• Development and Reproduction
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• v.19 no.4
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• pp.227-234
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• 2015

The objective of this study was to investigate the expression of bovine luteum expressed sequence tags (ESTs), vascular endothelial growth factor (VEGF), and tumor necrosis factor receptor 1 (TNFR1) and the presence of functional ESTs in the bovine corpus luteum (CL) during different stages of the estrus cycle. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed a difference in the expression of ESTs during the CL stage. Concentration of ESTs in the CL tissue increased significantly from the mid-luteal stage and decreased thereafter. RT-PCR analysis showed higher levels of the EST genes in the CL of the mid-luteal stage than in other stages, and the same level of expression of VEGF. Immunohistochemistry analysis of the tissue from CL formation to regression showed low cytosol and aggregation of the nucleus. And activity caspase 3 (apoptosis detector) was most strongly detected in the CL1 stage of bovine. During the estrous cycle, the cytosol was magnified and differentiation of the nucleus was clearly manifested. The ESTs affected the CL, and the relationship between VEGF and TNFR1 played a pivotal role for CL development and activation, dependent on the stage of CL. These results suggest local production of ESTs, the presence of functional ESTs in the bovine CL, and that ESTs play a role in regulating the function of cell death in bovine CL.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.192-192
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• 2005

• Proceedings of the Zoological Society Korea Conference
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• 2003.08a
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• pp.182.4-182
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• 2003

No Abstract, See Full Text

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.1
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• pp.116-121
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• 2010

Long-chain polyunsaturated fatty acids (LC-PUFA) promote the development of brain and vision of the fetus, relieve inflammation, inhibit oral dysplasia of rumor cell, decrease the incidence of cardiovascular disease and regulate arrhythmia. ${\Delta}-6$ desaturase is the rate-limited enzyme in the desaturation process. This study reports the cloning, characterization and tissue expression of a ${\Delta}-6$ desaturase gene in the chicken. PCR primers were designed based on the predicted sequence of chicken ${\Delta}-6$ desaturase (accession number: XM421053) and used to isolate a cDNA fragment of 1,323 bp from chicken liver. Based on the 1,323 bp fragment an EST (BI390105) was obtained by BLAST. The EST and 5'nd of the 1,323 bp fragment were partially overlapped. Gene specific primers derived from the EST were used for amplification of the 5'nd. Another gene-specific primer derived from the 1,323 bp fragment was used for amplification of the 3'nd by 3'ACE. Then the three overlapping cDNA sequences obtained were assembled with DNAMAN software and a full-length ${\Delta}-6$ desaturase of 2,153 bp was obtained. The full-length cDNA contained an ORF of 1,335 bp with a 5'ntranslated region of 147 nucleotides followed by an ATG initiation codon. Stop codon TGA was at position 1,481-1,483 bp. The deduced amino acids shared an homology above 77% with bovine, mice, orangutan, rat and human. The protein sequence had three histidine-rich regions HDFGH (HisI region), HFQHH (HisII region) and HH (HisIII region), a cytochrome $b_{5}$-like domain containing a heme-binding motif and two transmembrane domains. Sequence analysis of the chicken genomic DNA revealed that the coding sequence of chicken ${\Delta}-6$ desaturase included 12 exons and 11 introns. Semi-quantitative RT-PCR showed that the ${\Delta}-6$ desaturase expression levels were in turn liver, spleen, pancreas, lung, breast muscle, heart, and abdominal fat. The expression of ${\Delta}-6$ desaturase in liver was significantly higher than that in breast muscle (p<0.01). The expression of ${\Delta}-6$ desaturase in lung was significantly higher than that in abdominal fat (p<0.01). This is the first clone of chicken ${\Delta}-6$ desaturase.

• Journal of Animal Science and Technology
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• v.51 no.1
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• pp.1-8
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• 2009

We generated 57,598 expressed sequence tags (ESTs) from 3 cDNA libraries of Hanwooo (Korean Cattle), fat, loin, liver. Liver, intermuscular fat and longissimus dorsi tissues were obtained from a 24-month-old Hanwoo steer immediately after slaughter. cDNA library was constructed according to the oligocapped method. The EST data were clustered and assembled into unique sequences, 4,759 contigs and 7,587 singletons. To carry out functional analysis, Gene Ontology annotation and identification of significant leaf nodes were performed that were detected by searching significant p-values from $2^{nd}$ level GO terms to leaf nodes using Bonferroni correction. We found that 13, 26 and 8 significant leaf nodes are unique in the transcripts according to 3 GO categories, molecular function, biological process and cellular component. Also digital gene expression profiling using the Audic's test was performed and tissue specific genes were detected in the above 3 libraries.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.55 no.2
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• pp.151-158
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• 2010

Camelina sativa L., known as popular names "gold-of-pleasure" or "false flax" is an alternative oilseed crop that can be grown under different climatic and soil conditions. Up to date, however, the genomic information of Camelina has not been studied in detail. Therefore, a cDNA library was constructed and characterized from young leaves. The constructed cDNA library incorporated of 1334 cDNA clones and the size of the insertion fragments average was 736 base pair. We generated a total of 1269 high-quality expressed sequence tags (ESTs) sequences. The result of cluster analysis of EST sequences showed that the number of unigene was 851. According to subsequent analysis, the 476 (55.9%) unigenes were highly homologous to known function genes and the other 375 (44.1%) unigenes were unknown. Remaining 63 (7.4%) unigenes had no homology with any other peptide in NCBI database, indicating that these seemed to be novel genes expressed in leaves of Camelina. The database-matched ESTs were further classified into 17 categories according to their functional annotation. The most abundant of categories were "protein with binding function or cofactor requirement (27%)", "metabolism (11%)", "subcellular localization (11%)", "cellular transport, transport facilities and transport routes (7%)", "energy (6%)", "regulation of metabolism and protein function (6%)". Our result in this study provides an overview of mRNA expression profile and a basal genetic information of Camelina as an oilseed crop.

• Journal of Photoscience
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• v.9 no.2
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• pp.267-268
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• 2002

A vertebrate retina is an organ belonging to the central nerve system (CNS), and is usually difficult to regenerate except at an embryonic stage in life. However, certain species of urodele amphibians, such as newts and salamanders, possess the ability to regenerate a functional retina from retinal pigment epithelial (RPE) cells even as adults. After surgical removal of neural retinas from adult newt eyes, the remaining RPE cells lose their pigment granules, transdifferentiate into retinal progenitor cells, which further differentiate into various retinal neurons, and then finally reform a functional neural network. To understand the molecular mechanisms of CNS regeneration, we attempted to investigate the genes expressing in regenerating newt retina. mRNAs were isolated from regenerating retinas at 18-19 days after the surgical removal of the normal retina, and a cDNA library (regenerating retinal cDNA library) were constructed. Our EST analysis of 112 clones in the regenerating cDNA library revealed that about 70% clones are closely related to the genes previously identified. About 40% clones are housekeeping genes, and about 15% clones encode proteins related to the regulation of gene expression and to the proliferation of the cells. Sequences similar to neural retina- and RPE-specific genes were not detected at all. These results led us to suppose that the regenerating retinal cells are in a state considerably different from those of neither neural retina nor RPE cells.

• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.44-44
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• 2003

Gene expression in five tissues of the abalone (Haliotis discus hannai) was investigated using an expressed sequence tag (EST) analysis. Randomly selected clones were obtained from cDNA libraries constructed with gill (GI), digestive diverticula(DD), hepatopancreas (HP), foot/mucus (FM) and rectangular muscle (RM). Of 1,235 clonesanalyzed (288 clones for GI, DD, HP each,166 for FM, and 205 for RM), 741 (60.0%) clones in total turned out to share significant similarity with the sequences from NCBI GenBank (less than 10/sup -3/ of e-values), 423 sequences showed poor similarity (> 10/sup -3/), and 71 sequences didn't match with any sequences in GenBank. The percent unique sequence (singleton) was ranged from 56.1% (RM) to 74.7% (FM) among libraries. On the other hand, overall percent singleton was 55.3% when all the ESTs from five libraries were assembled into contigs. Analysis of the organisms represented by the best hit for each EST (e-values < 10/sup -3/) showed that 23.8% matched with mammalian entries, 24.0% with mollusks, 14.4% with insects, 11.6% with fish and 26.2% with others. The expressed patterns differed among the tissues when judged by the categorization of the sequences from each library into 10 broad functional classes. In all the libraries, the class I (no hit o. poor similarity) was the largest category with an average of 40.1%. This largest class was followed by class V (general metabolisms) in DD (21.9%), GI (14.6%) and HP (16.7%), while the 'cell structure and motility'(class VI) was the second largest class in remaining two libraries (31.2% for RM and 9.6% for FM). The class IX (cell division and proliferation) was the smallest class in all the libraries (less than 3%). This report provides the first tissue-specific lists of expressed abalone genes, which could be a fundamental basis for genomics program of abalone species.

• Journal of Microbiology and Biotechnology
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• v.19 no.8
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• pp.774-780
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• 2009

Flammulina velutipes is a popular edible basidiomycete mushroom found in East Asia and is commonly known as winter mushroom. Mushroom development showing dramatic morphological changes by different environmental factors is scientifically and commercially interesting. To create a genetic database and isolate genes regulated during mushroom development, cDNA libraries were constructed from three developmental stages of mycelium, primordium, and fruit body in F. velutipes. We generated a total of 5,431 expressed sequence tags (ESTs) from randomly selected clones from the three cDNA libraries. Of these, 3,332 different unique genes (unigenes) were consistent with 2,442 (73%) singlets and 890 (27%) contigs. This corresponds to a redundancy of 39%. Using a homology search in the gene ontology database, the EST unigenes were classified into the three categories of molecular function (28%), biological process (29%), and cellular component (6%). Comparative analysis found great variations in the unigene expression pattern among the three different unigene sets generated from the cDNA libraries of mycelium, primordium, and fruit body. The 19-34% of total unigenes were unique to each unigene set and only 3% were shared among all three unigene sets. The unique and common representation in F. velutipes unigenes from the three different cDNA libraries suggests great differential gene expression profiles during the different developmental stages of F. velutipes mushroom.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.1
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• pp.11-18
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• 2008

We created a cDNA microarray representing approximately 3,500 pig genes for functional genomic studies. The array elements were selected from 6,494 cDNA clones identified in a large-scale expressed sequence tag (EST) project. These cDNA clones came from normalized and subtracted porcine adipose tissue cDNA libraries. Sequence similarity searches of the 3,426 ESTs represented on the array using BLASTN identified 2,790 (81.4%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. We used the gene microarray to profile transcripts expressed by adipose tissue of fatty Chinese Xiang pig (XP) and muscley Large White (LW). Microarray analysis of RNA extracted from adipose tissue of fatty XP and muscley LW identified 81 genes that were differently expressed two fold or more. Transcriptional differences of four of these genes, adipocyte fatty acid binding protein (aP2), stearyl-CoA desaturase (SCD), sterol regulatory element binding transcription factor 1 (SREBF1) and lipoprotein lipase (LPL) were confirmed using SYBR Green quantitative RT-PCR technology. Our results showed that high expression of SCD and SREBF1 may be one of the reasons that larger fat deposits are observed in the XP. In addition, our findings also illustrate the potential power of microarrays for understanding the molecular mechanisms of porcine development, disease resistance, nutrition, fertility and production traits.