Journal of Genetics最新文献_第9页

Exploring the influences of geographical variation on sequence signatures in the human gut microbiome 探索地理差异对人类肠道微生物组序列特征的影响

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-11-16 DOI: 10.1007/s12041-023-01448-4

Gauraw Kumar, Punyasloke Bhadury

{"title":"Exploring the influences of geographical variation on sequence signatures in the human gut microbiome","authors":"Gauraw Kumar, Punyasloke Bhadury","doi":"10.1007/s12041-023-01448-4","DOIUrl":"https://doi.org/10.1007/s12041-023-01448-4","url":null,"abstract":"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.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"346 2","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138506351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The formate dehydrogenase enhances aluminum tolerance of tobacco 甲酸脱氢酶增强烟草对铝的耐受性

4区生物学

Journal of Genetics Pub Date : 2023-10-11 DOI: 10.1007/s12041-023-01447-5

Yonghong Xie, Yunmin Wei, Rongrong Han, Shitian Yu, Hui Xu, Caode Jiang, Yongxiong Yu

引用次数: 0

AICRF: ancestry inference of admixed population with deep conditional random field 具有深度条件随机场的混合种群的祖先推断

4区生物学

Journal of Genetics Pub Date : 2023-10-06 DOI: 10.1007/s12041-023-01445-7

Farhad Alizadeh, Hamid Jazayeriy, Omid Jazayeri, Fatemeh Vafaee

引用次数: 0

Mendel did not study common, naturally occurring phenotypes 孟德尔没有研究常见的、自然发生的表型

4区生物学

Journal of Genetics Pub Date : 2023-09-20 DOI: 10.1007/s12041-023-01446-6

David Curtis

引用次数: 0

Serum exosomal hsa_circRNA_0001842 is the potential biomarker for diagnosing lower limb vascular disease in type 2 diabetes mellitus 血清外泌体hsa_circRNA_0001842是诊断2型糖尿病下肢血管疾病的潜在生物标志物

4区生物学

Journal of Genetics Pub Date : 2023-09-16 DOI: 10.1007/s12041-023-01442-w

Qian-Qian Liu, Xing-Hui Liu, Hai-Ming Wang, Li-Min Xu, Xiao-Jing Zhao, Shu-Guang Han, Zuo-Hua Lu

引用次数: 0

In silico genotyping of blood group alleles using WGS data: a comparative study of the Orang Asli in Peninsular Malaysia. 利用WGS数据进行血型等位基因的计算机基因分型:马来西亚半岛阿斯利猩猩的比较研究。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Mercy Rophina, Teh Lay Kek, Sridhar Sivasubbu, Vinod Scaria, Mohd Zaki Salleh

{"title":"In silico genotyping of blood group alleles using WGS data: a comparative study of the Orang Asli in Peninsular Malaysia.","authors":"Mercy Rophina, Teh Lay Kek, Sridhar Sivasubbu, Vinod Scaria, Mohd Zaki Salleh","doi":"","DOIUrl":"","url":null,"abstract":"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.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10220547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome sequencing and characterization of microsatellite markers of Pterocarpus santalinus L.f.: an economically important endangered tree of Eastern Ghats, India. 印度东高止山脉一种重要的濒危经济树种——紫檀树的基因组测序及微卫星标记特征。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

M V Sneha, A H Madhushree, S Tapas Ranjan, B N Divakara, P Mohana Kumara, H R Prabuddha

{"title":"Genome sequencing and characterization of microsatellite markers of Pterocarpus santalinus L.f.: an economically important endangered tree of Eastern Ghats, India.","authors":"M V Sneha, A H Madhushree, S Tapas Ranjan, B N Divakara, P Mohana Kumara, H R Prabuddha","doi":"","DOIUrl":"","url":null,"abstract":"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 (FST) of 0.19 (FST˂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.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9841876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the influences of geographical variation on sequence signatures in the human gut microbiome. 探索地理变异对人类肠道微生物群序列特征的影响。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Gauraw Kumar, Punyasloke Bhadury

{"title":"Exploring the influences of geographical variation on sequence signatures in the human gut microbiome.","authors":"Gauraw Kumar, Punyasloke Bhadury","doi":"","DOIUrl":"","url":null,"abstract":"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.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138805330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LncRNA TTN-AS1 exacerbates extracellular matrix accumulation via miR-493-3p/FOXP2 axis in diabetic nephropathy. LncRNA TTN-AS1通过miR-493-3p/FOXP2轴加剧糖尿病肾病的细胞外基质积累。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Lin Jia, Wenzhe Wang, Hui Liu, Fan Zhu, Yunfang Huang

引用次数: 0

Is the fundamental pathology in Duchenne's muscular dystrophy caused by a failure of glycogenolysis-glycolysis in costameres? 杜氏肌萎缩症的基本病理是由糖原溶解失败引起的吗?

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Vishakha Nesari, Suresh Balakrishnan, Upendra Nongthomba

{"title":"Is the fundamental pathology in Duchenne's muscular dystrophy caused by a failure of glycogenolysis-glycolysis in costameres?","authors":"Vishakha Nesari, Suresh Balakrishnan, Upendra Nongthomba","doi":"","DOIUrl":"","url":null,"abstract":"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.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10754139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0