• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.374-389
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• 2023

Organophosphorus (OP) pesticides, particularly malathion, parathion, diazinon, and chlorpyrifos, are widely used in both agricultural and residential contexts. This refractory quality is shared by certain organ phosphorus insecticides, and it may have unintended consequences for certain non-target soil species. Bioremediation cleans organic and inorganic contaminants using microbes and plants. Organophosphate-hydrolyzing enzymes can transform pesticide residues into non-hazardous byproducts and are increasingly being considered viable solutions to the problem of decontamination. When coupled with system analysis, the multi-omics technique produces important data for functional validation and genetic manipulation, both of which may be used to boost the efficiency of bioremediation systems. RNA-guided nucleases and RNA-guided base editors include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR), which are used to alter genes and edit genomes. The review sheds light on key knowledge gaps and suggests approaches to pesticide cleanup using a variety of microbe-assisted methods. Researches, ecologists, and decision-makers can all benefit from having a better understanding of the usefulness and application of systems biology and gene editing in bioremediation evaluations.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.7
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• pp.927-932
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• 2018

The demand for beef as a protein source is increasing worldwide, although in most countries beef accounts for considerably less than half of total meat consumption. Beef also provides a highly desirable eating experience in developed countries and, increasingly, in developing countries. The sustainability of beef production has different meanings in the various geographical and socio-economic regions of the world. Natural resources including land mass and uses, rainfall and access to livestock feed, and the robustness of the economy are major determinants of the perception of beef sustainability. In this overview of the 2016 International Symposium on "Future Beef in Asia" and this subsequent Special Edition of the Asian-Australasian Journal of Animal Sciences on "Current Situation and Future Prospects for Global Beef Production", the contributions have been grouped into the following categories: Countries in Southeast Asia; Europe; and Countries producing highly marbled beef for export and/or domestic consumption. They also include reference to Special Topics including marbled beef production, and use of "omics" technologies to enhance beef quality assurance. Among these broad categories, notable differences exist across countries in the production and marketing of beef. These reflect differences in factors including natural resource availability and climate, population size, traditional culture and degree of economic development including industrial and technological developments. We trust that the International Symposium and this Special Edition on Current Situation and Future Prospects for Global Beef Production, the contents of which that are briefly summarized in this paper, will serve as a valuable resource for the livestock industries, researchers and students with an interest in enhancing the prospects for sustainable, efficient beef production that satisfies the growing size and complexity of consumer demands and markets for beef.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.425-431
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• 2005

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

• Molecular & Cellular Toxicology
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• v.1 no.1
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• pp.17-25
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• 2005

There are some critical drawbacks in the use of biomarkers for a global assessment of the toxicological impacts many chemicals and environmental pollutants have, primarily due to an individual biomarker's specificity for an explicit chemical or toxicant. In other words, the biomarker-based assessment methodology used to analyze toxicological effects lacks a high-throughput capability. Therefore, eco-toxicogenomics, or the study of toxicogenomics with organisms present within a given environmental locale, has recently been introduced with the advent of the so-called "-omics" era, which began with the creation of microarray technologies. Fish are comparable with humans in their toxicological responses and thus data from toxicogenomic studies performed with fish could be applied, with appropriate tools and implementation protocols, to the evaluation of environments where human or animal health is of concern. At present, there have been very active research streams for developing expression sequence tag (EST) databases (DBs) for zebra fish and rainbow trout. Even though few reports involve toxicogenomic studies with fish, a few groups have successfully fabricated and used cDNA microarrays or oligo DNA chips when studying the toxicological impacts of hypoxia or some toxicants with fish. Furthermore, it is strongly believed that this technology can also be implemented with non-model fish. With the standardization of DNA microarray technologies and ample progress in bioinformatics and proteomic technologies, data obtained from DNA microarray technologies offer not only multiple biomarker assays or an analysis of gene expression profiles, but also a means of elucidating gene networking, gene-gene relations, chemical-gene interactions, and chemical-chemical relationships. Accordingly, the ultimate target of eco-toxicogenomics should be to predict and map the pathways of stress propagation within an organism and to analyze stress networking.

• Molecular & Cellular Toxicology
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• v.4 no.3
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• pp.260-266
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• 2008

Recently, there has been scientific discussion on the utility of -omics techniques such as genomics, proteomics, and metabolomics within toxicological research and mechanism-based risk assessment. Toxicogenomics is a novel approach integrating the expression analysis of genes (genomic) or proteins (proteomic) with traditional toxicological methods. Since 1999, the toxicogenomic approach has been extensively applied for regulatory purposes in order to understand the potential toxic mechanisms that result from chemical compound exposures. Therefore, this article's purpose was to consider the utility of toxicogenomic profiles for improved risk assessment, explore the current limitations in applying toxicogenomics to regulation, and finally, to rationalize possible avenues to resolve some of the major challenges. Based on many recent works, the significant impact toxicogenomic techniques would have on human health risk assessment is better identification of toxicity pathways or mode-of-actions (MOAs). In addition, the application of toxicogenomics in risk assessment and regulation has proven to be cost effective in terms of screening unknown toxicants prior to more extensive and costly experimental evaluation. However, to maximize the utility of these techniques in regulation, researchers and regulators must resolve many parallel challenges with regard to data collection, integration, and interpretation. Furthermore, standard guidance has to be prepared for researchers and assessors on the scientifically appropriate use of toxicogenomic profiles in risk assessment. The National Institute of Toxicological Research (NITR) looks forward to an ongoing role as leader in addressing the challenges associated with the scientifically sound use of toxicogenomics data in risk assessment.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.96-103
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• 2010

Oligosaccharyltransferase (OTase) catalyzes the transfer of a lipid-linked oligosaccharide (LLO) to the nascent polypeptide. Most eukaryotes have an OTase composed of a multisubunit protein complex. However, the kinetoplastid Leishmania major and the bacterium Campylobacter jejuni have only a single subunit for OTase activity, Stt3p and PglB, respectively. In this study, a new in vitro assay for OTase was developed by using a fluorescent peptide containing N-glycosylation sequon, Asn-Xaa-Thr/Ser, where Xaa can be any amino acid residue except Pro. L. major Stt3p and C. jejuni PglB as a model OTase enzyme demonstrated the formation of glycopeptides from a fluorescent peptide through OTase activities. For separation and measurement of the glycopeptides produced by the OTases, Tricine-SDS-PAGE, a lectin column and fluorospectrophotometer, and HPLC were applied. Comparison of these assay methods for analyzing a fluorescent glycopeptide showed HPLC analysis is the best method for separation of glycopeptides and nonglycosylated peptides as well as for quantify the peptides than other methods.

• Biomolecules & Therapeutics
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• v.28 no.3
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• pp.282-291
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• 2020

Inhaled solvents such as toluene are of particular concern due to their abuse potential that is easily exposed to the environment. The inhalation of toluene causes various behavioral problems, but, the effect of short-term exposure of toluene on changes in emotional behaviors over time after exposure and the accompanying pathological characteristics have not been fully identified. Here, we evaluated the behavioral and neurochemical changes observed over time in mice that inhaled toluene. The mice were exposed to toluene for 30 min at a concentration of either 500 or 2,000 ppm. Toluene did not cause social or motor dysfunction in mice. However, increased anxiety-like behavior was detected in the short-term after exposure, and depression-like behavior appeared as delayed effects. The amount of striatal dopamine metabolites was significantly decreased by toluene, which continued to be seen for up to almost two weeks after inhalation. Additionally, an upregulation of serotonin 1A (5-HT_1A) receptor in the hippocampus and the substantia nigra, as well as reduced immunoreactivity of neurogenesis markers in the dentate gyrus, was observed in the mice after two weeks. These results suggest that toluene inhalation, even single exposure, mimics early anxiety-and delayed depression-like emotional disturbances, underpinned by pathological changes in the brain.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.438-447
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• 2011

Deinococcus radiodurans is extremely resistant to various genotoxic conditions and chemicals. In this study, we characterized the effect of a sublethal concentration (100 ${\mu}M$) of cadmium (Cd) on D. radiodurans using a whole-genome DNA microarray. Time-course global gene expression profiling showed that 1,505 genes out of 3,116 total ORFs were differentially expressed more than 2-fold in response to Cd treatment for at least one timepoint. The majority of the upregulated genes are related to iron uptake, cysteine biosynthesis, protein disulfide stress, and various types of DNA repair systems. The enhanced upregulation of genes involved in cysteine biosynthesis and disulfide stress indicate that Cd has a high affinity for sulfur compounds. Provocation of iron deficiency and growth resumption of Cd-treated cells by iron supplementation also indicates that CdS forms in iron-sulfur-containing proteins such as the [Fe-S] cluster. Induction of base excision, mismatch, and recombinational repair systems indicates that various types of DNA damage, especially base excision, were enhanced by Cd. Exposure to sublethal Cd stress reduces the growth rate, and many of the downregulated genes are related to cell growth, including biosynthesis of cell membrane, translation, and transcription. The differential expression of 52 regulatory genes suggests a dynamic operation of complex regulatory networks by Cd-induced stress. These results demonstrate the effect of Cd exposure on D. radiodurans and how the related genes are expressed by this stress.

• Molecules and Cells
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• v.41 no.3
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• pp.214-223
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• 2018

Oligoadenylate synthetase (OAS) protein family is the major interferon (IFN)-stimulated genes responsible for the activation of RNase L pathway upon viral infection. OAS-like (OASL) is also required for inhibition of viral growth in human cells, but the loss of one of its mouse homolog, OASL1, causes a severe defect in termination of type I interferon production. To further investigate the antiviral activity of OASL1, we examined its subcellular localization and regulatory roles in IFN production in the early and late stages of viral infection. We found OASL1, but not OASL2, formed stress granules trapping viral RNAs and promoted efficient RLR signaling in early stages of infection. Stress granule formation was dependent on RNA binding activity of OASL1. But in the late stages of infection, OASL1 interacted with IRF7 transcripts to inhibit translation resulting in down regulation of IFN production. These results implicate that OASL1 plays context dependent functions in the antiviral response for the clearance and resolution of viral infections.

• Molecules and Cells
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• v.41 no.3
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• pp.179-187
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• 2018

Proteomic analysis of extracellular vesicles (EVs) from biological fluid is a powerful approach to discover potential biomarkers for human diseases including cancers, as EV secreted to biological fluids are originated from the affected tissue. In order to investigate significant molecules related to the pathogenesis of bladder cancer, EVs were isolated from patient urine which was analyzed by mass spectrometry based proteomics. Comparison of the EV proteome to the whole urine proteome demonstrated an increased number of protein identification in EV. Comparative MS analyses of urinary EV from control subjects and bladder cancer patients identified a total of 1,222 proteins. Statistical analyses provided 56 proteins significantly increased in bladder cancer urine, including proteins for which expression levels varied by cancer stage (P-value < 0.05). While urine represents a valuable, non-invasive specimen for biomarker discovery in urologic cancers, there is a high degree of intra- and inter-individual variability in urine samples. The enrichment of urinary EV demonstrated its capability and applicability of providing a focused identification of biologically relevant proteins in urological diseases.