• Journal of Microbiology and Biotechnology
• /
• 제19권8호
• /
• pp.774-780
• /
• 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.

• Animal cells and systems
• /
• 제13권4호
• /
• pp.381-389
• /
• 2009

Using the DDRT-PCR, a series of differentially expressed genes in human primary cervical cancer was isolated. Among the 250 PCR amplimers, 88 gene fragments were confirmed by reverse Northern hybridization. Homology searches indicated that 26 out of 88 were previously known genes including calmodulin, human BBC1, histone H3.3, a series of ribosomal proteins (RPL19, RPS19, and RPS12), translation initiation factor (eIF-4AI), lactoferrin, integrin ${\alpha}6$, cell-surface antigens (CD9 and CD59), transcription factor (mbp-1), and mitochondrial proteins. Several unknown clones showed sequence homology with known genes. Furthermore, six of the unknown genes showed identical sequence with expressed sequence tags (EST) of unknown function. Differential expression patterns of identified genes were further examined and confirmed with multiple pairs of cervical cancer samples using Northern hybridization. Our profiling of differentially expressed genes may provide useful information about the underlying genetic alterations in human cervical carcinoma and diagnostic markers for this disease. The precise roles of these genes in cancer development remain to be elucidated.

• 한국패류학회지
• /
• 제30권2호
• /
• pp.155-163
• /
• 2014

동양달팽이의 EST 에서 serpin 유전자는 2가지 type이 추정되었다. Ns-serpin type 1 (partial) 서열의 코딩 영역은 총 819 bp 이었으며, 272개의 아미노산으로 이루어져 있었으며, Ns-serpin type 2 (partial) 의 코딩영역은 총 555 bp, 185개의 아미노산으로 이루어져 있었다. Laminarin 처리 전에는 Ns-serpin type 1이 2개 발현되었으며 처리 후에는 Ns-serpin type 2가 1개 발현되고 있었다. BLAST 결과를 바탕으로 유사도가 높은 17개의 참고 서열과 동양달팽이의 Ns-serpin type 1, 2의 아미노산 서열을 MEGA6 프로그램의 clustalW 엔진을 이용하여 multiple sequence alignment 를 수행한 결과, 척색동물의 포유강 9종, 조류강 1종, 양서강 1종과 척색동물인 해초강, 절지동물의 거미강 1종과 곤충강 1종이 같은 군으로 묶였으며, 연체동물문의 경우 동양달팽이의 두 가지 type 을 포함한 복족강 4종이 같은 군으로 묶이는 것을 확인하였다. Psipred 프로그램을 활용하여 예측한 2D 구조도 multiple align 및 phylodendrogram 결과와 연관이 있음을 확인할 수 있었다. EST를 통해 밝힌 동양달팽이의 두 가지 type의 Ns-serpin 서열은 Aplysia californica 등의 근연종들의 서열과 유사하였다. 본 연구에서는 무척추동물에서의 선천성 면역과 연관이 있는 것으로 잘 알려진 두 종류의 serpin 유전자 서열을 동양달팽이 EST 결과에서 발굴 하였으며, 동양달팽이에서도 여러 가지 type의 serpin 이 존재 할 수 있음을 입증하였다.

• Fisheries and Aquatic Sciences
• /
• 제6권3호
• /
• pp.110-115
• /
• 2003

Expressed sequence tag (EST) analysis was conducted using a cDNA library made from the liver mRNA of olive flounder (Paralichthys olivaceus). In the survey of 421 ESTs, 362 showed significant homology to previously described genes while 59 were unidentified or novel. Comparative analysis of the identified ESTs showed that 69 $(19.0\%)$ clones were identified as homologous to the previously reported olive flounder ESTs, and 279 $(77.1\%)$ clones were identified as orthologs of known genes from other organisms. The remaining 14 $(3.9\%)$ clones were identified as orthologs of known sequences with unknown functions. These tagged cDNA clones, identified and unidentified, could provide fundamental baseline data for genomic studies of this species.

• 한국수산과학회지
• /
• 제36권5호
• /
• pp.442-448
• /
• 2003

Melanin concentrating hormone (MCH) regulating color change of fish skin was identified from brain cDNA library of Olive flounder (Paralichthys olivaceus) during the analysis of Expressed Sequence Tags (ESTs). Olive flounder MCH gene consisted of 598 nucleotides encoding 150 amino acids. Olive flounder MCH protein revealed to contain signal peptide of 19 amino acid residues, pro-MCH of 131 amino acids being processed to biologically active and mature form of hormone with 25 amino acid residues at the carboxyl terminus. A comparative structural analysis revealed that Olive flounder MCH precursor had low sequence identity with other fish species and mammalian counterparts, while the amino acid sequences of mature hormone had a relatively high identity and more conserved. RT-PCR analysis revealed that olive flounder MCH precersor gene was expressed spectically only in the brain and not in other tissues.

• 한국어병학회지
• /
• 제23권2호
• /
• pp.229-238
• /
• 2010

We constructed a rock bream (Oplegnathus fasciatus) liver cDNA library and a total of 1533 expressed sequence tag (EST) clones were generated. Gene annotation procedures and homology searches of the sequenced ESTs were analyzed using BLASTX. Of the 1533 EST clones, 1165 different ESTs showed significant homology to previously described genes while 368 ESTs were unidentified, hypothetical, or unnamed proteins. Encoding 106 different sequences were identified as putative bio-defense genes or genes associated with immune response.

• 원예과학기술지
• /
• 제31권5호
• /
• pp.598-606
• /
• 2013

약은 생식과 화형을 결정짓는 꽃의 주요한 기관 중 하나이다. 오리엔탈나리인 아카풀코로부터 만든 약 특이적 cDNA library로부터 2000개의 ESTs를 무작위로 선발하였다. 잎과 약을 cDNA 탐침으로 이용한 differential slot blot이 약에서 발현되는 클론들을 얻기 위해 사용되었으며 570개의 비반복적 ESTs를 얻었고 염기서열분석을 하였다. BLASTX 알고리즘을 이용하여 GenBank에 비교해서 191개의 클론이 의미 있는 유사성을 보였지만 나머지(66.5%)는 기존에 보고된 염기서열에 확인되지 않았다. Gene ontology(GO) annotation에 따른 기능분류결과 대체적으로 세포와 세포구성 부분에서 주요하게 단백질이 확인되었다. 7개의 다른 기관과 발달 단계에서 전사체 분석은 약특이적일 적으로 추정되는 30개의 클론을 가지고 노던혼성화반응을 이용하여 수행하였다. 이러한 결과는 differential slot blot을 이용하여 약에 발현되는 유전자를 선별하는 것이 매우 효과적인 방법인 것으로 간주되며 또한 지금의 연구가 앞으로 나리의 화분을 포함한 약에 대한 기초정보를 제공할 수 있을 것으로 생각한다.

• BMB Reports
• /
• 제39권2호
• /
• pp.183-188
• /
• 2006

Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.

• BMB Reports
• /
• 제44권4호
• /
• pp.238-243
• /
• 2011

We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean Jindo dog. An additional 365,909 ESTs from other dog breeds were identified from the NCBI dbEST database, and all ESTs were clustered into 28,514 consensus sequences using StackPack. We selected the 7,305 consensus sequences that could be assembled from at least five ESTs and estimated that 12,533 high-quality single nucleotide polymorphisms (SNPs) were present in 97,835 putative SNPs from the 7,305 consensus sequences. We identified 58 Jindo dog-specific SNPs in comparison to other breeds and predicted seven synonymous SNPs and ten non-synonymous SNPs. Using PolyPhen, a program that predicts changes in protein structure and potential effects on protein function caused by amino acid substitutions, three of the non-synonymous SNPs were predicted to result in changes in protein function for proteins expressed by three different genes (TUSC3, ITIH2, and NAT2).

• Journal of Microbiology and Biotechnology
• /
• 제15권5호
• /
• pp.1060-1066
• /
• 2005

Under environmental stress, such as strong irradiance or nitrogen deficiency, unicellular green algae of the genus Haematococcus accumulate secondary carotenoids, i.e. astaxanthin, in the cytosol. The induction and regulation of astaxanthin biosynthesis in microalgae has recently received considerable attention owing to the increasing use of secondary carotenoids as a source of pigmentation for fish aquacultures, and as a potential drug in cancer prevention as a free-radical quencher. Accordingly, this study generated expressed sequence tags (ESTs) from a library constructed from astaxanthin-induced Haematococcus pluvialis. Partial sequences were obtained from the 5' ends of 1,858 individual cDNAs, and then grouped into 1,025 non-overlapping sequences, among which 708 sequences were singletons, while the remainder fell into 317 clusters. Approximately $63\%$ of the EST sequences showed similarity to previously described sequences in public databases. H. pluvialis was found to consist of a relatively high percentage of genes involved in genetic information processing ($15\%$) and metabolism ($11\%$), whereas a relatively low percentage of sequences was involved in the signal transduction ($3\%$), structure ($2\%$), and environmental information process ($3\%$). In addition, a relatively large fraction of H. pluvialis sequences was classified as genes involved in photosynthesis ($9\%$) and cellular process ($9\%$). Based on this EST analysis, the full-length cDNA sequence for superoxide dismutase (SOD) of H. pluvialis was cloned, and the expression of this gene was investigated. The abundance of SOD changed substantially in response to different culture conditions, indicating the possible regulation of this gene in H. pluvialis.