Search results for: Gene expression data

Authors: Le Thuy Mai, Vu Nguyen Thanh

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β-Glucosidase is an important enzyme for production of ethanol from lignocellulose. With hydrolytic activity on cellooligosaccharides, especially cellobiose, β-glucosidase removes product inhibitory effect on cellulases and forms fermentable sugars. In this study, β-glucosidase encoding gene (BGL1) from traditional starter yeast Saccharomycosis fibuligera BMQ908 was cloned and expressed in Pichia pastoris. BGL1 of S. fibuligera BMQ 908 shared 98% nucleotide homology with the closest GenBank sequence (M22475) but identity in amino-acid sequences of catalytic domains. Recombinant plasmid pPICZαA/BGL1 containing the sequence encoding BGL1 mature protein and α-factor secretion signal was constructed and transformed into methylotrophic yeast P. pastoris by electroporation. The recombinant strain produced single extracellular protein with molecular weight of 120 kDa and cellobiase activity of 60 IU/ml. The optimum pH of the recombinant β-glucosidase was 5.0 and the optimum temperature was 50°C.

Keywords: β-Glucosidase, Pichia pastoris, Saccharomycopsisfibuligera, recombinant enzyme.

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

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In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

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Authors: I. Boroňová, J. Bernasovská, J. Kmec, E. Petrejčíková

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Dilated cardiomyopathy (DCM) is a severe cardiovascular disorder characterized by progressive systolic dysfunction due to cardiac chamber dilatation and inefficient myocardial contractility often leading to chronic heart failure. Recently, a genome-wide association studies (GWASs) on DCM indicate that the ZBTB17 gene rs10927875 single nucleotide polymorphism is associated with DCM. The aim of the study was to identify the distribution of ZBTB17 gene rs10927875 polymorphism in 50 Slovak patients with DCM and 80 healthy control subjects using the Custom Taqman®SNP Genotyping assays. Risk factors detected at baseline in each group included age, sex, body mass index, smoking status, diabetes and blood pressure. The mean age of patients with DCM was 52.9±6.3 years; the mean age of individuals in control group was 50.3±8.9 years. The distribution of investigated genotypes of rs10927875 polymorphism within ZBTB17 gene in the cohort of Slovak patients with DCM was as follows: CC (38.8%), CT (55.1%), TT (6.1%), in controls: CC (43.8%), CT (51.2%), TT (5.0%). The risk allele T was more common among the patients with dilated cardiomyopathy than in normal controls (33.7% versus 30.6%). The differences in genotype or allele frequencies of ZBTB17 gene rs10927875 polymorphism were not statistically significant (p=0.6908; p=0.6098). The results of this study suggest that ZBTB17 gene rs10927875 polymorphism may be a risk factor for susceptibility to DCM in Slovak patients with DCM. Studies of numerous files and additional functional investigations are needed to fully understand the roles of genetic associations.

Keywords: Dilated cardiomyopathy, SNP polymorphism, ZBTB17 gene.

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Authors: N. Hussain, G. Jaffery, A.N. Sabri, S. Hasnain

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The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.

Keywords: American College of Rheumatology criteria, autoimmune disease, Cytotoxic T Lymphocyte Antigen-4, Polymerase Chain Reaction, Systemic Lupus Erythematosus

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Authors: Sitansu Kumar Verma, Soni Yadav, Jitendra Singh, Shraddha, Ajay Kumar

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MicroRNAs (miRNAs), a class of approximately 22 nucleotide long non coding RNAs which play critical role in different biological processes. The mature microRNA is usually 19–27 nucleotides long and is derived from a bigger precursor that folds into a flawed stem-loop structure. Mature micro RNAs are involved in many cellular processes that encompass development, proliferation, stress response, apoptosis, and fat metabolism by gene regulation. Resent finding reveals that certain viruses encode their own miRNA that processed by cellular RNAi machinery. In recent research indicate that cellular microRNA can target the genetic material of invading viruses. Cellular microRNA can be used in the virus life cycle; either to up regulate or down regulate viral gene expression Computational tools use in miRNA target prediction has been changing drastically in recent years. Many of the methods have been made available on the web and can be used by experimental researcher and scientist without expert knowledge of bioinformatics. With the development and ease of use of genomic technologies and computational tools in the field of microRNA biology has superior tremendously over the previous decade. This review attempts to give an overview over the genome wide approaches that have allow for the discovery of new miRNAs and development of new miRNA target prediction tools and databases.

Keywords: MicroRNAs, computational tools, gene regulation, databases, RNAi.

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Authors: M. Maimunah, G. A. Froemming, H. Nawawi, M. I. Nafeeza, O. Effat, M. Y. Rosmadi, M. S. Mohamed Saifulaman

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Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.

Keywords: Atherosclerosis, GeneFishing™ PCR, cathepsin B gene.

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Authors: S. Bag, S. Ramaiah, P. Anitha, K. M. Kumar, P. Lavanya, V. Sivasakhthi, A. Anbarasu

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Gene networks present a graphical view at the level of gene activities and genetic functions and help us to understand complex interactions in a meaningful manner. In the present study, we have analyzed the gene interaction of PPAR-γ (peroxisome proliferator-activated receptor gamma) by search tool for retrieval of interacting genes. We find PPAR-γ is highly networked by genetic interactions with 10 genes: RXRA (retinoid X receptor, alpha), PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), NCOA1 (nuclear receptor coactivator 1), NR0B2 (nuclear receptor subfamily 0, group B, member 2), HDAC3 (histone deacetylase 3), MED1 (mediator complex subunit 1), INS (insulin), NCOR2 (nuclear receptor co-repressor 2), PAX8 (paired box 8), ADIPOQ (adiponectin) and it augurs well for the fact that obesity and several other metabolic disorders are inter related.

Keywords: Gene networks, NCOA1, PPARγ, PPARGC1A, RXRA.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: Minh T. N. Le, Cathleen Teh, Ng Shyh-Chang, Vladimir Korzh, Harvey F. Lodish, Bing Lim

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MicroRNAs are an important class of gene expression regulators that are involved in many biological processes including embryogenesis. miR-125b is a conserved microRNA that is enriched in the nervous system. We have previously reported the function of miR-125b in neuronal differentiation of human cell lines. We also discovered the function of miR-125b in regulating p53 in human and zebrafish. Here we further characterize the brain defects in zebrafish embryos injected with morpholinos against miR-125b. Our data confirm the essential role of miR-125b in brain morphogenesis particularly in maintaining the balance between proliferation, cell death and differentiation. We identified lunatic fringe (lfng) as an additional target of miR-125b in human and zebrafish and suggest that lfng may mediate the function of miR-125b in neurogenesis. Together, this report reveals new insights into the function of miR- 125b during neural development of zebrafish.

Keywords: microRNA, miR-125b, neurogenesis, zebrafish.

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Authors: Khadijat T. Bamigbade, Olufade F. W. Onifade

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The field of automatic facial expression analysis has been an active research area in the last two decades. Its vast applicability in various domains has drawn so much attention into developing techniques and dataset that mirror real life scenarios. Many techniques such as Local Binary Patterns and its variants (CLBP, LBP-TOP) and lately, deep learning techniques, have been used for facial expression recognition. However, the problem of occlusion has not been sufficiently handled, making their results not applicable in real life situations. This paper develops a simple, yet highly efficient method tagged Local Binary Pattern-Histogram of Gradient (LBP-HOG) with occlusion detection in face image, using a multi-class SVM for Action Unit and in turn expression recognition. Our method was evaluated on three publicly available datasets which are JAFFE, CK, SFEW. Experimental results showed that our approach performed considerably well when compared with state-of-the-art algorithms and gave insight to occlusion detection as a key step to handling expression in wild.

Keywords: Automatic facial expression analysis, local binary pattern, LBP-HOG, occlusion detection.

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Authors: Jana Kisková, Dana Gabriková

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Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4- repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance of specific haplotype groups of SNPs and interaction of MAOA with others genes (e. g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: Autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism.

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Authors: H. M. Abdelmoneim, N. A. Babtain, A. S. Barhamain, A. Z. Kufiah, A. S. Malibari, S. F. Munassar, R. S. Rawa

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Introduction: Prostate cancer is one of the most common causes of morbidity and mortality in men in developed countries. Cancer Stem Cells (CSCs) could be responsible for the progression and relapse of cancer. Therefore, CSCs markers could provide a prognostic strategy for human malignancies. Aldehyde dehydrogenase 1A1 (ALDH1A1) activity has been shown to be associated with tumorigenesis and proposed to represent a functional marker for tumor initiating cells in various tumor types including prostate cancer. Material & Methods: We analyzed the immunohistochemical expression of ALDH1A1 in benign prostatic hyperplasia (BPH), prostatic intraepithelial neoplasia (PIN) and prostatic adenocarcinoma and assessed their significant correlations in 50 TURP sections. They were microscopically interpreted and the results were correlated with histopathological types and tumor grade. Results: In different prostatic histopathological lesions we found that ALDH1A1 expression was low in BPH (13.3%) and PIN (6.7%) and then its expression increased with prostatic adenocarcinoma (40%), and this was statistically highly significant (P value = 0.02). However, in different grades of prostatic adenocarcinoma we found that the higher the Gleason grade the higher the expression for ALDH1A1 and this was statistically significant (P value = 0.02). We compared the expression of ALDH1A1 in PIN and prostatic adenocarcinoma. ALDH1A1 expression was decreased in PIN and highly expressed in prostatic adenocarcinoma and this was statistically significant (P value = 0.04). Conclusion: Increasing ALDH1A1 expression is correlated with aggressive behavior of the tumor. Immunohistochemical expression of ALDH1A1 might provide a potential approach to study tumorigenesis and progression of primary prostate carcinoma.

Keywords: ALDH1A1, BPH, PIN, prostatic adenocarcinoma.

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Authors: Rohayu Izanwati M. R., Muhamad Ridhwan M. R., Abbe Maleyki M. J., Ahmad Zubaidi A. L., Zahri M. K.

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PPARs function as regulators of lipid and lipoprotein metabolism. The aim of the study was to compare the lipid profile between two phases of fasting and to examine the frequency and relationship of peroxisome proliferator-activated receptor, PPARα gene polymorphisms to lipid profile in fasting respondents. We conducted a case-control study protocol, which included 21 healthy volunteers without gender discrimination at the age of 18 years old. 3 ml of blood sample was drawn before the fasting phase and during the fasting phase (in Ramadhan month). 1ml of serum for the lipid profile was analyzed by using the automated chemistry analyser (Olympus, AU 400) and the data were analysed using the Paired T-Test (SPSS ver.20). DNA was extracted and PCR was conducted utilising 6 sets of primer. Primers were designed within 6 exons of interest in PPARα gene. Genetic and metabolic characteristics of fasting respondents and controls were estimated and compared. Fasting respondents were significantly have lowered the LDL levels (p=0.03). There were no polymorphisms detected except in exon 1 with 5% of this population study respectively. The polymorphisms in exon 1 of the PPARα gene were found in low frequency. Regarding the 1375G/T and 1386G/T polymorphisms in the exon 1 of the PPARα gene, the T-allele in fasting phase had no association with the decreased LDL levels (Fisher Exact Test). However this association is more promising when the sample size is larger in order to elucidate the precise impact of the polymorphisms on lipid profile in the population. In conclusion, the PPARα gene polymorphisms do not appear to affect the LDL of fasting respondents.

Keywords: Fasting, LDL, Peroxisome proliferator activated receptor alpha (PPAR-α), Polymorphisms.

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Authors: Yasser M. Saad, Heba El-Sebaie Abd El-Sadek

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Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.

Keywords: Crustacean, Genetics, cox1, phylogeny.

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Authors: Fawzi Irshaid, Adnan Jaran, Fatiha Dilmi, Khaled Tarawneh, Raji Hadeth, Ahad Al-Khatib

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The aim of this study was to estimate the frequency of EBV infection in Hodgkin's lymphoma (HL) and non-Hodgkin's lymphoma (NHL) occurring in Jordanian patients. A total of 55 patients with lymphoma were examined in this study. Of 55 patients, 30 and 25 were diagnosed as HL and NHL, respectively. The four HL subtypes were observed with the majority of the cases exhibited the mixed cellularity (MC) subtype followed by the nodular sclerosis (NS). The high grade was found to be the commonest subtype of NHL in our sample, followed by the low grade. The presence of EBV virus was detected by immunostating for expression of latent membrane protein-1 (LMP-1). The frequency of LMP-1 expression occurred more frequent in patients with HL (60.0%) than in patients with NHL (32.0%). The frequency of LMP-1 expression was also higher in patients with MC subtype (61.11%) than those patients with NS (28.57%). No age or gender difference in occurrence of EBV infection was observed among patient with HL. By contrast, the prevalence of EBV infection in NHL patients aged below 50 was lower (16.66%) than in NHL patients aged 50 or above (46.15%). In addition, EBV infection was more frequent in females with NHL (38.46%) than in male with NHL (25%). In NHL cases, the frequency of EBV infection in intermediate grade (60.0%) was high when compared with frequency of low (25%) or high grades (25%). In conclusion, analysis of LMP-1 expression indicates an important role for this viral oncogene in the pathogenesis of EBV-associated malignant lymphomas. These data also support the previous findings that people with EBV may develop lymphoma and that efforts to maintain low lymphoma should be considered for people with EBV infection.

Keywords: Hodgkin lymphoma, Epstein Barr virus, hematoxylin, infection, LMP-1 expression.

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Authors: S. Manzoor, A. Nadeem, M. Javed, ME. Babar

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A major goal in animal genetics is to understand the role of common genetic variants in diseases susceptibility and production traits. Sahiwal cattle can be considered as a global animal genetic resource due to its relatively high milk producing ability, resistance against tropical diseases and heat tolerant. CYP11B1 gene provides instructions for making a mitochondrial enzyme called steroid 11-beta-hydroxylase. It catalyzes the 11deoxy-cortisol to cortisol and 11deoxycorticosterone to corticosterone in cattle. The bovine CYP11B1 gene is positioned on BTA14q12 comprises of eight introns and nine exons and protein is associated with mitochondrial epithelium. The present study was aimed to identify the single-nucleotide polymorphisms in CYP11B1 gene in Sahiwal cattle breed of Pakistan. Four polymorphic sites were identified in exon one of CYP11B1 gene through sequencing approach. Significant finding was the incidence of the C→T polymorphism in 5'-UTR, causing amino acid substitution from alanine to valine (A30V) in Sahiwal cattle breed. That Ala/Val polymorphism may serve as a powerful genetic tool for the development of DNA markers that can be used for the particular traits for different local cattle breeds.

Keywords: CYP11B1, single nucleotide polymorphism, sahiwal cattle, Pakistan.

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Authors: R. K. Agrawal, Rajni Bala

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Developing an accurate classifier for high dimensional microarray datasets is a challenging task due to availability of small sample size. Therefore, it is important to determine a set of relevant genes that classify the data well. Traditionally, gene selection method often selects the top ranked genes according to their discriminatory power. Often these genes are correlated with each other resulting in redundancy. In this paper, we have proposed a hybrid method using feature ranking and wrapper method (Genetic Algorithm with multiclass SVM) to identify a set of relevant genes that classify the data more accurately. A new fitness function for genetic algorithm is defined that focuses on selecting the smallest set of genes that provides maximum accuracy. Experiments have been carried on four well-known datasets1. The proposed method provides better results in comparison to the results found in the literature in terms of both classification accuracy and number of genes selected.

Keywords: Gene selection, genetic algorithm, microarray datasets, multi-class SVM.

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, molecular characterization, cattle, Bangladesh.

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires were returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age ranges from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge; however, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non- significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: Gene Profiling, Knowledge, Malaysia, Physician.

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Authors: P. Visutsak

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The study of the interaction between humans and computers has been emerging during the last few years. This interaction will be more powerful if computers are able to perceive and respond to human nonverbal communication such as emotions. In this study, we present the image-based approach to emotion classification through lower facial expression. We employ a set of feature points in the lower face image according to the particular face model used and consider their motion across each emotive expression of images. The vector of displacements of all feature points input to the Adaptive Support Vector Machines (A-SVMs) classifier that classify it into seven basic emotions scheme, namely neutral, angry, disgust, fear, happy, sad and surprise. The system was tested on the Japanese Female Facial Expression (JAFFE) dataset of frontal view facial expressions [7]. Our experiments on emotion classification through lower facial expressions demonstrate the robustness of Adaptive SVM classifier and verify the high efficiency of our approach.

Keywords: emotion classification, facial expression, adaptive support vector machines, facial expression classifier.

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Authors: Mehrdad Hashemi, Mitra Behrooz Aghdam, Reza Mahdian, Ahmad Reza Kamyab

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Cytogenetic analysis still remains the gold standard method for prenatal diagnosis of trisomy 21 (Down syndrome, DS). Nevertheless, the conventional cytogenetic analysis needs live cultured cells and is too time-consuming for clinical application. In contrast, molecular methods such as FISH, QF-PCR, MLPA and quantitative Real-time PCR are rapid assays with results available in 24h. In the present study, we have successfully used a novel MGB TaqMan probe-based real time PCR assay for rapid diagnosis of trisomy 21 status in Down syndrome samples. We have also compared the results of this molecular method with corresponding results obtained by the cytogenetic analysis. Blood samples obtained from DS patients (n=25) and normal controls (n=20) were tested by quantitative Real-time PCR in parallel to standard G-banding analysis. Genomic DNA was extracted from peripheral blood lymphocytes. A high precision TaqMan probe quantitative Real-time PCR assay was developed to determine the gene dosage of DSCAM (target gene on 21q22.2) relative to PMP22 (reference gene on 17p11.2). The DSCAM/PMP22 ratio was calculated according to the formula; ratio=2 -ΔΔCT. The quantitative Real-time PCR was able to distinguish between trisomy 21 samples and normal controls with the gene ratios of 1.49±0.13 and 1.03±0.04 respectively (p value <0.001). These results represent the presence of 3 copies of target gene in DS samples Vs 2 copies in normal controls. The results of quantitative Real-time PCR were in complete agreement with results of cytogenetic analysis. This study confirms previous reports regarding successful implementation of quantitative Real-time PCR for detection of trisomy 21. However, the assay has been improved by using MGB probes and more accurate data analysis. This assay, in particular, when performed in combination with another molecular assay such as QF-PCR or MLPA, can be used as a reliable technique for rapid prenatal diagnosis of trisomy 21.

Keywords: Trisomy 21, Real-time PCR, MGB-TaqMan Probes, Gene Dosage.

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Authors: Praseeda Lekshmi.V, Dr.M.Sasikumar

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Facial expression analysis is rapidly becoming an area of intense interest in computer science and human-computer interaction design communities. The most expressive way humans display emotions is through facial expressions. In this paper we present a method to analyze facial expression from images by applying Gabor wavelet transform (GWT) and Discrete Cosine Transform (DCT) on face images. Radial Basis Function (RBF) Network is used to classify the facial expressions. As a second stage, the images are preprocessed to enhance the edge details and non uniform down sampling is done to reduce the computational complexity and processing time. Our method reliably works even with faces, which carry heavy expressions.

Keywords: Face Expression, Radial Basis Function, GaborWavelet Transform, Human Computer Interaction.

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Authors: A. Molee, N. Duanghaklang, P. Mernkrathoke

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The objective was to determine the single gene and interaction effect of composite genotype of beta-kappa casein and DGAT1 gene on milk yield (MY) and milk composition, content of milk fat (%FAT), milk protein (%PRO), solid not fat (%SNF), and total solid (%TS) in crossbred Holstein cows. Two hundred and thirty- one cows were genotyped with PCR-RFLP for DGAT1 and composite genotype data of beta-kappa casein from previous work were used. Two model, (1), and (2), was used to estimate single gene effect, and interaction effect on the traits, respectively. The significance of interaction effects on all traits were detected. Most traits have consistent pattern of significant when model (1), and (2) were compared, except the effect of composite genotype of betakappa casein on %FAT, and the effect of DGAT1 on MY, which the significant difference was detected in only model (1).The results suggested that when the optimum of all traits was necessary, interaction effect should be concerned.

Keywords: composite genotype of beta-kappa casein, DGAT1gene, Milk composition, Milk yield

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Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

Abstract:

Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

Abstract:

Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: V. T. S. Dao, T. G. Etoh, C. Vo Le, H. D. Nguyen, K. Takehara, T. Akino, K. Nishi

Abstract:

We present an explicit expression to estimate driving voltage attenuation through RC networks representation of an ultrahigh- speed image sensor. Elmore delay metric for a fundamental RC chain is employed as the first-order approximation. By application of dimensional analysis to SPICE simulation data, we found a simple expression that significantly improves the accuracy of the approximation. Estimation error of the resultant expression for uniform RC networks is less than 2%. Similarly, another simple closed-form model to estimate 50 % delay through fundamental RC networks is also derived with sufficient accuracy. The framework of this analysis can be extended to address delay or attenuation issues of other VLSI structures.

Keywords: Dimensional Analysis, Elmore model, RC network, Signal Attenuation, Ultra-High-Speed Image Sensor.

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Authors: Shyue-Ran Li, Kuohsiang Chen

Abstract:

The study explored varied types of human smiles and extracted most of the key factors affecting the smiles. These key factors then were converted into a set of control points which could serve to satisfy the needs for creation of facial expression for 3D animators and be further applied to the face simulation for robots in the future. First, hundreds of human smile pictures were collected and analyzed to identify the key factors for face expression. Then, the factors were converted into a set of control points and sizing parameters calculated proportionally. Finally, two different faces were constructed for validating the parameters via the process of simulating smiles of the same type as the original one.

Keywords: 3D animation, facial expression, numerical, robot, smile parameter.

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

Abstract:

Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: Fuad M. Alkoot

Abstract:

DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: Biometrics, identity verification, genetic data, k-nearest neighbor.

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