Search results for: material genome

Authors: Micheale Yifter Weldemichael

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

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Authors: Mine Koyaz, M. Cem Altun

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Selection of the materials satisfying the expected performances is significantly important for any design. Today, with the constantly evolving and developing technologies, the material options are so wide that the necessity of the use of some support tools in the selection process is arising. Therefore, as a sub process of building element design, a systematic material selection tool is developed, that defines four main steps of the material selection; definition, research, comparison and decision. The main purpose of the tool is being an educational instrument that would show a methodic way of material selection in architectural detailing for the use of architecture students. The tool predefines the possible uses of various material databases and other sources of information on material properties. Hence, it is to be used as a guidance for designers, especially with a limited material knowledge and experience. The material selection tool not only embraces technical properties of materials related with building elements’ functional requirements, but also its sensual properties related with the identity of design and its environmental impacts with respect to the sustainability of the design. The method followed in the development of the tool has two main sections; first the examination and application of the existing methods and second the development of trial versions and their applications. Within the scope of the existing methods; design support tools, methodic approaches for the building element design and material selection process, material properties, material databases, methodic approaches for the decision making process are examined. The existing methods are applied by architecture students and newly graduate architects through different design problems. With respect to the results of these applications, strong and weak sides of the existing material selection tools are presented. A main flow chart of the material selection tool has been developed with the objective to apply the strong aspects of the existing methods and develop their weak sides. Through different stages, a different aspect of the material selection process is investigated and the tool took its final form. Systematic material selection tool, within the building element design process, guides the users with a minimum background information, to practically and accurately determine the ideal material that is to be chosen, satisfying the needs of their design. The tool has a flexible structure that answers different needs of different designs and designers. The trial version issued in this paper shows one of the paths that could be followed and illustrates its application over a design problem.

Keywords: architectural education, building element design, material selection tool, systematic approach

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Authors: Ryan Masoodi, Hossein Rostami

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Aluminum has been credited for the massive advancement of many industrial products, from aerospace and automotive to electronics and even household appliances. These developments have come with a cost, which is a toxic by-product. The rise of aluminum production has been accompanied by the rise of a waste material called Bauxite Residue or Red Mud. This toxic material has been proved to be harmful to the environment, yet, there is no proper way to dispose or recycle it. Herewith, a new experimental method to utilize this waste in the building material is proposed. A method to mix red mud, fly ash, and some other ingredients is explored to create a new construction material that can satisfy the minimum required strength for bricks. It concludes that it is possible to produce bricks with enough strength that is suitable for constriction in environments with low to moderate weather conditions.

Keywords: bauxite residue, brick, red mud, recycling

Procedia PDF Downloads 169

Authors: Ren Zuo Wang

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In this paper, in order to investigate the behavior of the wood structure, the non-linearity of wood material model in LS-DYNA is adopted. It is difficult and less efficient to conduct the experiment of the ancient wood structure, hence LS-DYNA software can be used to simulate nonlinear responses of ancient wood structure. In LS-DYNA software, there is material model called *MAT_WOOD or *MAT_143. This model is to simulate a single-element response of the wood subjected to tension and compression under the parallel and the perpendicular material directions. Comparing with the exact solution and numerical simulations results using LS-DYNA, it demonstrates the accuracy and the efficiency of the proposed simulation method.

Keywords: LS-DYNA, wood structure, single-element simulations, MAT_143

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Authors: Bharath Kenchappa, Kunigal Shivakumar

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Lightweight, low thermal conductivity and high temperature resistant materials or the system with moderate mechanical properties and capable of taking high heating rates are needed in both commercial and military applications. A single material with these attributes is very difficult to find and one needs to come with innovative ideas to make such material system using what is available. To bring down the cost of the system, one has to be conscious about the cost of basic materials. Such a material system can be called as the thermal barrier system. This paper focuses on developing, testing and characterization of material system for thermal barrier applications. The material developed is porous, low density, low thermal conductivity of 0.1062 W/m C and glass transition temperature about 310 C. Also, the thermal properties of the developed material was measured in both longitudinal and thickness direction to highlight the fact that the material shows isotropic behavior. The material is called modified Eco-Core which uses only less than 9% weight of high-char resin in the composite. The filler (reinforcing material) is a component of fly ash called Cenosphere, they are hollow micro-bubbles made of ceramic materials. Special mixing-technique is used to surface coat the fillers with a thin layer of resin to develop a point-to-point contact of particles. One could use commercial ceramic micro-bubbles instead of Cenospheres, but it is expensive. The bulk density of Cenospheres is about 0.35 g/cc and we could accomplish the composite density of about 0.4 g/cc. One percent filler weight of 3mm length standard drywall grade fibers was used to bring the added toughness. Both thermal and mechanical characterization was performed and properties are documented. For higher temperature applications (up to 1,000 C), a hybrid system was developed using an aerogel mat. Properties of combined material was characterized and documented. Thermal tests were conducted on both the bare modified Eco-Core and hybrid materials to assess the suitability of the material to a thermal barrier application. The hybrid material system was found to meet the requirement of the application.

Keywords: aerogel, fly ash, porous material, thermal barrier

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Authors: Youcef Faci, Djillali Allou, Ahmed Mebtouche, Badredine Maalem

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The inclination of the bolt in a fastened joint of composite material during a tensile test can be influenced by several parameters, including material properties, bolt diameter and length, the type of composite material being used, the size and dimensions of the bolt, bolt preload, surface preparation, the design and configuration of the joint, and finally testing conditions. These parameters should be carefully considered and controlled to ensure accurate and reliable results during tensile testing of composite materials with fastened joints. Our work focuses on the effect of the stacking sequence and the geometry of specimens. An experimental test is carried out to obtain the inclination of a bolt during a tensile test of a composite material using acoustic emission and digital image correlation. Several types of damage were obtained during load. Digital image correlation techniques permit to obtain the inclination of bolt angle value during tensile test. We concluded that the inclination of the bolt during a tensile test of a composite material can be related to the damage that occurs in the material. It can cause stress concentrations and localized deformation in the material, leading to damage such as delamination, fiber breakage, matrix cracking, and other forms of failure.

Keywords: damage, digital image correlation, bolt inclination angle, joint

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Authors: Lucélia Alcântara

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Reading has been seen as a passive skill by many people for a long time. However, when one comes to study it deeply and in a such a way that the act of reading equals acquiring knowledge through living an experience that belongs to him/her, passive definitely becomes active. Material development with a focus on reading has to consider much more than reading strategies. The following questions are asked: Is the material appropriate to the students’ reality? Does it make students think and state their points of view? With that in mind a lesson has been developed to illustrate theory becoming practice. Knowledge, criticality, intercultural experience and social interaction. That is what reading is for.

Keywords: reading, culture, material development, learning

Procedia PDF Downloads 536

Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

Procedia PDF Downloads 593

Authors: Antonela Matana, Dubravka Brdar, Vesela Torlak, Marijana Popovic, Ivana Gunjaca, Ozren Polasek, Vesna Boraska Perica, Maja Barbalic, Ante Punda, Caroline Hayward, Tatijana Zemunik

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Parathyroid hormone (PTH) plays a critical role in the regulation of bone mineral metabolism and calcium homeostasis. Higher PTH levels are associated with heart failure, hypertension, coronary artery disease, cardiovascular mortality and poorer bone health. A twin study estimated that 60% of the variation in PTH concentrations is genetically determined. Only one GWAS of PTH concentration has been reported to date. Identified loci explained 4.5% of the variance in circulating PTH, suggesting that additional genetic variants remain undiscovered. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels in a general population. We have performed a GWAS meta-analysis on 2596 individuals originating from three Croatian cohorts: City of Split and the Islands of Korčula and Vis, within a large-scale project of “10,001 Dalmatians”. A total of 7 411 206 variants, imputed using the 1000 Genomes reference panel, with minor allele frequency ≥ 1% and Rsq ≥ 0.5 were analyzed for the association. GWAS within each data set was performed under an additive model, controlling for age, gender and relatedness. Meta-analysis was conducted using the inverse-variance fixed-effects method. Furthermore, to identify sex-specific effects, we have conducted GWAS meta-analyses analyzing males and females separately. In addition, we have performed biological pathway analysis. Four SNPs, representing one locus, reached genome-wide significance. The most significant SNP was rs11099476 on chromosome 4 (P=1.15x10-8), which explained 1.14 % of the variance in PTH. The SNP is located near the protein-coding gene RASGEF1B. Additionally, we detected suggestive association with SNPs, rs77178854 located on chromosome 2 in the DPP10 gene (P=2.46x10-7) and rs481121 located on chromosome 1 (P=3.58x10-7) near the GRIK1 gene. One of the top hits detected in the main meta-analysis, intron variant rs77178854 located within DPP10 gene, reached genome-wide significance in females (P=2.21x10-9). No single locus was identified in the meta-analysis in males. Fifteen biological pathways were functionally enriched at a P<0.01, including muscle contraction, ion homeostasis and cardiac conduction as the most significant pathways. RASGEF1B is the guanine nucleotide exchange factor, known to be associated with height, bone density, and hip. DPP10 encodes a membrane protein that is a member of the serine proteases family, which binds specific voltage-gated potassium channels and alters their expression and biophysical properties. In conclusion, we identified 2 novel loci associated with PTH levels in a general population, providing us with further insights into the genetics of this complex trait.

Keywords: general population, genome-wide association analysis, parathyroid hormone, single nucleotide polymorphisms.

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Authors: Mustafa Albayrak, Mete Onur Kaman, Ilyas Bozkurt

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In this study, the necessary material parameters were determined to be able to conduct progressive damage analysis of layered composites under low velocity impact by using the MAT162 material module in the LS-DYNA program. The material module MAT162 based on Hashin failure criterion requires 34 parameters in total. Some of these parameters were obtained directly as a result of dynamic and quasi-static mechanical tests, and the remaining part was calibrated and determined by comparing numerical and experimental results. Woven glass/epoxy was used as the composite material and it was produced by vacuum infusion method. In the numerical model, composites are modeled as three-dimensional and layered. As a result, the acquisition of MAT162 material module parameters, which will enable progressive damage analysis, is given in detail and step by step, and the selection methods of the parameters are explained. Numerical data consistent with the experimental results are given in graphics.

Keywords: Composite Impact, Finite Element Simulation, Progressive Damage Analyze, LS-DYNA, MAT162

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

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

Keywords: BCaRV, Betanucleorhabdovirus, Ribes, RNA-seq

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Authors: Gaokai Liu

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The distribution of material grain sizes reflects the strength, fracture, corrosion and other properties, and the grain size can be acquired via the grain boundary. In recent years, the automatic grain boundary detection is widely required instead of complex experimental operations. In this paper, an effective solution is applied to acquire the grain boundary of material images. First, the initial superpixel segmentation result is obtained via a superpixel approach. Then, a region merging method is employed to merge adjacent regions based on certain similarity criterions, the experimental results show that the merging strategy improves the superpixel segmentation result on material datasets.

Keywords: grain boundary detection, image segmentation, material images, region merging

Procedia PDF Downloads 170

Authors: Yea-Chyi Lin, Shinn-Dar Wu, Chien-Ping Chung

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Tea is not only part of the daily lives of the Chinese people, but also represents an essence of their culture. A manufactured tea is prepared with other complicated steps for self-cultivation. Tea drinking promotes friendship and is etiquette in Chinese ceremony. Tea was discovered in China and introduced worldwide. Tea is generally used as herbal medicine. Paowan of tea can be used as plant composts and deodorant as well as for moisture proof-package. Tea prepared via carbon material technology resulted in the increase of its value. Carbon material technology uses graphite. With the battery anode material, tea can also become a new carbon material element. It has a fiber carbon structure that can retain the advantage of tea ontology. Therefore, this study provides a new preparation method through special sintering technology equipment with a gas counter-current system of 300°C to 400°C and 400°C to 900°C. The recovery of carbonization was up to 80% or more. This study addresses tea recycling technology and shows charred sintering method and loss from solving grinder to obtain a good fiber carbon structure.

Keywords: recycling technology, tea, carbonization, sintering technology, manufacturing

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Authors: Chi Zhang, Jun Jiang

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Constitutive equations are very important in finite element (FE) modeling, and the accuracy of the material constants in the equations have significant effects on the accuracy of the FE models. A wide range of constitutive equations are available; however, fitting the material constants in the constitutive equations could be complex and time-consuming due to the strong non-linearity and relationship between the constants. This work will focus on the development of a set of unified MATLAB programs for fitting the material constants in the constitutive equations efficiently. Users will only need to supply experimental data in the required format and run the program without modifying functions or precisely guessing the initial values, or finding the parameters in previous works and will be able to fit the material constants efficiently.

Keywords: constitutive equations, FE modelling, MATLAB program, non-linear curve fitting

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Authors: V. Singh, S. Singh, S. S. Garewal

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Metal matrix composites with aluminum as the matrix material have been heralded as the next great development in advanced engineering materials. Aluminum metal matrix composites (AMMC) refer to the class of light weight high performance material systems. Properties of AMMCs can be tailored to the demands of different industrial applications by suitable combinations of matrix, reinforcement and processing route. AMMC finds its application in automotive, aerospace, defense, sports and structural areas. This paper presents an overview of AMMC material systems on aspects relating to processing, types and applications with case studies.

Keywords: aluminum metal matrix composites, applications of aluminum metal matrix composites, lighting material processing of aluminum metal matrix composites

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Authors: Kwok Tak Kit

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Combating climate change is becoming a hot topic in various sectors. Building construction and infrastructure sectors contributed a significant proportion of waste and GHGs emissions in the economy of different countries and cities. Many types of research had conducted and discussed the topic of waste management and waste management being a macro-level control is well developed in the building and construction industry. However, there is little research and studies on the micro-level of waste management, “building construction material wastage management,” and fewer reviews about regulatory control in the building construction sector. In this paper, we will focus on the potentialities and importance of material wastage management and review the deficiencies of the current standard to take into account the reduction of material wastage in a systematic and quantitative approach.

Keywords: quantitative measurement, material wastage management plan, waste management, uncalculated waste, circular economy

Procedia PDF Downloads 154

Authors: Chetan Mahawar, Sarath Chandran, Sridhar Panigrahi, V. P. Shaji

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The ever-growing advancement in space exploration has led to an alarming concern for space debris removal as it restricts further launch operations and adventurous space missions; hence numerous studies have come up with technologies for re-entry predictions and material selection processes for mitigating space debris. The selection of material and operating conditions is determined with the objective of lightweight structure and ability to demise faster subject to spacecraft survivability during its mission. Since the demisability of spacecraft depends on evolving thermal material properties such as emissivity, specific heat capacity, thermal conductivity, radiation intensity, etc. Therefore, this paper presents the analysis of evolving thermal material properties of spacecraft, which affect the demisability process and thus estimate demise time using the demisability model by incorporating evolving thermal properties for sensible heating followed by the complete or partial break-up of spacecraft. The demisability analysis thus concludes the best suitable spacecraft material is based on the least estimated demise time, which fulfills the criteria of design-for-survivability and as well as of design-for-demisability.

Keywords: demisability, emissivity, lightweight, re-entry, survivability

Procedia PDF Downloads 117

Authors: A. M. Naraghi, V. Gonzalez, M. O'Sullivan, C. G. Walker, M. Poshdar, F. Ying, M. Abdelmegid

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Discrete Event Simulation (DES) and Agent Based Simulation (ABS) are two simulation approaches that have been proposed to support decision-making in the construction industry. Despite the wide use of these simulation approaches in the construction field, their applications for production and material planning is still limited. This is largely due to the dynamic and complex nature of construction material supply chain systems. Moreover, managing the flow of construction material is not well integrated with site logistics in traditional construction planning methods. This paper presents a hybrid of DES and ABS to simulate on-site and off-site material supply processes. DES is applied to determine the best production scenarios with information of on-site production systems, while ABS is used to optimize the supply chain network. A case study of a construction piling project in New Zealand is presented illustrating the potential benefits of using the proposed hybrid simulation model in construction material flow planning. The hybrid model presented can be used to evaluate the impact of different decisions on construction supply chain management.

Keywords: construction supply-chain management, simulation modeling, decision-support tools, hybrid simulation

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Authors: Un-Hwan Park, Jun-Hyeok Heo, In-Sung Lee, Tae-Hyeon Oh, Dae-Gyu Park

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Automotive interior material consisting of several material layers has the sound-absorbing function. It is difficult to predict sound absorbing coefficient because of several material layers. So, many experimental tunings are required to achieve the target of sound absorption. Therefore, while the car interior materials are developed, so much time and money is spent. In this study, we present a method to predict the sound absorbing performance of the material with multi-layer using physical properties of each material. The properties are predicted by Foam-X software using the sound absorption coefficient data measured by impedance tube. Then, we will compare and analyze the predicted sound absorption coefficient with the data measured by scaled reverberation chamber and impedance tubes for a prototype. If the method is used instead of experimental tuning in the development of car interior material, the time and money can be saved, and then, the development effort can be reduced because it can be optimized by simulation.

Keywords: multi-layer nonwoven, sound absorption coefficient, scaled reverberation chamber, impedance tubes

Procedia PDF Downloads 377

Authors: Anyaphat Srithanasuwan, Noppason Pangprasit, Montira Intanon, Phongsakorn Chuammitri, Witaya Suriyasathaporn, Ynte H. Schukken

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Streptococcus uberis is one of the most common mastitis-causing pathogens, with a wide range of intramammary infection (IMI) durations and pathogenicity. This study aimed to compare shared or unique virulence factor gene clusters distinguishing persistent and transient strains of S. uberis. A total of 139 S. uberis strains were isolated from three small-holder dairy herds with a high prevalence of S. uberis mastitis. The duration of IMI was used to categorize bacteria into two groups: transient and persistent strains with an IMI duration of less than 1 month and longer than 2 months, respectively. Six representative S. uberis strains, three from each group (transience and persistence) were selected for analysis. All transient strains exhibited multi-locus sequence types (MLST), indicating a highly diverse population of transient S. uberis. In contrast, MLST of persistent strains was available in an online database (pubMLST). Identification of virulence genes was performed using whole-genome sequencing (WGS) data. Differences in genomic size and number of virulent genes were found. For example, the BCA gene or alpha-c protein and the gene associated with capsule formation (hasAB), found in persistent strains, are important for attachment and invasion, as well as the evasion of the antimicrobial mechanisms and survival persistence, respectively. These findings suggest a genetic-level difference between the two strain types. Consequently, a comprehensive study of 139 S. uberis isolates will be conducted to perform an in-depth genetic assessment through WGS analysis on an Illumina platform.

Keywords: Streptococcus Uberis, mastitis, whole genome sequence, intramammary infection, persistent S. Uberis, transient s. Uberis

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Authors: Khin Thanda Win, Chunying Zhang, Sanghyeob Lee

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Mildew resistance locus o (Mlo), a plant-specific gene family with seven-transmembrane (TM), plays an important role in plant resistance to powdery mildew (PM). PM caused by Podosphaera xanthii is a widespread plant disease and probably represents the major fungal threat for many Cucurbits. The recent Cucurbita maxima genome sequence data provides an opportunity to identify and characterize the MLO gene family in this species. Total twenty genes (designated CmaMLO1 through CmaMLO20) have been identified by using an in silico cloning method with the MLO gene sequences of Cucumis sativus, Cucumis melo, Citrullus lanatus and Cucurbita pepo as probes. These CmaMLOs were evenly distributed on 15 chromosomes of 20 C. maxima chromosomes without any obvious clustering. Multiple sequence alignment showed that the common structural features of MLO gene family, such as TM domains, a calmodulin-binding domain and 30 important amino acid residues for MLO function, were well conserved. Phylogenetic analysis of the CmaMLO genes and other plant species reveals seven different clades (I through VII) and only clade IV is specific to monocots (rice, barley, and wheat). Phylogenetic and structural analyses provided preliminary evidence that five genes belonged to clade V could be the susceptibility genes which may play the importance role in PM resistance. This study is the first comprehensive report on MLO genes in C. maxima to our knowledge. These findings will facilitate the functional analysis of the MLOs related to PM susceptibility and are valuable resources for the development of disease resistance in pumpkin.

Keywords: Mildew resistance locus o (Mlo), powdery mildew, phylogenetic relationship, susceptibility genes

Procedia PDF Downloads 182

Authors: Mitra Shokrollahi, Mia Stanic, Anisha Hundal, Janet N. Y. Chan, Defne Urman, Chris A. Jordan, Anne Hakem, Roderic Espin, Jun Hao, Rehna Krishnan, Philipp G. Maass, Brendan C. Dickson, Manoor P. Hande, Miquel A. Pujana, Razqallah Hakem, Karim Mekhail

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Current models suggest that DNA double-strand breaks (DSBs) can move to the nuclear periphery for repair. It is unclear to what extent human DSBs display such repositioning. Here we show that the human nuclear envelope localizes to DSBs in a manner depending on DNA damage response (DDR) kinases and cytoplasmic microtubules acetylated by α-tubulin acetyltransferase-1 (ATAT1). These factors collaborate with the linker of nucleoskeleton and cytoskeleton complex (LINC), nuclear pore complex (NPC) protein NUP153, the nuclear lamina and kinesins KIF5B and KIF13B to generate DSB-capturing nuclear envelope tubules (dsbNETs). dsbNETs are partly supported by nuclear actin filaments and the circadian factor PER1 and reversed by kinesin KIFC3. Although dsbNETs promote repair and survival, they are also co-opted during poly (ADP-ribose) polymerase (PARP) inhibition to restrain BRCA1-deficient breast cancer cells and are hyper-induced in cells expressing the aging-linked lamin A mutant progerin. In summary, our results advance understanding of nuclear structure-function relationships, uncover a nuclear-cytoplasmic DDR and identify dsbNETs as critical factors in genome organization and stability.

Keywords: DNA damage response, genome stability, nuclear envelope, cancer, age-related disorders

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Authors: Bakur Gulua

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In this work, we consider some boundary value problems for the plate. The plate is the elastic material with voids. The state of plate equilibrium is described by the system of differential equations that is derived from three-dimensional equations of equilibrium of an elastic material with voids (Cowin-Nunziato model) by Vekua's reduction method. Its general solution is represented by means of analytic functions of a complex variable and solutions of Helmholtz equations. The problem is solved analytically by the method of the theory of functions of a complex variable.

Keywords: the elastic material with voids, boundary value problems, Vekua's reduction method, a complex variable

Procedia PDF Downloads 129

Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Muhammad Adeel Arshad, Faiz-Ul Hassan, Yanfen Cheng

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According to FAO, enteric methane (CH4) production is about 44% of all greenhouse gas emissions from the livestock sector. Ruminants produce CH4 as a result of fermentation of feed in the rumen especially from roughages which yield more CH4 per unit of biomass ingested as compared to concentrates. Efficient ruminal fermentation is not possible without abating CO2 and CH4. Methane abatement strategies are required to curb the predicted rise in emissions associated with greater ruminant production in future to meet ever increasing animal protein requirements. Ecology of ruminal methanogenesis and avenues for its mitigation can be identified through various genomic and transcriptomic techniques. Programs such as Hungate1000 and the Global Rumen Census have been launched to enhance our understanding about global ruminal microbial communities. Through Hungate1000 project, a comprehensive reference set of rumen microbial genome sequences has been developed from cultivated rumen bacteria and methanogenic archaea along with representative rumen anaerobic fungi and ciliate protozoa cultures. But still many species of rumen microbes are underrepresented especially uncultivable microbes. Lack of sequence information specific to the rumen's microbial community has inhibited efforts to use genomic data to identify specific set of species and their target genes involved in methanogenesis. Metagenomic and metatranscriptomic study of entire microbial rumen populations offer new perspectives to understand interaction of methanogens with other rumen microbes and their potential association with total gas and methane production. Deep understanding of methanogenic pathway will help to devise potentially effective strategies to abate methane production while increasing feed efficiency in ruminants.

Keywords: Genome sequences, Hungate1000, methanogens, ruminal fermentation

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Authors: Faisal Nouroz, Mukaramin Mukaramin

Abstract:

Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Yang Song, Xiaojun Qiu

Abstract:

Multilayer materials are applied to much acoustics area. Multilayer porous materials are dominant in room absorber. Multilayer viscoelastic materials are the basic parts in underwater absorption coating. In most cases, the one-way sound absorption performance of multilayer material is concentrated according to the sound source site. But the two-way sound absorption performance is also necessary to be known in some special cases which sound is produced in both sides of the material and the both sides especially might contact with different media. In this article, this kind of case was research. The multilayer material was composed of viscoelastic layer and steel plate and the porous layer. The two sides of multilayer material contact with water and air, respectively. A theory model was given to describe the sound propagation and impedance in multilayer absorption material. The two-way sound absorption properties of several multilayer materials were calculated whose two sides all contacted with different media. The calculated results showed that the difference of two-way sound absorption coefficients is obvious. The frequency, the relation of layers thickness and parameters of multilayer materials all have an influence on the two-way sound absorption coefficients. But the degrees of influence are varied. All these simulation results were analyzed in the article. It was obtained that two-way sound absorption at different frequencies can be promoted by optimizing the configuration parameters. This work will improve the performance of underwater sound absorption coating which can absorb incident sound from the water and reduce the noise radiation from inside space.

Keywords: different media, multilayer material, sound absorption coating, two-way sound absorption

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Authors: Naoki Yamamoto, Hidenobu Ozaki, Taiichiro Ookawa, Youming Liu, Kazunori Okada, Aiping Zheng

Abstract:

Rice sheath blight is one of the destructive fungal diseases in rice. We have thought that rice sheath blight resistance is a polygenic trait. Host-pathogen interactions and secondary metabolites such as lignin and phytoalexins are likely to be involved in defense against R. solani. However, to our knowledge, it is still unknown how sheath blight resistance can be enhanced in rice breeding. To seek for an alternative genetic factor that contribute to sheath blight resistance, we mined relevant allelic variations from rice core collections created in Japan. Based on disease lesion length on detached leaf sheath, we selected 30 varieties of the top tail-end and the bottom tail-end, respectively, from the core collections to perform genome-wide association mapping. Re-sequencing reads for these varieties were used for calling single nucleotide polymorphisms among the 60 varieties to create a SNP panel, which contained 1,137,131 homozygous variant sites after filitering. Association mapping highlighted a locus on the long arm of chromosome 11, which is co-localized with three sheath blight QTLs, qShB11-2-TX, qShB11, and qSBR-11-2. Based on the localization of the trait-associated alleles, we identified an ankyryn repeat-containing protein gene (ANK-M) as an uncharacterized candidate factor for rice sheath blight resistance. Allelic distributions for ANK-M in the whole rice population supported the reliability of trait-allele associations. Gene expression characteristics were checked to evaluiate the functionality of ANK-M. Since an ANK-M homolog (OsPIANK1) in rice seems a basal defense regulator against rice blast and bacterial leaf blight, ANK-M may also play a role in the rice immune system.

Keywords: allele mining, GWAS, QTL, rice sheath blight

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Authors: A. Fettahoglu

Abstract:

Theory of viscoelasticity is used by many researchers to represent the behavior of many materials such as pavements on roads or bridges. Several researches used analytical methods and rheology to predict the material behaviors of simple models. Today, more complex engineering structures are analyzed using Finite Element Method, in which material behavior is embedded by means of three dimensional viscoelastic material laws. As a result, structures of unordinary geometry and domain can be analyzed by means of Finite Element Method and three dimensional viscoelastic equations. In the scope of this study, rheological models embedded in ANSYS, namely, generalized Maxwell model and Prony series, which are two methods used by ANSYS to represent viscoelastic material behavior, are presented explicitly. Afterwards, a guide is illustrated to ease using of viscoelasticity tool in ANSYS.

Keywords: ANSYS, generalized Maxwell model, finite element method, Prony series, viscoelasticity, viscoelastic material curve fitting

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

Abstract:

The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

Procedia PDF Downloads 224