Search results for: sequencing strategies

Authors: H. Bahbahani, H. Musa, F. Al Mathen

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The dromedary camels (Camelus dromedarius) are single-humped even-toed ungulates populating the African Sahara, Arabian Peninsula, and Southwest Asia. The genome of this desert-adapted species has been minimally investigated using autosomal microsatellite and mitochondrial DNA markers. In this study, the genomes of 33 dromedary camel samples from different parts of the Arabian Peninsula were sequenced using Illumina Next Generation Sequencing (NGS) platform. These data were combined with Genotyping-by-Sequencing (GBS) data from African (Sudanese) dromedaries to investigate the genomic relationship between African and Arabian Peninsula dromedary camels. Principle Component Analysis (PCA) and average genome-wide admixture analysis were be conducted on these data to tackle the objectives of these studies. Both of the two analyses conducted revealed phylogeographic distinction between these two camel populations. However, no breed-wise genetic classification has been revealed among the African (Sudanese) camel breeds. The Arabian Peninsula camel populations also show higher heterozygosity than the Sudanese camels. The results of this study explain the evolutionary history and migration of African dromedary camels from their center of domestication in the southern Arabian Peninsula. These outputs help scientists to further understand the evolutionary history of dromedary camels, which might impact in conserving the favorable genetic of this species.

Keywords: dromedary, genotyping-by-sequencing, Arabian Peninsula, Sudan

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Authors: Nasser Al-Rawahi

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The study aims at determining self-regulated learning strategies used by Omani physical education candidates to learn sport skills. The data were collected by a self-regulated learning theory questionnaire. The sample of the study comprised of 145 undergraduate physical education students enrolled in the department of physical education at the College of Education, Sultan Qaboos University. The findings of the study revealed that the most commonly used strategies for learning sport skills by Omani physical education candidate are ‘the effort learning strategies, planning learning strategies and evaluation learning strategies’. However, the reflection learning strategies, self-monitoring and self-efficacy learning strategies were revealed as the least used strategies by the PE candidates in learning and acquiring sport skills. Based on these findings, suggestions and recommendations for future research were provided.

Keywords: learning strategies, physical education candidates, self-regulated learning theory, Oman

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Authors: Negin Parsamanesh, Saman Ameri-Mahabadi, Ali Nikfar, Mojdeh Mansouri, Hossein Chiti, Gita Fatemi Abhari

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Duchenne muscular dystrophy (DMD) is a severe progressive X-linked neuromuscular illness that affects movement through mutations in dystrophin gene. The mutation leads to insufficient, lack of or dysfunction of dystrophin. The cause of DMD was determined in an Iranian family. Exome sequencing was carried out along with a complete physical examination of the family. In silico methods were applied to find the alteration in the protein structure. The homozygous variant in DMD gene (NM-004006.2) was defined as c.2732-2733delTT (p.Phe911CysfsX8) in exon 21. In addition, phylogenetic conservation study of the human dystrophin protein sequence revealed that phenylalanine 911 is one of the evolutionarily conserved amino acids. In conclusion, our study indicated a new deletion in the DMD gene in the affected family. This deletion with an X-linked inheritance pattern is new in Iran. These findings could facilitate genetic counseling for this family and other patients in the future.

Keywords: duchenne muscular dystrophy, whole exome sequencing, iran, metabolic syndrome

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Authors: Jianxin Zhu, Na Liu

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Entry strategies play a vital role in the development of new enterprises in the catering industry. Different entry strategies will have different effects on the development of new enterprise. Based on the research of scholars at home and abroad, and combining the characteristics of the catering industry, the entry strategies are divided into low-price entry strategies and high-quality entry strategies. Facing the entry of new enterprise, the strategies of incumbent enterprises are divided into response strategies and non-response strategies. This paper uses evolutionary game theory to study the strategic interaction mechanism between incumbent companies and new enterprises. When different initial values and parameter values are set, which strategy will the two-game subjects choose, respectively? Using matlab2016 for numerical simulation, the results show that the choice of strategies for new enterprise and incumbent enterprise is influenced by more than one factor, and the system has different evolution trends under different circumstances. When the parameters were set, the choice of two subjects' strategies mainly depends on the net profit between the strategies.

Keywords: catering industry, entry strategy, evolutionary game, strategic interaction mechanism

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

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

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

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Authors: M. Hadavi, Z. Hashemi

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Learning strategies play an important role in the development of language skills. Vocabulary learning strategies as the backbone of these strategies have become a major part of English language teaching. This study is a comparative analysis of Vocabulary Learning Strategies (VLS) use and preference among freshmen and senior EFL medical sciences students with different fields of study. 449 students (236 freshman and 213 seniors) participated in the study. 64.6% were female and 35.4% were male. The instrument utilized in this research was a questionnaire consisting of 41 items related to the students’ approach to vocabulary learning. The items were classified under eight sections as dictionary strategies, guessing strategies, study preferences, memory strategies, autonomy, note- taking strategies, selective attention, and social strategies. The participants were asked to answer each item with a 5-point Likert-style frequency scale as follows:1) I never or almost never do this, 2) I don’t usually do this, 3) I sometimes do this, 4) I usually do this, and 5)I always or almost always do this. The results indicated that freshmen students and particularly surgical technology students used more strategies compared to the seniors. Overall guessing and dictionary strategies were the most frequently used strategies among all the learners (p=0/000). The mean and standard deviation of using VLS in the students who had no previous history of participating in the private English language classes was less than the students who had attended these type of classes (p=0/000). Female students tended to use social and study preference strategies whereas male students used mostly guessing and dictionary strategies. It can be concluded that the senior students under instruction from the university have learned to rely on themselves and choose the autonomous strategies more, while freshmen students use more strategies that are related to the study preferences.

Keywords: vocabulary leaning strategies, medical sciences, students, linguistics

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

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

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

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Authors: Ali W. N. Alattabi, Clare B. Harris, Rafid M. Alkhaddar, Montserrat Ortoneda, David A. Phipps, Ali Alzeyadi, Khalid S. Hashim

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This study was performed to optimise the hydraulic retention time (HRT) and study its effects on the sludge characteristics and the effluent quality in an aerobic suspension sequencing batch reactor (ASSBR) treating synthetic wastewater. The results showed that increasing the HRT from 6 h to 12 h significantly improved the COD and Nitrate removal efficiency; it was increased from 78.7% - 75.7% to 94.7% – 97% for COD and Nitrate respectively. However, increasing the HRT from 12 h to 18 h reduced the COD and Nitrate removal efficiency from 94.7% - 97% to 91.1% – 94.4% respectively. Moreover, Increasing the HRT from 18 h to 24 h did not affect the COD and Nitrate removal efficiency. Sludge volume index (SVI) was used to monitor the sludge settling performance. The results showed a direct relationship between the HRT and SVI value. Increasing the HRT from 6 h to 12 h led to decrease the SVI value from 123 ml/g to 82.5 ml/g, and then it remained constant despite of increasing the HRT from 12 h to 18 h and to 24 h. The results obtained from this study showed that the HRT of 12 h was better for COD and Nitrate removal and a good settling performance occurred during that range.

Keywords: COD, hydraulic retention time, nitrate, sequencing batch reactor, sludge characteristics

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Authors: Amin Mojiri, Hamidi Abdul Aziz

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Leachate is created while water penetrates through the waste in a landfill, carrying some forms of pollutants. In literature, for treatment of wastewater and leachate, different ways of biological treatment were used. Sequencing batch reactor (SBR) is a kind of biological treatment. This study investigated the co-treatment of landfill leachate and domestic waste water by SBR and powdered activated carbon augmented (PAC) SBR process. The response surface methodology (RSM) and central composite design (CCD) were employed. The independent variables were aeration rate (L/min), contact time (h), and the ratio of leachate to wastewater mixture (%; v/v)). To perform an adequate analysis of the aerobic process, three dependent parameters, i.e. COD, color, and ammonia-nitrogen (NH3-N or NH4-N) were measured as responses. The findings of the study indicated that the PAC-SBR showed a higher performance in elimination of certain pollutants, in comparison with SBR. With the optimal conditions of aeration rate (0.6 L/min), leachate to waste water ratio (20%), and contact time (10.8 h) for the PAC-SBR, the removal efficiencies for color, NH3-N, and COD were 72.8%, 98.5%, and 65.2%, respectively.

Keywords: co-treatment, landfill Leachate, wastewater, sequencing batch reactor, activate carbon

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Authors: Proud Arunrangsiwed

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Crisis management strategies could be found in various curriculums, not only in schools of business, but also schools of communication. Young students, such as freshmen and sophomores of undergraduate schools, may not care about learning crisis management strategies. Moreover, crisis management strategies are not a topic art students are familiar with. The current paper discusses a way to adapt entertainment media into a crisis management lesson, and the importance of learning crisis management strategies in the school of animation. Students could learn crisis management strategies by watching movies with content about a crisis and responding to crisis responding. The students should then participate in follow up discussions related to the strategies that were used to address the crisis, as well as their success in solving the crisis.

Keywords: situational crisis communication theory, crisis response strategies, media effect, unintentional effect

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Authors: Pailin Klinkesorn

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The research aimed to study the use of learning strategies for Japanese language among college students with different learning achievements who study Japanese as a foreign language in the Higher Education’s level. The survey was conducted by using a questionnaire adapted from Strategy Inventory for language Learning or SILL (Oxford, 1990), consisting of two parts: questions about personal data and questions about the use of learning strategies for Japanese language. The samples of college students in the Japanese language program were purposively selected from Suansunandha Rajabhat University. The data from the questionnaire was statistically analyzed by using mean scores and one-way ANOVA. The results showed that Social Strategies was used by the greatest number of college students, whereas Memory Strategies was used by the least number of students. The students in different levels used various strategies, including Memory Strategies, Cognitive Strategies, Metacognitive Strategies and Social Strategies, at the significance level of 0.05. In addition, the students with different learning achievements also used different strategies at the significance level of 0.05. Further studies can explore learning strategies of other groups of Japanese learners, such as university students or company employees. Moreover, learning strategies for language skills, including listening, speaking, reading and writing, can be analyzed for better understanding of learners’ characteristics and for teaching applications.

Keywords: language learning strategies, achievement, Japanese, college students

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Authors: S. Fahiminiya, J. Nadaf, F. Rauch, L. Jerome-Majewska, J. Majewski

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Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation.

Keywords: whole exome sequencing data, non-coding variants, copy number variations, rare diseases

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Authors: Simin Sadeghi-Saeb

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Metacognitive strategies consistently play important roles in reading comprehension. The metacognitive strategies involve the active monitoring and consequent regulation and orchestration of the cognitive processes in relation to the cognitive objects or data on which they bear. In this paper, the effect of instruction in using metacognitive strategies on reading academic materials, type of metacognitive strategies were mostly used by college university students before and after the instruction and the level they use those strategies before and after the instruction were studied. For these aims, 50 female college students were chosen. Then, they were divided randomly into two groups, experimental and control groups. At first session, students in both groups took the standard TOFEL exam. After the pre-test had been administered, the instruction began. After treatment, a post-test was taken. It is useful to state that after pre-test and post-test the same questionnaire was handed to the students of experimental group. The results of this research show that the instruction of metacognitive strategies has positive effect on the students' scores in reading comprehension tests. Furthermore, it showed that before and after the instruction, the students' usage of metacognitive strategies changed. Also, it demonstrated that the instruction affected the students' level of metacognitive strategies' usage.

Keywords: EFL students, English reading comprehension, instruction, metacognitive strategies

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Authors: Collins Molua

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This paper investigated the effect of Teaching Strategies on Academic Achievement in Secondary Physics Education as a quality assurance process for the teaching and learning of the subject. Teaching strategies investigated were the interactive, independent and dependent strategies. Three null hypotheses were tested at p< 0.05 using one instrument, physics achievement test(PAT).The data were analyzed using analysis of covariance (ANCOVA).Results showed that teaching strategies have significant effect on students achievement; the joint effect of the teaching strategies was also significant on students achievement in Physics. The interactive teaching strategies was recommended for teaching the subject and the students should be exposed to practical, computer literacy to stimulate interest and curiosity to enhance quality.

Keywords: quality, assurance, secondary education, strategies, physics

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Sunil Dutta

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Synchronization is defined as ‘the sequencing and re-sequencing of all relative and absolute activities in time and space and continuous alignment of those actions with purposeful objective in a complex and dynamic atmosphere. In a complex and dynamic production / maintenance setup, no single group can work in isolation for long. In addition, many activities in projects take place simultaneously at the same time. Work of every section / group is interwoven with work of others. The various activities / interactions which take place in production / overhaul workshops are interlinked because of physical requirements (information, material, workforces, equipment, and space) and dependencies. The activity sequencing is determined by physical dependencies of various department / sections / units (e.g., inventory availability must be ensured before stripping and disassembling of equipment), whereas resource dependencies do not. Theory of constraint facilitates identification, analyses and exploitation of the constraint in methodical manner. These constraints (equipment, manpower, policies etc.) prevent the department / sections / units from getting optimum exploitation of available resources. The significance of theory of constraints for achieving synchronization at overhaul workshop is illustrated in this paper.

Keywords: synchronization, overhaul, throughput, obsolescence, uncertainty

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

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

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

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Authors: Parvaneh Mahmoudi, Ahmad Moeni, Seyed Mojtaba Khayam Nekoei, Mohsen Mardi, Mehrshad Zeinolabedini, Ghasem Hosseini Salekdeh

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Saffron (Crocus sativus L.) is one of the most important spice and medicinal plants. The three-branch style of C. sativus flowers are the most important economic part of the plant and known as saffron, which has several medicinal properties. Despite the economic and biological significance of this plant, knowledge about its molecular characteristics is very limited. In the present study, we, for the first time, constructed a comprehensive dataset for C. sativus stigma through de novo transcriptome sequencing. We performed de novo transcriptome sequencing of C. sativus stigma using the Illumina paired-end sequencing technology. A total of 52075128 reads were generated and assembled into 118075 unigenes, with an average length of 629 bp and an N50 of 951 bp. A total of 66171unigenes were identified, among them, 66171 (56%) were annotated in the non-redundant National Center for Biotechnology Information (NCBI) database, 30938 (26%) were annotated in the Swiss-Prot database, 10273 (8.7%) unigenes were mapped to 141 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, while 52560 (44%) and 40756 (34%) unigenes were assigned to Gen Ontology (GO) categories and Eukaryotic Orthologous Groups of proteins (KOG), respectively. In addition, 65 candidate genes involved in three stages of crocin biosynthesis were identified. Finally, transcriptome sequencing of saffron stigma was used to identify 6779 potential microsatellites (SSRs) molecular markers. High-throughput de novo transcriptome sequencing provided a valuable resource of transcript sequences of C. sativus in public databases. In addition, most of candidate genes potentially involved in crocin biosynthesis were identified which could be further utilized in functional genomics studies. Furthermore, numerous obtained SSRs might contribute to address open questions about the origin of this amphiploid spices with probable little genetic diversity.

Keywords: saffron, transcriptome, NGS, bioinformatic

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Authors: Katalin Gombos, Bence Gálik, Krisztina Ildikó Kalács, Krisztina Gödöny, Ákos Várnagy, József Bódis, Attila Gyenesei, Gábor L. Kovács

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Although non-invasive pre-implantation genetic testing for aneuploidy (NIPGT-A) is potentially appropriate to assess chromosomal ploidy of the embryo, practical application of it in a routine IVF center has not been started in the absence of a recommendation. We developed a comprehensive workflow for a clinically applicable strategy for NIPGT-A based on next-generation sequencing (NGS) technology. We performed MALBAC whole genome amplification and NGS on spent blastocyst culture media of Day 3 embryos fertilized with intra-cytoplasmic sperm injection (ICSI). Spent embryonic culture media of morphologically good quality score embryos were enrolled in further analysis with the blank culture media as background control. Chromosomal abnormalities were identified by an optimized bioinformatics pipeline applying a copy number variation (CNV) detecting algorithm. We demonstrate a comprehensive workflow covering both wet- and dry-lab procedures supporting a clinically applicable strategy for NIPGT-A. It can be carried out within 48 h which is critical for the same-cycle blastocyst transfer, but also suitable for “freeze all” and “elective frozen embryo” strategies. The described integrated approach of non-invasive evaluation of embryonic DNA content of the culture media can potentially supplement existing pre-implantation genetic screening methods.

Keywords: next generation sequencing, in vitro fertilization, embryo assessment, non-invasive pre-implantation genetic testing

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Authors: Mina Hojat Ansari, Kamran Bagheri Lankarani, Mohammad Reza Fattahi, Ali Reza Safarpour

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Irritable bowel syndrome (IBS) is a common bowel disorder which is usually diagnosed through the abdominal pain, fecal irregularities and bloating. Alteration in the intestinal microbial composition is implicating to inflammatory and functional bowel disorders which is recently also noted as an IBS feature. Owing to the potential importance of microbiota implication in both efficiencies of the treatment and prevention of the diseases, we examined the association between the intestinal microbiota and different bowel patterns in a cohort of subjects with IBS and healthy controls. Fresh fecal samples were collected from a total of 50 subjects, 30 of whom met the Rome IV criteria for IBS and 20 Healthy control. Total DNA was extracted and library preparation was conducted following the standard protocol for small whole genome sequencing. The pooled libraries sequenced on an Illumina Nextseq platform with a 2 × 150 paired-end read length and obtained sequences were analyzed using several bioinformatics programs. The majority of sequences obtained in the current study assigned to bacteria. However, our finding highlighted the significant microbial taxa variation among the studied groups. The result, therefore, suggests a significant association of the microbiota with symptoms and bowel characteristics in patients with IBS. These alterations in fecal microbiota could be exploited as a biomarker for IBS or its subtypes and suggest the modification of the microbiota might be integrated into prevention and treatment strategies for IBS.

Keywords: irritable bowel syndrome, intestinal microbiota, small whole genome sequencing, fecal samples, Illumina

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Authors: Corey F. Fitzgerald

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This study provides a comprehensive examination of the biomechanical sequencing inherent in pitching motions, coupled with an advanced methodology for interpreting gathered data to inform programming strategies. The analysis is conducted utilizing state-of-the-art biomechanical laboratory equipment capable of detecting subtle changes and deviations, facilitating highly informed decision-making processes. Through this presentation, the intricate dynamics of pitching sequences are meticulously discussed to highlight the complex movement patterns accessible and actionable for performance enhancement purposes in the weight room.

Keywords: sport science, applied biomechanics, strength and conditioning, applied research

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Authors: Pouya Karimi, Ramin Gasemi Shayan, Parsa Sheykhzade

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Ease shotgun DNA sequencing is changing the microbial sciences. Sequencing instruments are compelling to the point that example planning is currently the key constraining element. Here, we present a microfluidic test readiness stage that incorporates the key strides in cells to grouping library test groundwork for up to 96 examples and decreases DNA input prerequisites 100-overlay while keeping up or improving information quality. The universally useful microarchitecture we show bolsters work processes with subjective quantities of response and tidy up or catch steps. By decreasing the example amount necessities, we empowered low-input (∼10,000 cells) entire genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil miniaturized scale settlements with prevalent outcomes. We additionally utilized the upgraded throughput to succession ∼400 clinical Pseudomonas aeruginosa libraries and exhibit magnificent single-nucleotide polymorphism discovery execution that clarified phenotypically watched anti-toxin opposition. Completely coordinated lab-on-chip test arrangement beats specialized boundaries to empower more extensive organization of genomics across numerous fundamental research and translational applications.

Keywords: clinical microbiology, DNA, microbiology, microbial genomics

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Authors: Khalda Amr, Noha Eltaweel, Sherif Ismail, Hala Raslan

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Introduction: Osteoarthritis is the most common form of arthritis that involves the wearing away of the cartilage that caps the bones in the joints. While rheumatoid arthritis is an autoimmune disease in which the immune system attacks the joints, beginning with the lining of joints. In this study, we aimed to study the top deregulated miRNAs that might be the cause of pathogenesis in both diseases. Methods: Eight cases were recruited in this study: 4 rheumatoid arthritis (RA), 2 osteoarthritis (OA) patients, as well as 2 healthy controls. Total RNA was isolated from plasma to be subjected to miRNA profiling by NGS. Sequencing libraries were constructed and generated using the NEBNextR UltraTM small RNA Sample Prep Kit for Illumina R (NEB, USA), according to the manufacturer’s instructions. The quality of samples were checked using fastqc and multiQC. Results were compared RA vs Controls and OA vs. Controls. Target gene prediction and functional annotation of the deregulated miRNAs were done using Mienturnet. The top deregulated miRNAs in each disease were selected for further validation using qRT-PCR. Results: The average number of sequencing reads per sample exceeded 2.2 million, of which approximately 57% were mapped to the human reference genome. The top DEMs in RA vs controls were miR-6724-5p, miR-1469, miR-194-3p (up), miR-1468-5p, miR-486-3p (down). In comparison, the top DEMs in OA vs controls were miR-1908-3p, miR-122b-3p, miR-3960 (up), miR-1468-5p, miR-15b-3p (down). The functional enrichment of the selected top deregulated miRNAs revealed the highly enriched KEGG pathways and GO terms. Six of the deregulated miRNAs (miR-15b, -128, -194, -328, -542 and -3180) had multiple target genes in the RA pathway, so they are more likely to affect the RA pathogenesis. Conclusion: Six of our studied deregulated miRNAs (miR-15b, -128, -194, -328, -542 and -3180) might be highly involved in the disease pathogenesis. Further functional studies are crucial to assess their functions and actual target genes.

Keywords: next generation sequencing, mirnas, rheumatoid arthritis, osteoarthritis

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Authors: Habib Onsori, Somayeh Akrami, Mohammad Rahmati

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Deafness is the most common sensory disorder with the frequency of 1/1000 in many populations. Mutations in the GJB2 (CX26) gene at the DFNB1 locus on chromosome 13q12 are associated with congenital hearing loss. Approximately 80% of congenital hearing loss cases are recessively inherited and 15% dominantly inherited. Mutations of the GJB2 gene, encoding gap junction protein Connexin 26 (Cx26), are the most common cause of hereditary congenital hearing loss in many countries. This report presents two cases of different mutations from Iranian patients with bilateral hearing loss. DNA studies were performed for the GJB2 gene by PCR and sequencing methods. In one of them, direct sequencing of the gene showed a heterozygous T→C transition at nucleotide 604 resulting in a cysteine to arginine amino acid substitution at codon 202 (C202R) in the fourth extracellular domain (TM4) of the protein. The analyses indicate that the C202R mutation appeared de novo in the proband with a possible dominant effect (GenBank: KF 638275). In the other one, DNA sequencing revealed a compound heterozygous mutation (35delG, 363delC) in the Cx26 gene that is strongly associated with congenital non-syndromic hearing loss (NSHL). So screening the mutations for hearing loss individuals referring to genetics counseling centers before marriage and or pregnancy is recommended.

Keywords: CX26, deafness, GJB2, mutation

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Authors: Xiaoxing Ye

Abstract:

To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

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Authors: Asmuddin Natsir, A. Mujnisa, Syahriani Syahrir, Marhamah Nadir, Nurul Purnomo

Abstract:

Bacteria, protozoa, Archaea, and fungi are the dominant microorganisms found in the rumen ecosystem that has an important role in converting feed ingredients into components that can be digested and utilized by the livestock host. This study was conducted to assess the diversity of rumen bacteria of bali cattle raised under traditional farming condition. Three adult bali cattle were used in this experiment. The rumen fluid samples from the three experimental animals were obtained by the Stomach Tube method before the morning feeding. The results of study indicated that the Illumina sequencing was successful in identifying 301,589 sequences, averaging 100,533 sequences, from three rumen fluid samples of three cattle. Furthermore, based on the SILVA taxonomic database, there were 19 kinds of phyla that had been successfully identified. Of the 19 phyla, there were only two dominant groups across the three samples, namely Bacteroidetes and Firmicutes, with an average percentage of 83.68% and 13.43%, respectively. Other groups such as Synergistetes, Spirochaetae, Planctomycetes can also be identified but in relatively small percentage. At the genus level, there were 157 sequences obtained from all three samples. Of this number, the most dominant group was Prevotella 1 with a percentage of 71.82% followed by 6.94% of Christencenellaceae R-7 group. Other groups such as Prevotellaceae UCG-001, Ruminococcaceae NK4A214 group, Sphaerochaeta, Ruminococcus 2, Rikenellaceae RC9 gut group, Quinella were also identified but with very low percentages. The sequencing results were able to detect the presence of 3.06% and 3.92% respectively for uncultured rumen bacterium and uncultured bacterium. In conclusion, the results of this experiment can provide an opportunity for a better understanding of the rumen bacterial diversity of the bali cattle raised under traditional farming condition and insight regarding the uncultured rumen bacterium and uncultured bacterium that need to be further explored.

Keywords: 16S rRNA sequencing, bali cattle, rumen microbial diversity, uncultured rumen bacterium

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Authors: Zixi You

Abstract:

With the demand of multilingual speakers increasing in the job market, multi-language learning programs have become more and more popular among undergraduate students. A study on multi-language learning strategies is therefore highly demanded on both practical and theoretical levels. Based on previous classification of learning strategies in SLA, and an investigation of BA Modern Language program students (with post-A level L2 and ab initio L3 learning experience from year one), this study explores and compares different types of learning strategies used by multi-language speakers and learners, transferable learning strategies between L2 and L3, and factors affecting the transfer. The results indicate that all the 23 types of learning strategies of L2 are employed when learning L3 from ab initio level, yet with different tendencies. Learning strategy transfer from L2 to L3 (i.e., the learners attribute the applying of these L3 learning strategies to be a direct result of their L2 learning experience) are observed in all 23 types of learning strategies. Comparatively, six types of “cognitive strategies” have higher transfer tendency than others. With regard to the failure of the transfer of some particular L2 strategies and the development of independent L3 strategies of individual learners, factors such as language proficiency, language typology and learning environment have played important roles among others. The presentation of this study will provide audiences with detailed data, insightful analysis and discussion on both theoretical and practical aspects of multi-language learning that will benefit both students and educators.

Keywords: learning strategy, multi-language acquisition, second language acquisition, strategy transfer

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Authors: Hamed Saremi, Shahla Saremi

Abstract:

In today's competitive world, organizations are expected to surpass the competitors and benefit from the resources and benefits. Therefore, organizations need to improve the current performance is felt more than ever that this requires to identify organizational optimal strategies, and consider all strategies simultaneously. In this study, to enhance competitive advantage and according to customer requirements, alignment between business, production and marketing strategies, House of Quality (QFD) approach has been used and zero-one linear programming model has been studied. First, the alignment between production and marketing strategies with business strategy, independent weights of these strategies is calculated. Then with using QFD approach the aligned weights of optimal strategies in each production and marketing field will be obtained and finally the aligned marketing strategies selection with the purpose of allocating budget and specialist human resource to marketing functions will be done that lead to increasing competitive advantage and benefit.

Keywords: marketing strategy, business strategy, strategy alignment, house of quality deployment, production strategy

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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

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Authors: Hamed Saremi, Suzan Taghavy, Shahla Saremi

Abstract:

In today's competitive world, organizations are expected to surpass the competitors and benefit from the resources and benefits. Therefore, organizations need to improve the current performance is felt more than ever that this requires to identify organizational optimal strategies, and consider all strategies simultaneously. In this study, to enhance competitive advantage and according to customer requirements, alignment between business, production and marketing strategies, House of Quality (QFD) approach has been used and zero-one linear programming model has been studied. First, the alignment between production and marketing strategies with business strategy, independent weights of these strategies is calculated. Then with using QFD approach the aligned weights of optimal strategies in each production and marketing field will be obtained and finally the aligned marketing strategies selection with the purpose of allocating budget and specialist human resource to marketing functions will be done that lead to increasing competitive advantage and benefit.

Keywords: strategy alignment, house of quality deployment, production strategy, marketing strategy, business strategy

Procedia PDF Downloads 413