Search results for: gene frequency

Authors: Mengistu G. Woldu, Hani Y. Zaki, Areeg Faggad, Badreldin E. Abdalla

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Background: Type 2 diabetes mellitus (T2DM) is a complex, degenerative, and multi-factorial disease, which is culpable for huge mortality and morbidity worldwide. Even though relatively significant numbers of studies are conducted on the genetics domain of this disease in the developed world, there is huge information gap in the sub-Saharan Africa region in general and in Eritrea in particular. Objective: The principal aim of this study was to investigate the association of common variants of the Insulin Receptor Substrate 1 (IRS1) and Transcription Factor 7-Like 2 (TCF7L2) genes with T2DM in the Eritrean population. Method: In this cross-sectional case control study 200 T2DM patients and 112 non-diabetes subjects were participated and genotyping of the IRS1 (rs13431179, rs16822615, 16822644rs, rs1801123) and TCF7L2 (rs7092484) tag SNPs were carries out using PCR-RFLP method of analysis. Haplotype analyses were carried out using Plink version 1.07, and Haploview 4.2 software. Linkage disequilibrium (LD), and Hardy-Weinberg equilibrium (HWE) analyses were performed using the Plink software. All descriptive statistical data analyses were carried out using SPSS (Version-20) software. Throughout the analysis p-value ≤0.05 was considered statistically significant. Result: Significant association was found between rs13431179 SNP of the IRS1 gene and T2DM under the recessive model of inheritance (OR=9.00, 95%CI=1.17-69.07, p=0.035), and marginally significant association found in the genotypic model (OR=7.50, 95%CI=0.94-60.06, p=0.058). The rs7092484 SNP of the TCF7L2 gene also showed markedly significant association with T2DM in the recessive (OR=3.61, 95%CI=1.70-7.67, p=0.001); and allelic (OR=1.80, 95%CI=1.23-2.62, p=0.002) models. Moreover, eight haplotypes of the IRS1 gene found to have significant association withT2DM (p=0.013 to 0.049). Assessments made on the interactions of genotypes of the rs13431179 and rs7092484 SNPs with various parameters demonstrated that high density lipoprotein (HDL), low density lipoprotein (LDL), waist circumference (WC), and systolic blood pressure (SBP) are the best T2DM onset predicting models. Furthermore, genotypes of the rs7092484 SNP showed significant association with various atherogenic indexes (Atherogenic index of plasma, LDL/HDL, and CHLO/HDL); and Eritreans carrying the GG or GA genotypes were predicted to be more susceptible to cardiovascular diseases onset. Conclusions: Results of this study suggest that IRS1 (rs13431179) and TCF7L2 (rs7092484) gene polymorphisms are associated with increased risk of T2DM in Eritreans.

Keywords: IRS1, SNP, TCF7L2, type 2 diabetes

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Authors: Ahmed H. Abdullah, Pavel Kroupa

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Globular clusters (GC) are important objects for tracing the early evolution of a galaxy. We study the correlation between the cluster population and the global properties of the host galaxy. We found that the correlation between cluster population (NGC) and the baryonic mass (Mb) of the host galaxy are best described as 10 −5.6038Mb. In order to understand the origin of the U -shape relation between the GC specific frequency (SN) and Mb (caused by the high value of SN for dwarfs galaxies and giant ellipticals and a minimum SN for intermediate mass galaxies≈ 1010M), we derive a theoretical model for the specific frequency (SNth). The theoretical model for SNth is based on the slope of the power-law embedded cluster mass function (β) and different time scale (Δt) of the forming galaxy. Our results show a good agreement between the observation and the model at a certain β and Δt. The model seems able to reproduce higher value of SNth of β = 1.5 at the midst formation time scale.

Keywords: galaxies: dwarf, globular cluster: specific frequency, number of globular clusters, formation time scale

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Authors: Norihiro Kato, Yuriko Takayama

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

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

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Authors: S. Ozeri, D. Shmilovitz

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Micro‐Turbine Generators (MTG) are small size power plants that consist of a high speed, gas turbine driving an electrical generator. MTGs may be fueled by either natural gas or kerosene and may also use sustainable and recycled green fuels such as biomass, landfill or digester gas. The typical ratings of MTGs start from 20 kW up to 200 kW. The primary use of MTGs is for backup for sensitive load sites such as hospitals, and they are also considered a feasible power source for Distributed Generation (DG) providing on-site generation in proximity to remote loads. The MTGs have the compressor, the turbine, and the electrical generator mounted on a single shaft. For this reason, the electrical energy is generated at high frequency and is incompatible with the power grid. Therefore, MTGs must contain, in addition, a power conditioning unit to generate an AC voltage at the grid frequency. Presently, this power conditioning unit consists of a rectifier followed by a DC/AC inverter, both rated at the full MTG’s power. The losses of the power conditioning unit account to some 3-5%. Moreover, the full-power processing stage is a bulky and costly piece of equipment that also lowers the overall system reliability. In this study, we propose a new type of power conditioning stage in which only a small fraction of the power is processed. A low power converter is used only to program the rotor current (i.e. the excitation current which is substantially lower). Thus, the MTG's output voltage is shaped to the desired amplitude and frequency by proper programming of the excitation current. The control is realized by causing the rotor current to track the electrical frequency (which is related to the shaft frequency) with a difference that is exactly equal to the line frequency. Since the phasor of the rotation speed and the phasor of the rotor magnetic field are multiplied, the spectrum of the MTG generator voltage contains the sum and the difference components. The desired difference component is at the line frequency (50/60 Hz), whereas the unwanted sum component is at about twice the electrical frequency of the stator. The unwanted high frequency component can be filtered out by a low-pass filter leaving only the low-frequency output. This approach allows elimination of the large power conditioning unit incorporated in conventional MTGs. Instead, a much smaller and cheaper fractional power stage can be used. The proposed technology is also applicable to other high rotation generator sets such as aircraft power units.

Keywords: gas turbine, inverter, power multiplier, distributed generation

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Authors: D. J. Kalita

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Cancer is one of the prime causes of early death worldwide. Mutation of the gene involve in DNA repair and damage, like BRCA2 (Breast cancer gene two) genes, can be detected efficiently by PCR-RFLP to early breast cancer diagnosis and adopt the suitable method of treatment. Host Defense Peptide can be used as blueprint for the design and synthesis of novel anticancer drugs to avoid the side effect of conventional chemotherapy and chemo resistance. The change at nucleotide position 392 of a -› c in the cancer sample of dog mammary tumour at BRCA2 (exon 7) gene lead the creation of a new restriction site for SsiI restriction enzyme. This SNP may be a marker for detection of canine mammary tumour. Support vector machine (SVM) algorithm was used to design and predict the anticancer peptide from the mature functional peptide. MTT assay of MCF-7 cell line after 48 hours of post treatment showed an increase in the number of rounded cells when compared with untreated control cells. The ability of the synthesized peptide to induce apoptosis in MCF-7 cells was further investigated by staining the cells with the fluorescent dye Hoechst stain solution, which allows the evaluation of the nuclear morphology. Numerous cells with dense, pyknotic nuclei (the brighter fluorescence) were observed in treated but not in control MCF-7 cells when viewed using an inverted phase-contrast microscope. Thus, PCR-RFLP is one of the attractive approach for early diagnosis, and synthetic cationic peptide can be used for the treatment of canine mammary tumour.

Keywords: cancer, cationic peptide, host defense peptides, Breast cancer genes

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Authors: Bo Hu, Shibo Wang, Haoyang Zhang, Jie Shi

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With the development of sonar detection technology, the acoustic stealth technology of underwater vehicles is facing severe challenges. The underwater acoustic coating is developing towards the direction of low-frequency absorption capability and broad absorption frequency bandwidth. In this paper, an acoustic model of underwater acoustic coating of composite material embedded with periodical steel structure is presented. The model has multiple high absorption peaks in the frequency range of 1kHz-8kHz, where achieves high sound absorption and broad bandwidth performance. It is found that the frequencies of the absorption peaks are related to the classic half-wavelength transmission principle. The sound absorption performance of the acoustic model is investigated by the finite element method using COMSOL software. The sound absorption mechanism of the proposed model is explained by the distributions of the displacement vector field. The influence of geometric parameters of periodical steel structure, including thickness and distance, on the sound absorption ability of the proposed model are further discussed. The acoustic model proposed in this study provides an idea for the design of underwater low-frequency broadband acoustic coating, and the results shows the possibility and feasibility for practical underwater application.

Keywords: acoustic coating, composite material, broad frequency bandwidth, sound absorption performance

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Authors: Mohammadreza Aghasadeghi, Mojtaba Hamidi-Fard, Seyed Amir Sadeghi, Ashkan Noorbakhsh

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Introduction: HIV is known as one of the most important pathogens and mortality in all human societies, but unfortunately, no definitive cure has been found for it. Due to its weakened immune system, this virus causes a variety of primary and secondary opportunistic infections. Cytomegalovirus (CMV) is one of the most relevant opportunistic viruses seen in HIV-positive people that cause various infections in HIV-positive people. This virus causes various infections in HIV-positive people, such as retinal infection (CMVR), gastrointestinal infections, diarrhea, severe weight loss, and cerebrospinal fluid problems. These various infections make it important to evaluate the prevalence of CMV in HIV-positive people to diagnose it quickly and in a timely manner. This infection in HIV-positive people reduces life expectancy and causes serious harm to patients. However, a simple test in HIV-positive people can prevent the virus from progressing. Material and Methods: In this study, we collected 200 blood samples (including 147 men and 53 women) from HIV-positive individuals and examined the frequency of CMV-DNA in these cases by real-time PCR method. In the next step, the data was analyzed by SPSS software, and then we obtained the relationship between age, sex, and the frequency of CMV in HIV-positive individuals. Results: The total frequency of CMV DNA was about 59%, which is a relatively high prevalence due to the age range of the subjects. The frequency in men was 61.2% and 52.8% in women. This frequency was also higher in males than females. We also observed more frequency in two age groups of 16 to 30 years and 31 to 45 years. Discussion: Due to the high prevalence of CMV in HIV-positive individuals and causing serious problems in this group of people, this study was shown that both the patients and the community should pay more attention to this issue. Ministry of Health, as a stakeholder organization, can make CMV DNA testing mandatory as soon as a person is HIV positive.

Keywords: CMV, HIV, AIDS, real-time PCR, SPSS

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Authors: E. Grochowska-Niedworok, K. Brukało, M. Hadasik, M. Kardas

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Consumption of vegetables by school children and adolescents is essential for their normal growth, development and health, but a significant minority of the world's population consumes the right amount of these products. The aim of the study was to evaluate the preferences and frequency of consumption of vegetables by school children and adolescents. It has been assumed that effectively implemented nutrition education programs should have an impact on increasing the frequency of vegetable consumption among the recipients. The study covered 514 students of five schools in the Opole Voivodeship aged 9 years to 22 years. The research tool was an author's questionnaire, which consisted of closed questions on the frequency of vegetable consumption and the use of 10 ways to treat them. Preferences and frequencies are shown in percentages, while correlations were estimated on the basis of Cramer`s V and gamma coefficients. In each of the examined age groups, the relationship between sex and vegetable consumption (the Cramer`s V coefficient value was 0.06 to 0.38) was determined and the various methods of culinary processing were used (V Craméra was 0.08 to 0.34). For both sexes, the relationship between age and frequency of vegetable consumption was shown (gamma values ranged from ~ 0.00 to 0.39) and different cooking methods (gamma values were 0.01 to 0.22). The most important determinant of nutritional choices is the taste and availability of products. The fact that they have a positive effect on their health is only in third position. As has been shown, obesity prevention programs can not only address nutrition education but also teach about new flavors and increase the availability of healthy foods. In addition, the frequency of vegetable consumption can be a good indicator reflecting the healthy behaviors of children and adolescents.

Keywords: children and adolescents, frequency, welfare rate, vegetables

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Authors: Rami A. Maher, Ibraheem K. Ibraheem

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This work presents a comparison study between the state-space and polynomial methods for the design of the robust governor for load frequency control of steam turbine power systems. The robust governor is synthesized using the two approaches and the comparison is extended to include time and frequency domains performance, controller order, and uncertainty representation, weighting filters, optimality and sub-optimality. The obtained results are represented through tables and curves with reasons of similarities and dissimilarities.

Keywords: robust control, load frequency control, steam turbine, H∞-norm, system uncertainty, load disturbance

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Authors: Mehrnoosh Azimi Sanavi, Hamed Ghazvini, Mehryar Zargari, Hossein Ghalehnoei, Zahra Hosseini-khah

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Objectives: Calcium Voltage-Gated Channel Subunit Alpha1 C (CACNA1C) is one of the most important genes associated with schizophrenia. Methods: 45 male Wistar rats were divided into 5 groups: saline, control, ketamine, clozapine, and risperidone. Animals in ketamine, risperidone, and clozapine groups received ketamine (30 mg/ kg-i.p.) for 10 days. After the last injection of ketamine, we started injecting clozapine (7.5 mg/kg-i.p.) risperidone (1 mg/kg-i.p.) for up to 28 days. Twenty-four hours after the last injection, open field, social interaction, and elevated plus-maze tests, and gene expression in the hippocampus were performed. Results: The results of the social interaction test revealed a significant decrease in cumulative time with ketamine compared with the saline group and an increase with clozapine and risperidone compared with the ketamine group. Moreover, results from the elevated plus-maze test demonstrated a critical decrease in open-arm time and an increase in close-arm time with ketamine compared with saline, as well as an increase in open-arm time with risperidone compared with ketamine. Further results revealed a significant increase in rearing and grooming with ketamine compared to saline, as well as a decrease with risperidone and clozapine compared to ketamine. There were no significant differences in CACNA1C gene expression between groups in the rat hippocampus. In brief, the results of this study indicated that clozapine and risperidone could partially improve cognitive impairments in the rat. However, our findings demonstrated that this treatment is not related to CACNA1C gene expression.

Keywords: schizophrenia, ketamine, clozapine, risperidone

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Authors: Ferreira RC, Simons HZ, Thompson WS, Cutler AJ, Dopico XC, Smyth DJ, Mashar M, Schuilenburg H, Walker NM, Dunger DB, Wallace C, Todd JA, Wicker LS, Pekalski ML

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Type 1 diabetes is caused by autoimmune destruction of insulin-secreting beta cells in the pancreas. T cells are known to play an important role in this immune-mediated destruction; however, there is no general consensus regarding alterations in cytokine production or T cell subsets in peripheral blood of patients with type 1 diabetes. Using polychromatic flow cytometry of peripheral blood mononuclear cells (PBMCs), we assessed production of the proinflammatory cytokines IL-21, IFN-γ and IL-17 by memory CD4 T effector (Teff) cells in 69 patients with type 1 diabetes and 61 healthy donors. We found a 21.9% (95% CI 5.8, 40.2; p = 3.9 × 10(-3)) higher frequency of IL-21(+) CD45RA(-) memory CD4(+) Teffs in patients with type 1 diabetes (geometric mean 5.92% [95% CI 5.44, 6.44]) compared with healthy donors (geometric mean 4.88% [95% CI 4.33, 5.50]). In a separate cohort of 30 patients with type 1 diabetes and 32 healthy donors, we assessed the frequency of circulating T follicular helper (Tfh) cells in whole blood. Consistent with the increased production of IL-21, we also found a 14.9% increase in circulating Tfh cells in the patients with type 1 diabetes (95% CI 2.9, 26.9; p = 0.016). Analysis of IL-21 production by PBMCs from a subset of 46 of the 62 donors immunophenotyped for Tfh showed that frequency of Tfh cells was associated with the frequency of IL-21+ cells (r2 = 0.174, p = 0.004). These results indicate that increased IL-21 production is likely to be an aetiological factor in the pathogenesis of type 1 diabetes that could be considered as a potential therapeutic target.

Keywords: T follicular helper cell, IL-21, IL-17, type 1 diabetes

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Authors: Sai Radavaram

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A wideband low-profile circularly-polarized antenna, consisting of 2×2 sequentially-rotated, differentially-fed, slotted rectangular patch elements, is proposed. To realize the right-hand circular polarization, an anti-clockwise phase rotation of 0o, -90o, -180o and -270o is applied between the antenna elements. The proposed antenna, with a height of only 0.02lambda (where lambda is the wavelength of the antenna at the center frequency of the antenna), exhibits a 68% impedance bandwidth from 2 to 4.05 GHz with a 3dB axial ratio bandwidth in the order of 56% from 2.25 to 4.05 GHz. Moreover, a wide 3dB axial ratio beamwidth of 140o is obtained at the center frequency of 3 GHz, along with symmetrical radiation patterns over the operating frequency band.

Keywords: circular polarization, sequentially rotated, slotted patch antennas, wideband

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Authors: Beldjilali Bilal, Benadda Belkacem, Kahlouche Salem

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Due to the Doppler effect caused by the high velocity of satellite and in some case receivers, the frequency of the Global Positioning System (GPS) signals are transformed into a new ones. Several acquisition algorithms frequency of the Global Positioning System (GPS) signals are transformed can be used to estimate the new frequency and phase shifts values. Numerous algorithms are based on the frequencies domain calculation. Our developed algorithm is a new approach dedicated to the Global Positioning System signal acquisition based on the fast Fourier transform. Our proposed new algorithm is easier to implement and has fast execution time compared with elder ones.

Keywords: global positioning system, acquisition, FFT, GPS/L1, software receiver, weak signal

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Authors: Mafalda Moreira, Diana Alba, Inês Paiva Ferreira, Rita Calejo, Ana Rita Soares, Leonilde Machado

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Intellectual disability (ID) is characterized by deficits in intellectualfunctioningassociatedwithalterations in the adaptive behaviour, whose onset is inthedevelopmentalperiod. Itaffects 3% of the population, ofwhich 10% have a geneticaetiology. One of those causes isAlwadeiSyndrome, with 3 cases describedworldwide. It results from a homozygous nonsense mutation in theRUSC2 gene andisassociatedwithintellectualdisabilityanddysmorphic facialfeatures. Theauthorsreportthe case of a 5-year-old-boy, born to a healthymotherafter a full-termuneventfulpregnancy, thatwasreferred to Neurodevelopmentalconsultationdue toglobal developmentaldelay. Familyhistoryrevealedlearningdifficulties in the paternal brotherhood. Milddismorphicfeatureswereevidentsuch as darkinfraorbitalregion, low-set ears, beakednose, retrognathism, high-archedpalateandjointhyperlaxity. WechslerIntelligenceScale for Children III fullscaleIQ quoted 61. Karyotypeandchromosomalmicroarrayanalysiswerenormal, as well as the fragile X molecular study. DNA sequencingwasthenperformedandallowedtheidentificationof amutation in the RUSC2 gene. Theetiologicaldiagnosisof ID remains unknown in up to 80% of cases, creatinguncertainty in children’sfamilies. Theadvances in DNA sequencingtechnologieshaveincreasedourknowledgeofthegeneticdiseasesinvolved, as theAlwadeisyndromewasonlydescribedsince 2016. Thegeneticdiagnosisof ID allowsfamilygeneticcounselingandenablesthedevelopmentof target therapeutic approaches.

Keywords: intellectual disability, genetic aetiology, alwadei syndrome, RUSC2

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Authors: Siriniya Siribrahmanakul

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Introduction:SARsCOVID-19 is rapidly spreading, and some people may exhibit severe symptoms. Mortality rate of 2.0–3.0% with COVID-19 infection atworldwide. Human leukocyte antigen (HLA), located on chromosome 6, consist of HLA class I and class II. HLA are used by the immune system to attach self-antigens. Previous studies, HLA-DRB1*01:01,HLA-DRB1*12:01and HLA-DRB1*14:04 were, showed significant difference with severe COVID-19 in the Chinese population by p-value < 0.05. Objective: We investigated the prevalence of HLA-DRB1 alleles associated with severe COVID-19 in Thai population. Materials and Methods:200 DNA samples were isolated from EDTA blood using the MagNAprue Compact Nucleic Acid Isolation kits.HLA-DRB1alleles were genotyped using sequence-specific oligonucleotides (PCR-SSOs). Results:The frequency of HLA-DRB1 alleles in Thai population wereHLA-DRB1*12:02 (15.75%), HLA-DRB1*15:02 (14.50%), HLA-DRB1*09:01 (11.50%), HLA-DRB1*07:01 (9.50%), HLA-DRB1*03:01,HLA-DRB1*05:01 (5.75%), HLA-DRB1*14:01 (5.50%), HLA-DRB1*16:02 (4.50%), HLA-DRB1*04:05 (4.00%), HLA-DRB1*14:03 (3.25%), HLA-DRB1*10:01 (2.25%) and HLA-DRB1*13:02 (2.00%). Particularly, HLA-DRB1*12:02 allele was the highest allele frequency presented in the four regions groups of Thai population. Furthermore, the HLA-DRB1* alleles associated with severe COVID-19, which consists ofHLA-DRB1*14:04(2.00 %) and HLA-DRB1*12:01(0.50%) in Thai population, whereas HLA-DRB1*01:01 allele was not found in this population. HLA-DRB1*14:04 and HLA-DRB1*12:01alleles were similarly distributed in four regions populations in Thailand (p-value > 0.05). The alleles frequencies of HLA-DRB1*14:04 and HLA-DRB1*12:01, which associated with severe COVID-19, had no significant differences between Thai population, South China population, South Africa population, and South Koreapopulation (p-value > 0.05). Conclusions: Particularly, this study has focused on allele frequency of HLA-DRB1*14:04in a healthy Thai population to evaluating their impact on the severe COVID-19. Furthermore, our research needs to be done in larger numbers of Thai patients.

Keywords: HLA-DRB1, allele frequency, Thai population, COVID-19 marker

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Authors: Alaa M. M. Badr Eldin, Marwa I. Ezzat, Mohammed S. Sedeek, Manal S. Afifi, Omar M. Sabry

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Cytotoxic activity of the total methanol extract against breast cancer cell line MCF-7 was amazing IC50 at 54 ug/ml. 130 polyphenolic compounds were tentatively identified in pomegranate peel (Punica granatum L.) methanol extract using HPLC-MS/MS technique. The antiestrogenic activity of the polyphenolic constituents found in pomegranate extract was confirmed experimentally in-vitro and by the in-silico molecular docking using gallagic acid, ellagic acid, and Punicalagin as these are considered model compounds confirmed in pomegranate peel extract. The methanolic extract was found to suppress ER, TGF-β, and NF-kB in-vitro gene expression strongly, and that was verified by qPCR and Western Blot gel electrophoresis techniques.

Keywords: HPLC-MS/MS, pomegranate, breast cancer, ovarian cancer, ER, TGF-β, NF-kB

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Authors: Yugander Arra, Florence Auguy, Melissa Stiebner, Sophie Chéron, Michael M. Wudick, Van Schepler-Luu, Sébastien Cunnac, Wolf B. Frommer, Laurence Albar

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Rice yellow mottle virus (RYMV) is one of the most important diseases affecting rice in Africa. The most promising strategy to reduce yield losses is the use of highly resistant varieties. The resistance gene RYMV2 is homolog of the Arabidopsis constitutive expression of pathogenesis related protein-5 (AtCPR5) nucleoporin gene. Resistance alleles are originating from African cultivated rice Oryza glaberrima, rarely cultivated, and are characterized by frameshifts or early stop codons, leading to a non-functional or truncated protein. Rice possesses two paralogs of CPR5 and function of these genes are unclear. Here, we evaluated the role of the two rice candidate nucleoporin paralogs OsCPR5.1 (pathogenesis-related gene 5; RYMV2) and OsCPR5.2 by CRISPR/Cas9 genome editing. Despite striking sequence and structural similarity, only loss-of-function of OsCPR5.1 led to full resistance, while loss-of-function oscpr5.2 mutants remained susceptible. Short N-terminal deletions in OsCPR5.1 also did not lead to resistance. In contrast to Atcpr5 mutants, neither OsCPR5.1 nor OsCPR5.2 knock out mutants showed substantial growth defects. Taken together, the candidate nucleoporin OsCPR5.1, but not its close homolog OsCPR5.2, plays a specific role for the susceptibility to RYMV, possibly by impairing the import of viral RNA or protein into the nucleus. Whereas gene introgression from O. glaberrima to high yielding O. sativa varieties is impaired by strong sterility barriers and the negative impact of linkage drag, genome editing of OsCPR5.1, while maintaining OsCPR5.2 activity, thus provides a promising strategy to generate O. sativa elite lines that are resistant to RYMV.

Keywords: CRISPR Cas9, genome editing, knock out mutant, recessive resistance, rice yellow mottle virus

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Authors: Syed A. Bukhari, Ankur Goswmai, Dale Hume, Thomas Thundat

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Here we demonstrate mechanical detection of photo-induced Insulator to metal transition (MIT) in ultra-thin vanadium dioxide (VO₂) micro strings by using < 100 µW of optical power. Highly focused laser beam heated the string locally resulting in through plane and along axial heat diffusion. Localized temperature increase can cause temperature rise > 60 ºC. The heated region of VO₂ can transform from insulating (monoclinic) to conducting (rutile) phase leading to lattice compressions and stiffness increase in the resonator. The mechanical frequency of the resonator can be tuned by changing optical power and wavelength. The first mode resonance frequency was tuned in three different ways. A decrease in frequency below a critical optical power, a large increase between 50-120 µW followed by a large decrease in frequency for optical powers greater than 120 µW. The dynamic mechanical response was studied as a function of incident optical power and gas pressure. The resonance frequency and amplitude of vibration were found to be decreased with increasing laser power from 25-38 µW and increased by1-2 % when the laser power was further increased to 52 µW. The transition in films was induced and detected by a single pump and probe source and by employing external optical sources of different wavelengths. This trend in dynamic parameters of the strings can be co-related with reversible Insulator to metal transition in VO₂ films which creates change in density of the material and hence the overall stiffness of the strings leading to changes in string dynamics. The increase in frequency at a particular optical power manifests a transition to a more ordered metallic phase which tensile stress onto the string. The decrease in frequency at higher optical powers can be correlated with poor phonon thermal conductivity of VO₂ in conducting phase. Poor thermal conductivity of VO₂ can force in-plane penetration of heat causing the underneath SiN supporting VO₂ which can result as a decrease in resonance frequency. This noninvasive, non-contact laser-based excitation and detection of Insulator to metal transition using micro strings resonators at room temperature and with laser power in few µWs is important for low power electronics, and optical switching applications.

Keywords: thermal conductivity, vanadium dioxide, MEMS, frequency tuning

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Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck, Jason Stanley, Leroy Whilby

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major threat to fruit and vegetable industries in the United States. The establishment of pest fruit fly in the agricultural industries and produce severe ecological and economic impacts on agricultural diversification and trade. Detection and identification of these agricultural pests in a timely manner will facilitate the possibility of eradication from newly invaded areas. Identification of larval stages to species level is difficult, but is required to determine pest loads and their pathways into the United States. The aim of this study is the New World genus, Anastrepha which includes pests of major economic importance. Mitochondrial cytochrome c oxidase I (COI) gene sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level. During phylogenetics analysis numerous nuclear mitochondrial pseudogenes (numts) were discovered in different specimens. The numts are nonfunctional copies of the mtDNA present in the nucleus and are easily coamplified with the mitochondrial COI gene copy by using conserved universal primers. This is problematic for DNA Barcoding, which attempts to characterize all living organisms by using the COI gene. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed.

Keywords: tephritid, Anastrepha fraterculus, COI, numts

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Authors: Fadzil Ahmad, Noor Ashidi Mat Isa

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This study introduces an improved genetic algorithm procedure that focuses search around near optimal solution corresponded to a group of elite chromosome. This is achieved through a novel crossover technique known as Segmented Multi Chromosome Crossover. It preserves the highly important information contained in a gene segment of elite chromosome and allows an offspring to carry information from gene segment of multiple chromosomes. In this way the algorithm has better possibility to effectively explore the solution space. The improved GA is applied for the automatic and simultaneous parameter optimization and feature selection of artificial neural network in pattern recognition of medical problem, the cancer and diabetes disease. The experimental result shows that the average classification accuracy of the cancer and diabetes dataset has improved by 0.1% and 0.3% respectively using the new algorithm.

Keywords: genetic algorithm, artificial neural network, pattern clasification, classification accuracy

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Authors: Sheila M. Wicks, Gail Mahady, Udesh Patel, Joanna Michel, Armando Caceres

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Introduction: The genus piperaceae contains approximately 1000 species of herbs scrubs small trees and hanging vines distributed in both hemispheres. During our ethno medical work in Guatemala of the 27 plant families documented for us e by the Qeqchi Maya for reproductive disorders the most prominent were the Piperaceae (15%) and Menispermiaceae. Our Previous work showed that extracts from form Piper and Cissampelos species bound to both and progesterone and the estrogen receptors. In this work active extracts from Piper aeruginosibaccum Trelease, P auritum, P tuerckheimii and Cissampels tropaeolifolia were tested in functionalized cell based assays including a SEAP reporter gene and by qPCR of ER-responsive gene expression in MCF-7cells. In the reporter gene assay P aeruginosibaccum was estrogenic and enhanced E2 EFFECTS IN MCF-7 CELLS. P. tuerckheimi was not estrogenic alone but significantly enhanced the effects of E2 on SEAP reporter gene expression. Both altered mRNA expression of E2 responsive genes in MCF-7. Methods: this is collaborative project between University of Illinois at Chicago and University of San Carlos Guatemala City. 144 spices of plants were collected in Guatemala of which 57 used to treat a variety of women's reproductive health. The Genus Piperaraceae contains approximately 1000 species of herbs scrubs and small trees. Active extracts of the plants were tested in functionalized in cell-based bioassays including SEAP reporter genes. Results demonstrated altered mRNA expression of E2 responsive genes in MC-7 cells plants were collected in Guatemala of which 57 used. Conclusion of the 5 plants tested all were shown to contain components of binding to estrogenic receptor to a greater or lesser degree. These effects support the use of QEqchi Maya women in Guatemala for reproductive.

Keywords: reporter genes, MC7, guatemala piperaceae, reproductive health

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Authors: Yazid Alkraimeen

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Precise prediction of dielectric stresses and high voltages of power transformers require the accurate calculation of frequency-dependent parameters. A lack of accuracy can result in severe damages to transformer windings. Transient conditions is stuided by digital computers, which require the implementation of accurate models. This paper analyzes the computation of frequency-dependent skin and proximity losses included in the transformer winding model, using analytical equations and Finite Element Method (FEM). A modified formula to calculate the proximity and the skin losses is presented. The results of the frequency-dependent parameter calculations are verified using the Finite Element Method. The time-domain transient voltages are obtained using Numerical Inverse Laplace Transform. The results show that the classical formula for proximity losses is overestimating the transient voltages when compared with the results obtained from the modified method on a simple transformer geometry.

Keywords: fast front transients, proximity losses, transformer winding modeling, skin losses

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Authors: Ha T. T. Ly, Truc B. Truc, Hai N. Truong, Mai P. T. Nguyen, Ngoc D. Ngo, Khanh V. Tran, Hai T. Le

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Beta thalassemia is one of the most common inherited blood disorders, which is characterized by decreased or absent in beta globin expression. Patients with Beta thalassemia whose anemia is not so severe as to necessitate transfusions are said to have thalassemia intermedia. Objective: The goal of this study is prenatal diagnosis for pregnancy woman with Beta thalassemia intermedia and her husband with Beta thalassemia carrier at high risk of Beta thalassemia major in Northern of Vietnam. Material and method: The family has a 6 years-old compound heterozygous thalassemia major for CD71/72(+A) and Hbb:c. -78A>G/nt-28(A>G) male child. The father was heterozygous for CD71/72(+A) mutation which is Beta plus type and the mother was compound heterozygosity of two different variants, namely, Hbb: c. -78A>G/nt-28(A>G) and CD26(A-G) HbE. Prenatal Beta thalassemia mutation detection in fetal DNA was carried out using multiplex Amplification-refractory mutation system ARMS-PCR and confirmed by direct Sanger-sequencing Hbb gene. Prenatal diagnoses were perfomed by amniotic fluid sampling from pregnant woman in the 16-18th week of pregnancy after the genotypes of parents of the probands were identified. Result: When amniotic fluid sample was analyzed for Beta globin gene (Hbb), we found that the genotype is heterozygous for CD71/72(+A) and CD26(A-G) HbE. This genotype is different from the 1st child of this family. Conclusion: Prenatal diagnosis helps the parents to know the genotype and the thalassemia status of the fetus, so they can have early decision on their pregnancy. Genetic diagnosis provided a useful method in diagnosis for familial members in pedigree, genetic counseling and prenatal diagnosis.

Keywords: beta thalassemia intermedia, Hbb gene, pedigree, prenatal diagnosis

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Authors: Yiming Jin, Ping Dong

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The primary resonance of a pipeline close to a plane boundary is investigated in this paper. Based on classic Van der Pol equation and added a nonlinear item, a new wake oscillator model is proposed to predict the vortex-induced vibration (VIV) of a circular cylinder close to a plane boundary. Then, with the multi-scale method, the approximate solution for the case of the primary resonance is obtained. Besides, to study the characteristic of the primary resonance, the effects of the mass ration, frequency, damp ratio and gap ratio on the frequency-response curves of the pipeline are analysed. On the whole, the trend of the numerical results match up with that of the experimental data well and the mass ration, frequency, damp ratio and gap ratio play an important role in the vortex-induced vibration (VIV) of a circular cylinder close to a plane boundary, especially, the smaller is the mass ratio, the larger impact the gap ratio has on the frequency-response curves of the primary resonance.

Keywords: primary resonance, gap ratio, vortex-induced vibration, multi-scale method

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Authors: Gigih Priyandoko, Mohd Fairusham Ghazali, Tan Siew Fun

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This paper discusses about the defect detection of plastic pipe by using nonlinear acoustic wave modulation method. It is a sensitive method for damage detection and it is based on the propagation of high frequency acoustic waves in plastic pipe with low frequency excitation. The plastic pipe is excited simultaneously with a slow amplitude modulated vibration pumping wave and a constant amplitude probing wave. The frequency of both the excitation signals coincides with the resonances of the plastic pipe. A PVP pipe is used as the specimen as it is commonly used for the conveyance of liquid in many fields. The results obtained are being observed and the difference between uncracked specimen and cracked specimen can be distinguished clearly.

Keywords: plastic pipe, defect detection, nonlinear acoustic modulation, excitation

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Authors: Mustapha Sadouk

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This study investigates the sensitivity of high-frequency acoustic parameters in a rigid air-saturated porous bilayer material within the framework of the equivalent fluid theory, a specific case of the Biot model. The study specifically focuses on the sensitivity analysis in the frequency domain. The interaction between the fluid and solid phases of the porous medium incorporates visco-inertial and thermal exchange, characterized by two functions: the dynamic tortuosity α(ω) proposed by Johnson et al. and the dynamic compressibility β(ω) proposed by Allard, refined by Sadouki for the low-frequency domain of ultrasound. The parameters under investigation encompass porosity, tortuosity, viscous characteristic length, thermal characteristic length, as well as viscous and thermal shape factors. A +30% variation in these parameters is considered to assess their impact on the transmitted wave amplitudes. By employing this larger variation, a more comprehensive understanding of the sensitivity of these parameters is obtained. The outcomes of this study contribute to a better comprehension of the high-frequency wave behavior in porous bilayer materials, providing valuable insights for the design and optimization of such materials across various applications.

Keywords: bilayer materials, ultrasound, sensitivity analysis, equivalent fluid theory, dynamic tortuosity., porous material

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

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Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Shubhita Mathur, Ritika Kar Bahal, Priyanka Chauhan, Anil K. Tyagi

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Mycobacterium tuberculosis, the causative agent of human tuberculosis, is a major cause of mortality. Bacillus Calmette-Guérin (BCG), the only licensed vaccine available for protection against tuberculosis confers highly variable protection ranging from 0%-80%. Thus, novel vaccine strains need to be evaluated for their potential as a vaccine against tuberculosis. We had previously constructed a triple gene mutant of M. tuberculosis (MtbΔmms), having deletions in genes encoding for phosphatases mptpA, mptpB, and sapM that are involved in host-pathogen interaction. Though vaccination with Mtb∆mms strain induced protection in the lungs of guinea pigs, the mutant strain was not able to control the hematogenous spread of the challenge strain to the spleens. Additionally, inoculation with Mtb∆mms resulted in some pathological damage to the spleens in the early phase of infection. In order to overcome the pathology caused by MtbΔmms in the spleens of guinea pigs and also to control the dissemination of the challenge strain, MtbΔmms was genetically modified by disrupting bioA gene to generate MtbΔmmsb strain. Further, in vivo attenuation of MtbΔmmsb was evaluated, and its protective efficacy was assessed against virulent M. tuberculosis challenge in guinea pigs. Our study demonstrates that Mtb∆mmsb mutant was highly attenuated for growth and virulence in guinea pigs. Vaccination with Mtb∆mmsb mutant generated significant protection in comparison to sham-immunized animals at 4 and 12 weeks post-infection in lungs and spleens of the infected animals. Our findings provide evidence that deletion of genes involved in signal transduction and biotin biosynthesis severely attenuates the pathogen and the single immunization with the auxotroph was able to provide significant protection as compared to sham-immunized animals. The protection imparted by Mtb∆mmsb fell short in comparison to the protection observed in BCG-immunized animals. This study nevertheless indicates the importance of attenuated multiple gene deletion mutants of M. tuberculosis in generating protection against tuberculosis.

Keywords: Mycobacterium tuberculosis, BCG, MtbΔmmsb, bioA, guinea pigs

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Authors: Fiston Masudi Tambwe, Lwanga Charles, Arfang Badji, Unzimai Innocent

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The development of maize varieties combining Provitamin A (PVA), high yield, and Striga resistance is an effective and affordable strategy to contribute to food security in sub-Saharan Africa, where maize is a staple food crop. There has been limited research on introgressing PVA genes into Striga-resistant maize genotypes. The objectives of this study were to: i) determine the mode of gene action controlling PVA carotenoid accumulation in Striga-resistant maize, ii) identify Striga-resistant maize hybrids with high PVA content and stable yield, and iii) validate the presence of PVA functional markers in offspring. Six elite, Striga-resistant inbred females were crossed with six high-PVA inbred males in a North Carolina Design II and their offspring were evaluated in four environments, following a 5x8 alpha lattice design with four hybrid checks. Results revealed that both additive and non-additive gene action control carotenoid accumulation in the present study, with a predominance of non-additive gene effects for PVA. Hybrids STR1004xCLHP0352 and STR1004xCLHP0046 - identified as Striga-resistant because they supported fewer Striga plants – were the highest-yielding genotypes with a moderate PVA concentration of 5.48 and 5.77 µg/g, respectively. However, those two hybrids were not stable in terms of yield across all environments. Hybrid STR1007xCLHP0046, however, supported fewer Striga plants, had a yield of 4.52 T/ha, a PVA concentration of 4.52 µg/g, and was also stable. Gel-based marker systems of CrtRB1 and LCYE were used to screen the hybrids and favorable alleles of CrtRB1 primers were detected in 20 hybrids, confirming good levels of PVA carotenoids. Hybrids with favorable alleles of LCYE had the highest concentration of non-PVA carotenoids. These findings will contribute to the development of high-yielding PVA-rich maize varieties in Uganda.

Keywords: gene action, stability, striga resistance, provitamin A markers, beta-carotene hydroxylase 1, CrtRB1, beta-carotene, beta-cryptoxanthin, lycopene epsilon cyclase, LCYE

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Authors: L. M. Al-Harbi, A. M. Shokry, J. S. M. Sabir, A. Chaudhary, J. Manikandan, K. S. Saini

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Breast cancer is the second most common cause of cancer death worldwide and is the most common malignancy among Saudi females. During breast carcinogenesis, a wide-array of cytogenetic changes involving deletions, or amplification, or translocations, of part or whole of chromosome regions have been observed. Because of the limitations of various earlier technologies, newer tools are developed to scan for changes at the genomic level. Recently, Array Comparative Genomic Hybridization (aCGH) technique has been applied for detecting segmental genomic alterations at molecular level. In this study, aCGH was performed on twenty breast cancer tumors and their matching non-tumor (normal) counterparts using the Agilent 2x400K. Several regions were identified to be either amplified or deleted in a tumor-specific manner. Most frequent alterations were amplification of chromosome 1q, chromosome 8q, 20q, and deletions at 16q were also detected. The amplification of genetic events at 1q and 8q were further validated using FISH analysis using probes targeting 1q25 and 8q (MYC gene). The copy number changes at these loci can potentially cause a significant change in the tumor behavior, as deletions in the E-Cadherin (CDH1)-tumor suppressor gene as well as amplification of the oncogenes-Aurora Kinase A. (AURKA) and MYC could make these tumors highly metastatic. This study validates the use of aCGH in Saudi breast cancer patients and sets the foundations necessary for performing larger cohort studies searching for ethnicity-specific biomarkers and gene copy number variations.

Keywords: breast cancer, molecular biology, ecology, environment

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