• Asian Pacific Journal of Cancer Prevention
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• 제17권sup3호
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• pp.305-309
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• 2016

PTEN protein is an important tumour suppressor factor detectable by immunohistochemistry. The goal of the present study was to investigate the prognostic role of PTEN gene expression focusing on length of survival in breast cancer patients. This descriptive-analytical study was conducted on 100 breast cancer cases referred to Sabzevar hospitals in the north east of Iran between 2010 and 2011, followed up to 2015. The PTEN gene expression of tumour tissue samples was determined using specific monoclonal antibodies. The data were analyzed using Chi-square test and Fisher's exact test. Patient length of survival was analyzed after 4 years of follow-up using the Cox regression model. The PTEN gene was expressed in 70 of 100 samples, while being found at a high level in all noncancerous samples. There was an inverse significant relationship between expression of PTEN and tumour stage and grade (p<0.001). In addition, expression of PTEN in invasive ductal tumours was less than in non-invasive tumours. There was also an inverse significant relationship between the likelihood of death and PTEN gene expression (p<0.01). These findings indicate that lack of PTEN gene expression can be sign for a worse prognosis and poor survival in breast cancer.

• Molecules and Cells
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• 제21권3호
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• pp.376-380
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• 2006

Gene expression is regulated in large part at the level of transcription under the control of sequence-specific transcriptional regulatory proteins. Therefore, the ability to affect gene expression at will using sequencespecific artificial transcription factors would provide researchers with a powerful tool for biotechnology research and drug discovery. Previously, we isolated 56 novel sequence-specific DNA-binding domains from the human genome by in vivo selection. We hypothesized that these domains might be more useful for regulating gene expression in higher eukaryotic cells than those selected in vitro using phage display. However, an unpredictable factor, termed the "context effect", is associated with the construction of novel zinc finger transcription factors--- DNA-binding proteins that bind specifically to 9-base pair target sequences. In this study, we directly selected active artificial zinc finger proteins from a zinc finger protein library. Direct in vivo selection of constituents of a zinc finger protein library may be an efficient method for isolating multi-finger DNA binding proteins while avoiding the context effect.

• Fisheries and Aquatic Sciences
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• 제13권1호
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• pp.56-62
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• 2010

To determine whether long double-stranded RNA (dsRNA) induces RNA interference and type I interferon (IFN) responses in fish, long dsRNAs encoding enhanced green fluorescent protein (EGFP), GFPuv, and polyinosinic-polycytidylic acid sequences were co-injected with an EGFP expressing plasmid, into rock bream (Oplegnathus fasciatus). We investigated the EGFP mRNA and protein levels, and the transcriptional responses of dsRNA-dependent protein kinase and Mx1 genes. Long dsRNAs were strong inducers of a type I IFN response in rock bream, resulting in nonspecific suppression of exogenous gene expression. Furthermore, sequence-specific knockdown of exogenous gene expression at the mRNA level was detected at an early phase (24 h). These results suggested that long dsRNA may inhibit exogenous gene expression through an early mRNA interference response and a later type I IFN response in fish.

• Asian-Australasian Journal of Animal Sciences
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• 제18권11호
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• pp.1552-1556
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• 2005

The UCPs are members of the mitochondrial inner membrane transporter family, present in the mitochondrial inner membrane. Their main function is increasing the energy expenditure via diminishing the resulting production of ATP from mitochondrial oxidative phosphorylation instead of yielding dissipative heat. They are associated with the metabolism of fat and regulation of energy expenditure. The UCP gene can be viewed as the candidate gene for chicken fatness. In the present study, RT-PCR and Northern Blot methods were developed to investigate the expression of the UCP gene in ten tissues including heart, liver, spleen, lung, kidney, gizzard, intestine, brain, breast muscle and abdominal fat of chicken. The results of both RT-PCR and Northern Blot methods showed that the UCP gene expressed specific in breast muscle. The expression levels of UCP gene in breast muscles from egg-type and meat-type chickens of hatching, 2, 4, 6 and 8 wk of age were detected by RT-PCR assay and results showed that the expression levels of UCP gene were related to breeds. Expression level of UCP gene in layers was higher than that in broilers at various weeks of age except at 6 wk. The UCP gene's expression was higher at 6 wk and had no significant difference among other weeks of age in broilers; in layers the expression level of UCP gene had no significant difference among weeks of age. The experiment results also showed that insulin could increase the expression level of UCP gene by 40% compared with control group.

• Environmental Analysis Health and Toxicology
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• 제25권1호
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• pp.1-10
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• 2010

Monitoring toxicity levels in specific biological compartments is necessary to evaluate the ecotoxicological risk associated with soil environmental pollution. Gene expression, as potential biomarker, is increasingly used as rapid early warning systems in environmental monitoring and ecological risk assessment procedures. Various representative species are currently used for the purpose of assessing soil toxicity, however, investigations on toxicological assessments using endpoint based on gene-level have been limited. In this review, we will present the current trends in organisms and endpoints used in soil toxicity study and report gene expression related to toxicity using soil organism, and C. elegans as promising organisms for this approach.

• Asian Pacific Journal of Cancer Prevention
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• 제16권10호
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• pp.4251-4256
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• 2015

Background: Exposure to cigarette may affect human health and increase risk of a wide range of diseases including pulmonary diseases, such as chronic obstructive pulmonary disease (COPD), asthma, lung fibrosis and lung cancer. However, the molecular mechanisms of pathogenesis induced by cigarettes still remain obscure even with extensive studies. With systemic view, we attempted to identify the specific gene modules that might relate to injury caused by cigarette smoke and identify hub genes for potential therapeutic targets or biomarkers from specific gene modules. Materials and Methods: The dataset GSE18344 was downloaded from the Gene Expression Omnibus (GEO) and divided into mouse cigarette smoke exposure and control groups. Subsequently, weighted gene co-expression network analysis (WGCNA) was used to construct a gene co-expression network for each group and detected specific gene modules of cigarette smoke exposure by comparison. Results: A total of ten specific gene modules were identified only in the cigarette smoke exposure group but not in the control group. Seven hub genes were identified as well, including Fip1l1, Anp32a, Acsl4, Evl, Sdc1, Arap3 and Cd52. Conclusions: Specific gene modules may provide better understanding of molecular mechanisms, and hub genes are potential candidates of therapeutic targets that may possible improve development of novel treatment approaches.

• Communications for Statistical Applications and Methods
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• 제22권2호
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• pp.181-199
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• 2015

In a short history, RNA-seq data have established a revolutionary tool to directly decode various scenarios occurring on whole genome-wide expression profiles in regards with differential expression at gene, transcript, isoform, and exon specific quantification, genetic and genomic mutations, and etc. RNA-seq technique has been rapidly replacing arrays with seq-based platform experimental settings by revealing a couple of advantages such as identification of alternative splicing and allelic specific expression. The remarkable characteristics of high-throughput large-scale expression profile in RNA-seq are lied on expression levels of read counts, structure of correlated samples and genes, larger number of genes compared to sample size, different sampling rates, inevitable systematic RNA-seq biases, and etc. In this study, we will comprehensively review how robust Bayesian and non-parametric methods have a better performance than classical statistical approaches by explicitly incorporating such intrinsic RNA-seq specific features with flexible and more appropriate assumptions and distributions in practice.

• 한국독성학회:학술대회논문집
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• 한국독성학회 2000년도 국제심포지움 및 추계학술대회
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• pp.31-41
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• 2000

The major issue in the post genome sequencing era is determination of gene expression patterns in variety of biological systems. A microarray system is a powerful technology for analyzing the expression profile of thousands of genes at one experiment. In this study, we constructed cDNA microarray which carries 2,304 cDNAS derived from oligo-capped mouse cDNA library. Using this hand-made microarray we determined gene expression in various biological systems. To determine tissue specific genes, we compared Nine genes were highly-expressed in adult mouse brain compared to kidney, liver, and skeletal muscle. Tissue distribution analysis using DNA microarray extracted 9 genes that were predominantly expressed in the brain. A database search showed that five of the 9 genes, MBP, SC1, HiAT3, S100 protein-beta, and SNAP25, were previously known to be expressed at high level in the brain and in the nervous system. One gene was highly sequence similar to rat S-Rex-s/human NSP-C, suggesting that the gene is a mouse homologue. The remaining three genes did not match to known genes in the GenBank/EMBL database, indicating that these are novel genes highly-expressed in the brain. Our DNA microarray was also used to detect differentiation specific genes, hormone dependent genes, and transcription-factor-induced genes. We conclude that DNA microarray is an excellent tool for identifying differentially expressed genes.

• 식물조직배양학회지
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• 제25권2호
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• pp.89-93
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• 1998

Tomato phenylalanine ammonia-lyase 5 (tPAL5) was identified that alternate initiation sites were utilized differentially in response to environmental stimuli (Lee et al, 1992b). In this study, we tried to look into tissue -or cell- specific expression pattern of tPAL5 gene by fusing with ${\beta}-glucuronidase$ (GUS) gene in transgenic tobacco plants. In transgenic plants, root and stem extracts contained 8~12 fold higher levels of GUS activity than petiole or leaf tissue while the highest levels of induction was observed from leaf tissue by mechanical wounding (5~11 fold). In trans-sections of stems and petioles, GUS activity was restricted to phloem cells(outer region) of developing vascular bundle and mainly at apical tip region in the root tissues. The levels of GUS activity was drastically reduced (10~12 fold reduction) when the 5'-upstream region of tPAL5 gene (-1151bp from ATG codon) was deleted up to -665. The levels of GUS expression, however, raised up by 6~8 fold when deleted up to -455. Therefore, we conclude that there are positive cis-elements at the region -1151 to -1008 and at -455 to -195 while the negative cis-element is at -1008 to -455.

• International Journal of Industrial Entomology and Biomaterials
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• 제2권1호
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• pp.79-81
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• 2001

A study was conducted to establish the degree of genetic divergence between different hybrid forms and rearing conditions through estimation of the minimum number of genes (allelic pairs) differentiating parents in terms of specific quantitative traits. It was established that the minimum gene numbers differentiating parental lines in the inheritance of cocoon was 1, of cocoon shell weight- between 1 and 2, and of silk filament length- between 2 and 3. The variability in the specific genetic parameter could be explained by the reliability of the statistical-and-genetic method used and the expression of genes affecting the formation of each of the characters tested. Gene expression, in its turns is conditioned both by the gene interaction within the genotypes and the different genotype response to environmental change. To go deep in the problem, experiments should be conducted under strictly controlled conditions, reducing the mathematical-and-genetic analysis to a physiological levels and hence to analyse the genetic nature of the specific quantitative character formation and its genetic control.