Search results for: gene transfer

Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: Muhammad Imran, Sarfraz Shafiq, Xiangru Tang

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

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

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Authors: Farahnaz Motamedi Sedeh, Homayoon Mahravani, Parvin Shawrang, Mehdi Behgar

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Most countries use inactivated binary ethylenimine (BEI) vaccines to control and prevent Foot-and-Mouth Disease (FMD). However, this vaccine induces a short-term humoral immune response in animals. This study investigated the cellular and humoral immune responses in homologous and prime-boost (PB) groups in the BALB/c mouse model. FMDV strain O/IRN/1/2007 was propagated in the BHK-21 cell line and inactivated by three methods, including a chemical with BEI to produce a conventional vaccine (CV), a gamma irradiation vaccine (GIV), and an electron irradiated vaccine (EIV). Three vaccines were formulated with the adjuvant aluminum hydroxide gel. In addition, a DNA vaccine was prepared by amplifying the virus VP1 gene pcDNA3.1 plasmid. In addition, the plasmid encoding the granulocyte-macrophage colony-stimulating factor gene (GM-CSF) was used as a molecular adjuvant. Eleven groups of five mice each were selected, and the vaccines were administered as homologous and heterologous strategy prime-boost (PB) in three doses two weeks apart. After the evaluation of neutralizing antibodies, interleukin (IL)-2, IL-4, IL-10, interferon-gamma (INF-γ), and MTT assays were compared in the different groups. The pcDNA3.1+VP1 cassette was prepared and confirmed as a DNA vaccine. The virus was inactivated by gamma rays and electron beams at 50 and 55 kGy as GIV and EIV, respectively. Splenic lymphocyte proliferation in the inactivated vaccinated homologous groups was significantly lower (P≤0.05) compared with the heterologous prime-boosts (PB1, PB2, PB3) and DNA + GM-CSF groups (P≤0.05). The highest SNT titer was observed in the inactivated vaccine groups. IFN-γ and IL-2 were higher in the vaccinated groups. It was found that although there was a protective humoral immune response in the groups with inactivated vaccine, there was adequate cellular immunity in the group with the DNA vaccine. However, the strongest cellular and humoral immunity was observed in the PB groups. The primary injection was accompanied by DNA vaccine + GM-CSF and boosted injection with GIV or CV.

Keywords: foot and mouth disease, irradiated vaccine, immune responses, DNA vaccine, prime boost strategy

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Authors: Pakize Ozlem Kurt Polat

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GMO (genetically modified organism) is the result of a laboratory process where genes from the DNA of one species are extracted and artificially forced into the genes of an unrelated plant or animal. This technology includes; nucleic acid hybridization, recombinant DNA, RNA, PCR, cell culture and gene cloning techniques. The studies are divided into three groups of properties transferred to the transgenic plant. Up to 59% herbicide resistance characteristic of the transfer, 28% resistance to insects and the virus seems to be related to quality characteristics of 13%. Transgenic crops are not included in the commercial production of each product; mostly commercial plant is soybean, maize, canola, and cotton. Day by day increasing GMO interest can be listed as follows; Use in the health area (Organ transplantation, gene therapy, vaccines and drug), Use in the industrial area (vitamins, monoclonal antibodies, vaccines, anti-cancer compounds, anti -oxidants, plastics, fibers, polyethers, human blood proteins, and are used to produce carotenoids, emulsifiers, sweeteners, enzymes , food preservatives structure is used as a flavor enhancer or color changer),Use in agriculture (Herbicide resistance, Resistance to insects, Viruses, bacteria, fungi resistance to disease, Extend shelf life, Improving quality, Drought , salinity, resistance to extreme conditions such as frost, Improve the nutritional value and quality), we explain all this methods step by step in this research. GMO has advantages and disadvantages, which we explain all of them clearly in full text, because of this topic, worldwide researchers have divided into two. Some researchers thought that the GMO has lots of disadvantages and not to be in use, some of the researchers has opposite thought. If we look the countries law about GMO, we should know Biosafety law for each country and union. For this Biosecurity reasons, the problems caused by the transgenic plants, including Turkey, to minimize 130 countries on 24 May 2000, ‘the United Nations Biosafety Protocol’ signed nudes. This protocol has been prepared in addition to Cartagena Biosafety Protocol entered into force on September 11, 2003. This protocol GMOs in general use by addressing the risks to human health, biodiversity and sustainable transboundary movement of all GMOs that may affect the prevention, transit covers were dealt and used. Under this protocol we have to know the, ‘US Regulations GMO’, ‘European Union Regulations GMO’, ‘Turkey Regulations GMO’. These three different protocols have different applications and rules. World population increasing day by day and agricultural fields getting smaller for this reason feeding human and animal we should improve agricultural product yield and quality. Scientists trying to solve this problem and one solution way is molecular biotechnology which is including the methods of GMO too. Before decide to support or against the GMO, should know the GMO protocols and it effects.

Keywords: biotechnology, GMO (genetically modified organism), molecular marker

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Authors: Maciej Sobczak, Julita Pietrzak, Tomasz Płoszaj, Agnieszka Robaszkiewicz

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Brg1, a member of SWI/SNF complex, plays a role in chromatin remodeling, therefore, regulates expression of many genes. Brg1 is an ATPase of SWI/SNF complex, thus its activity requires ATP. Through its bromodomain recognizes acetylated histone residues and evicts them, thus promoting transcriptionally active state of chromatin. One of the enzymes that is responsible for acetylation of histone residues is Ep300. It was previously shown in the literature that cooperation of Brg1 and Ep300 occurs at the promoter regions that have binding sites for E2F-family transcription factors as well as CpG islands. According to literature, approximately 20% of human cancer possess mutation in Brg1 or any other crucial SWI/SNF subunit. That phenomenon makes Brg1-Ep300 a very promising target for anti-cancer therapy. Therefore in our study, we investigated if physical interaction between Brg1 and Ep300 exists and what impact those two proteins have on key for breast cancer cells processes such as DNA damage repair and cell proliferation. Bioinformatical analysis pointed out, that genes involved in cell proliferation and DNA damage repair are overexpressed in MCF7 and MDA-MB-231 cells. Moreover, promoter regions of these genes are highly acetylated, which suggests high transcriptional activity of those sites. Notably, many of those gene possess within their promoters an E2F, Brg1 motives, as well as CpG islands and acetylated histones. Our data show that Brg1 physically interacts with Ep300, and together they regulate expression of genes involved in DNA damage repair and cell proliferation. Upon inhibiting Brg1 or Ep300, expression of vital for cancer cell survival genes such as CDK2/4, BRCA1/2, PCNA, and XRCC1 is decreased in MDA-MB-231 and MCF7 cells. Moreover, inhibition or silencing of either Brg1 or Ep300 leads to cell cycle arrest in G1. After inhibition of BRG1 or Ep300 on tested gene promoters, the repressor complex including Rb, HDAC1, and EZH2 is formed, which inhibits gene expression. These results highlight potentially significant target for targeted anticancer therapy to be introduced as a supportive therapy.

Keywords: brg1, ep300, breast cancer, epigenetics

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Authors: Ian Campbell, Gillian Mitchell, Paul James, Na Li, Ella Thompson

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The genetic cause of the majority of multiple-case breast cancer families remains unresolved. Next generation sequencing has emerged as an efficient strategy for identifying predisposing mutations in individuals with inherited cancer. We are conducting whole exome sequence analysis of germ line DNA from multiple affected relatives from breast cancer families, with the aim of identifying rare protein truncating and non-synonymous variants that are likely to include novel cancer predisposing mutations. Data from more than 200 exomes show that on average each individual carries 30-50 protein truncating mutations and 300-400 rare non-synonymous variants. Heterogeneity among our exome data strongly suggest that numerous moderate penetrance genes remain to be discovered, with each gene individually accounting for only a small fraction of families (~0.5%). This scenario marks validation of candidate breast cancer predisposing genes in large case-control studies as the rate-limiting step in resolving the missing heritability of breast cancer. The aim of this study is to screen genes that are recurrently mutated among our exome data in a larger cohort of cases and controls to assess the prevalence of inactivating mutations that may be associated with breast cancer risk. We are using the Agilent HaloPlex Target Enrichment System to screen the coding regions of 168 genes in 1,000 BRCA1/2 mutation-negative familial breast cancer cases and 1,000 cancer-naive controls. To date, our interim analysis has identified 21 genes which carry an excess of truncating mutations in multiple breast cancer families versus controls. Established breast cancer susceptibility gene PALB2 is the most frequently mutated gene (13/998 cases versus 0/1009 controls), but other interesting candidates include NPSR1, GSN, POLD2, and TOX3. These and other genes are being validated in a second cohort of 1,000 cases and controls. Our experience demonstrates that beyond PALB2, the prevalence of mutations in the remaining breast cancer predisposition genes is likely to be very low making definitive validation exceptionally challenging.

Keywords: predisposition, familial, exome sequencing, breast cancer

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Authors: Abhishek Kumar, Mohamed Awadein, Georg Gramse, Luyang Song, He Sun, Wolfgang Schofberger, Stefan Müllegger

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Electron transfer is a crucial part of chemical reactions which drive everyday processes. With the help of an electro-chemical radio frequency scanning tunneling microscopy (EC-RF-STM) setup, we are observing single electron mediated oxidation-reduction processes in molecules like ferrocene and transition metal corroles. Combining the techniques of scanning microwave microscopy and cyclic voltammetry allows us to monitor such processes with attoampere sensitivity. A systematic study of such phenomena would be critical to understanding the nano-scale behavior of catalysts, molecular sensors, and batteries relevant to the development of novel material and energy applications.

Keywords: radiofrequency, STM, cyclic voltammetry, ferrocene

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Authors: M. Lizzy Madiwani, Ignatious Ncube, Evelyn Madoroba

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This study was designed to determine the distribution of pathogenic bacteria in household raised chickens and study their virulence and antibiotic profiles. For this purpose, 40 chickens were purchased from families in the Capricorn district and sacrificed for sampling. Tissues were cultured on different bacteriological media followed by biotyping using Matrix-assisted Laser Desorption Ionization-time of Flight (MALDI-TOF). Disk diffusion test was performed to determine the antibiotic susceptibility profiles of these bacteria. Out of a total of 160 tissue samples evaluated, E. coli and Salmonella were detected in these tissues. Furthermore, determination of the pathogenic E. coli and Salmonella strains at species level using primer sets that target selected genes of interest in the polymerase chain reaction (PCR) assay was employed. The invA gene, a confirmatory gene of Salmonella was detected in all the Salmonella isolates. The study revealed that there is a high distribution of Salmonella and pathogenic E. coli in these chickens. Therefore, further studies on identification at the species level are highly recommended to provide management and sanitation practices to lower this prevalence. The antimicrobial susceptibly data generated from this study can be a valuable reference to veterinarians for treating bacterial diseases in poultry.

Keywords: antimicrobial, Escherichia coli, pathogens, Salmonella

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Authors: Jung Hyun Kim, Gyo Woo Lee

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In this study, the enhancement of the heat release performance of an extruded-type heat sink to prepare the large-capacity solar inverter thru the flow holes in the base plate near the heat sources was investigated. Optimal location and number of the holes in the baseplate were determined by using a commercial computation program. The heat release performance of the shape-modified heat sink was measured experimentally and compared with that of the simulation. The heat sink with 12 flow holes in the 18-mm-thick base plate has a 8.1% wider heat transfer area, a 2.5% more mass flow of air, and a 2.7% higher heat release rate than those of the original heat sink. Also, the surface temperature of the base plate was lowered 1.5°C by the holes.

Keywords: heat sink, forced convection, heat transfer, performance evaluation, flow holes

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Authors: Stavros Palavouzis, Alexandra Triantafyllopoulou, Aliki Tzima, Epaminondas Paplomatas

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Mating-type genes are present in most filamentous fungi, even though teleomorphs for all species have not been recorded. Our study tries to explore the effect of different growth conditions on the expression of MAT genes in Neofusicoccum mediterraneum. As such, selected isolates were grown in potato dextrose broth or in water agar supplemented with pine needles under a 12 h photoperiod, as well as in constant darkness. Mycelia and spores were collected at different time points, and RNA extraction was performed, with the extracted product being used for cDNA synthesis. New primers for MAT gene expression were designed while qPCR results are underway. The second part of the study involved the isolation and cloning in a selected pGEM-T vector of the Botryosphaeria dothidea MAT1 1 1 and MAT1 2 1 mating genes, including flanking regions. As a next step, the genes were amplified using newly designed primers with engineered restriction sites. Amplicons were excised and subsequently sub-cloned in appropriate binary vectors. The constructs were afterward inserted into Agrobacterium tumefaciens and utilized for Agrobacterium-mediated transformation (ATMT) of Neofusicoccum mediterraneum. At the same time, the transformation of a Verticillium dahliae tomato race 1 strain (70V) was performed as a control. While the procedure was successful in regards to V. dahliae, transformed strains of N. mediterraneum could not be obtained. At present, a new transformation protocol, which utilizes a combination of protoplast and Agro transformation, is being evaluated.

Keywords: anamorph, heterothallism, perithecia, pycnidia, sexual stage

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Authors: Bahman Ghaderi, Hedayat Hosseini, Parviz Kafche

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The role of knowledge management processes in achieving the strategic goals of organizations is crucial. To this end, understanding the relationship between knowledge management processes and different aspects of strategic thinking (followed by long-term organizational planning) should be considered. This research examines the relationship between each of the five knowledge management processes (creation, storage, transfer, audit, and deployment) with each dimension of strategic thinking (vision, creativity, thinking, communication and analysis) in one of the major sectors of the food industry in Iran. In this research, knowledge management and its dimensions (knowledge acquisition, knowledge storage, knowledge transfer, knowledge auditing, and finally knowledge utilization) as independent variables and strategic thinking and its dimensions (creativity, systematic thinking, vision, strategic analysis, and strategic communication) are considered as the dependent variable. The statistical population of this study consisted of 245 managers and employees of Minoo Food Industrial Group in Tehran. In this study, a simple random sampling method was used, and data were collected by a questionnaire designed by the research team. Data were analyzed using SPSS 21 software. LISERL software is also used for calculating and drawing models and graphs. Among the factors investigated in the present study, knowledge storage with 0.78 had the most effect, and knowledge transfer with 0.62 had the least effect on knowledge management and thus on strategic thinking.

Keywords: knowledge management, strategic thinking, knowledge management processes, food industry

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Authors: Michel Kulhandjian, Dimitris A. Pados

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The objective of this work is to develop a theoretical framework for reliable digital recording system identification from digital audio files alone, for forensic purposes. A digital recording system consists of a microphone and a digital sound processing card. We view the cascade as a system of unknown transfer function. We expect same manufacturer and model microphone-sound card combinations to have very similar/near identical transfer functions, bar any unique manufacturing defect. Input voice (or other) signals are modeled as non-stationary processes. The technical problem under consideration becomes blind deconvolution with non-stationary inputs as it manifests itself in the specific application of digital audio recording equipment classification.

Keywords: blind system identification, audio fingerprinting, blind deconvolution, blind dereverberation

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Authors: S. Pradhan, D. Pradhan, G. Tripathy, T. Dasmohapatra

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Suppressors of cytokine signalling (SOCS3), a newly indentified anti-apoptotic molecule is a downstream effecter of the receptor tyrosine kinase-Ras signalling pathway. Current study has uncovered that SOCS3 may have wide and imperative capacities, particularly because of its close correlation with malignant tumors. To investigate the impact of SOCS3 on MDR, we analyzed the expression of P-gp and SOCS3 by immune-histochemistry and found there was positive correlation between them. At that point we effectively interfered with RNA translation by the contamination of siRNA of SOCS3 into MCF7/ADM breast cancer cell lines through a lentivirus, and the expression of the target gene was significantly inhibited. After RNAi the drug resistance was reduced altogether and the expression of MDR1 mRNA and P-gp in MCF7/ADM cell lines demonstrated a significant decrease. Likewise the expression of P53 protein increased in a statistically significant manner (p ≤ 0.01) after RNAi exposure. Moreover, flowcytometry analysis uncovers that cell cycle and anti-apoptotic enhancing capacity of cells changed after RNAi treatment. These outcomes proposed SOCS3 may take part in breast cancer MDR by managing MDR1 and P53 expression, changing cell cycle and enhancing the anti-apoptotic ability.

Keywords: SOCS3gene, breast cancer, multidrug resistance, MDR1 gene, RNA interference

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Authors: Zhao Wang, Hong Yan

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In this paper, a unified-gas kinetic scheme (UGKS) for the gas-particle flow is constructed. UGKS is a direct modeling method for both continuum and rarefied flow computations. The dynamics of particle and gas are described as rarefied and continuum flow, respectively. Therefore, we use the Bhatnagar-Gross-Krook (BGK) equation for the particle distribution function. For the gas phase, the gas kinetic scheme for Navier-Stokes equation is solved. The momentum transfer between gas and particle is achieved by the acceleration term added to the BGK equation. The new scheme is tested by a 2cm-in-thickness dense bed comprised of glass particles with 1.5mm in diameter, and reasonable agreement is achieved.

Keywords: gas-particle flow, unified gas-kinetic scheme, momentum transfer, shock-induced fluidization

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Authors: Ghazanfar Ali, Fahad N Almajhdi

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This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: influenza A (H3N2), genetic characterization, viral isolation, RT-PCR, Saudi Arabia

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Authors: Chengcao Sun, Shujun Li, Cuili Yang, Yongyong Xi, Liang Wang, Feng Zhang, Dejia Li

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Recently, the long non-coding RNA (lncRNA) NEAT1 has been identified as an oncogenic gene in multiple cancer types and elevated expression of NEAT1 was tightly linked to tumorigenesis and cancer progression. However, the molecular basis for this observation has not been characterized in progression of non-small cell lung cancer (NSCLC). In our studies, we identified NEAT1 was highly expressed in NSCLC patients and was a novel regulator of NSCLC progression. Patients whose tumors had high NEAT1 expression had a shorter overall survival than patients whose tumors had low NEAT1 expression. Further, NEAT1 significantly accelerates NSCLC cell growth and metastasis in vitro and tumor growth in vivo. Additionally, by using bioinformatics study and RNA pull down combined with luciferase reporter assays, we demonstrated that NEAT1 functioned as a competing endogenous RNA (ceRNA) for has-miR-377-3p, antagonized its functions and led to the de-repression of its endogenous targets E2F3, which was a core oncogene in promoting NSCLC progression. Taken together, these observations imply that the NEAT1 modulated the expression of E2F3 gene by acting as a competing endogenous RNA, which may build up the missing link between the regulatory miRNA network and NSCLC progression.

Keywords: long non-coding RNA NEAT1, hsa-miRNA-377-3p, E2F3, non-small cell lung cancer, tumorigenesis

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Authors: Dogan Ciloglu, Abdurrahim Bolukbasi, Harun Cifci

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In this study, the experiments were carried out to determine the best coolant for the quenching process among water-based silica, alumina, titania and copper oxide nanofluids (0.1 vol%). A sphere made up off brass material was used in the experiments. After the spherical test specimen was heated at high temperatures, it was suddenly plunged into the nanofluid suspensions. All experiments were performed at saturated conditions and under atmospheric pressure. Using the temperature-time data of the specimen, the cooling curves were obtained. The experimental results showed that the cooling performance of test specimen depended on the type of nanofluids. The silica nanoparticles enhanced the performance of boiling heat transfer and it is the best coolant for the quenching among other nanoparticles.

Keywords: quenching, nanofluid, pool boiling, heat transfer

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Authors: Nagri Sateesh, Kundavarapu Vengalrao, Kopparthi Phaneendra Kumar

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Vacuum assisted resin transfer molding (VARTM) is one of the manufacturing technique that is viable for production of fiber reinforced polymer composite components suitable for aerospace, marine and commercial applications. However, the repeatable quality of the product can be achieved by critically fixing the process parameters such as Vacuum Pressure (VP) and permeability of the preform. The present investigation is aimed at studying the effect of permeability for production of Glass Fiber Reinforced Plastic (GFRP) components with consistent quality. The VARTM mould is made with an acrylic transparent top cover to observe and record the resin flow pattern. Six layers of randomly placed glass fiber under five different vacuum pressures VP1 = 0.013, VP2 = 0.026, VP3 = 0.039, VP4 = 0.053 and VP5 = 0.066 MPa were studied. The laminates produced by this process under the above mentioned conditions were characterized with ASTM D procedures so as to study the effect of these process parameters on the quality of the laminate. Moreover, as mentioned there is a considerable effect of permeability on the impact strength and the void content in the laminates under different vacuum pressures. SEM analysis of the impact tested fractured GFRP composites showed the bonding of fiber and matrix.

Keywords: permeability, vacuum assisted resin transfer molding (VARTM), ASTM D standards, SEM

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Authors: Elham Ahmadi, Mehrdad Ravanshad, Joyce Fingeroth, Mazyar Ziyaeyan, Rajesh Panigrahi, Jun Xie, Gao Guangping

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B-cell proliferative disorders often occur among persons that are T-cell compromised. These disorders are primarily EBV+ and can first present with a focal lesion. Direct introduction of oncolytic viruses into localized tumors provides theoretical advantages over chemotherapy and immunotherapy by reducing systemic toxicity, to which the immunocompromised host is most vulnerable. Widely studied as a vehicle for gene therapy, AAV has only rarely been applied to treat cancer. As a prelude to development of a therapeutic vehicle, we assessed the ability of 15 distinct recombinant AAV serotypes (rAAV1, rAAV2, rAAV3b, rAAV4, rAAV5, rAAV6, rAAV6.2, rAAV6TM, rAAV7, rAAV8, rAAVrh8, rAAV9, rAAVrh10, rAAV39, rAAV43) bearing eGFP to infect human B-cell tumor lines compared with primary B-cells in vitro. Enhanced infection of tumor lines by AAV 6.2 was demonstrated by flow cytometry. EBV superinfection of EBV negative B-cell tumor lines increased susceptibility to AAV6.2 infection. As proof of concept, AAV6.2 bearing HSV-1 thymidine kinase in place of eGFP eliminated tumor cells upon exposure to ganciclovir.

Keywords: AAV, gene therapy, lymphoma, malignancy, tropism

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Authors: L. Musak, J. Valachova, T. Vasicko, O. Osina

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Stainless steel is resistant to electrochemical corrosion by passivation. Welders are greatly exposed to welding fumes of toxic metals, which added to this steel. The content of chromium (Cr) is above 11.5%, Ni and Mo from 2 to 6.5%. The aim of the study was the evaluation of occupational exposure to Cr, chromosome analysis and valuation of individual susceptibility polymorphism of gene CCND1 c.870 G>A. The exposed group was consisted from 117 welders of stainless steels. The average age was 38.43 years and average exposure time 7.14 years. Smokers represented 40.17%. The control group consisted of 123 non-exposed workers with an average age of 39.74 years and time employment 16.67 years. Smokers accounted for 22.76%. Analysis of Cr in blood and urine was performed by atomic absorption spectrophotometry (AAS Varian SpectraAA 30P) with electrothermal decomposition of the sample in the graphite furnace. For the evaluation of chromosomal aberrations (CA) cytogenetic analysis of peripheral blood lymphocytes was used. Gene polymorphism was determined by PCR-RFLP reaction using appropriate primers and restriction enzymes. For statistic analysis the Mann-Whitney U-test was used. The mean Cr level in blood of exposed group was 0.095 µmol/l (0.019 min - max 0.504). No value exceeds the average normal value. The mean value Cr in urine was 7.9 µmol/mol creatinine (min 0.026 to max 19.26). The total number of CA was 1.86% in compared to 1.70% controls. (CTA-type 0.90% vs. 0.80% and CSA-type 0.96% vs. 0.90%). In the number of total CA statistical difference was observed between smokers and non-smokers of exposed group (S-1.57% vs. NS-2.04%, P<0.05). In CCND1 gene polymorphisms was observed the increasing of the total CA with wild-type allele (WT) via heterozygous to the VAR genotype (1.44% <1.82% <2.13%). A statistically higher incidence of CTA-type aberrations in variant genotypes between exposed and control groups was observed (1.22% vs. 0.59%, P <0.05). The work place is usually higher source of exposure to harmful factors. Workers need consistent and frequent health control. In assessing the risk of adverse effects of metals it is important to consider their persistence, behavior and bioavailability. Prolonged exposure to carcinogens may not manifest symptoms of poisoning, but delayed effects may occur, which resulted in a higher incidence of malignant tumors.

Keywords: CCND1, genotoxicity, polymorphism, stainless steel, welders

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Authors: Shokoufeh Roudashti, Shahin Bahari, Fakhri Haghi, Habib Zeighami, Ghazal Naderi, Paniz Shirmast

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Background: Mycobacterium tuberculosis complex (MTBC) causes tuberculosis (TB) in humans and animals. Mycobacterium MTBC is one of the most important species of zoonotic pathogens that can be transmitted from cattle to humans. The disease can transmit to human by direct contact with the infected animals, drinking unpasteurized milk and consumption of uncooked meat. The presence of these opportunistic, pathogenic bacteria in bovine milk has emerged as a public-health concern, especially among individuals who consume raw milk. Tuberculosis MTBC is the predominant infectious cause of morbidity and morality worldwide, It is estimated that one third of the world population (approx. 1.8 billion persons) is infected with M. tuberculosis and each year there are 8 million new cases worldwide. The aim of this study, to detect Mycobacterium MTBC in raw milk samples using polymerase chain reaction (PCR). Materials and Methods: In the present study, 60 raw milk samples were collected from rural areas in Zanjan, Iran. After extraction of DNAs and using special primers for Is6110 gene as a marker, PCR was applied to detect the presence or non-presence of the related gene. Results: According to the findings of this study, 8 (13.5 %) out of 60 milk samples were positive for Mycobacterium spp (P < 0.1). Conclusions: The Outbreak of genus Mycobacteria spp in milk samples were determined to be relatively high in Zanjan, Iran.

Keywords: Mycobacteria spp, raw milk, PCR, Zanjan

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Authors: Louaifi Hamaili Samira, Mataoui Amina, Cheraitia Tadjeddine

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This investigation proposes a numerical analysis of two turbulent parallel jets impinging a heated plate. The heat transfer enhancement is carried out according of the main parameters of the jet-wall interaction. The numerical solution of the stationary equations (RANS) is performed by the finite volume method using the k - ε model. A parametric study is performed to evaluate simultaneously the effect of nozzle-plate distance and velocity ratios in the range 0≤λ≤1. It is found that good local cooling is obtained for λ= 0.25 when the impinging distance is between 4w and 8w than for velocity ratios λ=1 and λ= 0.75. On the other hand, for impinging distances exceeding 8w, the velocity ratio λ =0.75 is more appropriate for good local cooling of the plate.

Keywords: two unequal jets, turbulence, mixing, heat transfer, CFD

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Authors: Swarkar Sharma, Ekta Rai, Ankit Mahajan, Parvinder Kumar, Manoj K Dhar, Sushil Razdan, Kumarasamy Thangaraj, Carol Wise, Shiro Ikegawa M.D., K.K. Pandita M.D.

Abstract:

Rare disorders are poorly understood hence, remain uncharacterized or patients are misdiagnosed and get poor medical attention. A rare mysterious skeletal disorder that remained unidentified for decades and rendered many people physically challenged and disabled for life has been reported in an isolated remote village ‘Arai’ of Poonch district of Jammu and Kashmir. This village is located deep in mountains and the population residing in the region is highly consanguineous. In our survey of the region, 70 affected people were reported, showing similar phenotype, in the village with a population of approximately 5000 individuals. We were able to collect samples from two multi generational extended families from the village. Through Whole Exome sequencing (WES), we identified a rare variation NM_003880.3:c.156C>A NP_003871.1:p.Cys52Ter, which results in introduction of premature stop codon in WISP3 gene. We found this variation perfectly segregating with the disease in one of the family. However, this variation was absent in other family. Interestingly, a novel splice site mutation at position c.643+1G>A of WISP3 gene, perfectly segregating with the disease was observed in the second family. Thus, exploiting WES and putting different evidences together (familial histories and genetic data, clinical features, radiological and biochemical tests and findings), the disease has finally been diagnosed as a very rare recessive hereditary skeletal disease “Progressive Pseudorheumatoid Arthropathy of Childhood” (PPAC) also known as “Spondyloepiphyseal Dysplasia Tarda with Progressive Arthropathy” (SEDT-PA). This genetic characterization and identification of the disease causing mutations will aid in genetic counseling, critically required to curb this rare disorder and to prevent its appearance in future generations in the population. Further, understanding of the role of WISP3 gene the biological pathways should help in developing treatment for the disorder.

Keywords: whole exome sequencing, Next Generation Sequencing, rare disorders

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Authors: Hongmeng Su, Luyu Zhao, Yanyan Qian, Hong Fan

Abstract:

Aim: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors that endanger human health seriously. RNA methylation, especially N6-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C), a crucial epigenetic transcriptional regulatory mechanism, plays an important role in tumorigenesis, progression and prognosis. This research aims to systematically evaluate the prognostic value of m⁶A and m⁵C modulators in HCC patients. Methods: Twenty-four modulators of m⁶A and m⁵C were candidates to analyze their expression level and their contribution to predict the prognosis of HCC. Consensus clustering analysis was applied to classify HCC patients. Cox and LASSO regression were used to construct the risk model. According to the risk score, HCC patients were divided into high-risk and low/medium-risk groups. The clinical pathology factors of HCC patients were analyzed by univariate and multivariate Cox regression analysis. Results: The HCC patients were classified into 2 clusters with significant differences in overall survival and clinical characteristics. Nine-gene risk model was constructed including METTL3, VIRMA, YTHDF1, YTHDF2, NOP2, NSUN4, NSUN5, DNMT3A and ALYREF. It was indicated that the risk score could serve as an independent prognostic factor for patients with HCC. Conclusion: This study constructed a Nine-gene risk model by modulators of m⁶A and m⁵C and investigated its effect on the clinical prognosis of HCC. This model may provide important consideration for the therapeutic strategy and prognosis evaluation analysis of patients with HCC.

Keywords: hepatocellular carcinoma, m⁶A, m⁵C, prognosis, RNA methylation

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Authors: Z. Aziz, S. Terkhi, Y. Sefir, R. Djelti, S. Bentata

Abstract:

The effect of a uniform electric field across multi-barrier systems (InAs/InxGa1-xAs) is exhaustively explored by a computational model using exact Airy function formalism and the transfer-matrix technique. In the case of biased DFHBSL structure a strong reduction in transmission properties was observed and the width of the mini-band structure linearly decreases with the increase of the applied bias. This is due to the confinement of the states in the mini-band structure, which becomes increasingly important (Wannier-Stark Effect).

Keywords: dimer fibonacci height barrier superlattices, singular extended state, exact Airy function and transfer matrix formalism, bioinformatics

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Authors: Aziz Zoubir, Sefir Yamina, Djelti Redouan, Bentata Samir

Abstract:

The effect of a uniform electric field across multibarrier systems (GaAs/AlxGa1-xAs) is exhaustively explored by a computational model using exact Airy function formalism and the transfer-matrix technique. In the case of biased Dimer Fibonacci Height Barrier superlattices (DFHBSL) structure a strong reduction in transmission properties was observed and the width of the miniband structure linearly decreases with the increase of the applied bias. This is due to the confinement of the states in the miniband structure, which becomes increasingly important (Wannier-Stark effect).

Keywords: Dimer Fibonacci Height Barrier superlattices, singular extended states, exact Airy function, transfer matrix formalism

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Authors: Karthik Mittal

Abstract:

This study performs an unsupervised machine learning analysis to find clusters of related SNPs which highlight biological pathways that are important for the biological mechanisms of breast cancer. Studying genetic variations in isolation is illogical because these genetic variations are known to modulate protein production and function; the downstream effects of these modifications on biological outcomes are highly interconnected. After extracting the SNPs and their effect on different types of breast cancer using the MRBase library, two unsupervised machine learning clustering algorithms were implemented on the genetic variants: a k-means clustering algorithm and a hierarchical clustering algorithm; furthermore, principal component analysis was executed to visually represent the data. These algorithms specifically used the SNP’s beta value on the three different types of breast cancer tested in this project (estrogen-receptor positive breast cancer, estrogen-receptor negative breast cancer, and breast cancer in general) to perform this clustering. Two significant genetic pathways validated the clustering produced by this project: the MAPK signaling pathway and the connection between the BRCA2 gene and the ESR1 gene. This study provides the first proof of concept showing the importance of unsupervised machine learning in interpreting GWAS summary statistics.

Keywords: breast cancer, computational biology, unsupervised machine learning, k-means, PCA

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Authors: Tripta Dixit, Smita Sahu, William Selvamurthy, Sadhana Srivastava

Abstract:

India is battling with the issues of accessibility, affordability and availability of quality health to the masses. Indian medical heritage which dated back to 3000 BC unveils the rich knowledge pool which has undergone a perceptible change over years, such as eradication of many communicable diseases, increasing individual awareness of quality health and import driven medical device market etc. Despite a slew of initiatives the holistic slogan of ‘health for all’ remains elusive and a concern for the nation. The 21st-century projects a myriad of challenges like cultural diversity, large population, demographic dividend and geographical segmentation leading to varied needs of people as per their regional conditions of climate, disease prevalence, nutrition and sanitation. But these challenges are also opportunities for the development of indigenous, low cost and accessible technologies to tackle them. This requires reinforcing the potential of indigenous technologies in coordination with prevailing health issues in various regions of country. This paper emphasis on the strategy for exploring the indigenous technologies with entrusted up-scaling to meet the diverse needs of the people. This review proposes to adopt technology transfer as a strategy to establish a vibrant ecosystem for identifying and up-scaling the indigenous medical technologies with diligent hand-holding for public health.

Keywords: health, indigenous, medical technology, technology transfer

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Authors: H. F. Shi, C. L. Zhang

Abstract:

Visible-light-responsive g-C3N4/NaNbO3 nanowires photocatalysts were fabricated by introducing polymeric g-C3N4 on NaNbO3 nanowires. The microscopic mechanisms of interface interaction, charge transfer and separation, as well as the influence on the photocatalytic activity of g-C3N4/NaNbO3 composite were systematic investigated. The HR-TEM revealed that an intimate interface between C3N4 and NaNbO3 nanowires formed in the g-C3N4/NaNbO3 heterojunctions. The photocatalytic performance of photocatalysts was evaluated for CO2 reduction under visible-light illumination. Significantly, the activity of g-C3N4/NaNbO3 composite photocatalyst for photoreduction of CO2 was higher than that of either single-phase g-C3N4 or NaNbO3. Such a remarkable enhancement of photocatalytic activity was mainly ascribed to the improved separation and transfer of photogenerated electron-hole pairs at the intimate interface of g-C3N4/NaNbO3 heterojunctions, which originated from the well-aligned overlapping band structures of C3N4 and NaNbO3. Pt loaded NaNbO3-xNx (Pt-NNON), a visible-light-sensitive photocatalyst, was synthesized by an in situ photodeposition method from H2PtCl6•6H2O onto NaNbO3-xNx (NNON) sample. Pt-NNON exhibited a much higher photocatalytic activity for gaseous 2-propanol (IPA) degradation under visible-light irradiation in contrast to NNON. The apparent quantum efficiency (AQE) of Pt-NNON sample for IPA photodegradation achieved up to 8.6% at the wavelength of 419 nm. The notably enhanced photocatalytic performance was attributed to the promoted charge separation and transfer capability in the Pt-NNON system. This work suggests that surface nanosteps possibly play an important role as an electron transfer at high way, which facilitates to the charge carrier collection onto Pt rich zones and thus suppresses recombination between photogenerated electrons and holes. This method can thus be considered as an excellent strategy to enhance photocatalytic activity of organic decomposition in addition to the commonly applied noble metal doping method.

Keywords: CO2 reduction, NaNbO3, nanowires, g-C3N4

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Authors: Dmytro Symak

Abstract:

Drying is a complex technologic, thermal and energy process. Energy cost of drying processes in many cases is the most costly stage of production, and can be over 50% of total costs. As we know, in Ukraine over 85% of Portland cement is produced moist, and the finished product energy costs make up to almost 60%. During the wet cement production, energy costs make up over 5500 kJ / kg of clinker, while during the dry only 3100 kJ / kg, that is, switching to a dry Portland cement will allow result into double cutting energy costs. Therefore, to study raw materials drying process in the manufacture of Portland cement is very actual task. The fine ferrous materials drying (small pyrites, red mud, clay Kyoko) is recommended to do by filtration method, that is one of the most intense. The essence of filtration method drying lies in heat agent filtering through a stationary layer of wet material, which is located on the perforated partition, in the "layer-dispersed material - perforated partition." For the optimum drying purposes, it is necessary to establish the dependence of pressure loss in the layer of dispersed material, and the values of heat and mass transfer, depending on the speed of the gas flow filtering. In our research, the experimentally determined pressure loss in the layer of dispersed material was generalized based on dimensionless complexes in the form and coefficients of heat exchange. We also determined the relation between the coefficients of mass and heat transfer. As a result of theoretic and experimental investigations, it was possible to develop a methodology for calculating the optimal parameters for the thermal agent and the main parameters for the filtration drying installation. The comparison of calculated by known operating expenses methods for the process of small pyrites drying in a rotating drum and filtration method shows to save up to 618 kWh per 1,000 kg of dry material and 700 kWh during filtration drying clay.

Keywords: drying, cement, heat and mass transfer, filtration method

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