In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and isease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within 20 A (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.
Computational Biology ; Crystallization ; Humans ; Hydrophobic and Hydrophilic Interactions ; Isoelectric Point ; Molecular Biology ; Point Mutation ; Protein Engineering ; Proteins

Visualization of the homology information is an important method to analyze the evolutionary and functional meanings of genes. With a database containing model genomes of Homo sapiens, Mus muculus, and Rattus norvegicus, we constructed a web-based comparative analysis tool, BioCovi, to visualize the homology information of mammalian sequences on a very large scale. The user interface has several features: it marks regions whose identity is greater than that specified, it shows or hides gaps from the result of global sequence alignment, and it inverts the graph when total identity is higher than the threshold specified.
Animals ; Genome ; Genomics* ; Humans ; Mice ; Rats ; Sequence Alignment

BOD is an FTP service management tool on the Internet. It was developed for biological researchers in South Korea. It enables easier and faster access of bioinformation without having to go through foreign FTP sites. BOD includes an automatic downloader with a management and email alert service from which the user can easily select and schedule any biological database. Once listed in BOD, the user can check and modify the download status and data from an additional email alert service.
Appointments and Schedules ; Electronic Mail ; Internet ; Korea

BACKGROUND: Androgenic alopecia (AGA) is the most common type of hair loss. It is likely inherited genetically and is promoted by dihydrotestosterone. 5α-reductase has been proven a good target through finasteride use. However, the pathogenesis of AGA cannot be fully explained based only on dihydrotestosterone levels. OBJECTIVE: To identify similar hairloss inhibition activity of RE-ORGA with mode of action other than finasteride. METHODS: We prepared RE-ORGA from Korean herb mixtures. We performed MTT assays for cytotoxicity, Cell Counting Kit-8 assays for cell proliferation, and western blot to identify expression levels of 5α-reductase and Bax. RNA-sequencing was performed for the expression patterns of genes in dihydrotestosterone-activated pathways. Anti-inflammatory activity was also assessed by the expression levels of tumor necrosis factor-alpha (TNF-α) and interleukin 6. RESULTS: REORGA could promote the proliferation of human dermal papilla cells and showed low cytotoxicity. It also inhibited the expression of 5α-reductases and Bax in the cells. RNA-sequencing results verified that the mRNA expressions of SRD5A1, Bax, transforming growth factor-beta 1 (TGF-β1), and TGF-β1 induced transcript 1 (TGFβ1I1) were decreased, whereas expression of protein tyrosine kinase 2 beta (PTK2β) was more elevated. REORGA also showed anti-inflammatory activity through decreased mRNA levels of TNF-α. CONCLUSION: Transcriptionally, up-regulation of PTK2β and concomitant down-regulation of TGFβ1I1 imply that RE-ORGA can modulate androgen receptor sensitivity, decreasing the expression of 5α-reductase type II and Bax together with TGF-β1 transcripts; RE-ORGA also showed partial anti-inflammatory activity. Overall, RE-ORGA is expected to alleviate hair loss by regulating 5α-reductase activity and the receptor's androgen sensitivity.
Alopecia ; Blotting, Western ; Cell Count ; Cell Proliferation ; Cholestenone 5 alpha-Reductase ; Dihydrotestosterone ; Down-Regulation ; Finasteride ; Hair ; Humans ; Interleukin-6 ; Protein-Tyrosine Kinases ; Receptors, Androgen ; RNA, Messenger ; Tumor Necrosis Factor-alpha ; Up-Regulation

The main mechanism of evolution is that biological entities change, are selected, and reproduce. We propose a different concept in terms of the main agent or atom of evolution: in the biological world, not an individual object,but its interactive network is the fundamental unit of evolution. The interaction network is composed of interaction pairs of information objects that have order information. This indicates a paradigm shift from 3D biological objects to an abstract network of information entities as the primary agent of evolution. It forces us to change our views about how organisms evolve and therefore the methods we use to analyze evolution.

1,2-Diacetylbenzene (DAB) is a metabolite of 1,2-diethylbenzene, which is commonly used in the manufacture of plastics and gasoline. We examined the neurotoxic effects of DAB in young and old rats, particularly its effects on hippocampus. Previously, we reported DAB impairs hippocampal neurogenesis but that the underlying mechanism remained unclear. In this study, we evaluate the toxicities exhibited by DAB in the hippocampi of 6-month-old (young) and 20-month-old (old) male SD rats by treating animals intraperitoneally with DAB at 3 mg/kg/day for 1 week. Hippocampal areas were dissected from brains and RNA was extracted and subjected to RNA-seq analysis. RNA results showed animals exhibited age-dependent sensitivity to the neurotoxic effects of DAB. We observed that inflammatory pathways were up-regulated in old rats but that metabolism- and detoxification-related pathways were up-regulated in young rats. This result in old rats, especially upregulation of the TREM1 signaling pathway (an inflammatory response involved in Alzheimer’s disease (AD)) was confirmed by RT-PCR. Our study results provide a better understanding of age-dependent responses to DAB and new insight into the association between DAB and AD.

1,2-Diacetylbenzene (DAB) is a metabolite of 1,2-diethylbenzene, which is commonly used in the manufacture of plastics and gasoline. We examined the neurotoxic effects of DAB in young and old rats, particularly its effects on hippocampus. Previously, we reported DAB impairs hippocampal neurogenesis but that the underlying mechanism remained unclear. In this study, we evaluate the toxicities exhibited by DAB in the hippocampi of 6-month-old (young) and 20-month-old (old) male SD rats by treating animals intraperitoneally with DAB at 3 mg/kg/day for 1 week. Hippocampal areas were dissected from brains and RNA was extracted and subjected to RNA-seq analysis. RNA results showed animals exhibited age-dependent sensitivity to the neurotoxic effects of DAB. We observed that inflammatory pathways were up-regulated in old rats but that metabolism- and detoxification-related pathways were up-regulated in young rats. This result in old rats, especially upregulation of the TREM1 signaling pathway (an inflammatory response involved in Alzheimer’s disease (AD)) was confirmed by RT-PCR. Our study results provide a better understanding of age-dependent responses to DAB and new insight into the association between DAB and AD.