Search results for: horizontal gene transfer

Authors: Fitria D. Ayuningtyas, Anggraini Barlian

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Green turtle (Chelonia mydas) is one of TSD (Temperature-dependent Sex Determination, TSD) animals which sex is determined by the egg’s incubation temperature. GSD (Genotypic Sex Determination) homologous genes such as Wilms’ Tumor (Wt1) and Forkhead Box L2 (FoxL2) play a role in TSD animal sex determination process. Wt1 plays a role in both male pathway, as a transcription factor for Sf1 gene and in female pathway, as a transcription factor for Dax1. FoxL2 plays a role specifically in female sex determination, and known as transcriptional factor for Aromatase gene. Until now, research on the pattern of Wt1 and FoxL2 genes expression in C.mydas has not been conducted yet. The aim of this research is to know the pattern of Wt1 and FoxL2 genes expression in Mesonephros-Gonad (MG) complexes of Chelonia mydas embryos incubated in masculinizing temperature (MT) and feminizing temperature (FT). Eggs of C.mydas incubated in 3 different stage of TSP (Thermosensitive Period) at masculinizing temperature (26±10C, MT) and feminizing temperature (31±10C FT). Mesonefros-gonad complexes were isolated at Pre-TSP stage (FT at days 14th, MT at days 24th), TSP stage (FT at days 24th, MT at days 36th) and differentiated stage (FT at days 40th, MT at days 58th). RNA from mesonephros-gonad (MG) complexes were converted into cDNA by RT-PCR process, and the pattern of Wt1 and FoxL2 genes expression is analyzed by quantitative Real Time PCR (qPCR) method, β-actin gene is used as an internal control. The pattern of Wt1 gene expression in Pre-TSP stage was almost the same between MG complexes incubated at MT or FT, while TSP and differentiation stage, the pattern of Wt1 gene expression in MG complexes incubated at MT or FT was increased. Wt1 gene expression of MG complexes that incubated at FT was higher than at MT. There was a difference pattern between Wt1 gene expression in this research compared to the previous research in protein level. It could be assumed that the difference caused by post-transcriptional regulation mechanisms before mRNA of Wt1 gene translated into protein structure. The pattern of FoxL2 gene expression in Pre-TSP stage was almost the same between MG complexes that incubated at MT and FT, and increased in both TSP and differentiated stage. The FoxL2 gene expression in MG complexes that incubated in FT is higher than MT on TSP and differentiated stage. Based on the results of this research, it can be assumed that Wt1 and FoxL2 gene were expressed in MG complexes that incubated both at MT and FT since Pre-TSP stage. The pattern of Wt1 gene expression was increased in every stage of gonadal development, and so do the pattern of FoxL2 gene expression. Wt1 and FoxL2 gene expressions were higher in MG complexes incubated at FT than MT.

Keywords: chelonia mydas, FoxL2, gene expression, TSD, Wt1

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Authors: M. Yusuf

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The recent discovery of the phenomenon of RNA interference has led to its application in various aspects of plant improvement. Crops can be modified by engineering novel RNA interference pathways that create small RNA molecules to alter gene expression in crops or plant pests. RNA interference can generate new crop quality traits or provide protection against insects, nematodes and pathogens without introducing new proteins into food and feed products. This is an advantage in contrast with conventional procedures of gene transfer. RNA interference has been used to develop crop varieties resistant to diseases, pathogens and insects. Male sterility has been engineered in plants using RNA interference. Better quality crops have been developed through the application of RNA interference etc. The objective of this paper is to highlight the application of RNA interference in crop improvement and to project its potential future use to solve problems of agricultural production in relation to plant breeding.

Keywords: RNA interference, application, crop Improvement, agricultural production

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Authors: Houda Jalali, Hassan Abbassi

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In this numerical work, natural convection and entropy generation of Al₂O₃–water nanofluid in square cavity have been studied. A two-dimensional steady laminar natural convection in a differentially heated square cavity of length L, filled with a nanofluid is investigated numerically. The horizontal walls are considered adiabatic. Vertical walls corresponding to x=0 and x=L are respectively maintained at hot temperature, T_h and cold temperature, T_c. The resolution is performed by the CFD code "FLUENT" in combination with GAMBIT as mesh generator. These simulations are performed by maintaining the Rayleigh numbers varied as 10³ ≤ Ra ≤ 10⁶, while the solid volume fraction varied from 1% to 5%, the particle size is fixed at dp=33 nm and a range of the temperature from 20 to 70 °C. We used models of thermophysical nanofluids properties based on experimental measurements for studying the effect of adding solid particle into water in natural convection heat transfer and entropy generation of nanofluid. Such as models of thermal conductivity and dynamic viscosity which are dependent on solid volume fraction, particle size and temperature. The average Nusselt number is calculated at the hot wall of the cavity in a different solid volume fraction. The most important results is that at low temperatures (less than 40 °C), the addition of nanosolids Al₂O₃ into water leads to a decrease in heat transfer and entropy generation instead of the expected increase, whereas at high temperature, heat transfer and entropy generation increase with the addition of nanosolids. This behavior is due to the contradictory effects of viscosity and thermal conductivity of the nanofluid. These effects are discussed in this work.

Keywords: entropy generation, heat transfer, nanofluid, natural convection

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Authors: S. Ali Ashrafizadeh, M. Amidpour, N. Hedayat

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Driving forces along with transfer coefficient affect on heat transfer rate, on the other hand, with regard to the relation of these forces with irriversibilities they are effective on exergy losses. Therefore, the driving forces can be used as a relation between heat transfer rate, transfer coefficients and exergy losses. In this paper, first, the relation of the exergetic efficiency and resistant forces is obtained, next the relation between exergy efficiency, relative driving force, heat transfer rate and heat resistances is considered. In all cases, results are argued graphically. Finally, a case study inspected by obtained results.

Keywords: heat transfer, exergy losses, exergetic efficiency, driving forces

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Authors: Stephy Saavedra, Annsy C. Arredondo, Gisele Monteiro, Adalberto Pessoa Jr, Carol N. Flores-Fernandez, Amparo I. Zavaleta

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L-asparaginase from bacterial sources is used in leukemic treatment and food industry. This enzyme is classified based on its affinity towards L-asparagine and L-glutamine. Likewise, ansZ genes express L-asparaginase with higher affinity to L-asparagine. The aim of this work was to clone and express of ansZ gene from Bacillus sp. CH11 isolated from Chilca salterns in Peru. The gene encoding L-asparaginase was cloned into pET15b vector and transformed in Escherichia coli BL21 (DE3) pLysS. The expression was carried out in a batch culture using LB broth and 0.5 mM IPTG. The recombinant L-asparaginase showed a molecular weight of ~ 39 kDa by SDS PAGE and a specific activity of 3.19 IU/mg of protein. The cloning and expression of ansZ gene from this halotolerant Bacillus sp. CH11 allowed having a biological input to improve a future scaling-up.

Keywords: ansZ gene, Bacillus sp, Chilca salterns, recombinant L-asparaginase

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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: Bandar Ali Al-Asbahi, Mohammad Hafizuddin Haji Jumali

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Forster energy transfer between poly (9,9'-di-n-octylfluorenyl-2,7-diyl) (PFO)/TiO2 nanoparticles (NPs) as a donor and Fluorol 7GA as an acceptor has been studied. The energy transfer parameters were calculated by using mathematical models. The dominant mechanism responsible for the energy transfer between the donor and acceptor molecules was Forster-type, as evidenced by large values of quenching rate constant, energy transfer rate constant and critical distance of energy transfer. Moreover, these composites which were used as an emissive layer in organic light emitting diodes, were investigated in terms of current density–voltage and electroluminescence spectra.

Keywords: energy transfer parameters, forster-type, electroluminescence, organic light emitting diodes

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Authors: Belmiloud Mohamed Amine, Sad Chemloul Nord-Eddine

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In this study we investigated numerically heat transfer by mixed convection coupled to radiation in a square cavity; the upper horizontal wall is movable. The purpose of this study is to see the influence of the emissivity and the varying of the Richardson number on the variation of the average Nusselt number. The vertical walls of the cavity are differentially heated, the left wall is maintained at a uniform temperature higher than the right wall, and the two horizontal walls are adiabatic. The finite volume method is used for solving the dimensionless governing equations. Emissivity values used in this study are ranged between 0 and 1, the Richardson number in the range 0.1 to10. The Rayleigh number is fixed to Ra = 10000 and the Prandtl number is maintained constant Pr = 0.71. Streamlines, isothermal lines and the average Nusselt number are presented according to the surface emissivity. The results of this study show that the Richardson number and emissivity affect the average Nusselt number.

Keywords: mixed convection, square cavity, wall emissivity, lid-driven, numerical study

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Authors: Damiaa Saad Khudor

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The paper describes an investigation for the thermal design of a fluidized bed cooler and prediction of heat transfer rate among the media categories. It is devoted to the thermal design of such equipment and their application in the industrial fields. It outlines the strategy for the fluidization heat transfer mode and its implementation in industry. The thermal design for fluidized bed cooler is used to furnish a complete design for a fluidized bed cooler of Sodium Bicarbonate. The total thermal load distribution between the air-solid and water-solid along the cooler is calculated according to the thermal equilibrium. The step by step technique was used to accomplish the thermal design of the fluidized bed cooler. It predicts the load, air, solid and water temperature along the trough. The thermal design for fluidized bed cooler revealed to the installation of a heat exchanger consists of (65) horizontal tubes with (33.4) mm diameter and (4) m length inside the bed trough.

Keywords: fluidization, powder technology, thermal design, heat exchangers

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Authors: Vinod Kumar, Navin Kumar, Surjit Angra, Prince Sharma

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This paper presents the design analysis of saddle support of a horizontal pressure vessel. Since saddle have the vital role to support the pressure vessel and to maintain its stability, it should be designed in such a way that it can afford the vessel load and internal pressure of the vessel due to liquid contained in the vessel. A model of horizontal pressure vessel and saddle support is created in Ansys. Stresses are calculated using mathematical approach and Ansys software. The analysis reveals the zone of high localized stress at the junction part of the pressure vessel and saddle support due to operating conditions. The results obtained by both the methods are compared with allowable stress value for safe designing.

Keywords: ANSYS, pressure vessel, saddle, support

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Authors: Ankita Shukla, Tiratha Raj Singh

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Colorectal cancer (CRC) imposes serious mortality burden worldwide and it has been increasing for past consecutive years. Continuous efforts have been made so far to diagnose the disease condition and to identify the root cause for it. In this study, we performed the pathway level as well as the differential gene expression studies for CRC. We analyzed the gene expression profile GSE24514 from Gene Expression Omnibus (GEO) along with the gene pathways involved in the CRC. This analysis helps us to understand the behavior of the genes that have shown differential expression through their targeted pathways. Pathway analysis for the targeted genes covers the wider area which therefore decreases the possibility to miss the significant ones. This will prove to be beneficial to expose the ones that have not been given attention so far. Through this analysis, we attempt to understand the various neighboring genes that have close relationship to the targeted one and thus proved to be significantly controlling the CRC. It is anticipated that the identified hub and neighboring genes will provide new directions to look at the pathway level differently and will be crucial for the regulatory processes of the disease.

Keywords: mismatch repair, microsatellite instability, carcinogenesis, morbidity

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Authors: Qian Pei, Hengjian Tong, Weitao Chen, Hai Wang, Yanrong Feng

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Horizontal parallax is the foundation of stereoscopic viewing. However, the human eye will feel uncomfortable and it will occur diplopia if horizontal parallax is larger than eye separation. Therefore, we need to do parallax refining before conducting stereoscopic observation. Although some scholars have been devoted to online remote sensing refining, the main work of image refining is completed on the server side. There will be a significant delay when multiple users access the server at the same time. The emergence of HTML5 technology in recent years makes it possible to develop rich browser web application. Authors complete the image parallax refining on the browser side based on HTML5, while server side only need to transfer image data and parallax file to browser side according to the browser’s request. In this way, we can greatly reduce the server CPU load and allow a large number of users to access server in parallel and respond the user’s request quickly.

Keywords: 3D remote sensing images, parallax, online refining, rich browser web application, HTML5

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Authors: Ch. Ramreddy, P. Naveen, D. Srinivasacharya

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The objective of the present study is to investigate the effect of nonlinear temperature and concentration on the mixed convective flow of micropolar fluid over an inclined flat plate in a non-Darcy porous medium in the presence of convective boundary condition. In order to analyze all the essential features, the transformed nonlinear conservation equations are worked out numerically by spectral method. By insisting the comparison between vertical, horizontal and inclined plates, the physical quantities of the flow and its characteristics are exhibited graphically and quantitatively with various parameters. An increase in the coupling number and inclination of angle tend to decrease the skin friction, mass transfer rate and the reverse change is there in wall couple stress and heat transfer rate. The nominal effect on the wall couple stress and skin friction is encountered whereas the significant effect on the local heat and mass transfer rates are found for high enough values of Biot number.

Keywords: convective boundary condition, micropolar fluid, non-darcy porous medium, non-linear convection, spectral method

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Authors: Kang Hyun Yi

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Wireless power transfer technologies are inductive coupling, magnetic resonance, and capacitive coupling methods, typically. Among them, the capacitive coupling wireless power transfer, also named Capacitive Coupling Wireless Power Transfer (CCWPT), has been researched to overcome the drawbacks of other approaches. The CCWPT has many advantages such as a simple structure, low standing power loss, reduced Electromagnetic Interference (EMI) and the ability to transfer power through metal barriers. In this paper, the CCWPT system with 6.78MHz class D inverter is proposed and analyzed. The proposed system is consisted of the 6.78MHz class D inverter with the LC low pass filter, the capacitor between a transmitter and a receiver and impedance transformers. The system is verified with a prototype for charging mobile devices.

Keywords: wireless power transfer, capacitive coupling power transfer, class D inverter, 6.78MHz

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Authors: I. Boroňová, J. Bernasovská, J. Kmec, E. Petrejčíková

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Dilated cardiomyopathy (DCM) is a severe cardiovascular disorder characterized by progressive systolic dysfunction due to cardiac chamber dilatation and inefficient myocardial contractility often leading to chronic heart failure. Recently, a genome-wide association studies (GWASs) on DCM indicate that the ZBTB17 gene rs10927875 single nucleotide polymorphism is associated with DCM. The aim of the study was to identify the distribution of ZBTB17 gene rs10927875 polymorphism in 50 Slovak patients with DCM and 80 healthy control subjects using the Custom Taqman®SNP Genotyping assays. Risk factors detected at baseline in each group included age, sex, body mass index, smoking status, diabetes and blood pressure. The mean age of patients with DCM was 52.9±6.3 years; the mean age of individuals in control group was 50.3±8.9 years. The distribution of investigated genotypes of rs10927875 polymorphism within ZBTB17 gene in the cohort of Slovak patients with DCM was as follows: CC (38.8%), CT (55.1%), TT (6.1%), in controls: CC (43.8%), CT (51.2%), TT (5.0%). The risk allele T was more common among the patients with dilated cardiomyopathy than in normal controls (33.7% versus 30.6%). The differences in genotype or allele frequencies of ZBTB17 gene rs10927875 polymorphism were not statistically significant (p=0.6908; p=0.6098). The results of this study suggest that ZBTB17 gene rs10927875 polymorphism may be a risk factor for susceptibility to DCM in Slovak patients with DCM. Studies of numerous files and additional functional investigations are needed to fully understand the roles of genetic associations.

Keywords: ZBTB17 gene, rs10927875 polymorphism, dilated cardiomyopathy, cardiovascular disorder

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Authors: Gül Ebru Orhun

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A half diallel crossing design was carried out during 2011 and 2012 growing seasons under Çanakkale-Turkey ecological conditions. In this research, 20 F1 maize hybrids obtained by 6x6 half diallel crossing were used. Gene action for protein content and grain yield traits were explored in half set involving six elite inbred lines. According to the results diallel analysis dominance and additive gene variances were determined for protein content. Variance/Co-variance graphs revealed for grain yield and protein content traits. In this study, inheritance of grain yield and protein content demonstrated over-dominance type of gene action.

Keywords: protein, maize, inheritance, gene action

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Authors: Ashraf Ali, Kriti Upadhyay, Puja Sohal, Anant Mohan, Randeep Guleria

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Background: Gene silencing by aberrant promoter hypermethylation is common in lung cancer and is an initiating event in its development. Aim: To evaluate the gene promoter hypermethylation frequency in serum and tissue of lung cancer patients. Method: 95 newly diagnosed untreated advance stage lung cancer patients and 50 cancer free matched controls were studied. Bisulfite modification of tissue and serum DNA was done; modified DNA was used as a template for methylation-specific PCR analysis. Survival was assessed for one year. Results: Of 95 patients, 82% were non-small cell lung cancer (34% squamous cell carcinoma, 34% non-small cell lung cancer and 14% adenocarcinoma) and 18% were small cell lung cancer. Biopsy revealed that tissue of 89% and 75% of lung cancer patients and 85% and 52% of controls had promoter hypermethylated for MGMT (p=0.35) and p16(p<0.001) gene, respectively. In serum, 33% and 49% of lung cancer patients and 28% and 43% controls were positive for MGMT and p16 gene. No significant correlation was found between survival and clinico-pathological parameters. Conclusion: High gene promoter methylation frequency of p16 gene in tissue biopsy may be linked with early stages of carcinogenesis. Appropriate follow-up is required for confirmation of this finding.

Keywords: lung cancer, MS- PCR, methylation, molecular biology

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Authors: M. V. Bartashevich

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The problem of heat transfer at thin laminar liquid film is solved numerically. A thin film of liquid flows down an inclined surface under conditions of variable heat flux on the wall. The use of thin films of liquid allows to create the effective technologies for cooling surfaces. However, it is important to investigate the most suitable cooling regimes from a safety point of view, in order, for example, to avoid overheating caused by the ruptures of the liquid film, and also to study the most effective cooling regimes depending on the character of the distribution of the heat flux on the wall, as well as the character of the blowing of the film surface, i.e., the external shear stress on its surface. In the statement of the problem on the film surface, the heat transfer coefficient between the liquid and gas is set, as well as a variable external shear stress - the intensity of blowing. It is shown that the combination of these factors - the degree of uniformity of the distribution of heat flux on the wall and the intensity of blowing, affects the efficiency of heat transfer. In this case, with an increase in the intensity of blowing, the cooling efficiency increases, reaching a maximum, and then decreases. It is also shown that the more uniform the heating of the wall, the more efficient the heat sink. A separate study was made for the flow regime along the horizontal surface when the liquid film moves solely due to external stress influence. For this mode, the analytical solution is used for the temperature at the entrance region for further numerical calculations downstream. Also the influence of the degree of uniformity of the heat flux distribution on the wall and the intensity of blowing of the film surface on the heat transfer efficiency was also studied. This work was carried out at the Kutateladze Institute of Thermophysics SB RAS (Russia) and supported by FASO Russia.

Keywords: Heat Flux, Heat Transfer Enhancement, External Blowing, Thin Liquid Film

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Authors: M. D. Asemoloye, S. G. Jonathan, A. Rafiq, O. J. Olawuyi, D. O. Adejoye

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Calmodulin is one of the intracellular calcium proteins that regulates large spectrum of enzymes and cellular functions including metabolism of cyclic nucleotides and glycogen. The potentials of calmodulin gene in fungi necessitates their genetic response and their strong cassette of enzyme secretions for pesticide degradation. Therefore, this study was carried out to investigate the ‘Transcriptomic’ response of calmodulin encoding genes in Talaromyces fungi in response to 2, 2-dichlorovinyl dimethyl phosphate (DDVP or Dichlorvos) an organophosphate pesticide and γ-Hexachlorocyclohexane (Lindane) an organochlorine pesticide. Fungi strains isolated from rhizosphere from grasses rhizosphere in pesticide polluted sites were subjected to percentage incidence test. Two most frequent fungi were further characterized using ITS gene amplification (ITS1 and ITS4 combinations), they were thereafter subjected to In-vitro DDVP and lindane tolerance tests at different concentrations. They were also screened for presence and expression of calmodulin gene (caM) using RT-PCR technique. The two Talaromyces strains had the highest incidence of 50-72% in pesticide polluted site, they were both identified as Talaromyces astroroseus asemoG and Talaromyces purpurogenum asemoN submitted in NCBI gene-bank with accession numbers KY488464 and KY488468 respectively. T. astroroseus KY488464 tolerated DDVP (1.23±0.023 cm) and lindane (1.11±0.018 cm) at 25 % concentration while T. purpurogenum KY488468 tolerated DDVP (1.33±0.061 cm) and lindane (1.54±0.077 cm) at this concentration. Calmodulin gene was detected in both strains, but RT-PCR expression of caM gene revealed at 900-1000 bp showed an under-expression of caM in T. astrorosues KY488464 but overexpressed in T. purpurogenum KY488464. Thus, the calmodulin gene response of these fungal strains to both pesticides could be considered in monitoring the potentials of fungal strains to pesticide tolerance and bioremediation of pesticide in polluted soil.

Keywords: Calmodulin gene, pesticide, RT-PCR, talaromyces, tolerance

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Authors: Sarah Devi Silvian, Hanna Shobrina Iqomatul Haq, Fara Cholidatun Nabila, Agustin Krisna Wardani

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Bacteria ability to survive in antibiotic is controlled by the presence of gene that encodes the antibiotic resistance protein. The instability of the antibiotic resistance gene can be observed by exposing the bacteria under the lethal dose of antibiotic. Low concentration of antibiotic can induce mutation, which may take a role in bacterial adaptation through the antibiotic concentration. Lactobacillus casei FNCC 0090 is one of the probiotic bacteria that has an ability to survive in tetracycline by expressing the tetM gene. The aims of this study are to observe the possibilities of mutation happened in L.casei FNCC 0090 by exposing in sub-lethal dose of tetracycline and also observing the instability of the tetM gene by comparing the sequence between the wild type and mutant. L.casei FNCC 0090 has a lethal dose in 60 µg/ml, low concentration is applied to induce the mutation, the range from 10 µg/ml, 15 µg/ml, 30 µg/ml, 45 µg/ml, and 50 µg/ml. L.casei FNCC 0090 is exposed to the low concentration from lowest to the highest concentration to induce the adaptation. Plasmid is isolated from the highest concentration culture which is 50 µg/ml by using modified alkali lysis method with the addition of lysozyme. The tetM gene is isolated by using PCR (Polymerase Chain Reaction) method, then PCR amplicon is purified and sequenced. Sequencing is done on both samples, wild type and mutant. Both sequences are compared and the mutations can be traced in the presence of nucleotides changes. The changing of the nucleotides means that the tetM gene is instable.

Keywords: L. casei FNCC 0090, probiotic, tetM, tetracycline

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Authors: Vanessa Funk, Steven Blum, Stephanie Cole, Jorge Maciel, Matthew Lux

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Paper-based synthetic gene circuits offer a new paradigm for programmable, fieldable biodetection. We demonstrate that by freeze-drying gene circuits with in vitro expression machinery, we can use complimentary RNA sequences to trigger colorimetric changes upon rehydration. We have successfully utilized both green fluorescent protein and luciferase-based reporters for easy visualization purposes in solution. Through several efforts, we are aiming to use this new platform technology to address a variety of needs in portable detection by demonstrating several more expression and reporter systems for detection functions on paper. In addition to RNA-based biodetection, we are exploring the use of various mechanisms that cells use to respond to environmental conditions to move towards all-hazards detection. Examples include explosives, heavy metals for water quality, and toxic chemicals.

Keywords: cell-free lysates, detection, gene circuits, in vitro

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Authors: Paul Shize Li, Frank Alber

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A fundamental task of clinical genomics is to unravel the functions of genes and their associations with disorders. Although experimental biology has made efforts to discover and elucidate the molecular mechanisms of individual genes in the past decades, still about 40% of human genes have unknown functions, not to mention the diseases they may be related to. For those biologists who are interested in a particular gene with unknown functions, a powerful computational method tailored for inferring the functions and disease relevance of uncharacterized genes is strongly needed. Studies have shown that genes strongly linked to each other in multiple biological networks are more likely to have similar functions. This indicates that the densely connected subgraphs in multiple biological networks are useful in the functional and phenotypic annotation of uncharacterized genes. Therefore, in this work, we have developed an integrative network approach to identify the frequent local clusters, which are defined as those densely connected subgraphs that frequently occur in multiple biological networks and consist of the query gene that has few or no disease or function annotations. This is a local clustering algorithm that models multiple biological networks sharing the same gene set as a three-dimensional matrix, the so-called tensor, and employs the tensor-based optimization method to efficiently find the frequent local clusters. Specifically, massive public gene expression data sets that comprehensively cover dynamic, physiological, and environmental conditions are used to generate hundreds of gene co-expression networks. By integrating these gene co-expression networks, for a given uncharacterized gene that is of biologist’s interest, the proposed method can be applied to identify the frequent local clusters that consist of this uncharacterized gene. Finally, those frequent local clusters are used for function and disease annotation of this uncharacterized gene. This local tensor clustering algorithm outperformed the competing tensor-based algorithm in both module discovery and running time. We also demonstrated the use of the proposed method on real data of hundreds of gene co-expression data and showed that it can comprehensively characterize the query gene. Therefore, this study provides a new tool for annotating the uncharacterized genes and has great potential to assist clinical genomic diagnostics.

Keywords: local tensor clustering, query gene, gene co-expression network, gene annotation

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Authors: Alieh Farshbaf

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Introduction: Current anti-retroviral drugs have some restrictions for treatment of HIV-1 infection. The efficacy of retroviral drugs is not same in different infected patients and the virus rebound from latent reservoirs after stopping them. Recently, the engineering of stem cells and gene therapy provide new approaches to eliminate some drug problems by induction of resistance to HIV-1. Literature review: Up to now, AIDS-restriction genes (ARGs) were suitable candidate for gene and cell therapies, such as cc-chemokine receptor-5 (CCR5). In this manner, CCR5 provide effective cure in Berlin and Boston patients by inducing of HIV-1 resistance with allogeneic stem cell transplantation. It is showed that Zinc Finger Nuclease (ZFN) could induce HIV-1 resistance in stem cells of infected patients by homologous recombination or non-end joining mechanism and eliminate virus loading after returning the modified cells. Then, gene modification by HIV restriction factors, as TRIM5, introduced another gene candidate for HIV by interfering in infection process. These gene modifications/editing provided by stem cell futures that improve treatment in refractory disease such as HIV-1. Conclusion: Although stem cell transplantation has some complications, but in compare to retro-viral drugs demonstrated effective cure by elimination of virus loading. On the other hand, gene therapy is cost-effective for an infected patient than retroviral drugs payment in a person life-long. The results of umbilical cord blood stem cell transplantation showed that gene and cell therapy will be applied easier than previous treatment of AIDS with high efficacy.

Keywords: stem cell, AIDS, gene modification, cell engineering

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Authors: Wang Liguang, Zhang Xueqing

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The build-operate-transfer (BOT) project delivery system has provided effective routes to mobilize private sector funds, innovative technologies, management skills and operational efficiencies for public infrastructure development and have been widely used in China during the last 20 years. Many BOT projects in China will be smoothly transferred to the government soon and the transfer stage, which is considered as the last stage, must be studied carefully and handled well to achieve the overall success of BOT projects. There will be many issues faced by both the public sector and private sector in the transfer stage of BOT projects, including project post-assessment, technology and documents transfer, personal training and staff transition, etc. and sometimes additional legislation is needed for future operation and management of facilities. However, most previous studies focused on the bidding, financing, and building and operation stages instead of transfer stage. This research identifies nine key issues in the transfer stage of BOT projects through a comprehensive study on three cases in China, and the expert interview and expert discussion meetings are held to validate the key issues and give detail analysis. A proposed framework of transfer management is prepared based on the experiences derived and lessons drawn from the case studies and expert interview and discussions, which is expected to improve the transfer management of BOT projects in practice.

Keywords: BOT project, key issues, transfer management, transfer stage

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Authors: Habib Onsori, Somayeh Akrami, Mohammad Rahmati

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Deafness is the most common sensory disorder with the frequency of 1/1000 in many populations. Mutations in the GJB2 (CX26) gene at the DFNB1 locus on chromosome 13q12 are associated with congenital hearing loss. Approximately 80% of congenital hearing loss cases are recessively inherited and 15% dominantly inherited. Mutations of the GJB2 gene, encoding gap junction protein Connexin 26 (Cx26), are the most common cause of hereditary congenital hearing loss in many countries. This report presents two cases of different mutations from Iranian patients with bilateral hearing loss. DNA studies were performed for the GJB2 gene by PCR and sequencing methods. In one of them, direct sequencing of the gene showed a heterozygous T→C transition at nucleotide 604 resulting in a cysteine to arginine amino acid substitution at codon 202 (C202R) in the fourth extracellular domain (TM4) of the protein. The analyses indicate that the C202R mutation appeared de novo in the proband with a possible dominant effect (GenBank: KF 638275). In the other one, DNA sequencing revealed a compound heterozygous mutation (35delG, 363delC) in the Cx26 gene that is strongly associated with congenital non-syndromic hearing loss (NSHL). So screening the mutations for hearing loss individuals referring to genetics counseling centers before marriage and or pregnancy is recommended.

Keywords: CX26, deafness, GJB2, mutation

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Authors: Mezigheche Nawel, Gouasmia Abdelhacine, Athmani Allaeddine, Merzoud Mouloud

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Masonry infill walls are inevitable in the self-supporting structures, but their contribution in the resistance of earthquake loads is generally neglected in the structural analyses. The principal aim of this work through a numerical study of the behavior of masonry infill walls in structures subjected to horizontal load is to propose by finite elements numerical modeling, a more reliable approach, faster and close to reality. In this study, 3D finite element analysis was developed to study the behavior of masonry infill walls in structures subjected to horizontal load: The finite element software being used was ABAQUS, it is observed that more rigidity of the masonry filling is significant, more the structure is rigid, so we can conclude that the filling brings an additional rigidity to the structure not to be neglected. It is also observed that when the framework is subjected to horizontal loads, the framework separates from the filling on the level of the tended diagonal.

Keywords: finite element, masonry infill walls, rigidity of the masonry, tended diagonal

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Authors: Ekaterina M. Myasnikova, Andrey A. Makashov, Alexander V. Spirov

Abstract:

First manifestation of a segmentation pattern in the early Drosophila development is the formation of expression domains (along with the main embryo axis) of genes belonging to the trunk gene class. Highly variable expression of genes from gap family in early Drosophila embryo is strongly reduced by the start of gastrulation due to the gene cross-regulation. The dynamics of gene expression is described by a gene circuit model for a system of four gap genes. It is shown that for the formation of a steep and stationary border by the model it is necessary that there existed a nucleus (modeling point) in which the gene expression level is constant in time and hence is described by a stationary equation. All the rest genes expressed in this nucleus are in a dynamic equilibrium. The mechanism of border formation associated with the existence of a stationary nucleus is also confirmed by the experiment. An important advantage of this approach is that properties of the system in a stationary nucleus are described by algebraic equations and can be easily handled analytically. Thus we explicitly characterize the cross-regulation properties necessary for the robustness and formulate the conditions providing this effect through the properties of the initial input data. It is shown that our formally derived conditions are satisfied for the previously published model solutions.

Keywords: drosophila, gap genes, reaction-diffusion model, robustness

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Authors: Kien-Trinh Thi Bui, Cuong Manh Nguyen

Abstract:

In order to simulate and reproduce the operational characteristics of a dam visually, it is necessary to capture the displacement at different measurement points and analyze the observed movement data promptly to forecast the dam safety. The accuracy of forecasts is further improved by applying machine learning methods to data analysis progress. In this study, the horizontal displacement monitoring data of the Ialy hydroelectric dam was applied to machine learning algorithms: Gaussian processes, multi-layer perceptron neural networks, and the M5-rules algorithm for modelling and forecasting of horizontal displacement of the Ialy hydropower dam (Vietnam), respectively, for analysing. The database which used in this research was built by collecting time series of data from 2006 to 2021 and divided into two parts: training dataset and validating dataset. The final results show all three algorithms have high performance for both training and model validation, but the MLPs is the best model. The usability of them are further investigated by comparison with a benchmark models created by multi-linear regression. The result show the performance which obtained from all the GP model, the MLPs model and the M5-Rules model are much better, therefore these three models should be used to analyze and predict the horizontal displacement of the dam.

Keywords: Gaussian processes, horizontal displacement, hydropower dam, Ialy dam, M5-Rules, multi-layer perception neural networks

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Authors: Sittipong Jarernprasert, Enrique Bazan-Zurita, Paul C. Rizzo

Abstract:

Currently, seismic probabilistic risk assessments (SPRA) for nuclear facilities use In-Structure Response Spectra (ISRS) in the calculation of fragilities for systems and components. ISRS are calculated via dynamic analyses of the host building subjected to two orthogonal components of horizontal ground motion. Each component is defined as the median motion in any horizontal direction. Structural engineers applied the components along selected X and Y Cartesian axes. The ISRS at different locations in the building are also calculated in the X and Y directions. The choice of the directions of X and Y are not specified by the ground motion model with respect to geographic coordinates, and are rather arbitrarily selected by the structural engineer. Normally, X and Y coincide with the “principal” axes of the building, in the understanding that this practice is generally conservative. For SPRA purposes, however, it is desirable to remove any conservatism in the estimates of median ISRS. This paper examines the effects of the direction of horizontal seismic motion on the ISRS on typical nuclear structure. We also evaluate the variability of ISRS calculated along different horizontal directions. Our results indicate that some central measures of the ISRS provide robust estimates that are practically independent of the selection of the directions of the horizontal Cartesian axes.

Keywords: seismic, directionality, in-structure response spectra, probabilistic risk assessment

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Authors: Tovondahiniriko Fanjirindratovo, Olga Ramiarinjanahary, Paulisimone Rasoavonjy

Abstract:

The sunshine duration, which is the sum of all the moments when the solar beam radiation is up to a minimal value, is an important parameter for climatology, tourism, agriculture and solar energy. Its measure is usually given by a pyrheliometer installed on a two-axis solar tracker. Due to the high cost of this device and the availability of global radiation on a horizontal surface, on the other hand, several studies have been done to make a correlation between global radiation and sunshine duration. Most of these studies are fitted for the northern hemisphere using a pyrheliometric database. The aim of the present work is to list and assess all the existing methods and apply them to Reunion Island, a tropical region in the southern hemisphere. Using a database of ten years, global, diffuse and beam radiation for a horizontal surface are employed in order to evaluate the uncertainty of existing algorithms for a tropical region. The methodology is based on indirect comparison because the solar beam radiation is not measured but calculated by the beam radiation on a horizontal surface and the sun elevation angle.

Keywords: Carpentras method, data fitting, global radiation, sunshine duration, Slob and Monna algorithm, step algorithm

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