• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.10
• /
• pp.1473-1477
• /
• 2007

Four-and-a-half LIM-only protein 3 (FHL3) is a member of the LIM protein superfamily and can participate in mediating protein-protein interaction by binding one another through their LIM domains. In this study, the 5'- and 3'- cDNA ends were characterized by RACE (Rapid Amplification of the cDNA Ends) methodology in combination with in silico cloning based on the partial cDNA sequence obtained. Bioinformatics analysis showed FHL3 protein contained four LIM domains and four LIM zinc-binding domains. In silico mapping assigned this gene to the gene cluster MTF1-INPP5B-SF3A3-FHL3-CGI-94 on pig chromosome 6 where several QTL affecting intramuscular fat and eye muscle area had previously been identified. Transcription of the FHL3 gene was detected in spleen, liver, kidney, small intestine, skeletal muscle, fat and stomach, with the greatest expression in skeletal muscle. The A/G polymorphism in exon II was significantly associated with birth weight, average daily gain before weaning, drip loss rate, water holding capacity and intramuscular fat in a Landrace-derived pig population. Together, the present study provided the useful information for further studies to determine the roles of FHL3 gene in the regulation of skeletal muscle cell growth and differentiation in pigs.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.221-228
• /
• 2003

This paper presents a novel method that can identify the individual's haplotype from the given genotypes. Because of the limitation of the conventional single-locus analysis, haplotypes have gained increasing attention in the mapping of complex-disease genes. Conventionally there are two approaches which resolve the individual's haplotypes. One is the molecular haplotypings which have many potential limitations in cost and convenience. The other is the in-silico haplotypings which phase the haplotypes from the diploid genotyped populations, and are cost effective and high-throughput method. In-silico haplotyping is divided into two sub-categories - statistical and computational method. The former computes the frequencies of the common haplotypes, and then resolves the individual's haplotypes. The latter directly resolves the individual's haplotypes using the perfect phylogeny model first proposed by Dan Gusfield [7]. Our method combines two approaches in order to increase the accuracy and the running time. The individuals' haplotypes are resolved by considering the MLE (Maximum Likelihood Estimation) in the process of computing the frequencies of the common haplotypes.

• Molecules and Cells
• /
• v.24 no.3
• /
• pp.394-408
• /
• 2007

Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 93-11 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region [Kottapalli et al. (2006)]. Transcriptional profiling of FR13A and IET8585 using a rice 22K oligo array validated the above findings. Based on in silico analysis and arraying we observed that both cultivars respond to the above stresses through a common signaling system involving protein kinases, adenosine mono phosphate kinase, leucine rich repeat, PDZ/DHR/GLGF, and response regulator receiver protein. The combined approaches suggest that transcription factor EREBP on long arm of chromosome 5 regulates both submergence tolerance and blb resistance. Pyruvate decarboxylase and alcohol dehydrogenase, co-located in the same region, are candidate downstream genes for submergence tolerance at the seedling stage, and t-snare for bs-blb resistance. We also detected up-regulation of novel defense/stress-related genes including those encoding fumaryl aceto acetate (FAA) hydrolase, scramblase, and galactose oxidase, in response to the imposed stresses.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.4
• /
• pp.621-629
• /
• 2021

Shigella flexneri is a facultative intracellular pathogen that causes bacillary dysentery in humans. Infection with S. flexneri can result in more than a million deaths yearly and most of the victims are children in developing countries. Therefore, identifying novel and unique drug targets against this pathogen is instrumental to overcome the problem of drug resistance to the antibiotics given to patients as the current therapy. In this study, a comparative analysis of the metabolic pathways of the host and pathogen was performed to identify this pathogen's essential enzymes for the survival and propose potential drug targets. First, we extracted the metabolic pathways of the host, Homo sapiens, and pathogen, S. flexneri, from the KEGG database. Next, we manually compared the pathways to categorize those that were exclusive to the pathogen. Further, all enzymes for the 26 unique pathways were extracted and submitted to the Geptop tool to identify essential enzymes for further screening in determining the feasibility of the therapeutic targets that were predicted and analyzed using PPI network analysis, subcellular localization, druggability testing, gene ontology and epitope mapping. Using these various criteria, we narrowed it down to prioritize 5 novel drug targets against S. flexneri and one vaccine drug targets against all strains of Shigella. Hence, we suggest the identified enzymes as the best putative drug targets for the effective treatment of S. flexneri.

• The Korean Journal of Physiology and Pharmacology
• /
• v.20 no.5
• /
• pp.507-514
• /
• 2016

Although 3D-complex fractionated atrial electrogram (CFAE) mapping is useful in radiofrequency catheter ablation for persistent atrial fibrillation (AF), the directions and configuration of the bipolar electrodes may affect the electrogram. This study aimed to compare the spatial reproducibility of CFAE by changing the catheter orientations and electrode distance in an in -silico left atrium (LA). We conducted this study by importing the heart CT image of a patient with AF into a 3D-homogeneous human LA model. Electrogram morphology, CFAE-cycle lengths (CLs) were compared for 16 different orientations of a virtual bipolar conventional catheter (conv-cath: size 3.5 mm, inter-electrode distance 4.75 mm). Additionally, the spatial correlations of CFAE-CLs and the percentage of consistent sites with CFAE-CL<120 ms were analyzed. The results from the conv-cath were compared with that obtained using a mini catheter (mini-cath: size 1 mm, inter-electrode distance 2.5 mm). Depending on the catheter orientation, the electrogram morphology and CFAE-CLs varied (conv-cath: $11.5{\pm}0.7%$ variation, mini-cath: $7.1{\pm}1.2%$ variation), however the mini-cath produced less variation of CFAE-CL than conv-cath (p<0.001). There were moderate spatial correlations among CFAE-CL measured at 16 orientations (conv-cath: $r=0.3055{\pm}0.2194$ vs. mini-cath: $0.6074{\pm}0.0733$, p<0.001). Additionally, the ratio of consistent CFAE sites was higher for mini catheter than conventional one ($38.3{\pm}4.6%$ vs. $22.3{\pm}1.4%$, p<0.05). Electrograms and CFAE distribution are affected by catheter orientation and electrode configuration in the in-silico LA model. However, there was moderate spatial consistency of CFAE areas, and narrowly spaced bipolar catheters were less influenced by catheter direction than conventional catheters.

• The Plant Pathology Journal
• /
• v.38 no.6
• /
• pp.572-582
• /
• 2022

Sheath blight disease caused by the necrotrophic, soilborne pathogen Rhizoctonia solani Kuhn, is the global threat to rice production. Lack of reliable stable resistance sources in rice germplasm pool for sheath blight has made resistance breeding a very difficult task. In the current study, 101 rice landraces were screened against R. solani under artificial epiphytotics and identified six moderately resistant landraces, Jigguvaratiga, Honasu, Jeer Sali, Jeeraga-2, BiliKagga, and Medini Sannabatta with relative lesion height (RLH) range of 21-30%. Landrace Jigguvaratiga with consistent and better level of resistance (21% RLH) than resistant check Tetep (RLH 28%) was used to develop mapping population. DNA markers associated with ShB resistance were identified in F₂ mapping population developed from Jigguvaratiga × BPT5204 (susceptible variety) using bulk segregant analysis. Among 56 parental polymorphic markers, RM5556, RM6208, and RM7 were polymorphic between the bulks. Single marker analysis indicated the significant association of ShB with RM5556 and RM6208 with phenotypic variance (R²) of 28.29 and 20.06%, respectively. Co-segregation analysis confirmed the strong association of RM5556 and RM6208 located on chromosome 8 for ShB trait. This is the first report on association of RM6208 marker for ShB resistance. In silico analysis revealed that RM6208 loci resides the stearoyl ACP desaturases protein, which is involved in defense mechanism against plant pathogens. RM5556 loci resides a protein, with unknown function. The putative candidate genes or quantitative trait locus harbouring at the marker interval of RM5556 and RM6208 can be further used to develop ShB resistant varieties using molecular breeding approaches.

• KSBB Journal
• /
• v.26 no.2
• /
• pp.131-138
• /
• 2011

Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.

• Journal of Life Science
• /
• v.31 no.5
• /
• pp.453-463
• /
• 2021

Hearing loss is a group of clinically and genetically heterogeneous disorders characterized by congenital- to adult-onset deafness with frequent additional symptoms such as myopathy, nephropathy, and optic disorders. It is commonly divided into two types: syndromic, with no other symptoms, and nonsyndromic, with other symptoms. Autosomal recessive hearing loss is relatively frequent in Pakistan, which may be due in part to frequent consanguineous marriages. This study was performed by whole exome sequencing to determine the genetic causes in two Pakistani consanguineous families with autosomal recessive hearing loss. We identified a pathogenic homozygous variant (p.Leu326Gln in MYO7A) in a family with prelingual-onset hearing loss and two variants of uncertain significance (p.Val3094Ile in GPR98 and p.Asp56Gly in PLA2G6) in a family with early-onset hearing loss concurrent with muscular atrophy. The missense mutations in MYO7A and PLA2G6 were located in the highly conserved sites, and in silico analyses predicted pathogenicity, while the GPR98 mutation was located in the less conserved site, and most in silico analysis programs predicted its nonpathogenic effect. Homozygosity mapping showed that both alleles of the homozygous mutations identified in each family originated from a single founder; spread from this single source might be due to consanguineous marriages. This study will help provide exact molecular diagnosis and treatment for autosomal recessive hearing loss patients in Pakistan.

• Journal of Plant Biotechnology
• /
• v.35 no.4
• /
• pp.265-274
• /
• 2008

Glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family divided into Phi, Tau, Theta, Zeta, Lambda and DHAR classes on the basis of sequence identity. The Phi(F) and Tau(U) classes are plant-specific and ubiquitous. Their roles have been defined as herbicide detoxification and responses to biotic and abiotic stresses. Fifty-two members of the GST super-family were identified in the Arabidopsis thaliana genome, 13 members of which belong to the Phi class of GSTs (AtGSTFs). Based on the sequence similarities of AtGSTFs, 11 BAC clones were identified from Brassica rapa. Seven unique sequences of ORFs designated the Phi class candidates of GST derived from B. rapa (BrGSTFs) were detected from these 11 BAC clones by blast search and sequence alignment. Some of BrGSTFs were present in the same BAC clones indicating that BrGSTFs could also be clustered as usual in plant. They were mapped on B. rapa linkage group 2, 3, 9 and 10 and their nucleotide and amino acid sequences were highly similar to those of AtGSTFs. In addition, in silico analysis of BrGSTFs using Korea Brassica Genome Project 24K oligochip and microarray database for cold, salt and drought stresses revealed 15 unigenes to be highly similar to AtGSTFs and six of these were identical to one of BrGSTFs identified in the BAC clones indicating their expression. The sequences of BrGSTFs and unigenes identified in this study will facilitate further studies to apply GST genes to medical and agriculture purposes.

• Asian-Australasian Journal of Animal Sciences
• /
• v.18 no.9
• /
• pp.1237-1241
• /
• 2005

Mannose-P-dolichol utilization defect 1 (MPDU1) gene is required for utilization of the mannose donor MPD in synthesis of both lipid-linked oligosaccharides (LLOs) and glycosylphosphatidylinositols (GPI) which are important for functions such as protein folding and membrane anchoring. The full length cDNA of the porcine MPDU1 was determined by in silico cloning and rapid amplification of cDNA ends (RACE). The deduced amino acid showed 91% identity to the corresponding human sequence with five predicted transmembrane regions. RT-PCR was performed to detect its expression pattern in five tissues and results showed that it is expressed ubiquitously among the tissues checked. A single nucleotide substitution resulting in the amino acid change (137 Tyr-137 His) was detected within exon 5. Allele frequencies in six pig breeds showed distinctive differences between those Chinese indigenous pigs breeds and European pigs. Using the pig/rodent somatic cell hybrid panel (SCHP), we mapped the porcine MPDU1 gene to SSC12, which is consistent with the comparative mapping result as conservative syntenic groups presented between human chromosome 17 and pig chromosome 12.