Search results for: sequencing skill

Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

Abstract:

Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

Procedia PDF Downloads 111

Authors: Manasvi Pinnaka, Brianna Chrisman

Abstract:

Cystic fibrosis patients often develop lung infections that range anywhere in severity from mild to life-threatening due to the presence of thick and sticky mucus that fills their airways. Since many of these infections are chronic, they not only affect a patient’s ability to breathe but also increase the chances of mortality by respiratory failure. With a publicly available dataset of DNA sequences from bacterial species in the lung microbiome of cystic fibrosis patients, the correlations between different microbial species in the lung and the extent of deterioration of lung function were investigated. 16S sequencing technologies were used to determine the microbiome composition of the samples in the dataset. For the statistical analyses, referencing helped distinguish between taxonomies, and the proportions of certain taxa relative to another were determined. It was found that the Fusobacterium, Actinomyces, and Leptotrichia microbial types all had a positive correlation with the FEV1 score, indicating the potential displacement of these species by pathogens as the disease progresses. However, the dominant pathogens themselves, including Pseudomonas aeruginosa and Staphylococcus aureus, did not have statistically significant negative correlations with the FEV1 score as described by past literature. Examining the lung microbiology of cystic fibrosis patients can help with the prediction of the current condition of lung function, with the potential to guide doctors when designing personalized treatment plans for patients.

Keywords: bacterial infections, cystic fibrosis, lung microbiome, 16S sequencing

Procedia PDF Downloads 71

Authors: Hana Barak, Alex Sivan, Ariel Kushmaro

Abstract:

Microorganisms are the most diverse and abundant life forms on Earth and account for a large portion of the Earth’s biomass and biodiversity. To date though, our knowledge regarding microbial life is lacking, as it is based mainly on information from cultivated organisms. Indeed, microbiologists have borrowed from astrophysics and termed the ‘uncultured microbial majority’ as ‘microbial dark matter’. The realization of how diverse and unexplored microorganisms are, actually stems from recent advances in molecular biology, and in particular from novel methods for sequencing microbial small subunit ribosomal RNA genes directly from environmental samples termed next-generation sequencing (NGS). This has led us to use NGS that generates several gigabases of sequencing data in a single experimental run, to identify and classify environmental samples of microorganisms. In metagenomics sequencing analysis (both 16S and shotgun), sequences are compared to reference databases that contain only small part of the existing microorganisms and therefore their taxonomy assignment may reveal groups of unknown microorganisms or origins. These unknowns, or the ‘microbial sequences dark matter’, are usually ignored in spite of their great importance. The goal of this work was to develop an improved bioinformatics method that enables more complete analyses of the microbial communities in numerous environments. Therefore, NGS was used to identify previously unknown microorganisms from three different environments (industrials wastewater, Negev Desert’s rocks and water wells at the Arava valley). 16S rRNA gene metagenome analysis of the microorganisms from those three environments produce about ~4 million reads for 75 samples. Between 0.1-12% of the sequences in each sample were tagged as ‘Unassigned’. Employing relatively simple methodology for resequencing of original gDNA samples through Sanger or MiSeq Illumina with specific primers, this study demonstrates that the mysterious ‘Unassigned’ group apparently contains sequences of candidate phyla. Those unknown sequences can be located on a phylogenetic tree and thus provide a better understanding of the ‘sequences dark matter’ and its role in the research of microbial communities and diversity. Studying this ‘dark matter’ will extend the existing databases and could reveal the hidden potential of the ‘microbial dark matter’.

Keywords: bacteria, bioinformatics, dark matter, Next Generation Sequencing, unknown

Procedia PDF Downloads 226

Authors: M. Kouyate, M. Sangare, S. Samake, S. Keita, H. G. Kim, D. H. Geschwind

Abstract:

Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder.

Keywords: bioinformatics, endonucleases, autism, Sanger sequencing, point mutations

Procedia PDF Downloads 55

Authors: Pradeep Kumar Sahoo

Abstract:

Facilitating writing skill among the young techies seems a bit challenging. Various factors may owe to this difficulty. Inappropriate syllabus, inadequate infrastructure, to some extent, untrained faculty members and above all the background of learners may be treated as the components that make the process challenging. In order to convert/create/prepare writing skill friendly, the focused items will have to be different from the classroom the present day traditional classroom situation. This paper focuses on the multiple contemporary strategies for approaching a wide range of typical problems that the writers face in a specific technical university of Odisha.

Keywords: background of learners, classroom friendly approach, inappropriate syllabus, traditional classroom situation

Procedia PDF Downloads 318

Authors: Mustafa M. Bob, Siti Izaidah Azmi, Mohd Hakim Ab Halim, Nur Syahida Abdul Jamal, Aznah Nor-Anuar, Zaini Ujang

Abstract:

In this research, the formation and development of aerobic granular sludge (AGS) for domestic wastewater treatment application in hot climate conditions was studied using a sequencing batch reactor (SBR). The performance of the developed AGS in the removal of organic matter and nutrients from wastewater was also investigated. The operation of the reactor was based on the sequencing batch system with a complete cycle time of 3 hours that included feeding, aeration, settling, discharging and idling. The reactor was seeded with sludge collected from the municipal wastewater treatment plant in Madinah city, Saudi Arabia and operated at a temperature of 40ºC using synthetic wastewater as influent. Results showed that granular sludge was developed after an operation period of 30 days. The developed granular sludge had a good settling ability with the average size of the granules ranging from 1.03 to 2.42 mm. The removal efficiency of chemical oxygen demand (COD), ammonia nitrogen (NH3-N) and total phosphorus (TP) were 87.31%, 91.93% and 61.25% respectively. These results show that AGS can be developed at elevated temperatures and it is a promising technique to treat domestic wastewater in hot and low humidity climate conditions such as those encountered in Saudi Arabia.

Keywords: aerobic granular sludge, hot climate, sequencing batch reactor, domestic wastewater treatment

Procedia PDF Downloads 337

Authors: Pataraporn Kheawwan

Abstract:

Preceptorship represents an important aspect in new nurse orientation. However, there was no formal preceptor training program developed for nurse preceptor in Thailand. The purposes of this study were to develop and evaluate formal preceptor training program for nurse preceptors in King Chulalongkorn Memorial Hospital, Thailand. A research and development study design was utilized in this study. Participants were 37 nurse preceptors. The program contents were delivered by e-learning material, class lecture, group discussion followed by simulation training. Knowledge of the participants was assessed pre and post program. Skill and critical thinking were assessed using Preceptor Skill and Decision Making Evaluation form at the end of program. Statistical significant difference in knowledge regarding preceptor role and coaching strategies between pre and post program were found. All participants had satisfied skill and decision making score after completed the program. Most of participants perceived benefits of preceptor training course. In conclusion, The results of this study reveal that the newly developed preceptorship course is an effective formal training course for nurse preceptors.

Keywords: preceptor, preceptorship, new nurse, clinical education

Procedia PDF Downloads 236

Authors: Zulhisyam Salleh, Fizatul Aini Patakor, Rosilah Wahab, Awangku Khairul Ridzwan Awangku Jaya

Abstract:

Autism is a lifelong developmental disability that affects how people perceive the world and interact with others. Most of these children have difficulty with fine motor skills which typically struggle with handwriting and fine activities in their routine life such as getting dressed and controlled use of the everyday tool. Because fine motor activities encompass so many routine functions, a fine motor delay can have a measurable negative impact on a person's ability to handle daily practical tasks. This project proposed a simple fine motor exercise aid plus the game (exergame) for autistic children who discover from fine motor difficulties. The proposed exergame will be blinking randomly and user needs to bend their finger accordingly. It will notify the user, whether they bend the right finger or not. The system is realized using Arduino, which is programmed to control all the operated circuit. The feasibility studies with six autistic children were conducted and found the child interested in using exergame and could quickly get used to it. This study provides important guidance for future investigations of the exergame potential for accessing and improving fine motor skill among autistic children.

Keywords: autism children, Arduino project, fine motor skill, finger exergame

Procedia PDF Downloads 130

Authors: Yi-Hsuan Gloria Lo

Abstract:

The educational objective of vocational high schools (VHSs) is to equip VHS students with practical skills and knowledge that can be applied in the job-related market. However, with the increasing number of technological universities over the past two decades, the majority of VHS students have chosen to receive higher education rather than enter the job market. VHS English education has been confronting a dilemma: Should an English for specific purposes (ESP) approach, which aligns with the educational goal of VHS education, be taken or should an English for general purposes (EGP) approach, which prepares VHS students for advanced studies in universities, be followed? While ESP theorists proposed that that ESP can be taught to secondary learners, little was known about VHS students’ perspective on this ESP-versus-EGP dilemma. Scant research has investigated different facets of students’ needs (necessities, wants, and lacks) for both ESP and EGP in terms of the four language skills and the factors that contribute to any differences. To address the gap in the literature, 100 VHS students responded to statements related to their necessities, wants, and lacks in learning ESP and EGP on a 6-point Likert scale. Six VHS students were interviewed to tap into the reasons for different facets of the needs for learning EGP and ESP. The statistical analysis indicates that at this stage of learning English, VHS subjects believed that EGP was more necessary than ESP; EGP was more desirable than ESP. However, they reported that they were more lacking in ESP than in EGP learning. Regarding EGP, the results show that the VHS subjects rated speaking as their most necessary skill, speaking as the most desirable skill, and writing as the most lacking skill. A significant difference was found between perceived learning necessities and lacks and between perceived wants and lacks. No statistical difference was found between necessities and wants. In the aspect of ESP, the results indicate that the VHS subjects marked reading as their most necessary skill, speaking as the most desirable skill, and writing as the most lacking skill. A significant difference exists between their perceived necessities and lacks and between their wants and lacks. However, there is no statistically significant difference between their perceived lacks and wants. Despite the lack of a significant difference between learning necessities and wants, the qualitative interview data reveal that the reasons for their perceived necessities and wants were different. The findings of the study confirm previous research that demonstrates that ‘needs’ is a multiple and conflicting construct. What VHS students felt most lacking was not necessarily what they believed they should learn or would like to learn. Although no statistical difference was found, different reasons were attributed to their perceived necessities and wants. Both theoretical and practical implications have been drawn and discussed for ESP research in general and teaching ESP in VHSs in particular.

Keywords: vocational high schools (VHSs), English for General Purposes (EGP), English for Specific Purposes (ESP), needs analysis

Procedia PDF Downloads 152

Authors: Majed Zobairy, Payam Mohammadpanahi

Abstract:

Introduction: Skill movement education is one of extremely important duty for sport coaches and sport teachers. Researchers have done lots of studies in this filed to gain the best methodology in movement learning. One of the essential aspects in skill movement education is observational learning. Observational learning, or learning by watching demonstrations, has been characterized as one of the most important methods by which people learn variety of skill and behaviours.The purpose of this study was determined the effect of observational practice on the volleyball service learning with emphasis on the Role of Self–Efficacy. Methods: The Sample consisted of100 male students was assigned accessible sampling technique and homogeneous manner with emphasis on the Role of Self–Efficacy level to 4 groups. The first group performed physical training, the second group performed observational practice task, the third practiced physically and observationally and the fourth group served as the control group. The experimental groups practiced in a one day acquisition and performed the retention task, after 72 hours. Kolmogorov-Smirnov test and independent t-test were used for Statistical analyses. Results and Discussion: Results shows that observation practice task group can significantly improve volleyball services skills acquisition (T=7.73). Also mixed group (physically and observationally) is significantly better than control group regarding to volleyball services skills acquisition (T=7.04). Conclusion: Results have shown observation practice task group and mixed group are significantly better than control group in acquisition test. The present results are in line with previous studies, suggesting that observation learning can improve performance. On the other hand, results shows that self-efficacy level significantly effect on acquisition movement skill. In other words, high self-efficacy is important factor in skill learning level in volleyball service.

Keywords: observational practice, volleyball service, self–efficacy, sport science

Procedia PDF Downloads 371

Authors: Amira Potter

Abstract:

Since three years, ESPRIT has adopted project-based learning across its curricula. The philosophy behind this reform is to prepare its future engineers to become more operational once they integrate the workplace. It allows them to learn all the required skills expected from them by their future employers. This learner-centered method helps the students take responsibility for their own learning, solve real-world problems and carry out muli-faceted projects. Therefore, the teacher who used to be considered as the detainer of the knowledge has become more of a facilitator and a coach, encouraging their students’ learning process. This innovative way to English teaching has enabled the students to learn the English language differently. The target language is learnt cooperatively through group work, presentations, debating and many other communicative activities. The speaking skill in English language remains by far the most challenging skill for Tunisian students with an educational background based on Arabic as a first language and French as a second language. The student’s initial resistance to speak English in front of their classmates and the way they end up performing their work, shows the real progress they managed to achieve through PBL approach. The article will focus on the positive impact PBL has had on oral fluency among Esprit engineering students and how it has been achieved. It will also describe how speaking skill is taught and assessed at ESPRIT.

Keywords: cooperative, engineer, innovative, project-based learning

Procedia PDF Downloads 299

Authors: Amin Mojiri, Akiyoshi Ohashi, Tomonori Kindaichi

Abstract:

Synthetic domestic wastewater was treated via combining treatment methods, including electrochemical oxidation, adsorption, and sequencing batch reactor (SBR). In the upper part of the reactor, an anode and a cathode (Ti/RuO₂-IrO₂) were organized in parallel for the electrochemical oxidation procedure. Sodium sulfate (Na₂SO₄) with a concentration of 2.5 g/L was applied as the electrolyte. The voltage and current were fixed on 7.50 V and 0.40 A, respectively. Then, 15% working value of the reactor was filled by activated sludge, and 85% working value of the reactor was added with synthetic wastewater. Powdered cockleshell, 1.5 g/L, was added in the reactor to do ion-exchange. Response surface methodology was employed for statistical analysis. Reaction time (h) and pH were considered as independent factors. A total of 97.0% biochemical oxygen demand, 99.9% phosphorous and 88.6% cadmium were eliminated at the optimum reaction time (80.0 min) and pH (6.4).

Keywords: adsorption, electrochemical oxidation, metals, SBR

Procedia PDF Downloads 185

Authors: Kennedy Efosa Ehimwenma, Sujatha Krishnamoorthy, Safiya Al‑Sharji

Abstract:

The probability computation of events is in the interval of [0, 1], which are values that are determined by the number of outcomes of events in a sample space S. The probability Pr(A) that an event A will never occur is 0. The probability Pr(B) that event B will certainly occur is 1. This makes both events A and B a certainty. Furthermore, the sum of probabilities Pr(E₁) + Pr(E₂) + … + Pr(Eₙ) of a finite set of events in a given sample space S equals 1. Conversely, the difference of the sum of two probabilities that will certainly occur is 0. This paper first discusses Bayes, the complement of probability, and the difference of probability for occurrences of learning-events before applying them in the prediction of learning objects in student learning. Given the sum of 1; to make a recommendation for student learning, this paper proposes that the difference of argMaxPr(S) and the probability of student-performance quantifies the weight of learning objects for students. Using a dataset of skill-set, the computational procedure demonstrates i) the probability of skill-set events that have occurred that would lead to higher-level learning; ii) the probability of the events that have not occurred that requires subject-matter relearning; iii) accuracy of the decision tree in the prediction of student performance into class labels and iv) information entropy about skill-set data and its implication on student cognitive performance and recommendation of learning.

Keywords: complement of probability, Bayes’ rule, prediction, pre-assessments, computational education, information theory

Procedia PDF Downloads 135

Authors: Eyup Ozkan, Ozkan U. Nalbantoglu, Aycan Gundogdu, Mehmet Hora, A. Emre Onuk

Abstract:

The human microbiome has been associated with cardiological conditions and this relationship is becoming to be defined beyond the gastrointestinal track. In this study, we investigate the alteration in circulatory microbiota in the context of Coronary Artery Disease (CAD). We received circulatory blood samples from suspected CAD patients and maintain 16S ribosomal RNA sequencing to identify each patient’s microbiome. It was found that Corynebacterium and Methanobacteria genera show statistically significant differences between healthy and CAD patients. The overall biodiversities between the groups were observed to be different revealed by machine learning classification models. We also achieve and demonstrate the performance of a diagnostic method using circulatory blood microbiome-based estimation.

Keywords: coronary artery disease, blood microbiome, machine learning, angiography, next-generation sequencing

Procedia PDF Downloads 132

Authors: Mohammed Ali

Abstract:

A flexible manufacturing system has been studied under different manufacturing strategies. The aim of this paper is to test the impact of number of pallets and routing flexibility (design strategy) on system performance operating at different sequencing and dispatching rules (control strategies) at unbalanced load condition (planning strategies). A computer simulation model is developed to evaluate the effects of aforementioned strategies on the make-span time, which is taken as the system performance measure. The impact of number of pallets is shown with the different levels of routing flexibility. In this paper, the same manufacturing system is modeled under different combination of sequencing and dispatching rules. The result of the simulation shows that there is definite range of pallets for each level of routing flexibility at which the systems performs satisfactorily.

Keywords: flexible manufacturing system, manufacturing, strategy, makespan

Procedia PDF Downloads 645

Authors: Hammad Khan, Wookeun Bae

Abstract:

Major concerns regarding nitritation of low-strength ammonium wastewaters include low ammonium loading rates (usually below 0.2 kg/m3-d) and uncertainty about long-term stability of the process. The purpose of this study was to test a sequencing batch reactor (SBR) filled with cell-immobilized polyethylene glycol (PEG) pellets to see if it could achieve efficient and stable nitritation under various environmental conditions. SBR was fed with synthetic ammonium wastewater of 30±2 mg-N/L and pH: 8±0.05, maintaining the dissolved oxygen concentration of 1.7±0.2 mg/L and the temperature at 30±1oC. The reaction was easily converted to partial nitrification mode within a month by feeding relatively high ammonium substrate (~100 mg-N/L) in the beginning. We observed stable nitritation over 300 days with high ammonium loading rates (as high as ~1.1 kg-N/m3-d), nitrite accumulation rates (mostly over 97%) and ammonium removal rate (mostly over 95%). DO was a major limiting substrate when the DO concentration was below ~4 mg/L and the NH4+-N concentration was above 5 mg/L, giving almost linear increase in the ammonium oxidation rate with the bulk DO increase. Low temperatures mainly affected the reaction rate, which could be compensated for by increasing the pellet volume (i.e. biomass). Our results demonstrated that an SBR filled with small cell-immobilized PEG pellets could achieve very efficient and stable nitritation of a low-strength ammonium wastewater.

Keywords: ammonium loading rate (ALR), cell-immobilization, long-term nitritation, sequencing batch reactor (SBR), sewage treatment

Procedia PDF Downloads 250

Authors: Alisa Kazarina, Guntis Gerhards, Elina Petersone-Gordina, Ilva Pole, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka

Abstract:

Human body is inhabited by a vast number of microorganisms, collectively known as the human microbiome, and there is a tremendous interest in evolutionary changes in human microbial ecology, diversity and function. The field of paleomicrobiology, study of ancient human microbiome, is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including the taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify the hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results, we suggest that wider range of primers used can provide more accurate recapitulation of microbial communities in archaeological samples. Acknowledgements. This work was supported by the ERAF grant Nr. 1.1.1.1/16/A/101.

Keywords: 16S rRNA gene, ancient human microbiome, archaeology, bioinformatics, genomics, microbiome, molecular biology, next-generation sequencing

Procedia PDF Downloads 165

Authors: Narges Nemati, Mohammadreza Fallahpour, Hossein Bozorgian

Abstract:

Reading is one of the receptive skills which has an important role in improving other skills like writing and speaking. Furthermore, language learners can acquire plenty of vocabularies and become more acquainted with written expression through reading. Also, negative attitudes toward reading can cause negligible reading comprehension, which could prompt poor performance in the English language. Considering the fact that reading instruction was discussed as a low priority skill in the field of EFL teacher education, this study attempted to investigate EFL teachers’ attitudes toward reading instruction. Therefore, to serve the purpose of this study, a mixed-method approach was utilized by inviting 100 Iranian EFL teachers who taught at English language institutes of Iran to fill out a validated questionnaire on teachers’ attitude toward reading. Subsequently, 10 participants were randomly selected for further observations and interview sessions to evaluate the differences between their stated attitude and their actual practices. The findings from analyzing questionnaires, observations, and interviews revealed that EFL teachers’ stated attitude toward reading instruction was positive; whereas, due to some reasons like lack of time, scarcity of interesting passages, and lack of interest in reading long passages, teachers did not show positive actual attitude toward teaching reading skill.

Keywords: English as foreign language classroom, English language, reading skill, teachers' attitude

Procedia PDF Downloads 128

Authors: Cheng-Yang Lee, Petrus Tang, Tzu-Hao Chang

Abstract:

Copy number variations (CNVs) have played an important role in many kinds of human diseases, such as Autism, Schizophrenia and a number of cancers. Many diseases are found in genome coding regions and whole exome sequencing (WES) is a cost-effective and powerful technology in detecting variants that are enriched in exons and have potential applications in clinical setting. Although several algorithms have been developed to detect CNVs using WES and compared with other algorithms for finding the most suitable methods using their own samples, there were not consistent datasets across most of algorithms to evaluate the ability of CNV detection. On the other hand, most of algorithms is using command line interface that may greatly limit the analysis capability of many laboratories. We create a series of simulated WES datasets from UCSC hg19 chromosome 22, and then evaluate the CNV detective ability of 19 algorithms from OMICtools database using our simulated WES datasets. We compute the sensitivity, specificity and accuracy in each algorithm for validation of the exome-derived CNVs. After comparison of 19 algorithms from OMICtools database, we construct a platform to install all of the algorithms in a virtual machine like VirtualBox which can be established conveniently in local computers, and then create a simple script that can be easily to use for detecting CNVs using algorithms selected by users. We also build a table to elaborate on many kinds of events, such as input requirement, CNV detective ability, for all of the algorithms that can provide users a specification to choose optimum algorithms.

Keywords: whole exome sequencing, copy number variations, omictools, pipeline

Procedia PDF Downloads 288

Authors: Chia-Jung Li, Li-Te Lin, Kuan-Hao Tsui

Abstract:

The study identifies SPP1 as a potential gene associated with ovarian aging, revealing a significant decline in its expression in aged ovaries. SPP1, also known as osteopontin (OPN), is a multifunctional glycoprotein involved with regulatory proteins and pro-inflammatory immune chemokines. However, its genetic links to ovarian aging have not been extensively explored. Spatial transcriptomic analyses were conducted on ovaries from young and aged female mice, along with a sample from a 73-year-old individual. Additionally, single-cell RNA sequencing analysis was performed to identify associations between SPP1 and key genes. The study focused on crucial genes, including ITGAV, ITGB1, CD44, MMP3, and FN1, with a particular emphasis on the correlation between SPP1 and ITGB1. The findings indicate a significant decline in SPP1 expression in aged ovaries, which was consistent in the 73-year-old sample. Single-cell RNA sequencing unveiled associations between SPP1 and key genes, emphasizing a strong co-expression correlation between SPP1 and ITGB1. While the study provides valuable insights, further research is necessary to understand the broader implications and potential applications of SPP1 in ovarian aging. Translating these findings to clinical settings requires careful consideration. The identification of SPP1 as a gene implicated in ovarian aging opens new avenues for advancing precision medicine and refining treatment strategies for conditions related to ovarian aging.

Keywords: SPP1, ovarian aging, spatial transcriptomic, single-cell RNA sequencing

Procedia PDF Downloads 8

Authors: Priyanka Dargode, Suhas Gore, Manju Sharma, Arvind Lali

Abstract:

Anaerobic digestion has been widely used for production of methane from different biowastes. However, the complexity of microbial communities involved in the process is poorly understood. The performance of biogas production process concerning the process productivity is closely coupled to its microbial community structure and syntrophic interactions amongst the community members. The present study aims at understanding taxonomic variations occurring in any starter inoculum when acclimatised to different lignocellulosic biomass (LBM) feedstocks relating to time of digestion. The work underlines use of high throughput Next Generation Sequencing (NGS) for validating the changes in taxonomic patterns of microbial communities. Biomethane Potential (BMP) batches were set up with different pretreated and non-pretreated LBM residues using the same microbial consortium and samples were withdrawn for studying the changes in microbial community in terms of its structure and predominance with respect to changes in metabolic profile of the process. DNA of samples withdrawn at different time intervals with reference to performance changes of the digestion process, was extracted followed by its 16S rRNA amplicon sequencing analysis using Illumina Platform. Biomethane potential and substrate consumption was monitored using Gas Chromatography(GC) and reduction in COD (Chemical Oxygen Demand) respectively. Taxonomic analysis by QIIME server data revealed that microbial community structure changes with different substrates as well as at different time intervals. It was observed that biomethane potential of each substrate was relatively similar but, the time required for substrate utilization and its conversion to biomethane was different for different substrates. This could be attributed to the nature of substrate and consequently the discrepancy between the dominance of microbial communities with regards to different substrate and at different phases of anaerobic digestion process. Knowledge of microbial communities involved would allow a rational substrate specific consortium design which will help to reduce consortium adaptation period and enhance the substrate utilisation resulting in improved efficacy of biogas process.

Keywords: amplicon sequencing, biomethane potential, community predominance, taxonomic analysis

Procedia PDF Downloads 503

Authors: Elizabeth Starzycka-Korbas, Michal Starzycki, Wojciech Rybinski, Mirosława Dabert

Abstract:

For a few years, the populations of pathogenic fungi occurring in winter oilseed rape in Malyszyn were analyzed. Brassica napus L. in Poland and in the world is a source of energy for both the men (oil), and animals, as post-extraction middling, as well as a motor fuel (oil, biofuel) therefore studies of this type are very important. The species composition of pathogenic fungi can be an indicator of seed yield. The occurrence of oilseed rape pathogens during several years were analyzed using the sequencing method DNA ITS. The results were compared in the gene bank using the program NCBI / BLAST. In field conditions before harvest of oilseed rape presence of pathogens infesting B. napus has been assessed. For example, in 2015, 150 samples have been isolated and applied to PDA medium for the identification of belonging species. From all population has been selected mycelium of 83 isolates which were sequenced. Others (67 isolates) were pathogenic fungi of the genus Alternaria which are easily to recognize. The population of pathogenic species on oilseed rape have been identified after analyzing the DNA ITS and include: Leptosphaeria sp. 38 (L. maculans 25, L. biglobosa 13), Alternaria sp. 29, Fusarium sp. 3, Sclerotinia sclerotiorum 7, heterogeneous 6, total of 83 isolates. The genus Alternaria sp. fungi wear the largest share of B. napus pathogens in particular years. Another dangerous species for oilseed rape was Leptosphaeria sp. Populations of pathogens in each year were different. The number of pathogens occurring in the field and their composition is very important for breeders and farmers because of the possible selection of the most resistant genotypes for sowing in the next growing season.

Keywords: B. napus, DNA ITS Sequencing, pathogenic fungi, population

Procedia PDF Downloads 265

Authors: Elizabeth A. Montero

Abstract:

The project contemplated in this study particularly aimed at enabling public school children of ages ten to twelve who belong to low and middle income families. The pupils were provided training on communication, work, computer and social skills. In this study, the researcher hypothesized that children given the opportunity to develop a skill through guidance and proper supervision will significantly learn, improve and develop a skill. Since children’s minds are highly absorbent like a sponge absorbing anything within its capacity to take, it is ideal and necessary that education should provide an environment that is rich offering an array of meaningful experiences. The context of this study is well balanced since it catered to the children’s communication, work, computer and social skills.

Keywords: Munting Kamay, Munting Gawa, children’s development training, UCU experience

Procedia PDF Downloads 408

Authors: Shalini TV, Gangadharan GG, Sriranjini S Jaideep, ASN Seshasayee, Awadhesh Pandit

Abstract:

Introduction: Prakriti (body-mind constitution of an individual) is a conventional, customized and unique understanding of which is essential for the personalized medicine described in Ayurveda, Indian System of Medicine. Based on the Doshas( functional, bio humoral unit in the body), individuals are categorized into three major Prakriti- Vata, Pitta, and Kapha. The human gut microbiome hosts plenty of highly diverse and metabolically active microorganisms, mainly dominated by the bacteria, which are known to influence the physiology of an individual. Few researches have shown the correlation between the Prakriti and the biochemical parameters. In this study, an attempt was made to explore any correlation between the Prakriti (phenotype of an individual) with the Genetic makeup of the gut microbiome in healthy individuals. Materials and methods: 270 multi-ethnic, healthy volunteers of both sex with the age group between 18 to 40 years, with no history of antibiotics in the last 6 months were recruited into three groups of Vata, Pitta, and Kapha. The Prakriti of the individual was determined using Ayusoft, a software designed by CDAC, Pune, India. The volunteers were subjected to initial screening for the assessment of their height, weight, Body Mass Index, Vital signs and Blood investigations to ensure they are healthy. The stool and saliva samples of the recruited volunteers were collected as per the standard operating procedure developed, and the bacterial DNA was isolated using Qiagen kits. The extracted DNA was subjected to 16s rRNA sequencing using the Illumina kits. The sequencing libraries are targeting the variable V3 and V4 regions of the 16s rRNA gene. Paired sequencing was done on the MiSeq system and data were analyzed using the CLC Genomics workbench 11. Results: The 16s rRNA sequencing of the V3 and V4 regions showed a diverse pattern in both the oral and stool microbial DNA. The study did not reveal any specific pattern of bacterial flora amongst the Prakriti. All the p-values were more than the effective alpha values for all OTUs in both the buccal cavity and stool samples. Therefore, there was no observed significant enrichment of an OTU in the patient samples from either the buccal cavity or stool samples. Conclusion: In healthy volunteers of multi-ethnicity, due to the influence of the various factors, the correlation between the Prakriti and the gut microbiome was not seen.

Keywords: gut microbiome, ayurveda Prakriti, sequencing, multi-ethnic urban population

Procedia PDF Downloads 110

Authors: Mohd Yusri Ibrahim

Abstract:

Youth participation in social work is essential in social and community development. Although many studies have been conducted to identify the determinant of youth involvement, few studies were discussed interaction between communication skills and youth participation in volunteerism. This article will discuss a cross-sectional study that was conducted to identify the relationship between communication skills and youth participation in social work. The results were successfully developed an interaction model of communication skills as predictor to participation criteria among youth. Finally, the article was suggested several ways to encourage youth participation in community by developing their communication skill in various stages.

Keywords: youth, participation, communication skill, social work

Procedia PDF Downloads 340

Authors: Tarek Aboueldahab, Hanan Farag

Abstract:

Parallel Job Shop Scheduling Problem (JSP) is a multi-objective and multi constrains NP- optimization problem. Traditional Artificial Intelligence techniques have been widely used; however, they could be trapped into the local minimum without reaching the optimum solution, so we propose a hybrid Artificial Intelligence model (AI) with Discrete Breeding Swarm (DBS) added to traditional Artificial Intelligence to avoid this trapping. This model is applied in the cost minimization of the Car Sequencing and Operator Allocation (CSOA) problem. The practical experiment shows that our model outperforms other techniques in cost minimization.

Keywords: parallel job shop scheduling problem, artificial intelligence, discrete breeding swarm, car sequencing and operator allocation, cost minimization

Procedia PDF Downloads 155

Authors: Bolormaa Dalanbayar, Batsaikhan Ulaankhuu, Bayarmaa Tsogtbaatar

Abstract:

In this study, we surveyed employers and students to identify compliance between employers' needs and student self-assessment of skills. Employers' survey consisted of fifteen questions to determine employers' assessment of the knowledge and skills of graduates in heavy equipment repairer's programs from four TVET schools. We also compared a survey questionnaire with Liebherr brands' job duty requirements, which determines the training needs and qualification level of their new workers. The study shows more than 76% of employers assessed professional knowledge as sufficient, more than 47% of employers assessed vocational skills as sufficient and more than 43% of employers rated attitudes as sufficient. Therefore, we can state there is a skill mismatch between the employer's assessment and students' self-assessment.

Keywords: skill mismatch, employers needs, competence-based curriculum

Procedia PDF Downloads 12

Authors: Ali Alattabi, Clare Harris, Rafid Alkhaddar, Ali Alzeyadi

Abstract:

Petroleum refinery wastewater (PRW) can be considered as one of the most significant source of aquatic environmental pollution. It consists of oil and grease along with many other toxic organic pollutants. In recent years, a new technique was implemented using different types of membranes and sequencing batch reactors (SBRs) to treat PRW. SBR is a fill and draw type sludge system which operates in time instead of space. Many researchers have optimised SBRs’ operating conditions to obtain maximum removal of undesired wastewater pollutants. It has gained more importance mainly because of its essential flexibility in cycle time. It can handle shock loads, requires less area for operation and easy to operate. However, bulking sludge or discharging floating or settled sludge during the draw or decant phase with some SBR configurations are still one of the problems of SBR system. The main aim of this study is to develop and innovative design for the SBR optimising the process variables to result is a more robust and efficient process. Several experimental tests will be developed to determine the removal percentages of chemical oxygen demand (COD), Phenol and nitrogen compounds from synthetic PRW. Furthermore, the dissolved oxygen (DO), pH and oxidation-reduction potential (ORP) of the SBR system will be monitored online to ensure a good environment for the microorganisms to biodegrade the organic matter effectively.

Keywords: petroleum refinery wastewater, sequencing batch reactor, hydraulic retention time, Phenol, COD, mixed liquor suspended solids (MLSS)

Procedia PDF Downloads 235

Authors: Mohammed Ali

Abstract:

In this paper, evaluation of flexible manufacturing system is made under different manufacturing strategies. The objective of this paper is to test the impact of pallets and routing flexibility on system performance operating at different sequencing rules, dispatching rules and at unbalanced load condition. A computer simulation model is developed to evaluate the effects of aforementioned manufacturing strategies on the make-span performance of flexible manufacturing system. The impact of number of pallets is shown with the different levels of routing flexibility. In this paper, the same manufacturing system is modeled under different combination of sequencing and dispatching rules. A series of simulation experiments are conducted and results analyzed. The result of the simulation shows that there is impact of pallets and routing flexibility on the performance of the system.

Keywords: flexibility, flexible manufacturing system, pallets, make-span, simulation

Procedia PDF Downloads 398

Authors: Huajuan Shi

Abstract:

Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

Procedia PDF Downloads 63