Search results for: Genome profiling (GP)

Authors: Shamim Ahmed Koichi Nishigaki

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Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.

Keywords: Fluctuation, Genome profiling (GP), Pattern similarity score (PaSS), Robustness, Spiddos-shift.

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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: Cj Gletus Matthews Cn Jacobs, Kogilah Narayanasamy

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This article explores the sociological perspectives on social problems and the role of the media which has a delicate role to tread in balancing its duty to the public and the victim Whilst social problems have objective conditions, it is the subjective definition of such problems that ensure which social problem comes to the fore and which doesn-t. Further it explores the roles and functions of policymakers when addressing social problems and the impact of the inception of media profiling as well as the advantages and disadvantages of media profiling towards social problems. It focuses on the inception of media profiling due to its length and a follow up article will explore how current media profiling towards social problems have evolved since its inception.

Keywords: Media Profiling, Policy Response, Social Problems

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Authors: E. Al Daoud

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The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.

Keywords: Genome, species, blastp, conserved genes, cronobacter.

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Authors: Somayyeh Azizi, Saeed Kaboli, Atsushi Yagi

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Whole genome duplication (WGD) increased the number of yeast Saccharomyces cerevisiae chromosomes from 8 to 16. In spite of retention the number of chromosomes in the genome of this organism after WGD to date, chromosomal rearrangement events have caused an evolutionary distance between current genome and its ancestor. Studies under evolutionary-based approaches on eukaryotic genomes have shown that the rearrangement distance is an approximable problem. In the case of S. cerevisiae, we describe that rearrangement distance is accessible by using dedoubled adjacency graph drawn for 55 large paired chromosomal regions originated from WGD. Then, we provide a program extracted from a C program database to draw a dedoubled genome adjacency graph for S. cerevisiae. From a bioinformatical perspective, using the duplicated blocks of current genome in S. cerevisiae, we infer that genomic organization of eukaryotes has the potential to provide valuable detailed information about their ancestrygenome.

Keywords: Whole-genome duplication, Evolution, Double-cutand- join operation, Yeast.

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Authors: Essam Al Daoud

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Genome rearrangement is an important area in computational biology and bioinformatics. The basic problem in genome rearrangements is to compute the edit distance, i.e., the minimum number of operations needed to transform one genome into another. Unfortunately, unsigned genome rearrangement problem is NP-hard. In this study an improved ant colony optimization algorithm to approximate the edit distance is proposed. The main idea is to convert the unsigned permutation to signed permutation and evaluate the ants by using Kaplan algorithm. Two new operations are added to the standard ant colony algorithm: Replacing the worst ants by re-sampling the ants from a new probability distribution and applying the crossover operations on the best ants. The proposed algorithm is tested and compared with the improved breakpoint reversal sort algorithm by using three datasets. The results indicate that the proposed algorithm achieves better accuracy ratio than the previous methods.

Keywords: Ant colony algorithm, Edit distance, Genome breakpoint, Genome rearrangement, Reversal sort.

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Authors: Jiaji Zhou, Le Liang, Long Chen

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Geographic Profiling has successfully assisted investigations for serial crimes. Considering the multi-cluster feature of serial criminal spots, we propose a Multi-point Centrography model as a natural extension of Single-point Centrography for geographic profiling. K-means clustering is first performed on the data samples and then Single-point Centrography is adopted to derive a probability distribution on each cluster. Finally, a weighted combinations of each distribution is formed to make next-crime spot prediction. Experimental study on real cases demonstrates the effectiveness of our proposed model.

Keywords: Geographic profiling, Centrography model, K-means algorithm

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Authors: M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, A. Malekpour, M. Foroughmand, S. Goliaei, M. Totonchi, N. Ansari–Pour

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The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.

Keywords: Cancer risk, extrinsic factors, genome sequencing, intrinsic factors.

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Authors: Ioannis P. Panapakidis, Marios N. Moschakis

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With the continuous increment of smart meter installations across the globe, the need for processing of the load data is evident. Clustering-based load profiling is built upon the utilization of unsupervised machine learning tools for the purpose of formulating the typical load curves or load profiles. The most commonly used algorithm in the load profiling literature is the K-means. While the algorithm has been successfully tested in a variety of applications, its drawback is the strong dependence in the initialization phase. This paper proposes a novel modified form of the K-means that addresses the aforementioned problem. Simulation results indicate the superiority of the proposed algorithm compared to the K-means.

Keywords: Clustering, load profiling, load modeling, machine learning, energy efficiency and quality.

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Authors: Khaled M. Khan, Armstrong Nhlabatsi

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This article attempts to analyse behavioural traits of lone-wolves who struck and killed innocents in six different attacks in Europe in last nine months. The main objective of this study is to develop a profiling template in order to capture commonality of characteristics of these attackers. This study tries to understand the homogeneity of lone-wolves in terms of their social background and state of mind. The commonality among them can possibly be used to build a profiling template that could help detecting vulnerable persons who are prone to be self-radicalised or radicalised by someone else. The result of this study provides us an understanding of their commonality in terms of their state of mind and social characteristics.

Keywords: Behavioral pattern, terrorism, profiling, commonality.

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

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De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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Authors: Gry M, Bergström J, Lengquist J, Lindberg J, Drobin K, Schwenk J, Nilsson P, Schuppe-Koistinen I.

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Sensitive and predictive DILI (Drug Induced Liver Injury) biomarkers are needed in drug R&D to improve early detection of hepatotoxicity. The discovery of DILI biomarkers that demonstrate the predictive power to identify individuals at risk to DILI would represent a major advance in the development of personalized healthcare approaches. In this healthy volunteer acetaminophen study (4g/day for 7 days, with 3 monitored nontreatment days before and 4 after), 450 serum samples from 32 subjects were analyzed using protein profiling by antibody suspension bead arrays. Multiparallel protein profiles were generated using a DILI target protein array with 300 antibodies, where the antibodies were selected based on previous literature findings of putative DILI biomarkers and a screening process using pre dose samples from the same cohort. Of the 32 subjects, 16 were found to develop an elevated ALT value (2Xbaseline, responders). Using the plasma profiling approach together with multivariate statistical analysis some novel findings linked to lipid metabolism were found and more important, endogenous protein profiles in baseline samples (prior to treatment) with predictive power for ALT elevations were identified.

Keywords: DILI, Plasma profiling, PLSDA, Randomforest.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

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Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: P. Pasomboon, P. Chumnanpuen, T. E-kobon

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Hyaluronic acid (HA) consists of linear heteropolysaccharides repeat of D-glucuronic acid and N-acetyl-D-glucosamine. HA has various useful properties to maintain skin elasticity and moisture, reduce inflammation, and lubricate the movement of various body parts without causing immunogenic allergy. HA can be found in several animal tissues as well as in the capsule component of some bacteria including Pasteurella multocida. This study aimed to modify a genome-scale metabolic model of Escherichia coli using computational simulation and flux analysis methods to predict HA productivity under different carbon sources and nitrogen supplement by the addition of two enzymes (GLMU2 and HYAD) from P. multocida to improve the HA production under the specified amount of carbon sources and nitrogen supplements. Result revealed that threonine and aspartate supplement raised the HA production by 12.186%. Our analyses proposed the genome-scale metabolic model is useful for improving the HA production and narrows the number of conditions to be tested further.

Keywords: Pasteurella multocida, Escherichia coli, hyaluronic acid, genome-scale metabolic model, bioinformatics.

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Authors: S. Moghaddaszadeh-Ahrabi, S. Farajnia, Gh. Rahimi-Mianji, A. Nejati-Javaremi

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In recent years, there has been an increasing interest toward the use of bovine genotyped embryos for commercial embryo transfer programs. Biopsy of a few cells in morulla stage is essential for preimplantation genetic diagnosis (PGD). Low amount of DNA have limited performing the several molecular analyses within PGD analyses. Whole genome amplification (WGA) promises to eliminate this problem. We evaluated the possibility and performance of an improved primer extension preamplification (I-PEP) method with a range of starting bovine genomic DNA from 1-8 cells into the WGA reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure (~3h). This optimized WGA method was assessed by 6 loci specific polymerase chain reactions (PCRs), included restriction fragments length polymorphism (RFLP). Optimized WGA procedure possesses enough sensitivity for molecular genetic analyses through the few input cells. This is a new era for generating characterized bovine embryos in preimplantation stage.

Keywords: Whole genome amplification (WGA), Genotyping, Bovine, Preimplantation genetic diagnosis (PGD)

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Authors: Sarabjeet Kaur Kochhar

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With a surge of stream processing applications novel techniques are required for generation and analysis of association rules in streams. The traditional rule mining solutions cannot handle streams because they generally require multiple passes over the data and do not guarantee the results in a predictable, small time. Though researchers have been proposing algorithms for generation of rules from streams, there has not been much focus on their analysis. We propose Association rule profiling, a user centric process for analyzing association rules and attaching suitable profiles to them depending on their changing frequency behavior over a previous snapshot of time in a data stream. Association rule profiles provide insights into the changing nature of associations and can be used to characterize the associations. We discuss importance of characteristics such as predictability of linkages present in the data and propose metric to quantify it. We also show how association rule profiles can aid in generation of user specific, more understandable and actionable rules. The framework is implemented as SUPAR: System for Usercentric Profiling of Association Rules in streaming data. The proposed system offers following capabilities: i) Continuous monitoring of frequency of streaming item-sets and detection of significant changes therein for association rule profiling. ii) Computation of metrics for quantifying predictability of associations present in the data. iii) User-centric control of the characterization process: user can control the framework through a) constraint specification and b) non-interesting rule elimination.

Keywords: Data Streams, User subjectivity, Change detection, Association rule profiles, Predictability.

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Authors: L. Agneni, F. Carta, C. Micheletta, V. Tersigni

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The development of a qualitative method to profile jobseekers is needed to improve the quality of the Public Employment Services (PES) in Italy. This is why the National Agency for Active Labour Market Policies (ANPAL) decided to introduce a Qualitative Profiling Service in the context of the activities carried out by local employment offices’ operators. The qualitative profiling service provides information and data regarding the jobseeker’s personal transition status, through a semi-structured questionnaire administered to PES clients during the guidance interview. The questionnaire responses allow PES staff to identify, for each client, proper activities and policy measures to support jobseekers in their reintegration into the labour market. Data and information gathered by the qualitative profiling tool are the following: frequency, modalities and motivations for clients to apply to local employment offices; clients’ expectations and skills; difficulties that they have faced during the previous working experiences; strategies, actions undertaken and activated channels for job search. These data are used to assess jobseekers’ personal and career characteristics and to measure their employability level (qualitative profiling index), in order to develop and deliver tailor-made action programmes for each client. This paper illustrates the use of the above-mentioned qualitative profiling service on the national territory and provides an overview of the main findings of the survey: concerning the difficulties that unemployed people face in finding a job and their perception of different aspects related to the transition in the labour market. The survey involved over 10.000 jobseekers registered with the PES. Most of them are beneficiaries of the “citizens' income”, a specific active labour policy and social inclusion measure. Furthermore, data analysis allows classifying jobseekers into a specific group of clients with similar features and behaviours, on the basis of socio-demographic variables, customers' expectations, needs and required skills for the profession for which they seek employment. Finally, the survey collects PES staff opinions and comments concerning clients’ difficulties in finding a new job and also their strengths. This is a starting point for PESs’ operators to define adequate strategies to facilitate jobseekers’ access or reintegration into the labour market.

Keywords: Labour market transition, Public Employment Services, qualitative profiling, vocational guidance.

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Authors: O. Yavuz, L. Ozyilmaz

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HIV-1 genome is highly heterogeneous. Due to this variation, features of HIV-I genome is in a wide range. For this reason, the ability to infection of the virus changes depending on different chemokine receptors. From this point of view, R5 HIV viruses use CCR5 coreceptor while X4 viruses use CXCR5 and R5X4 viruses can utilize both coreceptors. Recently, in Bioinformatics, R5X4 viruses have been studied to classify by using the experiments on HIV-1 genome. In this study, R5X4 type of HIV viruses were classified using Auto Regressive (AR) model through Artificial Neural Networks (ANNs). The statistical data of R5X4, R5 and X4 viruses was analyzed by using signal processing methods and ANNs. Accessible residues of these virus sequences were obtained and modeled by AR model since the dimension of residues is large and different from each other. Finally the pre-processed data was used to evolve various ANN structures for determining R5X4 viruses. Furthermore ROC analysis was applied to ANNs to show their real performances. The results indicate that R5X4 viruses successfully classified with high sensitivity and specificity values training and testing ROC analysis for RBF, which gives the best performance among ANN structures.

Keywords: Auto-Regressive Model, HIV, Neural Networks, ROC Analysis.

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Authors: Martin Bader

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During the last years, the genomes of more and more species have been sequenced, providing data for phylogenetic recon- struction based on genome rearrangement measures. A main task in all phylogenetic reconstruction algorithms is to solve the median of three problem. Although this problem is NP-hard even for the sim- plest distance measures, there are exact algorithms for the breakpoint median and the reversal median that are fast enough for practical use. In this paper, this approach is extended to the transposition median as well as to the weighted reversal and transposition median. Although there is no exact polynomial algorithm known even for the pairwise distances, we will show that it is in most cases possible to solve these problems exactly within reasonable time by using a branch and bound algorithm.

Keywords: Comparative genomics, genome rearrangements, me-dian, reversals, transpositions.

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Authors: Hikmat A. M. Abd-El-Jaber, Tengku M. T. Sembok

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The information on the Web increases tremendously. A number of search engines have been developed for searching Web information and retrieving relevant documents that satisfy the inquirers needs. Search engines provide inquirers irrelevant documents among search results, since the search is text-based rather than semantic-based. Information retrieval research area has presented a number of approaches and methodologies such as profiling, feedback, query modification, human-computer interaction, etc for improving search results. Moreover, information retrieval has employed artificial intelligence techniques and strategies such as machine learning heuristics, tuning mechanisms, user and system vocabularies, logical theory, etc for capturing user's preferences and using them for guiding the search based on the semantic analysis rather than syntactic analysis. Although a valuable improvement has been recorded on search results, the survey has shown that still search engines users are not really satisfied with their search results. Using ontologies for semantic-based searching is likely the key solution. Adopting profiling approach and using ontology base characteristics, this work proposes a strategy for finding the exact meaning of the query terms in order to retrieve relevant information according to user needs. The evaluation of conducted experiments has shown the effectiveness of the suggested methodology and conclusion is presented.

Keywords: information retrieval, user profiles, semantic Web, ontology, search engine.

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Authors: Chintanu K. Sarmah, Sandhya Samarasinghe, Don Kulasiri, Daniel Catchpoole

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Gene expression profiling is rapidly evolving into a powerful technique for investigating tumor malignancies. The researchers are overwhelmed with the microarray-based platforms and methods that confer them the freedom to conduct large-scale gene expression profiling measurements. Simultaneously, investigations into cross-platform integration methods have started gaining momentum due to their underlying potential to help comprehend a myriad of broad biological issues in tumor diagnosis, prognosis, and therapy. However, comparing results from different platforms remains to be a challenging task as various inherent technical differences exist between the microarray platforms. In this paper, we explain a simple ratio-transformation method, which can provide some common ground for cDNA and Affymetrix platform towards cross-platform integration. The method is based on the characteristic data attributes of Affymetrix- and cDNA- platform. In the work, we considered seven childhood leukemia patients and their gene expression levels in either platform. With a dataset of 822 differentially expressed genes from both these platforms, we carried out a specific ratio-treatment to Affymetrix data, which subsequently showed an improvement in the relationship with the cDNA data.

Keywords: Gene expression profiling, microarray, cDNA, Affymetrix, childhood leukaemia.

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Authors: Chang Kug Kim, Dong Suk Park, Young Joo Seol, Jang Ho Hahn

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The National Agricultural Biotechnology Information Center (NABIC) plays a leading role in the biotechnology information database for agricultural plants in Korea. Since 2002, we have concentrated on functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on bioinformatics of major agricultural resources such as rice, Chinese cabbage, and microorganisms. In the NABIC, integration-based biotechnology database provides useful information through a user-friendly web interface that allows analysis of genome infrastructure, multiple plants, microbial resources, and living modified organisms.

Keywords: biotechnology, database, genome information

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Authors: Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.

Keywords: Genome-scale metabolic model, Zymomonas mobilis, uncoupled growth, flux distribution, ATP dissipation.

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Authors: Dmitry S. Sitnikov, Andrey V. Ovchinnikov

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Research results and optimal parameters investigation of laser cut and profiling of diamond and quartz substrates by femtosecond laser pulses are presented. Profiles 10 μm in width, ~25 μm in depth and several millimeters long were made. Investigation of boundaries quality has been carried out with the use of AFM «Vecco». Possibility of technological formation of profiles and micro-holes in diamond and quartz substrates with nanometer-scale boundaries is shown. Experimental results of multilayer dielectric cover treatment are also presented. Possibility of precise upper layer (thickness of 70–140 nm) removal is demonstrated. Processes of thin metal film (60 nm and 350 nm thick) treatment are considered. Isolation tracks (conductance ~ 10-11 S) 1.6–2.5 μm in width in conductive metal layers are formed.

Keywords: Femtosecond laser ablation, microhole and nanoprofileformation, micromachining

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Authors: Y. J. Chen, T. M. Yue, Z. N. Guo

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This paper reports the effects of laser energy on the characteristics of bubbles generated in the weld zone and the formation of new chemical bonds at the Polyethylene Terephthalate (PET)/Ti joint interface in laser joining of PET to Ti. The samples were produced by using different laser energies ranging from 1.5 J – 6 J in steps of 1.5 J, while all other joining parameters remained unchanged. The types of chemical bonding at the joint interface were analysed by the x-ray photoelectron spectroscopy (XPS) depth-profiling method. The results show that the characteristics of the bubbles and the thickness of the chemically bonded interface, which contains the laser generated bonds of Ti–C and Ti–O, increase markedly with increasing laser energy input. The tensile failure load of the joint depends on the combined effect of the amount and distribution of the bubbles formed and the chemical bonding intensity of the joint interface.

Keywords: Laser direct joining, Ti/PET interface, laser energy, XPS depth profiling, chemical bond, tensile failure load.

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Authors: Benjamin Y. M. Kwan, Jennifer Y. Y. Kwan, Hon Keung Kwan

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In the paper, the relative performances on spectral classification of short exon and intron sequences of the human and eleven model organisms is studied. In the simulations, all combinations of sixteen one-sequence numerical representations, four threshold values, and four window lengths are considered. Sequences of 150-base length are chosen and for each organism, a total of 16,000 sequences are used for training and testing. Results indicate that an appropriate combination of one-sequence numerical representation, threshold value, and window length is essential for arriving at top spectral classification results. For fixed-length sequences, the precisions on exon and intron classification obtained for different organisms are not the same because of their genomic differences. In general, precision increases as sequence length increases.

Keywords: Exons and introns classification, Human genome, Model organism genome, Spectral analysis

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Authors: Stephen Akinlabi, Mukul Shukla, Esther Akinlabi, Marwala Tshilidzi

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This paper reports the evolving properties of a 3 mm low carbon steel plate after Laser Beam Forming achieve this objective, the chemical analyse material and the formed components were carried thereafter both were characterized through microhardness profiling microstructural evaluation and tensile testing. showed an increase in the elemental concentration of the component when compared to the as received attributed to the enhancement property of the LBF process Ultimate Tensile Strength (UTS) and the Vickers the formed component shows an increase when compared to the as received material, this was attributed to strain hardening and grain refinement brought about by the LBF process. The microstructure of the as received steel consists of equiaxed ferrit that of the formed component exhibits elongated orming process (LBF). To es of the as received out and compared; profiling, The chemical analyses formed material; this can be process. The microhardness of ferrite and pearlite while grains.

Keywords: Laser beam forming, deformation , deformation, elongated grains

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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Authors: Zeyneb Kurt, Oguzhan Yavuz

Abstract:

The feature of HIV genome is in a wide range because of it is highly heterogeneous. Hence, the infection ability of the virus changes related with different chemokine receptors. From this point, R5 and X4 HIV viruses use CCR5 and CXCR5 coreceptors respectively while R5X4 viruses can utilize both coreceptors. Recently, in Bioinformatics, R5X4 viruses have been studied to classify by using the coreceptors of HIV genome. The aim of this study is to develop the optimal Multilayer Perceptron (MLP) for high classification accuracy of HIV sub-type viruses. To accomplish this purpose, the unit number in hidden layer was incremented one by one, from one to a particular number. The statistical data of R5X4, R5 and X4 viruses was preprocessed by the signal processing methods. Accessible residues of these virus sequences were extracted and modeled by Auto-Regressive Model (AR) due to the dimension of residues is large and different from each other. Finally the pre-processed dataset was used to evolve MLP with various number of hidden units to determine R5X4 viruses. Furthermore, ROC analysis was used to figure out the optimal MLP structure.

Keywords: Multilayer Perceptron, Auto-Regressive Model, HIV, ROC Analysis

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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