• BMB Reports
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• v.38 no.6
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• pp.739-747
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• 2005

Full-length cDNA sequences of four novel SPATA4 genes in chimpanzee, cow, chicken and ascidian were identified by bioinformatic analysis using mouse or human SPATA4 cDNA fragment as electronic probe. All these genes have 6 exons and have similar protein molecular weight and do not localize in sex chromosome. The mouse SPATA4 sequence is identified as significantly changed in cryptorchidism, which shares no significant homology with any known protein in swissprot databases except for the homologous genes in various vertebrates. Our searching results showed that all SPATA4 proteins have a putative conserved domain DUF1042. The percentages of putative SPATA4 protein sequence identity ranging from 30% to 99%. The high similarity was also found in 1 kb promoter regions of human, mouse and rat SPATA4 gene. The similarities of the sequences upstream of SPATA4 promoter also have a high proportion. The results of searching SymAtlas (http://symatlas.gnf.org/SymAtlas/) showed that human SPATA4 has a high expression in testis, especially in testis interstitial, leydig cell, seminiferous tubule and germ cell. Mouse SPATA4 was observed exclusively in adult mouse testis and almost no signal was detected in other tissues. The pI values of the protein are negative, ranging from 9.44 to 10.15. The subcellular location of the protein is usually in the nucleus. And the signal peptide possibilities for SPATA4 are always zero. Using the SNPs data in NCBI, we found 33 SNPs in human SPATA4 gene genomic DNA region, with the distribution of 29 SNPs in the introns. CpG island searching gives the data about CpG island, which shows that the regions of the CpG island have a high similarity with each other, though the length of the CpG island is different from each other.This research is a fundamental work in the fields of the bioinformational analysis, and also put forward a new way for the bioinformatic analysis of other genes.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1710-1720
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• 2008

A comprehensive genome profiling study was undertaken based on automated genotyping and analysis of 20 microsatellite markers that involved 155 birds representing eight different populations. The distribution of microsatellite markers in each of these breeds helped us to decipher genetic heterogeneity, population genetic structure and evolutionary relationships of the present day chicken populations in India. All the microsatellite loci utilized for the analysis were polymorphic and reasonably informative. A total of 285 alleles were documented at 20 loci with a mean of 14.25 alleles/locus. A total of 103 alleles were found to be population/strain specific of which, only 30 per cent had a frequency of more than 10. The mean PIC values ranged from 0.39 for the locus ADL158 to 0.71 for loci MCW005 or ADL267 across the genomes and 0.55 in Dahlem Red to 0.71 in Desi (non-descript), among the populations. The overall mean expected and observed heterozygosity estimates for our populations were 0.68 and 0.64, respectively. The overall mean inbreeding coefficients (FIS) varied between -0.05 (Babcock) and 0.16 (Rhode Island Red). The pairwise FST estimates ranged from 0.06 between Aseel and Desi (non-descript) to 0.14 between Dahlem Red and Babcock. The Nei's genetic distance varied from 0.30 (WLH-IWD and WLH-IWF) to 0.80 (Dahlem Red and Babcock. Phylogenetic analysis grouped all the populations into two main clusters, representing i) the pure breeds, Dahlem Red and Rhode Island Red, and ii) the remaining six populations/strains. All the chicken populations studied were in the state of mild to moderate inbreeding except for commercial birds. A planned breeding is advised for purebreds to revive their genetic potential. High genetic diversity exists in Desi (non-descript), local birds, which can be exploited to genetically improve the birds suitable for backyard poultry.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.170-176
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• 2009

Culture-independent 16S rDNA-DGGE profiling and phylogenetic analysis were used to examine the predominant bacterial communities associated with the two sponges, Dictyonella sp. and Spirastrella abata from Jeju island. The culture-independent approach involved extraction of total bacterial DNA, PCR amplification of the 16S ribosomal DNA using primer pair 341f-GC and 518r, and separation of the amplicons on a denaturing gradient gel. Denaturing gradient gel electrophoresis banding patterns indicated 8 and 7 bands from the two sponge species, Dictyonella sp. and Spirastrella abata, respectively. There were not common major bands in two different sponges. Comparative sequence analysis of variable DGGE bands revealed from 93% to 98% similarity to the known published sequences. The dominant bacterial group of Dictyonella sp. belonged to uncultured Gammaproteobacteria, while, that of Spirastrella abata belonged to uncultured Alphaproeobacteria and Firmicutes. DGGE analysis indicated predominant communities of the sponge-associated bacteria differ in the two sponges from the same geographical location. This result revealed that bacterial community profiles of the sponges were host species-specific.

• Journal of Information Processing Systems
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• v.12 no.1
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• pp.1-34
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• 2016

Gene identification is at the center of genomic studies. Although the first phase of the Encyclopedia of DNA Elements (ENCODE) project has been claimed to be complete, the annotation of the functional elements is far from being so. Computational methods in gene identification continue to play important roles in this area and other relevant issues. So far, a lot of work has been performed on this area, and a plethora of computational methods and avenues have been developed. Many review papers have summarized these methods and other related work. However, most of them focus on the methodologies from a particular aspect or perspective. Different from these existing bodies of research, this paper aims to comprehensively summarize the mainstream computational methods in gene identification and tries to provide a short but concise technical reference for future studies. Moreover, this review sheds light on the emerging trends and cutting-edge techniques that are believed to be capable of leading the research on this field in the future.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.188-194
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• 2023

Microbacterium elymi KUDC0405^T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405^T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405^T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 ㎛. Based on 16S rRNA gene sequences, KUDC0405^T was most closely related to Microbacterium bovistercoris NEAU-LLE^T (97.8%) and Microbacterium pseudoresistens CC-5209^T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405^T and M. bovistercoris NEAU-LLE^T and M. pseudoresistens CC-5209^T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405^T, M. bovistercoris NEAU-LLE^T, and M. pseudoresistens CC-5209^T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405^T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C_17:0 and iso-C_16:0. Strain KUDC0405^T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405^T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405^T (=KCTC 49411^T, =CGMCC1.18472^T).

• Clinical and Experimental Pediatrics
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• v.53 no.3
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• pp.432-436
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• 2010

Transient neonatal diabetes mellitus (TNDM) has been associated with paternal uniparental isodisomy of chromosome 6, paternally inherited duplication of 6q24, or a methylation defect at a CpG island of the ZAC or HYMAI gene. We experienced a case of TNDM in which the patient presented with hyperglycemia, macroglossia, and intrauterine growth retardation, caused by a paternally derived HYMAI. An 18-day-old female infant was admitted to the hospital because of macroglossia and recurrent hyperglycemia. In addition to the macroglossia, she also presented with large fontanelles, micrognathia, and prominent eyes. Serum glucose levels were 200-00 mg/dL and they improved spontaneously 2 days after admission. To identify the presence of a maternal methylated allele, bisulfite-treated genomic DNA from peripheral blood was prepared and digested with BssHII after polymerase chain reaction (PCR) amplification with methylation-specific HYMAI primers. PCR and restriction fragment length polymorphism analysis showed that the patient had only the paternal origin of the HYMA1 gene. TNDM is associated with a methylation defect in chromosome 6, suggesting that an imprinted gene on chromosome 6 is responsible for this phenotype.

• Journal of Life Science
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• v.31 no.6
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• pp.537-542
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• 2021

Schisandra nigra Max., a dioecious plant native to Jeju Island in Korea, is cultivated on a small scale for fruit production. As fruit-producing female individuals are generally considered to be more valuable than male, early identification of plant sex at the seedling stage is important. In this study, a sequence-characterized amplified region (SCAR) marker associated with a female-specific region in the genome of S. nigra was investigated. Of 120 randomly amplified polymorphic DNA (RAPD) primers, one primer (OPB-03) consistently amplified a 749 bp band in female plants. The female-specific PCR product was isolated and cloned, and the nucleotide sequences were then determined. Southern hybridization performed using the female-specific fragment as a probe produced positive signals only in genomic DNA from the female plants. This result revealed that the 749 bp segment of DNA was present in the genome of female plants but absent in the genome of male plants. A SCAR primer pair was designed based on the RAPD marker to amplify a 436 bp fragment in the genomic DNA of female plants. This primer pair amplified the expected size of DNA fragment in female plants and four monoecious individuals collected from a natural population. The SCAR marker identified in this study can be used to distinguish female-flowering individuals at the seedling stage.

• The Plant Pathology Journal
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• v.38 no.1
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• pp.12-24
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• 2022

In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.

• Microbiology and Biotechnology Letters
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• v.44 no.4
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• pp.512-521
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• 2016

A bacterial strain was isolated from a soil sample collected on Jeju Island, Korea. The strain, designated WJ-2, exhibited a high xylanase activity, whereas cellulase activity was not detected. The 16S rRNA gene sequence of WJ-2 was highly similar to type strains of the genus Streptomyces. A neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WJ-2 is phylogenetically related to Streptomyces atrovirens. Furthermore, DNA-DNA hybridization analysis confirmed that strain WJ-2 is a novel subspecies of Streptomyces atrovirens. The genomic DNA G+C content was 73.98 mol% and the major fatty acid present was anteiso-C15:0 (36.19%). The growth and xylanase production of strain WJ-2 were significantly enhanced by using soytone and xylan as nitrogen and carbon sources, respectively. Crude enzyme preparations from the culture broth of strain WJ-2 exhibited maximal total xylanase activities at pH 7.0 and $55^{\circ}C$. Thin-layer chromatography analysis revealed that the crude enzyme degrades beechwood xylan to yield xylobiose and xylotriose as the principal hydrolyzed end products.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.