Search results for: primer sequences

Authors: Fulufhelo Amanda Doboro, Kgomotso Sebeko, Stephen Njiro, Moritz Van Vuuren

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Ovine herpesvirus 2 (OvHV-2) genome obtained from the lymphopblastoid cell line of a BJ1035 cow was recently sequenced in the United States of America (USA). Information on the sequences of OvHV-2 genes obtained from South African strains from bovine or other African countries and molecular characterization of OvHV-2 is not documented. Present investigation provides information on the nucleotide and derived amino acid sequences and genetic diversity of Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes, of these genes from OvHV-2 strains circulating in South Africa. Gene-specific primers were designed and used for PCR of DNA extracted from 42 bovine blood samples that previously tested positive for OvHV-2. The expected PCR products of 495 bp, 253 bp, 890 bp and 1632 bp respectively for Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes were sequenced and multiple sequence analysis done on the selected regions of the sequenced PCR products. Two genotypes for ORF 27 and ORF 73 gene sequences, and three genotypes for Ov 7 and Ov 8 ex2 gene sequences were identified, and similar groupings for the derived amino acid sequences were obtained for each gene. Nucleotide and amino acid sequence variations that led to the identification of the different genotypes included SNPs, deletions and insertions. Sequence analysis of Ov 7 and ORF 27 genes revealed variations that distinguished between sequences from SA and reference OvHV-2 strains. The implication of geographic origin among SA sequences was difficult to evaluate because of random distribution of genotypes in the different provinces, for each gene. However, socio-economic factors such as migration of people with animals, or transportation of animals for agricultural or business use from one province to another are most likely to be responsible for this observation. The sequence variations observed in this study have no impact on the antibody binding activities of glycoproteins encoded by Ov 7, Ov 8 ex2 and ORF 27 genes, as determined by prediction of the presence of B cell epitopes using BepiPred 1.0. The findings of this study will be used for selection of gene candidates for the development of diagnostic assays and vaccine development as well.

Keywords: amino acid, genetic diversity, genes, nucleotide

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Authors: Tulin Coskun

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We investigate the approximation of analytic functions of several variables in polydisc by the sequences of linear k-positive operators in Gadjiev sence. The approximation of analytic functions of complex variable by linear k-positive operators was tackled, and k-positive operators and formulated theorems of Korovkin's type for these operators in the space of analytic functions on the unit disc were introduced in the past. Recently, very general results on convergence of the sequences of linear k-positive operators on a simply connected bounded domain within the space of analytic functions were proved. In this presentation, we extend some of these results to the approximation of analytic functions of several complex variables by sequences of linear k-positive operators.

Keywords: analytic functions, approximation of analytic functions, Linear k-positive operators, Korovkin type theorems

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Authors: Bin Liu

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Prokaryotic promoter, consisted of two short DNA sequences located at in -35 and -10 positions, is responsible for controlling the initiation and expression of gene expression. Different types of promoters have different functions, and their consensus sequences are similar. In addition, their consensus sequences may be different for the same type of promoter, which poses difficulties for promoter identification. Unfortunately, all existing computational methods treat promoter identification as a binary classification task and can only identify whether a query sequence belongs to a specific promoter type. It is desired to develop computational methods for effectively identifying promoters and their types. Here, a two-layer predictor is proposed to try to deal with the problem. The first layer is designed to predict whether a given sequence is a promoter and the second layer predicts the type of promoter that is judged as a promoter. Meanwhile, we also analyze the importance of feature and sequence conversation in two aspects: promoter identification and promoter type identification. To the best knowledge of ours, it is the first computational predictor to detect promoters and their types.

Keywords: promoter, promoter type, random forest, sequence information

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Authors: Saed Khawaldeh, Mohamed Elsharnouby, Alaa Eddin Alchalabi, Usama Pervaiz, Tajwar Aleef, Vu Hoang Minh

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Taxonomic classification has a wide-range of applications such as finding out more about the evolutionary history of organisms that can be done by making a comparison between species living now and species that lived in the past. This comparison can be made using different kinds of extracted species’ data which include DNA sequences. Compared to the estimated number of the organisms that nature harbours, humanity does not have a thorough comprehension of which specific species they all belong to, in spite of the significant development of science and scientific knowledge over many years. One of the methods that can be applied to extract information out of the study of organisms in this regard is to use the DNA sequence of a living organism as a marker, thus making it available to classify it into a taxonomy. The classification of living organisms can be done in many machine learning techniques including Neural Networks (NNs). In this study, DNA sequences classification is performed using Convolutional Neural Networks (CNNs) which is a special type of NNs.

Keywords: deep networks, convolutional neural networks, taxonomic classification, DNA sequences classification

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Authors: B. M. Md-Zain, N. A. Rahman, M. A. B. Abdul-Latiff, W. M. R. Idris

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We conducted molecular research to portray phylogenetic relationships of Malaysian primates particularly in the genus of Macaca. We have sequenced cytochrome C oxidase subunit I (COI) of mitochondrial DNA of several individuals from M. fascicularis and M. arctoides. PCR amplifications were performed and COI DNA sequences were aligned using ClustalW. Phylogenetic trees were constructed using distance analyses by employing neighbor-joining algorithm (NJ). We managed to sequence 700 bp of COI DNA sequences. The tree topology showed that M. fascicularis did not clump based on phyleogeography division in Peninsular Malaysia. Individuals from Negeri Sembilan merged together with samples from Perak and Penang into one clade. In addition, phylogenetic analyses indicated that M. arctoides was classified into sinica group instead of fascicularis group supported by genetic distance data. COI gene is an effective locus to clarify phylogenetic position of M. arctoides but not in discriminating M. fascicularis population in Peninsular Malaysia.

Keywords: cercopithecine, long-tailed macaque, Macaca fascicularis, Macaca arctoides

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Authors: Anas Hallak, Latifa Seblini, Juergen Wilde

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In mechatronics or sensor technology, plastic housings are used to protect sensitive components from harmful environmental influences, such as moisture, media, or reactive substances. Connections, preferably in the form of metallic lead-frame structures, through the housing wall are required for their electrical supply or control. In this system, an insufficient connection between the plastic component, e.g., Polyamide66, and the metal surface, e.g., copper, due to the incompatibility is dominating. As a result, leakage paths can occur along with the plastic-metal interface. Since adhesive bonding has been established as one of the most important joining processes and its use has expanded significantly, driven by the development of improved high-performance adhesives and bonding techniques, this technology has been involved in metal-plastic hybrid structures. In this study, an epoxy bonding agent from DELO (DUALBOND LT2266) has been used to improve the mechanical and chemical binding between the metal and the polymer. It is an adhesion promoter with two reaction stages. In these, the first stage provides fixation to the lead frame directly after the coating step, which can be done by UV-Exposure for a few seconds. In the second stage, the material will be thermally hardened during injection molding. To analyze the two reaction stages of the primer, dynamic DSC experiments were carried out and correlated with Fourier-transform infrared spectroscopy measurements. Furthermore, the number of crosslinking bonds formed in the system in each reaction stage has also been estimated by a rheological characterization. Those investigations have been performed with different times of UV exposure: 12, 96 s and in an industrial preferred temperature range from -20 to 175°C. The shear viscosity values of primer have been measured as a function of temperature and exposure times. For further interpretation, the storage modulus values have been calculated, and the so-called Booij–Palmen plot has been sketched. The next approach in this study is the self-healing mechanisms in the hydride system in which the primer should flow into micro-damage such as interface, cracks, inhibit them from growing, and close them. The ability of the primer to flow in and penetrate defined capillaries made in Ultramid was investigated. Holes with a diameter of 0.3 mm were produced in injection-molded A3EG7 plates with 4 mm thickness. A copper substrate coated with the DUALBOND was placed on the A3EG7 plate and pressed with a certain force. Metallographic analyses were carried out to verify the filling grade, which showed an almost 95% filling ratio of the capillaries. Finally, to estimate the self-healing mechanism in metal-plastic hybrid systems, characterizations have been done on a simple geometry with a metal inlay developed by the Institute of Polymer Technology in Friedrich-Alexander-University. The specimens have been modified with tungsten wire which was to be pulled out after the injection molding to create a micro-hole in the specimen at the interface between the primer and the polymer. The capability of the primer to heal those micro-cracks upon heating, pressing, and thermal aging has been characterized through metallographic analyses.

Keywords: hybrid structures, self-healing, thermoplastic housing, adhesive

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Authors: Rouhollah Radjabi, Mojtaba Zarei, Elham Sanatgar, Hossein Shouhani

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RAPD molecular markers in order to discrimination of the Iranian native Bombyx mori silkworm breeds were used. DNA extraction using phenol - chloroform was and the qualitative and quantitative measurements of extracted DNA and its dilution, the obtained bands on agarose gel 1.5 percent were marked and analyzed. Results showed that the bands are observed between 250-2500 bp and most bands have been observed as Gilani-orange, the lowest bands observed are Khorasani-lemon. Primer 3 with 100% polymorphism with the highest polymorphism and primer 2 with 61.5 polymorphism had the lowest percentage of polymorphism. Cluster analysis of races and placed them in three main groups, races Gilani - orange, Baghdad and Khorasani -pink if the first group, camel's thorn, Herati - yellow race was alone in the second group and Khorasani – lemon was alone in the third group. The greatest similarity between the races, between Khorasani- pink and Baghdad (0.64). RAPD markers have been determined different silkworm races based on various morphological or economic characteristics except geographic origin.

Keywords: silkworm, molecular marker, RAPD, Iran

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Authors: Hana Barak, Alex Sivan, Ariel Kushmaro

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

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

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: Mohammed Abdullah Basahi

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The objective of the present study was to identify the phylogenetic relationships and determine genetic diversity among Suaeda genotypes growing in Saudi Arabia and to find out whether these could be a potential source for genetic diversity. A set of nineteen genotypes was analyzed using twenty-four ISSR primers. Clear amplified polymorphic DNA products were obtained from the screening of twenty-four ISSR primers on nineteen genotypes that allowed selection of ten primers and the results were reproducible. Nineteen genotypes were revealed a unique profile with ten ISSR primers and thus it can be used for the DNA fingerprinting. Different primers produced a different level of polymorphism among the nineteen genotypes. The number of polymorphic bands per primer varied from 5 to 14 with an average of 8 bands per primer. The results revealed that the genotypes differed for ISSR markers. The genetic similarity based on Nei and Li’s ranged from 0.450 to 0.930. Cluster analysis was conducted based on ISSR data to group the Suaeda genotypes and to construct a dendrogram. Four groups can be distinguished by truncating the dendrogram at GS value of 0.54. ISSR markers showed high level of polymorphism among the genotypes examined. The present study indicates that ISSR markers could be successfully used in genetic characterization and diversity in Suaeda.

Keywords: suaeda, DNA fingerprinting, ISSR, Saudi Arabia

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Authors: Bilal Wajid, Erchin Serpedin

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The health industry is aiming towards personalized medicine. If the patient’s genome needs to be sequenced it is important that the entire analysis be completed quickly. This paper explores use of parallel computing to analyze very large sequences. Two cases have been considered. In the first case, the sequence is kept constant and the effect of increasing the number of MPI-based processes is evaluated in terms of execution time, speed and efficiency. In the second case the number of MPI-based processes have been kept constant whereas, the length of the sequence was increased.

Keywords: parallel computing, alignment, genome assembly, alignment

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Authors: Fernandes A. C. B. C. J., de Jesus V. C., Sepideh N., Vilela OFGG, Somarin K. K., França R., Pinheiro F. H. S. L.

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Objective: The purpose of this study was to look at the effect of pre-treatment of enamel with pumice and/or 37% phosphoric acid on the shear bond strength (SBS) of orthodontic tubes bonded to enamel while simultaneously evaluating the efficacy of orthodontic tubes bonded by self-etch primer (SEP). Materials and Methods: 39 of the crown halves were divided into 3 groups at random. Group, I was the control group utilizing both prophy paste and the conventional double etching pre-treatment method. Group II excluded the use of prophy paste prior to double etching. Group III excluded the use of both prophy paste and double etching and only utilized SEP. Bond strength of the orthodontic tubes was measured by SBS. One way ANOVA and Tukey’s HSD test were used to compare SBS values between the three groups. The statistical significance was set to p<0.05. Results: The difference in SBS values of groups I (36.672 ± 9.315 Mpa), II (34.242 ± 9.986 Mpa), and III (39.055 ± 5.565) were not statistically significant (P<0.05). Conclusion: This study suggested that the use of prophy paste or pre-acid etch of the enamel surface did not provide a statistically significant difference in SBS between the three groups.

Keywords: shear bond strength, orthodontic bracket, self-etch primer, pumice, prophy

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Authors: Priya Arora, Ashutosh Mishra

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Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

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Authors: Perdana Rakhmana Putra, Hansen Wijaya, Sri Budiyani, Muhamad Natsir, Alexis badai Samudra

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The Palembang Sub-Basin (PSB) located in southern part of South Sumatera basin (SSB) consist of half-graben complex trending N-S to NW-SE. These geometries are believe as an impact of strike-slip regime developed in Eocene-Oligocene. Generally, most of the wells in this area produced hydrocarbon from late stage of syn-rift sequences called Lower Talang Akar (LTAF) and post-rift sequences called Batu Raja Formation (BRF) and drilled to proved hydrocarbon on structural trap; three-way dip anticline, four-way dip anticline, dissected anticline, and stratigraphy trap; carbonate build-up and stratigraphic pinch out. Only a few wells reached the deeper syn-rift sequences called Lahat Formation (LAF) and Lemat Formation (LEF). The new interpretation of subsurface data was done by the tectonostratigraphy concept and focusing on syn-rift sequence. Base on seismic characteristic on basin centre, it divided into four sequences: pre-rift sequence, rift initiation, maximum rift and late rift. These sequences believed as a new exploration target on PSB mature basin. This paper will demonstrate the paleo depositional setting during Paleogene and exploration play concept of syn-rift sequence in PSB. The main play for this area consists of stratigraphic and structure play, where the stratigraphic play is Eocene-Oligocene sediment consist of LAF sandstone, LEF-Benakat formation, and LAF with pinch-out geometry. The pinch-out, lenses geometry and on-lap features can be seen on the seismic reflector and formed at the time of the syn-rift sequence. The structural play is dominated by a 3 Way Dip play related to reverse fault trap.

Keywords: syn-rift, tectono-stratigraphy, exploration play, basin center play, south sumatera basin

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Authors: Corey F. Fitzgerald

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

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

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Authors: Yili Liu, Honghao Ren, Mariko Kondo

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In the field of second language (L2) speech learning, it is well-known that that learner’s first language (L1) phonetic and phonological characteristics will be transferred into their L2 production and perception, which lead to foreign accent. For L1 Mandarin learners of Japanese, the confusion of /u/ and /o/ in /CjV/ sequences has been observed in their utterance frequently. L1 transfer is considered to be the cause of this issue, however, other factors which influence the identification of /Cju/ and /Cjo/ sequences still under investigation. This study investigates the perception of Japanese /Cju/ and /Cjo/ units by L1 Mandarin learners of Japanese. It further examined whether learners’ proficiency, syllable position, phonetic features of preceding consonants and background noise affect learners’ performance in perception. Fifty-two Mandarin-speaking learners of Japanese and nine native Japanese speakers were recruited to participate in an identification task. Learners were divided into beginner, intermediate and advanced level according to their Japanese proficiency. The average correct rate was used to evaluate learners’ perceptual performance. Furthermore, the comparison of the correct rate between learners’ groups and the control group was conducted as well to examine learners’ nativelikeness. Results showed that background noise tends to pose an adverse effect on distinguishing /u/ and /o/ in /CjV/ sequences. Secondly, Japanese proficiency has no influence on learners’ perceptual performance in the quiet and in background noise. Then all learners did not reach a native-like level without the distraction of noise. Beginner level learners performed less native-like, although higher level learners appeared to have achieved nativelikeness in the multi-talker babble noise. Finally, syllable position tends to affect distinguishing /Cju/ and /Cjo/ only under the noisy condition. Phonetic features of preceding consonants did not impact learners’ perception in any listening conditions. Findings in this study can give an insight into a further understanding of Japanese vowel acquisition by L1 Mandarin learners of Japanese. In addition, this study indicates that L1 transfer is not the only explanation for the confusion of /u/ and /o/ in /CjV/ sequences, factors such as listening condition and syllable position are also needed to take into consideration in future research. It also suggests the importance of perceiving speech in a noisy environment, which is close to the actual conversation required more attention to pedagogy.

Keywords: background noise, Chinese learners of Japanese, /Cju/ and /Cjo/ sequences, second language perception

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Authors: F. Berna Benli, Özgür Keskin

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Lately, many mathematicians have been studied the statistical convergence of a sequence of fuzzy numbers. We know that Lambda-statistically convergence is a kind of convergence between ordinary convergence and statistical convergence. In this paper, we will introduce the new kind of convergence such as λ-levelwise statistical convergence. Then, we will define the concept of the λ-levelwise statistical cluster and limit points of a sequence of fuzzy numbers. Also, we will discuss the relations between the sets of λ-levelwise statistical cluster points and λ-levelwise statistical limit points of sequences of fuzzy numbers. This work has been extended in this paper, where some relations have been considered such that when lambda-statistical limit inferior and lambda-statistical limit superior for lambda-statistically convergent sequences of fuzzy numbers are equal. Furthermore, lambda-statistical boundedness condition for different sequences of fuzzy numbers has been studied.

Keywords: fuzzy number, λ-levelwise statistical cluster points, λ-levelwise statistical convergence, λ-levelwise statistical limit points, λ-statistical cluster points, λ-statistical convergence, λ-statistical limit points

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Authors: Okolie Pius Ifeanyi, Emerenini Emilymary Chima

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Aims: The study investigated the diversity and identities of Lactic Acid Bacteria (LAB) isolated from different fresh fruits using Molecular Nested PCR analysis and the efficacy of cell free supernatants from Lactic Acid Bacteria (LAB) isolated from fresh fruits for in vitro control of some tomato pathogens. Study Design: Nested PCR approach was used in this study employing universal 16S rRNA gene primers in the first round PCR and LAB specific Primers in the second round PCR with the view of generating specific Nested PCR products for the LAB diversity present in the samples. The inhibitory potentials of supernatant obtained from LAB isolates of fruits origin that were molecularly characterized were investigated against some tomato phytopathogens using agar-well method with the view to develop biological agents for some tomato disease causing organisms. Methodology: Gram positive, catalase negative strains of LAB were isolated from fresh fruits on Man Rogosa and Sharpe agar (Lab M) using streaking method. Isolates obtained were molecularly characterized by means of genomic DNA extraction kit (Norgen Biotek, Canada) method. Standard methods were used for Nested Polymerase Chain Reaction (PCR) amplification targeting the 16S rRNA gene using universal 16S rRNA gene and LAB specific primers, agarose gel electrophoresis, purification and sequencing of generated Nested PCR products (Macrogen Inc., USA). The partial sequences obtained were identified by blasting in the non-redundant nucleotide database of National Center for Biotechnology Information (NCBI). The antimicrobial activities of characterized LAB against some tomato phytopathogenic bacteria which include (Xanthomonas campestries, Erwinia caratovora, and Pseudomonas syringae) were obtained by using the agar well diffusion method. Results: The partial sequences obtained were deposited in the database of National Centre for Biotechnology Information (NCBI). Isolates were identified based upon the sequences as Weissella cibaria (4, 18.18%), Weissella confusa (3, 13.64%), Leuconostoc paramensenteroides (1, 4.55%), Lactobacillus plantarum (8, 36.36%), Lactobacillus paraplantarum (1, 4.55%) and Lactobacillus pentosus (1, 4.55%). The cell free supernatants of LAB from fresh fruits origin (Weissella cibaria, Weissella confusa, Leuconostoc paramensenteroides, Lactobacillus plantarum, Lactobacillus paraplantarum and Lactobacillus pentosus) can inhibits these bacteria by creating clear zones of inhibition around the wells containing cell free supernatants of the above mentioned strains of lactic acid bacteria. Conclusion: This study shows that potentially LAB can be quickly characterized by molecular methods to specie level by nested PCR analysis of the bacteria isolate genomic DNA using universal 16S rRNA primers and LAB specific primer. Tomato disease causing organisms can be most likely biologically controlled by using extracts from LAB. This finding will reduce the potential hazard from the use of chemical herbicides on plant.

Keywords: nested pcr, molecular characterization, 16s rRNA gene, lactic acid bacteria

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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: Delphine Ribes Lemay, Valentine Bernasconi, André Andrade, Lara DéFayes, Mathieu Salzmann, FréDéRic Kaplan, Nicolas Henchoz

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Digitization and preservation of large heritage induce high maintenance costs to keep up with the technical standards and ensure sustainable access. Creating impactful usage is instrumental to justify the resources for long-term preservation. The Museum für Gestaltung of Zurich holds one of the biggest poster collections of the world from which 52’000 were digitised. In the process of building a digital installation to valorize the collection, one objective was to develop an algorithm capable of predicting the next poster to show according to the ones already displayed. The work presented here describes the steps to build an algorithm able to automatically create sequences of posters reflecting associations performed by curator and professional designers. The exposed challenge finds similarities with the domain of song playlist algorithms. Recently, artificial intelligence techniques and more specifically, deep-learning algorithms have been used to facilitate their generations. Promising results were found thanks to Recurrent Neural Networks (RNN) trained on manually generated playlist and paired with clusters of extracted features from songs. We used the same principles to create the proposed algorithm but applied to a challenging medium, posters. First, a convolutional autoencoder was trained to extract features of the posters. The 52’000 digital posters were used as a training set. Poster features were then clustered. Next, an RNN learned to predict the next cluster according to the previous ones. RNN training set was composed of poster sequences extracted from a collection of books from the Gestaltung Museum of Zurich dedicated to displaying posters. Finally, within the predicted cluster, the poster with the best proximity compared to the previous poster is selected. The mean square distance between features of posters was used to compute the proximity. To validate the predictive model, we compared sequences of 15 posters produced by our model to randomly and manually generated sequences. Manual sequences were created by a professional graphic designer. We asked 21 participants working as professional graphic designers to sort the sequences from the one with the strongest graphic line to the one with the weakest and to motivate their answer with a short description. The sequences produced by the designer were ranked first 60%, second 25% and third 15% of the time. The sequences produced by our predictive model were ranked first 25%, second 45% and third 30% of the time. The sequences produced randomly were ranked first 15%, second 29%, and third 55% of the time. Compared to designer sequences, and as reported by participants, model and random sequences lacked thematic continuity. According to the results, the proposed model is able to generate better poster sequencing compared to random sampling. Eventually, our algorithm is sometimes able to outperform a professional designer. As a next step, the proposed algorithm should include a possibility to create sequences according to a selected theme. To conclude, this work shows the potentiality of artificial intelligence techniques to learn from existing content and provide a tool to curate large sets of data, with a permanent renewal of the presented content.

Keywords: Artificial Intelligence, Digital Humanities, serendipity, design research

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Authors: Sabeen Alam, Mehboob Alam

Abstract:

The research work entitled “Effect of Bacillus pumilus strains on heavy metal accumulation in lettuce grown on contaminated soil” focused on functional role of Bacillus pumilus strains inoculated with lettuce seed in mitigating heavy metal in chromite mining soil. In this experiment, factor A was three Bacillus pumilus strains (sequence C-2PMW-8, C-1 SSK-8 and C-1 PWK-7) while soil used for this experiment was collected from Prang Ghar mining site and lettuce seeds were grown in three levels of chromite mining soil (2.27, 4.65 and 7.14 %). For mining soil minimum days to germinate noted in lettuce grown on garden soil inoculated with sequence. Maximum germination percentage noted was for C-1 SSK-8 grown on garden soil, maximum lettuce height for sequence C-2 PWM-8, fresh leaf weight for C-1 PWK-7 inoculated lettuce, dry weight of lettuce leaf for lettuce inoculated with C-1 SSK-8 and C-1 PWK-7 strains, number of leaves per plant for lettuce inoculated with C-1 SSK-8, leaf area for C-2 PMW-8 inoculated lettuce, survival percentage for C-1 SSK-8 treated lettuce and chlorophyll content for C-2 PMW-8. Results related to heavy metals accumulation showed that minimum chromium was in lettuce and in soil for all three sequences, cadmium (Cd) in lettuce and in soil for all three sequences, manganese (Mn) in lettuce and in soil for three sequences, lead (Pb) in lettuce and in soil for three sequences. It can be concluded that chromite mining soil significantly reduced the growth and survival of lettuce, but when lettuce was inoculated with Bacillus.pumilus strains, it enhances growth and survival. Similarly, minimum heavy metal accumulation in plant and soil, regardless of type of Bacillus pumilus used, all three sequences has same mitigating effect on heavy metal in both soil and lettuce. All the three Bacillus pumilus strains ensured reduction in heavy metals content (Mn, Cd, Cr) in lettuce, below the maximum permissible limits of WHO 2011.

Keywords: bacillus pumilus, heavy metals, permissible limits, lettuce, chromite mining soil, mitigating effect

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Authors: Nidhi S. Chandra, Veena Agrawal, Debprasad Chattopadhyay

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Background: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in developing countries. It spreads feco orally mainly due to contamination of drinking water by sewage. There is limited data on the genotypic comparison of HEV isolates from sewage water and humans. The aim of this study was to identify genotype and conduct phylogenetic analysis of HEV isolates from sewage water and humans. Materials and Methods: 14 sewage water and 60 serum samples from acute sporadic hepatitis E cases (negative for hepatitis A, B, C) were tested for HEV-RNA by nested polymerase chain reaction (RTnPCR) using primers designed with in RdRp (RNA dependent RNA polymerase) region of open reading frame-1 (ORF-1). Sequencing was done by ABI prism 310. The sequences (343 nucleotides) were compared with each other and were aligned with previously reported HEV sequences obtained from GeneBank, using Clustal W software. A Phylogenetic tree was constructed by using PHYLIP version 3.67 software. Results: HEV-RNA was detected in 49/ 60 (81.67%) serum and 5/14 (35.71%) sewage samples. The sequences obtained from 17 serums and 2 sewage specimens belonged to genotype I with 85% similarity and clustering with previously reported human HEV sequences from India. HEV isolates from human and sewage in North West India are genetically closely related to each other. Conclusion: These finding suggest that sewage acts as reservoir of HEV. Therefore it is important that measures are taken for proper waste disposal and treatment of drinking water to prevent outbreaks and epidemics due to HEV.

Keywords: hepatitis E virus, nested polymerase chain reaction, open reading frame-1, nucleotidies

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Authors: Henni Sid Ahmed, Belbachir Mohamed Faouzi, Jean Caelen

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Behavior recognition has been studied for realizing drivers assisting system and automated navigation and is an important studied field in the intelligent Building. In this paper, a recognition method of behavior recognition separated from a real image was studied. Images were divided into several categories according to the actual weather, distance and angle of view etc. SIFT was firstly used to detect key points and describe them because the SIFT (Scale Invariant Feature Transform) features were invariant to image scale and rotation and were robust to changes in the viewpoint and illumination. My goal is to develop a robust and reliable system which is composed of two fixed cameras in every room of intelligent building which are connected to a computer for acquisition of video sequences, with a program using these video sequences as inputs, we use SIFT represented different images of video sequences, and SVM (support vector machine) Lights as a programming tool for classification of images in order to classify people’s behaviors in the intelligent building in order to give maximum comfort with optimized energy consumption.

Keywords: video analysis, people behavior, intelligent building, classification

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Authors: J. Trarbach, S. Schosser, B. Vogt

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Decision-makers tend to prefer the first alternative over subsequent alternatives which is called the primacy effect. To reliably measure this effect, we conducted an experiment with real consequences for preference statements. Therefore, we elicit preferences of subjects using a rating scale, i.e. hypothetical preferences, and willingness to pay, i.e. real preferences, for two sequences of pain. Within these sequences, both overall intensity and duration of pain are identical. Hence, a rational decision-maker should be indifferent, whereas the primacy effect predicts a stronger preference for the first sequence. What we see is a primacy effect only for hypothetical preferences. This effect vanishes for real preferences.

Keywords: decision making, primacy effect, real incentives, willingness to pay

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Authors: Alexander A. Tokmakov

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Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility. Two groups are albumin and globulin dissolving in water and salt solutions possessing metabolic activities. Two other groups are inactive and non-dissolvable and contain glutelins or glutenins and prolamins or gliadins. Gliadins are major components of the storage proteins in wheat endosperm. Gliadin proteins are separated into three groups based on electrophoretic mobility: α/β-gliadin, γ-gliadin, and ω-gliadin. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, involving coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus, three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 37 of the 40 accessions (93%) carried 210 bp allele, and three accessions (8%) did not yield any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: diploied wheat, gliadin, Triticum boeoticum, Triticum urartu

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Authors: Marianna Bolla

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The aim of this paper is to compare spectral, discrepancy, and degree properties of expanding graph sequences. As we can prove equivalences and implications between them and the definition of the generalized (multiclass) quasirandomness of Lovasz–Sos (2008), they can be regarded as generalized quasirandom properties akin to the equivalent quasirandom properties of the seminal Chung-Graham-Wilson paper (1989) in the one-class scenario. Since these properties are valid for deterministic graph sequences, irrespective of stochastic models, the partial implications also justify for low-dimensional embedding of large-scale graphs and for discrepancy minimizing spectral clustering.

Keywords: generalized random graphs, multiway discrepancy, normalized modularity spectra, spectral clustering

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Authors: Ergun Sakalar, Kubra Bilgic

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In the last decades, real-time PCR has become a reliable tool preferred to use in many laboratories for pathogen detection. This technique allows for monitoring target amplification via fluorescent molecules besides admit of quantitative analysis by enabling of convert outcomes of thermal cycling to digital data. Sensitivity and traceability of real-time PCR are based on measuring of fluorescence that appears only when fluorescent reporter dye bound to specific target DNA.The fluorescent reporter systems developed for this purpose are divided into two groups. The first group consists of intercalator fluorescence dyes such as SYBR Green, EvaGreen which binds to double-stranded DNA. On the other hand, the second group includes fluorophore-labeled oligonucleotide probes that are separated into three subgroups due to differences in mechanism of action; initial primer-probes such as Cyclicons, Angler®, Amplifluor®, LUX™, Scorpions, and the second one hydrolysis probes like TaqMan, Snake assay, finally hybridization probes, for instance, Molecular Beacons, Hybprobe/FRET, HyBeacon™, MGB-Eclipse, ResonSense®, Yin-Yang, MGB-Pleiades. In addition nucleic acid analogues, an increase of probe affinity to target site is also employed with fluorescence-labeled probes. Consequently, abundant real-time PCR detection chemistries are chosen by researcher according to the field of application, mechanism of action, advantages, and proper structures of primer/probes.

Keywords: fluorescent dye, food safety, molecular probes, nucleic acid analogues

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Authors: Adam Rosiński

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This paper discusses an experiment conducted with two groups of participants, composed of musicians and non-musicians, in order to investigate the impact of the speed of a sound sequence and the order of sounds on the grouping of sounds into sequences of six tones. Significant differences were observed between musicians and non-musicians with respect to the threshold sequence speed at which the sequence was split into two streams. The differences in the results for the two groups suggest that the musical education of the participating listeners may be a vital factor. The criterion of musical education should be taken into account during experiments so that the results obtained are reliable, uniform, and free from interpretive errors.

Keywords: auditory scene analysis, education, hearing, psychoacoustics

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Authors: T. Padma, Jayashree S. Pillai

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Random entities are an essential component in any cryptographic application. The suitability of a number theory based novel pseudorandom sequence called Pseudorandom Partial Quotient Sequence (PPQS) generated from the continued fraction expansion of irrational numbers, in cryptographic applications, is analyzed in this paper. An approach to build the algorithm around a hard mathematical problem has been considered. The PQ sequence is tested for randomness and its suitability as a cryptographic key by performing randomness analysis, key sensitivity and key space analysis, precision analysis and evaluating the correlation properties is established.

Keywords: pseudorandom sequences, key sensitivity, correlation, security analysis, randomness analysis, sensitivity analysis

Procedia PDF Downloads 594