RESUMEN
BACKGROUND: Few studies have annotated the whole mitochondrial DNA (mtDNA) genome associated with drug responses in Asian populations. This study aimed to characterize mtDNA genetic profiles, especially the distribution and frequency of well-known genetic biomarkers associated with diseases and drug-induced toxicity in a Korean population. METHOD: Whole mitochondrial genome was sequenced for 118 Korean subjects by using a next-generation sequencing approach. The bioinformatic pipeline was constructed for variant calling, haplogroup classification and annotation of mitochondrial mutation. RESULTS: A total of 681 variants was identified among all subjects. The MT-TRNP gene and displacement loop showed the highest numbers of variants (113 and 74 variants, respectively). The m.16189T > C allele, which is known to reduce the mtDNA copy number in human cells was detected in 25.4% of subjects. The variants (m.2706A > G, m.3010A > G, and m.1095T > C), which are associated with drug-induced toxicity, were observed with the frequency of 99.15%, 30.51%, and 0.08%, respectively. The m.2150T > A, a genotype associated with highly disruptive effects on mitochondrial ribosomes, was identified in five subjects. The D and M groups were the most dominant groups with the frequency of 34.74% and 16.1%, respectively. CONCLUSIONS: Our finding was consistent with Korean Genome Project and well reflected the unique profile of mitochondrial haplogroup distribution. It was the first study to annotate the whole mitochondrial genome with drug-induced toxicity to predict the ADRs event in clinical implementation for Korean subjects. This approach could be extended for further study for validation of the potential ethnic-specific mitochondrial genetic biomarkers in the Korean population.
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ADN Mitocondrial , Mitocondrias , Pueblo Asiatico/genética , ADN Mitocondrial/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Mitocondrias/genética , República de CoreaRESUMEN
A mesophilic, facultatively anaerobic, autotrophic bacterium, designated strain Su4(T), was isolated from marine sediment. The isolate was able to utilize reduced sulfur compounds including thiosulfate, tetrathionate, sulfur and sulfide but not sulfite as the energy source. Growth occurred under aerobic and denitrifying chemolithoautotrophic conditions in the presence of thiosulfate as an electron donor and bicarbonate as a carbon source. The G+C content of the genomic DNA was 64.5 mol%. Comparative 16S rRNA gene sequence studies showed that strain Su4(T) was clearly affiliated with the class Gammaproteobacteria. The isolate was Gram-negative-staining and rod-shaped, lacked flagella and grew in artificial seawater medium at 10-40 °C (optimum 28-32 °C) and in 1-5â% (w/v) NaCl (optimum 3â% NaCl). Strain Su4(T) possessed C16:0, C16:1ω7c/iso-C15:0 2-OH and C18:1ω7c/ω9t/ω12t as the major fatty acids. On the basis of phenotypic and phylogenetic analysis, the isolate represents a novel species of a novel genus, for which the name Thioalbus denitrificans is proposed. The type strain is Su4(T) (â=âKCTC 5699(T) â=âJCM 15568(T)).
Asunto(s)
Gammaproteobacteria/clasificación , Gammaproteobacteria/aislamiento & purificación , Sedimentos Geológicos/microbiología , Compuestos de Azufre/metabolismo , Aerobiosis , Anaerobiosis , Técnicas de Tipificación Bacteriana , Composición de Base , Bicarbonatos/metabolismo , Carbono/metabolismo , Crecimiento Quimioautotrófico , Análisis por Conglomerados , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/química , ADN Ribosómico/genética , Ácidos Grasos/análisis , Gammaproteobacteria/genética , Gammaproteobacteria/fisiología , Datos de Secuencia Molecular , Oxidación-Reducción , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Cloruro de Sodio/metabolismo , TemperaturaRESUMEN
A taxonomic study was performed on two isolates, strains RF3(T) and RF21, recovered from a thiosulfate-oxidizing enrichment culture. Comparative 16S rRNA gene sequence analysis showed that these isolates were clearly affiliated with the class Betaproteobacteria. Strains RF3(T) and RF21 were most closely related to Diaphorobacter nitroreducens NA10B(T) (97.9 and 98.2 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains RF3(T) and RF21 was 99.8 %. The two isolates were Gram-negative, aerobic and denitrifying. Growth was observed at 7-35 degrees C. Physiological and biochemical properties of strains RF3(T) and RF21 were different from those of D. nitroreducens NA10B(T) in that strains RF3(T) and RF21 were able to utilize l-histidine, 2-ketogluconate and caprate, but unable to utilize suberate. The G+C contents of the genomic DNA of strains RF3(T) and RF21 were 62.9 and 62.8 mol%, respectively, and the predominant quinone was ubiquinone-8. Strains RF3(T) and RF21 possessed C(16 : 0), C(17 : 0) cyclo, and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH as major fatty acids. DNA-DNA relatedness data indicated that strains RF3(T) and RF21 represent a genomic species separate from D. nitroreducens. On the basis of the evidence presented from this polyphasic analysis, it is suggested that strains RF3(T) and RF21 represent a novel species of the genus Diaphorobacter, for which the name Diaphorobacter oryzae sp. nov. is proposed. The type strain is RF3(T) (=KCTC 22225(T)=LMG 24467(T)).
Asunto(s)
Comamonadaceae/clasificación , Tiosulfatos/metabolismo , Técnicas Bacteriológicas , Comamonadaceae/química , Comamonadaceae/genética , Comamonadaceae/metabolismo , Medios de Cultivo , Ácidos Grasos , Datos de Secuencia Molecular , Oxidación-Reducción , Fenotipo , ARN Ribosómico 16S/genética , Especificidad de la EspecieRESUMEN
Our newly designed primers were evaluated for the molecular analysis of specific groups of the sqr gene encoding sulfide : quinone reductase (SQR) in sediment environments. Based on the phylogenetic analysis, we classified the sqr sequences into six groups. PCR primers specific for each group were developed. We successfully amplified sqr-like gene sequences related to groups 1, 2 and 4 from diverse sediments including a marine sediment (SW), a tidal flat (TS), a river sediment (RS) and a lake sediment (FW). We recovered a total of 82 unique phylotypes (based on a 95 % amino acid sequence similarity cutoff) from 243 individual sqr-like gene sequences. Phylotype richness varied widely among the groups of sqr-like gene sequences (group 1>group 2>group 4) and sediments (SW>TS>RS>FW). Most of the sqr-like gene sequences were affiliated with the Proteobacteria clade and were distantly related to the reference sqr gene sequences from cultivated strains (less than approximately 80 % amino acid sequence similarity). Unique sqr-like gene sequences were associated with individual sediment samples in groups 1 and 2. This molecular tool has also enabled us to detect sqr-like genes in a sulfur-oxidizing enrichment from marine sediments. Collectively, our results support the presence of previously unrecognized sqr gene-containing micro-organisms that play important roles in the global biogeochemical cycle of sulfur.
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Sedimentos Geológicos/microbiología , NAD(P)H Deshidrogenasa (Quinona)/genética , Proteobacteria/genética , Bacterias Reductoras del Azufre/genética , Cartilla de ADN , ADN Bacteriano/genética , Agua Dulce/microbiología , Variación Genética , Datos de Secuencia Molecular , Filogenia , Proteobacteria/enzimología , Agua de Mar/microbiología , Alineación de Secuencia , Análisis de Secuencia de ADN , Azufre/metabolismo , Microbiología del AguaRESUMEN
Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.