• Title/Summary/Keyword: Major Genes

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Copy Number Deletion Has Little Impact on Gene Expression Levels in Racehorses

  • Park, Kyung-Do;Kim, Hyeongmin;Hwang, Jae Yeon;Lee, Chang-Kyu;Do, Kyoung-Tag;Kim, Heui-Soo;Yang, Young-Mok;Kwon, Young-Jun;Kim, Jaemin;Kim, Hyeon Jeong;Song, Ki-Duk;Oh, Jae-Don;Kim, Heebal;Cho, Byung-Wook;Cho, Seoae;Lee, Hak-Kyo
    • Asian-Australasian Journal of Animal Sciences
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    • v.27 no.9
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    • pp.1345-1354
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    • 2014
  • Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

Current Status of Comparative Mapping in Livestock

  • Lee, J.H.;Moran, C.;Park, C.S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.16 no.10
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    • pp.1411-1420
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    • 2003
  • Comparative maps, representing chromosomal locations of homologous genes in different species, are useful sources of information for identifying candidate disease genes and genes determining complex traits. They facilitate gene mapping and linkage prediction in other species, and provide information on genome organization and evolution. Here, the current gene mapping and comparative mapping status of the major livestock species are presented. Two techniques were widely used in comparative mapping: FISH (Fluorescence In Situ Hybridization) and PCR-based mapping using somatic cell hybrid (SCH) or radiation hybrid (RH) panels. New techniques, using, for example, ESTs (Expressed Sequence Tags) or CASTS (Comparatively Anchored Sequence Tagged Sites), also have been developed as useful tools for analyzing comparative genome organization in livestock species, further enabling accurate transfer of valuable information from one species to another.

The Effects of Genetic and Nutritional Factors on Pork Quality - Review -

  • Ellis, M.;McKeith, F.K.;Miller, K.D.
    • Asian-Australasian Journal of Animal Sciences
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    • v.12 no.2
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    • pp.261-270
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    • 1999
  • Consumers are increasingly quality orientated and an understanding of the factors that influence product quality is a prerequisite to the development of programs to produce quality pork to meet market requirements. Pork quality is comprised of many components and is multi-factorial in nature. This review focuses on genetic and environmental influences on muscle color, water holding capacity, and palatability attributes. The impact of genetic factors such as breed variation and the influence of major genes (the Halothane and Rendement Napole genes), as well as relationships between carcass leanness and quality, are considered. In addition, the effect of nutrition, including vitamins and minerals, feeding level, and dietary energy:protein ratio, on pork quality is reviewed. Finally, the impact of diet on fat composition and quality is summarized.

Transcriptional Response According to Strength of Calorie Restriction in Saccharomyces cerevisiae

  • Lee, Yae-Lim;Lee, Cheol-Koo
    • Molecules and Cells
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    • v.26 no.3
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    • pp.299-307
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    • 2008
  • To characterize gene expression that is dependent on the strength of calorie restriction (CR), we obtained transcriptome at different levels of glucose, which is a major energy and carbon source for budding yeast. To faithfully mimic mammalian CR in yeast culture, we reconstituted and grew seeding yeast cells in fresh 2% YPD media before inoculating into 2%, 1%, 0.5% and 0.25% YPD media to reflect different CR strengths. We collected and characterized 160 genes that responded to CR strength based on the rigorous statistical analyses of multiple test corrected ANOVA (adjusted p value < 0.1 or raw p value < 0.0031) and Pearson correlation (|r| > 0.7). Based on the individual gene studies and the GO Term Finder analysis of 160 genes, we found that CR dose-dependently and gradually increased mitochondrial function at the transcriptional level. Therefore, we suggest these 160 genes are markers that respond to CR strength and that might be useful in elucidating CR mechanisms, especially how stronger CR extends life span more.

Cloning and Expression of Nucleocapsid Genes of Hantaviruses in Escherichia coli (대장균에서 한타바이러스 뉴클레오캡시드 유전자의 발현에 관한 연구)

  • 노갑수;하석훈;김종완;홍선표;김형배;최차용
    • KSBB Journal
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    • v.13 no.6
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    • pp.649-655
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    • 1998
  • Hantaviruses are rodent hosts-borne viruses belonging to the family Bunyaviridae, and are etiologic agents for two acute diseases, i.e., Haemorrhagic Fever with Renal Syndrome (HFRS) and Hantavirus Pulmonary Syndrome (HPS). There have been a lot of reports on prophylactic vaccines and diagnostics for the diseases, but most of viral antigens have been prepared by eukaryotic cell culture. Nucleocapsid proteins of Hantaviruses are known as the major viral antigens. Thereby, we prepared nucleocapsid genes of Hantaan virus and Seoul virus by RT-PCR and cloned into plasmid vectors, pET-3a and pKK223-3. Both genes were expressed in Escherichia coli with higher expression level of Seoul viral nucleocapsid protein compared to that of Hantaan in pET-3a. Hantaan viral gene was expressed much higher level in plasmid pET-3a that in pKK223-3. About 30% of expressed nucleocapsid protein was soluble and the rest was remained in insoluble fraction.

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Deciphering Key Genes of Proliferative and Secretory Phase Using Integrated Transcriptomics and Network Analysis

  • Payal Gupta;Shriya Dube;Payal Priyadarshini;Shanvi Singh;Anasuya Pravallika R;Vijay Lakshmi Srivastava;Abhishek Sengupta;Priyanka Narad
    • Microbiology and Biotechnology Letters
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    • v.51 no.3
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    • pp.317-324
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    • 2023
  • Endometrium receptivity is a complex mechanism of intricate pathways that lead to the shift from the proliferative to the secretory phase. Our goal was to identify high-ranking differentially expressed genes and study the pathways associated with the phenomenon. Raw data were retrieved from six GEO datasets and 705 DEGs were identified through robust ranking aggregation after the integration of five datasets. 20 key genes were identified that were further re-validated in an additional dataset. Supporting evidence through the experimental references confirms them as major biomarkers of the shift from the proliferative to the secretory phase.

Draft Genome Sequence of the Neodothiora populina-Like Yeast Strain JAF-11, Which Produces the Biosurfactant myo-Inositol Lipids

  • Jeong-Seon Kim;Parthiban Subramanian;Seunghwan Kim;Jun Heo;Bong-Sik Yun;Yiseul Kim
    • Microbiology and Biotechnology Letters
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    • v.51 no.3
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    • pp.328-331
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    • 2023
  • Genomic information of biotechnologically and industrially important microorganisms provides the basis for understanding their metabolic potential. Here, we report the draft genome sequence of the Neodothiora populina-like yeast strain JAF-11 capable of producing biosurfactant myo-inositol lipids. The draft genome contained genes associated with secondary metabolite biosynthesis, including transport and metabolism of lipids, which are a major component of fungal surfactants. Identification of myo-inositol and acyl chain synthesis genes in the draft genome corresponded to the specific biosurfactant produced by strain JAF-11. Further experimental studies could help to elucidate the genes responsible for the production of biosurfactant by strain JAF-11.

Co-expression of MDRI and HLA-B7 Genes in a Mammalian Cell Using a Retrovirus

  • Lee, Seong-Min;Lee, Kyoo-Hyung;Kim, Hag-Dong;Lee, Je-Hwan;Lee, Jung-Shin;Kim, Joon
    • BMB Reports
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    • v.34 no.2
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    • pp.176-181
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    • 2001
  • Using a retrovirus, foreign genes can be introduced into mammalian cells. The purpose of this study is to produce a retrovirus that can make the infected cells express two genes; the human multidrug resistance gene (MDR1) and the HLA-B7 gene, which is one of the major human histocompatibility complex (MHC) class I genes. For the expression of these genes, the internal ribosome entry site (IRES) was used, which was derived from the encephalomyocarditis (EMC) virus. In order to produce retroviruses, a retroviral vector was transfected into a packaging cell line and the transfected cells were treated with vincristine, which is an anti-cancer drug and a substrate for the MDRI gene product. This study revealed that two genes were incorporated into chromosomes of selected cells and expressed in the same cells. The production of the retrovirus was confirmed by the reverse transcription (RT)-PCR of the viral RNA. The retrovirus that was produced infected mouse fibroblast cells as well as the human U937. This study showed that packaging cells produced the retroviruses, which can infect the target cells. Once the conditions for the high infectivity of retrovirus into human cells are optimized, thus virus will be used to infect hematopoietic stem cells to co-express MDRl and HLA-B7 genes, and develop the lymphocytes that can be used for the immnogene therapy.

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Current Status on Molecular Genetic Study and Comparative Genomic Analysis of Virulence Related Genes in Xanthomonas oryzae pv. oryzae (벼 흰잎마름병균(Xanthomonas oryzae pv. oryzae)의 병원성 유전자의 분자유전학적 연구현황 및 비교유전체 분석)

  • Kang, Hee-Wan;Park, Young-Jin;Lee, Byeong-Moo
    • Korean Journal of Microbiology
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    • v.44 no.1
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    • pp.1-9
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    • 2008
  • Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight on rice. In this paper, current status on molecular genetic study of major virulence genes, hypersensitive response and pathogenicity (hrp), productions of extracellular polysaccharide (EPS), extracellular enzymes and lipopolysaccharides (LPS), avr genes were reviewed. The IS elements with 611 copies including 133 ORF IS were inserted in various regions of the Xoo genome and in expecially regions franking virulence genes. Whole genome sequence of X. oryzae pv. oryzae KACC10331 were used for defining genetic organization of the virulence genes. Futhermore, the virulence genes in Xoo genome were compared to those of other Xanthomonas species in Blast GenBank data base.

Comparative Transcriptome Analysis Reveals Differential Response of Phytohormone Biosynthesis Genes in Glumous Flowers of Cold-Tolerant and Cold-Sensitive Rice Varieties Upon Cold Stress at Booting Stage

  • Park, Myoung Ryoul;Kim, Ki-Young;Tyagi, Kuldeep;Baek, So-Hyeon;Yun, Song Joong
    • Korean Journal of Breeding Science
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    • v.43 no.1
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    • pp.1-13
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    • 2011
  • Low temperature stress is one of the major negative factors affecting vegetative and reproductive growth of rice. To better understand responses of rice plants to low temperature we analyzed transcriptome expression patterns in glumous flower of cold-tolerant japonica rice variety, Stejaree45, and cold-susceptible variety, HR19621-AC6 at booting stage under cold water irrigation. A total of 2,411 probes were differentially expressed by low temperature in glumous flowers of the two varieties. Some important genes involved in hormone biosynthesis showed variety-specific regulation. Expression of GA20ox3 and GA2ox, among the genes involved in GA biosynthesis, was regulated differentially in the two varieties. Among the genes involved in IAA biosynthesis, YUCCA1 and TAA1:1 showed variety-specific regulation. Among the genes involved in cytokinin biosynthsis and signaling, expression of LOG, HK1 and HK3 was significantly down-regulated only in the cold-susceptible variety. Among the genes involved in ABA biosynthesis, NSY and AAO3 were down-regulated only in the cold-tolerant variety. In general, genes involved in GA, IAA and cytokinin biosynthesis responded to cold temperature in such a way that capacity of those bioactive hormones is maintained at relatively higher levels under cold temperature in the cold-tolerant variety, which can help minimize cold stress imposed to developing reproductive organs in the cold-tolerant variety.