance, thereby impacting the accuracy of DNA identification. Secondly, sequence-based polymorphism can be unveiled by next-generation sequencing technology, which could significantly enhance the detectable polymorphic information of core STR loci and improve the efficiency of individual identification and kinship analysis. Thirdly, different populations exhibit distinct STR sequence characteristics. Over the past decade, studies on sequence-based polymorphisms of STR loci have increased alongside the application of next-generation sequencing technology, and sequence-based polymorphisms from multiple populations were reported. However, previously studied populations and data were scattered, and different formats of repeat region sequences were used in various studies. These limitations result in the absence of a systematic summary and analysis of sequence polymorphism for core STR loci, hindering its further application in forensic practices. A comprehensive understanding of core STR loci sequence characteristics is crucial for individual identification from trace DNA, deconvolution of mixed samples, and determination of mutation origins in paternity testing. In this review, we focus on 19 autosomal core STRs and systematically review the sequence polymorphisms of these loci based on population data reported in the literature. We summarize variations in repeat regions, analyze variation patterns, present high-frequency variations in flanking regions within the Chinese population, and discuss potential challenges encountered in STR sequence analyses, with the aim to provide a reference for the analyses and application of STR sequence, the identification of rare alleles in criminal case testing, and the development of STR genotyping panel.

Chromatin-associated RNAs (caRNAs), closely related to chromatin structure and functions, are a class of RNAs that interact with chromatin in cis, trans, or cis-trans cooperation modes, regulating gene expression and maintaining the orderly progression of cellular processes. N⁶-methyladenosine (m⁶A) is a ubiquitous and dynamically reversible epigenetic modification in eukaryotic RNAs, playing an important regulatory role in a variety of biological processes. m⁶A modification of chromatin-associated RNAs can regulate chromatin accessibility and gene expression at the transcriptional level, maintaining the normal functions of organisms. In this review, we summarize the mechanisms of m⁶A-modified caRNAs-chromatin interactions and their role in gene expression, with the aim of providing scientific basis and ideas for the analysis of the molecular mechanisms of gene transcriptional regulation.

In the field of forensic science, mixed DNA evidence obtained from crime scenes often contains genetic information from multiple individuals, and its accurate interpretation is crucial for case investigation and judicial decision-making. With the advancement of forensic genetic technologies, although detection capabilities have significantly improved, there are still substantial bottlenecks in the interpretation of multi-contributor DNA profiles. Traditional methods are often unable to simultaneously and precisely infer both the genotypes of suspects and their respective contribution proportions, which makes them insufficient to meet the stringent requirements of complex mixture analysis. To address these challenges, we propose a continuous gamma distribution model algorithm based on probabilistic residual optimization in this study. By constructing a two-step probabilistic evaluation framework, the algorithm first generates candidate genotype combinations through allelic permutations and estimates preliminary contributor proportions. It then introduces the gamma distribution hypothesis to build a probability density function, dynamically optimizes the shape parameter (α) and the scale parameter (β) to calculate residual probability weights, and employs an iterative maximum likelihood estimation process to simultaneously optimize genotype combinations and contributor proportion parameters. The final results are derived by integrating population allele frequency databases to output the maximum likelihood solution. This algorithm provides a reliable and quantifiable analytical tool for forensic identification, significantly improving the accuracy of complex mixture interpretation and enhancing the practical utility of mixed DNA in criminal investigations. It holds substantial significance in advancing forensic science technologies and safeguarding judicial fairness.

Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease with multi-organ involvement. The FAM167A-BLK locus at 8p23 has been identified as a genetic susceptibility locus for SLE by previous genome-wide association studies (GWAS). To explore the role of functional single-nucleotide polymorphisms (SNPs) within this locus on the regulation of BLK and FAM167A genes, we perform comprehensive functional annotation using GCTA and fnGWAS approaches to identify candidate functional SNPs，and verify them through dual-luciferase reporter assays, shRNA knockdown experiments, and CRISPR/dCas9 knockdown experiments. The results show that four functional SNPs exhibit allele-specific enhancing effect on BLK expression, while showing no discernible regulatory influence on FAM167A expression. Importantly, BLK is shown to regulate the expression of FAM167A. These findings highlight FAM167A as a potential pathogenic gene contributing to SLE. This study expands the mechanistic understanding of genetic regulation at the FAM167A-BLK locus and provides new insights into SLE development.

Extracellular vesicles (EVs) are membrane-bound particles released by cells into the extracellular microenvironment. In the nervous system, EVs serve as critical mediators of biomolecule trafficking and intercellular communication. These vesicles are deeply involved in orchestrating physiological homeostasis and pathological cascades, while demonstrating significant potential for therapeutic and diagnostic applications. In this review, we systematically summarize the functional heterogeneity and research advances in neuron- and glial cell-derived EVs, aiming to provide a theoretical basis for understanding the diverse roles of EVs in the nervous system.

Microglia, as the resident immune cells of the central nervous system (CNS), maintain neural homeostasis by orchestrating the clearance of necrotic neurons, cellular debris, and pathogens through phagocytosis. This intracellular process involves a dynamic cascade of protein-mediated events, including cargo recognition and phagosome formation, phagosome maturation, and lysosomal degradation. Phagosome maturation critically relies on V-ATPase-driven acidification, with proton transport efficiency predominantly determined by its a subunit. In mammals, the V-ATPase a subunit has four isoforms (a1, a2, a3 and a4), whereas zebrafish (Danio rerio) possess only the three isoforms (a1, a2 and a3), with marked differences observed in their targeted cell types and suborganellar localization patterns. Notably, the V-ATPase a3 subunit is primarily localized on osteoclast lysosomes, facilitating bone resorption by acidification. The preliminary studies have revealed its conserved lysosomal localization in zebrafish microglia; however, its functional role in microglial development and regulatory mechanisms underlying phagosome maturation remain elusive. To address this knowledge gap, we employed a V-ATPase a3 subunit-deficient (tcirg1b^-/-) zebrafish model, integrating whole-mount in situ hybridization, immunofluorescence, co-immunoprecipitation (Co-IP), and apoptosis assays. Key findings include: The a3 subunit is expressed during early zebrafish development; a3 subunit deficiency caused abnormal phagosome accumulation, microglial swelling and decreased activity, showing an "indigestion-like" phenotype; By exogenous labeling of late phagosomes and immunofluorescence staining, it was confirmed that the defect of V-ATPase a3 subunit impaired late phagosome-lysosome fusion in microglia; Co-IP demonstrated direct binding between the a3 subunit and Rab7. Rab7 knockdown phenocopied the "indigestion" morphology, suggesting a cooperative role in phagosome degradation. These results demonstrate that the V-ATPase a3 subunit regulates microglial phagosome maturation by mediating Rab7-dependent phagolysosomal fusion. In conclusion, this study not only elucidates the molecular mechanism underlying microglial phagocytic capacity but also provides novel insights into the evolutionarily conserved roles of V-ATPase isoforms in cellular clearance pathways.

Nitrogen is an indispensable macronutrient for plant growth, and nitrate is the main source of nitrogen for plants. The relationship between supply and demand of nitrate has a decisive impact on plant development. The NRT1/PTR family (nitrate transporter 1/peptide transporter family, NPF) is a major nitrate transporter family, playing a key role in nitrate uptake. In plant research, this type of protein can regulate its function through post-translational modification, thereby regulating nitrate sense, uptake, and plant development. NRT1.1 (NPF6.3/CHL1), a key member of the NPF family, functions both as a nitrate transporter and a nitrate sensor. In this review, we elucidate the role of NPF nitrate transporter proteins in regulating nitrate uptake and utilization in Arabidopsis thaliana, Oryza sativa, and Zea mays, and summarize the effects of post-translational modification on nitrate transport and plant development. Finally, the prospect of related research in trees is discussed, in order to provide scientific basis and technical support for improving nitrogen fertilizer utilization efficiency, enhancing plant resistance to adverse conditions, and protecting ecological environment.