• Natural Product Sciences
• /
• v.26 no.4
• /
• pp.259-267
• /
• 2020

Snakebite is a severe medical, economic, and social problem across the world, mostly in the tropical and subtropical area. These regions of the globe have typical of the world's venomous snakes present where access to prompt treatment is limited or not available. Snake venom is a complex mixture of toxin proteins like neurotoxin and cardiotoxin, and other enzymes like phospholipase A2 (PLA2), haemorrhaging, transaminase, hyaluronidase, phosphodiesterase, acetylcholinesterase, cytolytic and necrotic toxins. Snake venom shows a wide range of biological effects like anticoagulation or platelet aggregation, hemolysis, hypotension and edema. Phospholipase A2 is the principal constituent of snake venom; it catalyzes the hydrolysis of the sn-2 position of membrane glycerophospholipids to liberate arachidonic acid, which is the precursor of eicosanoids including prostaglandins and leukotrienes. The information regarding the structure and function of the phospholipase A2 enzyme may help in treating the snakebite victims. This review article constitutes a brief description of the structure, types, mechanism occurrence, and tests of phospholipase A2 and role of components of medicinal plants used to inhibit phospholipase A2.

• Korean Journal of Clinical Laboratory Science
• /
• v.53 no.1
• /
• pp.68-80
• /
• 2021

An uncertified facility is a facility not certified, as defined in the Biological Agents and Toxins Act (BATA) in Singapore, but has met the requirements of the Ministry of Health to possess First and Fifth Schedule biological agents and toxins. This type of facility is also known as a Biosafety Level 2 Plus (BSL 2+) facility. Registration as an uncertified facility or a BSL 2+ facility requires a certain process and procedure to be sought with the Biosafety Branch of the ministry. This review, shares first-hand knowledge on the journey to achieving registration of the authors' facility. The procedure involved considerable preparation, setting up facility requirements, biosafety precautions, procedures and practices, and training and competence of laboratory users. The ministry conducted a thorough onsite facility audit to ensure that the facility requirements and biosafety procedures and practices were in place. It then issued an approval letter of possession for the first-time use of biological agents and registered the laboratory as an uncertified facility. The expectation is that the comprehensive information shared may be of great benefit to other facilities with similar interests.

• Genomics & Informatics
• /
• v.19 no.3
• /
• pp.27.1-27.4
• /
• 2021

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural language understanding. Biological named entity recognition (NER) and named entity normalisation (NEN) are two common tasks aiming at identifying and linking biologically important entities such as genes or gene products mentioned in the literature to biological databases. In this paper, we present an updated version of OryzaGP, a gene and protein dataset for rice species created to help natural language processing (NLP) tools in processing NER and NEN tasks. To create the dataset, we selected more than 15,000 abstracts associated with articles previously curated for rice genes. We developed four dictionaries of gene and protein names associated with database identifiers. We used these dictionaries to annotate the dataset. We also annotated the dataset using pretrained NLP models. Finally, we analysed the annotation results and discussed how to improve OryzaGP.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.388-391
• /
• 2005

The Protein Structural and Functional Conservation need a common language for data definition. With the help of common language provided by Protein Ontology the high level of sequence and functional conservation can be extended to all organisms with the likelihood that proteins that carry out core biological processes will again be probable orthologues. The structural and functional conservation in these proteins presents both opportunities and challenges. The main opportunity lies in the possibility of automated transfer of protein data annotations from experimentally traceable model organisms to a less traceable organism based on protein sequence similarity. Such information can be used to improve human health or agriculture. The challenge lies in using a common language to transfer protein data annotations among different species of organisms. First step in achieving this huge challenge is producing a structured, precisely defined common vocabulary using Protein Ontology. The Protein Ontology described in this paper covers the sequence, structure and biological roles of Protein Complexes in any organism.

• Journal of Environmental Impact Assessment
• /
• v.10 no.2
• /
• pp.99-108
• /
• 2001

This study was performed to develop an information processing system for the sound conservation of soil and groundwater resources. The system contains numerical models and geographic information systems for underground flow and contamination. Multidimensional Finite Element Model for Subsurface Environment (MFEMSE) was invented to analyze underground flow and pollution problems of water and gas phases. Newly developed and conventional models (MODFLOW, MOC3D, MT3D, PMPATH, PEST, UCODE) were integrated with GIS (ArcView) for the construction of an integrated information management system of subsurface environment. This system was applied to the management of three mineral water companies located in clean high mountain basin. Desirable management criteria and operational strategies were suggested using this system. The system was constructed to be applied for the broad sense of decision supporting tools in related topics of this study, so that it can be used not only for the prevention regulations, but also for clean up projects.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.2
• /
• pp.178-183
• /
• 2006

Microbes are one of the most important bioresources in bioindustry and provide high economic values. Although there are currently about 6,000 bacterial species with validly published names, microbiologists generally assume that the number may account for less than 1% of the bacterial species present on Earth. To discover the remaining species, studies of metagenomes, metabolomes, and proteomes related to microbes have recently been carried out in various fields. We have constructed an information system that integrates various data on microbial resources and manages bioinformation to support efficient research of microorganisms. We have designated this system 'Bio-Meta Information System (Bio-MIS).' Bio-MIS consists of an integrated microbial resource database, a microbial resource input system, an integrated microbial resource search engine, a microbial resource online distribution system, a portal service, and management via the Internet. In the future, this system is expected to be connected with various public databases. We plan to implement useful bioinformatics software for analyzing microbial genome resources. The Web site is accessible at http://biomis.probionic.com.

• Proceedings of the Korean Biophysical Society Conference
• /
• 2003.06a
• /
• pp.65-65
• /
• 2003

After many genome projects, algorithms and software to process explosively growing biological information have been developed. To process huge amount of biological information, high performance computing equipments are essential. If we use the remote resources such as computing power, storages etc., through a Grid to share the resources in the Internet environment, we will be able to obtain great efficiency to process data at a low cost. Here we present the performance improvement of the protein secondary structure prediction (PSIPred) by using the Grid platform, distributing protein sequence data on the Grid where each computer node analyzes its own part of protein sequence data to speed up the structure prediction. On the Grid, genome scale secondary structure prediction for Mycoplasma genitalium, Escherichia coli, Helicobacter pylori, Saccharomyces cerevisiae and Caenorhabditis slogans were performed and analyzed by a statistical way to show the protein structural deviation and comparison between the genomes. Experimental results show that the Grid is a viable platform to speed up the protein structure prediction and from the predicted structures.

• Investigative Magnetic Resonance Imaging
• /
• v.26 no.2
• /
• pp.96-103
• /
• 2022

Purpose: The survival of organisms critically depends on avoidance responses to life-threatening stimuli. Information about dangerous situations needs to be remembered to produce defensive behavior. To investigate underlying brain regions to process information of danger, manganese-enhanced MRI (MEMRI) was used in olfactory fear-conditioned rats. Materials and Methods: Fear conditioning was conducted in male Sprague-Dawley rats. The animals received nasal injections of manganese chloride solution to monitor brain activation for olfactory information processing. Twenty-four hours after manganese injection, rats were exposed to electric foot shocks with odor cue for one hour. Control rats were exposed to the same odor cue without foot shocks. Forty-eight hours after the conditioning, rats were anesthetized and their brains were scanned with 9.4T MRI. Acquired images were processed and statistical analyses were performed using AFNI. Results: Manganese injection enhanced brain areas involved in olfactory information pathways in T1 weighted images. Rats that received foot shocks showed higher brain activation in the central nucleus of the amygdala, septum, primary motor cortex, and preoptic area. In contrast, control rats displayed greater signals in the orbital cortex and nucleus accumbens. Conclusion: Nasal delivery of manganese solution enhanced olfactory signal pathways in rats. Odor cue paired with foot shocks activated amygdala, the central brain region in fear, and related brain circuits. Use of MEMRI in fear conditioning provides a reliable monitoring technique of brain activation for fear learning.

• IMMUNE NETWORK
• /
• v.2 no.3
• /
• pp.125-132
• /
• 2002

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.379-382
• /
• 2005

We demonstrate workflows in biological data retrieval and analysis using the DDBJ Web Service; specifically introduce a workflow for the analysis of proteins or proteomics data sets. The workflow mechanically extracts the gene whose protein structure and function are known from all the genes of a human genome in Ensembl (http://www.ensembl.org/) based on cross-references among Ensembl, Swiss-Prot (http://www.ebi.ac.uk/swissprot) and PDB (Protein Data Bank; http://www.wwpdb.org/). The workflow discovered ‘hidden’ linkages among databases. We will be able to integrate distributed and heterogeneous data systems into workflows, if they are provided based on standards for Web services.