Search results for: chronological sequence of discharges

Authors: Narjes Ebrahimi, Soheila Alyasin, Navid Nezafat, Hossein Esmailzadeh, Younes Ghasemi, Seyed Hesamodin Nabavizadeh

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Immunotherapy with allergy vaccines is of great importance in allergen-specific immunotherapy. In recent years, B-cell epitope-based vaccines have attracted considerable attention and the prediction of epitopes is crucial to design these types of allergy vaccines. B-cell epitopes might be linear or conformational. The prerequisite for the identification of conformational epitopes is the information about allergens' tertiary structures. Bioinformatics approaches have paved the way towards the design of epitope-based allergy vaccines through the prediction of tertiary structures and epitopes. Mite allergens are one of the major allergy contributors. Several mite allergens can elicit allergic reactions; however, their structures and epitopes are not well established. So, B-cell epitopes of various groups of mite allergens (24 allergens in 6 allergen groups) were predicted in the present work. Tertiary structures of 17 allergens with unknown structure were predicted and refined with RaptorX and GalaxyRefine servers, respectively. The predicted structures were further evaluated by Rampage, ProSA-web, ERRAT and Verify 3D servers. Linear and conformational B-cell epitopes were identified with Ellipro, Bcepred, and DiscoTope 2 servers. To improve the accuracy level, consensus epitopes were selected. Fifty-four conformational and 133 linear consensus epitopes were predicted. Furthermore, overlapping epitopes in each allergen group were defined, following the sequence alignment of the allergens in each group. The predicted epitopes were also compared with the experimentally identified epitopes. The presented results provide valuable information for further studies about allergy vaccine design.

Keywords: B-cell epitope, Immunotherapy, In silico prediction, Mite allergens, Tertiary structure

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

Procedia PDF Downloads 216

Authors: Lee Ping Ang, Salvatore Tomasello, Jun Wen, Marc S. Appelhans

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With about 225 species, Zanthoxylum L. is the second most species rich genus in Rutaceae. It is the only genus with a pantropical distribution. Economically, it is used in several Asian countries as traditional medicine and spice. In the past Zanthoxylum was divided into two genera, the temperate Zanthoxylum sensu strictu (s.s.) and the (sub)tropical Fagara, due to the large differences in flower morphology: heterochlamydeous in Fagara and homochlamydeous in Zanthoxylum s.s.. This genus is much under studied and previous phylogenetic studies using Sanger sequencing did not resolve the relationships sufficiently. In this study, we use Hybrid Capture with a specially designed bait set for Zanthoxylum to sequence 347 putatively single-copy genes. The taxon sampling has been largely improved as compared to previous studies and the preliminary results will be based on 371 specimens representing 133 species from all continents and major island groups. Our preliminary results reveal similar tree topology as the previous studies while providing more details to the backbone of the phylogeny. The phylogenetic tree consists of four main clades: A) African/Malagasy clade, B) Z. asiaticum clade - a clade consisting widespread species occurring in (sub)tropical Asia and Africa as well as Madagascar, C) Asian/Pacific clade and D) American clade, which also includes the temperate Asian species. The merging of Fagara and Zanthoxylum is supported by our results and the homochlamydeous flowers of Zanthoxylum s.s. are likely derived from heterochlamydeous flowers. Several of the morphologically defined sections within Zanthoxylum are not monophyletic. The study dissemination will (1) introduce the framework of this project; (2) present preliminary results and (3) the ongoing progress of the study.

Keywords: Zanthoxylum, phylogenomic, hybrid capture, pantropical

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Authors: Letizia Maria Drammis, Maria Antonella Brandimonte

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The idea that people use space representations to think about time and number received support from several lines of research. However, how these representations develop in children and then shape space-time and space-number mappings is still a debated issue. In the present study, 40 children (20 pre-schoolers and 20 elementary-school children) performed 4 main tasks, which required the use of more concrete (non-symbolic) or more abstract (symbolic) space-time and space-number associations. In the non-symbolic conditions, children were required to order pictures of everyday-life events occurring in a specific temporal order (Temporal sequences) and of quantities varying in numerosity (Numerical sequences). In the symbolic conditions, they were asked to perform the typical time-to-position and number-to-position tasks by mapping time-related words and numbers onto lines. Results showed that children performed reliably better in the non-symbolic Time conditions than the symbolic Time conditions, independently of age, whereas only pre-schoolers performed worse in the Number-to-position task (symbolic) as compared to the Numerical sequence (non-symbolic) task. In addition, only older children mapped time-related words onto space following the typical left-right orientation, pre-schoolers’ performance being somewhat mixed. In contrast, mapping numbers onto space showed a clear left-right orientation, independently of age. Overall, these results indicate a cross-domain difference in the way younger and older children process time and number, with time-related tasks being more difficult than number-related tasks only when space-time tasks require symbolic representations.

Keywords: space-time associations, space-number associations, orientation, children

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Authors: Hojjat Mohammadi, Randall Divito, Gary J. E. Kramer

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Tunnelling and pipe jacking in very soft soils (fat clays), even with an Earth Pressure Balance tunnel boring machine (EPBM), can cause large ground displacements. In this study, the short-term and long-term ground and tunnel response is predicted for twin, pipe-jacked EPBM 3 meter diameter tunnels with a narrow pillar width. Initial modelling indicated complete closure of the annulus gap at the tail shield onto the centrifugally cast, glass-fiber-reinforced, polymer mortar jacking pipe (FRP). Numerical modelling was employed to simulate the excavation and support installation sequence, examine the ground response during excavation, confirm the adequacy of the pillar width and check the structural adequacy of the installed pipe. In the numerical models, Mohr-Coulomb constitutive model with the effect of unloading was adopted for the fat clays, while for the bedrock layer, the generalized Hoek-Brown was employed. The numerical models considered explicit excavation sequences and different levels of ground convergence prior to support installation. The well-studied excavation sequences made the analysis possible for this study on a very soft clay, otherwise, obtaining the convergency in the numerical analysis would be impossible. The predicted results indicate that the ground displacements around the tunnel and its effect on the pipe would be acceptable despite predictions of large zones of plastic behaviour around the tunnels and within the entire pillar between them due to excavation-induced ground movements.

Keywords: finite element modeling (FEM), pipe-jacked tunneling, very soft clay, EPBM

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Authors: Francimar Alves, Marcos Castro, Marllus Lustosa

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In the context of the teaching of computer programming, the choice of tool to use is very important in the initiation and continuity of learning a programming language. The literature tools do not always provide usability and pedagogical dynamism clearly and accurately for effective learning. This hypothesis implies fall in productivity and difficulty of learning a particular programming language by students. The integrated development environments (IDEs) Dev-C ++ and Code :: Blocks are widely used in introductory courses for undergraduate courses in Computer Science for learning C and C ++ languages. However, after several years of discontinuity maintaining the source code of Dev-C ++ tool, the continued use of the same in the teaching and learning process of the students of these institutions has led to difficulties, mainly due to the lack of update by the official developers, which resulted in a sequence of problems in using it on educational settings. Much of the users, dissatisfied with the IDE Dev-C ++, migrated to Code :: Blocks platform targeting the more dynamic range in the learning process of the C and C ++ languages. Nevertheless, there is still the need to create a tool that can provide the resources of most IDE's software development literature, however, more interactive, simple, accurate and efficient. This motivation led to the creation of Falcon C ++ tool, IDE that brings with features that turn it into an educational platform, which focuses primarily on increasing student learning index in the early disciplines of programming and algorithms that use the languages ​​C and C ++ . As a working methodology, a field research to prove the truth of the proposed tool was used. The test results and interviews with entry-level students and intermediate in a postsecondary institution gave basis for the composition of this work, demonstrating a positive impact on the use of the tool in teaching programming, showing that the use of Falcon C ++ software is beneficial in the teaching process of the C and C ++ programming languages.

Keywords: ide, education, learning, development, language

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Authors: Mirosław Krzemieniewski, Marcin Zieliński, Marcin Dębowski

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Electrokinetic disintegration is one of the high-voltage electric methods. The design of systems is exceptionally simple. Biomass flows through a system of pipes with alongside mounted electrodes that generate an electric field. Discharges in the electric field deform cell walls and lead to their successive perforation, thereby making their contents easily available to bacteria. The spark-over occurs between electrode surface and pipe jacket which is the second pole and closes the circuit. The value of voltage ranges from 10 to 100kV. Electrodes are supplied by normal “power grid” monophase electric current (230V, 50Hz). Next, the electric current changes into direct current of 24V in modules serving for particular electrodes, and this current directly feeds the electrodes. The installation is completely safe because the value of generated current does not exceed 250mA and because conductors are grounded. Therefore, there is no risk of electric shock posed to the personnel, even in the case of failure or incorrect connection. Low values of the electric current mean small energy consumption by the electrode which is extremely low – only 35W per electrode – compared to other methods of disintegration. Pipes with electrodes with diameter of DN150 are made of acid-proof steel and connected from both sides with 90º elbows ended with flanges. The available S and U types of pipes enable very convenient fitting with system construction in the existing installations and rooms or facilitate space management in new applications. The system of pipes for electrokinetic disintegration may be installed horizontally, vertically, askew, on special stands or also directly on the wall of a room. The number of pipes and electrodes is determined by operating conditions as well as the quantity of substrate, type of biomass, content of dry matter, method of disintegration (single or circulatory), mounting site etc. The most effective method involves pre-treatment of substrate that may be pumped through the disintegration system on the way to the fermentation tank or recirculated in a buffered intermediate tank (substrate mixing tank). Biomass structure destruction in the process of electrokinetic disintegration causes shortening of substrate retention time in the tank and acceleration of biogas production. A significant intensification of the fermentation process was observed in the systems operating in the technical scale, with the greatest increase in biogas production reaching 18%. The secondary, but highly significant for the energetic balance, effect is a tangible decrease of energy input by agitators in tanks. It is due to reduced viscosity of the biomass after disintegration, and may result in energy savings reaching even 20-30% of the earlier noted consumption. Other observed phenomena include reduction in the layer of surface scum, reduced sewage capability for foaming and successive decrease in the quantity of bottom sludge banks. Considering the above, the system for electrokinetic disintegration seems a very interesting and valuable solutions meeting the offer of specialist equipment for the processing of plant biomass, including Virginia fanpetals, before the process of methane fermentation.

Keywords: electrokinetic disintegration, biomass, biogas production, fermentation, Virginia fanpetals

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Authors: Saidalavi Kannattippadi

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It is a culture based study on revealing how the indebtedness of the west belongs to the moral and scientific culture of Islam, even to such a way to be said there was no room for renaissance and the enlightment of the west without the active intervention of the Islamic culture in thoughts and activities of the European thinkers. The study focuses on the exact causes that led the west to the renaissance and goes through analyzing each of historical evidences for confirming the continuous cultural assimilations that occurred between east and west, through transmissions of knowledge, translations of unique treatises, study trips and so on. The west had deeply influenced by the thought and culture of Islam after having a long bitter experience from the blind rituals and customs introduced by the church and was expecting for a movement that can raise them upwards from the bankruptcy of morality and spirituality. The sequence of crusades and voyages of thinkers from west to eastern wards made the western people aware of the best culture ever found in the world as in name of Islam and they become ready to assimilate its notable cultural values and to borrow its cultural achievements. The west had two types of influences from the Islam; moral and scientific. the uprooting of untouchablitlity and racism from western society and their accepting the ideologies of equality and fraternity are moral influence and the innumerable inventions and discoveries found in modern science and technology are the scientific influences. Without the frantic efforts of Muslims in translating, modifying and commenting the science and philosophy of the Greek the west would not have even a chance to peep to the cultural values of the Greek. Here the Muslims are the guides and channels through which the west got educated and well cultured. The study also briefly sheds light on the cultural achievements of Muslims in material science, human science, etc.

Keywords: cultural assimilation, culture and civilization, indebtedness, Muslim world, west, translation, transmission

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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: Martina I. Reinhold, Theresa Bacon-Baguley

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A core challenge of physician assistant education is preparing professionals for lifelong learning. While this conventionally has encompassed scientific advances, students must also embrace new care delivery models and technologies. Telemedicine, the provision of care via two-way audio and video, is an example of a technological advance reforming health care. During a three-semester sequence of Hospital Community Experiences, physician assistant students were assigned experiences with Answer Health on Demand, a telemedicine collaborative. Preceding the experiences, the agency lectured on the application of telemedicine. Students were then introduced to the technology and partnered with a provider. Prior to observing the patient-provider interaction, patient consent was obtained. Afterwards, students completed a reflection paper on lessons learned and the potential impact of telemedicine on their careers. Thematic analysis was completed on the students’ reflection papers (n=13). Preceding the lecture and experience, over 75% of students (10/13) were unaware of telemedicine. Several stated they were 'skeptical' about the effectiveness of 'impersonal' health care appointments. After the experience, all students remarked that telemedicine will play a large role in the future of healthcare and will provide benefits by improving access in rural areas, decreasing wait time, and saving cost. More importantly, 30% of students (4/13) commented that telemedicine is a technology they can see themselves using in their future practice. Initial results indicate that collaborative interaction between students and telemedicine providers enhanced student learning and exposed students to technological advances in the delivery of care. Further, results indicate that students perceived telemedicine more favorably as a viable delivery method after the experience.

Keywords: collaboration, physician assistant education, teaching innovative health care delivery method, telemedicine

Procedia PDF Downloads 173

Authors: F. Farzan Nasab, H. J. M. Geijselaers, I. Baran, A. De Boer

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A method is introduced for the coupled skin-rib optimization of a wing box where mass minimization is the objective and local buckling is the constraint. The structure is made of composite materials where continuity of plies in multiple adjacent panels (blending) has to be satisfied. Blending guarantees the manufacturability of the structure; however, it is a highly challenging constraint to treat and has been under debate in recent research in the same area. To fulfill design guidelines with respect to symmetry, balance, contiguity, disorientation and percentage rule of the layup, a reference for the stacking sequences (stacking sequence table or SST) is generated first. Then, an innovative fully gradient-based optimization approach in relation to a specific SST is introduced to obtain the optimum thickness distribution all over the structure while blending is fulfilled. The proposed optimization approach aims to turn the discrete optimization problem associated with the integer number of plies into a continuous one. As a result of a wing box deflection, a rib is subjected to load values which vary nonlinearly with the amount of deflection. The bending stiffness of a skin affects the wing box deflection and thus affects the load applied to a rib. This indicates the necessity of a coupled skin-rib optimization approach for a more realistic optimized design. The proposed method is examined with the optimization of the layup of a composite stiffened skin and rib of a wing torsion box subjected to in-plane normal and shear loads. Results show that the method can successfully prescribe a valid design with a significantly cheap computation cost.

Keywords: blending, buckling optimization, composite panels, wing torsion box

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Authors: Stephanie Khater, Ali Chehade, Lamis Chalak

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The progressive replacement of the Lebanese autochthonous grapevine cultivars during the last decade by the imported foreign varieties almost resulted in the genetic erosion of the local germplasm and the confusion with cultivars' names. Hence there is a need to characterize these local cultivars and to assess the possible existing variability at the cultivar level. This work was conducted in an attempt to evaluate the intra-varietal diversity within Lebanese traditional cultivars 'Aswad', 'Maghdoushe', 'Maryame', 'Merweh', 'Meksese' and 'Obeide'. A total of 50 accessions distributed over five main geographical areas in Lebanon were collected and submitted to both ampelographic description and ISSR DNA analysis. A set of 35 ampelographic descriptors previously established by the International Office of Vine and Wine and related to leaf, bunch, berry, and phenological stages, were examined. Variability was observed between accessions within cultivars for blade shape, density of prostrate and erect hairs, teeth shape, berry shape, size and color, cluster shape and size, and flesh juiciness. At the molecular level, nine ISSR (inter-simple sequence repeat) primers, previously developed for grapevine, were used in this study. These primers generated a total of 35 bands, of which 30 (85.7%) were polymorphic. Totally, 29 genetic profiles were differentiated, of which 9 revealed within 'Obeide', 6 for 'Maghdoushe', 5 for 'Merweh', 4 within 'Maryame', 3 for 'Aswad' and 2 within 'Meksese'. Findings of this study indicate the existence of several genotypes that form the basis of the main indigenous cultivars grown in Lebanon and which should be further considered in the establishment of new vineyards and selection programs.

Keywords: ampelography, autochthonous cultivars, ISSR markers, Lebanon, Vitis vinifera L.

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Authors: Prittesh Patel, Rushabh Shah, Krishnamurthy Ramar, Vakulbhushan Bhaskar

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The present research work aims at finding genetic differences in the genomes of sugarcane red rot isolates Colletotrichum falcatum Went using Random Amplified Polymorphic DNA (RAPD) and interspersed simple sequence repeat (ISSR) molecular markers. Ten isolates of C. falcatum isolated from different red rot infected sugarcane cultivars stalk were used in present study. The amplified bands were scored across the lanes obtained in 15 RAPD primes and 21 ISSR primes successfully. The data were analysed using NTSYSpc 2.2 software. The results showed 80.6% and 68.07% polymorphism in RPAD and ISSR analysis respectively. Based on the RAPD analysis, ten genotypes were grouped into two major clusters at a cut-off value of 0.75. Geographically distant C. falcatum isolate cfGAN from south Gujarat had a level of similarity with Coimbatore isolate cf8436 presented on separate clade of bootstrapped dendrograms. First and second cluster consisted of five and three isolates respectively, indicating the close relation among them. The 21 ISSR primers produced 119 distinct and scorable loci in that 38 were monomorphic. The number of scorable loci for each primer varied from 2 (ISSR822) to 8 (ISSR807, ISSR823 and ISSR15) with an average of 5.66 loci per primer. Primer ISSR835 amplified the highest number of bands (57), while only 16 bands were obtained by primers ISSR822. Four primers namely ISSR830, ISSR845, ISSR4 and ISSR15 showed the highest value of percentage of polymorphism (100%). The results indicated that both of the marker systems RAPD and ISSR, individually can be effectively used in determination of genetic relationship among C falcatum accessions collected from different parts of south Gujarat.

Keywords: Colletotrichum falcatum, ISSR, RAPD, Red Rot

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Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Salah R. Al Zaidee, Ali S. Mahdi

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Except for simple problems of statically determinate structures, optimum design problems in structural engineering have implicit objective functions where structural analysis and design are essential within each searching loop. With these implicit functions, the structural engineer is usually enforced to write his/her own computer code for analysis, design, and searching for optimum design among many feasible candidates and cannot take advantage of available software for structural analysis, design, and searching for the optimum solution. The meta-model is a regression model used to transform an implicit objective function into objective one and leads in turn to decouple the structural analysis and design processes from the optimum searching process. With the meta-model, well-known software for structural analysis and design can be used in sequence with optimum searching software. In this paper, the meta-model has been used to develop an explicit objective function for plane steel frames subjected to dead, live, and seismic forces. Frame topology is assumed as predefined based on architectural and functional requirements. Columns and beams sections and different connections details are the main design variables in this study. Columns and beams are grouped to reduce the number of design variables and to make the problem similar to that adopted in engineering practice. Data for the implicit objective function have been generated based on analysis and assessment for many design proposals with CSI SAP software. These data have been used later in SPSS software to develop a pure quadratic nonlinear regression model for the explicit objective function. Good correlations with a coefficient, R², in the range from 0.88 to 0.99 have been noted between the original implicit functions and the corresponding explicit functions generated with meta-model.

Keywords: meta-modal, objective function, steel frames, seismic analysis, design

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Authors: Azam Fazelpour, Saeed R. Dehghani, Vlastimil Masek, Yuri S. Muzychka

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The study uses an image analysis technique employing thermal imaging to measure the percentage of areas with various temperatures on a freezing surface. An image segmentation method using threshold values is applied to a sequence of image recording the freezing process. The phenomenon is transient and temperatures vary fast to reach the freezing point and complete the freezing process. Freezing salt water is subjected to the salt rejection that makes the freezing point dynamic and dependent on the salinity at the phase interface. For a specific area of freezing, nucleation starts from one side and end to another side, which causes a dynamic and transient temperature in that area. Thermal cameras are able to reveal a difference in temperature due to their sensitivity to infrared radiance. Using Experimental setup, a video is recorded by a thermal camera to monitor radiance and temperatures during the freezing process. Image processing techniques are applied to all frames to detect and classify temperatures on the surface. Image processing segmentation method is used to find contours with same temperatures on the icing surface. Each segment is obtained using the temperature range appeared in the image and correspond pixel values in the image. Using the contours extracted from image and camera parameters, stratified areas with different temperatures are calculated. To observe temperature contours on the icing surface using the thermal camera, the salt water sample is dropped on a cold surface with the temperature of -20°C. A thermal video is recorded for 2 minutes to observe the temperature field. Examining the results obtained by the method and the experimental observations verifies the accuracy and applicability of the method.

Keywords: ice contour boundary, image processing, image segmentation, salt ice, thermal image

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Alyaa Abdlwahab

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Cutaneous leishmaniasis represents a serious health problem in Syria; this problem has become noticeably aggravated after the civil war in the country. Leishmania tropica parasite is the main cause of cutaneous leishmaniasis in Syria. In order to control the disease, we need an effective vaccine against leishmania parasite. DNA vaccination remains one of the favorable approaches that have been used to face cutaneous leishmaniasis. Ribosomal protein S4 is responsible for important roles in Leishmania parasite life. DNA vaccine based on S4 gene has been used against infections by many species of Leishmania parasite but leishmania tropica parasite, so this gene represents a good candidate for DNA vaccine construction. After proving the existence of ribosomal protein S4 gene in a Syrian strain of Leishmania tropica (LCED Syrian 01), sequencing it and cloning it into pCI plasmid, BALB/C mice were inoculated with pCI-S4 DNA vaccine. The immune response was determined by monitoring the lesion progression in inoculated BALB/C mice for six weeks after challenging mice with Leishmania tropica (LCED Syrian 01) parasites. IL-12, IFN-γ, and IL-4 were quantified in draining lymph nodes (DLNa) of the immunized BALB/C mice by using the RT-qPCR technique. The parasite burden was calculated in the final week for the footpad lesion and the DLNs of the mice. This study proved the existence and the expression of the ribosomal protein S4 gene in Leishmania tropica (LCED Syrian 01) promastigotes. The sequence of ribosomal protein cDNA S4 gene was determined and published in Genbank; the gene size was 822 bp. Expression was also demonstrated at the level of cDNA. Also, this study revealed that pCI-S4 DNA vaccine induces TH1\TH2 response in immunized mice; this response prevents partially developing a dermal lesion of Leishmania.

Keywords: ribosomal protein S4, DNA vaccine, Leishmania tropica, BALB\c

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Authors: Ajmal Hussain

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In Indian music parlance, Rasa denotes a distinct aesthetic experience that builds up in the mind of the listeners while listening to a piece of Indian classical music. The distinction of the experience is rooted in the concept that it gives rise to an enhanced awareness about the Self or God and creates a mental state detached from mundane issues of everyday life. The theory of Rasa was initially proposed in the context of theatre but became a part of Indian musicological discourse roughly two thousand years ago, however, to this day, it remains shrouded in mystery due to its religious associations and connotations. This paper attempts to demystify the theory of Rasa in the light of available scientific knowledge fund particularly in Brain and Mind sciences. The paper initially describes the religious context of the theory of Rasa and then discusses its classical formulations by Bharata and Abhinavagupta including the steps and stages laid down by the latter to explain the creation of musical experience. The classical formulations are then interpreted with reference to the scientific knowledge fund about the human mind and mechanics of perception. The study uses the model of human mind as proposed by Portuguese-American neuroscientist Antonio Damasio in his theory ‘A Nesting Principle’. On the basis of the findings by Damasio, the paper interprets the experience of Rasa from a scientific perspective and clarifies the sequence of steps and stages involved in the making of musical experience. The study concludes that although the classical formulations of Rasa identify key aspects of musical experience, the association of Rasa with religion is misleading. The association with religion does not depend upon musical stimulus but the intellectual orientation of the listener. It further establishes that the function of Rasa is more profound as, from an evolutionary perspective, it can be seen as a catalyst for higher consciousness.

Keywords: aesthetic, consciousness, music, Rasa

Procedia PDF Downloads 106

Authors: Yujie Zhou, Hee-Seong Byun, Sang-In Bak, Eui-Joon Kil, Kyung Joo Min, Vivek Chavan, Won Kyong Cho, Sukchan Lee, Seung-Woo Hong, Tae-Sun Park

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Fast neutron irradiation (FNI) can cause mutations on plant genome but, in the most of cases, these irradiated plants have not shown significant characteristics phenotypically. In this study, we utilized RNA-Seq to generate a high-resolution transcriptome map of the tomato (Solanum lycopersicum) genome effected by FNI. To quantify the different transcription levels in tomato irradiated by FNI, tomato seeds were irradiated by using MC-50 cyclotron (KIRAMS, Korea) for 0, 30 and 90 minutes, respectively. To investigate the effects on the pre-soaking condition, experimental groups were divided into dry and soaked seeds, which were soaked for 8 hours before irradiation. There was no noticeable difference in the percentage germination (PG) among dry seeds, while irradiated soaked seeds have about 10 % lower PG compared to the unirradiated control group. Using whole transcriptome sequencing by HiSeq 2000, we analyzed the differential gene expression in response to different time of FNI in dry and soaked seeds. More than 1.4 million base pair reads were mapped onto the tomato reference genome and the expression pattern differences between irradiated and unirradiated seeds were assessed. In 0, 30 and 90 minutes irradiation, 12,135, 28,495 and 28,675 transcripts were generated, respectively. Gene ontology analysis suggested the different enrichment of transcripts involved in response to different FNI. The present study showed that FNI effects on plant gene expression, which can become a new parameters for evaluating the responses against FNI on plants. In addition, the comparative analysis of differentially expressed genes in D and S seeds by FNI will also give us a chance to deep explore novel candidate genes for FNI, which could be a good model system to understand the mechanisms behind the adaption of plant to space biology research.

Keywords: tomato (solanum lycopersicum), fast neutron irradiation, RNA-sequence, transcriptome expression

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Authors: Aouina Nabila Yasmina, Zine El Abidine Chaoui

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Recently, understanding the interactions of electrons with the DNA molecule and its components has attracted considerable interest because DNA is the main site damaged by ionizing radiation. The interactions of radiation with DNA induce a variety of molecular damage such as single-strand breaks, double-strand breaks, basic damage, cross-links between proteins and DNA, and others, or the formation of free radicals, which, by chemical reactions with DNA, can also lead to breakage of the strand. One factor that can contribute significantly to these processes is the effect of water hydration on the formation and reaction of radiation induced by these radicals in and / or around DNA. B-DNA requires about 30% by weight of water to maintain its native conformation in the crystalline state. The transformation depends on various factors such as sequence, ion composition, concentration and water activity. Partial dehydration converts it to DNA-A. The present study shows the results of theoretical calculations for positrons and electrons elastic scattering with DNA medium and water over a broad energy range from 10 eV to 100 keV. Indeed, electron elastic cross sections and elastic mean free paths are calculated using a corrected form of the independent atom method, taking into account the geometry of the biomolecule (SCAR macro). Moreover, the elastic scattering of electrons and positrons by atoms of the biomolecule was evaluated by means of relativistic (Dirac) partial wave analysis. Our calculated results are compared with theoretical data available in the literature in the absence of experimental data, in particular for positron. As a central result, our electron elastic cross sections are in good agreement with existing theoretical data in the range of 10 eV to 1 keV.

Keywords: elastic cross scrion, elastic mean free path, scar macro method, electron collision

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Authors: Tei Kim, Brooklynn McNeil, Kathryn Dunn, Douglas I. Walker

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To better characterize the relationship between complex chemical exposures and disease, our laboratory uses an approach that combines low-cost, polydimethylsiloxane (silicone) wristband samplers that absorb many of the chemicals we are exposed to with untargeted high-resolution mass spectrometry (HRMS) to characterize 1000’s of chemicals at a time. In studies with human populations, these wristbands can provide an important measure of our environment: however, there is a need to use this approach in large cohorts to study exposures associated with the disease. To facilitate the use of silicone samplers in large scale population studies, the goal of this research project was to establish automated sample preparation methods that improve throughput, robustness, and scalability of analytical methods for silicone wristbands. Using the Opentron OT2 automated liquid platform, which provides a low-cost and opensource framework for automated pipetting, we created two separate workflows that translate the manual wristband preparation method to a fully automated protocol that requires minor intervention by the operator. These protocols include a sequence generation step, which defines the location of all plates and labware according to user-specified settings, and a transfer protocol that includes all necessary instrument parameters and instructions for automated solvent extraction of wristband samplers. These protocols were written in Python and uploaded to GitHub for use by others in the research community. Results from this project show it is possible to establish automated and open source methods for the preparation of silicone wristband samplers to support profiling of many environmental exposures. Ongoing studies include deployment in longitudinal cohort studies to investigate the relationship between personal chemical exposure and disease.

Keywords: bioinformatics, automation, opentrons, research

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

Abstract:

Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: D. Kuvshinov, A. Siswanto, W. Zimmerman

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A phorbol-12-myristate-13-acetate (TPA) is a synthetic analogue of phorbol ester (PE), a natural toxic compound of Euphorbiaceae plant. The oil extracted from plants of this family is useful source for primarily biofuel. However this oil can also be used as a food stock due to its significant nutrition content. The limitations for utilizing the oil as a food stock are mainly due to a toxicity of PE. Nowadays a majority of PE detoxification processes are expensive as include multi steps alcohol extraction sequence. Ozone is considered as a strong oxidative agent. It reaction with PE it attacks the carbon double bond of PE. This modification of PE molecular structure results into nontoxic ester with high lipid content. This report presents data on development of simple and cheap PE detoxification process with water application as a buffer and ozone as reactive component. The core of this new technique is a simultaneous application of new microscale plasma unit for ozone production and patented gas oscillation technology. In combination with a reactor design the technology permits ozone injection to the water-TPA mixture in form of microbubbles. The efficacy of a heterogeneous process depends on diffusion coefficient which can be controlled by contact time and interface area. The low velocity of rising microbubbles and high surface to volume ratio allow fast mass transfer to be achieved during the process. Direct injection of ozone is the most efficient process for a highly reactive and short lived chemical. Data on the plasma unit behavior are presented and influence of the gas oscillation technology to the microbubbles production mechanism has been discussed. Data on overall process efficacy for TPA degradation is shown.

Keywords: microbubble, ozonolysis, synthetic phorbol ester, chemical engineering

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Authors: Elsie L. Echeverri-Carroll

Abstract:

Entrepreneurial ecosystems have become an important concept to explain the birth and sustainability of technology-based entrepreneurship within regions. However, as a theoretical concept, the temporal evolution of entrepreneurship systems remain underdeveloped, making it difficult to understand their dynamic contributions to entrepreneurs. This paper argues that successful technology-based ecosystems go over three cumulative spawning stages: corporate spawning, entrepreneurial spawning, and community spawning. The importance of corporate incubation in vibrant entrepreneurial ecosystems is well documented in the entrepreneurial literature. Similarly, entrepreneurial spawning processes for venture capital-backed startups are well documented in the financial literature. In contrast, there is little understanding of both the third stage of entrepreneurial spawning (when a community of entrepreneurs become a source of firm spawning) and the temporal sequence in which spawning effects occur in a region. We test this three-stage model of entrepreneurial spawning using data from two large databases on firm births—the Secretary of State (160,000 observations) and the National Establishment Time Series (NEST with 150,000 observations)—and information collected from 60 1½-hour interviews with startup founders and representatives of key entrepreneurial organizations. This temporal model is illustrated with case study of Austin, Texas ranked by the Kauffman Foundation as the number one entrepreneurial city in the United States in 2015 and 2016. The 1½-year study founded by the Kauffman Foundation demonstrates the importance of taken into consideration the temporal contributions of both large and entrepreneurial firms in understanding the factors that contribute to the birth and growth of technology-based entrepreneurial regions. More important, these learnings could offer an important road map for regions that pursue to advance their entrepreneurial ecosystems.

Keywords: entrepreneurial ecosystems, entrepreneurial industrial clusters, high-technology, temporal changes

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Authors: M. N. Zelenin, V. S. Mikhailov, R. P. Zhivotovsky

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It is known that residual welding deformations give negative effect to processability and operational quality of welded structures, complicating their assembly and reducing strength. Therefore, selection of optimal technology, ensuring minimum welding deformations, is one of the main goals in developing a technology for manufacturing of welded structures. Through years, JSC SSTC has been developing a theory for estimation of welding deformations and practical activities for reducing and compensating such deformations during welding process. During long time a methodology was used, based on analytic dependence. This methodology allowed defining volumetric changes of metal due to welding heating and subsequent cooling. However, dependences for definition of structures deformations, arising as a result of volumetric changes of metal in the weld area, allowed performing calculations only for simple structures, such as units, flat sections and sections with small curvature. In case of complex 3D structures, estimations on the base of analytic dependences gave significant errors. To eliminate this shortage, it was suggested to use finite elements method for resolving of deformation problem. Here, one shall first calculate volumes of longitudinal and transversal shortenings of welding joints using method of analytic dependences and further, with obtained shortenings, calculate forces, which action is equivalent to the action of active welding stresses. Further, a finite-elements model of the structure is developed and equivalent forces are added to this model. Having results of calculations, an optimal sequence of assembly and welding is selected and special measures to reduce and compensate welding deformations are developed and taken.

Keywords: residual welding deformations, longitudinal and transverse shortenings of welding joints, method of analytic dependences, finite elements method

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Authors: Natascha C. D'Amico, Enzo Grossi, Giovanni Valbusa, Ala Malasevschi, Gianpiero Cardone, Sergio Papa

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Purpose: To characterize, through a radiomic approach, the nature of areas classified PI-RADS (Prostate Imaging Reporting and Data System) 3/5, recognized in multiparametric prostate magnetic resonance with T2-weighted (T2w), diffusion and perfusion sequences with paramagnetic contrast. Methods and Materials: 24 cases undergoing multiparametric prostate MR and biopsy were admitted to this pilot study. Clinical outcome of the PI-RADS 3/5 was found through biopsy, finding 8 malignant tumours. The analysed images were acquired with a Philips achieva 1.5T machine with a CE- T2-weighted sequence in the axial plane. Semi-automatic tumour segmentation was carried out on MR images using 3DSlicer image analysis software. 45 shape-based, intensity-based and texture-based features were extracted and represented the input for preprocessing. An evolutionary algorithm (a TWIST system based on KNN algorithm) was used to subdivide the dataset into training and testing set and select features yielding the maximal amount of information. After this pre-processing 20 input variables were selected and different machine learning systems were used to develop a predictive model based on a training testing crossover procedure. Results: The best machine learning system (three-layers feed-forward neural network) obtained a global accuracy of 90% ( 80 % sensitivity and 100% specificity ) with a ROC of 0.82. Conclusion: Machine learning systems coupled with radiomics show a promising potential in distinguishing benign from malign tumours in PI-RADS 3/5 areas.

Keywords: machine learning, MR prostate, PI-Rads 3, radiomics

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

Abstract:

Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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