• Genomics & Informatics
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• v.14 no.4
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• pp.241-254
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• 2016

Environmental microbes like Bordetella petrii has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in B. petrii challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value. In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No. PRJNA28135) from genome database of National Centre for Biotechnology information. In this regards, the inhibitory effect of nine natural compounds like ajoene (Allium sativum), allicin (A. sativum), cinnamaldehyde (Cinnamomum cassia), curcumin (Curcuma longa), gallotannin (active component of green tea and red wine), isoorientin (Anthopterus wardii), isovitexin (A. wardii), neral (Melissa officinalis), and vitexin (A. wardii) have been acknowledged with anti-bacterial properties and hence tested against identified drug target of B. petrii by implicating computational approach. The in silico studies revealed the hypothesis that lpxD could be a potential drug target and with recommendation of a strong inhibitory effect of selected natural compounds against infection caused due to B. petrii, would be further validated through in vitro experiments.

• Journal of Computing Science and Engineering
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• v.11 no.4
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• pp.111-120
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• 2017

Post-translational modifications (PTMs) of proteins play substantial roles in the gene regulation of cell physiological functions and in the generation of major diseases. However, the majority of existing studies only explored a certain PTM of proteins, while very few have investigated the PTMs of two or more domains and the effects of their interactions. In this study, after collecting data regarding a large number of breast cancer-related and validated PTMs, a sequence and domain analysis of breast cancer proteins was carried out using bioinformatics methods. Then, protein-protein interaction network-related tools were applied in order to determine the crosstalks between the PTMs of the proteins. Finally, statistical and functional analyses were conducted to identify more modification sites of domains and proteins that may interact with at least two or more PTMs. In addition to exploring the associations between the interactive effects of PTMs, the present study also provides important information that would allow biologists to further explore the regulatory pathways of biological functions and related diseases.

• International journal of advanced smart convergence
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• v.8 no.3
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• pp.115-122
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• 2019

Recent and ongoing discoveries of mycoviruses with new properties demand the development of an appropriate research infrastructure to analyze their evolution and classification. In particular, the discovery of negative-sense single-stranded mycoviruses is worth noting in genome types in which double-stranded RNA virus and positive-sense single-stranded RNA virus were predominant. In addition, some genomic properties of mycoviruses are more interesting because they have been reported to have similarities with the pathogenic virus family that infects humans and animals. Genetic information on mycoviruses continues to accumulate in public repositories; however, these databases have some difficulty reflecting the latest taxonomic information and obtaining specialized data for mycoviruses. Therefore, in this study, we developed a bioinformatics-based pipeline to efficiently utilize this genetic information. We also designed a schema for data processing and database construction and an algorithm to keep taxonomic information of mycoviruses up to date. The pipeline and database (termed 'mycoVDB') presented in this study are expected to serve as useful foundations for improving the accuracy and efficiency of future research on mycoviruses.

• Genomics & Informatics
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• v.21 no.4
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• pp.49.1-49.11
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• 2023

Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.

• Proceedings of the Korea Contents Association Conference
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• 2007.11a
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• pp.3-6
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• 2007

KISTI(Korea Institute of Science & Technology Information) CCBB(Center for Computational Biology and Bioinformatics) Website has been providing bioinformatics contents(databases and analysis tools) services to construct IT-based bioinformatics infrastructure. It also carries out the services to support domestic bioinformatics R&D activity and to construct the infrastructure. But, these services are not actively available because this CCBB website is not wellknown to users. Therefore, we performed the user survey for the researchers who are studying in the field of biological science. The items of this survey consist of subjects on bioinformatics databases, analysis tools and BioInfoNet. After the user survey is rearranged and analyzed, the result of survey will be used to provide the good service to the users who are need of bioinformatics infrastructure such as databases and analysis tools etc.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.sup3
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• pp.65-70
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• 2016

Lung cancer is one of the most common malignancies in the world. Its incidence and mortality rates are on the rise in Pakistan. However, epidemiological studies to identify common lung cancer determinants in the Pakistani population have been limited. In this study, data of 440 cases and 323 controls were collected from different hospitals in Peshawar and Islamabad, along with information about socio-demographic factors including age, sex and smoking. Univariate and multi-factorial analyses of socio-demographic factors in association with each other were also performed. Overall survival analysis highlighted that, out of 440 patients in the lung cancer dataset, 204 people were uncensored with a median survival time of 13 months (95% CI=12-18). There were 41 femaleand 399 male patients. Differences were observed between length of survival in the males and females (${\chi}12$ = 6.1; p-value = 0.01). Gender was observed to be significantly related to survival (p-value< 0.01), with better survival in females (hazard ratio=2). Cox regression was extended to adjust for the covariate age (z = 2.5; p-value = 0.02). Survival analysis was also performed on the basis of smoking groups (current smokers, former smokers and never smoked individuals) and smoking duration (smoking duration >10 years, <10 years and never smoked). Smoking duration was significantly associated with survival (p-value < 0.01), with better survival in never smokers in comparison to both smoking for greater or less than 10 years. Strong associations were observed for smoking group with duration greater than 10 years, OR=6.1(3.9-9.5) on univariate and multifactorial analysis OR=11.3(CI=6.8-19.3).

• Journal of Animal Science and Technology
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• v.55 no.6
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• pp.515-520
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• 2013

Pyruvate kinase M2 (PKM2) is a key regulatory enzyme in the glycolytic pathway. It is one of four pyruvate kinase isoenzymes that widely differ in their occurrence according to tissue type. PKM2 is expressed in differentiated tissues, such as fat tissues, lung, as well as normal proliferating cells, embryonic cells, and tumor cells. The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) in the PKM2 gene with meat quality traits in Berkshire pigs. We detected a SNP (g.34341 A>G) in the 3'UTR region of the PKM2 gene in 670 Berkshire pigs through DNA sequencing. Three genotypes, AA, AG, and GG, were found for this SNP, but based on an association analysis with meat quality traits, genotype AA was significantly associated with thicker back fat than genotype GG (p=0.027). Therefore, the g.34341 A>G polymorphism in the 3'UTR region of the porcine PKM2 gene could be applied in pig breeding programs to improve back fat thickness.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.205-211
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• 2013

The swine is one of the most widespread mammalian throughout the whole world. Presently, many studies concerning microsatellites in swine, especially domestic pigs, have been carried out in order to investigate general diversity patterns among either populations or breeds. Until now, a lot of time and effort spend into a single PCR method. But simple and more rapid multiplex PCR methods have been developed. The purpose of this study is to develop a robust set of microsatellites markers (MS marker) for traceability and individual identification. Using multiplex-PCR method with 23 MS marker divided 2 set, various alleles occurring to 5 swine breed (Berkshire, Landrace, Yorkshire, Duroc and Korea native pig) used markers to determine allele frequency and heterozygosity. MS marker found 4 alleles at SW403, S0227, SWR414, SW1041 and SW1377. The most were found 10 alleles at SW1920. Heterozygosity represented the lowest value of 0.102 at SWR414 and highest value of 0.861 at SW1920. So, it was recognized appropriate allele frequency for individual identification in swine. Using multiplex-PCR method, MS markers used to determine individual identification biomarker and breed-specific marker for faster, more accurate and lower analysis cost. Based on this result, a scientific basis was established to the existing pedigree data by applying genetics additionally. Swine traceability is expected to be very useful system and be conducted nationwide in future.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.11
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• pp.1523-1528
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• 2013

To increase plumage color uniformity and understand the genetic background of Korean chickens, we performed a genome-wide association study of different plumage color in Korean native chickens. We analyzed 60K SNP chips on 279 chickens with GEMMA methods for GWAS and estimated the genetic heritability for plumage color. The estimated heritability suggests that plumage coloration is a polygenic trait. We found new loci associated with feather pigmentation at the genome-wide level and from the results infer that there are additional genetic effect for plumage color. The results will be used for selecting and breeding chicken for plumage color uniformity.

• CELLMED
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• v.4 no.1
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• pp.6.1-6.12
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• 2014

Anthrax is the deadly disease for human being caused by Bacillus anthracis. Instantaneous research work on the mode of infection of the organism revealed that different proteases are involved in different steps of pathogenesis. Present study reports the in silico characterization and the detection of pathogenic proteases involved in anthrax infection through protein-protein interaction. A total of 13 acid, 9 neutral, and 1 alkaline protease of Bacillus anthracis were selected for analysing the physicochemical parameter, the protein superfamily and family search, multiple sequence alignment, phylogenetic tree construction, protein-protein interactions and motif finding. Among the 13 acid proteases, 10 were found as extracellular enzymes that interact with immune inhibitor A (InhA) and help the organism to cross the blood brain barrier during the process of infection. Multiple sequence alignment of above acid proteases revealed the position 368, 489, and 498-contained 100% conserved amino acids which could be used to deactivate the protease. Among the groups analyzed, only acid protease were found to interact with InhA, which indicated that metalloproteases of acid protease group have the capability to develop pathogenesis during B. anthracis infection. Deactivation of conserved amino acid position of germination protease can stop the sporulation and germination of B anthracis cell. The detailed interaction study of neutral and alkaline proteases could also be helpful to design the interaction network for the better understanding of anthrax disease.