Genes最新文献

Background: Rhododendron is a globally distributed and extensive genus, comprising over 1000 species. In the southwestern mountains of China, there exists a remarkable diversity of Rhododendron, with Yunnan Province alone harboring more than 600 species. R. decorum Franch. has long been utilized by local communities for its medicinal and edible properties. However, the transcriptional regulation function, medicinal properties, and edibility characteristics of R. decorum Franch. currently lack a solid theoretical basis.

Methods: Total RNA was extracted from leaves, corollas and androecium/gynoecium of R. decorum Franch. in Heqing county, followed by the construction of cDNA libraries and the de novo assembly of transcriptomes.

Results: A total of 63,050 unigenes were extracted from the flowers and leaf organs of R. decorum Franch. Among these unigenes, 43,517 were predicted to be coding sequences, with 32,690 being effectively annotated. Differential gene expression enrichment was observed among different organs within their respective transcriptomes; notably floral organs exhibited significant defense against plant diseases along with signal transduction functions. Furthermore, during the flower harvesting period, all floral organs exhibited gene enrichment pathways associated with carbohydrate metabolism. Additionally, the stamen and pistil displayed flavonoid metabolism pathways, suggesting their potential applications as functional food or medicine.

Conclusions: Our results shed light on plant-pathogen defense mechanisms and the molecular bias of flavonoids biosynthesis on flower organs during the flowering period, which might help to understand the consumption of R. decorum Franch. corollas by the Bai nationality of Heqing county.

Background/Objectives: Maintaining an optimum transport density is essential for protecting water quality, lowering stress levels, and increasing fish survival rates. Transporting marine fish fry involves major dangers. The purpose of this study was to evaluate the impact of transport stress at varying densities on the immune-related gene expression, antioxidant capacity, and survival rate of yellowfin seabream (Acanthopagrus latus) fry. Methods: A 12 h simulated transport experiment was conducted with A. latus fry divided into six density groups. For 1-2 cm fry, densities of 900, 1200, and 1500 fry per pouch were used to assess antioxidant enzyme activity; and for 4-5 cm fry, densities of 100, 125, and 150 fry per pouch were used for gene expression analysis. The key parameters measured included survival rates, antioxidant enzyme activities in liver and intestinal tissues, and expression levels of HSP90α and caspase-3 genes. Results: The findings showed that recovery time and density both affected the observed responses and that transport density had a substantial effect on antioxidant enzyme activity in all tissues. The intestinal and liver tissues showed a considerable decrease in antioxidant enzyme activity, suggesting that these tissues may be able to respond to oxidative stress. Moreover, under high-density transport conditions, there were notable increases in the expression of caspase-3 and HSP90α, suggesting the activation of immune response systems. This research offers valuable new understandings into the relationship between transport density and immunological and antioxidant modulation in A. latus fry. Conclusions: The results provide a scientific foundation for enhancing aquaculture transport conditions, which will ultimately lead to decreased fish mortality and improved general health during transit, resulting in more sustainable and effective aquaculture methods.

Background/Objectives: Riboswitches are functional nucleic acids that regulate biological processes by interacting with small molecules, such as metabolites, influencing gene expression. Artificial functional nucleic acids, including deoxyribozymes, have been developed through in vitro selection for various catalytic functions. In a previous study, an l-histidine-dependent deoxyribozyme was identified, exhibiting RNA cleavage activity in the presence of l-histidine resembling ribonuclease catalytic mechanisms. This study aims to clarify the role of l-histidine in the activity and structural formation of the l-histidine-dependent deoxyribozyme (HD), focusing on the binding properties and conformational changes of its derivative HD3. Methods: Conformational changes in HD3 were analyzed using circular dichroism (CD) under varying concentrations of l-histidine. Direct binding analysis was conducted using carbon-14 (¹⁴C)-labeled l-histidine and a liquid scintillation counter. The catalytic activity of HD3 in the presence of different l-histidine concentrations was measured. Results: The binding constant for l-histidine-induced conformational changes (K_a(CD)) was found to be 2.0 × 10³ (M^-1), whereas for catalytic activity (K_a(Rxn)) and scintillation counting (K_a(RI)), it was approximately 1.0 × 10³ (M^-1). Conclusions: l-Histidine plays an essential role in both the catalytic activity and structural formation of the HD3 deoxyribozyme. The consistent binding constants across different experimental methods highlight the significant contribution of l-histidine to the active folding of deoxyribozymes.

Background/objectives: Infectious bronchitis (IB) is a highly infectious avian disease caused by the infectious bronchitis virus (IBV). The disease causes lesions mainly in the respiratory, reproductive, and renal systems and has a significant economic impact on the poultry industry worldwide.

Methods: We discovered two unique IBV isolates (T-62: PP737794.1 and CL-61: PP783617.1) circulating in Canada and molecularly characterized them.

Results: The phylogenetic analysis revealed that the IBV isolates belong to genotype I and fall between lineages 25 and 7. Further analysis of the T-62 IBV isolate indicated that it is a potential recombinant of the Iowa state isolate (IA1162/2020-MW) and that the CL-61 strain of the IBV is also a recombinant IBV with the Connecticut (Conn) vaccine strain as its major parent. The S1 glycoprotein of the CL-61 and T-62 strains of the IBV had 85.7% and 73.2% amino acid (aa) identities respectively compared to the Conn vaccine strain. There were 67 and 129 aa substitutions among the S1 glycoprotein of the CL-61 and T-62 strains of the IBV compared to the Conn vaccine, respectively. Importantly, two and nineteen of these aa variations were in hypervariable regions 1 (HVR1) and HVR3. Finally, the two IBV isolates possessed a higher affinity for the sialic acid ligand compared to the DMV/1639 and Mass/SES IBV strains.

Conclusions: Genetic recombination in the IBV results in the continual emergence of new variants, posing challenges for the poultry industry. As indicated by our analyses, live attenuated vaccine strains play a role in the genetic recombination of the IBV, resulting in the emergence of variants.

Background: Bouquet is a crucial characteristic indicative of wine quality that develops during the aging stage. The cytochrome P450 VvCYP76F14 multi-functionally catalyzes linalool into (E)-8-hydroxylinalool, (E)-8-oxolinalool, and (E)-8-carboxylinalool, which are direct precursors for wine bouquet. Wine bouquet was closely related to VvCYP76F14 activities.

Method: The VvCYP76F14 genes were cloned from five wine grape varieties using a homologous cloning method. The variation in residues of VvCYP76F14s were assessed by multiple alignment of amino acid sequences. Functional studies were implemented by in vitro enzyme activity and transient over-expression systems.

Results: D299T variation was observed in VvCYP76F14s of 'Yantai 2-2-08', 'Yantai 2-2-19', and 'Yantai 2-3-37' offspring lines, which was correlated with the decreased content of wine bouquet precursors of (E)-8-hydroxylinalool, (E)-8-oxolinalool, and (E)-8-carboxylinalool, respectively. Notably, the key amino acid residue D299 was located at the phase 0 intron positions of VvCYP76F14 genes isolated from distinct wine grape varieties or offspring lines, respectively. Notably, VvCYP76F14s of the 'Yantai2-2-08', 'Yantai 2-2-19', and 'Yantai 2-3-37' mutant lines exhibited lower in vitro enzymatic activities than those of 'L35' and 'Merlot'. In addition, the transient expression of VvCYP76F14 cloned from 'L35' and 'Merlot' restored the levels of wine bouquet precursors in berries of three D299T mutant lines, respectively, whereas VvCYP76F14 cloned from D299T mutant lines failed.

Conclusions: D299T variation was observed in three offspring lines and D299T mutation in VvCYP76F14 led to the decrease in wine bouquet precursor contents. VvCYP76F14 was implicated in the regulation of wine bouquet precursors in wine grapes.

Objective: Congenital, non-syndromic orofacial clefts (CL/P) are infrequently monogenic in etiology. However, heterozygous pathogenic CDH1 germline variants were reported in a few non-syndromic CL/P families, as well as in one syndromic form of CL/P: the blepharocheilodontic syndrome. CDH1 encodes epithelial cadherin (E-cadherin), and close to 300 different pathogenic CDH1 variants are listed in the ClinVar mutation database. The majority of CDH1 germline variants are implicated in hereditary diffuse gastric cancer (HDGC) susceptibility. The purpose of this study was to classify the CDH1 c.760G>A (p.Asp254Asn) mutation with respect to its resulting phenotype. Methods: Exome sequencing and targeted Sanger sequencing were performed in a family segregating CL/P. A review of pathogenic CDH1 variants in ClinVar and those identified in a PubMed/MEDLINE search was performed. Results: We identified a family with six individuals, who were 35-77 years old (mean 56 years) at their last examination, uniformly affected with bilateral CL/P. The CDH1 c.760G>A variant segregated with CL/P. This variant had been reported in 21 individuals, most often children and young adults, from six families. We determined a significant sex preponderance for this variant regarding CL/P: all 16 male and 5 of 11 female heterozygotes presented with CL/P. Furthermore, none of the heterozygous individuals in seven families reported any gastrointestinal tumors. Conclusions: The recurrent CDH1 c.760G>A mutation confers a high risk for CL/P, with strong male preponderance. This review of 27 mutation carriers, including 3 who were 68, 70, and 77 years of age, indicates that c.760G>A does not confer an increased risk for HDGC. The relevance of differentiating craniofacial from cancer phenotypes in mutation carriers is substantial for precision medicine and for counseling families.

Background/objectives: Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure.

Methods: This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry.

Results: Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. F_ROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility.

Conclusions: This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds.

Background/objectives: Bacterial wilt disease is a soil-borne disease caused by Ralstonia solanacearum that causes huge losses to crop economies worldwide.

Methods: In this work, strain MLY102 was isolated and further identified as R. solanacearum from a diseased tobacco stalk. The genomic properties of MLY102 were explored by performing biochemical characterization, genome sequencing, compositional analysis, functional annotation and comparative genomic analysis.

Results: MLY102 had a pinkish-red color in the center of the colony surrounded by a milky-white liquid with fluidity on TTC medium. The biochemical results revealed that MLY102 can utilize carbon sources, including D-glucose (dGLU), cane sugar (SAC) and D-trehalose dihydrate (dTRE). Genome sequencing through the DNBSEQ and PacBio platforms revealed a genome size of 5.72 Mb with a G+C content of 67.59%. The genome consists of a circular chromosome and a circular giant plasmid with 5283 protein-coding genes. A comparison of the genomes revealed that MLY102 is closely related to GMI1000 and CMR15 but has 498 special genes and 13 homologous genes in the species-specific gene family, indicating a high degree of genomic uniqueness.

Conclusions: The unique characteristics and genomic data of MLY102 can provide important reference values for the prevention and control of bacterial wilt disease.

Background: Idiopathic epilepsy (IE) disproportionately affects Belgian shepherd dogs and although genomic risk markers have been identified previously in the breed, causative variants have not been described.

Methods: The current study analyzed differences in whole blood RNA expression associated with IE and with a previously identified IE risk haplotype on canine chromosome (CFA) 14 using a transcriptomics RNA-seq approach.

Results: MFSD2A and a likely pseudogene of RPL19, both of which are genes implicated in seizure activity, were upregulated in dogs with IE. Genes in the interferon signaling pathway were downregulated in Belgian shepherds with IE. The CFA14 risk haplotype was associated with upregulation of CLIC1, ACE2, and PIGN and downregulation of EPDR1, all known to be involved with epilepsy or the Wnt/β-catenin signaling pathway.

Conclusions: These results highlight the value of assessing gene expression in canine IE research to uncover genomic contributory factors.

Tripartite motif protein 26 (TRIM26) is an E3 ubiquitin ligase and a member of the TRIM family. Similar to other TRIM proteins, TRIM26 consists of three domains, collectively termed RBCC: a Really Interesting New Gene (RING) domain, one B-Box domain, and a C terminal domain consisting of a PRY/SPRY domain. The PRY/SPRY domain exhibits relatively higher conservation compared with the RING and B-Box domains, suggesting potentially similar roles across TRIM26 proteins from various species. TRIM26 either directly interacts with viral proteins or modulates immune responses to engage with a viral infection, serving as either a protective or detrimental host factor depending on the circumvent of the viral infection. The present review focuses on understanding the mechanisms of TRIM26 during viral infection and its potential future applications.