Journal of Genetics最新文献

Differences in the distribution of RBC antigens defining the blood group types among different populations have been well established. Fewer studies exist that have explored the blood group profiles of indigenous populations worldwide. With the availability of population-scale genomic datasets, we have explored the blood group profiles of theOrang Aslis, who are the indigenous population in Peninsular Malaysia and provide a systematic comparison of the same with major global population datasets. Variant call files fromwhole genome sequence data (hg19) of 114 Orang Asli were retrieved from The Orang Asli Genome Project. Systematic variant annotations were performed using ANNOVAR and only those variants mapping back to genes associated with 43 blood group systems and transcription factors KLF1 and GATA1 were filtered. Blood group-associated allele and phenotype frequencies were determined and were duly compared with other datasets including Singapore SequencingMalay Project, aboriginal western desert Australians and global population datasets including The 1000 Genomes Project and gnomAD. This study reports four alleles (rs12075, rs7683365, rs586178 and rs2298720) of DUFFY, MNS, RH and KIDD blood group systems which were significantly distinct between indigenous Orang Asli and cosmopolitanMalaysians. Eighteen alleles that belong to 14 blood group systems were found statistically distinct in comparison to global population datasets. Although not much significant differences were observed in phenotypes of most blood group systems, major insights were observed when comparing Orang Asli with aboriginal Australians and cosmopolitanMalaysians.This study serves as the first of its kind to utilize genomic data to interpret blood group antigen profiles of the OrangAsli population. In addition, a systematic comparison of blood group profiles with related populations was also analysed and documented.

Pterocarpus santalinus L.f. (red sanders) is an endemic, endangered and economically important tree species distributed in the Eastern Ghats of Andhra Pradesh, India. This tree is well known for its blood-red coloured timber which has a high value in the international market. Due to its high timber demand, illegally logging of red sanders has resulted in fragmentation and depletion of its natural populations. Assessing the genetic diversity is a prerequisite for the identification of distinct populations of red sanders in the natural habitat for prioritizing conservation efforts. The present study has focussed on genome sequencing, identification and validation of microsatellite markers of P. santalinus. A total of 282,918 simple sequence repeat (SSR) loci were identified using whole genome sequence from P. santalinus leaf tissue. A total of 28 SSRs were selected for polymorphism analysis across the 52 individuals belonging to three populations of P. santalinus and identified a sum of 502 alleles with polymorphic information content of 0.83; observed heteozygosity (Ho) 0.42 and expected heterozygosity (He) 0.69. Genetic differentiation coefficient (F_ST) of 0.19 (F_ST˂0.25) which is indicating moderate genetic differentiation among the populations. Six SSRs from P. indicus Willd. and P. erinaceus Poir. were successfully amplified in P. santalinus and produced 131 alleles. These newly identified SSRs are useful in detecting genetic diversity and further developing conservation strategies for P. santalinus.

Diabetic nephropathy (DN), a common cause of chronic renal failure and end-stage renal disease, leads to a high mortality. However, the role of TTN-AS1 in extracellular matrix (ECM) accumulation during DN remains unclear. In our study, TTN-AS1 exhibited high expression in high glucose-treated mesangial cells, and TTN-AS1 silencing alleviated high glucose-induced ECM accumulation in mesangial cells. Additionally, animal study revealed that TTN-AS1 was upregulated in renal tissues of DN rats, and TTN-AS1 knockdown mitigated renal injury of DN rats. Mechanistically, TTN-AS1 was validated to bind to miR-493-3p, and miR-493-3p targeted forkhead box P2 (FOXP2) 3'untranslated region in mesangial cells. TTN-AS1 interacted with miR-493-3p to upregulate FOXP2 in vitro and in vivo. Moreover, FOXP2 overexpression counteracted the effects of TTN-AS1 silencing on the ECM accumulation. In conclusion, TTN-AS1 exacerbated ECM accumulation via the miR-493-3p/FOXP2 axis during DN development. This research may provide a potential new direction for DN treatment.

Duchenne muscular dystrophy (DMD) is the most common form of progressive childhood muscular dystrophy associated with weakness of limbs, loss of ambulation, heart weakness and early death. The mutations causing either loss-of-expression or function of the full-length protein dystrophin (Dp427) from the DMD gene are responsible for the disease pathology. Dp427 forms a part of the large dystroglycan complex, called DAPC, in the sarcolemma, and its absence derails muscle contraction. Muscle biopsies from DMD patients show an overactivation of excitation-contraction-coupling (ECC) activable calcium incursion, sarcolemmal ROS production, NHE1 activation, IL6 secretion, etc. The signalling pathways, like Akt/PBK, STAT3, p38MAPK, and ERK1/2, are also hyperactive in DMD. These pathways are responsible for post-mitotic trophic growth and metabolic adaptation, in response to exercise in healthy muscles, but cause atrophy and cell death in dystrophic muscles. We hypothesize that the metabolic background of repressed glycolysis in DMD, as opposed to excess glycolysis seen in cancers or healthy contracting muscles, changes the outcome of these 'growth pathways'. The reduced glycolysis has been considered a secondary outcome of the cytoskeletal disruptions seen in DMD. Given the cytoskeleton-crosslinking ability of the glycolytic enzymes, we hypothesize that the failure of glycogenolytic and glycolytic enzymes to congregate is the primary pathology, which then affects the subsarcolemmal cytoskeletal organization in costameres and initiates the pathophysiology associated with DMD, giving rise to the tissue-specific differences in disease progression between muscle, heart and brain. The lacunae in the regulation of the key components of the hypothesized metabolome, and the limitations of this theory are deliberated. The considerations for developing future therapies based on known pathological processes are also discussed.

Geography shapes the structure and function of human gut microbiomes. In this study, we have explored the available human gut microbiome 16S rRNA sequence datasets of cohorts representing large geographical gradients. The 16S rRNA sequences representing V3-V4 as well as V4 regions generated using Illumina sequencing chemistry in the MiSeq platform encompassing the United States of America, Chile, South Africa, Kuwait, and Malaysia were subjected to in-depth computational biology analyses. Firmicutes and Bacteroidetes were the most dominant phyla present in all studied cohorts but Actinobacteria was exclusively present in high abundance in cohorts from Malaysia (15.99%). The relative abundance of five families, namely Bacteroidaceae, Ruminococcaceae, Prevotellaceae, Clostridiaceae, and Eubacteriaceae were highest representing the studied cohorts. The permutational multivariate analysis of variance (PERMANOVA) showed that the dissimilarity in the gut microbiome structure of cohorts representing studied countries was significant (R² = 0.28, P<0.001). The calculated Firmicutes to Bacteroidetes (F : B) ratio was found to be lowest in cohorts from South Africa (1.11) and Chile (0.95). The cohorts from South Africa exhibited the highest alpha diversity based on Hill numbers at q=0, whereas at q=1 and 2, cohorts from Malaysia had the highest alpha diversity. The beta diversity analysis revealed that cohorts from Chile formed a distinct cluster among all the studied geographical locations. For the first time, the study also showed that cohorts from Malaysia representing short geographical distances exhibited distinct intrapopulation differences in the gut microbiome and may not be influenced by cultural and genetic factors.

Wilms' tumour (WT) is the most typical type of renal tumour in children, which has a poor prognosis and high recurrence rate. This study explored whether lncRNA EMX2 opposite strand / antisense RNA (EMX2OS) modulated the stemness, epithelial-mesenchymal transition (EMT) and metastasis of WTcells through the interaction with insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1). The expression levels of EMX2OS, IGF2BP1 and stem cell markers OCT4, Nanog, Sox2 and CD133 were detected by real time quantitative polymerase chain reaction (RT-qPCR). The stemness, migration and invasion of WTcells were determined by sphere formation assay, scratch and transwell assay, respectively. The levels of EMT-related proteins were detected by Western blotting. RNA pull down and RIP assays were utilized to validate the interaction between EMX2OS and IGF2BP1. The tumourigenicity of WTcells in vivo was analysed using a xenograft tumour assay. EMX2OS was downregulated in WT patients, while IGF2BP1 was upregulated. EMX2OS overexpression or IGF2BP1 knockdown suppressed WT cell sphere formation, migration and invasion. Moreover, EMX2OS could directly interact with RNA-binding protein IGF2BP1, and IGF2BP1 overexpression counteracted the inhibitory effect of EMX2OS on WT cell stemness, migration, invasion and EMT. The in vivo tumour growth, stemness and EMT were repressed by EMX2OS through the interaction with IGF2BP1. In conclusion, EMX2OS acted as a tumour suppressor for WT by interacting with IGF2BP1, which might be a novel target for WT diagnosis and therapy.

Milkfish (Chanos chanos) belongs to the family Chanidae and it is a potential candidate species for aquaculture with the best biological characteristics. This study investigates the genetic diversity and population structure of C. chanos along the Indian coast using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). A total of 90 samples collected from five different locations across the Indian coast were sequenced for analysis using cyt b. The sequencing of a 1100-bp cyt b mtDNA fragment revealed the presence of 38 haplotypes with a haplotype diversity value of 0.835 and a nucleotide diversity value of 0.00400. The variation within and among populations accounted for about 97.33% and 2.67%, respectively. The fixation index analysis indicated that there is no significant genetic divergence among the populations from different geographical areas. Neighbour-joining tree analysis of the haplotype data showed no distinct patterns of phylogeographic structure. Results from this study indicated that there is a lack of genetic divergence between the populations of C. chanos along the Indian coast. The haplotype network showed star-like geneology which indicated the demographic expansion of the C. chanos population in these locations. The recent demographic expansion of the C. chanos population was also supported by the results of Tajima's D statistics. Results from this study can be used for planning effective strategies for the conservation and management of the C. chanos population in the wild.

CRISPR-Cas9-based F0 knockout (KO) approach permits relatively simple and rapid generation of homozygous KOs and allows quick investigation of gene functions in zebrafish. However, F0 KO studies are largely performed using commercial synthetic guide RNAs (gRNAs) which are unaffordable by majority of the researchers. We tested (i) how effective is the CRISPR-Cas9-based F0 KO approach using in vitro transcribed gRNAs; (ii) how penetrant are the resulting phenotype at the later developmental stages and (iii) whether Coughlin's group pre-designed gRNAs are functional even without validating the gRNAs or testing for lack of SNP's in target loci. We targeted the rx3 gene that is required for the formation of the eye, a structure that exhibits robustness and can quickly recover from early phenotypes. Our results indicate that, in the majority of the samples, injection of Cas9 protein complex with four different in vitro transcribed gRNAs; targeting rx3 results in lack of eyes or disrupted eye development. Thus, the CRISPR-Cas9-based F0 KO approach using pre-designed, quadruple in vitro transcribed gRNAs can recapitulate the function of a gene at least until 5-dpf stage of larval zebrafish.

The single-nucleotide polymorphisms (SNP) ILDR1 rs2332035 has shown a high statistical association with presbycusis (hearing loss with age or age-related hearing impairment (ARHI)), according to genetic association studies in European populations. However, linked markers have not been surveyed. Here linkage disequilibrium (LD) of markers in ILDR1, in relation to rs2332035, is explored in the 2504 individuals from the 1000Genomes database. Of the 920 SNPs retrieved, 10 showed strong LD (r²= 0.8) in Europeans and Latin Americans, which are proposed here as candidate markers for both control-case association and cause-effect studies in both populations.

The ring chromosome 21[r(21)] syndrome is a rare disorder, and mainly occurs as a de novo event. However, a wide variation of the phenotype has been reported in r(21) cases depending on breakpoints, loss of genetic material, and mosaicism of cells with r(21) and monosomy 21, causing copy number alterations. A 29-month-old female was referred to the centre for seizures, developmental delay, microcephaly, hypotonia, deafness, and other congenital abnormalities. Physical examination revealed short stature and multiple facial dysmorphism. She was unable to sit, walk or stand by herself. Cytogenetic study with GTG banding revealed a karyotype of mos 46,XX,r(21)(p11.1q22.12)[70]/45,XX,-21[10]/47,XX,r(21),+r(21)[1]/46,XX[10]. Additionally, molecular cytogenetics refined the breakpoints and characterized the deleted region (RP11-410P24/CHR21: 32849565-33019511) in the clone with the r(21) as ~12-14 Mb contiguous region at 21q22.12 to 21qter. The present study has accurately detected copy number alterations caused by ring chromosome formation. The basis of the UCSC Genome Browser on Human (GRCh38/hg38) analysis suggests hemizygous expression of a deleted critical region of chromosome 21 in ring chromosome cell lines. This is likely to be the underlying cause of the present phenotypes in the patient. Overall, the genotype-phenotypic correlation in r(21) cases remains widely diverse, most likely due to tissue-specific mosaicism of the 45, XX,-21 cell line.