• Journal of Microbiology and Biotechnology
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• 제22권9호
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• pp.1185-1192
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• 2012

This study investigated the hydrocarbonoclastic microbial community present on weathered crude oil and their ability to degrade weathered oil in seawater obtained from the Gulf St. Vincent (SA, Australia). Examination of the native seawater communities capable of utilizing hydrocarbon as the sole carbon source identified a maximum recovery of just $6.6{\times}10^1\;CFU/ml$, with these values dramatically increased in the weathered oil, reaching $4.1{\times}10^4\;CFU/ml$. The weathered oil (dominated by > $C_{30}$ fractions; $750,000{\pm}150,000mg/l$) was subject to an 8 week laboratory-based degradation microcosm study. By day 56, the natural inoculums degraded the soluble hydrocarbons (initial concentrations $3,400{\pm}700mg/l$ and $1,700{\pm}340mg/l$ for the control and seawater, respectively) to below detectable levels, and biodegradation of the residual oil reached 62% ($254,000{\pm}40,000mg/l$) and 66% ($285,000{\pm}45,000mg/l$) in the control and seawater sources, respectively. In addition, the residual oil gas chromatogram profiles changed with the presence of short and intermediate hydrocarbon chains. 16S rDNA DGGE sequence analysis revealed species affiliated with the genera Roseobacter, Alteromonas, Yeosuana aromativorans, and Pseudomonas, renowned oil-degrading organisms previously thought to be associated with the environment where the oil contaminated rather than also being present in the contaminating oil. This study highlights the importance of microbiological techniques for isolation and characterisation, coupled with molecular techniques for identification, in understanding the role and function of native oil communities.

• Journal of Applied Biological Chemistry
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• 제53권3호
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• pp.121-125
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• 2010

지난 10년간 분자 식물 일주기성에 대해 분자 생물학적, 생화학적인 연구가 많이 진행되었다. 본 연구에서는 식물의 Arabidopsis, rice 그리고 algae에서 지금까지 발표된 연구들을 종합하고 고찰해보려 했다. 그 결과, 아직까지도 주기성 대사의 모든 부분을 설명하기엔 부족한 부분이 많다는 것을 알수 있었다. 최근 주기성 단백질들의 전사후, 번역 그리고 번역후 변형과정에 대해 많은 연구자들이 관심을 갖기 시작했다. 이러한 부분에서 다량의 단백질을 한번에 볼 수 있는 2-DE gel electrophoresis와 MS/MS 기술이 절실히 요구된다고 할 수 있겠다.

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 2007년도 Proceedings of The Convention
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• pp.19-27
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• 2007

An important potential of metabolomics-based approach is the possibility to develop fingerprints of diseases or cellular responses to classes of compounds with known common biological effect. Such fingerprints have the potential to allow classification of disease states or compounds, to provide mechanistic information on cellular perturbations and pathways and to identify biomarkers specific for disease severity and drug efficacy. Metabolic profiles of biological fluids contain a vast array of endogenous metabolites. Changes in those profiles resulting from perturbations of the system can be observed using analytical techniques, such as NMR and MS. $^1H$ NMR was used to generate a molecular fingerprint of serum or urinary sample, and then pattern recognition technique was applied to identity molecular signatures associated with the specific diseases or drug efficiency. Several metabolites that differentiate disease samples from the control were thoroughly characterized by NMR spectroscopy. We investigated the metabolic changes in human normal and clinical samples using $^1H$ NMR. Spectral data were applied to targeted profiling and spectral binning method, and then multivariate statistical data analysis (MVDA) was used to examine in detail the modulation of small molecule candidate biomarkers. We show that targeted profiling produces robust models, generates accurate metabolite concentration data, and provides data that can be used to help understand metabolic differences between healthy and disease population. Such metabolic signatures could provide diagnostic markers for a disease state or biomarkers for drug response phenotypes.

• BMB Reports
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• 제52권9호
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• pp.540-547
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• 2019

Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.

• 한국응용곤충학회지
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• 제40권2호
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• pp.155-196
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• 2001

Basically insect hormones include ecdysteroids (molting hormone), juvenile hormones, and neurohormones comprising neuropeptides and biogenic amines. This article reviewed their chemical structures and biological functions. The active molting hormone is 20-hydroxyecdysone in most insects but makisterone A in some other insects including the honey bee and several phytophagous hemipterans. Most insects use JH III, but lepidopterans JH I and II. Dipterans also use a different JH, so-called JH $B_3$(JH III bisepoxide) and we still do not know the exact chemical structure of JH utilized in hemipterans. Some other insects use methyl farnesoate or hydroxylated JH III analogues as their juvenile hormone. Most diverse pictures can be found in neurohormones (NH), especially in neuropeptides, in terms of their number and structure. There are more than 200 neuropeptides (NP), classified into more than 30 families, which structures have been identified, and more of them are expected to be reported in the near future, partly due to rapid development in molecular biological techniques and in analytical techniques. More than half of them are involved in controlling activity of visceral muscles. But function (s) of many NPs are not clarified yet, even though their amino acid sequences have been identified. It is partly due to the fact that a single NP may have multiple functions. Another interesting point is their gene structure, having many number of independent, active peptides in one gene, apparently working for similar or totally different functions. NH also includes amines, such as octopamine, dopamine, serotonin, etc. From now on, investigation will be concentrated on identifying their function (s) and receptors, and on possibilities of their utilization as control agents against pest insects.

• Bulletin of the Korean Chemical Society
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• 제33권8호
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• pp.2731-2736
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• 2012

The use of pyrimethamine as antibacterial drug is limited by the poor solubility. To enhance its solubility, we prepared complexes of pyrimethamine with low-molecular-weight succinoglycan isolated from Sinorhizobium meliloti. Low-molecular-weight succinoglycans are monomers, dimers, and trimers of the succinoglycan repeating unit. The monomers and dimers were separated into their three species (M1, M2, and M3) and four fractions (D1 to D4) using chromatographic techniques, which were shown to be nontoxic. The solubility of pyrimethamine was markedly increased up to 42 fold by succinoglycan D3, where the level of its solubility enhancement was even 8-20 fold higher comparing with cyclodextrin or its derivatives. The complex formation of succinoglycan D3 with pyrimethamine was confirmed by $^1H$ nuclear magnetic resonance spectroscopy, Fourier-transform infrared spectroscopy, differential scanning calorimetry, scanning electron microscopy, and molecular modeling studies. Herein, we suggest that the low-molecular-weight succinoglycans may be utilized as highly effective solubilizers of pyrimethamine for pharmaceutical purposes.

• ALGAE
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• 제35권1호
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• pp.17-32
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• 2020

Asterochloris is one of the most common genera of lichen phycobionts in Trebouxiophyceae. Asterochloris phycobionts associated with the lichenized fungi Cladonia and Stereocaulon in King George Island (Antarctica) and Morro Chico (Chile), were isolated and then used to establish clonal cultures. To understand the phylogenetic relationships and species diversity of Antarctic Asterochloris species, molecular and morphological data were analyzed by using three microscopy techniques (light, confocal laser and transmission electron) and a multi-locus phylogeny with data from the nuclear-encoded internal transcribed spacer (ITS) rDNA and the actin and plastid-encoded ribulose bisphosphate carboxylase large chain (rbcL) coding genes. Morphological data of three Antarctic strains showed significant species-specific features in chloroplast while molecular data segregated the taxa into distinct three clades as well. Each species had unique molecular signatures that could be found in secondary structures of the ITS1 and ITS2. The species diversity of Antarctic Asterochloris was represented by six taxa, namely, A. glomerata, A. italiana, A. sejongensis, and three new species (A. antarctica, A. pseudoirregularis, A. stereocaulonicola).

• 대한방사성의약품학회지
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• 제6권1호
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• pp.20-26
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• 2020

Accelerator mass spectrometry (AMS) is a powerful detection technique with the exquisite sensitivity and high precision compared with other traditional analytical techniques. Accelerator mass spectrometry can be widely applied in the technique of radiocarbon dating in the fields of archeology, geology and oceanography. The ability of accelerator mass spectrometry to measure rare ¹⁴C concentrations in microgram and even sub-microgram amounts suggests that extension of ¹⁴C-accelerator mass spectrometry to biomedical field is a natural and attractive application of the technology. Drug development processes are costly, risky, and time consuming. However, the use of ¹⁴C-accelerator mass spectrometry allows absorption, distribution, metabolism and excretion (ADME) studies easier to understand pharmacokinetics of drug candidates. Over the last few decades, accelerator mass spectrometry and its applications to preclinical/clinical trials have significantly increased. For accelerator mass spectrometry analysis of biological samples, graphitization processes of samples are important. In this paper, we present a detailed sample preparation procedure to apply to graphitization of biological samples for accelerator mass spectrometry.

• Molecules and Cells
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• 제44권2호
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• pp.79-87
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• 2021

Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. Conserved bromodomain-containing AAA+ ATPases play important roles in nucleosome organization as histone chaperones. Recently, the high-resolution cryo-electron microscopy structures of Schizosaccharomyces pombe Abo1 revealed that it forms a hexameric ring and undergoes a conformational change upon ATP hydrolysis. In addition, single-molecule imaging demonstrated that Abo1 loads H3-H4 histones onto DNA in an ATP hydrolysis-dependent manner. However, the molecular mechanism by which Abo1 loads histones remains unknown. Here, we investigated the details concerning Abo1-mediated histone loading onto DNA and the Abo1-DNA interaction using single-molecule imaging techniques and biochemical assays. We show that Abo1 does not load H2A-H2B histones. Interestingly, Abo1 deposits multiple copies of H3-H4 histones as the DNA length increases and requires at least 80 bp DNA. Unexpectedly, Abo1 weakly binds DNA regardless of ATP, and neither histone nor DNA stimulates the ATP hydrolysis activity of Abo1. Based on our results, we propose an allosteric communication model in which the ATP hydrolysis of Abo1 changes the configuration of histones to facilitate their deposition onto DNA.

• Journal of Microbiology and Biotechnology
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• 제27권5호
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• pp.878-895
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• 2017

Phosphorylation, a critical mechanism in biological systems, is estimated to be indispensable for about 30% of key biological activities, such as cell cycle progression, migration, and division. It is synergistically balanced by kinases and phosphatases, and any deviation from this balance leads to disease conditions. Pathway or biological activity-based abnormalities in phosphorylation and the type of involved phosphatase influence the outcome, and cause diverse diseases ranging from diabetes, rheumatoid arthritis, and numerous cancers. Protein tyrosine phosphatases (PTPs) are of prime importance in the process of dephosphorylation and catalyze several biological functions. Abnormal PTP activities are reported to result in several human diseases. Consequently, there is an increased demand for potential PTP inhibitory small molecules. Several strategies in structure-based drug designing techniques for potential inhibitory small molecules of PTPs have been explored along with traditional drug designing methods in order to overcome the hurdles in PTP inhibitor discovery. In this review, we discuss druggable PTPs and structure-based virtual screening efforts for successful PTP inhibitor design.