Genes最新文献

Background: Heat shock proteins (HSPs) play crucial roles in response to temperature changes and biotic stresses. However, the HSP gene family in the pufferfish (Takifugu fasciatus) herring has not been comprehensively investigated.

Methods and results: This study presents a systematic analysis of the HSP70 and HSP90 gene families in T. fasciatus, focusing on gene characterization, conserved structural domains, molecular evolutionary history, and expression patterns of the HSP gene family under stress conditions. The findings reveal that 16 HSP genes are evolutionarily conserved, while hspa4 and hsp90aa appear specific to teleost fish. HSP genes exhibit widespread expression across 11 examined tissues, with most demonstrating high expression levels in the heart, brain, and liver. Furthermore, T. fasciatus was subjected to cryogenic and biotic stresses, revealing distinct expression patterns of HSPs under various stress conditions. The response of HSPs to cold stress and Aeromonas hydrophila infection was sustained. In contrast, gene expression of HSPs significantly changed only in the pre-infection period following Ichthyophthirius multifiliis infection, gradually returning to normal levels in the later stages.

Conclusions: These experimental results provide a foundation for further in-depth investigations into the characteristics and functions of HSPs in T. fasciatus.

Background/objectives: The spruces of the Picea abies-P. obovata complex have a total range that is the most extensive in the world flora of woody conifers. Hybridization between the nominative species has led to the formation of a wide introgression zone, which probably increases the adaptive potential of the entire species complex. This study aimed to search the genes associated with drought resistance, develop primers for the informative loci of these genes, identify and analyze SNPs, and establish the parameters of nucleotide diversity in the studied populations.

Methods: The objects of this study were eight natural populations of the spruce complex in the Urals. Nucleotide sequences related to drought resistance spruce genes with pronounced single-nucleotide substitutions were selected, based on which 16 pairs of primers to their loci were developed and tested.

Results: Based on the developed primers, six pairs of primers were chosen to identify SNPs and assess the nucleotide diversity of the studied populations. All selected loci were highly polymorphic (6 to 27 SNPs per locus). It was found that the Pic01 locus is the most variable (Hd = 0.947; π = 0.011) and selectively neutral, and the Pic06 locus is the most conservative (Hd = 0.516; π = 0.002) and has the most significant adaptive value.

Conclusions: The nucleotide diversity data for the studied populations reveal similar values among the populations and are consistent with the literature data. The discovered SNPs can be used to identify adaptive genetic changes in spruce populations, which is essential for predicting the effects of climate change.

Background/Objectives: The pathogenetic role of 15q11.2 Copy Number Variations (CNVs) remains contentious in the scientific community, as microdeletions and microduplications in this region are linked to neurodevelopmental disorders with variable expressivity. This study aims to explore the diagnostic utility of Exome Sequencing (ES) in a cohort of pediatric patients with 15q11.2 CNVs. Methods: We enrolled 35 probands with 15q11.2 microdeletions or microduplications from two genetic centers between January 2021 and January 2023. Chromosomal Microarray Analysis (CMA) and ES were performed with written consent obtained from all parents. Pathogenic variants were classified according to ACMG guidelines. Results: CMA identified additional pathogenic CNVs in 3 of 35 children (9%). Subsequent ES revealed likely pathogenic or pathogenic variants in 11 of 32 children (34%). Notably, a higher percentage of isolated autism spectrum disorder (ASD) diagnoses was observed in patients without other CNVs or point mutations (p = 0.019). Conclusions: The ES analysis provided a diagnostic yield of 34% in this pediatric cohort with 15q11.2 CNVs. While the study does not dismiss the contribution of the CNV to the clinical phenotype, the findings suggest that ES may uncover the underlying causes of neurodevelopmental disorders. Continuous monitoring and further genetic testing are recommended for all 15q11.2 CNV carriers to optimize clinical management and familial counseling.

Background/objectives: Accipitridae mitogenomes exhibit unique structural variations, including duplicated control regions (CRs) that undergo gradual degeneration into pseudo-CRs, revealing a complex evolutionary landscape. However, annotation of this characteristic in a subset of accipitrid genomes is lacking. Due to the taxonomic diversity of Accipitridae and the presence of understudied species, comprehensive mitogenomic studies are essential. This study sought to expand and investigate the evolutionary characteristics of Accipitridae mitogenomes.

Methods: A comparative analysis was conducted using the newly acquired complete mitogenomes of Haliastur indus and Accipiter badius poliopsis along with 22 available accipitrid mitogenomes. Codon usage, selective pressure, phylogenetic relationships, and structural variations were comparatively analyzed.

Results: Accipitrid mitogenomes showed a strong AT bias with adenine preference. Most protein-coding genes (PCGs) were under purifying selection except for ND3, which underwent positive selection. The ATP8 gene exhibited relaxed purifying selection on codon usage patterns and showed high genetic variation. Selection for ATP8 and ND3 genes was specific to certain clades of accipitrids. Gene order re-examination revealed both non-degenerate CRs and highly degenerate CR2 fragments in the Accipitridae family. Non-degenerate CRs were found in early diverging species, such as Elanus caeruleus and Pernis ptilorhynchus orientalis, while more recent lineages had highly degenerate CR2 fragments with missing conserved element. Repeat motifs and sequence variations were observed in the functional CR.

Conclusions: These findings suggest that ATP8 and ND3 genes reflect metabolic adaptations, while CRs indicate potential diversification of these accipitrid species. This study provides valuable insights into mitochondrial genome evolution within the Accipitridae family.

Powdery mildew is a prevalent wheat disease that affects yield and quality. The characterization and fine mapping of genes associated with powdery mildew resistance can benefit marker-assisted breeding. In this study, quantitative trait loci (QTL) associated with powdery mildew were mapped using a high-density 35K DArT genetic linkage map developed from a population of double haploid lines (DHs) created by crossing "Jinmai 33 (a highly resistance line) with Yannong 19 (a highly susceptible line)". Three stable QTLs for powdery mildew were identified on chromosomes 1B, 2B, and 6A combined with the composite interval graphing method and multiple interval mapping, explaining phenotypic variations (PVE) that range from 4.98% to 13.25%. Notably, Qpm.sxn-1B and Qpm.sxn-2B were identified across three environments, with the PVE ranging from 9.37% to 13.25% and from 4.98% to 5.23%, respectively. The synergistic effects of these QTLs were contributed by the parental line "Jinmai 33". Qpm.sxn-1B was the major stable QTL, and Qpm.sxn-2B was close to Pm51. Furthermore, Qpm.sxn-6A was identified in two environments, accounting for PVE values of 7.13% and 7.65%, respectively, with the resistance effects originating from the male parent. Remarkably, this locus has not been reported previously, indicating that Qpm.sxn-6A represents a newly dis-covered QTL governing powdery mildew genes. Conclusions Five molecular markers available for mark-er-assisted selection were selected for tracking Qpm.sxn-1B and Qpm.sxn-2B in the program. The identification of this novel newly discovered QTL and markers reported in this study will be useful for marker-assisted selection of powdery mildew resistance.

Background/objectives: High-throughput single-cell RNA sequencing (scRNA-seq) workflows produce libraries that demand extensive sequencing. However, standard next-generation sequencing (NGS) methods remain expensive, contributing to the high running costs of single-cell experiments and often negatively affecting the sample numbers and statistical strength of such projects. In recent years, a plethora of new sequencing technologies have become available to researchers through several manufacturers, often providing lower-cost alternatives to standard NGS.

Methods: In this study, we compared data generated from mouse scRNA-seq libraries sequenced with both standard Illumina sequencing by synthesis (Illumina SBS) and MGI's DNA nanoball sequencing (DNBSEQ).

Results: Our findings reveal similar overall performance using both technologies. DNBSEQ exhibited mildly superior sequence quality compared to Illumina SBS, as evidenced by higher Phred scores, lower read duplication rates and a greater number of genes mapping to the reference genome. Yet these improvements did not translate into meaningful differences in single-cell analysis parameters in our experiments, including detection of additional genes within cells, gene expression saturation levels and numbers of identified cells, with both technologies demonstrating equally robust performance in these aspects. The data produced by both sequencing platforms also produced comparable analytical outcomes for single-cell analysis. No significant difference in the annotation of cells into different cell types was observed and the same top genes were differentially expressed between populations and experimental conditions.

Conclusions: Overall, our data demonstrate that alternative technologies can be applied to sequence scRNA-seq libraries, generating virtually indistinguishable results compared to standard methods, and providing cost-effective alternatives.

Background/objectives: Heterodera avenae is a highly significant plant-parasitic nematode, causing severe economic losses to global crop production each year. Trichoderma species have been found to parasitize nematodes and control them by producing enzymes that degrade eggshells. The T. longibrachiatum T6 (T6) strain has been demonstrated the parasitic and lethal effects on H. avenae cysts and eggs, associated with the increased serine protease activity and trypsin-like serine protease gene (PRA1) expression.

Methods: Our present study aimed to purify the recombinant PRA1 protease through a prokaryotic expression system and identify its nematicidal activity.

Results: The recombinant PRA1 protease was identified as S1 family trypsin-like serine protease, with a molecular weight of 43.16 kDa. The purified soluble protease exhibited the optimal activity at 35 °C and pH 8.0, and also demonstrating higher hydrolytic ability toward casein and skimmed milk. Meanwhile, the Ca²⁺ and Mg²⁺ enhanced its activity, while the inhibitor PMSF significantly reduced it. The contents of H. avenae eggs leaked out after treatment with the recombinant PRA1 protease, with egg hatching inhibition and relative hatching inhibition rates at 70.60% and 66.58%, respectively. In contrast, there was no sign of content dissolution, and embryos developed normally in the control group.

Conclusions: Our present study revealed that the PRA1 protease of T6 strain has a lethal effect on H. avenae eggs, which providing a theoretical basis for developing biocontrol agents to control nematodes.

Background/Objectives: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries and it can progress to Richter's syndrome (RS), a more aggressive condition. The NF-κB pathway is pivotal in CLL pathogenesis, driven mainly by B-cell receptor (BCR) signaling. However, recent evidence indicates that BCR signaling is reduced in RS, raising questions about whether and how NF-κB activity is maintained in RS. This study aims to elucidate the triggers and dynamics of NF-κB activation and the progression from CLL to RS. Methods: Integrated single-cell RNA sequencing data from peripheral blood samples of four CLL-RS patients were analyzed. NF-κB pathway activity and gene expression profiles were assessed to determine changes in NF-κB components and their targets. Tumor microenvironment composition and cell-cell communication patterns were inferred to explore NF-κB regulatory mechanisms. Results: RS samples showed increased proportions of malignant cells expressing NF-κB components, including NFKB1, NFKB2, RELA, IKBKG, MAP3K14, CHUK, and IKBKB, with significantly higher expression levels than in CLL. Enhanced NF-κB pathway activity in RS cells was associated with targets involved in immune modulation. The tumor microenvironment in RS displayed significant compositional changes, and signaling inference revealed enhanced cell-cell communication via BAFF and APRIL pathways, involving interactions with receptors such as BAFF-R and TACI on RS cells. Conclusions: The findings from this study reveal an active state of NF-κB in RS and suggest that this state plays a critical role in the evolution of CLL to RS, which is modulated by alternative signaling pathways and the influence of the tumor microenvironment.

Background: The genetic background of Toll-like receptor 4 (TLR4) proved to be important in the induction of immune protection against Bordetella pertussis infection in humans. Currently, the evaluation of the acellular pertussis (aP) vaccine depends largely on using different mouse strains, while the TLR4 genotype of different mouse strains in response to pertussis toxin (PT) is not carefully determined. The current study was designed to determine the differences in TLR4 genotype and TLR4 pathway-related cytokines in response to PT stimulation among mouse strains of ICR, NIH, and BALB/c.

Method: We first determined the single-nucleotide polymorphisms (SNPs) in the TLR4 gene by using first-generation sequencing. Then, the cellular response, including the TLR4 mRNA expression and TLR4 signaling-related cytokines, of immune cells from different mouse strains after PT stimulation was determined.

Result: Three missense mutation sites (rs13489092, rs13489093, rs13489097) of the TLR4 gene were found. ICR mice were homozygous without mutation, NIH mice were partially heterozygous, and BALB/c mice were homozygous with a missense mutation. The expression of TLR4 was repressed while the downstream cytokines were upregulated after PT stimulation differently among mouse strains. The IFN-β cytokine of the TRIF pathway was significantly increased in ICR mice (p < 0.05). The IL-6 cytokine of the MyD88-dependent pathway was significantly increased in BALB/c mice (p < 0.05). The identified SNPs of the TLR4 gene in different mouse strains might account for the differences in cytokines levels determined after PT stimulation.

Conclusions: Our studies might provide useful referees to reduce the mouse-derived difference in the determination of vaccine titer and increase the comparability of the vaccine from different origins, as different mouse strains were used for vaccine development in different countries.

Background/Objectives: Adverse childhood experiences (ACEs) are potent drivers of psychopathology and neurological disorders, especially within minoritized populations. Nonetheless, we lack a coherent understanding of the neuronal mechanisms through which ACEs impact gene expression and, thereby, the development of psychopathology. Methods: This observational pilot study used a novel marker of neuronal functioning (brain-derived micro ribonucleic acids, or miRNAs) collected via saliva to explore the connection between ACEs and neuronal gene expression in 45 adolescents with a collectively high ACE exposure (26 males and 19 females of diverse races/ethnicities, with six cumulative ACEs on average). We aimed to determine the feasibility of using salivary microRNA for probing neuronal gene expression with the goal of identifying cellular processes and genetic pathways perturbed by childhood adversity. Results: A total of 274 miRNAs exhibited reliable salivary expression (raw counts > 10 in > 10% of samples). Fourteen (5.1%) were associated with cumulative ACE exposure (p < 0.05; r's ≥ 0.31). ACE exposure correlated negatively with miR-92b-3p, 145a-5p, 31-5p, and 3065-5p, and positively with miR-15b-5p, 30b-5p, 30c-5p, 30e-3p, 199a-3p, 223-3p, 338-3p, 338-5p, 542-3p, and 582-5p. Most relations remained significant after controlling for multiple comparisons and potential retrospective bias in ACE reporting for miRNAs with particularly strong relations (p < 0.03). We examined KEGG pathways targeted by miRNAs associated with total ACE scores. Results indicated putative miRNA targets over-represented 47 KEGG pathways (adjusted p < 0.05) involved in neuronal signaling, brain development, and neuroinflammation. Conclusions: Although preliminary and with a small sample, the findings represent a novel contribution to the understanding of how childhood adversity impacts neuronal gene expression via miRNA signaling.