• Journal of Plant Biotechnology
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• v.45 no.1
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• pp.45-54
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• 2018

This research was conducted to study the gene expression of coffee (Coffea arabica L.) seedlings under salt stress condition. A solution of five percent ($2.3dS\;m^{-1}$) deep sea water was used for the salt treatment, and it was thereby compared to normal irrigation water ($0.2dS\;m^{-1}$) used for the control treatment. The mRNA was extracted from the leaves of the coffee seedlings for a comprehensive analysis. In this study, a total of 19,581 genes were identified and aligned to the reference sequences available in the coffee genome database. The gene ontology analysis was performed to estimate the number of genes associated with the identified biological processes, cellular components and molecular functions. Among the 19,581 genes, 7369 (37.64%) were associated with biological processes, 5909 (30.18%) with cellular components, and 5325 (27.19%) with molecular functions. The remaining 978 (4.99%) genes were therefore grouped as unclassified. A differential gene expression analysis was performed using the DESeq2 package to identify the genes that were differentially expressed between the treatments based on fold changes and p-values. Namely, a total of 611 differentially expressed genes were identified (treatment/control) in that case. Among these, 336 genes were up-regulated while 275 of the genes were down-regulated. Of the differentially expressed genes, 60 genes showed statistically significant (p < 0.05) expression, 44 of which were up-regulated and 16 which were down-regulated. We also identified 11 differentially expressed transcription factor genes, 6 of which were up-regulated and rest 5 genes were down-regulated. The data generated from this study will help in the continued interest and understanding of the responses of coffee seedlings genes associated with salinity stress, in particular. This study will also provide important resources for further functional genomics studies.

• Communications for Statistical Applications and Methods
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• v.14 no.1
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• pp.169-182
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• 2007

Receive operating characteristic (ROC) approach can be employed to rank candidate genes from a microarray experiment, in particular, for the biomarker development with the purpose of population screening of a cancer. In the cancer microarray experiment based on n patients the researcher often wants to compare the tumor tissue with the normal tissue within the same individual using a common reference RNA. Ideally, this experiment produces n pairs of microarray data. However, it is often the case that there are missing values either in the normal or tumor tissue data. Practically, we have $n_1$ pairs of complete observations, $n_2$ "normal only" and $n_3$ "tumor only" data for the microarray. We refer to this data set as a mixed data set. We develop a ROC approach on the mixed data set to rank candidate genes for the biomarker development for the colorectal cancer screening. It turns out that the correlation between two ranks in terms of ROC and t statistics based on the top 50 genes of ROC rank is less than 0.6. This result indicates that employing a right approach of ranking candidate genes for the biomarker development is important for the allocation of resources.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.3
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• pp.425-429
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• 2003

Staphylococcus aureus is a major pathogen for cattle, causing various forms of subclinical and clinical mastitis and could be a causative agent of food poisoning, it produces various superantigenic exotoxins which have a great public health significance. A total of 72 S. aureus clinical isolates from dairy farms located in Kyunggi Province Korea were examined for the species identification by biochemical method, and for the detection of $\beta$-lactamase, enterotoxin and other exotoxins genes by PCR. The results of species identification by biochemical method agreed with those of PCR done with species specific primer STA-AU. $\beta$-lactamase is an enzyme closely associated with the resistance to antibiotic penicillin, which is an important means of treatment of mastitis, all the isolates were positive for the presence of genes encoding $\beta$-lactamase, which were reproduced in penicillin susceptibility disc assay. Six types of toxin genes, Staphylococcal enterotoxin (SE)A, SEB, SEC, SEE, toxic shock syndrome toxin (TSST-1) and exfoliative toxin A (ET A) were detected in 72 isolates by PCR associated genotypic method in this study, none of the isolates carried the genes for enterotoxin D (SED) and exfoliative toxin B (ETB). The occurrence rate of exotoxin genes rated as 12.5%, and the precision of the PCR identification results has been confirmed using the reference strains.

• ALGAE
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• v.31 no.2
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• pp.167-174
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• 2016

Biological response of cells to variable conditions should affect the expression level of certain genes. Quantification of these changes in target genes needs stable internal controls. Real-time quantitative polymerase chain reaction (PCR) has traditionally used reference or ‘housekeeping’ genes, that are considered to maintain equal expression in different conditions, to evaluate changes in target genes between samples and experimental conditions. Recent studies showed that some housekeeping genes may vary considerably in certain biological samples. This has not been evaluated in red algae. In order to identify the optimal internal controls for real-time PCR, we studied the expression of eleven commonly used housekeeping genes; elongation factor 1-alpha, glyceraldehyde-3-phosphate dehydrogenase, β-actin, polyubiquitin, 30S ribosomal gene, 60S ribosomal gene, beta-tubulin, alpha-tubulin, translation initiation factor, ubiquitin-conjugating enzyme, and isocitrate dehydrogenase in different life-history stages of Bostrychia moritziana. Our results suggest that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 30S ribosomal gene, have the most stable gene expression levels between the different life history stages (male, female, carposporophyte, and tetrasporophyte), while the other genes are not satisfactory as internal controls. These results suggest that the combinations of GAPDH and 30S would be useful as internal controls to assess expression level changes in genes that may control different physiological processes in this organism or that may change in different life history stages. These results may also be useful in other red algal systems.

• Journal of Animal Science and Technology
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• v.62 no.2
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• pp.141-158
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• 2020

Skin is a major thermoregulatory organ in the body controlling homeothermy, a critical function for climate adaptation. We compared genes expressed between tropical- and temperate-adapted cattle to better understand genes involved in climate adaptation and hence thermoregulation. We profiled the skin of representative tropical and temperate cattle using RNA-seq. A total of 214,754,759 reads were generated and assembled into 72,993,478 reads and were mapped to unique regions in the bovine genome. Gene coverage of unique regions of the reference genome showed that of 24,616 genes, only 13,130 genes (53.34%) displayed more than one count per million reads for at least two libraries and were considered suitable for downstream analyses. Our results revealed that of 255 genes expressed differentially, 98 genes were upregulated in tropically-adapted White Fulani (WF; Bos indicus) and 157 genes were down regulated in WF compared to Angus, AG (Bos taurus). Fifteen pathways were identified from the differential gene sets through gene ontology and pathway analyses. These include the significantly enriched melanin metabolic process, proteinaceous extracellular matrix, inflammatory response, defense response, calcium ion binding and response to wounding. Quantitative PCR was used to validate six representative genes which are associated with skin thermoregulation and epithelia dysfunction (mean correlation 0.92; p < 0.001). Our results contribute to identifying genes and understanding molecular mechanisms of skin thermoregulation that may influence strategic genomic selection in cattle to withstand climate adaptation, microbial invasion and mechanical damage.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.51 no.1
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• pp.95-106
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• 2018

To evaluate appropriate reference genes for the normalization of quantitative reverse transcription PCR (RT-qPCR) data with embryonic and larval samples from Russian sturgeon Acipenser gueldenstaedtii, the expression stability of eight candidate housekeeping genes, including beta-actin (ACTB), elongation factor-1A (EF1A), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone 2A (H2A), ribosomal protein L5 (RPL5), ribosomal protein L7 (RPL7), succinate dehydrogenase (SDHA), and ubiquitin-conjugating enzyme E2 (UBE2A), were tested using embryonic samples from 12 developmental stages and larval samples from 11 ontogenic stages. Based on the stability rankings from three statistic software packages, geNorm, NormFinder, and BestKeeper, the expression stability of the embryonic subset was ranked as UBE2A>H2A>SDHA>GAPDH>RPL5>EF1A>ACTB>RPL7. On the other hand, the ranking in the larval subset was determined as UBE2A>GAPDH>SDHA>RPL5>RPL7>H2A>EF1A>AC TB. When the two subsets were combined, the overall ranking was UBE2A>SDHA>H2A>RPL5>GAPDH>EF1A>ACTB>RPL7. Taken together, our data suggest that UBE2A and SDHA are recommended as suitable references for developmental and ontogenic samples of this sturgeon species, whereas traditional housekeepers such as ACTB and GAPDH may not be suitable candidates.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.2
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• pp.224-230
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• 2015

Next generation sequencing technologies provide opportunities to reveal the genetic variants and differentially expressedgenes. The genetic variants are closely relevance to understanding of genes and phenotypic differences related to agronomic characteristics among cultivars. In this study, we conducted RNA-seq using two Korean soybean accessions, including Daewon and Hwangkeum, by using next generation sequencing against Williams 82 genome as reference. A number of variants such assingle nucleotide variants (SNV), multiple nucleotide variants (MNV), insertion/deletion (InDel) and replacement, was 34,411 and 55,544 in Daewon and Hwangkeum, respectively. Among these variants, 9,611 nonsynonymous variants were detected within 4,290 genes in Daewon and 13,225 non-synonymous variants were located on 5,672 genes in Hwangkeum. The distribution of nonsynonymous variants and expression values of genes can serve as invaluable resource for genotyping and study of traits within genes for soybean improvements.

• Journal of Microbiology and Biotechnology
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• v.21 no.12
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• pp.1228-1235
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• 2011

We compared the gene expression among four clinical and five environmental V. vulnificus isolates, using a cDNA microarray containing 131 genes possibly associated with pathogenicity, transport, signal transduction, and gene regulations in the pathogen. cDNAs from total RNAs of these isolates were hybridized into the cDNA microarray using the cDNA of the wild-type strain MO6-24/O as a reference. We focused on selecting differentially expressed (DE) genes between clinical and environmental isolates using a modified t-statistic. We could detect two statistically significant DE genes between virulent isolates and less-virulent isolates with a marginal statistical significance (p-value of 0.008). These were genes putatively encoding pilin and adenlyate cylase. Real time-PCR confirmed that these two selected genes transcribed in significantly higher levels in virulent isolates than in less-virulent isolates. Mutants with lesions in the gene encoding pilin showed significantly higher $LD_{50}$ values than that of wild type.

• Genomics & Informatics
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• v.1 no.2
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• pp.94-100
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• 2003

Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

• Molecules and Cells
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• v.21 no.2
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• pp.269-275
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• 2006

A recent report of the Korean Intellectual Property Office(KIPO) showed that the number of biological sequence-based patents is rapidly increasing in Korea. We present biological features of Korean patented sequences though bioinformatic analysis. The analysis is divided into two steps. The first is an annotation step in which the patented sequences were annotated with the Reference Sequence (RefSeq) database. The second is an association step in which the patented sequences were linked to genes, diseases, pathway, and biological functions. We used Entrez Gene, Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Through the association analysis, we found that nearly 2.6% of human genes were associated with Korean patenting, compared to 20% of human genes in the U.S. patent. The association between the biological functions and the patented sequences indicated that genes whose products act as hormones on defense responses in the extra-cellular environments were the most highly targeted for patenting. The analysis data are available at http://www.patome.net