Search results for: ion torrent personal genome machine (PGM)
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 5124

Search results for: ion torrent personal genome machine (PGM)

5124 DeepOmics: Deep Learning for Understanding Genome Functioning and the Underlying Genetic Causes of Disease

Authors: Vishnu Pratap Singh Kirar, Madhuri Saxena

Abstract:

Advancement in sequence data generation technologies is churning out voluminous omics data and posing a massive challenge to annotate the biological functional features. With so much data available, the use of machine learning methods and tools to make novel inferences has become obvious. Machine learning methods have been successfully applied to a lot of disciplines, including computational biology and bioinformatics. Researchers in computational biology are interested to develop novel machine learning frameworks to classify the huge amounts of biological data. In this proposal, it plan to employ novel machine learning approaches to aid the understanding of how apparently innocuous mutations (in intergenic DNA and at synonymous sites) cause diseases. We are also interested in discovering novel functional sites in the genome and mutations in which can affect a phenotype of interest.

Keywords: genome wide association studies (GWAS), next generation sequencing (NGS), deep learning, omics

Procedia PDF Downloads 51
5123 Applying Massively Parallel Sequencing to Forensic Soil Bacterial Profiling

Authors: Hui Li, Xueying Zhao, Ke Ma, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

Abstract:

Soil can often link a person or item to a crime scene, which makes it a valuable evidence in forensic casework. Several techniques have been utilized in forensic soil discrimination in previous studies. Because soil contains a vast number of microbiomes, the analyse of soil microbiomes is expected to be a potential way to characterise soil evidence. In this study, we applied massively parallel sequencing (MPS) to soil bacterial profiling on the Ion Torrent Personal Genome Machine (PGM). Soils from different regions were collected repeatedly. V-region 3 and 4 of Bacterial 16S rRNA gene were detected by MPS. Operational taxonomic units (OTU, 97%) were used to analyse soil bacteria. Several bioinformatics methods (PCoA, NMDS, Metastats, LEfse, and Heatmap) were applied in bacterial profiles. Our results demonstrate that MPS can provide a more detailed picture of the soil microbiomes and the composition of soil bacterial components from different region was individualistic. In conclusion, the utility of soil bacterial profiling via MPS of the 16S rRNA gene has potential value in characterising soil evidences and associating them with their place of origin, which can play an important role in forensic science in the future.

Keywords: bacterial profiling, forensic, massively parallel sequencing, soil evidence

Procedia PDF Downloads 521
5122 Massively Parallel Sequencing Improved Resolution for Paternity Testing

Authors: Xueying Zhao, Ke Ma, Hui Li, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

Abstract:

Massively parallel sequencing (MPS) technologies allow high-throughput sequencing analyses with a relatively affordable price and have gradually been applied to forensic casework. MPS technology identifies short tandem repeat (STR) loci based on sequence so that repeat motif variation within STRs can be detected, which may help one to infer the origin of the mutation in some cases. Here, we report on one case with one three-step mismatch (D18S51) in family trios based on both capillary electrophoresis (CE) and MPS typing. The alleles of the alleged father (AF) are [AGAA]₁₇AGAG[AGAA]₃ and [AGAA]₁₅. The mother’s alleles are [AGAA]₁₉ and [AGAA]₉AGGA[AGAA]₃. The questioned child’s (QC) alleles are [AGAA]₁₉ and [AGAA]₁₂. Given that the sequence variants in repeat regions of AF and mother are not observed in QC’s alleles, the QC’s allele [AGAA]₁₂ was likely inherited from the AF’s allele [AGAA]₁₅ by loss of three repeat [AGAA]. Besides, two new alleles of D18S51 in this study, [AGAA]₁₇AGAG[AGAA]₃ and [AGAA]₉AGGA[AGAA]₃, have not been reported before. All the results in this study were verified using Sanger-type sequencing. In summary, the MPS typing method can offer valuable information for forensic genetics research and play a promising role in paternity testing.

Keywords: family trios analysis, forensic casework, ion torrent personal genome machine (PGM), massively parallel sequencing (MPS)

Procedia PDF Downloads 266
5121 Genome Analyses of Pseudomonas Fluorescens b29b from Coastal Kerala

Authors: Wael Ali Mohammed Hadi

Abstract:

Pseudomonas fluorescens B29B, which has asparaginase enzymatic activity, was isolated from the surface coastal seawater of Trivandrum, India. We report the complete Pseudomonas fluorescens B29B genome sequenced, identified, and annotated from a marine source. We find the genome at most minuscule a 7,331,508 bp single circular chromosome with a GC content of 62.19% and 6883 protein-coding genes. Three hundred forty subsystems were identified, including two predicted asparaginases from the genome analysis of P. fluorescens B29B for further investigation. This genome data will help further industrial biotechnology applications of proteins in general and asparaginase as a target.

Keywords: pseudomonas, marine, asparaginases, Kerala, whole-genome

Procedia PDF Downloads 165
5120 Computing the Similarity and the Diversity in the Species Based on Cronobacter Genome

Authors: E. Al Daoud

Abstract:

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

Procedia PDF Downloads 452
5119 CRISPR-DT: Designing gRNAs for the CRISPR-Cpf1 System with Improved Target Efficiency and Specificity

Authors: Houxiang Zhu, Chun Liang

Abstract:

The CRISPR-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 system varies among different gRNA sequences. The published CRISPR-Cpf1 gRNA data was reanalyzed. Many sequences and structural features of gRNAs (e.g., the position-specific nucleotide composition, position-nonspecific nucleotide composition, GC content, minimum free energy, and melting temperature) correlated with target efficiency were found. Using machine learning technology, a support vector machine (SVM) model was created to predict target efficiency for any given gRNAs. The first web service application, CRISPR-DT (CRISPR DNA Targeting), has been developed to help users design optimal gRNAs for the CRISPR-Cpf1 system by considering both target efficiency and specificity. CRISPR-DT will empower researchers in genome editing.

Keywords: CRISPR-Cpf1, genome editing, target efficiency, target specificity

Procedia PDF Downloads 218
5118 Deleterious SNP’s Detection Using Machine Learning

Authors: Hamza Zidoum

Abstract:

This paper investigates the impact of human genetic variation on the function of human proteins using machine-learning algorithms. Single-Nucleotide Polymorphism represents the most common form of human genome variation. We focus on the single amino-acid polymorphism located in the coding region as they can affect the protein function leading to pathologic phenotypic change. We use several supervised Machine Learning methods to identify structural properties correlated with increased risk of the missense mutation being damaging. SVM associated with Principal Component Analysis give the best performance.

Keywords: single-nucleotide polymorphism, machine learning, feature selection, SVM

Procedia PDF Downloads 339
5117 An Improved Ant Colony Algorithm for Genome Rearrangements

Authors: Essam Al Daoud

Abstract:

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

Procedia PDF Downloads 302
5116 The Role and Importance of Genome Sequencing in Prediction of Cancer Risk

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

Abstract:

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

Procedia PDF Downloads 229
5115 Phenotype Prediction of DNA Sequence Data: A Machine and Statistical Learning Approach

Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 122
5114 Phenotype Prediction of DNA Sequence Data: A Machine and Statistical Learning Approach

Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 110
5113 The Right to Data Portability and Its Influence on the Development of Digital Services

Authors: Roman Bieda

Abstract:

The General Data Protection Regulation (GDPR) will come into force on 25 May 2018 which will create a new legal framework for the protection of personal data in the European Union. Article 20 of GDPR introduces a right to data portability. This right allows for data subjects to receive the personal data which they have provided to a data controller, in a structured, commonly used and machine-readable format, and to transmit this data to another data controller. The right to data portability, by facilitating transferring personal data between IT environments (e.g.: applications), will also facilitate changing the provider of services (e.g. changing a bank or a cloud computing service provider). Therefore, it will contribute to the development of competition and the digital market. The aim of this paper is to discuss the right to data portability and its influence on the development of new digital services.

Keywords: data portability, digital market, GDPR, personal data

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5112 Genome Editing in Sorghum: Advancements and Future Possibilities: A Review

Authors: Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Teklehaimanot Hailesslasie

Abstract:

The advancement of target-specific genome editing tools, including clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9), mega-nucleases, base editing (BE), prime editing (PE), transcription activator-like endonucleases (TALENs), and zinc-finger nucleases (ZFNs), have paved the way for a modern era of gene editing. CRISPR/Cas9, as a versatile, simple, cost-effective and robust system for genome editing, has dominated the genome manipulation field over the last few years. The application of CRISPR/Cas9 in sorghum improvement is particularly vital in the context of ecological, environmental and agricultural challenges, as well as global climate change. In this context, gene editing using CRISPR/Cas9 can improve nutritional value, yield, resistance to pests and disease and tolerance to different abiotic stress. Moreover, CRISPR/Cas9 can potentially perform complex editing to reshape already available elite varieties and new genetic variations. However, existing research is targeted at improving even further the effectiveness of the CRISPR/Cas9 genome editing techniques to fruitfully edit endogenous sorghum genes. These findings suggest that genome editing is a feasible and successful venture in sorghum. Newer improvements and developments of CRISPR/Cas9 techniques have further qualified researchers to modify extra genes in sorghum with improved efficiency. The fruitful application and development of CRISPR techniques for genome editing in sorghum will not only help in gene discovery, creating new, improved traits in sorghum regulating gene expression sorghum functional genomics, but also in making site-specific integration events.

Keywords: CRISPR/Cas9, genome editing, quality, sorghum, stress, yield

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5111 The 1st Personal Pronouns as Evasive Devices in the 2016 Taiwanese Presidential Debate

Authors: Yan-Chi Chen

Abstract:

This study aims to investigate the 1st personal pronouns as evasive devices used by presidential candidates in the 2016 Taiwanese Presidential Debate within the framework of critical discourse analysis (CDA). This study finds that the personal pronoun ‘I’ is the highest frequent personal pronoun in the 2016 Taiwanese Presidential Debate. Generally speaking, the first personal pronouns were used most in the presidential debate, compared with the second and the third personal pronouns. Hence, a further quantitative analysis is conducted to explore the correlation between the frequencies of the two 1st personal pronouns and the other pronouns. Results show that the number of the personal pronoun ‘I’ increases from 26 to 49, with the personal pronoun ‘we’ decreases from 43 to 15 during the debate. Though it seems the personal pronoun ‘I’ has a higher tendency in pronominal choice, statistical evidence demonstrated that the personal pronoun ‘we’ has the greater statistical significance (p<0.0002), compared with that of ‘I’ (p<0.0116). The comparatively small p-value of the personal pronoun ‘we’ means it ‘has a stronger correlation with the overall pronominal choice, and the personal pronoun ‘we’ is more likely to be used than the personal pronoun ‘I’. Therefore, this study concludes that the pronominal choice varies with different evasive strategies. The ingrained functions of these personal pronouns are mainly categorized as ‘agreement’ and ‘justification’. The personal pronoun ’we’ is preferred in the agreement evasive strategies, and ‘I’ is used for justifying oneself. In addition, the personal pronoun ‘we’ can be defined as both ‘inclusive’ and ‘exclusive’ personal pronoun, which rendered ‘we’ more functions not limited to agreement evasive strategies. In conclusion, although the personal pronoun ‘I’ has the highest occurrences, the personal pronoun ‘we’ is more related to the first pronoun choices.

Keywords: critical discourse analysis (CDA), evasive devices, the 1st personal pronouns, the 2016 Taiwanese Presidential Debate

Procedia PDF Downloads 131
5110 The Impact of Personal Identity on Self-Esteem among Muslim Adolescents

Authors: Nadia Ayub

Abstract:

The purpose of the study was to explore the impact of personal identity on self-esteem among adolescents. Two hypotheses were tested in the study, i.e., personal identity effects on self-esteem; and gender difference in the variables of personal identity and self-esteem. The total of 300 (150 female; 150 male) adolescents participated in the study. Personal identity scale (Ayub, N., In Press), and self-esteem scale (Rosenberg, 1985) were administered. The findings of the study suggest that positive personal identity impact on self-esteem and gender difference was found on the variables of personal identity and self-esteem. In conclusion, the results of the study are beneficial for researchers, policymakers, psychologists. The strong positive personal identity and self-esteem help in healthy mental development not only in adolescence but throughout the life of individuals.

Keywords: personal identity, self-esteem, adolescents, positive psychology

Procedia PDF Downloads 358
5109 Human Digital Twin for Personal Conversation Automation Using Supervised Machine Learning Approaches

Authors: Aya Salama

Abstract:

Digital Twin is an emerging research topic that attracted researchers in the last decade. It is used in many fields, such as smart manufacturing and smart healthcare because it saves time and money. It is usually related to other technologies such as Data Mining, Artificial Intelligence, and Machine Learning. However, Human digital twin (HDT), in specific, is still a novel idea that still needs to prove its feasibility. HDT expands the idea of Digital Twin to human beings, which are living beings and different from the inanimate physical entities. The goal of this research was to create a Human digital twin that is responsible for real-time human replies automation by simulating human behavior. For this reason, clustering, supervised classification, topic extraction, and sentiment analysis were studied in this paper. The feasibility of the HDT for personal replies generation on social messaging applications was proved in this work. The overall accuracy of the proposed approach in this paper was 63% which is a very promising result that can open the way for researchers to expand the idea of HDT. This was achieved by using Random Forest for clustering the question data base and matching new questions. K-nearest neighbor was also applied for sentiment analysis.

Keywords: human digital twin, sentiment analysis, topic extraction, supervised machine learning, unsupervised machine learning, classification, clustering

Procedia PDF Downloads 56
5108 Genomic Adaptation to Local Climate Conditions in Native Cattle Using Whole Genome Sequencing Data

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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5107 The Effects of Ethnicity, Personality and Religiosity on Desire for Personal Space

Authors: Ioanna Skoura

Abstract:

Past research shows that personal space has been investigated since the 1950s. Also, personality traits have been found to have a significant relationship with personal space. However, some of these studies have been criticized for being ethically inappropriate. In an attempt to avoid ethical issues, a new scale measuring desire for personal space has been created. The purpose of the present study is to investigate the impact of ethnicity on desire for personal space. Additionally, extraversion and neuroticism are expected to predict significantly desire for personal space. Furthermore, the study is looking for any impact of religiosity on desire for personal space. In order to test the previous hypotheses, 115 participants from three cultural groups (English, Greeks in Greece and Greeks in the UK) are recruited online. Results indicate that only extraversion and religiosity are significant predictors of desire for personal space. Implications of the findings are discussed and suggestions for future research are made.

Keywords: ethnicity, religiosity, personality, personal space

Procedia PDF Downloads 160
5106 Genome Sequencing, Assembly and Annotation of Gelidium Pristoides from Kenton-on-Sea, South Africa

Authors: Sandisiwe Mangali, Graeme Bradley

Abstract:

Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds.

Keywords: Gelidium pristoides, genome, genome sequencing and assembly, Ion S5 sequencing platform

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5105 Genome-Wide Association Study Identify COL2A1 as a Susceptibility Gene for the Hand Development Failure of Kashin-Beck Disease

Authors: Feng Zhang

Abstract:

Kashin-Beck disease (KBD) is a chronic osteochondropathy. The mechanism of hand growth and development failure of KBD remains elusive now. In this study, we conducted a two-stage genome-wide association study (GWAS) of palmar length-width ratio (LWR) of KBD, totally involving 493 Chinese Han KBD patients. Affymetrix Genome Wide Human SNP Array 6.0 was applied for SNP genotyping. Association analysis was conducted by PLINK software. Imputation analysis was performed by IMPUTE against the reference panel of the 1000 genome project. In the GWAS, the most significant association was observed between palmar LWR and rs2071358 of COL2A1 gene (P value = 4.68×10-8). Imputation analysis identified 3 SNPs surrounding rs2071358 with significant or suggestive association signals. Replication study observed additional significant association signals at both rs2071358 (P value = 0.017) and rs4760608 (P value = 0.002) of COL2A1 gene after Bonferroni correction. Our results suggest that COL2A1 gene was a novel susceptibility gene involved in the growth and development failure of hand of KBD.

Keywords: Kashin-Beck disease, genome-wide association study, COL2A1, hand

Procedia PDF Downloads 170
5104 Genome Characterization and Phylogeny Analysis of Viruses Infected Invertebrates, Parvoviridae Family

Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

Abstract:

The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

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5103 Genome-Wide Analysis of Long Terminal Repeat (LTR) Retrotransposons in Rabbit (Oryctolagus cuniculus)

Authors: Zeeshan Khan, Faisal Nouroz, Shumaila Noureen

Abstract:

European or common rabbit (Oryctolagus cuniculus) belongs to class Mammalia, order Lagomorpha of family Leporidae. They are distributed worldwide and are native to Europe (France, Spain and Portugal) and Africa (Morocco and Algeria). LTR retrotransposons are major Class I mobile genetic elements of eukaryotic genomes and play a crucial role in genome expansion, evolution and diversification. They were mostly annotated in various genomes by conventional approaches of homology searches, which restricted the annotation of novel elements. Present work involved de novo identification of LTR retrotransposons by LTR_FINDER in haploid genome of rabbit (2247.74 Mb) distributed in 22 chromosomes, of which 7,933 putative full-length or partial copies were identified containing 69.38 Mb of elements, accounting 3.08% of the genome. Highest copy numbers (731) were found on chromosome 7, followed by chromosome 12 (705), while the lowest copy numbers (27) were detected in chromosome 19 with no elements identified from chromosome 21 due to partially sequenced chromosome, unidentified nucleotides (N) and repeated simple sequence repeats (SSRs). The identified elements ranged in sizes from 1.2 - 25.8 Kb with average sizes between 2-10 Kb. Highest percentage (4.77%) of elements was found in chromosome 15, while lowest (0.55%) in chromosome 19. The most frequent tRNA type was Arginine present in majority of the elements. Based on gained results, it was estimated that rabbit exhibits 15,866 copies having 137.73 Mb of elements accounting 6.16% of diploid genome (44 chromosomes). Further molecular analyses will be helpful in chromosomal localization and distribution of these elements on chromosomes.

Keywords: rabbit, LTR retrotransposons, genome, chromosome

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5102 Predictive Pathogen Biology: Genome-Based Prediction of Pathogenic Potential and Countermeasures Targets

Authors: Debjit Ray

Abstract:

Horizontal gene transfer (HGT) and recombination leads to the emergence of bacterial antibiotic resistance and pathogenic traits. HGT events can be identified by comparing a large number of fully sequenced genomes across a species or genus, define the phylogenetic range of HGT, and find potential sources of new resistance genes. In-depth comparative phylogenomics can also identify subtle genome or plasmid structural changes or mutations associated with phenotypic changes. Comparative phylogenomics requires that accurately sequenced, complete and properly annotated genomes of the organism. Assembling closed genomes requires additional mate-pair reads or “long read” sequencing data to accompany short-read paired-end data. To bring down the cost and time required of producing assembled genomes and annotating genome features that inform drug resistance and pathogenicity, we are analyzing the performance for genome assembly of data from the Illumina NextSeq, which has faster throughput than the Illumina HiSeq (~1-2 days versus ~1 week), and shorter reads (150bp paired-end versus 300bp paired end) but higher capacity (150-400M reads per run versus ~5-15M) compared to the Illumina MiSeq. Bioinformatics improvements are also needed to make rapid, routine production of complete genomes a reality. Modern assemblers such as SPAdes 3.6.0 running on a standard Linux blade are capable in a few hours of converting mixes of reads from different library preps into high-quality assemblies with only a few gaps. Remaining breaks in scaffolds are generally due to repeats (e.g., rRNA genes) are addressed by our software for gap closure techniques, that avoid custom PCR or targeted sequencing. Our goal is to improve the understanding of emergence of pathogenesis using sequencing, comparative genomics, and machine learning analysis of ~1000 pathogen genomes. Machine learning algorithms will be used to digest the diverse features (change in virulence genes, recombination, horizontal gene transfer, patient diagnostics). Temporal data and evolutionary models can thus determine whether the origin of a particular isolate is likely to have been from the environment (could it have evolved from previous isolates). It can be useful for comparing differences in virulence along or across the tree. More intriguing, it can test whether there is a direction to virulence strength. This would open new avenues in the prediction of uncharacterized clinical bugs and multidrug resistance evolution and pathogen emergence.

Keywords: genomics, pathogens, genome assembly, superbugs

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5101 Genetic Diversity and Discovery of Unique SNPs in Five Country Cultivars of Sesamum indicum by Next-Generation Sequencing

Authors: Nam-Kuk Kim, Jin Kim, Soomin Park, Changhee Lee, Mijin Chu, Seong-Hun Lee

Abstract:

In this study, we conducted whole genome re-sequencing of 10 cultivars originated from five countries including Korea, China, India, Pakistan and Ethiopia with Sesamum indicum (Zhongzho No. 13) genome as a reference. Almost 80% of the whole genome sequences of the reference genome could be covered by sequenced reads. Numerous SNP and InDel were detected by bioinformatic analysis. Among these variants, 266,051 SNPs were identified as unique to countries. Pakistan and Ethiopia had high densities of SNPs compared to other countries. Three main clusters (cluster 1: Korea, cluster 2: Pakistan and India, cluster 3: Ethiopia and China) were recovered by neighbor-joining analysis using all variants. Interestingly, some variants were detected in DGAT1 (diacylglycerol O-acyltransferase 1) and FADS (fatty acid desaturase) genes, which are known to be related with fatty acid synthesis and metabolism. These results can provide useful information to understand the regional characteristics and develop DNA markers for origin discrimination of sesame.

Keywords: Sesamum indicum, NGS, SNP, DNA marker

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5100 Genomics of Aquatic Adaptation

Authors: Agostinho Antunes

Abstract:

The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: comparative genomics, adaptive evolution, bioinformatics, phylogenetics, genome mining

Procedia PDF Downloads 492
5099 Insights into the Annotated Genome Sequence of Defluviitoga tunisiensis L3 Isolated from a Thermophilic Rural Biogas Producing Plant

Authors: Irena Maus, Katharina Gabriella Cibis, Andreas Bremges, Yvonne Stolze, Geizecler Tomazetto, Daniel Wibberg, Helmut König, Alfred Pühler, Andreas Schlüter

Abstract:

Within the agricultural sector, the production of biogas from organic substrates represents an economically attractive technology to generate bioenergy. Complex consortia of microorganisms are responsible for biomass decomposition and biogas production. Recently, species belonging to the phylum Thermotogae were detected in thermophilic biogas-production plants utilizing renewable primary products for biomethanation. To analyze adaptive genome features of representative Thermotogae strains, Defluviitoga tunisiensis L3 was isolated from a rural thermophilic biogas plant (54°C) and completely sequenced on an Illumina MiSeq system. Sequencing and assembly of the D. tunisiensis L3 genome yielded a circular chromosome with a size of 2,053,097 bp and a mean GC content of 31.38%. Functional annotation of the complete genome sequence revealed that the thermophilic strain L3 encodes several genes predicted to facilitate growth of this microorganism on arabinose, galactose, maltose, mannose, fructose, raffinose, ribose, cellobiose, lactose, xylose, xylan, lactate and mannitol. Acetate, hydrogen (H2) and carbon dioxide (CO2) are supposed to be end products of the fermentation process. The latter gene products are metabolites for methanogenic archaea, the key players in the final step of the anaerobic digestion process. To determine the degree of relatedness of dominant biogas community members within selected digester systems to D. tunisiensis L3, metagenome sequences from corresponding communities were mapped on the L3 genome. These fragment recruitments revealed that metagenome reads originating from a thermophilic biogas plant covered 95% of D. tunisiensis L3 genome sequence. In conclusion, availability of the D. tunisiensis L3 genome sequence and insights into its metabolic capabilities provide the basis for biotechnological exploitation of genome features involved in thermophilic fermentation processes utilizing renewable primary products.

Keywords: genome sequence, thermophilic biogas plant, Thermotogae, Defluviitoga tunisiensis

Procedia PDF Downloads 461
5098 Genomics of Adaptation in the Sea

Authors: Agostinho Antunes

Abstract:

The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: marine genomics, evolutionary bioinformatics, human genome sequencing, genomic analyses

Procedia PDF Downloads 572
5097 Modified Genome-Scale Metabolic Model of Escherichia coli by Adding Hyaluronic Acid Biosynthesis-Related Enzymes (GLMU2 and HYAD) from Pasteurella multocida

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

Abstract:

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

Procedia PDF Downloads 86
5096 Reform of the Law Relating to Personal Property Security

Authors: Ji Lian Yap

Abstract:

This paper will critically consider developments in 2014 in relation to the law relating to security over personal property in Hong Kong. The rules governing the registration of charges under the Hong Kong Companies Ordinance will be examined. Case law relating to personal property security will also be discussed. The transplantation of the floating charge into China’s Property Law will also be considered.

Keywords: personal property, security law, reform of the law, law

Procedia PDF Downloads 383
5095 In silico Comparative Analysis of Chloroplast Genome (cpDNA) and Some Individual Genes (rbcL and trnH-psbA) in Pooideae Subfamily Members

Authors: Ibrahim Ilker Ozyigit, Ertugrul Filiz, Ilhan Dogan

Abstract:

An in silico analysis of Brachypodium distachyon, Triticum aestivum, Festuca arundinacea, Lolium perenne, Hordeum vulgare subsp. vulgare of the Pooideaea was performed based on complete chloroplast genomes including rbcL coding and trnH-psbA intergenic spacer regions alone to compare phylogenetic resolving power. Neighbor-joining, Minimum Evolution, and Unweighted Pair Group Method with arithmetic mean methods were used to reconstruct phylogenies with the highest bootstrap supported the obtained data from whole chloroplast genome sequence. The highest and lowest values from nucleotide diversity (π) analysis were found to be 0.315813 and 0.043495 in rbcL coding region in chloroplast genome and complete chloroplast genome, respectively. The highest transition/transversion bias (R) value was recorded as 1.384 in complete chloroplast genomes. F. arudinacea-L. perenne clade was uncovered in all phylogenies. Sequences of rbcL and trnH-psbA regions were not able to resolve the Pooideae phylogenies due to lack of genetic variation.

Keywords: chloroplast DNA, Pooideae, phylogenetic analysis, rbcL, trnH-psbA

Procedia PDF Downloads 339