Biochemical Genetics最新文献

The IUCN classifies two-endemic fishes of the Western Ghats in Peninsular India: Nilgiri mystus Hemibagrus punctatus is critically endangered, and Yellow catfish Horabagrus brachysoma is vulnerable. These are threatened by habitat degradation, excess fishing, and dam construction. ICAR-NBFGR, the premier research organisation in India for fish conservation, aims to conserve these two species through captive propagation, stock identification, and stock-specific ranching programs. The information on this species' genetic diversity and population structure is crucial for the successful rehabilitation of the species. Microsatellite markers are considered suitable markers for genetic stock structure analyses. An attempt was made to identify microsatellite markers in H. brachysoma (n = 27) and H. punctatus (n = 31) using Illumina Sequencing technology. The preliminary studies show that markers are efficient enough to differentiate the genetic stocks of these conservation-important species across their range of natural distribution. Three genetic stocks are identified in H. brachysoma and two in H.punctatus using the developed markers.

AKR1B1 is a member of aldo-keto-reductase (AKR) superfamily which catalyze the reduction of carbonyl groups to hydroxyl groups in NADPH-dependent ways. Previous studies have shown that AKR1B1 promotes cancer progression, but its exact role in acute leukemia was unclear. Cell counting and Luminescent Cell Viability Assay were performed to measure the cell proliferation and viability. Soft-Agar Colony Formation (CFU) assay was conducted to measure the capacity of single cells to form colonies in vitro. Cell apoptosis, cell cycle, and cell differentiation were assessed by flow cytometry. Western blotting and RT-qPCR were utilized to examine AKR1B1 expression in acute leukemia cells. In vivo leukemia growth and mouse survival were evaluated using a model of xenotransplantation mice. We explored the AKR1B1 effect and mechanism in acute leukemia cells using RNA-sequencing technology and transcriptomic analysis. AKR1B1 is highly expressed in acute leukemia cells. Knockdown of AKR1B1 inhibited acute leukemia cell proliferation, colony-forming capability, and cell cycle and promoted apoptosis. Additionally, xenograft experiments proved that knockdown of AKR1B1 delayed the progression of acute leukemia cell in vivo. RNA-sequencing data analysis demonstrated that AKR1B1 was involved in the epigenetic silencing of H3K27me3-targeted genes. EZH2 inhibitor UNC1999 combined with knockdown of AKR1B1 showed synergistic inhibitory effect on acute leukemia cells. AKR1B1 is essential for the leukemogenesis and may serve as a potential therapeutic target to treat acute leukemia patients.

Previous study has identified circRNAs as an important factor in cancer stem cells (CSCs) progression, which contributes to tumor initiation and progression. This study aspired to uncover the mechanisms of circ_0000972 on hepatocellular carcinoma (HCC) CSCs. RT-qPCR was utilized to quantify circ_0000972, miR-96-5p, and profilin 1(PFN1) expression in HCC tissues and cells. To evaluate the in vivo functions of circ_0000972, HCC cells with circ_0000972 overexpression were utilized to establish xenograft model through subcutaneous injection. The cell colony and sphere formation assays were adopted to evaluate the impact of circ_0000972 on the stemness characteristics of HCC cells. Additionally, the interaction between circ_0000972, miR-96-5p, and PFN1 was determined through bioinformatics analysis, dual-luciferase reporter assays, and rescue experiments. Circ_0000972 and PFN1 expression was significantly downregulated in HCC tissues and cells, while miR-96-5p exhibited an increased expression level. The overexpression of circ_0000972 was observed to inhibit the cell colony, sphere formation, and EMT of HCC CSCs. In xenograft model, circ_0000972 overexpression restrained the tumor volume and weight. Mechanistically, circ_0000972 stimulated PFN1 expression through the inhibition of miR-96-5p. More importantly, circ_0000972 overexpression could promote PFN1 expression and inhibit the stemness of HCC CSCs. Interestingly, the effect of circ_0000972 overexpression on such progresses was reversed by PFN1 silencing. This study elucidates that circ_0000972, an antitumor factor, sponges miR-96-5p to inhibit oncogenic cellular process in HCC by mediating PFN1 expression.

Annexins are a ubiquitous, evolutionarily conserved group of Ca²⁺-dependent phospholipid-binding proteins. They are a family of less numerous and more varied proteins that form a unique monophyletic group. They play an important role in various abiotic and biotic stress responses through Ca²⁺-mediated signaling. Chickpea (Cicer arietinum L.) is one of the most widely grown legume crops in the world. In recent years, intensive research has been carried out to identify and elucidate genes and molecular pathways that control stress responses in plants. The availability of the chickpea genome has hastened the functional genomics of chickpea. In the current study, we attempted Genome-wide identification and in silico analysis of Annexins in chickpea. Thirteen annexin sequences have been identified in the chickpea genome. Four conserved annexin domains were found in ten annexin members, while three annexins CaAnn5, CaAnn12, and CaAnn13, showed three, two, and one conserved domain, respectively. The gene structure analysis showed the presence of multiple exons in all thirteen annexins. Most Annexin genes are composed of 3-5 introns. Their chromosomal locations showed that out of thirteen genes, ten could be mapped on four chromosomes. Three genes were placed on the scaffold regions. The promoter sequence analysis of all thirteen annexins showed the presence of various elements related to growth and development and response to different phytohormones and abiotic stress. The gene expression data of different annexins in various tissues like leaf, shoot, root, flower bud, and young pod showed their differential expression. Analysis of expression data of roots in drought stress showed their differential expression with the different stages of plant growth. Overall, the current findings show the possible role of CaAnns in different stages of plant growth and development in normal and stressful conditions. Moreover, these findings will be helpful in the further characterization of CaAnn genes and their promoters.

Substance use disorder (SUD) is a complex condition involving psychological, sociocultural, and genetic factors. In this study, we examined the alternations in mitochondrial DNA copy number (mtDNAcn) and telomere length (TL) and their relationship to demographic, medical, heredity, and substance use characteristics in patients with SUD and healthy controls. We investigated a total cohort of 54 participants: 21 healthy individuals, 17 patients with alcohol dependence (AD), and 16 patients with drug dependence (DD). TL and mtDNAcn were measured using quantitative real-time PCR, with statistical methods used to assess the association between variables. We observed a significant decrease in mtDNAcn in both SUD groups, particularly associated with chronic diseases in the AD group. No significant differences in TL were found among the three groups. Sex-associated analysis revealed a significant mtDNAcn reduction in the DD males and elevated TL in AD males compared to control males. Correlation analyses showed associations between the two biomarkers and age, sex, and chronic diseases. Our findings suggest that leukocyte mtDNAcn is a more sensitive marker than TL in patients with SUD, indicating sex-specific patterns of alterations. These findings require confirmation through larger cohort recruitment.

As a multifactorial and endocrine disease, polycystic ovary syndrome (PCOS) affects approximately 5-20% of women worldwide. Recently, long noncoding RNAs (lncRNAs) have emerged as potent predictors of a particular phenotype in PCOS. Our preliminary study examines the link between polymorphisms in lncRNAs MEG3, HOTTIP, and GAS5 and the risk of PCOS. The present study included 200 women with PCOS and 200 healthy women. The studied variations were genotyped by applying the PCR-RFLP and the tetra-ARMS-PCR reaction) techniques. The effect of variation in lncRNA on miRNA:lncRNA interactions, lncRNA-RNA interaction network, and the impact of the variations on the splicing site were predicted using different computational databases. The codominant heterozygous (TC vs. TT) model, the dominant (TC + CC vs. TT) model, the overdominant (TT + CC vs. TC) model, the C allele of rs2023843, and the C allele of rs55829688 had a protective role against PCOS. The A allele of rs4081134 and G allele of rs7158663 of the MEG3 conferred an increased risk of PCOS by 1.37 and 1.44 folds, respectively. The interaction analysis revealed that TC/GG/AA/TC and TC/GG/GA/TC strongly decreased the risk of PCOS by 94 and 92%, respectively. Interestingly, MEG3 and HOTTIP variants can create or disrupt binding sites for several splicing factors. In our population, MEG3 rs4081134 and rs7158663, GAS5 rs55829688, and HOTTIP rs2023843 polymorphisms were associated with PCOS risk. Replication studies on larger sample sizes must be conducted to confirm these findings and investigate other potential causative factors involved in the pathophysiology of PCOS.

Cocobod introduced nationwide artificial hand pollination in Ghana in 2017 to supplement natural pollination of Theobroma cacao L. (cocoa) by insects (Forcipomyia midges) to increase yield. Hybrid farms of 8-20 years old are mostly selected. Pollen donor and receiver trees are selected based on morphological characteristics. This study analyzed the genetic diversity among donor and recipient trees of cocoa hand pollination in three farms in the Offinso Municipality of Ghana using SSR markers. Twelve forward and reverse primer pairs out of fifteen primers screened were used to evaluate genetic intraspecific and interspecific diversity among 25 accessions based on clear amplification and reproducible scorable bands. A total of 115 polymorphic bands were detected which ranged between 5.00 and 17.00 with a mean of 9.58 alleles per locus. Cluster analysis showed similarity coefficient range of 0.10 to 0.83. Analysis of molecular variance (AMOVA) showed13% genetic variation between populations and 87% within populations of T. cacao. PhiPT value of 0.130 recorded showed weak genetic differentiation between populations. Gene diversity varied from 0.64 to 0.88 with primers MTcCIR33 and MTcCIR07 respectively. Highest observed heterozygosity (Ho) of 0.60 and least Polymorphism Information Content (PIC) of 0.57 were recorded. Pollen donor and recipient trees selected from the same or nearby farms accounts for present genetic structure of low genetic diversity between populations. Though hand pollination designs focus much on high yields, improving genetic diversity to prevent inbreeding in cocoa is recommended.

There are many factors that affect male fertility such as chronic health problems, psychological factors, and illnesses. Male infertility can be caused abnormal sperm function, low sperm production or even blockages that prevent the delivery of sperm. The aim of the work is to determine the expression pattern of the circularANKLE2 and circularL3MBTL4 RNA in spermatozoa from fertile and infertile males, as well as the relationship between these circRNA transcripts and sperm quality. The study involved two groups: a control group comprising 40 healthy, fertile men and an experimental group of 90 infertile males. Semen samples were collected and processed for analysis using computer-assisted semen analysis. Following RNA extraction from sperm samples, reverse transcription and real-time PCR were performed to assess the levels of circular ANKLE2 and circular L3MBTL4 RNA. There was a significant up-regulation of circularANKLE2 RNA expression (p < 0.05), and a significant down-regulation of circularL3MBTL4 RNA expression (p < 0.05) in asthenozoospermia, astheno-teratozoospermia, and oligo-astheno-teratozoospermia groups, as well as, in immature spermatozoa separated from normozoospermic samples. Moreover, the altered expression of both circular L3MBTL4 and circular ANKLE2 RNA showed significant correlations with the associated sperm parameters. In conclusion, the expression of circular ANKLE2 RNA and circular L3MBTL4 RNA may play a significant role in male fertility and could serve as potential biomarkers of sperm quality, warranting further investigation for their application in infertility diagnostics.

DNA polymorphisms QTL analysis in crops is a valuable tool to study the genetic basis of complex traits in agricultural plants. Candidate gene for abiotic (salinity) stress was spotted in the QTL region spanning CaLG03 and CaLG06 in our previous study. In continuity to the same, we have picked up QTL-associated Cicer arietinum RD22 (CaRD22) gene which belongs to BURP-domain-containing group of proteins (BURPs) and studied its expression patterns in salinity-tolerant (ICCV10) and susceptible (DCP92-3) genotypes of chickpea. Earlier, few systematic categorizations of BURPs including RD22 gene were reported, but no QTL driven functional prediction w.r.t salinity stress is known so far. Here, a couple of in silico approaches were utilized followed by lab validation to speculate the features of RD22 BURP gene particularly Ca_23903 in Chickpea. A complete set of fifteen BURP genes located on chromosome 2, 4, 5, 6, 7, 8, and Scaffold 653 were studied. Motif analysis, gene structure study, phylogenetic analysis, cis-element analysis in promoter regions, and co-expression network analysis were performed in addition to the quantitative expression analysis. Expression profiling of RD22 gene and other interacting gene partners were performed in root and shoot tissues exposed to salt stress (200 mM). The findings predict the behavior of BURP genes specifically RD22 subtype during salinity conditions emphasizing their implications in associated physiological processes.

Ovarian cancer (OC) is a challenging cancer frequently detected at advanced stages. Regulatory B cells (Breg cells) can impair antitumor immunity in patients with OC. The imbalanced serum soluble CD40/CD40L pathway is associated with ovarian tumors. This study aimed to explore the mechanisms involving CD40/CD40L signaling through which Breg cells promote the progression of OC. Breg cells were isolated from peripheral blood samples of 20 patients with OC and 20 healthy controls and identified by flow cytometry. Then, the soluble CD40L concentration in peripheral blood serum of OC patients and healthy volunteers was measured by enzyme-linked immunosorbent assay (ELISA), and we found that the serum soluble CD40L level markedly increased and the proportion of Breg cells was positively correlated with CD40L level in peripheral blood of OC patients. Besides, Breg cells were isolated from spleens of female C57BL/6 WT mice and CD40^-/- mice. Reverse transcription-quantitative polymerase chain reaction, cell counting kit-8 assays, colony formation assays, flow cytometry, Western blotting, wound healing assays, and Transwell assays were conducted to assess the in vitro effect of Breg cells and CD40. We found that Breg cells contributed to cell proliferation, migration, and invasion and suppressed cell apoptosis in OC via the CD40/CD40L pathway. Moreover, we established a xenograft tumor model in female nude BALB/c mice. Tumor size and weight were evaluated, and Western blotting and ELISA were conducted, and we found that Breg cells promoted tumor growth via CD40 signaling. In conclusion, this study demonstrates that Breg cells activated by the CD40/CD40L pathway promotes the aggressiveness of OC cells and tumor growth, indicating that targeting the CD40/CD40L pathway might represent a novel therapeutic option for OC treatment.