Search results for: CRISPR/Cas9 genome editing

Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: metabolic network, gene knockout, flux balance analysis, microarray data, integration

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Authors: Priscila A. Bernardes, Marcos E. Buzanskas, Luciana C. A. Regitano, Ricardo V. Ventura, Danisio P. Munari

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The best linear unbiased predictor (BLUP) is a method commonly used in genetic evaluations of breeding programs. However, this approach can lead to higher inbreeding coefficients in the population due to the intensive use of few bulls with higher genetic potential, usually presenting some degree of relatedness. High levels of inbreeding are associated to low genetic viability, fertility, and performance for some economically important traits and therefore, should be constantly monitored. Unreliable pedigree data can also lead to misleading results. Genomic information (i.e., single nucleotide polymorphism – SNP) is a useful tool to estimate the inbreeding coefficient. Runs of homozygosity have been used to evaluate homozygous segments inherited due to direct or collateral inbreeding and allows inferring population selection history. This study aimed to evaluate runs of homozygosity (ROH) and inbreeding in a population of Nelore beef cattle. A total of 814 animals were genotyped with the Illumina BovineHD BeadChip and the quality control was carried out excluding SNPs located in non-autosomal regions, with unknown position, with a p-value in the Hardy-Weinberg equilibrium lower than 10⁻⁵, call rate lower than 0.98 and samples with the call rate lower than 0.90. After the quality control, 809 animals and 509,107 SNPs remained for analyses. For the ROH analysis, PLINK software was used considering segments with at least 50 SNPs with a minimum length of 1Mb in each animal. The inbreeding coefficient was calculated using the ratio between the sum of all ROH sizes and the size of the whole genome (2,548,724kb). A total of 25.711 ROH were observed, presenting mean, median, minimum, and maximum length of 3.34Mb, 2Mb, 1Mb, and 80.8Mb, respectively. The number of SNPs present in ROH segments varied from 50 to 14.954. The longest ROH length was observed in one animal, which presented a length of 634Mb (24.88% of the genome). Four bulls were among the 10 animals with the longest extension of ROH, presenting 11% of ROH with length higher than 10Mb. Segments longer than 10Mb indicate recent inbreeding. Therefore, the results indicate an intensive use of few sires in the studied data. The distribution of ROH along the chromosomes showed that chromosomes 5 and 6 presented a large number of segments when compared to other chromosomes. The mean, median, minimum, and maximum inbreeding coefficients were 5.84%, 5.40%, 0.00%, and 24.88%, respectively. Although the mean inbreeding was considered low, the ROH indicates a recent and intensive use of few sires, which should be avoided for the genetic progress of breed.

Keywords: autozygosity, Bos taurus indicus, genomic information, single nucleotide polymorphism

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Authors: Sharifa Alshahrani

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Comics is a multimodal text wherein meaning is created by taking in all modes of expression at once. It uses two different semiotic modes, the verbal and the visual modes, together to make meaning and these different semiotic modes can be socially and culturally shaped to give meaning. Therefore, comics translation cannot treat comics as a monomodal text by translating only the verbal mode inside or outside the speech balloons as the cultural differences are encoded in the visual mode as well. Due to the development of the internet and editing software, comics translation is not anymore confined to the publishing houses and official translation as scanlation, or the fan translation took the initiative in translating comics for being emotionally attracted to the culture and genre. Scanlation is carried out by volunteering fans who translate out of passion. However, quality is one of the debatable issues relating to scanlation and fan translation. This study will investigate how the dynamic multimodal relationship in comics is exploited and interpreted in the translation by exploring the translation strategies and procedures adopted by the publishing houses and scanlation in interpreting comics into Arabic using three analytical frameworks; cultural references model, multimodal relation model and translation strategies and procedures models.

Keywords: comics, multimodality, translation, scanlation

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Authors: Debbarma Asis, Guha Chandan

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Tumor Protein-53 (P53) is one of the tumor suppressor proteins. P53 regulates the cell cycle that conserves stability by preventing genome mutation. It is named so as it runs as 53-kilodalton (kDa) protein on Polyacrylamide gel electrophoresis although the actual mass is 43.7 kDa. Experimental evidence has indicated that P53 cancer mutants loses tumor suppression activity and subsequently gain oncogenic activities to promote tumourigenesis. Tumor-specific DNA has recently been detected in the plasma of breast cancer patients. Detection of tumor-specific genetic materials in cancer patients may provide a unique and valuable tumor marker for diagnosis and prognosis. Commercially available MDA-468 breast cancer cell line was used for the proposed study.

Keywords: tumor protein (P53), cancer mutants, MDA-468, tumor suppressor gene

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: Sukrat Sinha, Abhay Kumar, Shanthy Sundaram

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The Leishmania homologue of activated C kinase (LACK) is known T cell epitope from soluble Leishmania antigens (SLA) that confers protection against Leishmania challenge. This antigen has been found to be highly conserved among Leishmania strains. LACK has been shown to be protective against L. donovani challenge. A comprehensive analysis of several LACK sequences was completed. The analysis shows a high level of conservation, lower variability and higher antigenicity in specific portions of the LACK protein. This information provides insights for the potential consideration of LACK as a putative candidate in the context of visceral Leishmaniasis vaccine target.

Keywords: bioinformatics, genome assembly, leishmania activated protein kinase c (lack), next-generation sequencing

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Authors: Khan Farhan Rafat, M. Junaid Hussain

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Seamless modification of an entity for the purpose of hiding a message of significance inside its substance in a manner that the embedding remains oblivious to an observer is known as steganography. Together with today's pervasive registering frameworks, steganography has developed into a science that offers an assortment of strategies for stealth correspondence over the globe that must, however, need a critical appraisal from security breach standpoint. Microsoft Word is amongst the preferably used word processing software, which comes as a part of the Microsoft Office suite. With a user-friendly graphical interface, the richness of text editing, and formatting topographies, the documents produced through this software are also most suitable for stealth communication. This research aimed not only to epitomize the fundamental concepts of steganography but also to expound on the utilization of Microsoft Word document as a carrier for furtive message exchange. The exertion is to examine contemporary message hiding schemes from security aspect so as to present the explorative discoveries and suggest enhancements which may serve a wellspring of information to encourage such futuristic research endeavors.

Keywords: hiding information in plain sight, stealth communication, oblivious information exchange, conceal, steganography

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Authors: F. H. Abanda, B. Kamsu-Foguem, J. H. M. Tah

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Construction cost estimation is one of the most important aspects of construction project design. For generations, the process of cost estimating has been manual, time-consuming and error-prone. This has partly led to most cost estimates to be unclear and riddled with inaccuracies that at times lead to over- or under-estimation of construction cost. The development of standard set of measurement rules that are understandable by all those involved in a construction project, have not totally solved the challenges. Emerging Building Information Modelling (BIM) technologies can exploit standard measurement methods to automate cost estimation process and improves accuracies. This requires standard measurement methods to be structured in ontologically and machine readable format; so that BIM software packages can easily read them. Most standard measurement methods are still text-based in textbooks and require manual editing into tables or Spreadsheet during cost estimation. The aim of this study is to explore the development of an ontology based on New Rules of Measurement (NRM) commonly used in the UK for cost estimation. The methodology adopted is Methontology, one of the most widely used ontology engineering methodologies. The challenges in this exploratory study are also reported and recommendations for future studies proposed.

Keywords: BIM, construction projects, cost estimation, NRM, ontology

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

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Authors: Victoria Zenotz

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For Fairclough (1989) critical literacy is a tool to enable readers and writers to build up meaning in discourse. More recently other authors (Leu et al., 2004) have included the new technology context in their definition of literacy. In their view being literate nowadays means to “successfully use and adapt to the rapidly changing information and communication technologies and contexts that continuously emerge in our world and influence all areas of our personal and professional lives.” (Leu et al., 2004: 1570). In this presentation the concept of critical literacy will be related to the creation of digital stories. In the first part of the presentation concepts such as literacy and critical literacy are examined. We consider that real social practices will help learners may improve their literacy level. Accordingly, we show some research, which was conducted at a secondary school in the north of Spain (2013-2014), to illustrate how the “writing” of digital stories may contribute to the development of critical literacy. The use of several instruments allowed the collection of data at the different stages of their creative process including watching and commenting models for digital stories, planning a storyboard, creating and selecting images, adding voices and background sounds, editing and sharing the final product. The results offer some valuable insights into learners’ literacy progress.

Keywords: literacy, computer assisted language learning, esl

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Authors: Angela U. Makolo

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Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

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Authors: Jamileh Darsareh, Mohammad Nikafrooz

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Some teachers and e-content producers, based on their experiences, try to produce educational videos using screen recording software. There are many challenges that they may encounter while producing screen-recorded videos. These are in the domains of technical and pedagogical challenges like designing the roadmap, preparing the screen, setting the recording software and recording the screen, editing, etc. This study is a descriptive study and tries to present some procedures for producing acceptable and well-made videos. These procedures are presented in the form of an algorithm for producing screen-recorded video. This algorithm presents the main producing phases, including design, pre-production, production, post-production, and distribution. These phases consist of some steps which are supported by several technical and pedagogical considerations. Following these phases and steps according to the suggested order helps the producers to produce their intended and desired video by saving time and also facing fewer technical problems. It is expected that by using this algorithm, e-content producers and teachers gain better performance in producing educational videos.

Keywords: e-content producing algorithm, screen-recorded videos, screen recording software, technical and pedagogical considerations

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Authors: J. Areerut

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Experimental Film Class Project is supported by the Institute for Research and Development at Suan Sunandha Rajabhat University. This project is purported to provide academic and professional services to improve the quality standards of the community and locals in accordance with the mission of the university, which is to improve and expand knowledge for the community and to develop and transfer such knowledge and professions to the next generation. Eventually, it leads to sustainable development because the development of human resources is deemed as the key for sustainable development. Moreover, the Experimental Film Class is an integral part of the teaching of film production at Suan Sunandha International School of Art (SISA). By means of giving opportunities to students for participation in projects by sharing experience, skill and knowledge and participation in field activities, it helps students in the film production major to enhance their abilities and potentials as preparation for their readiness in the marketplace. Additionally, in this class, we provide basic film knowledge, screenwriting techniques, editing and subtitles including uploading videos on social media such as YouTube and Facebook for the participant students.

Keywords: experimental film class, Watbangkapom School, participant students, basic of film production, film workshop

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Authors: Wen Zhang

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The smartphone plays a significant role in media convergence, and smartphone photography is reconstructing the way we communicate and think. This article aims to explore the smartphone photography practices of urban Chinese smartphone users and images produced by smartphones from a techno-cultural perspective. The analysis consists of two types of data: One is a semi-structured interview of 21 participants, and the other consists of the images created by the participants. The findings are organised in two parts. The first part summarises the current tendencies of capturing, editing, sharing and archiving digital images via smartphones. The second part shows that food and selfie/anti-selfie are the preferred subjects of smartphone photographic images from a technical and multi-purpose perspective and demonstrates that screenshots and image texts are new genres of non-photographic images that are frequently made by smartphones, which contributes to improving operational efficiency, disseminating information and sharing knowledge. The analyses illustrate the positive impacts between smartphones and photography enthusiasm and practices based on the diffusion of innovation theory, which also makes us rethink the value of photographs and the practice of ‘photographic seeing’ from the screen itself.

Keywords: digital photography, image-text, media convergence, photographic- seeing, selfie/anti-selfie, smartphone, technological innovation

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Authors: Ayesha Selwyn, Annapoorni Chandrashekar, Kumar Ashwarya, Nishant Baghel

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Project-based learning (PBL) activities are typically implemented in technology-enabled schools by highly trained teachers. In rural India, students have limited access to technology and quality education. Implementing typical PBL activities is challenging. This study details how Pratham Education Foundation’s Hybrid Learning model was used to implement two PBL activities related to music in 900 remote Indian villages with 46,000 students aged 10-14. The activities were completed by 69% of groups that submitted a total of 15,000 videos (completed projects). Pratham’s H-Learning model reaches 100,000 students aged 3-14 in 900 Indian villages. The community-driven model engages students in 20,000 self-organized groups outside of school. The students are guided by 6,000 youth volunteers and 100 facilitators. The students partake in learning activities across subjects with the support of community stakeholders and offline digital content on shared Android tablets. A training and implementation toolkit for PBL activities is designed by subject experts. This toolkit is essential in ensuring efficient implementation of activities as facilitators aren’t highly skilled and have limited access to training resources. The toolkit details the activity at three levels of student engagement - enrollment, participation, and completion. The subject experts train project leaders and facilitators who train youth volunteers. Volunteers need to be trained on how to execute the activity and guide students. The training is focused on building the volunteers’ capacity to enable students to solve problems, rather than developing the volunteers’ subject-related knowledge. This structure ensures that continuous intervention of subject matter experts isn’t required, and the onus of judging creativity skills is put on community members. 46,000 students in the H-Learning program were engaged in two PBL activities related to Music from April-June 2019. For one activity, students had to conduct a “musical survey” in their village by designing a survey and shooting and editing a video. This activity aimed to develop students’ information retrieval, data gathering, teamwork, communication, project management, and creativity skills. It also aimed to identify talent and document local folk music. The second activity, “Pratham Idol”, was a singing competition. Students participated in performing, producing, and editing videos. This activity aimed to develop students’ teamwork and creative skills and give students a creative outlet. Students showcased their completed projects at village fairs wherein a panel of community members evaluated the videos. The shortlisted videos from all villages were further evaluated by experts who identified students and adults to participate in advanced music workshops. The H-Learning framework enables students in low resource settings to engage in PBL and develop relevant skills by leveraging community support and using video creation as a tool. In rural India, students do not have access to high-quality education or infrastructure. Therefore designing activities that can be implemented by community members after limited training is essential. The subject experts have minimal intervention once the activity is initiated, which significantly reduces the cost of implementation and allows the activity to be implemented at a massive scale.

Keywords: community supported learning, project-based learning, self-organized learning, education technology

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Authors: Michael Ngongeh Mombe

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This Paper seeks to investigate an assertion made by some colleagues that there is no need paying a human translator to translate their literary texts, that there are softwares such as Reverso that can be used to do the translation. The main objective of this study is to examine the veracity of this assertion using Reverso to translate a literary text without any post-editing by a human translator. The work is based on two theories: Skopos and Communicative theories of translation. The work is a documentary research where data were collected from published documents in libraries, on the internet and from the translation produced by Reverso. We made a comparative text analyses of both source and target texts in a bid to highlight the weaknesses and strengths of the software. Findings of this work revealed that those who advocate the use of only Machine translation do so in ignorance of the translation mistakes usually made by the software. From the review of all the 268 segments of translation, we found out that the translation produced by Reverso is fraught with errors. We therefore recommend the use of human translators to either do the translation of their literary texts or revise the translation produced by machine to conform to the skopos of the work. This paper is based on Reverso translation. Similar works in the near future will be based on the other translation softwares to determine their weaknesses and strengths.

Keywords: machine translation, human translator, Reverso, literary text

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Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

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Authors: Chisakan Papapankiad

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The purposes of this research were 1) to study the competency of condominium managers, 2) to create the training curriculum via electronic media for condominium managers, and 3) to evaluate the training curriculum for condominium managers. The research methods included document analysis, interview, questionnaire, and a try-out. A total of 20 experts were selected to collect data by using Delphi technique. The designed curriculum was tried out with 30 condominium managers. The important steps of conducting this research included analyzing and synthesizing, creating interview questions, conducting factor analysis and developing the training curriculum, editing by experts, and trying out with sample groups. The findings revealed that there were five core competencies: leadership, human resources management, management, communication, and self-development. The training curriculum was designed and all the learning materials were put into a CD. The evaluation of the training curriculum was performed by five experts and the training curriculum was found to be cohesive and suitable for use in the real world. Moreover, the findings also revealed three important issues: 1) the competencies of the respondents after the experiment were higher than before the experiment and this had a level of significance of 0.01, 2) the competencies remained with the respondents at least 12 weeks and this also had a level of significance of 0.01, and 3) the overall level of satisfaction from the respondents were 'the highest level'.

Keywords: competency training curriculum, condominium managers, electronic media

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Authors: Jian-Jun Shu

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The statistical properties of CRMs are explored by estimating similar-word set occurrence distribution. It is observed that CRMs tend to have a fat-tail distribution for similar-word set occurrence. Thus, the fat-tail test with two fatness coefficients is proposed to distinguish CRMs from non-CRMs, especially from exons. For the first fatness coefficient, the separation accuracy between CRMs and exons is increased as compared with the existing content-based CRM prediction method – fluffy-tail test. For the second fatness coefficient, the computing time is reduced as compared with fluffy-tail test, making it very suitable for long sequences and large data-base analysis in the post-genome time. Moreover, these indexes may be used to predict the CRMs which have not yet been observed experimentally. This can serve as a valuable filtering process for experiment.

Keywords: statistical approach, transcription factor binding sites, cis-regulatory modules, DNA sequences

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Authors: Jiwon Lee, Si-hwan Jang, Sanghyun Joo

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The popularity of emoticons are on the rise since the mobile messengers are generalized. At the same time, few problems of emoticons are also occurred due to innate characteristics of emoticons. Too many emoticons make difficult people to select one which is well-suited for user's intention. On the contrary to this, sometimes user cannot find the emoticon which expresses user's exact intention. Poor information delivery of emoticon is another problem due to a major part of current emoticons are focused on emotion delivery. In this situation, we propose a new concept of emoticons, editable emoticons, to solve above drawbacks of emoticons. User can edit the components inside the proposed editable emoticon and send it to express his exact intention. By doing so, the number of editable emoticons can be maintained reasonable, and it can express user's exact intention. Further, editable emoticons can be used as information deliverer according to user's intention and editing skills. In this paper, we propose the concept of editable emoticons and schema based editable emoticon description method. The proposed description method is 200 times superior to the compared screen capturing method in the view of transmission bandwidth. Further, the description method is designed to have compatibility since it follows MPEG-UD international standard. The proposed editable emoticons can be exploited not only mobile applications, but also various fields such as education and medical field.

Keywords: description schema, editable emoticon, emoticon transmission, mobile applications

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Authors: Gunta Resevica, Nikita Zrelovs, Ivars Silamikelis, Ieva Kalnciema, Helvijs Niedra, Gunārs Lācis, Toms Bartulsons, Inga Moročko-Bičevska, Arturs Stalažs, Kristīne Drevinska, Andris Zeltins, Ina Balke

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Newly discovered viruses provide novel knowledge for basic phytovirus research, serve as tools for biotechnology and can be helpful in identification of epidemic outbreaks. Blackcurrant-associated rhabdovirus (BCaRV) have been discovered in USA germplasm collection samples from Russia and France. As it was reported in one accession originating from France it is unclear whether the material was already infected when it entered in the USA or it became infected while in collection in the USA. Due to that BCaRV was definite as non-EU viruses. According to ICTV classification BCaRV is representative of Blackcurrant betanucleorhabdovirus specie in genus Betanucleorhabdovirus (family Rhabdoviridae). Nevertheless, BCaRV impact on the host, transmission mechanisms and vectors are still unknown. In RNA-seq data pool from Ribes plants resistance gene study by high throughput sequencing (HTS) we observed differences between sample group gene transcript heat maps. Additional analysis of the whole data pool (total 393660492 of 150 bp long read pairs) by rnaSPAdes v 3.13.1 resulted into 14424 bases long contig with an average coverage of 684x with shared 99.5% identity to the previously reported first complete genome of BCaRV (MF543022.1) using EMBOSS Needle. This finding proved BCaRV presence in EU and indicated that it might be relevant pathogen. In this study leaf tissue from twelve asymptomatic blackcurrant cv. Mara Eglite plants (negatively tested for blackcurrant reversion virus (BRV)) from Dobele, Latvia (56°36'31.9"N, 23°18'13.6"E) was collected and used for total RNA isolation with RNeasy Plant Mini Kit with minor modifications, followed by plant rRNA removal by a RiboMinus Plant Kit for RNA-Seq. HTS libraries were prepared using MGI Easy RNA Directional Library Prep Set for 16 reactions to obtain 150 bp pair-end reads. Libraries were pooled, circularized and cleaned and sequenced on DNBSEQ-G400 using PE150 flow cell. Additionally, all samples were tested by RT-PCR, and amplicons were directly sequenced by Sanger-based method. The contig representing the genome of BCaRV isolate Mara Eglite was deposited at European Nucleotide Archive under accession number OU015520. Those findings indicate a second evidence on the presence of this particular virus in the EU and further research on BCaRV prevalence in Ribes from other geographical areas should be performed. As there are no information on BCaRV impact on the host this should be investigated, regarding the fact that mixed infections with BRV and nucleorhabdoviruses are reported.

Keywords: BCaRV, Betanucleorhabdovirus, Ribes, RNA-seq

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Hao Yuan, Yongjian Shen, Xiangjun He, Yuheng Li, Zhouzhou Zhang, Pengyu Zhang, Minkang Cai

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Remote sensing data can provide support for decision-making in disaster assessment or disaster relief. The traditional processing methods of sensitive targets in remote sensing mapping are mainly based on manual retrieval and image editing tools, which are inefficient. Methods based on deep learning for sensitive target hiding are faster and more flexible. But these methods have disadvantages in training time and cost of calculation. This paper proposed a target hiding model Self Attention (SA) Deepfill, which used self-attention modules to replace part of gated convolution layers in image inpainting. By this operation, the calculation amount of the model becomes smaller, and the performance is improved. And this paper adds free-form masks to the model’s training to enhance the model’s universal. The experiment on an open remote sensing dataset proved the efficiency of our method. Moreover, through experimental comparison, the proposed method can train for a longer time without over-fitting. Finally, compared with the existing methods, the proposed model has lower computational weight and better performance.

Keywords: remote sensing mapping, image inpainting, self-attention mechanism, target hiding

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Authors: Abdul Wahid

Abstract:

Inner speech, also known as verbal thinking, self-talk or private speech, is characterized by the subjective language experience in the absence of overt or audible speech. It is a psychological form of verbal activity which is being rehearsed without the articulation of any sound wave. In Psychology, self-limiting speech means the type of speech which contains information that inhibits the development of the self. People, in most cases, experience inner speech in their first language. It is very frequent in Bangladesh where the Bangla (L1) speaking students lose track of speech during their presentations in English (L2). This paper investigates into the long pauses (more than 0.4 seconds long) in English (L2) presentations by Bangla speaking students (18-21 year old) and finds the intervention of Bangla (L1) inner speech as one of its causes. The overt speeches of the presenters are placed on Audacity Audio Editing software where the length of pauses are measured in milliseconds. Varieties of inner speech questionnaire (VISQ) have been conducted randomly amongst the participants out of whom 20 were selected who have similar phenomenology of inner speech. They have been interviewed to describe the type and content of the voices that went on in their head during the long pauses. The qualitative interview data are then codified and converted into quantitative data. It was observed that in more than 80% cases students experience self-limiting inner speech/self-talk during their unwanted pauses in L2 presentations.

Keywords: Bangla-English Bilinguals, inner speech, L1 intervention in bilingualism, motor schema, pauses, phonological loop, phonological store, working memory

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Authors: Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Fayez Gebali

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This paper presents a novel semi-systolic array architecture for an optimized parallel sequence alignment algorithm. This architecture has the advantage that it can be modified to be reused for multiple pass processing in order to increase the number of processing elements that can be packed into a single FPGA and to increase the number of sequences that can be aligned in parallel in a single FPGA. This resolves the potential problem of many FPGA resources left unused for designs that have large values of short read length. When using the previously published conventional hardware design. FPGA implementation results show that, for large values of short read lengths (M>128), the proposed design has a slightly higher speed up and FPGA utilization over the the conventional one.

Keywords: bioinformatics, genome sequence alignment, re-sequencing applications, systolic array

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Authors: John G. Skelly, Peter K. Dearden, Thomas W. R. Harrop, Sarah N. Inwood, Joseph Guhlin

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The Argentine stem weevil (ASW; L. bonariensis) is an economically important pasture pest in New Zealand, which causes about $200 million of damage per annum. Microctonus hyperodae (Mh), a parasite of the ASW in its natural range in South America, was introduced into New Zealand to curb the pasture damage caused by the ASW. Mh is an endoparasitic wasp that lays its eggs in the ASW halting its reproduction. Mh was initially successful at preventing ASW proliferation and reducing pasture damage. The effectiveness of Mh has since declined due to decreased parasitism rates and has resulted in increased pasture damage. Although the mechanism through which ASW has developed resistance to Mh has not been discovered, it has been proposed to be due to the different reproductive modes used by Mh and the ASW in New Zealand. The ASW reproduces sexually, whereas Mh reproduces asexually, which has been hypothesised to have allowed the ASW to ‘out evolve’ Mh. Other species within the Microctonus genus reproduce both sexually and asexually. Strains of Microctonus aethiopoides (Ma), a species closely related to Mh, reproduce either by sexual or asexual reproduction. Comparing the genomes of sexual and asexual Microctonus may allow for the identification of the mechanism of asexual reproduction and other characteristics that may improve Mh as a biocontrol agent. The genomes of Mh and three strains of Ma, two of which reproduce sexually and one reproduces asexually, have been sequenced and annotated. The French (MaFR) and Moroccan (MaMO) reproduce sexually, whereas the Irish strain (MaIR) reproduces asexually. Like Mh, The Ma strains are also used as biocontrol agents, but for different weevil species. The genomes of Mh and MaIR were subsequently upgraded using Hi-C, resulting in a set of high quality, highly contiguous genomes. A subset of the genes involved in mitosis and meiosis, which have been identified though the use of Hidden Markov Models generated from genes involved in these processes in other Hymenoptera, have been catalogued in Mh and the strains of Ma. Meiosis and mitosis genes were broadly conserved in both sexual and asexual Microctonus species. This implies that either the asexual species have retained a subset of the molecular components required for sexual reproduction or that the molecular mechanisms of mitosis and meiosis are different or differently regulated in Microctonus to other insect species in which these mechanisms are more broadly characterised. Bioinformatic analysis of the chemoreceptor compliment in Microctonus has revealed some variation in the number of olfactory receptors, which may be related to host preference. Phylogenetic analysis of olfactory receptors highlights variation, which may be able to explain different host range preferences in the Microctonus. Hi-C clustering implies that Mh has 12 chromosomes, and MaIR has 8. Hence there may be variation in gene regulation between species. Genome alignment of Mh and MaIR implies that there may be large scale genome structural variation. Greater insight into the genetics of these agriculturally important group of parasitic wasps may be beneficial in restoring or maintaining their biocontrol efficacy.

Keywords: argentine stem weevil, asexual, genomics, Microctonus hyperodae

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Authors: Danny Barash

Abstract:

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

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Authors: M. Nikafrooz, J. Darsareh

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Due to the COVID-19 pandemic, its impacts on education all over the world and the problems arising from the use of traditional methods in education, it was necessary to apply alternative solutions to achieve educational goals. In this regard, electronic content production through screen recording and giving educational services in virtual classes became popular among many teachers. But the production of screen recorded videos involves special technical and educational considerations so that educators could be able to produce valuable and well-made videos by taking those considerations into account. The purpose of this study was to extract and find the technical and educational considerations of producing screen recorded videos to provide a useful and comprehensive guideline for e-content producers to enable them to produce high-quality educational videos. This study is fundamental research and data collection has been done using the Delphi method. In this research, an attempt has been made to provide the necessary criteria and considerations regarding the design and production of screen recorded videos by studying the literatures, identifying and analyzing learners' and teachers' needs and expectations, reviewing the previously produced videos. The results of these studies led to the finding and extracting 129 indicators in the form of 6 criteria. Such considerations are expected to reduce production and editing time, increase the technical and educational quality, and finally facilitating and enhancing the processes of teaching and learning.

Keywords: e-content, screen recorded videos, screen recording software, technical and pedagogical considerations

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Authors: Felice Elefant, Akanksha Bhatnaghar, Keegan Krick, Elizabeth Heller

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Context: The severity of Alzheimer’s Disease (AD) progression involves an interplay of genetics, age, and environmental factors orchestrated by histone acetyltransferase (HAT) mediated neuroepigenetic mechanisms. While disruption of Tip60 HAT action in neural gene control is implicated in AD, alternative mechanisms underlying Tip60 function remain unexplored. Altered RNA splicing has recently been highlighted as a widespread hallmark in the AD transcriptome that is implicated in the disease. Research Aim: The aim of this study was to identify a novel RNA binding/splicing function for Tip60 in human hippocampus and impaired in brains from AD fly models and AD patients. Methodology/Analysis: The authors used RNA immunoprecipitation using RNA isolated from 200 pooled wild type Drosophila brains for each of the 3 biological replicates. To identify Tip60’s RNA targets, they performed genome sequencing (DNB-SequencingTM technology, BGI genomics) on 3 replicates for Input RNA and RNA IPs by Tip60. Findings: The authors' transcriptomic analysis of RNA bound to Tip60 by Tip60-RNA immunoprecipitation (RIP) revealed Tip60 RNA targets enriched for critical neuronal processes implicated in AD. Remarkably, 79% of Tip60’s RNA targets overlap with its chromatin gene targets, supporting a model by which Tip60 orchestrates bi-level transcriptional regulation at both the chromatin and RNA level, a function unprecedented for any HAT to date. Since RNA splicing occurs co-transcriptionally and splicing defects are implicated in AD, the authors investigated whether Tip60-RNA targeting modulates splicing decisions and if this function is altered in AD. Replicate multivariate analysis of transcript splicing (rMATS) analysis of RNA-Seq data sets from wild-type and AD fly brains revealed a multitude of mammalian-like AS defects. Strikingly, over half of these altered RNAs were bonafide Tip60-RNA targets enriched for in the AD-gene curated database, with some AS alterations prevented against by increasing Tip60 in fly brain. Importantly, human orthologs of several Tip60-modulated spliced genes in Drosophila are well characterized aberrantly spliced genes in human AD brains, implicating disruption of Tip60’s splicing function in AD pathogenesis. Theoretical Importance: The authors' findings support a novel RNA interaction and splicing regulatory function for Tip60 that may underlie AS impairments that hallmark AD etiology. Data Collection: The authors collected data from RNA immunoprecipitation experiments using RNA isolated from 200 pooled wild type Drosophila brains for each of the 3 biological replicates. They also performed genome sequencing (DNBSequencingTM technology, BGI genomics) on 3 replicates for Input RNA and RNA IPs by Tip60. Questions: The question addressed by this study was whether Tip60 has a novel RNA binding/splicing function in human hippocampus and whether this function is impaired in brains from AD fly models and AD patients. Conclusions: The authors' findings support a novel RNA interaction and splicing regulatory function for Tip60 that may underlie AS impairments that hallmark AD etiology.

Keywords: Alzheimer's disease, cognition, aging, neuroepigenetics

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