Search results for: missense mutations

Authors: I. Nassiri, B. Goliaei, M. Tavassoli

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The ability to distinguish missense nucleotide substitutions that contribute to harmful effect from those that do not is a difficult problem usually accomplished through functional in vivo analyses. In this study, instead current biochemical methods, the effects of missense mutations upon protein structure and function were assayed by means of computational methods and information from the databases. For this order, the effects of new missense mutations in exon 5 of PTEN gene upon protein structure and function were examined. The gene coding for PTEN was identified and localized on chromosome region 10q23.3 as the tumor suppressor gene. The utilization of these methods were shown that c.319G>A and c.341T>G missense mutations that were recognized in patients with breast cancer and Cowden disease, could be pathogenic. This method could be use for analysis of missense mutation in others genes.

Keywords: Bioinformatics, missense mutations, PTEN tumorsuppressor gene.

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Authors: S. Mozuriunaite

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Contemporary metropolitan areas and large cities are dynamic, rapidly growing and continuously changing. Thus, urban transformations and mutations are not a new phenomenon, but rather a continuous process. Basic factors of urban transformation are related to development of technologies, globalisation, lifestyle, etc., which in combination with local factors have generated an extremely great variety of urban development conditions. This article discusses the main urbanisation processes in Lithuania during last 50-year period and social factors affecting urban functional mutations.

Keywords: Dispersion, functional mutations, urbanisation, urban mutations, social factors.

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Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le, Chi V. Phan

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Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.

Keywords: ATP7B gene, mutation detection, presymptomatic diagnosis, Vietnamese Wilson’s disease.

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Authors: Ismail, N., Sarijan, S

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The phylogenetic analysis using the most conservative portions of 18S rRNA gene revealed the phylogenetic relationship among the two populations where DNA divergence showed that the nucleotides diversity value were -0.00838 for the Tanjung Dawai, Kedah and -0.00708 for the Cherating, Pahang populations respectively. The net nucleotide divergence among populations (Da) was -0.0073 indicating a low polymorphism among the populations studied. Total number of mutations in the Tanjung Dawai, Kedah samples was higher than Cherating, Pahang samples, which are 73 and 59 respectively while shared mutations across the populations were 8, and reveal the evolutionary in the genome of Malaysian T. gigas. The tree topology of both populations inferred using Neigbour-joining method by comparing 1791 bp of partial 18S rRNA sequence revealed that T. gigas haplotypes were clustered into seven clades, suggesting that they are genetically diverse among populations which derived from a common ancestor.

Keywords: Horseshoe crabs, Tachypleus gigas, 18S rRNA genesequences, phylogenetic analysis

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: Z. M. Biyasheva, M. Zh. Tleubergenova, Y. A. Zaripova, A. L. Shakirov, V. V. Dyachkov

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In recent years, interest in ecogenetic and biomedical problems related to the effects on the population of radon and its daughter decay products has increased significantly. Of particular interest is the assessment of the consequence of irradiation at hazardous radon areas, which includes the Almaty region due to the large number of tectonic faults that enhance radon emanation. In connection with the foregoing, the purpose of this work was to study the genetic effects of exposure to supernormal radon doses on the alpha-radiation model. Irradiation does not affect the growth of the cell, but rather its ability to differentiate. In addition, irradiation can lead to somatic mutations, morphoses and modifications. These damages most likely occur from changes in the composition of the substances of the cell. Such changes are epigenetic since they affect the regulatory processes of ontogenesis. Variability in the expression of regulatory genes refers to conditional mutations that modify the formation of signs of intraspecific similarity. Characteristic features of these conditional mutations are the dominant type of their manifestation, phenotypic asymmetry and their instability in the generations. Currently, the terms “morphosis” and “modification” are used to describe epigenetic variability, which are maintained in Drosophila melanogaster cultures using linkaged X- chromosomes, and the mutant X-chromosome is transmitted along the paternal line. In this paper, we investigated the epigenetic effects of alpha particles, whose source in nature is mainly radon and its daughter decay products. In the experiment, an isotope of plutonium-238 (Pu²³⁸), generating radiation with an energy of about 5500 eV, was used as a source of alpha particles. In an experiment in the first generation (F₁), deformities or morphoses were found, which can be called "radiation syndromes" or mutations, the manifestation of which is similar to the pleiotropic action of genes. The proportion of morphoses in the experiment was 1.8%, and in control 0.4%. In this experiment, the morphoses in the flies of the first and second generation looked like black spots, or melanomas on different parts of the imago body; "generalized" melanomas; curled, curved wings; shortened wing; bubble on one wing; absence of one wing, deformation of thorax, interruption and violation of tergite patterns, disruption of distribution of ocular facets and bristles; absence of pigmentation of the second and third legs. Statistical analysis by the Chi-square method showed the reliability of the difference in experiment and control at P ≤ 0.01. On the basis of this, it can be considered that alpha particles, which in the environment are mainly generated by radon and its isotopes, have a mutagenic effect that manifests itself, mainly in the formation of morphoses or deformities.

Keywords: Alpha-radiation, genotoxicity, morphoses, radioecology, radon.

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Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

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We study the biological effects induced by ionizing radiation in view of therapeutic exposure and the idea of space flights beyond Earth's magnetosphere. In particular, we examine the differences between base pair substitution induction by ionizing radiation in model haploid and diploid yeast Saccharomyces cerevisiae cells. Such mutations are difficult to study in higher eukaryotic systems. In our research, we have used a collection of six isogenic trp5-strains and 14 isogenic haploid and diploid cyc1-strains that are specific markers of all possible base-pair substitutions. These strains differ from each other only in single base substitutions within codon-50 of the trp5 gene or codon-22 of the cyc1 gene. Different mutation spectra for two different haploid genetic trp5- and cyc1-assays and different mutation spectra for the same genetic cyc1-system in cells with different ploidy — haploid and diploid — have been obtained. It was linear function for dose-dependence in haploid and exponential in diploid cells. We suggest that the differences between haploid yeast strains reflect the dependence on the sequence context, while the differences between haploid and diploid strains reflect the different molecular mechanisms of mutations.

Keywords: Base pair substitutions, γ-rays, haploid and diploid cells, yeast Saccharomyces cerevisiae.

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Authors: Zachariah Sinkala

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A systems approach model for prostate cancer in prostate duct, as a sub-system of the organism is developed. It is accomplished in two steps. First this research work starts with a nonlinear system of coupled Fokker-Plank equations which models continuous process of the system like motion of cells. Then extended to PDEs that include discontinuous processes like cell mutations, proliferation and deaths. The discontinuous processes is modeled by using intensity poisson processes. The model incorporates the features of the prostate duct. The system of PDEs spatial coordinate is along the proximal distal axis. Its parameters depend on features of the prostate duct. The movement of cells is biased towards distal region and mutations of prostate cancer cells is localized in the proximal region. Numerical solutions of the full system of equations are provided, and are exhibit traveling wave fronts phenomena. This motivates the use of the standard transformation to derive a canonically related system of ODEs for traveling wave solutions. The results obtained show persistence of prostate cancer by showing that the non-negative cone for the traveling wave system is time invariant. The traveling waves have a unique global attractor is proved also. Biologically, the global attractor verifies that evolution of prostate cancer stem cells exhibit the avascular tumor growth. These numerical solutions show that altering prostate stem cell movement or mutation of prostate cancer cells lead to avascular tumor. Conclusion with comments on clinical implications of the model is discussed.

Keywords: Fokker-Plank equations, global attractor, stem cell.

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Authors: Chrysline Margus N. Piñol, Jenifer DP. De Maligaya, Ahl G. Balitaon

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Stable nonzero populations without random deaths caused by the Verhulst factor (Verhulst-free) are a rarity. Majority either grow without bounds or die of excessive harmful mutations. To delay the accumulation of bad genes or diseases, a new environmental parameter Γ is introduced in the simulation. Current results demonstrate that stability may be achieved by setting Γ = 0.1. These steady states approach a maximum size that scales inversely with reproduction age.

Keywords: Aging, mutation accumulation, population dynamics.

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Authors: Omar M. Sallabi, Younis El-Haddad

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The Genetic Algorithm (GA) is one of the most important methods used to solve many combinatorial optimization problems. Therefore, many researchers have tried to improve the GA by using different methods and operations in order to find the optimal solution within reasonable time. This paper proposes an improved GA (IGA), where the new crossover operation, population reformulates operation, multi mutation operation, partial local optimal mutation operation, and rearrangement operation are used to solve the Traveling Salesman Problem. The proposed IGA was then compared with three GAs, which use different crossover operations and mutations. The results of this comparison show that the IGA can achieve better results for the solutions in a faster time.

Keywords: AI, Genetic algorithms, TSP.

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Authors: Dimitri Perrin, Heather J. Ruskin, Martin Crane

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This study focuses on examining why the range of experience with respect to HIV infection is so diverse, especially in regard to the latency period. An agent-based approach in modelling the infection is used to extract high-level behaviour which cannot be obtained analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties, contributing to the individual disease experience, and is included in a network which mimics the chain of lymph nodes. The model also accounts for stochastic events such as viral mutations. The size and complexity of the model require major computational effort and parallelisation methods are used.

Keywords: HIV, Immune modelling, Agent-based system, individual response.

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Authors: Correa Arias, César

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Today, Higher Education in a global scope is subordinated to the greater institutional controls through the policies of the Quality of Education. These include processes of over evaluation of all the academic activities: students- and professors- performance, educational logistics, managerial standards for the administration of institutions of higher education, as well as the establishment of the imaginaries of excellence and prestige as the foundations on which universities of the XXI century will focus their present and future goals and interests. But at the same time higher education systems worldwide are facing the most profound crisis of sense and meaning and attending enormous mutations in their identity. Based in a qualitative research approach, this paper shows the social configurations that the scholars at the Universities in Mexico build around the discourse of the Quality of Education, and how these policies put in risk the social recognition of these individuals.

Keywords: Higher education, quality of education, social recognition, social configurations.

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Authors: M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid

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Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Keywords: Simulated annealing, genetic algorithm, sequence alignment, multiple sequence alignment.

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Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

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Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: Biological molecular networks, essential genes, graph theory, network subgraphs.

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Authors: Tom Snir, Eitan Rubin

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Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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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: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: Gypsies, HK1, HSMN-Russe, rare disease.

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Authors: K .Belhadi, H. Bousselsela, M. Yahia, A. Zidani, S. Benbia

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Sickle cell anemia is a recessive genetic disease caused by the presence in the red blood cell, of abnormal hemoglobin called hemoglobin S. It results from the replacement in the beta chain of the acid glutamic acid by valin at position 6. Topics may be homozygous (SS) or heterozygous (AS) most often asymptomatic. Other mutations result in compound heterozygous: - Synthesis of hemoglobin C mutation in the sixth leucin codon (heterozygous SC); - ß-thalassemia (heterozygous S-ß thalassemia). SS homozygous, heterozygous SC and S- ß -thalassemia are grouped under the major sickle cell syndromes. To make a laboratory diagnosis of hemoglobinopathies in a portion of the population in region of Batna, our study was conducted on 115 patients with suspected sickle cell anemia, all cases have benefited from hematological tests as blood count (count RBC, calculated erythrocyte indices, MCV and MCHC, measuring the hemoglobin concentration) and a biochemical test in this case electrophoresis CAPILLARYS HEMOGLOBIN (E). The results showed: 27 cases of sickle cell anemia were found on 115 suspected cases, 73,03% homozygous sickle cell disease and 59,25% sickle cell trait. Finally, the double heterozygous S/C, represent the incidence rate of 3, 70%.

Keywords: Hemoglobin, sickle cell syndromes, laboratory diagnosis

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

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Gastric Cancer (GC) has high morbidity and fatality rate in various countries. It is still one of the most frequent and deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes are highly expressed in the normal stomach epithelium and play important roles in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age. They were investigated with gene expression analysis and mutation screening by monitoring RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of gastrokines inactivation. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age, or cancer type of patients. Reduced of gastrokine genes seem to occur at the initial steps of gastric cancer development.

Keywords: Diagnostic biomarker, gastric cancer, nucleotide sequencing, semi-quantitative RT-PCR.

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Authors: Permphan Dharmasaroja

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Mutations of the telomeric copy of the survival motor neuron 1 (SMN1) gene cause spinal muscular atrophy. A deletion of the Eef1a2 gene leads to lower motor neuron degeneration in wasted mice. Indirect evidences have been shown that the eEF1A protein family may interact with SMN, and our previous study showed that abnormalities of neuromuscular junctions in wasted mice were similar to those of Smn mutant mice. To determine potential colocalization between SMN and tissue-specific translation elongation factor 1A2 (eEF1A2), an immunochemical analysis of HeLa cells transfected with the plasmid pcDNA3.1(+)C-hEEF1A2- myc and a new quantitative test of colocalization by intensity correlation analysis (ICA) was used to explore the association of SMN and eEF1A2. Here the results showed that eEF1A2 redistributed from the cytoplasm to the nucleus in response to serum and epidermal growth factor. In the cytoplasm, compelling evidence showed that staining for myc-tagged eEF1A2 varied in synchrony with that for SMN, consistent with the formation of a SMN-eEF1A2 complex in the cytoplasm of HeLa cells. These findings suggest that eEF1A2 may colocalize with SMN in the cytoplasm and may be a component of the SMN complex. However, the limitation of the ICA method is an inability to resolve colocalization in components of small organelles such as the nucleus.

Keywords: Intensity correlation analysis, intensity correlation quotient.

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene.

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.

Keywords: Seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation.

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Authors: A. Gruzdz, A. Ihnatowicz, J. Siddiqi, B. Akhgar

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MATCH project [1] entitle the development of an automatic diagnosis system that aims to support treatment of colon cancer diseases by discovering mutations that occurs to tumour suppressor genes (TSGs) and contributes to the development of cancerous tumours. The constitution of the system is based on a) colon cancer clinical data and b) biological information that will be derived by data mining techniques from genomic and proteomic sources The core mining module will consist of the popular, well tested hybrid feature extraction methods, and new combined algorithms, designed especially for the project. Elements of rough sets, evolutionary computing, cluster analysis, self-organization maps and association rules will be used to discover the annotations between genes, and their influence on tumours [2]-[11]. The methods used to process the data have to address their high complexity, potential inconsistency and problems of dealing with the missing values. They must integrate all the useful information necessary to solve the expert's question. For this purpose, the system has to learn from data, or be able to interactively specify by a domain specialist, the part of the knowledge structure it needs to answer a given query. The program should also take into account the importance/rank of the particular parts of data it analyses, and adjusts the used algorithms accordingly.

Keywords: Bioinformatics, gene expression, ontology, selforganizingmaps.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo Eduardo Sánchez Gutiérrez, Pedro Pablo González Pérez

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A computational platform is presented in this contribution. It has been designed as a virtual laboratory to be used for exploring optimization algorithms in biological problems. This platform is built on a blackboard-based agent architecture. As a test case, the version of the platform presented here is devoted to the study of protein folding, initially with a bead-like description of the chain and with the widely used model of hydrophobic and polar residues (HP model). Some details of the platform design are presented along with its capabilities and also are revised some explorations of the protein folding problems with different types of discrete space. It is also shown the capability of the platform to incorporate specific tools for the structural analysis of the runs in order to understand and improve the optimization process. Accordingly, the results obtained demonstrate that the ensemble of computational tools into a single platform is worthwhile by itself, since experiments developed on it can be designed to fulfill different levels of information in a self-consistent fashion. By now, it is being explored how an experiment design can be useful to create a computational agent to be included within the platform. These inclusions of designed agents –or software pieces– are useful for the better accomplishment of the tasks to be developed by the platform. Clearly, while the number of agents increases the new version of the virtual laboratory thus enhances in robustness and functionality.

Keywords: genetic algorithms, multi-agent systems, bioinformatics, optimization, protein folding, structural biology.

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Authors: W. Abu Rayyan, A. Singh, A. M. Al-Jaafreh, W. Abu Dayyih, M. Bustami, S. Salem, N. Seder, K. Schröppel

Abstract:

Hyphal growth and the transcriptional regulation to the host environment are key issues during the pathogenesis of C. albicans. Tec1p is the C. albicans homolog of a TEA transcription factor family, which share a conserved DNA-binding TEA domain in their N-terminal. In order to define a structure-function relationship of the C. albicans Tec1p protein, we constructed several mutations on the N terminal, C terminal or in the TEA binding domain itself by homologous recombination technology. The modifications in the open reading frame of TEC1 were tested for reconstitution of the morphogenetic development of the tec1/tec1 mutant strain CaAS12. Mutation in the TEA consensus sequence did not confer transition to hyphae whereas the reconstitution of the full-length Tec1p has reconstituted hyphal development. A deletion in one of glutamine-rich regions either in the Tec1p N-terminal or the C-terminal in regions of 53-212 or 637–744 aa, respectively, did not restore morphological development in mutant CaAS12 strain. Whereas, the reconstitution with Tec1p mutants other than the glutamate-rich region has restored the morphogenetic switch. Additionally, the deletion of the glutamine-rich region has attenuated the invasive growth and the heat shock resistance of C. albicans. In conclusion, we show that a glutamine-rich region of Tec1p is essential for the hyphal development and mediating adaptation to the host environment of C. albicans.

Keywords: Candida albicans, transcription factor, TEA domain, hyphal formation, morphogenetic development, TEC1, Tet-induced.

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Authors: Surajit Debnath, Soma Addya

Abstract:

Human genome is not only the evolutionary summation of all advantageous events, but also houses lesions of deleterious foot prints. A single gene mutation sometimes may express multiple consequences in numerous tissues and a linear relationship of the genotype and the phenotype may often be obscure. ß Thalassemia minor, a transfusion independent mild anaemia, coupled with environment among other factors may articulate into phenotypic pleotropy with Hypocholesterolemia, Vitamin D deficiency, Tissue hypoxia, Hyper-parathyroidism and Psychological alterations. Occurrence of Pancreatic insufficiency, resultant steatorrhoea, Vitamin-D (25-OH) deficiency (13.86 ngm/ml) with Hypocholesterolemia (85mg/dl) in a 30 years old male ß Thal-minor patient (Hemoglobin 11mg/dl with Fetal Hemoglobin 2.10%, Hb A2 4.60% and Hb Adult 84.80% and altered Hemogram) with increased Para thyroid hormone (62 pg/ml) & moderate Serum Ca+2 (9.5mg/ml) indicate towards a cascade of phenotypic pleotropy where the ß Thalassemia mutation ,be it in the 5’ cap site of the mRNA , differential splicing etc in heterozygous state is effecting several metabolic pathways. Compensatory extramedulary hematopoiesis may not coped up well with the stressful life style of the young individual and increased erythropoietic stress with high demand for cholesterol for RBC membrane synthesis may have resulted in Hypocholesterolemia.Oxidative stress and tissue hypoxia may have caused the pancreatic insufficiency, leading to Vitamin D deficiency. This may in turn have caused the secondary hyperparathyroidism to sustain serum Calcium level. Irritability and stress intolerance of the patient was a cumulative effect of the vicious cycle of metabolic compromises. From these findings we propose that the metabolic deficiencies in the ß Thalassemia mutations may be considered as the phenotypic display of the pleotropy to explain the genetic epidemiology. According to the recommendations from the NIH Workshop on Gene-Environment Interplay in Common Complex Diseases: Forging an Integrative Model, study design of observations should be informed by gene-environment hypotheses and results of a study (genetic diseases) should be published to inform future hypotheses. Variety of approaches is needed to capture data on all possible aspects, each of which is likely to contribute to the etiology of disease. Speakers also agreed that there is a need for development of new statistical methods and measurement tools to appraise information that may be missed out by conventional method where large sample size is needed to segregate considerable effect. A meta analytic cohort study in future may bring about significant insight on to the title comment.

Keywords: Genetic disease, Genetic epidemiology, Heterozygous, Phenotype, Pleotropy, ß Thalassemia minor, Metabolic compromises.

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