Search results for: molecular genetic purity

Authors: Younis R. Elhaddad, Mohamed A. Alshaari

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Since 2700 B.C the problem of constructing magic squares attracts many researchers. Magic squares one of most difficult challenges for mathematicians. In this work, we describe how to construct and enumerate Pan- magic squares using genetic algorithm, using new chromosome encoding technique. The results were promising within reasonable time.

Keywords: genetic algorithm, magic square, pan-magic square, computational intelligence

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Authors: Ashraf M. Ward, Ruban S. Yu

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Data consisting of 2757 records from tow Holstein herds made between 2000 and 2010 were used to examine environmental factors affecting age at first calving (AFC) and calving intervals (CI) and consequently estimate genetic and phenotypic parameters and trends. The overall means and standard errors for AFC and CI were 39.4 ± 7.2 months and 487.5 ± 151.6 days respectively. The respective heritability estimates were 0.091 ± 0.05 and 0.044 ± 0.032, while the repeatability estimate for CI was 0.096 ± 0.001. The genetic trends for CI and AFC were -0.6 d/yr and -0.01 mo/yr respectively and were both significant (P < 0.001), indicating a decrease in mean breeding value over the study period. Phenotypic trends were -0.31 mo/yr and -0.35 d/yr for AFC and CI respectively though non-significant (P > 0.05). The low heritability for CI and AFC indicated that temporary environmental influences were much greater than genetic influences or permanent environmental influences on these traits.

Keywords: Holstein, reproductive, genetic parameters, heritability

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Authors: Rishabh Srivastav, Divyam Sharma

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We propose an algorithm to cluster categorical data named as ‘Genetic algorithm initialized rough set based fuzzy K-Modes for categorical data’. We propose an amalgamation of the simple K-modes algorithm, the Rough and Fuzzy set based K-modes and the Genetic Algorithm to form a new algorithm,which we hypothesise, will provide better Centroid Model clustering results, than existing standard algorithms. In the proposed algorithm, the initialization and updation of modes is done by the use of genetic algorithms while the membership values are calculated using the rough set and fuzzy logic.

Keywords: categorical data, fuzzy logic, genetic algorithm, K modes clustering, rough sets

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Leandro Moura da Silva

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The international community has strived to create legal mechanisms to protect their biodiversity, but this can represent, sometimes, particularly in the case of regulatory regime on access to genetic resources, an excessive nationalism which transforms itself into a significant obstacle to scientific progress causing damages to the country and to local farmers. Although it has been poorly publicized in the media, the international legal system was marked, in 2014, by the entry into force of the Nagoya Protocol, which regulates the access and benefit sharing of genetic resources of the States Party to that legal instrument. However, it’s not reasonable to think of regulating access to genetic resources without reflecting on the links of this important subject with other related issues, such as family farming and agribusiness, food safety, food security, intellectual property rights (on seeds, genetic material, new plant varieties, etc.), environmental sustainability, biodiversity, and biosafety.

Keywords: international law, regulation on agriculture, agronomy techniques, sustainability, genetic resources and new crop varieties, CBD, Nagoya Protocol, ITPGRFA

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Authors: V. Pourmostaghimi, M. Zadshakoyan

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Efficiency and productivity of the finish hard turning can be enhanced impressively by utilizing accurate predictive models for cutting tool wear. However, the ability of genetic programming in presenting an accurate analytical model is a notable characteristic which makes it more applicable than other predictive modeling methods. In this paper, the genetic equation for modeling of tool flank wear is developed with the use of the experimentally measured flank wear values and genetic programming during finish turning of hardened AISI D2. Series of tests were conducted over a range of cutting parameters and the values of tool flank wear were measured. On the basis of obtained results, genetic model presenting connection between cutting parameters and tool flank wear were extracted. The accuracy of the genetically obtained model was assessed by using two statistical measures, which were root mean square error (RMSE) and coefficient of determination (R²). Evaluation results revealed that presented genetic model predicted flank wear over the study area accurately (R² = 0.9902 and RMSE = 0.0102). These results allow concluding that the proposed genetic equation corresponds well with experimental data and can be implemented in real industrial applications.

Keywords: cutting parameters, flank wear, genetic programming, hard turning

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Authors: A. Mirzaei, S. Zolghadri, M. Athari-Allaf, H. Yousefnia, A. R. Jalilian

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Rheumatoid arthritis is the most common autoimmune disease, leading to the destruction of the joints. The aim of this study was the preparation of 90Y-chitosan complex as a novel agent for radiosynovectomy. The complex was prepared in the diluted acetic acid solution. At the optimized condition, the radiochemical purity of higher than 99% was obtained by ITLC method on Whatman No. 1 and by using a mixture of methanol/water/acetic acid (4:4:2) as the mobile phase. The complex was stable in acidic media (pH=3) and its radiochemical purity was above 98% even after 48 hours. The biodistribution data in rats showed that there was no significant leakage of the injected activity even after 48 h. Considering all of the excellent features of the complex, 90Y-chitosan can be used to manipulate synovial inflammation effectively.

Keywords: chitosan, Y-90, radiosynovectomy, biodistribution

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Authors: H. Imad, Q. Cheah, J. Mohammad, O. Aamera

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The aim of this study is twofold. One is to determine the genetic structure of Iraq population and the second objective of the study was to evaluate the importance of these loci for forensic genetic purposes. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Twenty STR loci and Amelogenin including D3S1358, D13S317, PentaE, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433, and Amelogenin amplified by using power plex21® kit. PCR products detected by genetic analyzer 3730xL then data analyzed by PowerStatsV1.2. Based on the allelic frequencies, several statistical parameters of genetic and forensic efficiency have been estimated. This includes the homozygosity and heterozygosity, effective number of alleles (n), the polymorphism information content (PIC), the power of discrimination (DP), and the power of exclusion (PE). The power of discrimination values for all tested loci was from 75% to 96% therefore, those loci can be safely used to establish a DNA-based database for Iraq population.

Keywords: autosomal STR, genetic variation, Middle and South of Iraq, statistical parameters

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Authors: M. Mousavi-Daramoroudi, H. Yousefnia, F. Abbasi-Davani, S. Zolghadri

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In this study, ¹⁷⁷Lu-DOTATOC was prepared under optimized conditions (radiochemical purity: > 99%, radionuclidic purity: > 99%). The percentage of injected dose per gram (%ID/g) was calculated for organs up to 168 h post injection. Compartmental model was applied to mathematical description of the drug behaviour in tissue at different times. The biodistribution data showed the significant excretion of the radioactivity from the kidneys. The adrenal and pancreas, as major expression sites for somatostatin receptor (SSTR), had significant uptake. A pharmacokinetic model of ¹⁷⁷Lu-DOTATOC was presented by compartmental analysis which demonstrates the behavior of the complex.

Keywords: biodistribution, compartmental modeling, ¹⁷⁷Lu, Octreotide

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Authors: Snezana Mugosa, Zoran Todorovic, Zoran Bukumiric, Ivan Radosavljevic, Natasa Djordjevic

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Introduction: Various studies have shown that the frequency of clopidogrel resistance ranges from 4-40%. The aim of this study was to provide in depth analysis of genetic and non-genetic factors that influence clopidogrel resistance in cardiology patients. Methods: We have conducted a prospective study in 200 hospitalized patients hospitalized at Cardiology Centre of the Clinical Centre of Montenegro. CYP2C19 genetic testing was conducted, and the PREDICT score was calculated in 102 out of 200 patients treated with clopidogrel in order to determine the influence of genetic and non-genetic factors on outcomes of interest. Adverse cardiovascular events and adverse reactions to clopidogrel were assessed during 12 months follow up period. Results: PREDICT score and CYP2C19 enzymatic activity were found to be statistically significant predictors of expressing lack of therapeutic efficacy of clopidogrel by multivariate logistic regression, without multicollinearity or interaction between the predictors (p = 0.002 and 0.009, respectively). Conclusions: Pharmacogenetics analyses that were done in the Montenegrin population of patients for the first time suggest that these analyses can predict patient response to the certain therapy. Stepwise approach could be used in assessing the clopidogrel resistance in cardiology patients, combining the PREDICT score, platelet aggregation test, and genetic testing for CYP2C19 polymorphism.

Keywords: clopidogrel, pharmacogenetics, pharmacotherapy, PREDICT score

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Authors: Manjula Sutagundar, B. G. Sheeparamatti, D. S. Jangamshetti

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Micro Electro Mechanical Systems (MEMS) resonators have shown the potential of replacing quartz crystal technology for sensing and high frequency signal processing applications because of inherent advantages like small size, high quality factor, low cost, compatibility with integrated circuit chips. This paper presents the optimization and modelling and simulation of the optimized micro cantilever resonator. The objective of the work is to optimize the dimensions of a micro cantilever resonator for a specified range of resonant frequency and specific quality factor. Optimization is carried out using genetic algorithm. The genetic algorithm is implemented using MATLAB. The micro cantilever resonator is modelled in CoventorWare using the optimized dimensions obtained from genetic algorithm. The modeled cantilever is analysed for resonance frequency.

Keywords: MEMS resonator, genetic algorithm, modelling and simulation, optimization

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Authors: Prachi Sharma, Mukesh Kumar Rana

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In the present study, the simple sequence repeat(SSR) markers have been used in analysis of genetic diversity of 37 genotypes of Triticum aestivum. The DNA was extracted using cTAB method. The DNA was quantified using the fluorimeter. The annealing temperatures for 27 primer pairs were standardized using gradient PCR, out of which 16 primers gave satisfactory amplification at temperature ranging from 50-62⁰ C. Out of 16 polymorphic SSR markers only 10 SSR primer pairs were used in the study generating 34 reproducible amplicons among 37 genotypes out of which 30 were polymorphic. Primer pairs Xgwm533, Xgwm 160, Xgwm 408, Xgwm 120, Xgwm 186, Xgwm 261 produced maximum percent of polymorphic bands (100%). The bands ranged on an average of 3.4 bands per primer. The genetic relationship was determined using Jaccard pair wise similarity co-efficient and UPGMA cluster analysis with NTSYS Pc.2 software. The values of similarity index range from 0-1. The similarity coefficient ranged from 0.13 to 0.97. A minimum genetic similarity (0.13) was observed between VL 804 and HPW 288, meaning they are only 13% similar. More number of available SSR markers can be useful for supporting the genetic diversity analysis in the above wheat genotypes.

Keywords: wheat, genetic diversity, microsatellite, polymorphism

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Authors: J. Kaabi, Y. Harrath

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This paper studied the flow shop scheduling problem under machine availability constraints. The machines are subject to flexible preventive maintenance activities. The nonresumable scenario for the jobs was considered. That is, when a job is interrupted by an unavailability period of a machine it should be restarted from the beginning. The objective is to minimize the total tardiness time for the jobs and the advance/tardiness for the maintenance activities. To solve the problem, a genetic algorithm was developed and successfully tested and validated on many problem instances. The computational results showed that the new genetic algorithm outperforms another earlier proposed algorithm.

Keywords: flow shop scheduling, genetic algorithm, maintenance, priority rules

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Authors: Wafa’ Alma'Aitah, Khaled Almakadmeh

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this study presents an information retrieval system of using genetic algorithm to increase information retrieval efficiency. Using vector space model, information retrieval is based on the similarity measurement between query and documents. Documents with high similarity to query are judge more relevant to the query and should be retrieved first. Using genetic algorithms, each query is represented by a chromosome; these chromosomes are fed into genetic operator process: selection, crossover, and mutation until an optimized query chromosome is obtained for document retrieval. Results show that information retrieval with adaptive crossover probability and single point type crossover and roulette wheel as selection type give the highest recall. The proposed approach is verified using (242) proceedings abstracts collected from the Saudi Arabian national conference.

Keywords: genetic algorithm, information retrieval, optimal queries, crossover

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Authors: Adel Belayadi, Ahmed Mougari, Boualem Bourahla

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Molecular junctions are currently considered a promising style in the miniaturization of electronic devices. In this contribution, we provide a tight-binding model to investigate the quantum transport properties across-molecular junctions sandwiched between 2D-graphene nanoribbons in the zigzag direction. We investigate, in particular, the effect of embedded atoms such as Gold and Silicon across the molecular junction. The results exhibit a resonance behavior in terms of incident Fermi levels, depending on the molecular junction type. Additionally, the transport properties under a perpendicular magnetic field exhibit an oscillation for the transmittance versus the magnetic field strength.

Keywords: molecular junction, 2D-graphene nanoribbons, quantum transport properties, magnetic field

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Authors: Jeong-Hyun Yoo, Hanjung Kwon, Sung-Wook Cho

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Fused salt electrolysis was studied to make the high purity rare-earth metals using domestic rare-earth ore. The target metals of the fused salt electrolysis were Mm (Misch metal), La, Ce, Nd, etc. Fused salt electrolysis was performed with the supporting salt such as chloride and fluoride at the various temperatures and ampere. The metals made by fused salt electrolysis were analyzed to identify the phase and composition using the methods of XRD and ICP. As a result, the acquired rare-earth metals were the high purity ones which had more than 99% purity. Also, VIM (vacuum induction melting) was studied to make the kg level rare-earth alloy for the use of secondary battery and hydrogen storage. In order to indentify the physicochemical properties such as phase, impurity gas, alloy composition and hydrogen storage, the alloys were investigated. The battery characteristics were also analyzed through the various tests in the real production line of a battery company.

Keywords: domestic rare-earth ore, fused salt electrolysis, rare-earth materials, hydrogen storage alloy, secondary battery

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Authors: Asim Mehmood, Abdul Karim, Muhammad J. Jaskani, Faisal S. Awan, Muhammad W. Sajid

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Guava (Psidium guajava L.) is an important commercial fruit crop of Pakistan. It is an allogamous crop having 25-40% cross pollination which on the one hand leads to clonal degradation and on the other hand can add variations to generated new cultivars. Morpho-genetic characterization of 37 guava accessions was carried out for study of the genetic diversity among guava accessions located in province Punjab, Pakistan. For morphological analysis, 17 morphological traits were studied, and strong positive correlation was found among the 7 morphological traits which included thickness of outer flesh in relation to core diameter, fruit length, fruit width, fruit juiciness, fruit size, fruit sweetness and number of seeds. For genetic characterization, 18 microsatellites were used, and the sizes of reproducible and scorable bands ranged from 150 to 320 bp. These 18 primer pairs amplified a total of 85 alleles in P. guajava, with an average total number of 4.7 alleles per locus and no more than two displayed bands (nuclear SSR loci). The phylogenetic tree based on the morphological and genetic traits showed the diversity of these 37 guava genotypes into two major groups. These results indicated that Pakistani guava is quite diverse and a more detail study is needed to define the level of genetic variability.

Keywords: Psidium guajava L, genetic diversity, SSR markers, polymorphism, dendrogram

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Authors: Dorcas Ropo Abejide, Olamide Ahmed Falusi, Oladipupo Abdulazeez Yusuf Daudu, Bolaji Zuluqurineen Salihu, Muhammad Liman Muhammad

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This study evaluated the morpho-agronomic response of twenty-four (24) Nigerian Bambara groundnut landraces to water stress and genetic diversity of some selected accessions using SSR markers. The studies were carried out in the botanical garden of the Department of Plant Biology, Federal University of Technology, Minna, Niger State, Nigeria in a randomized complete block design using three replicates. Molecular analysis using SSR primers was carried out at the International Institute of Tropical Agriculture (IITA) Ibadan in order to characterize ten selected accessions comprising the seven most drought tolerant and three most susceptible accessions from the 24 accessions evaluated. Results revealed that water stress decreased morpho-agronomic traits such as plant height, leaf area, number of leaves per plant, seed yield, etc. A total of 22 alleles were detected by the SSR markers used with a mean number of 4 allelles. SSR markers MBamCO₃₃, Primer 65, and G358B2-D15 each detected 4 allelles, while Primer 3FR and 4FR detected 5 allelles each. The study revealed significantly high polymorphisms in 10 Loci. The mean value of polymorpic information content was 0.6997, implying the usefulness of the primers used in identifying genetic similarities and differences among the Bambara groundnut genotypes. The SSR analysis revealed a comparable pattern between genetic diversity and drought tolerance of the genotypes. The UPGMA dendrogram showed that at a genetic distance of 0.1, the accessions were grouped into three groups according to their level of tolerance to drought. The two most drought-tolerant accessions were grouped together, and the 5th and 6th most drought-tolerant accessions were also grouped together. This suggests that the genotypes grouped together may be genetically close, may possess similar genes, or have a common origin. The degree of genetic variants obtained from this profiling could be useful in Bambara groundnut breeding for drought tolerance. The identified drought tolerant Bambara groundnut landraces are important genetic resources for drought stress tolerance breeding programme of Bambara groundnut. The genotypes are also useful for germplasm conservation and global implications.

Keywords: Bambara groundnut, genetic diversity, germplasm, SSR markers, water stress

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

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The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, sport performance, Slovakia

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Authors: Michal Duchek, Jan Palán, Tomas Kubina

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Bars made of titanium grade 2 and grade 4 were subjected to rotary forging with up to 2.2 true strain reduction in the cross-section from 10 to 3.81 mm. During progressive deformation, grain refinement in the transverse direction took place. In the longitudinal direction, ultrafine microstructure has not developed. It has been demonstrated that titanium grade 2 strengthens more than grade 4. The ultimate tensile strength increased from 650 MPa to 1040 MPa in titanium grade 4. Hardness profiles on the cross section in both materials show an increase in the centre of the wire.

Keywords: commercial-purity titanium, wire, rotary swaging, tensile test, hardness, modulus of elasticity, microstructure

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Authors: Rouhollah Radjabi, Mojtaba Zarei, Elham Sanatgar, Hossein Shouhani

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RAPD molecular markers in order to discrimination of the Iranian native Bombyx mori silkworm breeds were used. DNA extraction using phenol - chloroform was and the qualitative and quantitative measurements of extracted DNA and its dilution, the obtained bands on agarose gel 1.5 percent were marked and analyzed. Results showed that the bands are observed between 250-2500 bp and most bands have been observed as Gilani-orange, the lowest bands observed are Khorasani-lemon. Primer 3 with 100% polymorphism with the highest polymorphism and primer 2 with 61.5 polymorphism had the lowest percentage of polymorphism. Cluster analysis of races and placed them in three main groups, races Gilani - orange, Baghdad and Khorasani -pink if the first group, camel's thorn, Herati - yellow race was alone in the second group and Khorasani – lemon was alone in the third group. The greatest similarity between the races, between Khorasani- pink and Baghdad (0.64). RAPD markers have been determined different silkworm races based on various morphological or economic characteristics except geographic origin.

Keywords: silkworm, molecular marker, RAPD, Iran

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Authors: Radhwan Yousif Sedik Al-Jawadi

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Optimization is necessary for finding appropriate solutions to a range of real-life problems. In particular, genetic (or more generally, evolutionary) algorithms have proved very useful in solving many problems for which analytical solutions are not available. In this paper, we present an optimization algorithm called Dynamic Schema with Dissimilarity and Similarity of Chromosomes (DSDSC) which is a variant of the classical genetic algorithm. This approach constructs new chromosomes from a schema and pairs of existing ones by exploring their dissimilarities and similarities. To show the effectiveness of the algorithm, it is tested and compared with the classical GA, on 15 two-dimensional optimization problems taken from literature. We have found that, in most cases, our method is better than the classical genetic algorithm.

Keywords: chromosome injection, dynamic schema, genetic algorithm, similarity and dissimilarity

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Authors: Peter James C. Icalia, Agapita J. Salces, Loida Valenzuela, Kangseok Seo, Geronima Ludan

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This study evaluated polymorphism of 11 microsatellite markers in four local genetic groups of cattle. Batanes cattle which has never been studied using microsatellites is evaluated for its genetic distance from the Ilocos cattle while Brahman and Holstein-Sahiwal are also included as there were insemination programs by the government using these two breeds. PCR products that were genotyped for each marker were analyzed using POPGENEv32. Results showed that 55% (Fst=0.5501) of the genetic variation is due to the differences between populations while the remaining 45% is due to individual variation. The Fst value also indicates that there were very great differences from population to population using the range proposed by Sewall and Wright. The constructed phylogenetic tree based on Nei’s genetic distance using the modified neighboor joining procedure of PHYLIPv3.5 showed the admixture of Brahman and Holstein-Sahiwal having them grouped in the same clade. Batanes and Ilocos cattle were grouped in a different cluster showing that they have descended from a single parental population. This would presumably address the claim that Batanes and Ilocos cattle are genetically distant from other groups and still exist despite the artificial insemination program of the government using Brahman and other imported breeds. The knowledge about the genetic structure of this population supports the development of conservation programs for the smallholder farmers.

Keywords: microsatellites, cattle, Philippines, populations, genetic structure

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Authors: Mafalda Moreira, Diana Alba, Inês Paiva Ferreira, Rita Calejo, Ana Rita Soares, Leonilde Machado

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Intellectual disability (ID) is characterized by deficits in intellectualfunctioningassociatedwithalterations in the adaptive behaviour, whose onset is inthedevelopmentalperiod. Itaffects 3% of the population, ofwhich 10% have a geneticaetiology. One of those causes isAlwadeiSyndrome, with 3 cases describedworldwide. It results from a homozygous nonsense mutation in theRUSC2 gene andisassociatedwithintellectualdisabilityanddysmorphic facialfeatures. Theauthorsreportthe case of a 5-year-old-boy, born to a healthymotherafter a full-termuneventfulpregnancy, thatwasreferred to Neurodevelopmentalconsultationdue toglobal developmentaldelay. Familyhistoryrevealedlearningdifficulties in the paternal brotherhood. Milddismorphicfeatureswereevidentsuch as darkinfraorbitalregion, low-set ears, beakednose, retrognathism, high-archedpalateandjointhyperlaxity. WechslerIntelligenceScale for Children III fullscaleIQ quoted 61. Karyotypeandchromosomalmicroarrayanalysiswerenormal, as well as the fragile X molecular study. DNA sequencingwasthenperformedandallowedtheidentificationof amutation in the RUSC2 gene. Theetiologicaldiagnosisof ID remains unknown in up to 80% of cases, creatinguncertainty in children’sfamilies. Theadvances in DNA sequencingtechnologieshaveincreasedourknowledgeofthegeneticdiseasesinvolved, as theAlwadeisyndromewasonlydescribedsince 2016. Thegeneticdiagnosisof ID allowsfamilygeneticcounselingandenablesthedevelopmentof target therapeutic approaches.

Keywords: intellectual disability, genetic aetiology, alwadei syndrome, RUSC2

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Authors: Michael Aupetit, Mahmoud Al-ismail, Khaled Mohamed

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Cancer is a major public health problem all over the world. Breast cancer has the highest incidence rate over all cancers for women in Qatar making its study a top priority of the country. Human cancer is a dynamic disease that develops over an extended period through the accumulation of a series of genetic alterations. A Darwinian process drives the tumor cells toward higher malignancy growing the branches of a progression tree in the space of genes expression. Although it is not possible to track these genetic alterations dynamically for one patient, it is possible to reconstruct the progression tree from the aggregation of thousands of tumor cells’ genetic profiles from thousands of different patients at different stages of the disease. Analyzing the progression tree is a way to detect pivotal molecular events that drive the malignant evolution and to provide a guide for the development of cancer diagnostics, prognostics and targeted therapeutics. In this work we present the development of a Visual Analytic web platform CanVis enabling users to upload gene-expression data and analyze their progression tree. The server computes the progression tree based on state-of-the-art techniques and allows an interactive visual exploration of this tree and the gene-expression data along its branching structure helping to discover potential driver genes.

Keywords: breast cancer, progression tree, visual analytics, web platform

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Authors: Fakhrosadat Sajjadian

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In the USA, about 5% of women diagnosed with breast cancer annually are affected by Inflammatory Breast Cancer (IBC), which is a highly aggressive type of Locally Advanced Breast Cancer (LABC). It is a type of LABC that is clinically and pathologically different, known for its rapid growth, invasiveness, and ability to promote the growth of blood vessels. Almost all women are found to have lymph nodes affected upon diagnosis, while around 36% show obvious distant metastases. Even with the latest improvements in multimodality therapies, the outlook for patients with IBC remains bleak, as the average disease-free survival time is less than 2.5 years. Recent research on the genetic factors responsible for the IBC phenotype has resulted in the discovery of genes that play a role in the advancement of this illness. The development of primary human cell lines and animal models has assisted in this research. These advancements offer new possibilities for future actions in identifying and treating IBC.

Keywords: breast cancer, inflammation, diagnosis, IBC, LABC

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Authors: Hernandez Pardo Diego F., Guiza Arguello Viviana R., Coy Echeverria Ana, Viejo Abrante Fernando

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The biological hydroxyapatite obtained from bovine bone arouses great interest in its application as a material for bone regeneration due to its better bioactive behavior in comparison with synthetic hydroxyapatite. For this reason, the objective of the present investigation was to determine the effect of chemical and thermal treatments in obtaining biological bovine hydroxyapatite of high purity and crystallinity. Two different chemical reagents were evaluated (NaOH and HCl) with the aim to remove the organic matrix of the bovine cortical bone. On the other hand, for analyzing the effect of thermal treatment temperature was ranged between 500 and 1000°C for a holding time of 4 hours. To accomplish the above, the materials before and after the chemical and thermal treatments were characterized by elemental compositional analysis (CHN), infrared spectroscopy by Fourier transform (FTIR), RAMAN spectroscopy, scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and X-ray diffraction (XRD) and energy dispersion X-ray spectroscopy (EDS). The results allowed to establish that NaOH is more effective in the removal of the organic matrix of the bone when compared to HCl, whereas a thermal treatment at 700ºC for 4 hours was enough to obtain biological hydroxyapatite of high purity and crystallinity.

Keywords: bovine bone, hydroxyapatite, biomaterials, thermal treatment

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Authors: Diana Larisa Vladoiu, Vasile Ostafe, Adriana Isvoran

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Molecular docking calculations reveal that pesticides provide favorable interactions with the bacterial chitinases. Pesticides interact with both hydrophilic and aromatic residues involved in the active site of the enzymes, their positions partially overlapping the substrate and the inhibitors locations. Molecular docking outcomes, in correlation with experimental literature data, suggest that the pesticides may be degraded or having an inhibitor effect on the activity of these enzymes, depending of the application dose and rate.

Keywords: chitinases, inhibition, molecular docking, pesticides

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Authors: Aran Abd Al Rahman

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Joubert syndrome regards as a congenital cerebellar ataxia caused by autosomal recessive carried on X chromosome. The disease diagnosed by brain imaging—the so-called molar tooth sign. Neurological signs were present from the neonatal period and include hypotonia progressing to ataxia, global developmental delay, ocular motor apraxia, and breathing dysregulation. These signs are variably associated with multiorgan involvement, mainly of the retina, kidneys, skeleton, and liver. 30 causative genes have been identified so far, all of which encode for proteins of the primary cilium or its apparatus, The purpose of our project was to detect the mutant gene (INPP5E gene) which cause Joubert syndrome. There were many methods used for diagnosis such as MRI and CT- scan and molecular diagnosis by doing ARMS PCR for detection of mutant gene that we were used in this research project. In this research for individual family which reported, the two children with parents, the two children were affected and were carrier.

Keywords: Joubert syndrome, genetic disease, Kurdistan region, Sulaimani

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Authors: Rugang Tian

Abstract:

In this study, we generated whole-genome sequence (WGS) data from110 native cattle. Together with whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of different cattle populations. Our findings revealed clustering of cattle groups in line with their geographic locations. We identified noticeable genetic diversity between indigenous cattle breeds and commercial populations. Among all studied cattle groups, lower genetic diversity measures were found in commercial populations, however, high genetic diversity were detected in some local cattle, particularly in Rashoki and Mongolian breeds. Our search for potential genomic regions under selection in native cattle revealed several candidate genes related with immune response and cold shock protein on multiple chromosomes such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis.

Keywords: cattle, whole-genome, population structure, adaptation

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