Search results for: Gene Profiling

Authors: Isam A. Mohamed Ahmed, Jiro Arima, Tsuyoshi Ichiyanagi, Emi Sakuno, Nobuhiro Mori

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The aim of this study was to screen for microorganism that able to utilize 3-N-trimethylamino-1-propanol (homocholine) as a sole source of carbon and nitrogen. The aerobic degradation of homocholine has been found by a gram-positive Rhodococcus sp. bacterium isolated from soil. The isolate was identified as Rhodococcus sp. strain A4 based on the phenotypic features, physiologic and biochemical characteristics, and phylogenetic analysis. The cells of the isolated strain grown on both basal-TMAP and nutrient agar medium displayed elementary branching mycelia fragmented into irregular rod and coccoid elements. Comparative 16S rDNA sequencing studies indicated that the strain A4 falls into the Rhodococcus erythropolis subclade and forms a monophyletic group with the type-strains of R. opacus, and R. wratislaviensis. Metabolites analysis by capillary electrophoresis, fast atom bombardment-mass spectrometry, and gas chromatography- mass spectrometry, showed trimethylamine (TMA) as the major metabolite beside β-alanine betaine and trimethylaminopropionaldehyde. Therefore, the possible degradation pathway of trimethylamino propanol in the isolated strain is through consequence oxidation of alcohol group (-OH) to aldehyde (-CHO) and acid (-COOH), and thereafter the cleavage of β-alanine betaine C-N bonds yielded trimethylamine and alkyl chain.

Keywords: Homocholine, 3-N-trimethylamino-1-propanol, Quaternary ammonium compounds, 16S rDNA gene sequence.

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Authors: Hanina M. N., Hairul Shahril M., Mohd Fazrullah Innsan M. F., Ismatul Nurul Asyikin I., Abdul Jalil A. K, Salina M. R., Ahmad I.B.

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Proteins levels produced by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antimicrobial agents or antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics or natural compounds in nature as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was focusing on the effect of essential oils from Cymbopogon flexuosus and C. nardus in regulating proteins production by Bacillus subtilis ATCC 21332. The Minimum Inhibition Concentrations (MICs) of both essential oils on B. subtilis were determined by using microdilution assay, resulting 0.2% and 1.56% for each C. flexuosus and C. nardus subsequently. The bacteria were further exposed to each essential oils at concentration of 0.01XMIC for 2 days. The proteins were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Protein profile showed that a band with approximate size of 250 kD was appeared for the treated bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in stressful condition with the presence of essential oils at low concentration could induce the protein production.

Keywords: Bacillus subtilis ATCC 21332, Cymbopogon essential oils, protein

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Authors: Ratnakar Tripathi, Rajnikant Mishra

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The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Fatma N. Talkhan, H. H. Abo-Assy, K. A. Soliman, Marwa M. Azzam, A. Z. E. Abdelsalam, A. S. Abdel-Razek

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The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.

Keywords: Bacillus thuringiensis, biological control, cry1 genes, multiplex PC, SDS- PAGE analysis.

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Authors: Mukesh Kumar Kirar, Ganga Agnihotri

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This paper investigates the preliminary sizing of generator set to design electrical system at the early phase of a project, dynamic behavior of generator-unit, as well as induction motors, during start-up of the induction motor drives fed from emergency generator unit. The information in this paper simplifies generator set selection and eliminates common errors in selection. It covers load estimation, step loading capacity test, transient analysis for the emergency generator set. The dynamic behavior of the generator-unit, power, power factor, voltage, during Direct-on-Line start-up of the induction motor drives fed from stand alone gene-set is also discussed. It is important to ensure that plant generators operate safely and consistently, power system studies are required at the planning and conceptual design stage of the project. The most widely recognized and studied effect of motor starting is the voltage dip that is experienced throughout an industrial power system as the direct online result of starting large motors. Generator step loading capability and transient voltage dip during starting of largest motor is ensured with the help of Electrical Transient Analyzer Program (ETAP).

Keywords: Sizing, induction motor starting, load estimation, Transient Analyzer Program (ETAP).

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Authors: Parmjit S. Panesar, Rupinder Kaur, Ram S. Singh

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Enzymes are the biocatalysts which catalyze the biochemical processes and thus have a wide variety of applications in the industrial sector. β-Galactosidase (E.C. 3.2.1.23) also known as lactase, is one of the prime enzymes, which has significant potential in the dairy and food processing industries. It has the capability to catalyze both the hydrolytic reaction for the production of lactose hydrolyzed milk and transgalactosylation reaction for the synthesis of prebiotics such as lactulose and galactooligosaccharides. These prebiotics have various nutritional and technological benefits. Although, the enzyme is naturally present in almonds, peaches, apricots and other variety of fruits and animals, the extraction of enzyme from these sources increases the cost of enzyme. Therefore, focus has been shifted towards the production of low cost enzyme from the microorganisms such as bacteria, yeast and fungi. As compared to yeast and bacteria, fungal β-galactosidase is generally preferred as being extracellular and thermostable in nature. Keeping the above in view, the present study was carried out for the isolation of the β-galactosidase producing fungal strain from the food as well as the agricultural wastes. A total of more than 100 fungal cultures were examined for their potential in enzyme production. All the fungal strains were screened using X-gal and IPTG as inducers in the modified Czapek Dox Agar medium. Among the various isolated fungal strains, the strain exhibiting the highest enzyme activity was chosen for further phenotypic and genotypic characterization. The strain was identified as Rhizomucor pusillus on the basis of 5.8s RNA gene sequencing data.

Keywords: β-galactosidase, enzyme, fungus, isolation.

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Authors: Bin Mu, Site Li, Shijin Yuan

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Under the circumstance of environment deterioration, people are increasingly concerned about the quality of the environment, especially air quality. As a result, it is of great value to give accurate and timely forecast of AQI (air quality index). In order to simplify influencing factors of air quality in a city, and forecast the city’s AQI tomorrow, this study used MATLAB software and adopted the method of constructing a mathematic model of PCA-GABP to provide a solution. To be specific, this study firstly made principal component analysis (PCA) of influencing factors of AQI tomorrow including aspects of weather, industry waste gas and IAQI data today. Then, we used the back propagation neural network model (BP), which is optimized by genetic algorithm (GA), to give forecast of AQI tomorrow. In order to verify validity and accuracy of PCA-GABP model’s forecast capability. The study uses two statistical indices to evaluate AQI forecast results (normalized mean square error and fractional bias). Eventually, this study reduces mean square error by optimizing individual gene structure in genetic algorithm and adjusting the parameters of back propagation model. To conclude, the performance of the model to forecast AQI is comparatively convincing and the model is expected to take positive effect in AQI forecast in the future.

Keywords: AQI forecast, principal component analysis, genetic algorithm, back propagation neural network model.

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Authors: H. Sakamoto, J. Tochimoto, S. Kurosawa, M. Suzuki, S. Oguri

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Salt stress adversely affects plant growth at various stages of development including seed germination, seedling establishment, vegetative growth and finally reproduction. Because of their immobile nature, plants have evolved mechanisms to sense and respond to salt stress. Seed dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. We identified a novel locus of Arabidopsis, designated SHG1 (salt hypersensitive germination 1), whose disruption leads to reduced germination rate under moderate salt stress conditions. SHG1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. The shg1-disrupted Arabidopsis mutant died at the cotyledon stage when sown on salt-containing medium, although wild-type plants could form true leaves under the same conditions. On the other hand, this mutant showed similar phenotypes to wild-type plants when sown on medium without salt and transferred to salt-containing medium at the vegetative stage. These results suggested that SHG1 played indispensable role in the seed germination and seedling establishment under moderate salt stress conditions. SHG1 may be involved in the release of seed dormancy.

Keywords: Germination, ankyrin repeat, Arabidopsis, salt tolerance.

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Authors: Nicolae Bold, Daniel Nijloveanu

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The idea of cropping-system is a method used by farmers. It is an environmentally-friendly method, protecting the natural resources (soil, water, air, nutritive substances) and increase the production at the same time, taking into account some crop particularities. The combination of this powerful method with the concepts of genetic algorithms results into a possibility of generating sequences of crops in order to form a rotation. The usage of this type of algorithms has been efficient in solving problems related to optimization and their polynomial complexity allows them to be used at solving more difficult and various problems. In our case, the optimization consists in finding the most profitable rotation of cultures. One of the expected results is to optimize the usage of the resources, in order to minimize the costs and maximize the profit. In order to achieve these goals, a genetic algorithm was designed. This algorithm ensures the finding of several optimized solutions of cropping-systems possibilities which have the highest profit and, thus, which minimize the costs. The algorithm uses genetic-based methods (mutation, crossover) and structures (genes, chromosomes). A cropping-system possibility will be considered a chromosome and a crop within the rotation is a gene within a chromosome. Results about the efficiency of this method will be presented in a special section. The implementation of this method would bring benefits into the activity of the farmers by giving them hints and helping them to use the resources efficiently.

Keywords: Genetic algorithm, chromosomes, genes, cropping, agriculture.

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Authors: Abu Salim Mustafa

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Water plays a major role in maintaining life on earth, but it can also serve as a matrix for pathogenic organisms, posing substantial health threats to humans. Although, outbreaks of diseases attributable to drinking water may not be common in industrialized countries, they still occur and can lead to serious acute, chronic, or sometimes fatal health consequences. The analysis of drinking water samples from different regions of Kuwait was performed in this study for bacterial and viral contaminations. Drinking tap water samples were collected from 15 different locations of the six Kuwait governorates. All samples were analyzed by confocal microscopy for the presence of bacteria. The samples were cultured in vitro to detect cultivable organisms. DNA was isolated from the cultured organisms and the identity of the bacteria was determined by sequencing the bacterial 16S rRNA genes, followed by BLAST analysis in the database of NCBI, USA. RNA was extracted from water samples and analyzed by real-time PCR for the detection of viruses with potential health risks, i.e. Astrovirus, Enterovirus, Norovirus, Rotavirus, and Hepatitis A. Confocal microscopy showed the presence of bacteria in some water samples. The 16S rRNA gene sequencing of culture grown organisms, followed by BLAST analysis, identified the presence of several non-pathogenic bacterial species. However, one sample had Acinetobacter baumannii, which often causes opportunistic infections in immunocompromised people, but none of the studied viruses could be detected in the drinking water samples analyzed. The results indicate that drinking water samples analyzed from various locations in Kuwait are relatively safe for drinking and do not contain many harmful pathogens.

Keywords: Drinking water, 16S rRNA, microbial diversity, viruses, Kuwait.

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Authors: Gholamhossein Hosseini

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Two earliness cotton genotypes I and II, which had been developed by hybridization and backcross methods between sindise-80 as an early maturing gene parent and two other lines i.e. Red leaf and Bulgare-557 as a second parent, are subjected to different environmental conditions. The early maturing genotypes with coded names of I and II were compared with four native cotton cultivars in randomized complete block design (RCBD) with four replications in three ecological regions of Iran from 2016-2017. Two early maturing genotypes along with four native cultivars viz. Varamin, Oltan, Sahel and Arya were planted in Agricultural Research Station of Varamin, Moghan and Kashmar for evaluation. Earliness data were collected for six treatments during two years in the three regions except missing data for the second year of Kashmar. Therefore, missed data were estimated and imputed. For testing the homogeneity of error variances, each experiment at a given location or year is analyzed separately using Hartley and Bartlett’s Chi-square tests and both tests confirmed homogeneity of variance. Combined analysis of variance showed that genotypes I and II were superior in Varamin, Moghan and Kashmar regions. Earliness means and their interaction effects were compared with Duncan’s multiple range tests. Finally combined analysis of variance showed that genotypes I and II were superior in Varamin, Moghan and Kashmar regions. Earliness means and their interaction effects are compared with Duncan’s multiple range tests.

Keywords: Cotton, combined, analysis, earliness.

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Authors: Kanthida Kusonmano, Michael Netzer, Bernhard Pfeifer, Christian Baumgartner, Klaus R. Liedl, Armin Graber

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Availability of high dimensional biological datasets such as from gene expression, proteomic, and metabolic experiments can be leveraged for the diagnosis and prognosis of diseases. Many classification methods in this area have been studied to predict disease states and separate between predefined classes such as patients with a special disease versus healthy controls. However, most of the existing research only focuses on a specific dataset. There is a lack of generic comparison between classifiers, which might provide a guideline for biologists or bioinformaticians to select the proper algorithm for new datasets. In this study, we compare the performance of popular classifiers, which are Support Vector Machine (SVM), Logistic Regression, k-Nearest Neighbor (k-NN), Naive Bayes, Decision Tree, and Random Forest based on mock datasets. We mimic common biological scenarios simulating various proportions of real discriminating biomarkers and different effect sizes thereof. The result shows that SVM performs quite stable and reaches a higher AUC compared to other methods. This may be explained due to the ability of SVM to minimize the probability of error. Moreover, Decision Tree with its good applicability for diagnosis and prognosis shows good performance in our experimental setup. Logistic Regression and Random Forest, however, strongly depend on the ratio of discriminators and perform better when having a higher number of discriminators.

Keywords: Classification, High dimensional data, Machine learning

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Authors: Aliaa M. El-Borai, Ehab A. Beltagy, Eman E. Gadallah, Samy A. ElAssar

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Bioremediation technology is now used for treatment instead of traditional metal removal methods. A strain was isolated from Marsa Alam, Red sea, Egypt showed high resistance to high lead concentration and was identified by the 16S rRNA gene sequencing technique as Halomonas sp. ES015. Medium optimization was carried out using Plackett-Burman design, and the most significant factors were yeast extract, casamino acid and inoculums size. The optimized media obtained by the statistical design raised the removal efficiency from 84% to 99% from initial concentration 250 ppm of lead. Moreover, Box-Behnken experimental design was applied to study the relationship between yeast extract concentration, casamino acid concentration and inoculums size. The optimized medium increased removal efficiency to 97% from initial concentration 500 ppm of lead. Immobilized Halomonas sp. ES015 cells on sponge cubes, using optimized medium in loop bioremediation column, showed relatively constant lead removal efficiency when reused six successive cycles over the range of time interval. Also metal removal efficiency was not affected by flow rate changes. Finally, the results of this research refer to the possibility of lead bioremediation by free or immobilized cells of Halomonas sp. ES015. Also, bioremediation can be done in batch cultures and semicontinuous cultures using column technology.

Keywords: Bioremediation, lead, Box–Behnken, Halomonas sp. ES015, loop bioremediation, Plackett-Burman.

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

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

Keywords: Genetic diversity, Monopterus cuchia, population, RAPD, Bangladesh.

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Authors: First G.M. Karthik, Second Ramachandra.V.Pujeri, Dr.

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Generalized Center String (GCS) problem are generalized from Common Approximate Substring problem and Common substring problems. GCS are known to be NP-hard allowing the problems lies in the explosion of potential candidates. Finding longest center string without concerning the sequence that may not contain any motifs is not known in advance in any particular biological gene process. GCS solved by frequent pattern-mining techniques and known to be fixed parameter tractable based on the fixed input sequence length and symbol set size. Efficient method known as Bpriori algorithms can solve GCS with reasonable time/space complexities. Bpriori 2 and Bpriori 3-2 algorithm are been proposed of any length and any positions of all their instances in input sequences. In this paper, we reduced the time/space complexity of Bpriori algorithm by Constrained Based Frequent Pattern mining (CBFP) technique which integrates the idea of Constraint Based Mining and FP-tree mining. CBFP mining technique solves the GCS problem works for all center string of any length, but also for the positions of all their mutated copies of input sequence. CBFP mining technique construct TRIE like with FP tree to represent the mutated copies of center string of any length, along with constraints to restraint growth of the consensus tree. The complexity analysis for Constrained Based FP mining technique and Bpriori algorithm is done based on the worst case and average case approach. Algorithm's correctness compared with the Bpriori algorithm using artificial data is shown.

Keywords: Constraint Based Mining, FP tree, Data mining, GCS problem, CBFP mining technique.

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Authors: M. Sangeetha, D. Chamundeeswari, C. Saravanababu, C. Rose, V. Gopal

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Rheumatoid arthritis (RA) is a chronic, progressive, systemic inflammatory disorder affecting the synovial joints and typically producing symmetrical arthritis that leads to joint destruction, which is responsible for the deformity and disability. Despite improvements in the treatment of RA over the past decade, there still is a need for new therapeutic agents that are efficacious, less expensive, and free of severe adverse reactions. The present study aimed to investigate role of inflammatory markers in arthritic rats treated with ethanolic bark extract of Albizia procera. The protective effect of ethanolic bark extract of Albizia procera against complete Freund’s adjuvant (CFA) induced arthritis in rats. Arthritis was induced by an intradermal injection of 0.1 ml FCA in the foot pad of left hind limb of rats. ETBE (100 and 200 mg/kg b.wt./p.o) and the reference drug diclofenac (25 mg/kg b.wt./p.o) were administered to arthritic rats. Paw volume was measured for all the animals before inducing arthritis and thereafter once in seven days by using plethysmometer for 42 days. Gene expression of inflammatory markers such as IL-1β and IL-10 were investigated in paw tissues. Up regulation of IL-1β and Down regulation IL-10 were observed in CFA injected rats when compared to normal rats. ETBE attenuated these alterations dose dependently when compared to the vehicle treated rats. These results provide insights into the mechanism of anti-arthritic activity, and unravel potential therapeutic use of Albizia procera in arthritis.

Keywords: CFA-Complete Freund’s adjuvant, ETBE, Ethanolic Bark Extract, IL- Interleukins, RA-Rheumatoid Arthritis.

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Authors: Oluyemi O. Awolusi, Abimbola M. Enitan, Sheena Kumari, Faizal Bux

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Nitrification is essential to biological processes designed to remove ammonia and/or total nitrogen. It removes excess nitrogenous compound in wastewater which could be very toxic to the aquatic fauna or cause serious imbalance of such aquatic ecosystem. Efficient nitrification is linked to an in-depth knowledge of the structure and dynamics of the nitrifying community structure within the wastewater treatment systems. In this study, molecular technique was employed for characterizing the microbial structure of activated sludge [ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB)] in a municipal wastewater treatment with intention of linking it to the plant efficiency. PCR based phylogenetic analysis was also carried out. The average operating and environmental parameters as well as specific nitrification rate of plant was investigated during the study. During the investigation the average temperature was 23±1.5oC. Other operational parameters such as mixed liquor suspended solids and chemical oxygen demand inversely correlated with ammonia removal. The dissolved oxygen level in the plant was constantly lower than the optimum (between 0.24 and 1.267 mg/l) during this study. The plant was treating wastewater with influent ammonia concentration of 31.69 and 24.47 mg/L. The influent flow rates (ML/Day) was 96.81 during period. The dominant nitrifiers include: Nitrosomonas spp. Nitrobacter spp. and Nitrospira spp. The AOB had correlation with nitrification efficiency and temperature. This study shows that the specific ammonia oxidizing rate and the specific nitrate formation rates can serve as good indicator of the plant overall nitrification performance.

Keywords: Ammonia monooxygenase α-subunit (amoA) gene, ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), specific nitrification rate, PCR.

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Authors: Yanju Zhang, Joost M. Woltering, Fons J. Verbeek

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It has been established that microRNAs (miRNAs) play an important role in gene expression by post-transcriptional regulation of messengerRNAs (mRNAs). However, the precise relationships between microRNAs and their target genes in sense of numbers, types and biological relevance remain largely unclear. Dissecting the miRNA-target relationships will render more insights for miRNA targets identification and validation therefore promote the understanding of miRNA function. In miRBase, miRanda is the key algorithm used for target prediction for Zebrafish. This algorithm is high-throughput but brings lots of false positives (noise). Since validation of a large scale of targets through laboratory experiments is very time consuming, several computational methods for miRNA targets validation should be developed. In this paper, we present an integrative method to investigate several aspects of the relationships between miRNAs and their targets with the final purpose of extracting high confident targets from miRanda predicted targets pool. This is achieved by using the techniques ranging from statistical tests to clustering and association rules. Our research focuses on Zebrafish. It was found that validated targets do not necessarily associate with the highest sequence matching. Besides, for some miRNA families, the frequency of their predicted targets is significantly higher in the genomic region nearby their own physical location. Finally, in a case study of dre-miR-10 and dre-miR-196, it was found that the predicted target genes hoxd13a, hoxd11a, hoxd10a and hoxc4a of dre-miR- 10 while hoxa9a, hoxc8a and hoxa13a of dre-miR-196 have similar characteristics as validated target genes and therefore represent high confidence target candidates.

Keywords: MicroRNA targets validation, microRNA-target relationships, dre-miR-10, dre-miR-196.

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Authors: Feng-Sheng Wang, Wu-Hsiung Wu, Kai-Cheng Hsu

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The optimization of biological systems, which is a branch of metabolic engineering, has generated a lot of industrial and academic interest for a long time. In the last decade, metabolic engineering approaches based on mathematical optimizations have been used extensively for the analysis and manipulation of metabolic networks. In practical optimization of metabolic reaction networks, designers have to manage the nature of uncertainty resulting from qualitative characters of metabolic reactions, e.g., the possibility of enzyme effects. A deterministic approach does not give an adequate representation for metabolic reaction networks with uncertain characters. Fuzzy optimization formulations can be applied to cope with this problem. A fuzzy multi-objective optimization problem can be introduced for finding the optimal engineering interventions on metabolic network systems considering the resilience phenomenon and cell viability constraints. The accuracy of optimization results depends heavily on the development of essential kinetic models of metabolic networks. Kinetic models can quantitatively capture the experimentally observed regulation data of metabolic systems and are often used to find the optimal manipulation of external inputs. To address the issues of optimizing the regulatory structure of metabolic networks, it is necessary to consider qualitative effects, e.g., the resilience phenomena and cell viability constraints. Combining the qualitative and quantitative descriptions for metabolic networks makes it possible to design a viable strain and accurately predict the maximum possible flux rates of desired products. Considering the resilience phenomena in metabolic networks can improve the predictions of gene intervention and maximum synthesis rates in metabolic engineering. Two case studies will present in the conference to illustrate the phenomena.

Keywords: Fuzzy multi-objective optimization problem, kinetic model, metabolic engineering.

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Authors: M. Jarrar, S. Behl, N. Shaheen, A. Fatima, R. Nasab

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Skin aging is a slow multifactorial process influenced by both internal as well as external factors. Ultra-violet radiations (UV), diet, smoking and personal habits are the most common environmental factors that affect skin aging. Fat contents and fibrous proteins as collagen and elastin are core internal structural components. The direct influence of UV on elastin integrity and health is central on aging of skin especially by time. The deposition of abnormal elastic material is a major marker in a photo-aged skin. Searching for compounds that may protect against cutaneous photodamage is exceedingly valued. Retinoids and alpha hydroxy acids have been endorsed by some researchers as possible candidates for protecting and or repairing the effect of UV damaged skin. For consolidating a better system of anti- and protective effects of such anti-aging agents, we evaluated the combinatory effects of various dosages of lactic acid and retinol on the dermal fibroblast’s elastin levels exposed to UV. The UV exposed cells showed significant reduction in the elastin levels. A combination of drugs with a higher concentration of lactic acid (30 -35 mM) and a lower concentration of retinol (10-15mg/mL) showed to work better in maintaining elastin concentration in UV exposed cells. We assume this preservation could be the result of increased tropo-elastin gene expression stimulated by retinol whereas lactic acid probably repaired the UV irradiated damage by enhancing the amount and integrity of the elastin fibers.

Keywords: Alpha Hydroxy Acid, Elastin, Retinol, Ultraviolet radiations.

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Authors: Abu Salim Mustafa

Abstract:

Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: Mycobacterium tuberculosis, Rv3873, peptides, vaccine

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Authors: Ajay Kumar Pandey, Mayank Kumar

Abstract:

White grub (Coleoptera: Scarabaeidae) is a major destructive pest in western Himalayan region of Uttarakhand. Beetles feed on apple, apricot, plum, walnut etc. during night while, second and third instar grubs feed on live roots of cultivated as well as non-cultivated crops. Collection and identification of scarab beetles through light trap was carried out at Crop Research Centre, Govind Ballab Pant University Pantnagar, Udham Singh Nagar (Uttarakhand) during 2018. Field trials were also conducted in 2018 to evaluate pre and post sown application of different insecticides against the white grub infesting soybean. The insecticides like Carbofuran 3 Granule (G) (750 g a.i./ha), Clothianidin 50 Water Dispersal Granule (WG) (120 g a.i./ha), Fipronil 0.3 G (50 g a.i./ha), Thiamethoxam 25 WG (80 g a.i./ha), Imidacloprid 70 WG (300 g a.i./ha), Chlorantraniliprole 0.4% G(100 g a.i./ha) and mixture of Fipronil 40% and Imidacloprid 40% WG (300 g a.i./ha) were applied at the time of sowing in pre sown experiment while same dosage of insecticides were applied in standing soybean crop during (first fortnight of July). Commutative plant mortality data were recorded after 20, 40, 60 days intervals and compared with untreated control. Total 23 species of white grub beetles recorded on the light trap and Holotrichia serrata Fabricious (Coleoptera: Melolonthinae) was found to be predominant species by recording 20.6% relative abundance out of the total light trap catch (i.e. 1316 beetles) followed by Phyllognathus sp. (14.6% relative abundance). H. rosettae and Heteronychus lioderus occupied third and fourth rank with 11.85% and 9.65% relative abundance, respectively. The emergence of beetles of predominant species started from 15th March, 2018. In April, average light trap catch was 382 white grub beetles, however, peak emergence of most of the white grub species was observed from June to July, 2018 i.e. 336 beetles in June followed by 303 beetles in the July. On the basis of the emergence pattern of white grub beetles, it may be concluded that the Peak Emergence Period (PEP) for the beetles of H. serrata was second fortnight of April for the total period of 15 days. In May, June and July relatively low population of H. serrata was observed. A decreasing trend in light trap catch was observed and went on till September during the study. No single beetle of H. serrata was observed on light trap from September onwards. The cumulative plant mortality data in both the experiments revealed that all the insecticidal treatments were significantly superior in protection-wise (6.49-16.82% cumulative plant mortality) over untreated control where highest plant mortality was 17.28 to 39.65% during study. The mixture of Fipronil 40% and Imidacloprid 40% WG applied at the rate of 300 g a.i. per ha proved to be most effective having lowest plant mortality i.e. 9.29 and 10.94% in pre and post sown crop, followed by Clothianidin 50 WG (120 g a.i. per ha) where the plant mortality was 10.57 and 11.93% in pre and post sown treatments, respectively. Both treatments were found significantly at par among each other. Production-wise, all the insecticidal treatments were found statistically superior (15.00-24.66 q per ha grain yields) over untreated control where the grain yield was 8.25 & 9.13 q per ha. Treatment Fipronil 40% + Imidacloprid 40% WG applied at the rate of 300 g a.i. per ha proved to be most effective and significantly superior over Imidacloprid 70WG applied at the rate of 300 g a.i. per ha.

Keywords: Bio efficacy, insecticide, Holotrichia, soybean, white grub.

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Authors: Achitphol Chookaew, Paramee Thongsukhsai, Patamarerk Engsontia, Narongwit Nakwan, Pritsana Raugrut

Abstract:

Lung cancer is one of the most common malignancies and primary cause of death due to cancer worldwide. Non-small cell lung cancer (NSCLC) is the main subtype in which majority of patients present with advanced-stage disease. Herein, we analyzed differentially expressed genes to find potential biomarkers for lung cancer diagnosis as well as prognostic markers. We used transcriptome data from our 2 NSCLC patients and public data (GSE81089) composing of 8 NSCLC and 10 normal lung tissues. Differentially expressed genes (DEGs) between NSCLC and normal tissue and between early-stage and late-stage NSCLC were analyzed by the DESeq2. Pairwise correlation was used to find the DEGs with false discovery rate (FDR) adjusted p-value £ 0.05 and |log2 fold change| ³ 4 for NSCLC versus normal and FDR adjusted p-value £ 0.05 with |log2 fold change| ³ 2 for early versus late-stage NSCLC. Bioinformatic tools were used for functional and pathway analysis. Moreover, the top ten genes in each comparison group were verified the expression and survival analysis via GEPIA. We found 150 up-regulated and 45 down-regulated genes in NSCLC compared to normal tissues. Many immnunoglobulin-related genes e.g., IGHV4-4, IGHV5-10-1, IGHV4-31, IGHV4-61, and IGHV1-69D were significantly up-regulated. 22 genes were up-regulated, and five genes were down-regulated in late-stage compared to early-stage NSCLC. The top five DEGs genes were KRT6B, SPRR1A, KRT13, KRT6A and KRT5. Keratin 6B (KRT6B) was the most significantly increased gene in the late-stage NSCLC. From GEPIA analysis, we concluded that IGHV4-31 and IGKV1-9 might be used as diagnostic biomarkers, while KRT6B and KRT6A might be used as prognostic biomarkers. However, further clinical validation is needed.

Keywords: Bioinformatics, differentially expressed genes, non-small cell lung cancer, transcriptomics.

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Authors: Norsakinah Mohammad Osman, Ali Etemad, Patimah Ismail

Abstract:

Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder that characterized by the presence of high glucose in blood that cause from insulin resistance and insufficiency due to deterioration β-cell Langerhans functions. T2DM is commonly caused by the combination of inherited genetic variations as well as our own lifestyle. Metallothionein (MT) is a known cysteine-rich protein responsible in helping zinc homeostasis which is important in insulin signaling and secretion as well as protection our body from reactive oxygen species (ROS). MT scavenged ROS and free radicals in our body happen to be one of the reasons of T2DM and its complications. The objective of this study was to investigate the association of MT1A and MT2A polymorphisms between T2DM and control subjects among Malay populations. This study involved 150 T2DM and 120 Healthy individuals of Malay ethnic with mixed genders. The genomic DNA was extracted from buccal cells and amplified for MT1A and MT2A loci; the 347bp and 238bp banding patterns were respectively produced by mean of the Polymerase Chain Reaction (PCR). The PCR products were digested with Mlucl and Tsp451 restriction enzymes respectively and producing fragments lengths of (158/189/347bp) and (103/135/238bp) respectively. The ANOVA test was conducted and it shown that there was a significant difference between diabetic and control subjects for age, BMI, WHR, SBP, FPG, HBA1C, LDL, TG, TC and family history with (P<0.05). While the HDL, CVD risk ratio and DBP does not show any significant difference with (P>0.05). The genotype frequency for AA, AG and GG of MT1A polymorphisms was 72.7%, 22.7% and 4.7% in cases and 15%, 55% and 30% in control respectively. As for MT2A, genotype frequency of GG, GC and CC was 42.7%, 27.3% and 30% in case and 5%, 40% and 55% for control respectively. Both polymorphisms show significant difference between two investigated groups with (P=0.000). The Post hoc test was conducted and shows a significant difference between the genotypes within each polymorphism (P=0. 000). The MT1A and MT2A polymorphisms were believed to be the reliable molecular markers to distinguish the T2DM subjects from healthy individuals in Malay populations.

Keywords: Type 2 Diabetes Mellitus (T2DM), Metallothionein (MT), MT1A (rs11076161), MT2A (rs10636), Malay, Genetic Polymorphism.

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Authors: Eryati Darwin, Eka Fithra Elfi, Indria Hafizah

Abstract:

Background: Physical exercise induces a pattern of hormonal and immunological responses that prevent endothelial dysfunction by maintaining the availability of nitric oxide (NO). Regular and moderate exercise stimulates NO release, that can be considered as protective factor of cardiovascular diseases, while strenuous exercise induces increased levels in a number of pro-inflammatory and anti-inflammatory cytokines. Pro-inflammatory cytokines tumor necrosis factor-α (TNF-α) triggers endothelial activation which results in an increased vascular permeability. Nuclear gene factor kappa B (NF-κB) activates biological effect of TNF-α. Aim of Study: To determine the effect of physical exercise on the endothelial and skeletal muscle, we measured the level of NF-κB on rats’ serum, macrophages, and myocytes after strenuous physical exercise. Methods: 30 male Rattus norvegicus in the age of eight weeks were randomly divided into five groups (each containing six), and there were treated groups (T) and control group (C). The treated groups obtain strenuous physical exercise by ran on treadmill at 32 m/minutes for 1 hour or until exhaustion. Blood samples, myocytes of gastrocnemius muscle, and intraperitoneal macrophages were collected sequentially. There were investigated immediately, 2 hours, 6 hours, and 24 hours (T1, T2, T3, and T4) after sacrifice. The levels of NF-κB were measured by ELISA methods. Results: From our study, we found that the levels of NF-κB on myocytes in treated group from which its specimen was taken immediately (T1), 2 hours after treadmill (T2), and 6 hours after treadmill (T3) were significantly higher than control group (p<0.05), while the group from which its specimen was taken 24 hours after treadmill, was no significantly different (p>0.05). Also on macrophages, NF-κB in treated groups T1, T2, and T3 was significantly higher than control group (p<0.05), but there was no difference between T4 and control group (p>0.05). The level of serum NF-κB was not significantly different between treatment group as well as compared to control group (p>0.05). Serum NF-κB was significantly higher than the level on macrophages and myocytes (p<0.05). Conclusion: This study demonstrated that strenuous physical exercise stimulates the activation of NF-κB that plays a role in vascular inflammation and muscular damage, and may be recovered after resting period.

Keywords: Endothelial function, inflammation, NF-κB, physical exercise.

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

Abstract:

Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast.

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