Search results for: genome mining

Authors: Neelma Ashraf

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Actinomycetes, particularly genus Streptomyces is of great importance due to their role in the discovery of new natural products, particularly antimicrobial secondary metabolites in the medicinal science and biotechnology industry. Different Streptomyces strains were isolated from Helianthus annuus plants and tested for antibacterial and antifungal activities. The most promising five strains were chosen for further investigation, and growth conditions for antibiotic synthesis were optimised. The supernatants were extracted in different solvents, and the extracted products were analyzed using liquid chromatography-mass spectrometry (LC-MS) and biological testing. From one of the potent strains Streptomyces globusus sp. BR123, a compound lavendamycin was identified using these analytical techniques. In addition, this potent strain also produces a strong antifungal polyene compound with a quasimolecular ion of 2072. Streptomyces sp. BR123 was genome sequenced because of its promising antimicrobial potential in order to identify the gene cluster responsible for analyzed compound “lavendamycin”. The genome analysis yielded candidate genes responsible for the production of this potent compound. The genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 with a GC content of 72.63% and 8103 protein coding genes was attained. Many antimicrobial, antiparasitic, and anticancerous compounds were detected through multiple biosynthetic gene clusters predicted by in-Silico analysis. Though, the novelty of metabolites was determined through the insignificant resemblance with known biosynthetic gene clusters. The current study gives insight into the bioactive potential of Streptomyces sp. isolate BR123 with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study revealed the connection of isolate BR123 with other Streptomyces strains, which could expand the knowledge of this genus and the mechanism involved in the discovery of new antimicrobial metabolites.

Keywords: streptomyces, secondary metabolites, genome, biosynthetic gene clusters, high performance liquid chromatography, mass spectrometry

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Authors: Kateryna Zharan, Jan C. Bongaerts

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Mining operations are energy intensive, and the share of energy costs in total costs is often quoted in the range of 40 %. Saving on energy costs is, therefore, a key element of any mine operator. With the improving reliability and security of renewable energy (RE) sources, and requirements to reduce carbon dioxide emissions, perspectives for using RE in mining operations emerge. These aspects are stimulating the mining companies to search for ways to substitute fossil energy with RE. Hereby, the main purpose of this study is to present the survey research assessment in matter of finding out the key issues related to the integration of RE into mining activities, based on the mining and renewable energy experts’ opinion. The purpose of the paper is to present the outcomes of a survey conducted among mining and renewable energy experts about the feasibility of RE in mining operations. The survey research has been developed taking into consideration the following categories: first of all, the mining and renewable energy experts were chosen based on the specific criteria. Secondly, they were offered a questionnaire to gather their knowledge and opinions on incentives for mining operators to turn to RE, barriers and challenges to be expected, environmental effects, appropriate business models and the overall impact of RE on mining operations. The outcomes of the survey allow for the identification of factors which favor and disfavor decision-making on the use of RE in mining operations. It concludes with a set of recommendations for further study. One of them relates to a deeper analysis of benefits for mining operators when using RE, and another one suggests that appropriate business models considering economic and environmental issues need to be studied and developed. The results of the paper will be used for developing a hybrid optimized model which might be adopted at mines according to their operation processes as well as economic and environmental perspectives.

Keywords: carbon dioxide emissions, mining industry, photovoltaic, renewable energy, survey research, wind generation

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Authors: Iman Farasat, Howard M. Salis

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The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

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Authors: M. Suwaibah, S. W. Tan, I. Aiini, K. Yusoff, A. R. Omar

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Respiratory diseases are the most important infectious diseases affecting poultry worldwide. One of the avian respiratory virus of global importance causing significant economic losses is Infectious Bronchitis Virus (IBV). The virus causes a wide spectrum disease known as Infectious Bronchitis (IB), affecting not only the respiratory system but also the kidney and the reproductive system, depending on its strain. IB and Newcastle disease are two of the most prevalent diseases affecting poultry in Malaysia. However, a study on the molecular characterization of Malaysian IBV is lacking. In this study, an IBV strain IBS130 which was isolated in 2015 was fully sequenced using next-gene sequencing approach. Sequence analysis of IBS130 based on the complete genome, polyprotein 1ab and S1 genes were compared with other IBV sequences available in Genbank, National Center for Biotechnology Information (NCBI). IBV strain IBS130 is characterised as QX-like strain based on whole genome and S1 gene sequence analysis. Comparisons of the virus with other IBV strains showed that the nucleotide identity ranged from 67% to 99.2%, depending on the region analysed. The similarity in whole genome nucleotide ranging from 84.9% to 90.7% with the least similar was from Singapore strains (84.9%) and highly similar with China QX-like strains. Meanwhile, the similarity in polyprotein 1ab ranging from 85.3% to 89.9% with the least similar to Singapore strains (85.3%) and highly similar with Mass strains from USA.

Keywords: infectious bronchitis virus, phylogenetic analysis, chicken, Malaysia

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Authors: Afsaneh Mohammadnejad, Marianne Nygaard, Jan Baumbach, Shuxia Li, Weilong Li, Jesper Lund, Jacob v. B. Hjelmborg, Lene Christensen, Qihua Tan

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Cognitive impairment in the elderly is a key issue affecting the quality of life. Despite a strong genetic background in cognition, only a limited number of single nucleotide polymorphisms (SNPs) have been found. These explain a small proportion of the genetic component of cognitive function, thus leaving a large proportion unaccounted for. We hypothesize that one reason for this missing heritability is the misspecified modeling in data analysis concerning phenotype distribution as well as the relationship between SNP dosage and the phenotype of interest. In an attempt to overcome these issues, we introduced a model-free method based on the generalized correlation coefficient (GCC) in a genome-wide association study (GWAS) of cognitive function in twin samples and compared its performance with two popular linear regression models. The GCC-based GWAS identified two genome-wide significant (P-value < 5e-8) SNPs; rs2904650 near ZDHHC2 on chromosome 8 and rs111256489 near CD6 on chromosome 11. The kinship model also detected two genome-wide significant SNPs, rs112169253 on chromosome 4 and rs17417920 on chromosome 7, whereas no genome-wide significant SNPs were found by the linear mixed model (LME). Compared to the linear models, more meaningful biological pathways like GABA receptor activation, ion channel transport, neuroactive ligand-receptor interaction, and the renin-angiotensin system were found to be enriched by SNPs from GCC. The GCC model outperformed the linear regression models by identifying more genome-wide significant genetic variants and more meaningful biological pathways related to cognitive function. Moreover, GCC-based GWAS was robust in handling genetically related twin samples, which is an important feature in handling genetic confounding in association studies.

Keywords: cognition, generalized correlation coefficient, GWAS, twins

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Authors: Surabhi Maiti, Prajakta Tamhankar, Prachi Uttam Mehta

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Since the accomplishment of the Human Genome Project, there has been an unparalled escalation in the sequencing of genomic data. This project has been the first major vault in the field of medical research, especially in genomics. This project won accolades by using a concept called Bigdata which was earlier, extensively used to gain value for business. Bigdata makes use of data sets which are generally in the form of files of size terabytes, petabytes, or exabytes and these data sets were traditionally used and managed using excel sheets and RDBMS. The voluminous data made the process tedious and time consuming and hence a stronger framework called Hadoop was introduced in the field of genetic sciences to make data processing faster and efficient. This paper focuses on using SPARK which is gaining momentum with the advancement of BigData technologies. Cloud Storage is an effective medium for storage of large data sets which is generated from the genetic research and the resultant sets produced from SPARK analysis.

Keywords: human genome project, Bigdata, genomic data, SPARK, cloud storage, Hadoop

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Authors: Mohammad Aljuhani, Yasamina Aljuhani

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The Mining Engineering Department at College of Engineering in NBU is under establishment. It is essential to establish such department in NBU. This is because, it is the only university in the region. Moreover, the mining industry is very active in the northern borders region. However, there is no mining engineering department in KSA except one in King Abdulziz University, which is 1400 km from the mining industry in the northern borders. As a result, department graduates from KAU find difficulties to get suitable jobs in their specialization in spite of their few numbers graduated per year and the presence of many jobs vacancies at the local mining sector. Therefore, the objectives of this research are to identify, measure and analyze the above mentioned problem from educational point of view. One more objective is to add a contribution towards solving such vital, society affecting problem. For achieving the first task of the research, that is problem size identification and analyses, a questionnaire was designed. The questionnaire was directed towards experienced engineers, in the mining and related industries, including the ministry of petroleum and minerals, Saudi Geological Survey, and Ma’aden Company as being prospective employers for the mining sector. The questionnaire target was to evaluate the Saudi mining engineers from an industrial point of view and to detect the main reasons behind their failure to find jobs. In addition, the study focuses in the demand of mining engineers in the northern borders region. Moreover, the study plan of the suggested department is designed based on the requirements of the mining industry. The feedback received from the industry reflected major educational shortcomings. In order to overcome the revealed defects, the second objective of the research was achieved where a suggested study plan “curriculum” has been prepared to take into consideration all the points of weakness so as to improve the graduates’ quality to fit the local mining work market.

Keywords: mining engineering, labor market, qualifications, curriculum, mining industry, mining engineers

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Authors: Davidson E. Egirani, Nanfe R. Poyi, Napoleon Wessey

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This paper would report the environmental challenges faced by stakeholders in the development and management of mineral resources in Mindanao mining region of the Philippines. The paper would proffer solutions via the development and management of integrated mineral resource framework. This is by interfacing the views of government, operating mining companies and the mining host communities. The project methods involved the desktop review of existing local, regional, national environmental and mining legislation. This was followed up with visits to mining sites and discussions were held with stakeholders in the mineral sector. The findings from a 2-year investigation would reveal lack of information, education, and communication campaign by stakeholders on environmental, health, political, and social issues in the mining industry. Small-scale miners lack the professional muscles for a balance shift of emphasis to sustainable and responsible mining to avoid environmental degradation and human health effect. Therefore, there is a need to balance ecological requirements, sustainability of the environment and development of mineral resources. This paper would provide an environmentally friendly mineral resource development framework.

Keywords: ecological requirements, environmental degradation, human health, mining legislation, responsible mining

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Authors: Borys Stegniy, Anton Gerilovych, Oleksii Solodiankin, Vitaliy Bolotin, Anton Stegniy, Denys Muzyka, Claudio Afonso

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New APMV was isolated from white fronted goose in Ukraine. This isolate was tested serologically using monoclonal antibodies in haemagglutination-inhibition tests against APMV1-9. As the results obtained isolate showed cross reactions with APMV7. Following investigations were provided for the full genome sequencing using random primers and cloning into pCRII-TOPO. Analysis of 100 transformed colonies of E.coli using traditional sequencing gave us possibilities to find only 3 regions, which could identify by BLAST. The first region with the length of 367 bp had 70 % nucleotide sequence identity to the APMV 12 isolate Wigeon/Italy/3920_1/2005 at genome position 2419-2784. Next region (344 bp) had 66 % identity to the same APMV 12 isolate at position 4760-5103. The last region (365 bp) showed 71 % identity to Newcastle disease virus strain M4 at position 12569-12928.

Keywords: APMV, Newcastle disease virus, Ukraine, full genome sequencing

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Authors: Bilal Wajid, Erchin Serpedin

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The health industry is aiming towards personalized medicine. If the patient’s genome needs to be sequenced it is important that the entire analysis be completed quickly. This paper explores use of parallel computing to analyze very large sequences. Two cases have been considered. In the first case, the sequence is kept constant and the effect of increasing the number of MPI-based processes is evaluated in terms of execution time, speed and efficiency. In the second case the number of MPI-based processes have been kept constant whereas, the length of the sequence was increased.

Keywords: parallel computing, alignment, genome assembly, alignment

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Authors: J. Suneetha, Vijayalaxmi

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Sequential Pattern Mining involves applying data mining methods to large data repositories to extract usage patterns. Sequential pattern mining methodologies used to analyze the data and identify patterns. The patterns have been used to implement efficient systems can recommend on previously observed patterns, in making predictions, improve usability of systems, detecting events, and in general help in making strategic product decisions. In this paper, identified performance of approximate sequential pattern mining defines as identifying patterns approximately shared with many sequences. Approximate sequential patterns can effectively summarize and represent the databases by identifying the underlying trends in the data. Conducting an extensive and systematic performance over synthetic and real data. The results demonstrate that ApproxMAP effective and scalable in mining large sequences databases with long patterns.

Keywords: multiple data, performance analysis, sequential pattern, sequence database scalability

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Authors: Filiz Ersoz, Taner Ersoz, Erkin Guler

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This paper addresses the issues and technique for textile industry using data mining techniques. Data mining has been applied to the stitching of garments products that were obtained from a textile company. Data mining techniques were applied to the data obtained from the CHAID algorithm, CART algorithm, Regression Analysis and, Artificial Neural Networks. Classification technique based analyses were used while data mining and decision model about the production per person and variables affecting about production were found by this method. In the study, the results show that as the daily working time increases, the production per person also decreases. In addition, the relationship between total daily working and production per person shows a negative result and the production per person show the highest and negative relationship.

Keywords: data mining, textile production, decision trees, classification

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Authors: Tanvi P. Patel, Warish D. Patel

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Association rule mining forms the core of data mining and it is termed as one of the well-known methodologies of data mining. Objectives of mining is to find interesting correlations, frequent patterns, associations or casual structures among sets of items in the transaction databases or other data repositories. Hence, association rule mining is imperative to mine patterns and then generate rules from these obtained patterns. For efficient targeted query processing, finding frequent patterns and itemset mining, there is an efficient way to generate an itemset tree structure named Memory Efficient Itemset Tree. Memory efficient IT is efficient for storing itemsets, but takes more time as compare to traditional IT. The proposed strategy generates maximal frequent itemsets from memory efficient itemset tree by using levelwise pruning. For that firstly pre-pruning of items based on minimum support count is carried out followed by itemset tree reconstruction. By having maximal frequent itemsets, less number of patterns are generated as well as tree size is also reduced as compared to MEIT. Therefore, an enhanced approach of memory efficient IT proposed here, helps to optimize main memory overhead as well as reduce processing time.

Keywords: association rule mining, itemset mining, itemset tree, meit, maximal frequent pattern

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Authors: Fahad Hanash Alzahrani

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This paper describes some recent advances in a quickly developing area of data storing and processing based on Data Warehouses and Data Mining techniques, which are associated with software, hardware, data mining algorithms and visualisation techniques having common features for any specific problems and tasks of their implementation.

Keywords: data warehouse, data mining, knowledge discovery in databases, on-line analytical processing

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Authors: Najiba Ouled Omar, Azza Harbaoui, Henda Ben Ghezala

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Current research practices sentiment analysis with a focus on social networks, DEfi Fouille de Texte (DEFT) (Text Mining Challenge) evaluation campaign focuses on opinion mining and sentiment analysis on social networks, especially social network Twitter. It aims to confront the systems produced by several teams from public and private research laboratories. DEFT offers participants the opportunity to work on regularly renewed themes and proposes to work on opinion mining in several editions. The purpose of this article is to scrutinize and analyze the works relating to opinions mining and sentiment analysis in the Twitter social network realized by DEFT. It examines the tasks proposed by the organizers of the challenge and the methods used by the participants.

Keywords: opinion mining, sentiment analysis, emotion, polarity, annotation, OSEE, figurative language, DEFT, Twitter, Tweet

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Authors: Hema Bhardwaj, D. Srinivasa Rao

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Technology for analysing, processing, and extracting meaningful data from enormous and complicated datasets can be termed as "big data." The technique of big data mining and big data analysis is extremely helpful for business movements such as making decisions, building organisational plans, researching the market efficiently, improving sales, etc., because typical management tools cannot handle such complicated datasets. Special computational and statistical issues, such as measurement errors, noise accumulation, spurious correlation, and storage and scalability limitations, are brought on by big data. These unique problems call for new computational and statistical paradigms. This research paper offers an overview of the literature on big data mining, its process, along with problems and difficulties, with a focus on the unique characteristics of big data. Organizations have several difficulties when undertaking data mining, which has an impact on their decision-making. Every day, terabytes of data are produced, yet only around 1% of that data is really analyzed. The idea of the mining and analysis of data and knowledge discovery techniques that have recently been created with practical application systems is presented in this study. This article's conclusion also includes a list of issues and difficulties for further research in the area. The report discusses the management's main big data and data mining challenges.

Keywords: big data, data mining, data analysis, knowledge discovery techniques, data mining challenges

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Authors: Harpreet Singh

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Finding relevant information on the World Wide Web is becoming highly challenging day by day. Web usage mining is used for the extraction of relevant and useful knowledge, such as user behaviour patterns, from web access log records. Web access log records all the requests for individual files that the users have requested from the website. Web usage mining is important for Customer Relationship Management (CRM), as it can ensure customer satisfaction as far as the interaction between the customer and the organization is concerned. Web usage mining is helpful in improving website structure or design as per the user’s requirement by analyzing the access log file of a website through a log analyzer tool. The focus of this paper is to enhance the accessibility and usability of a guitar selling web site by analyzing their access log through Deep Log Analyzer tool. The results show that the maximum number of users is from the United States and that they use Opera 9.8 web browser and the Windows XP operating system.

Keywords: web usage mining, web mining, log file, data mining, deep log analyzer

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Authors: Aishik Deb, Rituparna Sinha

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We have developed an algorithm to detect the abnormal segment/"structural variation in the genome across a number of samples. We have worked on simulated as well as real data from the BAM Files and have designed a segmentation algorithm where abnormal segments are detected. This algorithm aims to improve the accuracy and performance of the existing CNV-CH algorithm. The next-generation sequencing (NGS) approach is very fast and can generate large sequences in a reasonable time. So the huge volume of sequence information gives rise to the need for Big Data and parallel approaches of segmentation. Therefore, we have designed a map-reduce approach for the existing CNV-CH algorithm where a large amount of sequence data can be segmented and structural variations in the human genome can be detected. We have compared the efficiency of the traditional and map-reduce algorithms with respect to precision, sensitivity, and F-Score. The advantages of using our algorithm are that it is fast and has better accuracy. This algorithm can be applied to detect structural variations within a genome, which in turn can be used to detect various genetic disorders such as cancer, etc. The defects may be caused by new mutations or changes to the DNA and generally result in abnormally high or low base coverage and quantification values.

Keywords: cancer detection, convex hull segmentation, map reduce, next generation sequencing

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Authors: Taşkın Deniz Yıldız, Mustafa Topaloğlu, Orhan Kural

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The right to operate a fairly long periods of prior periods and after the 3213 Mining Law has been observed to be shortened in Turkey. Permit the realization of business activities (or concession) requested the purchase of the mine operated "found mine" position, as well as the financial and technical capability to have the owner of the right to operate the mines as well as the principle of equality is important in terms of assessing the best way be. In particular, in this context, license fields "negligence" (downsizing) have noted that the current arrangement for all periods. However, in the period after 3213 Mining Act and a permit to operate more effectively within the framework of implementation of negligence is laid down.

Keywords: mining legislation, operation, permit, Turkey

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Authors: Fuad Ali Mohammed Al-Yarimi

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Many algorithms have been proposed to provide privacy preserving in data mining. These protocols are based on two main approaches named as: the perturbation approach and the Cryptographic approach. The first one is based on perturbation of the valuable information while the second one uses cryptographic techniques. The perturbation approach is much more efficient with reduced accuracy while the cryptographic approach can provide solutions with perfect accuracy. However, the cryptographic approach is a much slower method and requires considerable computation and communication overhead. In this paper, a new scalable protocol is proposed which combines the advantages of the perturbation and distortion along with cryptographic approach to perform privacy preserving in distributed frequent itemset mining on horizontally distributed data. Both the privacy and performance characteristics of the proposed protocol are studied empirically.

Keywords: anonymity data, data mining, distributed frequent itemset mining, gaussian perturbation, perturbation approach, privacy preserving data mining

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Authors: Ghulam Muhammad Ali

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Unveiling of genes involved in drought and root architecture using transcriptomic analyses remained fragmented for further improvement of wheat through genome editing. The purpose of this research endeavor was to unveil the variations in different genes implicated in drought tolerance and root architecture in wheat through RNA-seq data analysis. In this study seedlings of 8 days old, 6 cultivars of wheat namely, Batis, Blue Silver, Local White, UZ888, Chakwal 50 and Synthetic wheat S22 were subjected to transcriptomic analysis for root and shoot genes. Total of 12 RNA samples was sequenced by Illumina. Using updated wheat transcripts from Ensembl and IWGC references with 54,175 gene models, we found that 49,621 out of 54,175 (91.5%) genes are expressed at an RPKM of 0.1 or more (in at least 1 sample). The number of genes expressed was higher in Local White than Batis. Differentially expressed genes (DEG) were higher in Chakwal 50. Expression-based clustering indicated conserved function of DRO1and RPK1 between Arabidopsis and wheat. Dendrogram showed that Local White is sister to Chakwal 50 while Batis is closely related to Blue Silver. This study flaunts transcriptomic sequence variations in different cultivars that showed mutations in genes associated with drought that may directly contribute to drought tolerance. DRO1 and RPK1 genes were fetched/isolated for genome editing. These genes are being edited in wheat through CRISPR-Cas9 for yield enhancement.

Keywords: transcriptomic, wheat, genome editing, drought, CRISPR-Cas9, yield enhancement

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Authors: J. K. Kavitha, D. Manjula, U. Kanimozhi

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Mining frequent and high utility item sets have gained much significance in the recent years. When the data arrives sporadically, incremental and interactive rule mining and utility mining approaches can be adopted to handle user’s dynamic environmental needs and avoid redundancies, using previous data structures, and mining results. The dependence on recommendation systems has exponentially risen since the advent of search engines. This paper proposes a model for building a recommendation system that suggests frequent and high utility item sets over dynamic datasets for a cluster based location prediction strategy to predict user’s trajectories using the Efficient Incremental Rule Mining (EIRM) algorithm and the Fast Update Utility Pattern Tree (FUUP) algorithm. Through comprehensive evaluations by experiments, this scheme has shown to deliver excellent performance.

Keywords: data sets, recommendation system, utility item sets, frequent item sets mining

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Authors: Zate Zewdneh Zana

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Coffea arabica (Arabica coffee), a cornerstone of the global beverage industry, necessitates rigorous genetic conservation due to its economic significance and genetic complexity. In this study, we performed whole-genome resequencing of wild species collected from its birthplace, Ethiopia. Advanced Illumina sequencing technology facilitated the mapping of a high percentage of clean reads to the C. arabica reference genome, revealing a substantial number of genetic variants, predominantly SNPs. Our comprehensive analysis not only uncovered a notable distribution of genomic variants across the coffee genome but also identified distinct genetic groups through phylogenetic and population structure analyses. This genomic study provides invaluable insights into the genetic diversity of C. arabica, highlighting the potential of identified SNPs and InDels in enhancing our understanding of key agronomic traits. The findings contribute significantly to genetic studies and support strategic breeding and conservation efforts essential for sustaining the global coffee industry.

Keywords: population genetics, wild species, evolutionary study, coffee plant

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Authors: Vinod Kumar Gupta, Narendrakumar M. Chaudhari, Suchismitha Iskepalli, Chitra Dutta

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Background-The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference draft genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium. Results-The analysis reveals the exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from the human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. The pan-genome for Prevotella remains “open”. Distribution of various functional COG categories differs appreciably among the habitat-specific genes, within Prevotella pan-genome and between the GIT-derived Bacteroides and Prevotella. The skin and GIT isolates of Prevotella are enriched in singletons involved in Signal transduction mechanisms, while the UGT and oral isolates show higher representation of the Defense mechanisms category. No niche-specific variations could be observed in the distribution of KEGG pathways. Conclusion-Prevotella may have developed distinct genetic strategies for adaptation to different anatomical habitats through selective, niche-specific acquisition and elimination of suitable gene-families. In addition, individual microorganisms tend to develop their own distinctive adaptive stratagems through large repertoires of singletons. Such in situ, habitat-driven refurbishment of the genetic makeup can impart substantial intra-lineage genome diversity within the microbes without perturbing their general taxonomic heritage.

Keywords: body niche adaptation, human microbiome, pangenome, Prevotella

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Authors: Burcu Oralhan, Zeki Oralhan, Nilsun Sariyer, Kumru Uyar

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Data mining has been becoming more and more important and a wide range of applications in recent years. Data mining is the process of find hidden and unknown patterns in big data. One of the applied fields of data mining is Customer Relationship Management. Understanding the relationships between products and customers is crucial for every business. Customer Relationship Management is an approach to focus on customer relationship development, retention and increase on customer satisfaction. In this study, we made an application of a data mining methods in telecommunication customer relationship management side. This study aims to determine the customers profile who likely to leave the system, develop marketing strategies, and customized campaigns for customers. Data are clustered by applying classification techniques for used to determine the churners. As a result of this study, we will obtain knowledge from international telecommunication industry. We will contribute to the understanding and development of this subject in Customer Relationship Management.

Keywords: customer churn analysis, customer relationship management, data mining, telecommunication industry

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Authors: Adel M. Zakri, Mohammed A. Al-Saleh, Judith. K. Brown, Ali M. Idris

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Betasatellites are small circular single stranded DNA molecules found associated with begomoviruses on field symptomatic plants. Their genome size is about half that of the helper begomovirus, ranging between 1.3 and 1.4 kb. The helper begomoviruses are usually members of the family Geminiviridae. Okra leaves showing vein thickening were collected from okra plants growing in Jazan, Saudi Arabia. Total DNA was extracted from leaves and used as a template to amplify circular DNA using rolling circle amplification (RCA) technology. Products were digested with PstI to linearize the helper viral genome(s), and associated DNA satellite(s), yielding a 2.8kbp and 1.4kbp fragment, respectively. The linearized fragments were cloned into the pGEM-5Zf (+) vector and subjected to DNA sequencing. The 2.8 kb fragment was identified as Cotton leaf curl Gezira virus genome, at 2780bp, an isolate closely related to strains reported previously from Saudi Arabia. A clone obtained from the 1.4 kb fragments he 1.4kb was blasted to GeneBank database found to be a betasatellite. The genome of betasatellite was 1357-bp in size. It was found to be a recombinant containing one fragment (877-bp) that shared 91% nt identity with Cotton leaf curl Gezira betasatellite [KM279620], and a smaller fragment [133--bp) that shared 86% nt identity with Tomato leaf curl Sudan virus [JX483708]. This satellite is thus a recombinant between a malvaceous-infecting satellite and a solanaceous-infecting begomovirus.

Keywords: begomovirus, betasatellites, cotton leaf curl Gezira virus, okra plants

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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Authors: Manvar Sagar, Nikul Virpariya

Abstract:

The advancement in data mining techniques plays an important role in many applications. In context of privacy and security issues, the problems caused by association rule mining technique are investigated by many research scholars. It is proved that the misuse of this technique may reveal the database owner’s sensitive and private information to others. Many researchers have put their effort to preserve privacy in Association Rule Mining. Amongst the two basic approaches for privacy preserving data mining, viz. Randomization based and Cryptography based, the later provides high level of privacy but incurs higher computational as well as communication overhead. Hence, it is necessary to explore alternative techniques that improve the over-heads. In this work, we propose an efficient, collusion-resistant cryptography based approach for distributed Association Rule mining using Shamir’s secret sharing scheme. As we show from theoretical and practical analysis, our approach is provably secure and require only one time a trusted third party. We use secret sharing for privately sharing the information and code based identification scheme to add support against malicious adversaries.

Keywords: Privacy, Privacy Preservation in Data Mining (PPDM), horizontally partitioned database, EMHS, MFI, shamir secret sharing

Procedia PDF Downloads 392

Authors: Rokhmatul Insani, Hira Laksmiwati Soemitro

Abstract:

Business Intelligence is a methodology that exploits the data to produce information and knowledge systematically, business intelligence can support the decision-making process. Some methods in business intelligence are data warehouse and data mining. A data warehouse can store historical data from transactional data. For data modelling in data warehouse, we apply dimensional modelling by Kimball. While data mining is used to extracting patterns from the data and get insight from the data. Data mining has many techniques, one of which is segmentation. For profiling of telecommunication customer, we use customer segmentation according to customer’s usage of services, customer invoice and customer payment. Customers can be grouped according to their characteristics and can be identified the profitable customers. We apply K-Means Clustering Algorithm for segmentation. The input variable for that algorithm we use RFM (Recency, Frequency and Monetary) model. All process in data mining, we use tools IBM SPSS modeller.

Keywords: business intelligence, customer segmentation, data warehouse, data mining

Procedia PDF Downloads 463

Authors: A. Argiri, A. Molla, Tzouvalekas, E. Skoufogianni, N. Danalatos

Abstract:

The release of heavy metals into the environment has increased over the last years. In this study, 25 soil samples (0-15 cm) from the fields near the mining area in Drama region were selected. The samples were analyzed in the laboratory for their physicochemical properties and for seven “pseudo-total’’ heavy metals content, namely Pb, Zn, Cd, Cr, Cu, Ni, and Mn. The total metal concentrations (Pb, Zn, Cd, Cr, Cu, Ni and Mn) in digests were determined by using the atomic absorption spectrophotometer. According to the results, the mean concentration of the listed heavy metals in 25 soil samples are Cd 1.1 mg/kg, Cr 15 mg/kg, Cu 21.7 mg/kg, Ni 30.1 mg/kg, Pd 50.8 mg/kg, Zn 99.5 mg/kg and Mn 815.3 mg/kg. The results show that the heavy metals remain in the soil even if the mining closed many years ago.

Keywords: Greece, heavy metals, mining, pollution

Procedia PDF Downloads 115