• Asian-Australasian Journal of Animal Sciences
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• 제26권8호
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.132-132
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• 2017

Plants, including Platycodon grandiflorum have been used globally across varied cultures as a safe natural source of medicines. From time immemorial, humans have relied on plants that could meet their basic necessities such as food, shelter, fuel and health. This study was executed to profile proteins from the hormone induced diploid and tetraploid roots using high throughput proteome approach. Two dimensional gels stained with CBB, a total of 64 differential expressed proteins were identified from the diploid root using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 20 differential expressed protein spots ( ${\geq}1.5-fold$) were analyzed using LTQ-FTICR MS whereas a total of 13 protein spots were up regulated and 7 protein spots were down-regulated. However, in the case of tetraploid root, a total of 78 differential expressed proteins were identified from tetraploid root of which a total of 28 differential expressed protein spots (${\geq}1.5-fold$) were analyzed by mass spectrometry whereas a total of 16 protein spots were up regulated and a total of 12 protein spots were down-regulated. However, proteins identified using iProClass databases revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding, oxidoreductase activity, transporter activity and isomers activity. The exclusive protein profile may provide insight clues for better understanding the characteristics of protein function and its metabolic activity that can help for the development of the nutritional and breeding aspects of this economically important medicinal plant.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.123-123
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• 2017

In spite of the potential medicinal significance and a wide range of pharmacologic properties of Platycodon grandiflorum, the molecular mechanism of its roots is still unknown. The present study was conducted to profile proteins from 3, 4 and 5 months aged diploid and tetraploid roots of Platycodon grandiflorum using high throughput proteome approach. Two-dimensional gels stained with CBB, a total of 68 differential expressed proteins were identified from the diploid root out of 767 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 29 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 24 protein spots were up-regulated and 5 protein spots were down-regulated. On the contrary, in the case of tetraploid root, a total of 86 differential expressed proteins were identified from tetraploid root out of 1033 protein spots of which a total of 39 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 21 protein spots were up-regulated and a total of 18 protein spots were down-regulated. It was revealed that the identified proteins from the explants were mainly associated with the nucleotide binding, oxidoreductase activity, transferase activity. Taken together, the identified proteins may be helpful to identify key candidate proteins for genetic improvement of plants.

• Asian Pacific Journal of Cancer Prevention
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• 제14권7호
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• pp.4393-4398
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• 2013

Background: Chromosomal translocations are genetic aberrations associated with specific non-Hodgkin lymphoma (NHL) subtypes. This study investigated the differential gene expression profile of Egyptian NHL cases based on a microarray approach. Materials and Methods: The study included tissue samples from 40 NHL patients and 20 normal lymph nodes used as controls. Total RNA was extracted and used for cDNA microarray assays. The quantitative real time polymerase chain reaction was used to identify the aberrantly expressed genes in cancer. Results: Significant associations of 8 up-regulated and 4 down-regulated genes with NHL were observed. Aberrant expression of a new group of genes not reported previously was apparent, including down-regulated NAG14 protein, 3 beta hydroxy-delta 5-c27 steroid oxi-reductase, oxi-glutarate dehydrogenase (lipo-amide), immunoglobulin lambda like polypeptide 3, protein kinase x linked, Hmt1, and caveolin 2 Tetra protein. The up-regulated genes were Rb binding protein 5, DKFZP586J1624 protein, protein kinase inhibitor gamma, zinc finger protein 3, choline ethanolamine phospho-transferase CEPT1, protein phosphatase, and histone deacetylase-3. Conclusions: This study revealed that new differentially expressed genes that may be markers for NHL patients and individuals who are at high risk for cancer development.

• Journal of Ginseng Research
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• 제46권2호
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• pp.255-265
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• 2022

Background: Ginsenoside Rb1, a bioactive component isolated from the Panax ginseng, acts as a remedy to prevent myocardial injury. However, it is obscure whether the cardioprotective functions of Rb1 are related to the regulation of endogenous metabolites, and its potential molecular mechanism still needs further clarification, especially from a comprehensive metabolomics profiling perspective. Methods: The mice model of acute myocardial ischemia (AMI) and oxygen glucose deprivation (OGD)-induced cardiomyocytes injury were applied to explore the protective effect and mechanism of Rb1. Meanwhile, the comprehensive metabolomics profiling was conducted by high-performance liquid chromatography and quadrupole time-of-flight mass spectrometry (HPLC-Q/TOF-MS) and a tandem liquid chromatography and mass spectrometry (LC-MS). Results: Rb1 treatment profoundly reduced the infarct size and attenuated myocardial injury. The metabolic network map of 65 differential endogenous metabolites was constructed and provided a new inspiration for the treatment of AMI by Rb1, which was mainly associated with mitophagy. In vivo and in vitro experiments, Rb1 was found to improve mitochondrial morphology, mitochondrial function and promote mitophagy. Interestingly, the mitophagy inhibitor partly attenuated the cardioprotective effect of Rb1. Additionally, Rb1 markedly facilitated the phosphorylation of AMP-activated protein kinase α (AMPKα), and AMPK inhibition partially weakened the role of Rb1 in promoting mitophagy. Conclusions: Ginsenoside Rb1 protects acute myocardial ischemia injury through promoting mitophagy via AMPKα phosphorylation, which might lay the foundation for the further application of Rb1 in cardiovascular diseases.

• 한국작물학회지
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• 제62권1호
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• pp.40-50
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• 2017

Seed storage proteins are used as carbon and nitrogen sources for the nutritional improvement of seeds. Since the composition of proteins from the Korean cultivars of proso millet is unknown, this study was conducted to obtain a reference map of millet seed proteins and identify the functional characteristics of the identified proteins. Proteins extracted from proso millet seeds of various cultivars were investigated using proteomic techniques such as 2-D electrophoresis coupled with mass fingerprinting; 1152 (differentially expressed) protein spots were detected on the 2-D gels. Among them, 26 reproducible protein spots were analyzed using matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. Out of the 26 proteins, 2 proteins were upregulated in all the millet cultivars, while 13 proteins were upregulated and 11 proteins were downregulated in 2 cultivars. Abundance of most of the identified protein species associated with polysaccharide and starch metabolism, transcription, and pathogenesis was significantly enhanced, while that of other protein species involved in glycolysis, stress response, and transduction was severely reduced. Taken together, the results suggest that the differential expression of the proteins from the four millet cultivars may be cultivar-specific. By conducting a proteomic investigation of millet seeds from different cultivars, we sought to better understand the functional categorization of individual proteins on the basis of their molecular functions. We believe that the identified proteins may help in investigating genetic variations in millet cultivars.

• Reproductive and Developmental Biology
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• 제33권3호
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• pp.183-187
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• 2009

This study analyzed change of proteins in granulosa cells during the porcine follicuar development by proteomics techniques. Granulosa cells of the follicles, of which the diameter is $2{\sim}4\;mm$ and $6{\sim}10\;mm$, were collected from ovary of slaughtered pig that each follicle of diameter $1{\sim}4\;mm$ and $6{\sim}10\;mm$. We extracted glanulosa cell proteins by M-PER Mammalian Protein Extraction Reagent. Proteins were refined by clean-up kit and quantified by Bradford method until total protein was $200{\mu}l$. Immobilized pH gradient(IPG) strip used 18 cm, $3{\sim}10\;NL$. SDS-PAGE used 10% acrylamide gel. After silver staining, Melanie 7 and naked eye test were used for spot analyzation. Increasing proteins in glanulosa cell of $6{\sim}10\;mm$ follicle were 7 spots. This spots were analyzed by MALDI-TOF MS and searched on NCBInr. In results, 7 spots were similar to zinc/ling finger protein 3 precursor (RING finger protein 203), angiomotin, heat shock 60 kDa protein 1 (chaperonin) isoform 1 (HSP60), similar to transducin-like enhancer protein 1 (TLE 1), SH3 and PX domains 2A (SH3PXD2A). Those proteins were related with transfer between cells. Increase of proteins has an effect on follicular development.

• 한국작물학회지
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• 제58권1호
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• pp.50-56
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• 2013

SELDI-TOF MS를 활용한 저분자 펩타이드 분석을 위해서는 분석시료에 대한 최적화 분석조건을 확립하는 것이 필수적으로 선행되어야 한다. 본 연구는 수수 종자 내 존재하는 10 kDa 이하의 저분자 펩타이드를 프로파일링하기 위하여 활용된 SELDI-TOF MS의 최적화 분석조건을 확립하는데 있다. 분석조건은 (1) 프로테인 칩: CM10(weak cation exchanger), Q10(strong anion exchanger), (2) 바인딩 버퍼의 희석배수: 1/2, 1/5, 1/10, 1/20, 1/50, 1/100, 1/200, (3) Q10의 바인딩 버퍼 강도: 10 mM, 100 mM, (4) 단백질 추출버퍼: sodium borate, sodium borate + acetone, phenol, TCA 버퍼로 하였다. 1. 바인딩 버퍼의 희석배수는 CM10과 Q10 모두 1/20과 1/50이 최적화로 나타났다. 2. Q10의 바인딩 버퍼 강도는 농도가 약한 10 mM에서 더 많은 피크가 검출되었다. 3. SELDI-TOF MS 분석에 적합한 수수 종자단백질 추출 버퍼로는 2~10 kDa 범위에서는 sodium borate 버퍼와 10~20 kDa 범위에서는 phenol 버퍼로 분석되었다.

• Advances in nano research
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• 제6권1호
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• pp.81-92
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• 2018

Biosynthesis of nanoparticles has acquired particular attention due to its economic feasibility, low toxicity and simplicity of the process. Extracellular synthesis of nanoparticles by bacteria and fungi has been stated to be brought about by enzymes and other reducing agents that may be secreted in the culture medium. The present study was carried out to determine the underlying mechanisms of extracellular silver nanoparticle synthesis by Pseudomonas hibiscicola isolated from the effluent of an electroplating industry in Mumbai. Synthesized nanoparticles were characterized by spectroscopy and electron microscopic techniques. Protein profiling studies were done using Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (1D-SDS PAGE) and subjected to identification by Mass Spectrometry. Characterization studies revealed synthesis of 50 nm nanoparticles of well-defined morphology. Total protein content and SDS PAGE analysis revealed a reduction of total protein content in test (nanoparticles solution) samples when compared to controls (broth supernatant). 45.45% of the proteins involved in the process of nanoparticle synthesis were identified to be oxidoreductases and are thought to be involved in either reduction of metal ions or capping of synthesized nanoparticles.

• BMB Reports
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• 제49권7호
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• pp.388-393
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• 2016

Although brown adipose tissue is important with regard to energy balance, the molecular mechanism of brown adipocyte differentiation has not been extensively studied. Specifically, regulation factors at the level of protein modification are largely unknown. In this study, we examine the changes in the expression level of enzymes which are involved in protein lysine methylation during brown adipocyte differentiation. Several enzymes, in this case SUV420H2, PRDM9, MLL3 and JHDM1D, were found to be up-regulated. On the other hand, Set7/9 was significantly down-regulated. In the case of SUV420H2, the expression level increased sharply during brown adipocyte differentiation, whereas the expression of SUV420H2 was marginally enhanced during the white adipocyte differentiation. The knock-down of SUV420H2 caused the suppression of brown adipocyte differentiation, as compared to a scrambled control. These results suggest that SUV420H2, a methyltransferase, is involved in brown adipocyte differentiation, and that the methylation of protein lysine is important in brown adipocyte differentiation.