• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.6
• /
• pp.2489-2493
• /
• 2015

Background: Loss of heterozygosity (LOH) on chromosomal regions is crucial in tumor progression and this study aimed to identify genome-wide LOH in pancreatic cancer. Materials and Methods: Single-nucleotide polymorphism (SNP) profiling data GSE32682 of human pancreatic samples snap-frozen during surgery were downloaded from Gene Expression Omnibus database. Genotype console software was used to perform data processing. Candidate genes with LOH were screened based on the genotype calls, SNP loci of LOH and dbSNP database. Gene annotation was performed to identify the functions of candidate genes using NCBI (the National Center for Biotechnology Information) database, followed by Gene Ontology, INTERPRO, PFAM and SMART annotation and UCSC Genome Browser track to the unannotated genes using DAVID (the Database for Annotation, Visualization and Integration Discovery). Results: The candidate genes with LOH identified in this study were MCU, MICU1 and OIT3 on chromosome 10. MCU was found to encode a calcium transporter and MICU1 could encode an essential regulator of mitochondrial $Ca^{2+}$ uptake. OIT3 possibly correlated with calcium binding revealed by the annotation analyses and was regulated by a large number of transcription factors including STAT, SOX9, CREB, NF-kB, PPARG and p53. Conclusions: Global genomic analysis of SNPs identified MICU1, MCU and OIT3 with LOH on chromosome 10, implying involvement of these genes in progression of pancreatic cancer.

• Environmental Analysis Health and Toxicology
• /
• v.26
• /
• pp.10.1-10.7
• /
• 2011

Objects: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. Method: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C.ripairus using pyrosequencing method. Results: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value${\leq}1^{-5}$) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. Conclusions: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

• Genomics & Informatics
• /
• v.21 no.2
• /
• pp.16.1-16.14
• /
• 2023

Coronavirus disease 2019 (COVID-19) is a viral infection produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus epidemic, which was declared a global pandemic in March 2020. The World Health Organization has recorded around 43.3 billion cases and 59.4 million casualties to date, posing a severe threat to global health. Severe COVID-19 indicates viral pneumonia caused by the SARS-CoV-2 infections, which can induce fatal consequences, including acute respiratory distress syndrome (ARDS). The purpose of this research is to better understand the COVID-19 and ARDS pathways, as well as to find targeted single nucleotide polymorphism. To accomplish this, we retrieved over 100 patients' samples from the Sequence Read Archive, National Center for Biotechnology Information. These sequences were processed through the Galaxy server next generation sequencing pipeline for variant analysis and then visualized in the Integrative Genomics Viewer, and performed statistical analysis using t-tests and Bonferroni correction, where six major genes were identified as DNAH7, CLUAP1, PPA2, PAPSS1, TLR4, and IFITM3. Furthermore, a complete understanding of the genomes of COVID-19-related ARDS will aid in the early identification and treatment of target proteins. Finally, the discovery of novel therapeutics based on discovered proteins can assist to slow the progression of ARDS and lower fatality rates.

• Research in Plant Disease
• /
• v.29 no.4
• /
• pp.363-376
• /
• 2023

Alternaria black spots or blights in cruciferous crops have been devastating diseases worldwide and led to economic losses in broccoli, Chinese cabbage, kale, radish, rapeseed, etc. These diseases are caused by different Alternaria spp., including A. brassicae, A. brassicicola and A. raphani transmitted from infected seeds or insect vectors. Efforts to excavate disease resistance traits of cruciferous crops against Alternaria black spots or blights have been demonstrated. Genetic resource of disease resistance was investigated in the wild relatives of cruciferous crops, and different cultivars were screened under different inoculation conditions. Development of the disease-resistant lines against Alternaria black spots or blights was also tried via genetic transformation of the cruciferous crops using diverse plant defence-associated genes. Plant immunity activated by pre-treatment with chemicals, i. e. β-amino-n-butyric acid and melatonin, was suggested for reducing Alternaria black spots or blights in cruciferous crops. The disease resistance traits have also been evaluated in model plant Arabidopsis originating from different habitats. Various plant immunity-related mutants showing different disease responses from wild-type Arabidopsis provided valuable information for managing Alternaria black spots or blights in cruciferous crops. In particular, redox regulation and antioxidant responses altered in the Alternaria-infected mutants were discussed in this review.

• Korean Journal of Poultry Science
• /
• v.43 no.2
• /
• pp.55-61
• /
• 2016

With the aim of investigating the differences in the quality traits of breast meat between spent hen and broiler chicken, the physicochemical characteristics, fatty acid profile and sensory attributes of breast meat from the two chicken types were assessed. A higher protein content and a lower moisture content were found in breast of spent hen compared to that of commercial broilers (P<0.05). No significant differences in crude fat and ash contents were detected between commercial broilers and the older spent hens (P>0.05). Spent hens showed a significantly lower pH value than did commercial broilers. Spent hen meat had a higher $L^*$ value than broiler chicken meat did (P<0.05). However, $a^*$ and $b^*$ values of breast meat were similar between spent hens and commercial broilers. Water holding capacity values measured in the breast meat were comparable between the two types of chicken used in this study (P>0.05). However, spent hen meat showed a higher cooking loss value than did broiler meat (P<0.05). Total polyunsaturated fatty acid content was significantly higher in spent hen meat compared to broiler meat, in particular eicosapentaenoic acid and docosahexaenoic acid. Nevertheless, sensory characteristics of breast meat were comparable between spent hen and broiler chicken. This information can help consumers to understand better the nutritive value and important quality traits of breast meat from commercial broilers and spent hens.

• Korean Journal of Environmental Biology
• /
• v.41 no.4
• /
• pp.677-682
• /
• 2023

Milky white spots appeared on red bean leaves in a red bean cultivation area located in Jangyeon-myeon, Goesan-gun, Chungbuk Province. After culturing the pathogen in PDA medium, their morphology was observed, and their genes were BLAST-searched in the National Center for Biotechnology Information (NCBI). The pathogen was identified as a fungus called Rhizopus arrhizus. As a result of reinoculating the isolated pathogen on red beans, the same symptoms as those in the isolated leaves occurred. Characteristic colonies of R. arrhizuson PDA medium initially showed a bright color and then changed to dark gray over time, with mostly spherical sporangia. The sporangiospores were spherical or elliptical, mostly irregular, and small in size. Therefore, based on these results, this disease has not yet been reported in red beans and was called red bean brown leaf blight caused by Rhizopus arrhizus A. Fisch (syn. R. oryzae).

• Journal of Life Science
• /
• v.22 no.12
• /
• pp.1644-1650
• /
• 2012

The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.

• Journal of Animal Science and Technology
• /
• v.51 no.2
• /
• pp.123-128
• /
• 2009

Recently, the $2^{nd}$ generation genome map of the Korean cattle (Hanwoo) has been constructed by comparison of the nucleotide sequence of the Korean cattle BAC clones with whole genome sequence of the bovine data-base (B_tau 2.1 build). The objective of this study was to update the $2^{nd}$ generation genome map of the Korean cattle using the similar approach. The nucleotide sequence of the Korean cattle BAC clones utilized in the construction of the $2^{nd}$ generation map was compared with the newly released bovine data-base (B_tau 3.1 build) to generate the $3^{rd}$ generation map. While, 5,105 BAC clones were localized on bovine chromosome in the $2^{nd}$ generation map, a total of 9,595 BAC clones, which spans about 37.27% of the bovine chromosome after eliminating the overlapping sequence among the clones, have been mapped on the bovine chromosome in the $3^{rd}$ generation map. Further analysis of the nucleotide sequence of the BAC clones will allow us to develop map and facilitate to pinpoint the genes that are important for the improvement of the performance in this cattle breed.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.7
• /
• pp.912-919
• /
• 2017

Objective: Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. Methods: By using fixation index ($F_{ST}$) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and $F_{ST}$. Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. Results: IL-32 is detected under positive selection using the $F_{ST}$ simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. Conclusion: This study provides evidence for IL-32 gene as under significant positive selection in goat.

• Journal of Plant Biotechnology
• /
• v.39 no.1
• /
• pp.33-48
• /
• 2012

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant $Arabidopsis$ was available. As a result, the whole $B.$ $rapa$ genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in $Brassica$ crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of $Brassica$ genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for high-resolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within $Brassica$ as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in $Brassica$ crop.