Search results for: genome scale sequencing

Authors: Faisal Nouroz, Mukaramin Mukaramin

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Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Maaza Saeed

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The current study examined the mediating roles of emotional intelligence (EI) and resilience in the relationship between mindfulness and life satisfaction among Chinese and Pakistani samples. 450 participants completed the mindful attention awareness scale, resilience scale, wong law emotional intelligence scale, and satisfaction with life scale from both cultures. Path analysis revealed that both emotional intelligence (EI) and resilience fully mediated the relationship between mindfulness and life satisfaction among participants of both cultures. Besides, a multi-group evaluation suggests that Chinese participants with significant EI scores are more likely to sustain greater life satisfaction than their Pakistani counterparts. Insinuation for prospective researches and current study pitfalls are discussed.

Keywords: mindfulness, life satisfaction, resilience, emotional intelligence

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Authors: Kang-In Lee, Woo-Jin Lee, Keun-Deuk Lee, Ju-Seung Chae

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In this study, small scale gap test (SSGT) was performed to measure shock sensitivity of nano-scaled 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) samples. The shock sensitivity of energetic materials is usually evaluated by the method of large-scale gap test (LSGT) that has a higher reliability than other methods. But LSGT has the disadvantage that it takes a high cost and time by using a large amount of explosive. In this experiment, nano-scaled RDX samples were prepared by spray crystallization in two different drying methods. In addition, 30μm RDX sample produced by precipitation crystallization and 5μm RDX sample produced by fluid energy mill process were tested to compare shock sensitivity. The study of shock sensitivity measured by small-scale gap test shows that small sized RDX particles have greater insensitivity. As a result, we infer SSGT method has higher reliability compared to the literature as measurement of shock sensitivity of energetic materials.

Keywords: nano-scaled RDX, SSGT(small scale gap test), shock sensitivity, RDX

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Authors: Arati Inamdar, Siddharth Bhattacharyya, Kester Haye

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Collision tumors are rare entities characterized by neoplasms of two different cell populations with distinct separating boundaries. Such tumors could be benign, malignant, or a combination of both. The exact mechanism of origin for collision tumors is predicted to be tumor heterogeneity or concurrent occurrence of neoplasm in the same organ. We present two cases of plasmacytoma presenting as a collision tumor, one with a tumor of hematological origin and another with a non-hematological origin, namely Chronic Lymphocytic Leukemia and Adenocarcinoma of the colon, respectively. The immunohistochemical stains and flowcytometry analysis performed on the specimens aided incorrect diagnosis. Interestingly, neoplastic cells of plasmacytoma in the first case demonstrated strong cytokeratin along with weak Epithelial Specific Antigen/ Epithelial cell adhesion molecule Monoclonal Antibody (MOC31) positivity, indicating that the tumor may influence the microenvironment of the tumor in the vicinity. Furthermore, the next-generation sequencing studies performed on the specimen with plasmacytoma and chronic lymphocytic lymphoma demonstrated BReast CAncer gene (BRCA2) and Tumor Necrosis Factor Alpha Induced Protein 3 (TNFAIP3) as a disease associated variants suggestive of risk for multiple tumors including collision tumors. Our reports highlight the unique collision tumors involving plasmacytoma, which have never been reported previously, as well as provide necessary insights about the underline genetic aberrations and tumor heterogeneity through sequencing studies and allow clonality assessment for subsequent tumors.

Keywords: BRCA2, collision tumor, chronic lymphocytic leukemia, plasmacytoma

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Authors: Bernard Doherty, Andrew Jelfs, Aveek Dasgupta, Patrick Holden

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Many companies have moved to agile and hybrid agile methodologies where portions of the Software Design Life-cycle (SDLC) and Software Test Life-cycle (STLC) can be time boxed in order to enhance delivery speed, quality and to increase flexibility to changes in software requirements. Despite widespread proliferation of agile practices, implementation often fails due to lack of adequate project management support, decreased motivation or fear of increased interaction. Consequently, few organizations effectively adopt agile processes with tailoring often required to integrate agile methodology in large scale environments. This paper provides an overview of the challenges in implementing an innovative large-scale tailored realization of the agile methodology termed the Agile Factory Model (AFM), with the aim of comparing and contrasting issues of specific importance to organizations undertaking large scale agile development. The conclusions demonstrate that agile practices can be effectively translated to a globally distributed development environment.

Keywords: agile, agile factory model, globally distributed development, large-scale agile

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Authors: Hamadi Khlif

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This paper deals with the understanding of the concept of e-management and the development of a measuring instrument adapted to the new problems encountered during the application of this new practice within the modern enterprise. Two principal e-management factors have been isolated in an exploratory study carried out among 260 participants. A confirmatory study applied to a second sample of 270 participants has been established in a cross-validation of the scale of measurement. The study presents the literature review specifically dedicated to e-management and the results of the exploratory and confirmatory phase of the development of this scale, which demonstrates satisfactory psychometric qualities. The e-management has two dimensions: a managerial dimension and a technological dimension.

Keywords: e-management, management, ICT deployment, mode of management

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Authors: Victor O. Abegunde, Melusi Sibanda

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There is need for a great deal of attention on small-scale agriculture for livelihood and food security because of the expanding global population. Small-scale agriculture has been identified as a major driving force of agricultural and rural development. However, the high dependence of the sector on natural and climatic resources has made small-scale farmers highly vulnerable to the adverse impact of climatic change thereby necessitating the need for embracing practices or concepts that will help absorb shocks from changes in climatic condition. This study examines the strategic position of small-scale farming in South African agriculture and in ensuring food security in the country, the vulnerability of small-scale agriculture to climate change and the potential of the concept of climate-smart agriculture to tackle the challenge of climate change. The study carried out a systematic review of peer-reviewed literature touching small-scale agriculture, climate change, food security and climate-smart agriculture, employing the realist review method. Findings revealed that increased productivity in the small-scale agricultural sector has a great potential of improving the food security of households in South Africa and reducing dependence on food purchase in a context of high food price inflation. Findings, however, also revealed that climate change affects small-scale subsistence farmers in terms of productivity, food security and family income, categorizing the impact on smallholder livelihoods into three major groups; biological processes, environmental and physical processes and impact on health. Analysis of the literature consistently showed that climate-smart agriculture integrates the benefits of adaptation and resilience to climate change, mitigation, and food security. As a result, farming households adopting climate-smart agriculture will be better off than their counterparts who do not. This study concludes that climate-smart agriculture could be a very good bridge linking small-scale agricultural sector and agricultural productivity and development which could bring about the much needed food security.

Keywords: climate change, climate-smart agriculture, food security, small-scale

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Authors: Hatice Karakoyun, Mustafa Akdag

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This study has been made to examine the attitudes of pre-school teachers towards values education. The study has been made as a general scanning model. The study’s working group contains 108 pre-school teachers who worked in Diyarbakır, Turkey. In this study Values Education Attitude Scale (VEAS), which developed by Yaşaroğlu (2014), was used. In order to analyze the data for sociodemographic structure, percentage and frequency values were examined. The Kolmogorov-Smirnov method was used in determination of the normal distribution of data. During analyzing the data, KolmogorovSimirnov test and the normal curved histograms were examined to determine which statistical analyzes would be applied on the scale and it was found that the distribution was not normal. Thus, the Mann Whitney U analysis technique which is one of the nonparametric statistical analysis techniques were used to test the difference of the scores obtained from the scale in terms of independent variables. According to the analyses, it seems that pre-school teachers’ attitudes toward values education are positive. According to the scale with the highest average, it points out that pre-school teachers think that values education is very important for students’ and children’s future. The variables included in the scale (gender, seniority, age group, education, school type, school place) seem to have no effect on the pre-school teachers’ attitude grades which joined to the study.

Keywords: attitude scale, pedagogy, pre-school teacher, values education

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Authors: Muhammad Sohail Sajid, Qurat-ul-Ain, Zafar Iqbal, Muhammad Nisar Khan, Asma Kausar, Adil Ejaz

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Rickettsiosis, caused by a Spotted Fever Group Rickettsiae (SFGR), is considered as an emerging infectious disease from public and veterinary perspective. The present study reports distribution of SFGR in the host (buffalo and cattle) and vector (ticks) population determined through gene specific amplification through PCR targeting outer membrane protein (ompA). Tick and blood samples were collected using standard protocols through convenient sampling from district Faisalabad. Ticks were dissected to extract salivary glands (SG). Blood and tick SG pools were subjected to DNA extraction and amplification of ompA using PCR. Overall prevalence of SFGR was reported as 21.5% and 33.6 % from blood and ticks, respectively. Hyalomma anatolicum was more prevalent tick associated with SFGR as compared to Rhipicephalus sp. Higher prevalence of SFGR was reported in cattle (25%) population as compared to that of buffalo (17.07%). On seasonal basis, high SFGR prevalence was recorded during spring season (48.1%, 26.32%, 17.76%) as compared to winter (27.9%, 21.43%, 15.38%) in vector and host (cattle and buffalo respectively) population. Sequencing analysis indicated that rickettsial endo-symbionts were associated with ticks of the study area. These results provided baseline information about the prevalence of SFGR in vector and host population.

Keywords: Rickettsia, livestock, polymerase chain reaction, sequencing, ticks, vectors

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Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

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The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

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Authors: Leo Nnamdi Ozurumba-Dwight

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Single-cell genomic analytical systems have proved to be a platform to isolate bulk cells into selected single cells for genomic, proteomic, and related metabolomic studies. This is enabling systematic investigations of the level of heterogeneity in a diverse and wide pool of cell populations. Single cell technologies, embracing techniques such as high parameter flow cytometry, single-cell sequencing, and high-resolution images are playing vital roles in these investigations on messenger ribonucleic acid (mRNA) molecules and related gene expressions in tracking the nature and course of disease conditions. This entails targeted molecular investigations on unit cells that help us understand cell behavoiur and expressions, which can be examined for their health implications on the health state of patients. One of the vital good sides of single-cell RNA sequencing (scRNA seq) is its probing capacity to detect deranged or abnormal cell populations present within homogenously perceived pooled cells, which would have evaded cursory screening on the pooled cell populations of biological samples obtained as part of diagnostic procedures. Despite conduction of just single-cell transcriptome analysis, scRNAseq now permits comparison of the transcriptome of the individual cells, which can be evaluated for gene expressional patterns that depict areas of heterogeneity with pharmaceutical drug discovery and clinical treatment applications. It is vital to strictly work through the tools of investigations from wet lab to bioinformatics and computational tooled analyses. In the precise steps for scRNAseq, it is critical to do thorough and effective isolation of viable single cells from the tissues of interest using dependable techniques (such as FACS) before proceeding to lysis, as this enhances the appropriate picking of quality mRNA molecules for subsequent sequencing (such as by the use of Polymerase Chain Reaction machine). Interestingly, scRNAseq can be deployed to analyze various types of biological samples such as embryos, nervous systems, tumour cells, stem cells, lymphocytes, and haematopoietic cells. In haematopoietic cells, it can be used to stratify acute myeloid leukemia patterns in patients, sorting them out into cohorts that enable re-modeling of treatment regimens based on stratified presentations. In immunotherapy, it can furnish specialist clinician-immunologist with tools to re-model treatment for each patient, an attribute of precision medicine. Finally, the good predictive attribute of scRNAseq can help reduce the cost of treatment for patients, thus attracting more patients who would have otherwise been discouraged from seeking quality clinical consultation help due to perceived high cost. This is a positive paradigm shift for patients’ attitudes primed towards seeking treatment.

Keywords: immunotherapy, transcriptome, re-modeling, mRNA, scRNA-seq

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Authors: Gul Selin Erben

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Precariousness can be evaluated as the new employment climate of the neo-liberal employment markets. As the word refers to a new mode of employment experience and working practices, it was felt as a necessity to reveal the basic characteristics of this kind of employment experience. Furthermore, according to the literature, precarious employment practices have some negative outcomes such as alienation, sense of anger, and anomy. Thus, it has quite significant to reveal the conditions' characteristics and practices of precarious employment. This study has the purpose to develop an instrument which measures the precarious employment practices. In order to develop a precariousness scale, the relevant literature was examined, and 30 statements were established as a result of the literature review. The development and validation of the scale were done by a sample of 123 individuals who work in different sectors in İstanbul as a white color employee. Convenience sampling was used as a sampling methodology. Reliability and factor analysis were conducted. As a result of the exploratory factor analysis, 3 dimensions were gathered.

Keywords: employment, employment experience, precariousness, scale development

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Authors: Chamilani Nikapitiya, Mahanama De Zoysa, Jehee Lee

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Most of the bacterial diseases are associated with high mortalities in aquaculture species and causing huge economic losses. Different approaches have been taken to prevent or control of bacterial diseases including use of vaccines, probiotics, chemotherapy, water quality management, etc. Antibiotics are widely applying as chemotherapy to control bacterial diseases, however, it has been shown that frequent use of antibiotics is favored to develop multi-drug resistance bacteria. Therefore, phages and phage encoded lytic proteins are known to be one of the most promising alternatives for antibiotics to avoid the emergence of antibiotic-resistant bacteria. We isolated and characterized the two lytic phages, namely pAh-1 and pAs-1 against pathogenic Aeromonas hydrophila and Aeromonas salmonicida, respectively. Morphological characteristics were analyzed by Transmission electron microscopy (TEM) and host strain specificities were tested with Aeromonas and other closely related bacterial strains. TEM analysis revealed that both pAh-1 and pAsm-1 are composed of an icosahedral head and a segmented tail, and we suggest that, they are new members of Myoviridae family. Genome sizes of isolated phages were estimated by restriction enzyme digestion of genomic DNA using selected endonucleases followed by agarose gel electrophoresis. Estimated genome size of pAh-1 and pAs-1 were approximately 64 Kbp and 120 Kbp, respectively. Both pAh-1 and pAs-1 have shown narrow host specificity. Moreover, protective effects of phage therapy against fish pathogenic A. hydrophila were investigated in zebrafish model. The survival rate was 40% higher when zebrafish received intra-peritoneal injection (i.p.) of pAh-1 were simultaneously challenge A. hydrophila (2 x 106 CFU/fish) compared to that without phage treatment. Overall results suggest that both pAh-1 and pAs-1 can be used as a potential phage therapy to control Aeromonas infections in aquaculture.

Keywords: Aeromonas infections, antibiotic resistance, bacteriophage, bio-control, lytic phage

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Authors: Chuping Lo

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This paper presents a simple model demonstrating that ceteris paribus countries with lower barriers to accessing global data tend to earn higher incomes than other countries. Therefore, large countries that inherently have greater data resources tend to have higher incomes than smaller countries, such that the former may be more hesitant than the latter to liberalize cross-border data flows to maintain this advantage. Furthermore, countries with higher artificial intelligence (AI) intensity in production technologies tend to benefit more from economies of scale in data aggregation, leading to higher income and more trade as they are better able to utilize global data.

Keywords: digital intensity, digital divide, international trade, scale of economics

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Authors: Andrew Anis Fakhrey Mosaad

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The goal of this study is to compare the efficacy of polarised light therapy with low-intensity laser therapy in treating oral mucositis brought on by chemotherapy in cancer patients. Evaluation procedures are the measurement of the WHO oral mucositis scale and the Common toxicity criteria scale. Techniques: Cancer patients (men and women) who had oral mucositis, ulceration, and discomfort and whose ages varied from 30 to 55 years were separated into two groups and received 40 chemotherapy treatments. Twenty patients in Group (A) received low-level laser therapy (LLLT) along with their regular oral mucositis medication treatment, while twenty patients in Group (B) received Bioptron light therapy (BLT) along with their regular oral mucositis medication treatment. Both treatments were applied for 10 minutes each day for 30 days. Conclusion and results: This study showed that the use of both BLT and LLLT on oral mucositis in cancer patients following chemotherapy greatly improved, as seen by the sharp falls in both the WHO oral mucositis scale (OMS) and the common toxicity criteria scale (CTCS). However, low-intensity laser therapy (LLLT) was superior to Bioptron light therapy in terms of benefits (BLT).

Keywords: Bioptron light therapy, low level laser therapy, oral mucositis, WHO oral mucositis scale, common toxicity criteria scale

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Authors: Pasquali Frederique, Manfreda Chiara, Crippa Cecilia, Indio Valentina, Ianieri Adriana, De Cesare Alessandra

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Microbiological hazards can be transmitted to humans through milk. In this study, we compared the microbiome composition and presence of foodborne pathogens in organic milk (n=6), organic hay milk (n=6), standard milk (n=6) and high-quality milk (n=6). The milk samples were collected during six samplings between December 2022 to January 2023 and between April and May 2024 to take into account seasonal variations. The 24 milk samples were submitted to DNA extraction and library preparation before shotgun sequencing on the Illumina HiScan™ SQ System platform. The total sequencing output was 600 GB. In all the milk samples, the phyla with the highest relative abundances were Pseudomonadota, Bacillota, Ascomycota, Actinomycetota and Apicomplexa, while the most represented genera were Pseudomonas, Streptococcus, Geotrichum, Acinetobacter and Babesia. The alpha and beta diversity indexes showed a clear separation between the microbiome of high-quality milk and those of the other milk types. Moreover, in the high-quality milk, the relative abundance of Staphylococcus (4.4%), Campylobacter (4.5%), Bacillus (2.5%), Enterococcus (2.4%), Klebsiella (1.3%) and Escherichia (0 .7%) was significantly higher in comparison to other types of milk. On the contrary, the relative abundance of Geotrichum (0.5%) was significantly lower. The microbiome results collected in this study showed significant differences in terms of the relative abundance of bacteria genera, including foodborne pathogen species. These results should be incorporated into risk assessment models tailored to different types of milk.

Keywords: raw milk, foodborne pathogens, microbiome, risk assessment

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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Authors: Abu Salim Mustafa

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

Keywords: drinking water, microbial contaminant, 16S rDNA, Kuwait

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Authors: Tugba Cinarli, Tugba Kavalali Erdogan, Sevil Masat, Dilek Kiymaz, Nida Kiyici, Zeliha Koc

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This study was conducted in a descriptive and cross-sectional manner, in order to determine the self-esteem, life satisfaction and depression/anxiety levels of the patients with stoma. The study was conducted between June 15, 2016 and June 15, 2017 among 196 oncology patients that were hospitalized in the general surgery clinic of a public hospital in Turkey. The case group consisted of 98 cancer patients with stoma and the control group consisted of 98 cancer patients without stoma. The data were collected through the Coopersmith Self-Esteem Scale, Life Satisfaction Scale, the Hospital Anxiety and Depression Scale, and a 21-question survey that aimed to determine the sociodemographic and clinical properties of the patients. The data were analyzed with percentage analysis, Mann Whitney U-test, Chi-square test and Spearmen’s correlation test. It was determined that for the case group; 44.9% had colon cancer, 29.6% had rectal cancer; 50% underwent temporary colostomia, 15.3% underwent permanent colostomia, 34.7% underwent temporary ileostomy. The experimental group's findings for the Coopersmith Self-Esteem Scale, Life Satisfaction Scale, the Anxiety Subscale and the Depression subscale were 64 (20 - 84), 17 (5 - 38), 10 (1 - 18), and 9 (1 - 19), respectively. The control group's findings for the Coopersmith Self-Esteem Scale, Life Satisfaction Scale, the Anxiety Subscale and the Depression Subscale were 68 (32 - 92), 21 (7 - 31), 8.5 (1 - 18), and 8 (1 - 18), respectively. It was found that the Coopersmith Self-Esteem Scale, Life Satisfaction Scale, and the Anxiety Subscale findings were significantly different for the experimental and control groups (p<0.05). It was determined that the self-esteem levels were positively correlated with life satisfaction and negatively correlated with anxiety and depression; also, the life satisfaction levels were negatively correlated with anxiety and depression. It is suggested that the nursing interventions should be planned in order to improve life-satisfaction and self-esteem levels of the patients, and to decrease depression and anxiety.

Keywords: anxiety, cancer, life satisfaction, self-esteem

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Authors: C. L. Wu, W. W. Tseng

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From the National Health Insurance (NHI) system was introduced in Taiwan in 2000, there have been some problems in transformed small-scale hospitals, such as mobility of patients, shortage of nursing staff, medical pipelines breaking fire compartments and insufficient fire protection systems. Due to shrinking of the funding scale and the aging society, fire safety in small-scale hospitals has recently given cause for concern. The aim of this study is to determine fire risk index for small-scale hospital through a systematic approach The selection of fire safety mitigation methods can be regarded as a multi-attribute decision making process which must be guaranteed by expert groups. First of all, identify and select safety related factors and identify evaluation criteria through literature reviews and experts group. Secondly, application of the Fuzzy Analytic Hierarchy Process method is used to ascertain a weighted value which enables rating of the importance each of the selected factors. Overall, Sprinkler type and Compartmentation are the most crucial indices in mitigating fire, that is to say, structural approach play an important role to decrease losses in fire events.

Keywords: Fuzzy Delphi Method, fuzzy analytic hierarchy, process risk assessment, fire events

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Authors: I. Wiedemann, A. R. Sharifi, A. Mählmeyer, C. Knorr

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A requirement for sperm motility is a morphologically intact flagellum with a central axoneme. The flagellar beating is caused by the varying activation and inactivation of dynein molecules which are located in the axoneme. DNAL4 (dynein, axonemal, light chain 4) is regarded as a possible functional candidate gene encoding a small subunit of the dyneins. In the present study, 5814bp of the porcine DNAL4 (GenBank Acc. No. AM284696.1, 6097 bp, 4 exons) were comparatively sequenced using three boars with a high motility (>68%) and three with a low motility (<60%). Primers were self-designed except for those covering exons 1, 2 and 3. Prior to sequencing, the PCR products were purified. Sequencing was performed with an ABI PRISM 3100 Genetic Analyzer using the BigDyeTM Terminator v3.1 Cycle Sequencing Reaction Kit. Finally, 23 SNPs were described and genotyped for 82 AI boars representing the breeds Piétrain, German Large White and German Landrace. The genotypes were used to assess possible associations with standard spermatological parameters (ejaculate volume, density, and sperm motility (undiluted (Motud), 24h (Mot1) and 48h (Mot2) after semen collection) that were regularly recorded on the AI station. The analysis included a total of 8,833 spermatological data sets which ranged from 2 to 295 sets per boar in five years. Only SNP g.1007A>G had a significant effect. Finally, the gene substitution effect using the following statistical model was calculated: Yijk= µ+αi+βj+αβij+b1Sijk+b2Aijk+b3T ijk + b4Vijk+b5(α*A)ijk +b6(β*A)ijk+b7(A*T)ijk+Uijk+eijk where Yijk is the semen characteristics, µ is the general mean, α is the main effect of breed, β is the main effect of season, S is the effect of SNP (g.1007A > G), A is the effect of age at semen collection, V is the effect of diluter, αβ, α*A, β*A, A*T are interactions between the fixed effects, b1-b7 are regression coefficients between y and the respective covariate, U is the random effect of repeated observation on animal and e is the random error. The results from the single marker regression analysis revealed highly significant effects (p < 0.0001) of SNP g.1007A > G on Mot1 resp. on Mot2, resulting in a marked reduction by 11.4% resp. 15.4%. Furthermore a loss of Motud by 4.6% was detected (p < 0.0178). Considering the SNP g.1007A > G as a main factor (dominant-recessive model), significant differences between genotypes AA and AG as well as AA and GG for Mot1 and Mot2 exist. For Motud there was a significant difference between AA and GG.

Keywords: association, DNAL4, porcine, sperm traits

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Authors: Samuel Abebe Ebebo

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Scale precipitation causes a major issue for geothermal power plants because it reduces the production rate of geothermal energy. Each geothermal power plant's different chemical and physical conditions can cause the scale to precipitate under a particular set of fluid-rock interactions. Depending on the mineral, it is possible to have scale in the production well, steam separators, heat exchangers, reinjection wells, and everywhere in between. The scale consists mainly of smectite and trace amounts of chlorite, magnetite, quartz, hematite, dolomite, aragonite, and amorphous silica. The smectite scale is one of the difficult scales at injection wells in geothermal power plants. X-ray diffraction and chemical composition identify this smectite as Stevensite. The characteristics and the scale of each injection well line are different depending on the fluid chemistry. The smectite scale has been widely distributed in pipelines and surface plants. Mineral water equilibrium showed that the main factors controlling the saturation indices of smectite increased pH and dissolved Mg concentration due to the precipitate on the equipment surface. This study aims to characterize the scales and geothermal fluids collected from the Onuma geothermal power plant in Akita Prefecture, Japan. Field tests were conducted on October 30–November 3, 2021, at Onuma to determine the pH control methods for preventing magnesium silicate scaling, and as exemplified, the formation of magnesium silicate hydrates (M-S-H) with MgO to SiO2 ratios of 1.0 and pH values of 10 for one day has been studied at 25 °C. As a result, M-S-H scale formation could be suppressed, and stevensite formation could also be suppressed when we can decrease the pH of the fluid by less than 8.1, 7.4, and 8 (at 97 °C) in the fluid from O-3Rb and O-6Rb, O-10Rg, and O-12R, respectively. In this context, the scales and fluids collected from injection wells at a geothermal power plant in Japan were analyzed and characterized to understand the formation conditions of Mg-silicate scales with on-site synthesis experiments. From the results of the characterizations and on-site synthesis experiments, the inhibition method of their scale formation is discussed based on geochemical modeling in this study.

Keywords: magnesium silicate, scaling, inhibitor, geothermal power plant

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Authors: Anuj Tyagi, Balwinder Singh, Naveen Kumar B. T., Niraj K. Singh

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Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment.

Keywords: antibiotic resistance, fish gut, metabolic pathways, microbial diversity

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Authors: Feng Ji Mervin Goh, Edmund Chee Jian Pua, Stuart Alexander Cook

Abstract:

Dilated cardiomyopathy (DCM) is a common cause of heart failure. Genetic mutations account for 50% of DCM cases with TTN mutations being the most common, accounting for up to 25% of DCM cases. However, the genetic architecture underlying Asian DCM patients is unknown. We evaluated 68 patients (female= 17) with DCM who underwent follow-up at the National Heart Centre, Singapore from 2013 through 2014. Clinical data were obtained and analyzed retrospectively. Genomic DNA was subjected to next-generation targeted sequencing. Nextera Rapid Capture Enrichment was used to capture the exons of a panel of 169 cardiac genes. DNA libraries were sequenced as paired-end 150-bp reads on Illumina MiSeq. Raw sequence reads were processed and analysed using standard bioinformatics techniques. The average age of onset of DCM was 46.1±10.21 years old. The average left ventricular ejection fraction (LVEF), left ventricular diastolic internal diameter (LVIDd), left ventricular systolic internal diameter (LVIDs) were 26.1±11.2%, 6.20±0.83cm, and 5.23±0.92cm respectively. The frequencies of mutations in major DCM-associated genes were as follows TTN (5.88% vs published frequency of 20%), LMNA (4.41% vs 6%), MYH7 (5.88% vs 4%), MYH6 (5.88% vs 4%), and SCN5a (4.41% vs 3%). The average callability at 10 times coverage of each major gene were: TTN (99.7%), LMNA (87.1%), MYH7 (94.8%), MYH6 (95.5%), and SCN5a (94.3%). In conclusion, TTN mutations are not common in Singaporean DCM patients. The frequencies of other major DCM-associated genes are comparable to frequencies published in the current literature.

Keywords: heart failure, dilated cardiomyopathy, genetics, next-generation sequencing

Procedia PDF Downloads 235

Authors: Andrey V. Khromov, Antonida V. Makhotenko, Ekaterina A. Snigir, Svetlana S. Makarova, Natalia O. Kalinina, Valentin V. Makarov, Mikhail E. Taliansky

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Due to its simplicity, CRISPR/Cas9 has become widely used and capable of inducing mutations in the genes of organisms of various kingdoms. The aim of this work was to develop applications for the efficient modification of DNA coding sequences of phytoene desaturase (PDS), coilin and vacuolar invertase (Solanum tuberosum) genes, and to develop a new nanoparticles carrier efficient technology to deliver the CRISPR/Cas9 system for editing the plant genome. For each of the genes - coilin, PDS and vacuolar invertase, five single RNA guide (sgRNAs) were synthesized. To determine the most suitable nanoplatform, two types of NP platforms were used: magnetic NPs (MNPS) and gold NPs (AuNPs). To test the penetration efficiency, they were functionalized with fluorescent agents - BSA * FITS and GFP, as well as labeled Cy3 small-sized RNA. To measure the efficiency, a fluorescence and confocal microscopy were used. It was shown that the best of these options were AuNP - both in the case of proteins and in the case of RNA. The next step was to check the possibility of delivering components of the CRISPR/Cas9 system to plant cells for editing target genes. AuNPs were functionalized with a ribonucleoprotein complex consisting of Cas9 and corresponding to target genes sgRNAs, and they were biolistically bombarded to axillary buds and apical meristems of potato plants. After the treatment by the best NP carrier, potato meristems were grown to adult plants. DNA isolated from this plants was sent to a preliminary fragment of the analysis to screen out the non-transformed samples, and then to the NGS. The present work was carried out with the financial support from the Russian Science Foundation (grant No. 16-16-04019).

Keywords: biobombardment, coilin, CRISPR/Cas9, nanoparticles, NPs, PDS, sgRNA, vacuolar invertase

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Authors: Meysam Naeimi, Zili Li, Rolf Dollevoet

Abstract:

A new small–scale test rig developed for rolling contact fatigue (RCF) investigations in wheel–rail material. This paper presents the scaling strategy of the rig based on dimensional analysis and mechanical modelling. The new experimental rig is indeed a spinning frame structure with multiple wheel components over a fixed rail-track ring, capable of simulating continuous wheel-rail contact in a laboratory scale. This paper describes the dimensional design of the rig, to derive its overall scaling strategy and to determine the key elements’ specifications. Finite element (FE) modelling is used to simulate the mechanical behavior of the rig with two sample scale factors of 1/5 and 1/7. The results of FE models are compared with the actual railway system to observe the effectiveness of the chosen scales. The mechanical properties of the components and variables of the system are finally determined through the design process.

Keywords: new test rig, rolling contact fatigue, rail, small scale

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Authors: K. Sathishkumar, V. Thiagarasu

Abstract:

Due to recent advances in DNA microarray technology, it is now feasible to obtain gene expression profiles of tissue samples at relatively low costs. Many scientists around the world use the advantage of this gene profiling to characterize complex biological circumstances and diseases. Microarray techniques that are used in genome-wide gene expression and genome mutation analysis help scientists and physicians in understanding of the pathophysiological mechanisms, in diagnoses and prognoses, and choosing treatment plans. DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. This work presents an analysis of several clustering algorithms proposed to deals with the gene expression data effectively. The existing clustering algorithms like Support Vector Machine (SVM), K-means algorithm and evolutionary algorithm etc. are analyzed thoroughly to identify the advantages and limitations. The performance evaluation of the existing algorithms is carried out to determine the best approach. In order to improve the classification performance of the best approach in terms of Accuracy, Convergence Behavior and processing time, a hybrid clustering based optimization approach has been proposed.

Keywords: microarray technology, gene expression data, clustering, gene Selection

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Authors: Karina C. Azzolin, Luis E. Kosteski, Alisson S. Milani, Raquel C. Zydeck

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This work aims to represent Numerically tests experimentally developed in reduced scale walls with horizontal and inclined cuts by using the Lattice Discrete Element Method (LDEM) implemented On de Abaqus/explicit environment. The cuts were performed with depths of 20%, 30%, and 50% On the walls subjected to centered and eccentric loading. The parameters used to evaluate the numerical model are its strength, the failure mode, and the in-plane and out-of-plane displacements.

Keywords: structural masonry, wall chases, small scale, numerical model, lattice discrete element method

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Authors: Supriya Manikrao Ovhal

Abstract:

In India, the summer monsoon rainfall occurs owing to large scale convection with reference to continental ITCZ. It was found that convection over tropical ocean increases with SST from 26 to 28 degree C, and when SST is above 29 degree C, it sharply decreases for warm pool areas of Indian and for monsoon areas of West Pacific Ocean. The reduction in convection can be influenced by large scale subsidence forced by nearby or remotely generated deep convection, thus it was observed that under the influence of strong large scale rising motion, convection does not decreases but increases monotonically with SST even if SST value is higher than 29.5 degree C. Since convection is related to SST gradient, that helps to generate low level moisture convergence and upward vertical motion in the atmosphere. Strong wind fields like cross equatorial low level jet stream on equator ward side of the warm pool are produced due to convection initiated by SST gradient. Areas having maximum SST have low SST gradient, and that result in feeble convection. Hence it is imperative to mention that the oceanic role (other than SST) could be prominent in influencing large Scale Atmospheric convection. Since warm oceanic surface somewhere or the other contributes to penetrate the heat radiation to the subsurface of the ocean, and as there is no studies seen related to oceanic subsurface role in large Scale Atmospheric convection, in the present study, we are concentrating on the oceanic subsurface contribution in large Scale Atmospheric convection by considering the SST gradient, mixed layer depth (MLD), thermocline, barrier layer. The present study examines the probable role of subsurface ocean parameters in influencing convection.

Keywords: sst, d20, olr, wind

Procedia PDF Downloads 86

Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

Abstract:

Gastric cancer (GC) has high morbidity and fatality rate in various countries and is still one of the most frequent and deadly diseases. Novel mitogenic and motogenic Gastrokine1 (GKN1) and Gastrokine 2 (GKN2) genes that are highly expressed in the normal stomach epithelium and plays an important role in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. Significant loss of copy number and mRNA transcript of GKN1 and GKN2 gene expression were frequently observed in all types of gastric cancer. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age were investigated with gene expression analysis and mutation screening by monetering RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of inactivation of gastrokines. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age or cancer type of patients. Reduced of gastrokine genes seems to occur at the initial steps of cancer development. In order to understand the investigation between gastric cancer and diagnostic biomarker; further analysis is necessary.

Keywords: gastric cancer, diagnostic biomarker, nucleotide sequencing, semi-quantitative RT-PCR

Procedia PDF Downloads 469