• Korean Journal of Poultry Science
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• v.34 no.1
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• pp.77-83
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• 2007

Poultry products including meat and eggs constitute a major protein source in the American diet and disease-causing pathogens represent major challenges to the poultry industry. More than 95% of pathogens enter the host through the mucosal surfaces of the respiratory, digestive and reproductive tracts and over the past few decades, the two main mechanisms used to control diseases have been the use of vaccines and antibiotics. However, in the poultry industry, there are mounting concerns over the ability of current vaccines to adequately protect against emerging hyper-virulent strains of pathogens and a lack of suitable, cost effective adjuvants. Thorough investigation of the immunogenetic responses involved in host-pathogen interactions will lead to the development of new and effective strategies for improving poultry health, food safety and the economic viability of the US poultry industry. In this paper, I describe the development of immunogenomic and proteomic tools to fundamentally determine and characterize the immunological mechanisms of the avian host to economically significant mucosal pathogens such as Eimeria. Recent completion of poultry genome sequencing and the development of several tissue-specific cDNA libraries in chickens are facilitating the rapid application of functional immunogenomics in the poultry disease research. Furthermore, research involving functional genomics, immunology and bioinformatics is providing novel insights into the processes of disease and immunity to microbial pathogens at mucosal surfaces. In this presentation, a new strategy of global gene expression using avian macrophage (AMM) to characterize the multiple pathways related to the variable immune responses of the host to Eimeria is described. This functional immunogenomics approach will increase current understanding of how mucosal immunity to infectious agents operates, and how it may be enhanced to enable the rational development of new and effective strategies against coccidiosis and other mucosal pathogens.

• Plant Biotechnology Reports
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• v.4 no.4
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• pp.311-319
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• 2010

Lettuce is an economically important leafy vegetable that accumulates a milk-like sap called latex in the laticifer. Previously, we conducted a large-scale lettuce latex proteomic analysis. However, the identified proteins were obtained only from lettuce ESTs and proteins deposited in NCBI databases. To extend the number of known latex proteins, we carried out an analysis identifying 302 additional proteins that were matched to the NCBI non-redundant protein database. Interestingly, the newly identified proteins were not recovered from lettuce EST and protein databases, indicating the usefulness of this hetero system in MudPIT analysis. Gene ontology studies revealed that the newly identified latex proteins are involved in many processes, including many metabolic pathways, binding functions, stress responses, developmental processes, protein metabolism, transport and signal transduction. Application of the non-redundant plant protein database led to the identification of an increased number of latex proteins. These newly identified latex proteins provide a rich source of information for laticifer research.

• Journal of Embryo Transfer
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• v.23 no.1
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• pp.25-30
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• 2008

This study was performed to identify and analyze the specifically expressed plasma proteins during early pregnancy in both pregnant and non-pregnant Hanwoo. Blood samples were collected at 0 (the day of AI), 2, 3, 4, 7, and 11 weeks after AI from pregnant (n=3) and non-pregnant (n=4) Hanwoo, respectively. The hematological parameters were measured. After 2-dimensional electrophoresis using serum, normalized protein spots were selected for the significant expression variation deviated over two fold in its expression level between two groups. Among 17 spots selected, 15 were identified as albumin, IgG1 heavy chain constant region, haptoglobin, ferrochelatase, fibrinogen, hemopexin. 5 spots were expressed only in non-pregnant specific. The spot identification of 1105 and 6106 was decreased after 3 weeks from AI. However, 2/17 spots were still unidentified. Further studies are needed to analyze the function of the proteins associated with early pregnancy.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2006.05a
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• pp.122-127
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• 2006

The innermost structures of synovium consist of one to three layers of cells generally identified as synovial lining cells(SLC). The present studies were initiated to determine the protein expression patterns of fibroblast-like synovial(FLS) cells derived from the synovia of rheumatoid arthritis. Post-traumatic arthritis(PTA) is one of the most common causes of secondary osteoarthritis, and usually affects younger people. The proteins were separated by two-dimensional polyacrylamide gel electrophoresis and RNA expression investigated by RT-PCR Proteome analyses led to the identification of more than 1,500 protein spots and of 11 differently expressed protein spots among them. Six proteins were down-regulated, and five proteins were up-regulated in ACL-transected synovial tissue. Among these, spots 3 and 8 were identified as cofilin-1 and smooth muscle protein $22-\alpha$, respectively, Therefore, the proteome analysis of synovial tissue is a useful approach to investigate a joint after an injury and can be used to understand the pathogenesis of PTA.

• The Plant Pathology Journal
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• v.32 no.6
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• pp.552-562
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• 2016

Pathogenesis-related proteins play multiple roles in plant development and biotic and abiotic stress tolerance. Here, we characterize a rice defense related gene named "jasmonic acid inducible pathogenesis-related class 10" (JIOsPR10) to gain an insight into its functional properties. Semi-quantitative RT-PCR analysis showed up-regulation of JIOsPR10 under salt and drought stress conditions. Constitutive over-expression JIOsPR10 in rice promoted shoot and root development in transgenic plants, however, their productivity was unaltered. Further experiments exhibited that the transgenic plants showed reduced susceptibility to rice blast fungus, and enhanced salt and drought stress tolerance as compared to the wild type. A comparative proteomic profiling of wild type and transgenic plants showed that overexpression of JIOsPR10 led to the differential modulation of several proteins mainly related with oxidative stresses, carbohydrate metabolism, and plant defense. Taken together, our findings suggest that JIOsPR10 plays important roles in biotic and abiotic stresses tolerance probably by activation of stress related proteins.

• Biomolecules & Therapeutics
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• v.16 no.4
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• pp.431-436
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• 2008

To identify genes whose expression correlated with biological features of therapy-related AML (t-AML), we analyzed the expression profiles of de novo AML t(9;11) and t-AML t(9;11) bone marrow samples using previously published SAGE data. Three-hundred twenty-nine transcripts that satisfied statistical (P<0.05) and magnitude-of-change ($\geq$ 4-fold) criteria were identified as differentially expressed between de novo AML t(9;11) and t-AML t(9;11) cells. Of these transcripts, 301 (91%) matched known genes or ESTs and were classified according to functional categories (http://david.abcc.ncifcrf.gov/). The majority of differentially expressed genes in t-AML t(9;11) were involved in the regulation of biological and metabolic processes. Especially prominent among these were genes related to immune and drug responses. These results establish a framework for developing new drugs for the treatment of t-AML.

• Journal of Microbiology
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• v.44 no.4
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• pp.375-382
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• 2006

From its initial colonization to causation of disease, Streptococcus pneumoniae has evolved strategies to cope with a number of stressful in vivo environmental conditions. In order to analyze a global view of this organism's response to heat shock, we established a 2-D electrophoresis proteome map of the S. pneumoniae D39 soluble proteins under in vitro culture conditions and performed the comparative proteome analysis to a 37 to $42^{\circ}C$ temperature up-shift in S. pneumoniae. When the temperature of an exponentially growing S. pneumoniae D39 culture was raised to $42^{\circ}C$, the expression level of 25 proteins showed changes when compared to the control. Among these 25 proteins, 12 were identified by MALDI-TOF and LC-coupled ESI MS/MS. The identified proteins were shown to be involved in the general stress response, energy metabolism, nucleotide biosynthesis pathways, and purine metabolism. These results provide clues for understanding the mechanism of adaptation to heat shock by S. pneumoniae and may facilitate the assessment of a possible role for these proteins in the physiology and pathogenesis of this pathogen.

• Reproductive and Developmental Biology
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• v.33 no.4
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• pp.237-242
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• 2009

Pregnancy is a unique event in which a fetus develops in the uterus despite being genetically and immunologically different from the mother, and the underlying mechanisms remain poorly understood. To analyze the differential gene expression profiles in nonpregnant and 7 days post coitus (dpc) pregnant uterus of mice, we performed a global proteomic study by 2-D gel electrophoresis (2-DE) and MALDI-TOF-MS. The uterine proteins were separated using 2-DE, Approximately 1,000 spots were detected on staining with Coomassie brilliant blue. An image analysis using Melanie III (Swiss Institute for Bioinformatics) was performed to detect variations in protein spots between pregnant and nonpregnant uterus. Twenty-one spots were identified as differentially expressed proteins, of which 10 were up-regulated proteins such as alpha-fetoprotein, chloride intracellular channel 1, transgelin, heat-shock protein beta-1, and carbonic anhydrase II, while 11 were down-regulated proteins such as X-box binding protein, glutathione S-transferase omega 1, olfactory receptor Olfr204, and metalloproteinase-disintegrin domain containing protein TECADAM. Most of the identified proteins appeared to be related with catabolism, cell growth, metabolism, regulation, cell protection, protein repair, or protection. Our results uncovered key proteins of mouse uterus involved in pregnancy.

• Korean Journal of Environmental Biology
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• v.38 no.3
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• pp.424-432
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• 2020

The present study aimed to analyze the metaproteome of the microbial community comprising harmful algal bloom (HAB) in the Daechung reservoir, Korea. HAB samples located at GPS coordinates of 36°29'N latitude and 127°28'E longitude were harvested in October 2013. Microscopic observation of the HAB samples revealed red signals that were presumably caused by the autofluorescence of chlorophyll and phycocyanin in viable cyanobacteria. Metaproteomic analysis was performed by a gelbased shotgun proteomic method. Protein identification was conducted through a two-step analysis including a forward search strategy (FSS) (random search with the National Center for Biotechnology Information (NCBI), Cyanobase, and Phytozome), and a subsequent reverse search strategy (RSS) (additional Cyanobase search with a decoy database). The total number of proteins identified by the two-step analysis (FSS and RSS) was 1.8-fold higher than that by one-step analysis (FSS only). A total of 194 proteins were assigned to 12 cyanobacterial species (99 mol%) and one green algae species (1 mol%). Among the species identified, the toxic microcystin-producing Microcystis aeruginosa NIES-843 (62.3%) species was the most dominant. The largest functional category was proteins belonging to the energy category (39%), followed by metabolism (15%), and translation (12%). This study will be a good reference for monitoring ecological variations at the meta-protein level of aquatic microalgae for understanding HAB.

• Mass Spectrometry Letters
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• v.5 no.1
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• pp.16-23
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• 2014

Liquid chromatography based mass spectrometry (LC-MS) is a key technology for analyzing highly complex and dynamic proteome samples. With highly accurate and sensitive LC-MS analysis of complex proteome samples, efficient data processing is another critical issue to obtain more information from LC-MS data. A typical proteomic data processing starts with protein database search engine which assigns peptide sequences to MS/MS spectra and finds proteins. Although several search engines, such as SEQUEST and MASCOT, have been widely used, there is no unique standard way to interpret MS/MS spectra of peptides. Each search engine has pros and cons depending on types of mass spectrometers and physicochemical properties of peptides. In this study, we describe a novel data process pipeline which identifies more peptides and proteins by correcting precursor ion mass numbers and unifying multi search engines results. The pipeline utilizes two open-source software, iPE-MMR for mass number correction, and iProphet to combine several search results. The integrated pipeline identified 25% more proteins in mouse epididymal adipose tissue compared with the conventional method. Also the pipeline was validated using control and colitis induced colon tissue. The results of the present study shows that the integrated pipeline can efficiently identify increased number of proteins compared to the conventional method which can be a breakthrough in identification of a potential biomarker candidate.