Search results for: genome rearrangement distance

Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: Neda Lovričević, Đilda Pečarić, Josip Pečarić

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The Jensen functional in its discrete form is brought in relation to the Csiszar divergence functional, this time via its monotonicity property. This approach presents a generalization of the previously obtained results that made use of interpolating Jensen-type inequalities. Thus the monotonicity property is integrated with the Zipf-Mandelbrot law and applied to f-divergences for probability distributions that originate from the Csiszar divergence functional: Kullback-Leibler divergence, Hellinger distance, Bhattacharyya distance, chi-square divergence, total variation distance. The Zipf-Mandelbrot and the Zipf law are widely used in various scientific fields and interdisciplinary and here the focus is on the aspect of the mathematical inequalities.

Keywords: Jensen functional, monotonicity, Csiszar divergence functional, f-divergences, Zipf-Mandelbrot law

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Authors: Suikinai Nobre Santos, Ranko Gacesa, Paul F. Long, Itamar Soares de Melo

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Extremophilic microorganism are adapted to biotopes combining several stress factors (temperature, pressure, radiation, salinity and pH), which indicate the richness valuable resource for the exploitation of novel biotechnological processes and constitute unique models for investigations their biomolecules (1, 2). The above information encourages us investigate bioprospecting synthesized compounds by a noval actinomycete, designated thermotolerant Streptomyces caatingaensis CMAA 1322, isolated from sample soil tropical dry forest (Caatinga) in the Brazilian semiarid region (3-17°S and 35-45°W). This set of constrating physical and climatic factores provide the unique conditions and a diversity of well adapted species, interesting site for biotechnological purposes. Preliminary studies have shown the great potential in the production of cytotoxic, pesticidal and antimicrobial molecules (3). Thus, to extend knowledge of the genes clusters responsible for producing biosynthetic pathways of natural products in strain CMAA1322, whole-genome shotgun (WGS) DNA sequencing was performed using paired-end long sequencing with PacBio RS (Pacific Biosciences). Genomic DNA was extracted from a pure culture grown overnight on LB medium using the PureLink genomic DNA kit (Life Technologies). An approximately 3- to 20-kb-insert PacBio library was constructed and sequenced on an 8 single-molecule real-time (SMRT) cell, yielding 116,269 reads (average length, 7,446 bp), which were allocated into 18 contigs, with 142.11x coverage and N50 value of 20.548 bp (BioProject number PRJNA288757). The assembled data were analyzed by Rapid Annotations using Subsystems Technology (RAST) (4) the genome size was found to be 7.055.077 bp, comprising 6167 open reading frames (ORFs) and 413 subsystems. The G+C content was estimated to be 72 mol%. The closest-neighbors tool, available in RAST through functional comparison of the genome, revealed that strain CMAA1322 is more closely related to Streptomyces hygroscopicus ATCC 53653 (similarity score value, 537), S. violaceusniger Tu 4113 (score value, 483), S. avermitilis MA-4680 (score value, 475), S. albus J1074 (score value, 447). The Streptomyces sp. CMAA1322 genome contains 98 tRNA genes and 135 genes copies related to stress response, mainly osmotic stress (14), heat shock (16), oxidative stress (49). Functional annotation by antiSMASH version 3.0 (5) identified 41 clusters for secondary metabolites (including two clusters for lanthipeptides, ten clusters for nonribosomal peptide synthetases [NRPS], three clusters for siderophores, fourteen for polyketide synthetase [PKS], six clusters encoding a terpene, two clusters encoding a bacteriocin, and one cluster encoding a phenazine). Our work provide in comparative analyse of genome and extract produced (data no published) by lineage CMAA1322, revealing the potential of microorganisms accessed from extreme environments as Caatinga” to produce a wide range of biotechnological relevant compounds.

Keywords: caatinga, streptomyces, environmental stresses, biosynthetic pathways

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Authors: Jareeluk Ratanaphan

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The purposed of this research were; 1. To survey the teacher’s needs on knowledge about special education management for special needs student 2. Development of distance training packages for teacher on special education management for special needs student 3. to study the effects of using the packages on trainee’s achievement 4. to study the effects of using the packages on trainee’s opinion on the distance training packages. The design of the experiment was research and development. The research sample for survey were 86 teachers, and 22 teachers for study the effects of using the packages on achievement and opinion. The research instrument comprised: 1) training packages on special education management for special needs student 2) achievement test 3) questionnaire. Mean, percentage, standard deviation, t-test and content analysis were used for data analysis. The findings of the research were as follows: 1. The teacher’s needs on knowledge about teaching for a learner with learning disability, mental retardation, autism, physical and health impairment and research in special education. 2. The package composed of special education management for special needs student document and manual of distance training packages. The document consisted by the name of packages, the explanation for the educator, content’s structure, concept, objectives, content and activities. Manual of distance training packages consisted by the explanation about a document, objectives, explanation about using the package, training schedule, and evaluation. The efficiency of packages was established at 79.50/81.35. 3. The results of using the packages were the posttest average scores of trainee’s achievement were higher than the pretest. 4. The trainee’s opinion on the package was at the highest level.

Keywords: distance training package, teacher, learner with special needs

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Authors: Alireza Shayegan, Morteza Amirabadi

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The y tool was developed to quantitatively compare dose distributions, either measured or calculated. Before computing ɣ, the dose and distance scales of the two distributions, referred to as evaluated and reference, are re-normalized by dose and distance criteria, respectively. The re-normalization allows the dose distribution comparison to be conducted simultaneously along dose and distance axes. Several two-dimensional images were acquired using a Scanning Liquid Ionization Chamber EPID and Extended Dose Range (EDR2) films for regular and irregular radiation fields. The raw images were then converted into two-dimensional dose maps. Transitional and rotational manipulations were performed for images using Matlab software. As evaluated dose distribution maps, they were then compared with the corresponding original dose maps as the reference dose maps.

Keywords: energetic electron, gamma function, penumbra, Matlab software

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Authors: Ante Turudic, Filip Varga, Zlatko Liber, Jernej Jakse, Zlatko Satovic, Ivan Radosavljevic, Martina Grdisa

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Microsatellites (SSRs) are highly informative repetitive sequences of 2-6 base pairs, which are the most used molecular markers in assessing the genetic diversity of plant species. Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip) is an outcrossing diploid (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repetitiveness and large size of the genome (haploid genome size of 9,58 pg), previous attempts to develop microsatellite markers using the standard methods were unsuccessful. A next-generation sequencing (NGS) approach was applied on genomic DNA extracted from fresh leaves of Dalmatian pyrethrum. The sequencing was conducted using NovaSeq6000 Illumina sequencer, after which almost 400 million high-quality paired-end reads were obtained, with a read length of 150 base pairs. Short reads were assembled by combining two approaches; (1) de-novo assembly and (2) joining of overlapped pair-end reads. In total, 6.909.675 contigs were obtained, with the contig average length of 249 base pairs. Of the resulting contigs, 31.380 contained one or multiple microsatellite sequences, in total 35.556 microsatellite loci were identified. Out of detected microsatellites, dinucleotide repeats were the most frequent, accounting for more than half of all microsatellites identifies (21,212; 59.7%), followed by trinucleotide repeats (9,204; 25.9%). Tetra-, penta- and hexanucleotides had similar frequency of 1,822 (5.1%), 1,472 (4.1%), and 1,846 (5.2%), respectively. Contigs containing microsatellites were further filtered by SSR pattern type, transposon occurrences, assembly characteristics, GC content, and the number of occurrences against the draft genome of T. cinerariifolium published previously. After the selection process, 50 microsatellite loci were used for primer design. Designed primers were tested on samples from five distinct populations, and 25 of them showed a high degree of polymorphism. The selected loci were then genotyped on 20 samples belonging to one population resulting in 17 microsatellite markers. Availability of codominant SSR markers will significantly improve the knowledge on population genetic diversity and structure as well as complex genetics and biochemistry of this species. Acknowledgment: This work has been fully supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir/ Sch. Bip.) insecticidal potential’ - (PyrDiv) (IP-06-2016-9034).

Keywords: genome assembly, NGS, SSR, Tanacetum cinerariifolium

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Authors: Leila Goosen, Dalize van Heerden

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The performance outcomes of first year Computer Science and Information Technology students across the world are of great concern, whether they are being taught in a face-to-face environment or via distance education. In the face-to-face environment, it is, however, somewhat easier to teach and support students than it is in a distance education environment. The face-to-face academic can more easily gauge the level of understanding and participation of students and implement interventions to address issues, which may arise. With the inroads that Web 2.0 and Web 3.0 technologies are making, the world of online teaching and learning are rapidly expanding, bringing about technologies, which allows for similar interactions between online academics and their students as available to their face-to-face counter parts. At the University of South Africa (UNISA), the Learning Management System (LMS) is called myUNISA and it is deployed on a SAKAI platform. In this paper, we will take a look at some of the myUNISA technologies implemented in the teaching of a first year programming course, how they are implemented and, in some cases, we will indicate how this affects the performance outcomes of students.

Keywords: computer science, Distance Education Technologies, Learning Management System, face-to-face environment

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Authors: Mohammad Mahdi Kioumarsi

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In this paper, using the response surface method (RSM), tornado diagram method and non-linear finite element analysis, the effect of four parameters on residual bending capacity of a corroded RC beam was investigated. The parameters considered are amount of localised cross section reduction, ratio of pit distance on adjacent bars to rebar distance, concrete compressive strength, and rebar tensile strength. The focus is on the influence on the bending ultimate limit state. Based on the obtained results, the effects of the ratio of pit distance to rebar distance (Lp⁄Lr) and the ratio of the localised cross section reduction to the original area of the rebar (Apit⁄A0) were found significant. The interference of localised corrosion on adjacent reinforcement bars reduces the bending capacity of under-reinforced concrete beam. Using the sensitivity analysis could lead to recognize uncertainty parameters, which have the most influences on the performance of the structure.

Keywords: localised corrosion, concrete beam, sensitivity analyses, ultimate capacity

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Authors: M. F. Miah, K. M. A. Zinnah, M. J. Raihan, H. Ali, M. N. Naser

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As genetic diversity is most important for existing, breeding and production of any fish; this study was undertaken for investigating genetic diversity of freshwater mud eel, Monopterus cuchia at population level where three ecological populations such as flooded area of Sylhet (P1), open water of Moulvibazar (P2) and open water of Sunamganj (P3) districts of Bangladesh were considered. Four arbitrary RAPD primers (OPB-12, C0-4, B-03 and OPB-08) were screened and RAPD banding patterns were analyzed among the populations considering 15 individuals of each population. In total 174, 138 and 149 bands were detected in the populations of P1, P2 and P3 respectively; however, each primer revealed less number of bands in each population. 100% polymorphic loci were recorded in P2 and P3 whereas only one monomorphic locus was observed in P1, recorded 97.5% polymorphism. Different genetic parameters such as inter-individual pairwise similarity, genetic distance, Nei genetic similarity, linkage distances, cluster analysis and allelic information, etc. were considered for measuring genetic diversity. The average inter-individual pairwise similarity was recorded 2.98, 1.47 and 1.35 in P1, P2 and P3 respectively. Considering genetic distance analysis, the highest distance 1 was recorded in P2 and P3 and the lowest genetic distance 0.444 was found in P2. The average Nei genetic similarity was observed 0.19, 0.16 and 0.13 in P1, P2 and P3, respectively; however, the average linkage distance was recorded 24.92, 17.14 and 15.28 in P1, P3 and P2 respectively. Based on linkage distance, genetic clusters were generated in three populations where 6 clades and 7 clusters were found in P1, 3 clades and 5 clusters were observed in P2 and 4 clades and 7 clusters were detected in P3. In addition, allelic information was observed where the frequency of p and q alleles were observed 0.093 and 0.907 in P1, 0.076 and 0.924 in P2, 0.074 and 0.926 in P3 respectively. The average gene diversity was observed highest in P2 (0.132) followed by P3 (0.131) and P1 (0.121) respectively.

Keywords: genetic diversity, Monopterus cuchia, population, RAPD, Bangladesh

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Authors: Soultana Konstantinidou, Tiziana Schmidt, Elena Landi, Alessandro De Carli, Giovanni Maltinti, Darius Witt, Alicja Dziadosz, Agnieszka Lindstaedt, Michele Lai, Mauro Pistello, Valentina Cappello, Luciana Dente, Chiara Gabellini, Piotr Barski, Vittoria Raffa

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CRISPR/Cas9 technology has gained the interest of researchers in the field of biotechnology for genome editing. Since its discovery as a microbial adaptive immune defense, this system has been widely adopted and is acknowledged for having a variety of applications. However, critical barriers related to safety and delivery are persisting. Here, we propose a new concept of genome engineering, which is based on a nano-formulation of Cas9. The Cas9 enzyme was conjugated to a gold nanoparticle (AuNP-Cas9). The AuNP-Cas9 maintained its cleavage efficiency in vitro, to the same extent as the ribonucleoprotein, including non-conjugated Cas9 enzyme, and showed high gene editing efficiency in vivo in zebrafish embryos. Since CRISPR/Cas9 technology is extensively used in cancer research, melanoma was selected as a validation target. Cell studies were performed in A375 human melanoma cells. Particles per se had no impact on cell metabolism and proliferation. Intriguingly, the AuNP-Cas9 internalized spontaneously in cells and localized as a single particle in the cytoplasm and organelles. More importantly, the AuNP-Cas9 showed a high nuclear localization signal. The AuNP-Cas9, overcoming the delivery difficulties of Cas9, could be used in cellular biology and localization studies. Taking advantage of the plasmonic properties of gold nanoparticles, this technology could potentially be a bio-tool for combining gene editing and photothermal therapy in cancer cells. Further work will be focused on intracellular interactions of the nano-formulation and characterization of the optical properties.

Keywords: CRISPR/Cas9, gene editing, gold nanoparticles, nanotechnology

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Authors: Feng-Sheng Wang, Chao-Ting Cheng

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Developing a drug from conception to launch is costly and time-consuming. Computer-aided methods can reduce research costs and accelerate the development process during the early drug discovery and development stages. This study developed a fuzzy multi-objective hierarchical optimization framework for identifying potential anticancer targets in a metabolic model. First, RNA-seq expression data of colorectal cancer samples and their healthy counterparts were used to reconstruct tissue-specific genome-scale metabolic models. The aim of the optimization framework was to identify anticancer targets that lead to cancer cell death and evaluate metabolic flux perturbations in normal cells that have been caused by cancer treatment. Four objectives were established in the optimization framework to evaluate the mortality of cancer cells for treatment and to minimize side effects causing toxicity-induced tumorigenesis on normal cells and smaller metabolic perturbations. Through fuzzy set theory, a multiobjective optimization problem was converted into a trilevel maximizing decision-making (MDM) problem. The applied nested hybrid differential evolution was applied to solve the trilevel MDM problem using two nutrient media to identify anticancer targets in the genome-scale metabolic model of colorectal cancer, respectively. Using Dulbecco’s Modified Eagle Medium (DMEM), the computational results reveal that the identified anticancer targets were mostly involved in cholesterol biosynthesis, pyrimidine and purine metabolisms, glycerophospholipid biosynthetic pathway and sphingolipid pathway. However, using Ham’s medium, the genes involved in cholesterol biosynthesis were unidentifiable. A comparison of the uptake reactions for the DMEM and Ham’s medium revealed that no cholesterol uptake reaction was included in DMEM. Two additional media, i.e., a cholesterol uptake reaction was included in DMEM and excluded in HAM, were respectively used to investigate the relationship of tumor cell growth with nutrient components and anticancer target genes. The genes involved in the cholesterol biosynthesis were also revealed to be determinable if a cholesterol uptake reaction was not induced when the cells were in the culture medium. However, the genes involved in cholesterol biosynthesis became unidentifiable if such a reaction was induced.

Keywords: Cancer metabolism, genome-scale metabolic model, constraint-based model, multilevel optimization, fuzzy optimization, hybrid differential evolution

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Authors: Tahir Mehmood, Mumtaz Akhter

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The global need for conflict management is greater now in the early 21st century than ever before. According to UNESCO, half of the world’s 195 countries will have to expand their stock of educationist significantly, some by tens of thousands, if the goal development targets are desired to achieve. Socioeconomic inequities, political instability, demographic changes and crises such as the HIV/AIDs epidemic have engendered huge shortfalls in teacher supply and low teacher quality in many developing countries. Education serves as back bone in development process. Open learning and distance education programs are serving as pivotal part of development process. It is now clear that ‘bricks and mortar’ approaches to expanding teacher education may not be adequate if the current and projected shortfalls in teacher supply and low teacher quality are to be properly addressed. The study is designed to measure the perceptions of teaching learning community about conflict management with special reference to open and distance learning. It was descriptive study which targeted teachers, students, community members and experts. Data analysis was carried out by using statistical techniques served by SPSS. Findings reflected that audience perceives open and distance learning as change agent and as development tool. It is noticed that target audience has driven prominent performance by using facility of open and distance learning.

Keywords: conflict management, open and distance learning, teachers, students

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Authors: Calogero Lo Destro

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Numerous nations around the world are facing exceptional challenges in employing measures to stop the spread of COVID-19. Following the recommendations of the World Health Organization, a series of preventive measures have been adopted. However, individuals must comply with these rules and recommendations in order to make these measures effective. While COVID-19 was climaxing, it seemed of crucial importance to analyze which psychosocial factors contribute to the acceptance of such preventive behavior, thus favoring the management of COVID-19 worldwide health crisis. In particular, the identification of aspects related to obstacles and facilitation of adherence to social distancing has been considered crucial in the containment of the virus spread. Since the virus was firstly detected in China, Asian people could be considered a relevant outgroup targeted for exclusion. We also hypothesized social distance could be influenced by characteristics of the target, such as smiling or coughing. 260 participants participated in this research on a voluntary basis. They filled a survey designed to explore a series of COVID-19 measures (such as exposure to virus and fear of infection). We also assessed participants state and trait anxiety. The dependent variable was social distance, based on a measure of seating distance designed ad hoc for the present work. Our hypothesis that participants could report greater distance in response to Asian people was not confirmed. On the other hand, significantly lower distance in response to smiling compared to coughing targets was reported. Adopting a regression analysis model, we found that participants' social distance, in response to both coughing and smiling targets, was predicted by fear of infection and by the perception COVID-19 could become a pandemic. Social distance in response to the coughing target was also significantly and positively predicted by age and state anxiety. In summary, the present work has sought to identify a set of psychological variables, which may still be predictive of social distancing.

Keywords: COVID-19, social distancing, health, preventive behaviors, risk of infection

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to re-investigate the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high internode certainty, relative gene support, and high gene concordance factor. The evidence stems from five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Keshek M.H, Mohamed M.A, El-Shafey M.A

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The aim of this research was increasing the productivity of solar distillation. In order to reach this aim, a solar distiller was created with three glass sides sloping 30o at the horizontal level, and the experiments were carried out on the solar distillation unit during the period from 24th August, 2016 till 24th May, 2017 at the Agricultural Engineering and Bio Systems Department, Faculty of Agriculture, Menoufia University. Three gap lengths were used between the water level and the inner glass cover, those were 3, 6, and 9 cm. As the result of change the gap length between the water level and the inner glass cover the total volume of basins were changed from 15.5, 13, and 11 L, respectively. The total basin volume was divided to three sections, to investigate the effect of water volume. The three water volumes were 100%, 75%, and 50%. Every section was supplied with one, two, or three heaters. The one heater power was 15 W. The results showed that, by increasing the distance between the basins edge and the inner edge of the glass cover, an increase occurs in the percentage of temperature difference with maximum value was 52% at distance 9 cm from each edge, an increase occurs in the productivity with maximum productivity was 3.3 L/m2 at distance 9 cm from each edge and an increase occurs in the efficiency with maximum efficiency was 70% at distance 9 cm from each edge.

Keywords: distillation, solar energy, still productivity, efficiency

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Authors: Satpal Yadav, Ashish Phulkar, Krishna K. Sahu

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Aim: The research aims at doing a 3 Dimension biomechanical analysis in the shot put techniques of International throwers to evaluate the performance. Research Method: The researcher adopted the descriptive method and the data was subjected to calculate by using Pearson’s product moment correlation for the correlation of the biomechanical parameters with the performance of shot put throw. In all the analyses, the 5% critical level (p ≤ 0.05) was considered to indicate statistical significance. Research Sample: Eight (N=08) international shot putters using rotational/glide technique in male category was selected as subjects for the study. The researcher used the following methods and tools to obtain reliable measurements the instrument which was used for the purpose of present study namely the tesscorn slow-motion camera, specialized motion analyzer software, 7.260 kg Shot Put (for a male shot-putter) and steel tape. All measurement pertaining to the biomechanical variables was taken by the principal investigator so that data collected for the present study was considered reliable. Results: The finding of the study showed that negative significant relationship between the angular velocity right shoulder, acceleration distance at pre flight (-0.70), (-0.72) respectively were obtained, the angular displacement of knee, angular velocity right shoulder and acceleration distance at flight (0.81), (0.75) and (0.71) respectively were obtained, the angular velocity right shoulder and acceleration distance at transition phase (0.77), (0.79) respectively were obtained and angular displacement of knee, angular velocity right shoulder, release velocity shot, angle of release, height of release, projected distance and measured distance as the values (0.76), (0.77), (-0.83), (-0.79), (-0.77), (0.99) and (1.00) were found higher than the tabulated value at 0.05 level of significance. On the other hand, there exists an insignificant relationship between the performance of shot put and acceleration distance [m], angular displacement shot, C.G at release and horizontal release distance on the technique of shot put.

Keywords: biomechanics, analysis, shot put, international throwers

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Authors: Zhang Kehan, Du Luona

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Wireless power transfer (WPT) systems have been widely investigated for advantages of convenience and safety compared to traditional plug-in charging systems. The research contents include impedance matching, circuit topology, transfer distance et al. for improving the efficiency of WPT system, which is a decisive factor in the practical application. What is more, coil structures such as spiral circular coil and helical coil with variable distance between two turns also have indispensable effects on the efficiency of WPT systems. This paper compares the efficiency of WPT systems utilizing spiral or helical coil with variable distance between two turns, and experimental results show that efficiency of spiral circular coil with an optimum distance between two turns is the highest. According to efficiency formula of resonant WPT system with series-series topology, we introduce M²/R₋₁ to measure the efficiency of spiral circular coil and helical coil WPT system. If the distance between two turns s is too close, proximity effect theory shows that the induced current in the conductor, caused by a variable flux created by the current flows in the skin of vicinity conductor, is the opposite direction of source current and has assignable impart on coil resistance. Thus in two coil structures, s affects coil resistance. At the same time, when the distance between primary and secondary coils is not variable, s can also make the influence on M to some degrees. The aforementioned study proves that s plays an indispensable role in changing M²/R₋₁ and then can be adjusted to find the optimum value with which WPT system achieves the highest efficiency. In actual application situations of WPT systems especially in underwater vehicles, miniaturization is one vital issue in designing WPT system structures. Limited by system size, the largest external radius of spiral circular coil is 100 mm, and the largest height of helical coil is 40 mm. In other words, the turn of coil N changes with s. In spiral circular and helical structures, the distance between each two turns in secondary coil is set as a constant value 1 mm to guarantee that the R2 is not variable. Based on the analysis above, we set up spiral circular coil and helical coil model using COMSOL to analyze the value of M²/R₋₁ when the distance between each two turns in primary coil sp varies from 0 mm to 10 mm. In the two structure models, the distance between primary and secondary coils is 50 mm and wire diameter is chosen as 1.5 mm. The turn of coil in secondary coil are 27 in helical coil model and 20 in spiral circular coil model. The best value of s in helical coil structure and spiral circular coil structure are 1 mm and 2 mm respectively, in which the value of M²/R₋₁ is the largest. It is obviously to select spiral circular coil as the first choice to design the WPT system for that the value of M²/R₋₁ in spiral circular coil is larger than that in helical coil under the same condition.

Keywords: distance between two turns, helical coil, spiral circular coil, wireless power transfer

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Authors: Jo-Han Chang, Chung-Jung Wu

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This study involves a design proposal. The objective of is to create a seat arrangement model for public reading spaces that enable free arrangement without disturbing the users. Through a subjective perception scale, this study explored whether distance between seats and direction of seats influence individual subjective perceptions in a public reading space. This study also involves analysis of user subjective perceptions when reading in the settings on 3 seats at different directions and with 5 distances between seats. The results may be applied to public chair design. This study investigated that (a) whether different directions of seats and distances between seats influence individual subjective perceptions and (b) the acceptable personal space between 2 strangers in a public reading space. The results are shown as follows: (a) the directions of seats and distances between seats influenced individual subjective perceptions. (b) subjective evaluation scores were higher for back-to-back seat directions with Distances A (10 cm) and B (62 cm) compared with face-to-face and side-by-side seat directions; however, when the seat distance exceeded 114 cm (Distance C), no difference existed among the directions of seats. (c) regarding reading in public spaces, when the distance between seats is 10 cm only, we recommend arranging the seats in a back-to-back fashion to increase user comfort and arrangement of face-to-face and side- by-side seat directions should be avoided. When the seat arrangement is limited to face-to-face design, the distance between seats should be increased to at least 62 cm. Moreover, the distance between seats should be increased to at least 114 cm for side- by-side seats to elevate user comfort.

Keywords: individual subjective perceptions, personal space, seat arrangement, direction, distances

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Authors: Daeung Jung

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Background: In case of patients with missing teeth, multiple implant restoration has been widely used and is inevitable. To increase its survival rate, it is important to understand the influence of different implant designs on inter-implant crestal bone resorption. There are several implant systems designed to minimize loss of crestal bone, and the Astra Tech and Brånemark Implant are two of them. Aim/Hypothesis: The aim of this 10-year study was to compare the height of inter-implant bone crest in two implant systems; the Astra Tech and the Brånemark implant system. Material and Methods: In this retrospective study, 40 consecutively treated patients were utilized; 23 patients with 30 sites for Astra Tech system and 17 patients with 20 sites for Brånemark system. The implant restoration was comprised of splinted crown in partially edentulous patients. Radiographs were taken immediately after 1st surgery, at impression making, at prosthetics setting, and annually after loading. Lateral distance from implant to bone crest, inter-implant distance was gauged, and crestal bone height was measured from the implant shoulder to the first bone contact. Calibrations were performed with known length of thread pitch distance for vertical measurement, and known diameter of abutment or fixture for horizontal measurement using ImageJ. Results: After 10 years, patients treated with Astra Tech implant system demonstrated less inter-implant crestal bone resorption when implants had a distance of 3mm or less between them. In cases of implants that had a greater than 3 mm distance between them, however, there appeared to be no statistically significant difference in crestal bone loss between two systems. Conclusion and clinical implications: In the situation of partially edentulous patients planning to have more than two implants, the inter-implant distance is one of the most important factors to be considered. If it is impossible to make sure of having sufficient inter-implant distance, the implants with less micro gap in the fixture-abutment junction, less traumatic 2nd surgery approach, and the adequate surface topography would be choice of appropriate options to minimize inter-implant crestal bone resorption.

Keywords: implant design, crestal bone loss, inter-implant distance, 10-year retrospective study

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Authors: So-Ra Jeon, Chan Byon

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This study investigates the heat transfer characteristics of aluminum foam heat sink and pin fin heat sink subjected to an impinging air jet under a fixed pumping power condition as well as fixed flow rate condition. The effects of dimensionless pumping power or the Reynolds number and the impinging distance ratio on the Nusselt number are considered. The result shows that the effect of the impinging distance on the Nusselt number is negligible under a fixed pumping power condition, while the Nusselt number increases with decreasing the impinging distance under a fixed pumping power condition. A correlation for the pressure drop is obtained as a function of the flow rate and the impinging distance ratio. And correlations for the stagnation Nusselt number of the impinging jet are developed as a function of the pumping power. The aluminum foam heat sinks did not show higher thermal performance compared to a conventional pin fin heat sink under a fixed pumping power condition.

Keywords: aluminum foam, heat sinks, impinging jet, pumping power

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Authors: Sumeet Rai, Anuj Tyagi, B. T. Naveen Kumar, Shubhkaramjeet Kaur, Niraj K. Singh

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Since their discovery, indiscriminate use of antibiotics in human, veterinary and aquaculture systems has resulted in global emergence/spread of multidrug-resistant bacterial pathogens. Thus, the need for alternative approaches to control bacterial infections has become utmost important. High selectivity/specificity of bacteriophages (phages) permits the targeting of specific bacteria without affecting the desirable flora. In this study, a lytic phage (Ahp1) specific to Aeromonas hydrophila subsp. hydrophila was isolated from finfish aquaculture pond. The host range of Ahp1 range was tested against 10 isolates of A. hydrophila, 7 isolates of A. veronii, 25 Vibrio cholerae isolates, 4 V. parahaemolyticus isolates and one isolate each of V. harveyi and Salmonella enterica collected previously. Except the host A. hydrophila subsp. hydrophila strain, no lytic activity against any other bacterial was detected. During the adsorption rate and one-step growth curve analysis, 69.7% of phage particles were able to get adsorbed on host cell followed by the release of 93 ± 6 phage progenies per host cell after a latent period of ~30 min. Phage nucleic acid was extracted by column purification methods. After determining the nature of phage nucleic acid as dsDNA, phage genome was subjected to next-generation sequencing by generating paired-end (PE, 2 x 300bp) reads on Illumina MiSeq system. De novo assembly of sequencing reads generated circular phage genome of 42,439 bp with G+C content of 58.95%. During open read frame (ORF) prediction and annotation, 22 ORFs (out of 49 total predicted ORFs) were functionally annotated and rest encoded for hypothetical proteins. Proteins involved in major functions such as phage structure formation and packaging, DNA replication and repair, DNA transcription and host cell lysis were encoded by the phage genome. The complete genome sequence of Ahp1 along with gene annotation was submitted to NCBI GenBank (accession number MF683623). Stability of Ahp1 preparations at storage temperatures of 4 °C, 30 °C, and 40 °C was studied over a period of 9 months. At 40 °C storage, phage counts declined by 4 log units within one month; with a total loss of viability after 2 months. At 30 °C temperature, phage preparation was stable for < 5 months. On the other hand, phage counts decreased by only 2 log units over a period of 9 during storage at 4 °C. As some of the phages have also been reported as glycerol sensitive, the stability of Ahp1 preparations in (0%, 15%, 30% and 45%) glycerol stocks were also studied during storage at -80 °C over a period of 9 months. The phage counts decreased only by 2 log units during storage, and no significant difference in phage counts was observed at different concentrations of glycerol. The Ahp1 phage discovered in our study had a very narrow host range and it may be useful for phage typing applications. Moreover, the endolysin and holin genes in Ahp1 genome could be ideal candidates for recombinant cloning and expression of antimicrobial proteins.

Keywords: Aeromonas hydrophila, endolysin, phage, narrow host range

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Authors: Paolo Fantozzi, Luigi Laura, Umberto Nanni

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The problem of Entity relation discovery in structured data, a well covered topic in literature, consists in searching within unstructured sources (typically, text) in order to find connections among entities. These can be a whole dictionary, or a specific collection of named items. In many cases machine learning and/or text mining techniques are used for this goal. These approaches might be unfeasible in computationally challenging problems, such as processing massive data streams. A faster approach consists in collecting the cooccurrences of any two words (entities) in order to create a graph of relations - a cooccurrence graph. Indeed each cooccurrence highlights some grade of semantic correlation between the words because it is more common to have related words close each other than having them in the opposite sides of the text. Some authors have used sliding windows for such problem: they count all the occurrences within a sliding windows running over the whole text. In this paper we generalise such technique, coming up to a Weighted-Distance Sliding Window, where each occurrence of two named items within the window is accounted with a weight depending on the distance between items: a closer distance implies a stronger evidence of a relationship. We develop an experiment in order to support this intuition, by applying this technique to a data set consisting in the text of the Bible, split into verses.

Keywords: cooccurrence graph, entity relation graph, unstructured text, weighted distance

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Authors: Shama, Asif Mahmood, Wen Zhang

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Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China. Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to library construction, which were then sequenced on the Illumina MiSeq platform. The sequenced reads were analyzed using a viral metagenomic analysis pipeline. A cardiovirus from the feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on the P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1. The complete genome of a cardiovirus was determined from the feces of wild rats, which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation.

Keywords: cardioviruses, viral metagenomics, novel viruses, virus-host interaction

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Authors: Mostert Jacques, Gulseven Osman, Williams Courtney

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The Covid-19 pandemic caused unparalleled disruption in the lives of the majority of the world. This included school closures and introduction of Online Learning. In this article we investigated the impact of distance learning on the self-efficacy and anxiety levels experienced by educators in South Africa. We surveyed 60 respondents from Independent Schools using a Likert Scale rating of 0 to 4. The results suggested that despite experiencing moderate anxiety, educators showed a sense of high self-efficacy during distance learning. This was specifically true for those with underlying health concerns. There was no significant difference between how the different genders experienced anxiety and self-efficacy. Further research into the impact on learners’ anxiety levels during distance learning will provide policymakers and educators with a better understanding of how the use of technology is influencing the effectiveness of teaching, learning, and assessment.

Keywords: COVID-19, education, self-efficacy, anxiety

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Authors: Jingyuan Hu, Zhandong Liu

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CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

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Authors: Santhita Tungkajiwangkoon, Yoshikazu Hoshi

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Three Japaneses Drosera species are the good model to study genome organization with highly specialized morphological group for insect trapping, and has revealed anti-inflammatory, and antibacterial effects, so there must be a reason for botanists are so appealing in these plants. Cytology and Flow cytometry were used to investigate the genetic stability and ploidy estimation in three related species. The cytological and Flow cytometry analysis were done in Drosera rotundifolia L., Drosera spatulata Labill and Drosera tokaiensis. The cytological studies by fluorescence staining (DAPI) showed that D. tokaiensis was an alloploid (2n=6x=60, hexaploid) which is a natural hybrid polyploids of D. rotundifolia and D. spatulata. D. rotundifolia was a diploid with the middle size of metaphase chromosomes (2n=2x=20) as a paternal origin and D. spatulata was a tetraploid with small size of metaphase chromosome (2n=4x=40) as a maternal origin. We confirmed by Flow cytometry analysis to determine the ploidy level and DNA content of the plants. The 2C-DNA values of D. rotundiflolia were 2.8 pg, D. spatulata was 1.6 pg and D. tokaiensis was 3.9 pg. However, 2C- DNA values of D. tokaiensis should be related from their parents but in the present study the 2C-DNA values of D. tokaiensis was no relation from the theoretical of hybrids representing additive parental. Possibility of D. tokaiensis is a natural hybrid, which is also hybridization in natural evolution can cause the genome reduction in plant.

Keywords: drosera, hybrid, cytology, flow cytometry

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Authors: S. Najafi, E. Bertini, M. Pezzotti, G.B. Tornielli, S. Zenoni

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Grapevine is an important agricultural fruit crop plant consumed worldwide and with a key role in the global economy. Grapevine is strongly affected by both biotic and abiotic stresses, which impact grape growth at different stages, such as during plant and berry development and pre- and post-harvest, consequently causing significant economic losses. Recently global warming has propelled the anticipation of the onset of berry ripening, determining the reduction of a grape color and increased volatilization of aroma compounds. Climate change could negatively alter the physiological characteristics of the grape and affect the berry and wine quality. Modern plant breeding can provide tools such as genome editing for improving grape resilience traits while maintaining intact the viticultural and oenological quality characteristics of the genotype. This study aims at developing a platform for genome editing application in grapevine plants with the final goal to improve berry quality, biotic, and abiotic resilience traits. We chose to directly deliver ribonucleoproteins (RNP, preassembled Cas protein and guide RNA) into plant protoplasts, and, from these cell structures, regenerate grapevine plants edited in specific selected genes controlling traits of interest. Edited plants regenerated by somatic embryogenesis from protoplasts will then be sequenced and molecularly characterized. Embryogenic calli of Sultana and Shiraz cultivars were initiated from unopened leaves of in-vitro shoot tip cultures and from stamens, respectively. Leaves were placed on NB2 medium while stamens on callus initiation medium (PIV) medium and incubated in the dark at 28 °C for three months. Viable protoplasts, tested by FDA staining, isolated from embryogenic calli were cultured by disc method at 1*105 protoplasts/ml. Mature well-shaped somatic embryos developed directly in the protoplast culture medium two months later and were transferred in the light into to shooting medium for further growth. Regenerated plants were then transferred to the greenhouse; no phenotypic alterations were observed when compared to non in-vitro cultured plants. The performed experiments allowed to established an efficient protocol of embryogenic calli production, protoplast isolation, and regeneration of the whole plant through somatic embryogenesis in both Sultana and Shiraz. Regenerated plants, through direct somatic embryogenesis deriving from a single cell, avoid the risk of chimerism during the regeneration process, therefore improving the genome editing process. As pre-requisite of genome editing, an efficient method for transfection of protoplast by yellow fluorescent protein (YFP) marker genes was also established and experiments of direct delivery of CRISPR–Cas9 ribonucleoproteins (RNPs) in protoplasts to achieve efficient DNA-free targeted mutations are in progress.

Keywords: CRISPR-cas9, plant regeneration, protoplast isolation, Vitis vinifera

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: cancer classification, feature selection, deep learning, genetic algorithm

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Authors: Amin Amini

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A Kinect sensor has been utilized as a cheap and accurate alternative to 3D laser scanners and electronic distance measurement (EDM) systems. This research presents an inexpensive and easy-to-setup system that utilizes the Microsoft Kinect v2 sensor as a surveying and measurement tool and investigates the possibility of using such a device as a replacement for conventional theodolite systems. The system was tested in an indoor environment where its accuracy in distance and angle measurements was tested using virtual markers in a 3D Cartesian environment. The system has shown an average accuracy of 97.94 % in measuring distances and 99.11 % and 98.84 % accuracy for area and perimeter, respectively, within the Kinect’s surveying range of 1.5 to 6 meters. The research also tested the system competency for relative angle determination between two objects.

Keywords: kinect v2, 3D measurement, depth map, ToF

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Authors: Yugander Arra, Florence Auguy, Melissa Stiebner, Sophie Chéron, Michael M. Wudick, Van Schepler-Luu, Sébastien Cunnac, Wolf B. Frommer, Laurence Albar

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Rice yellow mottle virus (RYMV) is one of the most important diseases affecting rice in Africa. The most promising strategy to reduce yield losses is the use of highly resistant varieties. The resistance gene RYMV2 is homolog of the Arabidopsis constitutive expression of pathogenesis related protein-5 (AtCPR5) nucleoporin gene. Resistance alleles are originating from African cultivated rice Oryza glaberrima, rarely cultivated, and are characterized by frameshifts or early stop codons, leading to a non-functional or truncated protein. Rice possesses two paralogs of CPR5 and function of these genes are unclear. Here, we evaluated the role of the two rice candidate nucleoporin paralogs OsCPR5.1 (pathogenesis-related gene 5; RYMV2) and OsCPR5.2 by CRISPR/Cas9 genome editing. Despite striking sequence and structural similarity, only loss-of-function of OsCPR5.1 led to full resistance, while loss-of-function oscpr5.2 mutants remained susceptible. Short N-terminal deletions in OsCPR5.1 also did not lead to resistance. In contrast to Atcpr5 mutants, neither OsCPR5.1 nor OsCPR5.2 knock out mutants showed substantial growth defects. Taken together, the candidate nucleoporin OsCPR5.1, but not its close homolog OsCPR5.2, plays a specific role for the susceptibility to RYMV, possibly by impairing the import of viral RNA or protein into the nucleus. Whereas gene introgression from O. glaberrima to high yielding O. sativa varieties is impaired by strong sterility barriers and the negative impact of linkage drag, genome editing of OsCPR5.1, while maintaining OsCPR5.2 activity, thus provides a promising strategy to generate O. sativa elite lines that are resistant to RYMV.

Keywords: CRISPR Cas9, genome editing, knock out mutant, recessive resistance, rice yellow mottle virus

Procedia PDF Downloads 87