Search results for: gene expression programming (GEP

Authors: R. Komsa-Penkova, G. Golemanov, G. Georgieva, K. Popovski, N. Slavov, P. Ivanov, K. Kovacheva, S. Rathee, E. Konova, A. Blajev

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Leptin and PAI-1 are important cytokines and may play a role in the regulation of PCOS development. PCOS is frequently associated with obesity, high BMI index and consequently with increased risk of metabolic disorders. The aim of the present study was to evaluate PAI-1 levels, genetic influence of the carriage of 675 4G/5G polymorphism in PAI-1 gene and leptin as a marker of obesity in the development of PCOS. Methods: Genotyping in 84 patients with PCOS and PCO and 100 healthy control subjects to detect single nucleotide deletion 675 G in the promoter of PAI-1 gene. The present study provides evidence that SNP 4G in the PAI-1 gene is associated with early pregnancy losses in patients with polycystosis. Further to this, there is a correlation between leptin levels, PAI-1 levels and BMI in the patients with PCOS, which confirms the role of obesity as a risk factor for PCOS.

Keywords: carriage of 675 4G/5G polymorphism, PCOS, early pregnancy losses, PAI-1 gene

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Abbasali Raz, Javad Dadgar Pakdel, Kourosh Azizi, Aboozar Soltani, Mohammad Djaefar Moemenbellah-Fard

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Background: Maggot debridement therapy is an appropriate, effective, and controlled method using sterilized larvae of Luciliasericata (L.sericata) to treat wounds. Netrin-A is an enzyme in the Laminins family which secreted from salivary gland of L.sericata with a central role in neural regeneration and angiogenesis. This study aimed to production of new recombinant Netrin-A protein of Luciliasericata larvae by baculovirus expression vector system (BEVS) in SF9. Material and methods: In the first step, gene structure was subjected to the in silico studies, which were include determination of Antibacterial activity, Prion formation risk, homology modeling, Molecular docking analysis, and Optimization of recombinant protein. In the second step, the Netrin-A gene was cloned and amplified in pTG19 vector. After digestion with BamH1 and EcoR1 restriction enzymes, it was cloned in pFastBac HTA vector. It was then transformed into DH10Bac competent cells, and the recombinant Bacmid was subsequently transfected into insect Sf9 cells. The expressed recombinant Netrin-A was thus purified in the Ni-NTA agarose. This protein evaluation was done using SDS-PAGE and western blot, respectively. Finally, its concentration was calculated with the Bradford assay method. Results: The Bacmid vector structure with Netrin-A was successfully constructed and then expressed as Netrin-A protein in the Sf9 cell lane. The molecular weight of this protein was 52 kDa with 404 amino acids. In the in silico studies, fortunately, we predicted that recombinant LSNetrin-A have Antibacterial activity and without any prion formation risk.This molecule hasa high binding affinity to the Neogenin and a lower affinity to the DCC-specific receptors. Signal peptide located between amino acids 24 and 25. The concentration of Netrin-A recombinant protein was calculated to be 48.8 μg/ml. it was confirmed that the characterized gene in our previous study codes L. sericata Netrin-A enzyme. Conclusions: Successful generation of the recombinant Netrin-A, a secreted protein in L.sericata salivary glands, and because Luciliasericata larvae are used in larval therapy. Therefore, the findings of the present study could be useful to researchers in future studies on wound healing.

Keywords: blowfly, BEVS, gene, immature insect, recombinant protein, Sf9

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Authors: P. Afsharian, S. Mousazadeh, M. Shahhoseini, R. Aflatoonian

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Introduction: Matrix MetalloProteinases (MMPs) degrade extracellular matrix components to provide normal remodeling and contribute to pathological tissue destruction and cell migration in endometriosis. It is accepted that MMPs are resistant to suppression by progesterone in endometriotic tissues. The physiological effects of progesterone are mediated by its two progesterone receptor (PGR) isoforms, namely PGR-A and PGR-B. The capacity of progesterone affect to gene expression is dependent on the PGR-A/PGR-B ratio. The imbalance ratio in endometriotic tissue may be an important mechanism to be resulted in Progesterone resistance and modify progesterone action via differential regulation of specific progesterone response genes and improve endometriosis disease. Material and methods: RNA was extracted from twenty ectopic (endometriotic) and eutopic (endometrial) tissue samples of women undergoing laparoscopy for endometriosis and 20 healthy fertile women at Royan Institute, Tehran, Iran. Analysis of PGR-A, PGR-B, MMP-2 and MMP-9 mRNA expression was performed using Real-time PCR in ectopic and eutopic tissues. Then, Statistical analysis was calculated according to the 2-ΔΔCT equation for all samples. Results: Quantitative RT–PCR analyses of PGR-A and PGR-B mRNA revealed that there were differences in both isoformes of PGRs mRNA expressions between ectopic and control eutopic tissues. We were able to demonstrate low expression levels of PGR-B isoforms in ectopic tissues. Although, PGR-A expression was significantly higher in the same ectopic samples compare to controls.This method permitted us to demonstrate significant overexpression of MMP-2 and MMP-9 in ectopic samples compared to control endometrial tissues, as well. Conclusions: Our data suggest that low expression levels of PGR-B and overexpression of PGR-A can alter PGR-A/PGR-B ratio in endometriotic ectopic tissues. Imbalance ratio of PGRs in endometriotic tissue may be able to consequence MMP-2 and MMP-9 overexpression which can be important in pathogenesis and treatment of disease.

Keywords: endometriosis, matrix metalloproteinases, progesterone receptor -A and -B, PGR-A/PGR-B ratio

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Authors: M. Al Zallouha, Y. Landkocz, J. Brunet, R. Cousin, J. M. Halket, E. Genty, P. J. Martin, A. Verdin, D. Courcot, S. Siffert, P. Shirali, S. Billet

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Toluene is one of the most used Volatile Organic Compounds (VOCs) in the industry. Amongst VOCs, Benzene, Toluene, Ethylbenzene and Xylenes (BTEX) emitted into the atmosphere have a major and direct impact on human health. It is, therefore, necessary to minimize emissions directly at source. Catalytic oxidation is an industrial technique which provides remediation efficiency in the treatment of these organic compounds. However, during operation, the catalysts can release some compounds, called byproducts, more toxic than the original VOCs. The catalytic oxidation of a gas stream containing 1000ppm of toluene on Pd/α-Al2O3 can release a few ppm of benzene, according to the operating temperature of the catalyst. The development of new catalysts must, therefore, include chemical and toxicological validation phases. In this project, A549 human lung cells were exposed in air/liquid interface (Vitrocell®) to gas mixtures derived from the oxidation of toluene with a catalyst of Pd/α-Al2O3. Both exposure concentrations (i.e. 10 and 100% of catalytic emission) resulted in increased gene expression of Xenobiotics Metabolising Enzymes (XME) (CYP2E1 CYP2S1, CYP1A1, CYP1B1, EPHX1, and NQO1). Some of these XMEs are known to be induced by polycyclic organic compounds conventionally not searched during the development of catalysts for VOCs degradation. The increase in gene expression suggests the presence of undetected compounds whose toxicity must be assessed before the adoption of new catalyst. This enhances the relevance of toxicological validation of such systems before scaling-up and marketing.

Keywords: BTEX toxicity, air/liquid interface cell exposure, Vitrocell®, catalytic oxidation

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Authors: Mrinal Jana, Geetanjali Panda

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In this paper a methodology is developed to solve a nonlinear fractional programming problem in which the coefficients of the objective function and constraints are interval parameters. This model is transformed into a general optimization problem and relation between the original problem and the transformed problem is established. Finally the proposed methodology is illustrated through a numerical example.

Keywords: fractional programming, interval valued function, interval inequalities, partial order relation

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Authors: Cheng-Yen Lu, Chin-Yuan Hsu

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Ambient temperature reduction (ATR) can extend the lifespan of an annual fish (Nothobranchius rachovii), but the underlying mechanism is unknown. In this study, the expression, concentration, and activity of cellular-degraded molecules were evaluated in the muscle of N. rachovii reared under high (30 °C), moderate (25 °C), and low (20 °C) ambient temperatures by biochemical techniques. The results showed that (i) the activity of the 20S proteasome, the expression of microtubule-associated protein 1 light chain 3-II (LC3-II), the expression of lysosome-associated membrane protein type 2a (Lamp 2a), and lysosome activity increased with ATR; (ii) the expression of the 70 kD heat shock cognate protein (Hsc 70) decreased with ATR; (iii) the expression of the 20S proteasome, the expression of lysosome-associated membrane protein type 1 (Lamp 1), the expression of molecular target of rapamycin (mTOR), the expression of phosphorylated mTOR (p-mTOR), and the p-mTOR/mTOR ratio did not change with ATR. These findings indicated that ATR activated the activity of proteasome, macroautophagy, and chaperone-mediated autophagy. Taken together these data reveal that ATR likely activates cellular degradation activity to extend the lifespan of N. rachovii.

Keywords: ambient temperature reduction, autophagy, degradation activity, lifespan, proteasome

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Authors: Muhammad Imran, Sarfraz Shafiq, Xiangru Tang

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Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcripts variability and proteome diversity in plants. Fragrant rice (Oryza sativa L.) has a high economic and nutritional value, and the application of micronutrients regulate 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular process in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars, indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars, and Zn treatment altered the editing frequency of SNPs in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway may also be post-transcriptionally regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis in fragrant rice.

Keywords: fragrant rice, 2-acetyl-1-pyrroline, gene expression, zinc, alternative splicing, SNPs

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Authors: M. Aherrahrou

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Moroccan education is currently facing many difficulties and problems due to traditional methods of teaching. Neuro -Linguistic Programming (NLP) appears to hold much potential for education at all levels. In this paper, the major aim is to explore the effect of certain Neuro -Linguistic Programming techniques in one educational institution in Morocco. Quantitative and Qualitative methods are used. The findings prove the effectiveness of this new approach regarding Moroccan education, and it is a promising tool to improve the quality of learning.

Keywords: learning and teaching environment, Neuro- Linguistic Programming, education, quality of learning

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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: Romeo A. Botes, Imelda Smit

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The demands of an ever changing and complex higher education environment, along with the profile of modern learners challenge current approaches to assessment and feedback. More learners enter the education system every year. The younger generation expects immediate feedback. At the same time, feedback should be meaningful. The assessment of practical activities in programming poses a particular problem, since both lecturers and learners in the information and computer science discipline acknowledge that paper-based assessment for programming subjects lacks meaningful real-life testing. At the same time, feedback lacks promptness, consistency, comprehensiveness and individualisation. Most of these aspects may be addressed by modern, technology-assisted assessment. The focus of this paper is the continuous development of an artefact that is used to assist the lecturer in the assessment and feedback of practical programming activities in a senior database programming class. The artefact was developed using three Design Science Research cycles. The first implementation allowed one programming activity submission per assessment intervention. This pilot provided valuable insight into the obstacles regarding the implementation of this type of assessment tool. A second implementation improved the initial version to allow multiple programming activity submissions per assessment. The focus of this version is on providing scaffold feedback to the learner – allowing improvement with each subsequent submission. It also has a built-in capability to provide the lecturer with information regarding the key problem areas of each assessment intervention.

Keywords: programming, computer-aided assessment, technology-assisted assessment, programming assessment software, design science research, mixed-method

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Authors: Anahit Hakobjanyan, Zdenka Navratilova, Gabriela Strakova, Martin Petrek

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Aging has a suppressive influence on human immune cells. Apoptosis may play important role in age-dependent immunosuppression and lymphopenia. Prevention of apoptosis may be promoted by BCL2-dependent and BCL2-independent manner. BCL2 is an antiapoptotic factor that has an antioxidative role by locating the glutathione at mitochondria and repressing oxidative stress. STAT3 may suppress apoptosis in BCL2-independent manner and promote cell survival blocking cytochrome-c release and reducing ROS production. The aim of our study was to estimate the influence of aging on BCL2-dependent and BCL2-independent prevention of apoptosis via measurement of BCL2 and STAT3 mRNAs expressions. The study was done on Armenian population (2 groups: 37 healthy young (mean age±SE; min/max age, male/female: 37.6±1.1; 20/54, 15/22), 28 healthy aged (66.7±1.5; 57/85, 12/16)). mRNA expression in peripheral blood leukocytes (PBL) was determined by RT-PCR using PSMB2 as the reference gene. Statistical analysis was done with Graph-Pad Prism 5; P < 0.05 considered as significant. The expression of BCL2 mRNA was lower in aged group (0.199) compared with young ones (0.643)(p < 0.01). Decrease expression was also recorded for female and male subgroups (p < 0.01). The expression level of STAT3 mRNA was increased (young, 0.228; aged, 0.428) (p < 0.05) during aging (in the whole age group and male/female subgroups). Decreased level of BCL2 mRNA may indicate about the suppression of BCL2-dependent prevention of apoptosis during aging in peripheral blood leukocytes. At the same time increased the level of STAT3 may suggest about activation of BCL2-independent prevention of apoptosis during aging.

Keywords: BCL2, STAT3, aging, apoptosis

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Authors: Mei Chen, Yingping Hou, Michelle Hao, Soheil Aghamohammadzadeh, Esteban Terzo, Roger Clark, Vijay Modur

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Background: Recessive Dystrophic Epidermolysis Bullosa (RDEB) is a genetic skin condition characterized by skin tearing and unremitting blistering upon minimal trauma. Repeated blistering, fibrosis, and scarring lead to aggressive squamous cell carcinoma later in life. RDEB is caused by mutations in the COL7A1 gene encoding collagen type VII (C7), the major component of anchoring fibrils mediating epidermis-dermis adherence. Nonsense mutations in the COL7A1 gene of a subset of RDEB patients leads to premature termination codons (PTC). Similarly, most Junctional Epidermolysis Bullosa (JEB) cases are caused by nonsense mutations in the LAMB3 gene encoding the β3 subunit of laminin 332. Currently, there is an unmet need for the treatment of RDEB and JEB. Zikani Therapeutics has discovered an array of macrocyclic compounds with ring structures similar to macrolide antibiotics that can facilitate readthrough activity of nonsense mutations in the COL7A1 and LAMB3 genes by acting as Ribosome Modulating Agents (RMAs). The medicinal chemistry synthetic advancements of these macrocyclic compounds have allowed targeting the human ribosome while preserving the structural elements responsible for the safety and pharmacokinetic profile of clinically used macrolide antibiotics. Methods: C7 expression was used as a measure of readthrough activity by immunoblot assays in two primary human fibroblasts from RDEB patients (R578X/R578X and R163X/R1683X-COL7A1). Similarly, immunoblot assays in C325X/c.629-12T > A-LAMB3 keratinocytes were used to measure readthrough activity for JEB. The relative readthrough activity of each compound was measured relative to Gentamicin. An imaging-based fibroblast migration assay was used as an assessment of C7 functionality in RDEB-fibroblasts over 16-20 hrs. The incubation period for the above experiments was 48 hrs for RDEB fibroblasts and 72 hours for JEB keratinocytes. Results: 9 RMAs demonstrated increased protein expression in both patient RDEB fibroblasts. The highest readthrough activity at tested concentrations without cytotoxicities increased protein expression up to 179% of Gentamicin (400 µg/ml), with favored readthrough activity in R163X/R1683X-COL7A1 fibroblasts. Concurrent with protein expression, fibroblast hypermotility phenotype observed in RDEB was rescued by reducing motility by ~35% to WT levels (the same level as 690 µM Gentamicin treated cells). Laminin β3 expression was also shown to be increased by 6 RMAs in keratinocytes to 33-83% of (400 µg/ml) Gentamicin. Conclusions: To date, 9 RMAs have been identified that enhance the expression of functional C7 in a mutation-dependent manner in two different RDEB patient fibroblast backgrounds (R578X/R578X and R163X/R1683X-COL7A1). A further 6 RMAs have been identified that enhance the readthrough of C325X-LAMB3 in JEB patient keratinocytes. Based on the clinical trial conducted by us with topical gentamycin in 2017, Zikani’s RMAs achieve clinically significant levels of read-through for the treatment of recessive dystrophic and Junctional Epidermolysis Bullosa.

Keywords: epidermolysis bullosa, nonsense mutation, readthrough, ribosome modulation

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Authors: Ahmad Ali Shahid, Mukhtar Ahmed

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The demand for long staple fiber having better strength and length is increasing with the introduction of modern spinning and weaving industry in Pakistan. Work on gene discovery from developing cotton fibers has helped to identify dozens of genes that take part in cotton fiber development and several genes have been characterized for their role in fiber development. Sucrose synthase (SuS) is a key enzyme in the metabolism of sucrose in a plant cell, in cotton fiber it catalyzes a reversible reaction, but preferentially converts sucrose and UDP into fructose and UDP-glucose. UDP-glucose (UDPG) is a nucleotide sugar act as a donor for glucose residue in many glycosylation reactions and is essential for the cytosolic formation of sucrose and involved in the synthesis of cell wall cellulose. The study was focused on successful Agrobacterium-mediated stable transformation of SuS gene in pCAMBIA 1301 into cotton under a CaMV35S promoter. Integration and expression of the gene were confirmed by PCR, GUS assay, and real-time PCR. Young leaves of SuS overexpressing lines showed increased total soluble sugars and plant biomass as compared to non-transgenic control plants. Cellulose contents from fiber were significantly increased. SEM analysis revealed that fibers from transgenic cotton were highly spiral and fiber twist number increased per unit length when compared with control. Morphological data from field plants showed that transgenic plants performed better in field conditions. Incorporation of genes related to cotton fiber length and quality can provide new avenues for fiber improvement. The utilization of this technology would provide an efficient import substitution and sustained production of long-staple fiber in Pakistan to fulfill the industrial requirements.

Keywords: agrobacterium-mediated transformation, cotton fiber, sucrose synthase gene, staple length

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Authors: Petra Borilova Linhartova, Michaela Ruckova, Sabina Sevcikova, Natalie Mlcuchova, Jan Bohm, Katerina Zukalova, Monika Vlachova, Jiri Dolina, Lumir Kunovsky, Radek Kroupa, Zdenek Pavlovsky, Zdenek Danek, Tereza Deissova, Lydie Izakovicova Holla, Ondrej Slaby, Zdenek Kala

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Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that frequently develops from Barrett's esophagus (BE), a premalignant pathologic change occurring in the lower end of the esophagus. Specific microRNAs (miRNAs), small non-coding RNAs that function as posttranscriptional regulators of gene expression, were repeatedly proved to play key roles in the pathogenesis of these diseases. This pilot study aimed to analyze four selected miRNAs in esophageal tissues from healthy controls (HC) and patients with reflux esophagitis (RE)/BE/EAC, as well as to compare expression at the site of Barrett's mucosa/adenocarcinoma and healthy esophageal tissue outside the area of the main pathology in patients with BE/EAC. In this pilot study, 22 individuals (3 HC, 8 RE, 5 BE, 6 EAC) were included and endoscopically examined. RNA was isolated from the fresh-frozen esophageal tissue (stored in the RNAlater™ Stabilization Solution −70°C) using the AllPrep DNA/RNA/miRNA Universal Kit. Subsequent RT-qPCR analysis was performed using selected TaqMan MicroRNA Assays for miR-21, miR-34a, miR-196a, miR-196b, and endogenous control (RNU44). While the expression of miR-21 in the esophageal tissue with the main pathology was decreased in BE and EAC patients in comparison to the group of HC and RE patients (p=0.01), the expression of miR-196a was increased in the BE and EAC patients (p<0.01). Correlations between those miRNAs expression in tissue and severity of diagnosis were observed (p<0.05). In addition, miR-196a was significantly more expressed at the site with the main pathology than in paired adjacent esophageal tissue in BE and EAC patients (p<0.01). In conclusion, our pilot results showed that miR-196a, which regulates the proliferation, invasion, and migration (and was previously associated with esophageal squamous cell carcinoma and marked as a potential therapeutic target), could be a diagnostic tissue biomarker for BE and EAC as well.

Keywords: microRNA, barrett´s esophagus, esophageal adenocarcinoma, biomarker

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Authors: Farideh K. Khosroushahi, Serkan Erdal, Mucip Geni̇şel

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Soil salinity is one of the major abiotic stress factors that restricts arable land and reduces crop productivity worldwide. High salt concentration adversely affects plant growth and development inducing water deficit, ionic toxicity, nutrient imbalance, and lead to oxidative stress. Although the stimulating role of mammalian sex hormones on various biological and biochemical processes under normal and stress condition have been proven, there is no study regarding with these hormone's effect on modulation of the alternative respiration pathway and AOX gene expression. In this study, changes in alternative respiration pathway in leaves of maize seedlings under salinity and the possible modulating effect of estrogen on these changes were investigated. Maize seedlings were grown in a hydroponic media for 11 days and then were exposed to salt stress for 3 days after being sprayed estrogen. The data obtained from oxygen consumption revealed that salt stress elevated cellular respiration value in the leaves. In addition, a marked increase was observed at alternative respiration level in salt-stressed seedlings. Compared to salt application alone, supplementation with estrogen resulted in a significant rise in alternative oxidase (AOX) activities. Similarly, while salt stress caused to rise in expressions of AOX gene compared to control seedlings, estrogen application resulted in further activation of these genes’ expression compared to stressed-seedlings alone. These data revealed that mitigating role of estrogen against the detrimental effects of salt stress is linked to modulation of alternative respiration pathway.

Keywords: alternative oxidase, estrogen, Ssalt stress, AOX, maize

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Authors: Rita Garcia

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Intelligent Programming Tutors, IPTs, are supplemental educational devices that assist in teaching software development. These systems provide customized learning allowing the user to select the presentation pace, pedagogical strategy, and to recall previous and additional teaching materials reinforcing learning objectives. In addition, IPTs automatically records individual’s progress, providing feedback to the instructor and student. These tutoring systems have an advantage over Tutoring Systems because Intelligent Programming Tutors are not limited to one teaching strategy and can adjust when it detects the user struggling with a concept. The Intelligent Programming Tutor is a category of Intelligent Tutoring Systems, ITS. ITS are available for many fields in education, supporting different learning objectives and integrate into other learning tools, improving the student's learning experience. This study provides a comparison of the IPTs currently adopted by the educational community and will focus on the different teaching methodologies and programming languages. The study also includes the ability to integrate the IPT into other educational technologies, such as massive open online courses, MOOCs. The intention of this evaluation is to determine one system that would best serve in a larger ongoing research project and provide findings for other institutions looking to adopt an Intelligent Programming Tutor.

Keywords: computer education tools, integrated software development assistance, intelligent programming tutors, tutoring systems

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Authors: Vera Lukasova, Eva Filova, Jana Dankova, Vera Sovkova, Matej Daniel, Michala Rampichova

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Proper bone implants should promote fast adhesion of cells, stimulate cell differentiation and support the formation of bone tissue. Nowadays titanium is used as a biocompatible material capable of bone tissue integration. This study was focused on comparison of bioactive properties of two titanium alloys - beta titanium alloy Ti36Nb6Ta and standard medical titanium alloy Ti6A14V. The advantage of beta titanium alloy Ti36Nb6Ta is mainly that this material does not contain adverse elements like vanadium or aluminium. Titanium alloys were sterilized in ethanol, placed into 48 well plates and seeded with porcine mesenchymal stem cells. Cells were cultivated for 14 days in standard growth cultivation media with osteogenic supplements. Cell metabolic activity was quantified using MTS assay (Promega). Cell adhesion on day 1 and cell proliferation on further days were verified immunohistochemically using beta-actin monoclonal antibody and secondary antibody conjugated with AlexaFluor®488. Differentiation of cells was evaluated using alkaline phosphatase assay. Additionally, gene expression of collagen I was measured by qRT-PCR. Porcine mesenchymal stem cells adhered and spread well on beta titanium alloy Ti36Nb6Ta on day 1. During the 14 days’ time period the cells were spread confluently on the surface of the beta titanium alloy Ti36Nb6Ta. The metabolic activity of cells increased during the whole cultivation period. In comparison to standard medical titanium alloy Ti6A14V, we did not observe any differences. Moreover, the expression of collagen I gene revealed no statistical differences between both titanium alloys. Therefore, a beta titanium alloy Ti36Nb6Ta promotes cell adhesion, metabolic activity, proliferation and collagen I expression equally to standard medical titanium alloy Ti6A14V. Thus, beta titanium is a suitable material that provides sufficient biocompatible properties. This project was supported by the Czech Science Foundation: grant No. 16-14758S.

Keywords: beta titanium alloy, biocompatibility, differentiation, mesenchymal stem cells

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Authors: Norihiro Kato, Yuriko Takayama

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Some gram-negative bacteria enable the simultaneous activation of gene expression involved in N-acylhomoserine lactone (AHL) dependent cell-to-cell communication system. Such regulatory system for the bacterial group behavior is termed as quorum sensing (QS) because a diffusible AHL signal can accumulate around the cell during the increase of the cell density and trigger activation of the sequential QS process. By blocking the QS, the expression of diverse genes related to infection, antibiotic production, and biofilm formation is inhibited. Conditioning of QS by regulation of the DNA-receptor-AHL interaction is a potential target for enhancing host defenses against pathogenicity. We focused on engineered application of transcriptional regulator SpnR produced in opportunistic human pathogen Serratia marcescens. The SpnR can interact with AHL signals at an N-terminal domain and also with a promoter region of a QS target gene at a C-terminal domain. As the initial process of the QS activation, the SpnR forms a complex with the AHL to enhance the expression of pig cluster; the SpnR normally acts as an activator for the expression of the QS-dependent gene. In this research, we attempt to artificially control QS by changing the role of SpnR. The QS-dependent prodigiosin production is expected to inhibit by externally added SpnR in the culture broth of AS-1 strain because the AHL concentration was kept below the threshold by AHL-SpnR complex formation. Maltose-binding protein (MBP)-tagged SpnR (MBP-SpnR) was overexpressed in Escherichia coli and purified using an affinity chromatography equipped with an amylose resin column. The specific interaction between AHL and MBP-SpnR was demonstrated by quartz crystal microbalance (QCM) sensor. AHL with amino end-group was coupled with COOH-terminated self-assembled monolayer prepared on a gold electrode of 27-MHz quartz crystal sensor using water-soluble carbodiimide. After the injection of MBP-SpnR into a cup-type sensor cell filled with the buffer solution, time course of resonant frequency change (ΔFs) was determined. A decrease of ΔFs clearly showed the uptake of MBP-SpnR onto the AHL-immobilized electrode. Furthermore, no binding affinity was observed after the heat-inactivation of MBP-SpnR at 80ºC. These results suggest that MBP-SpnR possesses a specific affinity for AHL. MBP-SpnR was added to the culture medium as an AHL trap to study inhibitory effects on intracellularly accumulated prodigiosin. With approximately 2 µM MBP-SpnR, the amount of prodigiosin induced was half that of the control without any additives. In conclusion, the function of SpnR could be switched by adding it to the cell culture. Exogenously added MBP-SpnR possesses high affinity for AHL derived from cells and acts as an inhibitor of AHL-mediated QS.

Keywords: intracellular signaling, microbial biotechnology, quorum sensing, transcriptional regulator

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: Irfan Ali, Srikant Gupta, Aquil Ahmed

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Every country needs a sustainable development (SD) for its economic growth by forming suitable policies and initiative programs for the development of different sectors of the country. This paper is comprised of modeling and optimization of different sectors of India that form a multi-criterion model. In this paper, we developed a fractional goal programming (FGP) model that helps in providing the efficient allocation of resources simultaneously by achieving the sustainable goals in gross domestic product (GDP), electricity consumption (EC) and greenhouse gasses (GHG) emission by the year 2030. Also, a weighted model of FGP is presented to obtain varying solution according to the priorities set by the policy maker for achieving future goals of GDP growth, EC, and GHG emission. The presented models provide a useful insight to the decision makers for implementing strategies in a different sector.

Keywords: sustainable and economic development, multi-objective fractional programming, fuzzy goal programming, weighted fuzzy goal programming

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Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

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Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

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Authors: Cristina-Maria Păcurar

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The paper presents an original Python-based application that outlines the advantages of combining some elementary notions of mathematics with the study of a programming language. The application support refers to some of the first lessons of analytic geometry, meaning conics and quadrics and their reduction to a standard form, as well as some related notions. The chosen programming language is Python, not only for its closer to an everyday language syntax – and therefore, enhanced readability – but also for its highly reusable code, which is of utmost importance for a mathematician that is accustomed to exploit already known and used problems to solve new ones. The purpose of this paper is, on one hand, to support the idea that one of the most appropriate means to initiate one into programming is throughout mathematics, and reciprocal, one of the most facile and handy ways to assimilate some basic knowledge in the study of mathematics is to apply them in a personal project. On the other hand, besides being a mean of learning both programming and analytic geometry, the application subject to this paper is itself a useful tool for it can be seen as an independent original Python package for analytic geometry.

Keywords: analytic geometry, conics, python, quadrics

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Authors: Sirous Eydivandi

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Diacylglycerol-O-acyltransferase (DGAT1) gene encodes diacylglycerol transferase enzyme that plays an important role in glycerol lipid metabolism. DGAT1 is considered to be the key enzyme in controlling the synthesis of triglycerides in adipocytes. This enzyme catalyzes the final step of triglyceride synthesis (transform triacylglycerol (DAG) into triacylglycerol (TAG). A total of 20 DGAT1 gene sequences and corresponding amino acids belonging to 4 species include cattle, goats, sheep and yaks were analyzed, and the differentiation within and among the species was also studied. The length of the DGAT1 gene varies greatly, from 1527 to 1785 bp, due to deletion, insertion, and stop codon mutation resulting in elongation. Observed genetic diversity was higher among species than within species, and Goat had more polymorphisms than any other species. Novel amino acid variation sites were detected within several species which might be used to illustrate the functional variation. Differentiation of the DGAT1 gene was obvious among species, and the clustering result was consistent with the taxonomy in the National Center for Biotechnology Information.

Keywords: DGAT1gene, bioinformatic, ruminnants, biotechnology information

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Authors: D. K. Rao, M. G. M. Khan, K. G. Reddy

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The focus of this paper is to develop a technique of solving a combined problem of determining Optimum Strata Boundaries (OSB) and Optimum Sample Size (OSS) of each stratum, when the population understudy is skewed and the study variable has a Pareto frequency distribution. The problem of determining the OSB is formulated as a Mathematical Programming Problem (MPP) which is then solved by dynamic programming technique. A numerical example is presented to illustrate the computational details of the proposed method. The proposed technique is useful to obtain OSB and OSS for a Pareto type skewed population, which minimizes the variance of the estimate of population mean.

Keywords: stratified sampling, optimum strata boundaries, optimum sample size, pareto distribution, mathematical programming problem, dynamic programming technique

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Authors: Nebras Gharbi, Itebeddine Ghorbel

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In the latest years and with the advancements of the multicore computing world, the constraint programming community tried to benefit from the capacity of new machines and make the best use of them through several parallel schemes for constraint solving. In this paper, we propose a survey of the different proposed approaches to solve Constraint Satisfaction Problems using parallel architectures. These approaches use in a different way a parallel architecture: the problem itself could be solved differently by several solvers or could be split over solvers.

Keywords: constraint programming, parallel programming, constraint satisfaction problem, speed-up

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Authors: Ghussoun Al-Jeiroudi

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Stochastic programming is one of the powerful technique which is used to solve real-life problems. Hence, the data of real-life problems is subject to significant uncertainty. Uncertainty is well studied and modeled by stochastic programming. Each day, problems become bigger and bigger and the need for a tool, which does deal with large scale problems, increase. Interior point method is a perfect tool to solve such problems. Interior point method is widely employed to solve the programs, which arise from stochastic programming. It is an iterative technique, so it is required a starting point. Well design starting point plays an important role in improving the convergence speed. In this paper, we propose a starting point for interior point method for multistage stochastic programming. Usually, the optimal solution of stage k+1 is used as starting point for the stage k. This point has the advantage of being close to the solution of the current program. However, it has a disadvantage; it is not in the feasible region of the current program. So, we suggest to take this point and modifying it. That is by adding to it a vector in the null space of the matrix of the unchanged constraints because the solution will change only in the null space of this matrix.

Keywords: interior point methods, stochastic programming, null space, starting points

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Authors: Yi H. Wong, Li L. Chan, Chee O. Leong, Stephen Ambu, Joon W. Mak, Priyadashi S. Sahu

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Background: Acanthamoeba is a free-living opportunistic protist which is ubiquitously distributed in the environment. Virulent Acanthamoeba can cause fatal encephalitis in immunocompromised patients and potential blinding keratitis in immunocompetent contact lens wearers. Approximately 24 species have been identified but only the A. castellanii, A. polyphaga and A. culbertsoni are commonly associated with human infections. Until to date, the precise molecular basis for Acanthamoeba pathogenesis remains unclear. Previous studies reported that Acanthamoeba virulence can be diminished through prolonged axenic culture but revived through serial mouse passages. As no clear explanation on this reversible pathogenesis is established, hereby, we postulate that the epigenetic regulators, DNA-methyltransferases (DNMT) and histone-deacetylases (HDAC), could possibly be involved in granting the virulence plasticity of Acanthamoeba spp. Methods: Four rounds of mouse passages were conducted to revive the virulence potential of the virulence-attenuated Acanthamoeba castellanii strain (ATCC 50492). Briefly, each mouse (n=6/group) was inoculated intraperitoneally with Acanthamoebae cells (2x 105 trophozoites/mouse) and incubated for 2 months. Acanthamoebae cells were isolated from infected mouse organs by culture method and subjected to subsequent mouse passage. In vitro cytopathic, encystment and gelatinolytic assays were conducted to evaluate the virulence characteristics of Acanthamoebae isolates for each passage. PCR primers which targeted on the 2 members (DNMT1 and DNMT2) and 5 members (HDAC1 to 5) of the DNMT and HDAC gene families respectively were custom designed. Quantitative real-time PCR (qPCR) was performed to detect and quantify the relative expression of the two gene families in each Acanthamoeba isolates. Beta-tubulin of A. castellanii (Genbank accession no: XP_004353728) was included as housekeeping gene for data normalisation. PCR mixtures were also analyzed by electrophoresis for amplicons detection. All statistical analyses were performed using the paired one-tailed Student’s t test. Results: Our pathogenicity tests showed that the virulence-reactivated Acanthamoeba had a higher degree of cytopathic effect on vero cells, a better resistance to encystment challenge and a higher gelatinolytic activity which was catalysed by serine protease. qPCR assay showed that DNMT1 expression was significantly higher in the virulence-reactivated compared to the virulence-attenuated Acanthamoeba strain (p ≤ 0.01). The specificity of primers which targeted on DNMT1 was confirmed by sequence analysis of PCR amplicons, which showed a 97% similarity to the published DNA-methyltransferase gene of A. castellanii (GenBank accession no: XM_004332804.1). Out of the five primer pairs which targeted on the HDAC family genes, only HDAC4 expression was significantly difference between the two variant strains. In contrast to DNMT1, HDAC4 expression was much higher in the virulence-attenuated Acanthamoeba strain. Conclusion: Our mouse passages had successfully restored the virulence of the attenuated strain. Our findings suggested that DNA-methyltransferase (DNMT1) and histone deacetylase (HDAC4) expressions are associated with virulence potential of Acanthamoeba spp.

Keywords: acanthamoeba, DNA-methyltransferase, histone deacetylase, virulence-associated proteins

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Authors: Debora P. Arce, Flavia J. Krsticevic, Marco R. Bertolaccini, Joaquín Ezpeleta, Estela M. Valle, Sergio D. Ponce, Elizabeth Tapia

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Small Heat Shock Proteins (sHSPs) are low molecular weight chaperones that play an important role during stress response and development in all living organisms. Fruit maturation and oxidative stress can induce sHSP synthesis both in Arabidopsis and tomato plants. RNA-Seq technology is becoming widely used in various transcriptomics studies; however, analyzing and interpreting the RNA-Seq data face serious challenges. In the present work, we de novo assembled the Solanum lycopersicum transcriptome for three different maturation stages (mature green, breaker and red ripe). Differential gene expression analysis was carried out during tomato fruit development. We identified 12 sHSPs differentially expressed that might be involved in breaker and red ripe fruit maturation. Interestingly, these sHSPs have different subcellular localization and suggest a complex regulation of the fruit maturation network process.

Keywords: sHSPs, maturation, tomato, RNA-Seq, assembly

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Authors: T. O. Ajewole, K. S. Olorunmiaye, D. A. Animasaun, M. Okpeku

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Drought impact on the production of food crops for the benefit of mankind cannot be overemphasized. This study shows the different kind of genes expressed at various level of drought regimes on Basella alba and rubra using a real-time PCR machine. The planting was done in the screen house while the gene expression study was carried out in the laboratory. Sandy-loamy soil was collected and four levels of drought regime was used as treatment and a control experiment was set up for the two vegetables. Drought interval of 5, 10, 15 and 20 days were used as treatments while a control experiment which was not starved of water at any point was also set up, five replicates were set up for each treatment. Stress was introduced at 12 Weeks after planting (WAP). From the result of this study, Basella alba shows the highest amplicon size of 34.6 and 52.32 for GmPCS5 and HVA1 respectively which by implication means these genes were expressed the more as the stress period interval increases.

Keywords: water stress, basella alba, basella rubra, HVA1

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Authors: Sun Gang

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A variety of functional spaces are distributed on the vast mountain waterfront. Their functional positioning presents a spontaneous form of settlement space, and the construction features show a passive impact on the natural environment. As the precious heritage of inheriting human civilization and promoting historical culture, the traditional settlement space in mountainous areas is also the local expression of landscape pattern pattern gene. Under the impact of rapid urban construction and the stimulation of the transformation of social consumption demand, the original texture, scale and ecology of the traditional mountain settlement space, especially the historical and cultural settlement space, have been affected, and the decline of characteristics hinders the development. This paper selects Anju Ancient Town, the fourth largest ancient city in China, which is located in the city of mountains and waters as the research object, and combines spatial analysis and other methods to study the characteristics and causes of its spatial morphology, analyze the internal logic in its formation and development process, build a genetic analysis map, explore the possibility of settlement inheritance and development, and provide reference for the construction, protection and inheritance of traditional mountain settlements.

Keywords: mountain traditional settlement, historical and cultural settlement space, spatial form, spatial gene

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