• Journal of Veterinary Science
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• v.25 no.1
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• pp.18.1-18.27
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• 2024

Mastitis is one of the most widespread infectious diseases that adversely affects the profitability of the dairy industry worldwide. Accurate diagnosis and identification of pathogens early to cull infected animals and minimize the spread of infection in herds is critical for improving treatment effects and dairy farm welfare. The major pathogens causing mastitis and pathogenesis are assessed first. The most recent and advanced strategies for detecting mastitis, including genomics and proteomics approaches, are then evaluated. Finally, the advantages and disadvantages of each technique, potential research directions, and future perspectives are reported. This review provides a theoretical basis to help veterinarians select the most sensitive, specific, and cost-effective approach for detecting bovine mastitis early.

• Clinical and Experimental Vaccine Research
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• v.12 no.3
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• pp.179-192
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• 2023

The world has watched the emergence of numerous animal viruses that may threaten animal health which were added to the perpetual growing list of animal pathogens. This emergence drew the attention of the experts and animal health groups to the fact that it has become necessary to work on vaccine development. The current review aims to explore the perspective vaccines for emerging viral diseases in farm animals. This aim was fulfilled by focusing on modern technologies as well as next generation vaccines that have been introduced in the field of vaccines, either in clinical developments pending approval, or have already come to light and have been applied to animals with acceptable results such as viral-vectored vaccines, virus-like particles, and messenger RNA-based platforms. Besides, it shed the light on the importance of differentiation of infected from vaccinated animals technology in eradication programs of emerging viral diseases. The new science of nanomaterials was explored to elucidate its role in vaccinology. Finally, the role of Bioinformatics or Vaccinomics and its assist in vaccine designing and developments were discussed. The reviewing of the published manuscripts concluded that the use of conventional vaccines is considered an out-of-date approach in eliminating emerging diseases. However, these types of vaccines are considered the suitable plan especially in countries with few resources and capabilities. Piloted vaccines that rely on genetic-based technologies with continuous analyses of current viruses should be the aim of future vaccinology. Smart genomics of emerging viruses will be the gateway to choosing appropriate vaccines, regardless of the evolutionary rates of viruses.

• Genomics & Informatics
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• v.10 no.1
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• pp.1-8
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• 2012

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/ Solexa systems, along with bioinformation analysis technologies of whole-genome $de$ $novo$ assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing $de$ $novo$ assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least $2{\times}$ and $30{\times}$ depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through $de$ $novo$ assembly in any whole-genome sequenced species. The $20{\times}$ and $50{\times}$ coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average $30{\times}$ coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.66-72
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• 2003

Toxicogenomics is now emerging as one of the most important genomics application because the toxicity test based on gene expression profiles is expected more precise and efficient than current histopathological approach in pre-clinical phase. One of the challenging points in Toxicogenomics is the construction of intelligent database management system which can deal with very heterogeneous and complex data from many different experimental and information sources. Here we present a new Toxicogenomics database developed as a part of 'Toxicogenomics for Efficient Safety Test (TEST) project'. The TEST database is especially focused on the connectivity of heterogeneous data and intelligent query system which enables users to get inspiration from the complex data sets. The database deals with four kinds of information; compound information, histopathological information, gene expression information, and annotation information. Currently, TEST database has Toxicogenomics information fer 12 molecules with 4 efficacy classes; anti cancer, antibiotic, hypotension, and gastric ulcer. Users can easily access all kinds of detailed information about there compounds and simultaneously, users can also check the confidence of retrieved information by browsing the quality of experimental data and toxicity grade of gene generated from our toxicology annotation system. Intelligent query system is designed for multiple comparisons of experimental data because the comparison of experimental data according to histopathological toxicity, compounds, efficacy, and individual variation is crucial to find common genetic characteristics .Our presented system can be a good information source for the study of toxicology mechanism in the genome-wide level and also can be utilized fur the design of toxicity test chip.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.

• Journal of Genetic Medicine
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• v.8 no.1
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• pp.28-34
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• 2011

Most clinicians understand clinical trials as the evaluation process for new medicine before their use. However, clinical trials can also be applied to laboratory diagnostic tests (LDTs) to verify diagnostic accuracy and efficacy before their clinical laboratory implementation for patients. The clinical trial of LDT has two distinctive characteristics that are different from the case of pharmaceuticals and thus worth special consideration. One of them is the level of evidence. The well-designed randomized controlled trials (RCTs) are known to provide the best evidence to prove the clinical efficacy of any pharmaceutical products. However, RCTs lose practicality when applied to LDTs due to various issues including ethical complications. For this reason, comparative study format is considered more feasible approach for LDTs. In addition pharmaceuticals and LDTs are different in that the user's intervention is not required for the former but critical to the latter. Moreover, in the case of pharmaceuticals, end-products are produced by manufacturers before being used by clinicians. However, in LDTs, once reagents and instruments are provided by manufacturers, they are first utilized by clinical laboratories to produce test results in order for clinicians to use them later. In other words, when it comes to LDTs, clinical laboratories play the role of manufacturers, providing reliable test results with improved quality assurance. Considering the distinctive characteristics of LDTs, we would like to offer detailed suggestions to successfully perform clinical trials in LDTs, which include analytical performance measures, clinical test performance measures, diagnostic test accuracy measures, clinical effectiveness measures, and post-implementation surveillance.

• Proceedings of the Korean Society of Crop Science Conference
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• 2004.04a
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• pp.12-27
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• 2004

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant sciences. Plant proteomics would be most useful when combined with other functional genomics tools and approaches. A combination of microarray and proteomics analysis will indicate whether gene regulation is controlled at the level of transcription or translation and protein accumulation. In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is a most prevalent technique to identify rapidly a large of proteins in proteome analysis. However, the conventional Western blotting/sequencing technique us still used in many laboratories. As a first step to efficiently construct protein data-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein spots are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins (i. e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 30% of total rice cDNA have been deposited in the database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that fumed out to be calreticulin, gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activate in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins (http://genome .c .kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Recently, we are separated proteins from grain filling and seed maturation in rice to perform ESI-Q-TOF/MS and MALDI-TOF/MS. This experiment shows a possibility to easily and rapidly identify a number of 2-DE separated proteins of rice by ESI-Q-TOF/MS and MALDI-TOF/MS. Therefore, the Information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful in the plant molecular breeding. Also, information from our study could provide a venue to plant breeder and molecular biologist to design their research strategies precisely.

• Genomics & Informatics
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• v.21 no.3
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• pp.33.1-33.11
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• 2023

Type 2 diabetes mellitus (T2DM) is a multifactorial, polygenic, and metabolically complicated disease. A large number of genes are responsible for the biogenesis of T2DM and calpain10 (CAPN10) is one of them. The association of numerous CAPN10 genetic polymorphisms in the development of T2DM has been widely studied in different populations and noticed inconclusive results. The present study is an attempt to evaluate the plausible association of CAPN10 polymorphism SNP-19 (rs3842570) with T2DM and T2DM-related anthropometric and metabolic traits in the Noakhali region of Bangladesh. This case-control study included 202 T2DM patients and 75 healthy individuals from different places in Noakhali. A significant association (p < 0.05) of SNP-19 with T2DM in co-dominant 2R/3R vs. 3R/3R (odds ratio [OR], 2.7; p=0.0014) and dominant (2R/3R) + (2R/2R) vs. 3R/3R (OR, 2.47; p=0.0011) genetic models was observed. High-risk allele 2R also showed a significant association with T2DM in the allelic model (OR, 1.67; p=0.0109). The genotypic frequency of SNP-19 variants showed consistency with Hardy-Weinberg equilibrium (p > 0.05). Additionally, SNP-19 genetic variants showed potential associations with the anthropometric and metabolic traits of T2DM patients in terms of body mass index, systolic blood pressure, diastolic blood pressure, total cholesterol, and triglycerides. Our approach identifies the 2R/3R genotype of SNP-19 as a significant risk factor for biogenesis of T2DM in the Noakhali population. Furthermore, a large-scale study could be instrumental to correlate this finding in overall Bangladeshi population.