Search results for: molecular diagnostics

Authors: Barbara Zapala, Marek Dziechciowski, Olaf Chmura, Monika Piwowar, Katarzyna Gawlik, Dorota Pawlicka-Gosiewska, Krzysztof Skotniczny, Bogdan Solnica, Kazimierz Pitynski

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BACKGROUND: Endometrial cancer is one of the most common gynecologic malignancy in developed countries.We hypothesized that amount of circulating micro-particles in blood may be connected with the development of endometrial hyperplasia and endometrial cancer. The aim of this study was to measure the micro-particles amount in uterine venous blood and in peripheral venous blood in women with atypical endometrial hyperplasia and endometrioid endometrial cancer. MATERIALS AND METHODS: By using flow cytometry (BD Canto II cytometer) we measured micro-particles amount in citrate plasma samples from peripheral and uterine venous blood of women with atypical hyperplasia of endometrium or endometrial cancer. We determined the amount of total (TF+), endothelial (CD144+) and monocytic (CD14+) micro- particles. RESULTS: Here we show statistically significant higher micro-particle levels in women with atypical hyperplasia of endometrium or endometrial cancer in comparison to healthy women. Performing measurements of the amounts of total, endothelial and monocytic microparticles allow for reliable differentiation between healthy, atypical hyperplasia and endometrial cancer groups. In blood samples from uterine veins the circulating micro-particle levels were significantly different from peripheral blood samples. The micro-particle levels in uterine blood samples were 7-fold higher than in those from peripheral blood of women with both atypical hyperplasia of endometrium and endometrial cancer when compared to the control group of healthy women. CONCLUSION: These results strongly suggested that the level of circulating micro-particles may be a sign of endometrial cancer development, however the detailed study is needed focusing on molecular processes passed through this small circulating molecules.

Keywords: endometrial cancer, endometrial hyperplasia, microvesicles, uterine blood

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Authors: S. Redjala, N. Ait Hocine, M. Gratton, N. Poirot, R. Ferhoum, S. Azem

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Polycarbonate (PC) is a promising polymer with high transparency in the range of the visible spectrum and is used in various fields, for example medical, electronic, automotive. Its low weight, chemical inertia, high impact resistance and relatively low cost are of major importance. In recent decades, some materials such as metals and ceramics have been replaced by polymers because of their superior advantages. However, some characteristics of the polymers are highly modified under the effect of ultraviolet (UV) radiation and temperature. The changes induced in the material by such aging depend on the exposure time, the wavelength of the UV radiation and the temperature level. The UV energy is sufficient to break the chemical bonds leading to a cleavage of the molecular chains. This causes changes in the mechanical, thermal, optical and morphological properties of the material. The present work is focused on the study of the effects of aging under ultraviolet (UV) radiation and under different temperature values on the physical-chemical and mechanical properties of a PC. Thus, various investigations, such as FTIR and XRD analyses, SEM and optical microscopy observations, micro-hardness measurements and monotonic and cyclic tensile tests, were carried out on the PC in the initial state and after aging. Results have shown the impact of aging on the properties of the PC studied. In fact, the MEB highlighted changes in the superficial morphology of the material by the presence of cracks and material de-bonding in the form of debris. The FTIR spectra reveal an attenuation of the peaks like the hydroxyl (OH) groups located at 3520 cm-1. The XRD lines shift towards a larger angle, reaching a maximum of 3°. In addition, Vickers micro-hardness measurements show that aging affects the surface and the core of the material, which results in different mechanical behaviours under monotonic and cyclic tensile tests. This study pointed out effects of aging on the macroscopic properties of the PC studied, in relationship with its microstructural changes.

Keywords: mechanical properties, physical-chemical properties, polycarbonate, UV aging, temperature aging

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Authors: Daina Jonkus, Solvita Petrovska, Dace Smiltina, Lasma Cielava

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The beta-lactoglobulin and kappa-casein are milk proteins which are important for milk composition. Cows with beta-lactoglobulin and kappa-casein gene BB genotypes have highest milk crude protein and fat content. The aim of the study was to determinate the frequencies of milk protein gene polymorphisms in local Latvian Brown (LB) cows breed and analyze the influence of beta-lactoglobulin and kappa-casein genotypes to milk productivity traits. 102 cows’ genotypes of milk protein genes were detected using Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) and electrophoresis on 3% agarose gel. For beta-lactoglobulin were observed 2 types of alleles A and B and for kappa-casein 3 types: A, B and E. Highest frequency in beta-lactoglobulin gene was observed for B allele – 0.926. Molecular analysis of beta-lactoglobulin gene shows 86.3% of individuals are homozygous by B allele and animals are with genotypes BB and 12.7% of individuals are heterozygous with genotypes AB. The highest milk yield 4711.7 kg was for 1st lactation cows with AB genotypes, whereas the highest milk protein content (3.35%) and fat content (4.46 %) was for BB genotypes. Analysis of the kappa-casein locus showed a prevalence of the A allele – 0.750. The genetic variant of B was characterized by a low frequency – 0.240. Moreover, the frequency of E occurred in the LB cows’ population with very low frequency – 0.010. 54.9 % of cows are homozygous with genotypes AA, and only 4.9 % are homozygous with genotypes BB. 32.8 % of individuals are heterozygous with genotypes AB, and 2.0 % are with AE. The highest milk productivity was for 1st lactation cows with AB genotypes: milk yield 4620.3 kg, milk protein content 3.39% and fat content 4.53 %. According to the results, in local Latvian brown there are only 2.9% of cows are with BB-BB genotypes, which is related to milk coagulation ability and affected cheese production yield. Acknowledgment: the investigation is supported by VPP 2014-2017 AgroBioRes Project No. 3 LIVESTOCK.

Keywords: beta-lactoglobulin, cows, genotype frequencies, kappa-casein

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Authors: Md. Z. Alam, Amal A. Elgharbawy, Muhammad Moniruzzaman, Nassereldeen A. Kabbashi, Parveen Jamal

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The enzymatic hydrolysis of lignocellulosic biomass is one of the obstacles in the process of sugar production, due to the presence of lignin that protects the cellulose molecules against cellulases. Although the pretreatment of lignocellulose in ionic liquid (IL) system has been receiving a lot of interest; however, it requires IL removal with an anti-solvent in order to proceed with the enzymatic hydrolysis. At this point, introducing a compatible cellulase enzyme seems more efficient in this process. A cellulase enzyme that was produced by Trichoderma reesei on palm kernel cake (PKC) exhibited a promising stability in several ILs. The enzyme called PKC-Cel was tested for its optimum pH and temperature as well as its molecular weight. One among evaluated ILs, 1,3-diethylimidazolium dimethyl phosphate [DEMIM] DMP was applied in this study. Evaluation of six factors was executed in Stat-Ease Design Expert V.9, definitive screening design, which are IL/ buffer ratio, temperature, hydrolysis retention time, biomass loading, cellulase loading and empty fruit bunches (EFB) particle size. According to the obtained data, IL-enzyme system shows the highest sugar concentration at 70 °C, 27 hours, 10% IL-buffer, 35% biomass loading, 60 Units/g cellulase and 200 μm particle size. As concluded from the obtained data, not only the PKC-Cel was stable in the presence of the IL, also it was actually stable at a higher temperature than its optimum one. The reducing sugar obtained was 53.468±4.58 g/L which was equivalent to 0.3055 g reducing sugar/g EFB. This approach opens an insight for more studies in order to understand the actual effect of ILs on cellulases and their interactions in the aqueous system. It could also benefit in an efficient production of bioethanol from lignocellulosic biomass.

Keywords: cellulase, hydrolysis, lignocellulose, pretreatment

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Authors: Fadime Eroglu

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Acanthamoeba genus belongs to kingdom protozoa, and it is known as free-living amoebae. Acanthamoeba genus has been isolated from human bodies, swimming pools, bottled mineral water, contact lens solutions, dust, and soil. The members of the genus Acanthamoeba causes Acanthamoeba Keratitis which is a painful sight-threatening disease of the eyes. In recent years, the prevalence of Acanthamoeba keratitis has been high rate reported. The eight different Acanthamoeba species are known to be effective in Acanthamoeba keratitis. These species are Acanthamoeba castellanii, Acanthamoeba polyphaga, Acanthamoeba griffini, Acanthamoeba hatchetti, Acanthamoeba culbertsoni and Acanhtamoeba rhysodes. The conventional diagnosis of Acanthamoeba Keratitis has relied on cytological preparations and growth of Acanthamoeba in culture. However molecular methods such as real-time PCR has been found to be more sensitive. The real-time PCR has now emerged as an effective method for more rapid testing for the diagnosis of infectious disease in decade. Therefore, a real-time PCR assay for the detection of Acanthamoeba keratitis and Acanthamoeba species have been developed in this study. The 18S rRNA sequences from Acanthamoeba species were obtained from National Center for Biotechnology Information and sequences were aligned with MEGA 6 programme. Primers and probe were designed using Custom Primers-OligoPerfectTMDesigner (ThermoFisherScientific, Waltham, MA, USA). They were also assayed for hairpin formation and degree of primer-dimer formation with Multiple Primer Analyzer ( ThermoFisherScientific, Watham, MA, USA). The eight different ATCC Acanthamoeba species were obtained, and DNA was extracted using the Qiagen Mini DNA extraction kit (Qiagen, Hilden, Germany). The DNA of Acanthamoeba species were analyzed using newly designed primer and probe set in real-time PCR assay. The early definitive laboratory diagnosis of Acanthamoeba Keratitis and the rapid initiation of suitable therapy is necessary for clinical prognosis. The results of the study have been showed that new primer and probes could be used for detection and distinguish for Acanthamoeba species. These new developing methods are helpful for diagnosis of Acanthamoeba Keratitis.

Keywords: Acathamoeba Keratitis, Acanthamoeba species, fast diagnosis, Real-Time PCR

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Authors: Gargi Ghoshal, Ashay Jain, Deepika Thakur, U. S. Shivhare, O. P. Katare

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The main objectives of this work were the rheological characterization of dispersions, emulsions at different pH used in the microcapsules preparation and the microcapsules obtain from gum arabic (A), guar gum (G), casein (C) and whey protein isolate (W) to keep β-carotene protected from degradation using the complex coacervation microencapsulation technique (CCM). The evaluation of rheological properties of dispersions, emulsions of different pH and so obtained microencapsules manifest the changes occur in the molecular structure of wall materials during the encapsulation process of β-carotene. These dispersions, emulsions of different pH and formulated microencapsules were subjected to go through various conducted experiments (flow curve test, amplitude sweep, and frequency sweep test) using controlled stress dynamic rheometer. Flow properties were evaluated as a function of apparent viscosity under steady shear rate ranging from 0.1 to 100 s-1. The frequency sweep test was conducted to determine the extent of viscosity and elasticity present in the samples at constant strain under changing angular frequency range from 0.1 to 100 rad/s at 25ºC. The dispersions and emulsion exhibited a shear thinning non-Newtonian behavior whereas microencapsules are considered as shear-thickening respectively. The apparent viscosity for dispersion, emulsions were decreased at low shear rates 20 s-1 and for microencapsules, it decreases up to ~50 s-1 besides these value, it has shown constant pattern. Oscillatory shear experiments showed a predominant viscous liquid behavior up to crossover frequencies of dispersions of C, W, A at 49.47 rad/s, 57.60 rad/s and 21.45 rad/s emulsion sample of AW at pH 5.0 it was 17.85 rad/s and GW microencapsules 61.40 rad/s respectively whereas no such crossover was found in G dispersion, emulsion with C and microencapsules still it showed more viscous behavior. Storage and loss modulus decreases with time also a shift of the crossover towards lower frequencies for A, W and C was observed respectively. However, their microencapsules showed more viscous behavior as compared to samples prior to blending.

Keywords: viscosity, gums, proteins, frequency sweep test, apparent viscosity

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Authors: Abbas Pourreza

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MicroRNAs (miRNAs) are small single-stranded non-coding RNAs. They are almost 18-25 nucleotides long and very conservative through evolution. They are involved in adjusting the expression of numerous genes due to the existence of a complementary region, generally in the 3' untranslated regions (UTR) of target genes, against particular mRNAs in the cell. Also, miRNAs have been proven to be involved in cell development, differentiation, proliferation, and apoptosis. More than 2000 miRNAs have been recognized in human cells, and these miRNAs adjust approximately one-third of all genes in human cells. Dysregulation of miRNA originated from abnormal DNA methylation patterns of the locus, cause to down-regulated or overexpression of miRNAs, and it may affect tumor formation or development of it. Breast cancer (BC) is the most commonly identified cancer, the most prevalent cancer (23%), and the second-leading (14%) mortality in all types of cancer in females. BC can be classified based on the status (+/−) of the hormone receptors, including estrogen receptor (ER), progesterone receptor (PR), and the Receptor tyrosine-protein kinase erbB-2 (ERBB2 or HER2). Currently, there are four main molecular subtypes of BC: luminal A, approximately 50–60 % of BCs; luminal B, 10–20 %; HER2 positive, 15–20 %, and 10–20 % considered Basal (triple-negative breast cancer (TNBC)) subtype. Aberrant expression of miR-145, miR-21, miR-10b, miR-125a, and miR-206 was detected by Stem-loop real-time RT-PCR in BC cases. Breast tumor formation and development may result from down-regulation of a tumor suppressor miRNA such as miR-145, miR-125a, and miR-206 and/or overexpression of an oncogenic miRNA such as miR-21 and miR-10b. MiR-125a, miR-206, miR-145, miR-21, and miR-10b are hugely predicted to be new tumor markers for the diagnosis and prognosis of BC. MiR-21 and miR-125a could play a part in the treatment of HER-2-positive breast cancer cells, while miR-145 and miR-206 could speed up the evolution of cure techniques for TNBC. To conclude, miRNAs will be presented as hopeful molecules to be used in the primary diagnosis, prognosis, and treatment of BC and battle as opposed to its developed drug resistance.

Keywords: breast cancer, HER2 positive, miRNA, TNBC

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Authors: Lola Brasseur, Guillaume Caulier, Marie Demeyer, Pascal Gerbaux, Igor Eeckhaut

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Seawater being an ideal dispersing agent, chemical communication stays predominant in marine ecosystems. However, if many molecules acting in chemical heterospecific communication have already been well described in terrestrial ecosystems, only three of these molecules were identified in marine ecosystems. Echinoderms and their symbiotic organisms constitute very good models to study heterospecific chemical communication because each class synthesizes a specific type of molecules and symbioses with echinoderms as hosts are very usual. In this study, the chemical communication that allows the commensal shrimps Tuleariocaris holthuisi Hipeau-Jacquotte, 1965 to live with their host Echinometra mathaei (Blainville, 1825) was investigated. The chemoreception of the shrimp was characterized using olfactometers and it was demonstrated that hosts and synthetic hydroxynaphthoquinones are attractive to the symbiotic shrimps. Hydroxynaphthoquinonic pigments also known as spinochromes are by the way synthesized by sea urchin and involved in all probability in a lot of mechanisms. To our knowledge, this study is the first highlighting the ecological function of naphthoquinones as kairomones. Chemical extractions were also performed on sea urchins in order to analyze and identify their specific hydroxynaphthoquinones using HPLC-ESI-MS. Accurate mass identification and elemental composition have been performed on various organs (gonads, coelomic liquid, digestive system and test) in different morphotypes of Echinometra mathaei for a better understanding of the molecular diversity of these semiochemicals. Moreover, some experiments were performed to investigate the dependence of T. holthuisi for their host. First, the analyses showed that the molecules involved in shrimp pigmentation are the same that the ones involved in E. mathaei, suggesting a potential feeding on the host. Secondly, a substantial shrimp depigmentation and an increase of the mortality rate were demonstrated after the symbionts-host separation which could mean a potential implication of spinochromes in the shrimp metabolism.

Keywords: crustacean, sea urchin, spinochrome, symbiosis

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Authors: Shalu Jain, Anju Bansal, Anup Kumar, Sunita Saxena

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Objectives: The novel TMPRSS2:ERG gene fusion is a common somatic event in prostate cancer that in some studies is linked with a more aggressive disease phenotype. Thus, this study aims to determine whether clinical variables are associated with the presence of TMPRSS2:ERG-fusion gene transcript in Indian patients of prostate cancer. Methods: We evaluated the clinical variables with presence and absence of TMPRSS2:ERG gene fusion in prostate cancer and BPH association of clinical patients. Patients referred for prostate biopsy because of abnormal DRE or/and elevated sPSA were enrolled for this prospective clinical study. TMPRSS2:ERG mRNA copies in samples were quantified using a Taqman chemistry by real time PCR assay in prostate biopsy samples (N=42). The T2:ERG assay detects the gene fusion mRNA isoform TMPRSS2 exon1 to ERG exon4. Results: Histopathology report has confirmed 25 cases as prostate cancer adenocarcinoma (PCa) and 17 patients as benign prostate hyperplasia (BPH). Out of 25 PCa cases, 16 (64%) were T2: ERG fusion positive. All 17 BPH controls were fusion negative. The T2:ERG fusion transcript was exclusively specific for prostate cancer as no case of BPH was detected having T2:ERG fusion, showing 100% specificity. The positive predictive value of fusion marker for prostate cancer is thus 100% and the negative predictive value is 65.3%. The T2:ERG fusion marker is significantly associated with clinical variables like no. of positive cores in prostate biopsy, Gleason score, serum PSA, perineural invasion, perivascular invasion and periprostatic fat involvement. Conclusions: Prostate cancer is a heterogeneous disease that may be defined by molecular subtypes such as the TMPRSS2:ERG fusion. In the present prospective study, the T2:ERG quantitative assay demonstrated high specificity for predicting biopsy outcome; sensitivity was similar to the prevalence of T2:ERG gene fusions in prostate tumors. These data suggest that further improvement in diagnostic accuracy could be achieved using a nomogram that combines T2:ERG with other markers and risk factors for prostate cancer.

Keywords: prostate cancer, genetic rearrangement, TMPRSS2:ERG fusion, clinical variables

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Authors: Nader Nciri, Suil Song, Namho Kim, Namjun Cho

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Properties and compositions of bitumen and bitumen-derived liquids have significant influences on the selection of recovery, upgrading and refining processes. Optimal process conditions can often be directly related to these properties. The end uses of bitumen and bitumen products are thus related to their compositions. Because it is not possible to conduct a complete analysis of the molecular structure of bitumen, characterization must be made in other terms. The present paper focuses on physico-chemical analysis of two different types of bitumens. These bitumen samples were chosen based on: the original crude oil (sand oil and crude petroleum), and mode of process. The aim of this study is to determine both the manufacturing effect on chemical species and the chemical organization as a function of the type of bitumen sample. In order to obtain information on bitumen chemistry, elemental analysis (C, H, N, S, and O), heavy metal (Ni, V) concentrations, IATROSCAN chromatography (thin layer chromatography-flame ionization detection), FTIR spectroscopy, and 1H NMR spectroscopy have all been used. The characterization includes information about the major compound types (saturates, aromatics, resins and asphaltenes) which can be compared with similar data for other bitumens, more importantly, can be correlated with data from petroleum samples for which refining characteristics are known. Examination of Asphalt Ridge froth bitumen showed that it differed significantly from representative petroleum pitches, principally in their nonhydrocarbon content, heavy metal content and aromatic compounds. When possible, properties and composition were related to recovery and refining processes. This information is important because of the effects that composition has on recovery and processing reactions.

Keywords: froth bitumen, oil sand, asphalt ridge, petroleum pitch, thin layer chromatography-flame ionization detection, infrared spectroscopy, 1H nuclear magnetic resonance spectroscopy

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Authors: Artemova Anastasiia, Shen Zexiang, Savilov Serguei

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The marine environment is very aggressive for a number of factors, such as moisture, temperature, winds, ultraviolet radiation, chloride ion concentration, oxygen concentration, pollution, and biofouling, all contributing to marine corrosion. Protective organic coatings provide protection either by a barrier action from the layer, which is limited due to permeability to water and oxygen or from active corrosion inhibition and cathodic protection due to the pigments in the coating. Carbon nanotubes can play not only barrier effect but also passivation effect via adsorbing molecular species of oxygen, hydroxyl, chloride and sulphate anions. Multiwall carbon nanotubes composite provide very important properties such as mechanical strength, non-cytotoxicity, outstanding thermal and electrical conductivity, and very strong absorption of ultraviolet radiation. The samples of stainless steel (316L) coated by epoxy resin with carbon nanotubes-based pigments were exposed to UV irradiation (340nm), and immersion to the sodium chloride solution for 1000h and corrosion behavior in 3.5 wt% sodium chloride (NaCl) solution was investigated. Experimental results showed that corrosion current significantly decreased in the presence of carbon nanotube-based materials, especially nitrogen-doped ones, in the composite coating. Importance of the structure and composition of the pigment materials and its composition was established, and the mechanism of the protection was described. Finally, the effect of nitrogen doping on the corrosion behavior was investigated. The pigment-polymer crosslinking improves the coating performance and the corrosion rate decreases in comparison with pure epoxy coating from 5.7E-05 to 1.4E-05mm/yr for the coating without any degradation; in more than 6 times for the coating after ultraviolet degradation; and more than 16% for the coatings after immersion degradation.

Keywords: corrosion, coating, carbon nanotubes, degradation

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Authors: Himanshu Singh, Rishi Kant, Shantanu Bhattacharya

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This paper adopts a top-down approach for mathematical modeling to predict the size reduction from micro to nano-scale through persistent etching. The process is simulated using a finite difference approach. Previously, various researchers have simulated the etching process for 1-D and 2-D substrates. It consists of two processes: 1) Convection-Diffusion in the etchant domain; 2) Chemical reaction at the surface of the particle. Since the process requires analysis along moving boundary, partial differential equations involved cannot be solved using conventional methods. In 1-D, this problem is very similar to Stefan's problem of moving ice-water boundary. A fixed grid method using finite volume method is very popular for modelling of etching on a one and two dimensional substrate. Other popular approaches include moving grid method and level set method. In this method, finite difference method was used to discretize the spherical diffusion equation. Due to symmetrical distribution of etchant, the angular terms in the equation can be neglected. Concentration is assumed to be constant at the outer boundary. At the particle boundary, the concentration of the etchant is assumed to be zero since the rate of reaction is much faster than rate of diffusion. The rate of reaction is proportional to the velocity of the moving boundary of the particle. Modelling of the above reaction was carried out using Matlab. The initial particle size was taken to be 50 microns. The density, molecular weight and diffusion coefficient of the substrate were taken as 2.1 gm/cm3, 60 and 10-5 cm2/s respectively. The etch-rate was found to decline initially and it gradually became constant at 0.02µ/s (1.2µ/min). The concentration profile was plotted along with space at different time intervals. Initially, a sudden drop is observed at the particle boundary due to high-etch rate. This change becomes more gradual with time due to declination of etch rate.

Keywords: particle size reduction, micromixer, FDM modelling, wet etching

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Authors: Suresh Kumar Verma, Jugal Kishore Das, Ealisha Jha, Mrutyunjay Suar, SKS Parashar

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In recent years nanoforms of inorganic metallic oxides has attracted a lot of interest due to their small size and significantly improved physical, chemical and biological properties compared to their molecular precursor. Some of the inorganic materials such as TiO2, ZnO, MgO, CaO, Al2O3 have been extensively used in biological applications. Zinc Oxide is a Wurtzite-type semiconductor and piezo-electric material exhibiting excellent electrical, optical and chemical properties with a band energy gap of 3.1-3.4 eV. Nanoforms of Zinc Oxide (ZnO) are increasingly recognised for their utility in biological application. The significant physical parameters such as surface area, particle size, surface charge and Zeta potential of Zinc Oxide (ZnO) nanoparticles makes it suitable for the uptake, persistance, biological, and chemical activities inside the living cells. The present study shows the effect of intrinsic defects of ZnO nanocrystals synthesized by high energy ball milling (HEBM) technique in their antibacterial activities. Bulk Zinc oxide purchased from market were ball milled for 7 h, 10 h, and 15 h respectively to produce nanosized Zinc Oxide. The structural and optical modification of such synthesized particles were determined by X-ray diffraction (XRD), Scanning Electron Microscopy and Electron Paramagnetic Resonance (EPR). The antibacterial property of synthesized Zinc Oxide nanoparticles was tested using well diffusion, minimum inhibitory Concentration, minimum bacteriocidal concentration, reactive oxygen species (ROS) estimation and membrane potential determination methods. In this study we observed that antibacterial activity of ZnO nanoparticles is because of the intrinsic defects that exist as a function of difference in size and milling time.

Keywords: high energy ball milling, ZnO nanoparticles, EPR, Antibacterial properties

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Authors: Sneha Kumari, Ravi Krishnan Elangovan

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This abstract describes the development of a high-speed tracking method by modification in motor components for nanoparticle attachment. Myosin motors are nano-sized protein machines powering movement that defines life. These miniature molecular devices serve as engines utilizing chemical energy stored in ATP to produce useful mechanical energy in the form of a few nanometre displacement events leading to force generation that is required for cargo transport, cell division, cell locomotion, translated to macroscopic movements like running etc. With the advent of in vitro motility assay (IVMA), detailed functional studies of the actomyosin system could be performed. The major challenge with the currently available IVMA for tracking actin filaments is a resolution limitation of ± 50nm. To overcome this, we are trying to develop Single Molecule IVMA in which nanoparticle (GNP/QD) will be attached along or on the barbed end of actin filaments using CapZ protein and visualization by a compact TIRF module called ‘cTIRF’. The waveguide-based illumination by cTIRF offers a unique separation of excitation and collection optics, enabling imaging by scattering without emission filters. So, this technology is well equipped to perform tracking with high precision in temporal resolution of 2ms with significantly improved SNR by 100-fold as compared to conventional TIRF. Also, the nanoparticles (QD/GNP) attached to actin filament act as a point source of light coffering ease in filament tracking compared to conventional manual tracking. Moreover, the attachment of cargo (QD/GNP) to the thin filament paves the way for various nano-technological applications through their transportation to different predetermined locations on the chip

Keywords: actin, cargo, IVMA, myosin motors and single-molecule system

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Authors: Martin C. Eze, Gao Min

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Lithium bis(trifluoromethanesulfonyl)imide (Li-TFSI) dopant is beneficial in improving the properties of 2,2′,7,7′-Tetrakis (N, N-di-p-methoxyphenylamino)-9,9′-spiro-bifluorene (Spiro-OMETAD) transport layer used in perovskite solar cells (PSCs). Properties such as electrical conductivity, band energy mismatch, and refractive index of Spiro-OMETAD layers are believed to play key roles in PSCs performance but only the dependence of electrical conductivity on Li-TFSI doping has been extensively studied. In this work, the effect of Li-TFSI doping level on highest occupied molecular orbital (HOMO) energy, electrical conductivity, and refractive index of Spiro-OMETAD film and PSC performance was demonstrated. The Spiro-OMETAD films were spin-coated at 4000 rpm for 30 seconds from solutions containing 73.4 mM of Spiro-OMeTAD, 23.6 mM of 4-tert-butylpyridine, 7.6 mM of tris(2-(1H-pyrazol-1-yl)-4-tert-butylpyridine) cobalt(III) tri[bis(trifluoromethane) sulfonimide] (FK209) dopant and Li-TFSI dopant varying from 37 to 62 mM in 1 ml of chlorobenzene. From ultraviolet photoelectron spectroscopy (UPS), ellipsometry, and 4-probe studies, the results show that films deposition from Spiro-OMETAD solution doped with 40 mM of Li-TFSI shows the highest electrical conductivity of 6.35×10-6 S/cm, the refractive index of 1.87 at 632.32 nm, HOMO energy of -5.22 eV and the lowest HOMO energy mismatch of 0.21 eV compared to HOMO energy of perovskite layer. The PSCs fabricated show the best power conversion efficiency, open-circuit voltage, and fill factor of 17.10 %, 1.1 V, and 70.12%, respectively, for devices based on Spiro-OMETAD solution doped with 40 mM of Li-TFSI. This study demonstrates that the optimum Spiro-OMETAD/ Li-TFSI doping ratio of 1.84 is the optimum doping level for Spiro-OMETAD layer preparation.

Keywords: electrical conductivity, homo energy mismatch, lithium bis(trifluoromethanesulfonyl)imide, power conversion efficiency, refractive index

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Authors: Makhosi Buthelezi

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Mitochondrial DNA cytochrome c oxidase I (COI) gene analyses linked the South African groundnut leaf miner (GLM) to the Australian soya bean moth Aproaerema simplexella (Walker) and Indian Aproaerema modicella (Deventer). Thus, the genetic relatedness of GLM, A. simplexela, and A. modicella was examined by performing mitochondrial and nuclear (COI, cytochrome oxidase subunit II (COII), mitochondrial cytochrome b (CYTB), nuclear ribosomal 28S (28S) and intergenic spacer elongation factor-1 alpha ( EF-1 ALPHA) on 44 specimens collected from South Africa, four from Mozambique, and three each from single locations in India and Australia. Phylogenetic analyses were conducted using the Maximum Parsimony (MP) and Neighbour-Joining (NJ) methods. All of the datasets of the five DNA gene regions that were sequenced were also analyzed using the Basic Local Alignment Search Tool (BLAST) to find the closest matches for inclusion in the phylogenetic trees as outgroups and for purposes of information. In the phylogenetic trees for COI, COII, cytb and EF-1 ALPHA, a similar pattern was observed in the way that the sequences assembled into different groups; i.e., some sequences of A. simplexella from Australia were grouped separately from the others, but some Australian sequences grouped with those of the GLM from South Africa, India, and Mozambique. In the phylogenetic tree for 28S, all sequences from South Africa, Australia, India, and Mozambique grouped together and formed one group. For COI, genetic pairwise distance ranged from 0.97 to 3.60 %, for COII it ranged from 0.19% to 2.32%, for cytb it ranged from 0.25 to 9.77% and for EF-1 ALPHA it ranged 0.48 to 6.99%. Results of this study indicate that these populations are genetically related and presumably constitute a single species. Thus, further molecular and morphological studies need to be undertaken in order to resolve this apparent conundrum on the taxonomy of these populations.

Keywords: aproaerema modicella, aproaerema simplexella, mitochondrial DNA, nuclear DNA

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Authors: Asieh Abbassi Daloii, Ahmad Abdi

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Introduction: Sports information suggests that physical inactivity increases the risk of many diseases, including atherosclerosis. Coronary heart disease, stroke and peripheral vascular disease, atherosclerosis and clinical protests. However, exercise can have beneficial effects on risk factors for atherosclerosis by reducing hyperlipidemia, hypertension, obesity, plaque density, increased insulin sensitivity and glucose tolerance is improved. Despite these findings, there is little information about the molecular mechanisms of interaction between the body and its relation to sport and there arteriosclerosis. The present study aims to investigate the effect of six weeks of progressive aerobic training and aqueous extract of crataegus monogyna on vascular endothelial growth factor (VEGF) variations and angiopoetin-1/2 (ANG- 1/2) in plasma and heart tissue in male Wistar rats. Methods: 30 male Wistar rats, 4-6 months old, were randomly divided into four groups: control crataegus monogyna (N=8), training crataegus monogyna (N=8), control saline (N=6), and training saline (N=8). The aerobic training program included running on treadmill at the speed of 34 meters per minute for 60 minutes per day. The training was conducted for six weeks, five days a week. Following each training session, both experimental and control subjects of crataegus monogyna groups were orally fed with 0.5 mg crataegus monogyna extract per gram of the body weight. The normal saline group was given the same amount of the normal saline solution (NS). Eventually, 72 hours after the last training session, blood samples were taken from inferior Verna cava. Conclusion: It is likely that crataegus monogyna extract compared with aerobic training and even combination of both training and crataegus monogyna extract is more effective on angiogenesis.

Keywords: angiopoietin 1, 2, vascular endothelial growth factor, aerobic exercise

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Authors: Alisa Kazarina, Guntis Gerhards, Elina Petersone-Gordina, Ilva Pole, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka

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Human body is inhabited by a vast number of microorganisms, collectively known as the human microbiome, and there is a tremendous interest in evolutionary changes in human microbial ecology, diversity and function. The field of paleomicrobiology, study of ancient human microbiome, is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including the taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify the hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results, we suggest that wider range of primers used can provide more accurate recapitulation of microbial communities in archaeological samples. Acknowledgements. This work was supported by the ERAF grant Nr. 1.1.1.1/16/A/101.

Keywords: 16S rRNA gene, ancient human microbiome, archaeology, bioinformatics, genomics, microbiome, molecular biology, next-generation sequencing

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Authors: Maryam Salehi, Gholamreza Bonyadinejad

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The application of agricultural plastic products like mulch, greenhouse covers, and silage films is increasing due to their economic benefits in providing an early and better-quality harvest. In 2015, the 4 million tons (valued a 10.6 million USD) global market for agricultural plastic films was estimated to grow by 5.6% per year through 2030. Despite the short-term benefits provided by plastic products, their long-term sustainability issues and negative impacts on soil health are not well understood. After their removal from the field, some plastic residuals remain in the soil. Plastic residuals in farmlands may fragment to small particles called microplastics (d<5mm). The microplastics' exposure to solar radiation could alter their surface chemistry and make them susceptible to fragmentation. Thus, this study examined the photodegradation of low density polyethylene as the model microplastics that are released to the agriculture farmland. The variation of plastic’s surface chemistry, morphology, and bulk characteristics were studied after accelerated UV-A radiation experiments and sampling from an agricultural field. The Attenuated Total Reflectance Fourier Transform Spectroscopy (ATR-FTIR) and X-ray Photoelectron Spectroscopy (XPS) demonstrated the formation of oxidized surface functional groups onto the microplastics surface due to the photodegradation. The Differential Scanning Calorimetry (DSC) analysis revealed an increased crystallinity for the photodegraded microplastics compared to the new samples. The gel permeation chromatography (GPC) demonstrated the reduced molecular weight for the polymer due to the photodegradation. This study provides an important opportunity to advance understanding of soil pollution. Understanding the plastic residuals’ variations as they are left in the soil is providing a critical piece of information to better estimate the microplastics' impacts on environmental biodiversity, ecosystem sustainability, and food safety.

Keywords: soil health, plastic pollution, sustainability, photodegradation

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Authors: S. Ahmad, C. Yuan, Q. Zhang

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The assorted architectural plasticity of a plant is majorly specified by stooling, a phenomenon tackled by a combination of developmental, environmental and hormonal accelerators of lateral buds. Chrysanthemums (Chrysanthemum morifolium) are one of the most economically important ornamental plants worldwide on the account of having plentiful architectural patterns, diverse shapes and attractive colors. Side branching is the major determinant guaranteeing the consistent demand of cut chrysanthemum in flower industry. Presence of immense number of axillary branches devalues the economic importance of this imperative plant and is a major challenge for mum growers to hold a stake in the cut flower market. Restricting branches to a minimum level, or no branches at all, is the dire need of the day in order to introducing novelty in cut chrysanthemums. Temperature is a potent factor which affects largely the escalation, development of chrysanthemum, and also the genetic expression of various vegetative traits like branching. It affects differently the developmental characteristics and phenotypic expressions of inherent qualities, thereby playing a significant role in differentiating the developmental responses in different cultivars of chrysanthemum. A detailed study pertaining to the affect of temperature on branching in chrysanthemum is a clear lacking throughout the literature on mums. Therefore, searching with temperature as an effective means of reducing side branching to a desired level could be an influencing extension of struggles about how to nullify stooling. This requires plenty of research in order to reveal the extended penetration of temperature in manipulating the genetic control of various important traits like branching, which is a burning issue now a days in producing cut flowers in chrysanthemum. The present review will highlight the impact of temperature on branching control mechanism in chrysanthemum at morpho-physiological, hormonal and molecular levels.

Keywords: branching, chrysanthemum, genetic control, hormonal, morpho-physiological, temperature

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Authors: S. S. Sree Sanker, K. N. Madhusoodanan

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Optical biosensors are dominant alternative for traditional analytical methods, because of their small size, simple design and high sensitivity. Photonic sensing method is one of the recent advancing technology for biosensors. It measures the change in refractive index which is induced by the difference in molecular interactions due to the change in concentration of the analyte. Glucose is an aldosic monosaccharide, which is a metabolic source in many of the organisms. The terahertz waves occupies the space between infrared and microwaves in the electromagnetic spectrum. Terahertz waves are expected to be applied to various types of sensors for detecting harmful substances in blood, cancer cells in skin and micro bacteria in vegetables. We have designed glucose sensors using silicon based 1D and 2D photonic crystal pillar arrays in terahertz frequency range. 1D photonic crystal has rectangular pillars with height 100 µm, length 1600 µm and width 50 µm. The array period of the crystal is 500 µm. 2D photonic crystal has 5×5 cylindrical pillar array with an array period of 75 µm. Height and diameter of the pillar array are 160 µm and 100 µm respectively. Two samples considered in the work are blood and glucose solution, which are labelled as sample 1 and sample 2 respectively. The proposed sensor detects the concentration of glucose in the samples from 0 to 100 mg/dL. For this, the crystal was irradiated with 0.3 to 3 THz waves. By analyzing the obtained S parameter, the refractive index of the crystal corresponding to the particular concentration of glucose was measured using the parameter retrieval method. Refractive indices of the two crystals decreased gradually with the increase in concentration of glucose in the sample. For 1D photonic crystals, a gradual decrease in refractive index was observed at 1 THz. 2D photonic crystal showed this behavior at 2 THz. The proposed sensor was simulated using CST Microwave studio. This will enable us to develop a model which can be used to characterize a glucose sensor. The present study is expected to contribute to blood glucose monitoring.

Keywords: CST microwave studio, glucose sensor, photonic crystal, terahertz waves

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Authors: Xin Li, Yan-Rong Guo, Jin-Fang Lin, Yi Feng, Håkan Billig, Ruijin Shao

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Background: Young women with polycystic ovary syndrome (PCOS) have a high risk of developing endometrial carcinoma. There is a need for the development of new medical therapies that can reduce the need for surgical intervention so as to preserve the fertility of these patients. The aim of the study was to describe and discuss cases of PCOS and insulin resistance (IR) women with early endometrial carcinoma while being co-treated with Diane-35 and metformin. Methods: Five PCOS-IR women who were scheduled for diagnosis and therapy for early endometrial carcinoma were recruited. The hospital records and endometrial pathology reports were reviewed. All patients were co-treated with Diane-35 and metformin for 6 months to reverse the endometrial carcinoma and preserve their fertility. Before, during, and after treatment, endometrial biopsies and blood samples were obtained and oral glucose tolerance tests were performed. Endometrial pathology was evaluated. Body weight (BW), body mass index (BMI), follicle-stimulating hormone (FSH), luteinizing hormone (LH), total testosterone (TT), sex hormone-binding globulin (SHBG), free androgen index (FAI), insulin area under curve (IAUC), and homeostasis model assessment of insulin resistance (HOMA-IR) were determined. Results: Clinical stage 1a, low grade endometrial carcinoma was confirmed before treatment. After 6 months of co-treatment, all patients showed normal epithelia. No evidence of atypical hyperplasia or endometrial carcinoma was found. Co-treatment resulted in significant decreases in BW, BMI, TT, FAI, IAUC, and HOMA-IR in parallel with a significant increase in SHBG. There were no differences in the FSH and LH levels after co-treatment. Conclusions: Combined treatment with Diane-35 and metformin has the potential to revert the endometrial carcinoma into normal endometrial cells in PCOS-IR women. The cellular and molecular mechanisms behind this effect merit further investigation.

Keywords: PCOS, progesterone resistance, insulin resistance, steroid hormone receptors, endometrial carcinoma

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Authors: Juan C. Reyes, Linnette Rodríguez, Héctor Villanueva, Jorge Vázquez, Ivonne Rivera

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On July 2020, a private non-profit community health center (HealthProMed) that serves people without a medical insurance plan or with limited resources in one of the most populated areas in San Juan, Puerto Rico, implemented a COVID-19 case investigation and contact-tracing surveillance system. Nursing personnel at the health center completed a computerized case investigation form that was translated, adapted, and modified from CDC’s Patient Under Investigation (PUI) Form. Between July 13, 2020, and March 17, 2022, a total of 9,233 SARS-CoV-2 tests were conducted at the health center, 16.9% of which were classified as confirmed cases (positive molecular test) and 27.7% as probable cases (positive serologic test). Most of the confirmed cases were females (60.0%), under 20 years old (29.1%), and living in their homes (59.1%). In the 14 days before the onset of symptoms, 26.3% of confirmed cases reported going to the supermarket, 22.4% had contact with a known COVID-19 case, and 20.7% went to work. The symptoms most commonly reported were sore throat (33.4%), runny nose (33.3%), cough (24.9%), and headache (23.2%). The most common preexisting medical conditions among confirmed cases were hypertension (19.3%), chronic lung disease including asthma, emphysema, COPD (13.3%), and diabetes mellitus (12.8). Multiple logistic regression analysis revealed that patients who used alcohol frequently during the last two weeks (OR=1.43; 95%CI: 1.15-1.77), those who were in contact with a positive case (OR=1.58; 95%CI: 1.33-1.88) and those who were obese (OR=1.82; 95%CI: 1.24-2.69) were significantly more likely to be a confirmed case after controlling for sociodemographic variables. Implementing a case investigation and contact-tracing component at community health centers can be of great value in the prevention and control of COVID-19 at the community level and could be used in future outbreaks.

Keywords: community health center, Puerto Rico, risk factors, SARS-CoV-2

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Authors: Sidra Shaw, Sarenna Shaw, Chae Joon Lee, Irimpan Mathews, Eric Koehn

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One of the biggest public health concerns of our time is increasing antimicrobial resistance. As of 2019, the CDC has documented more than 2.8 million serious antibiotic resistant infections in the United States. Currently, antibiotic resistant infections are directly implicated in over 750,000 deaths per year globally. On our current trajectory, British economist Jim O’Neill predicts that by 2050, an additional 10 million people (about half the population of New York) will die annually due to drug resistant infections. As a result, new biochemical pathways must be targeted to generate next generation antibiotic drugs that will be effective against drug resistant bacteria. One enticing target is the biosynthesis of DNA within bacteria, as few drugs interrupt this essential life process. Thymidylate synthase enzymes are essential for life as they catalyze the synthesis of a DNA building block, 2′-deoxythymidine-5′-monophosphate (dTMP). In humans, the thymidylate synthase enzyme (TSase) has been shown to be distinct from the flavin-dependent thymidylate synthase (FDTS) produced by many pathogenic bacteria. TSase and FDTS have distinct structures and mechanisms of catalysis, which should allow selective inhibition of FDTS over human TSase. Currently, C. diff is one of the most antibiotic resistant bacteria, and no drugs that target thymine biosynthesis exist for C. diff. Here we present the initial biochemical characterization of FDTS from C. diff. Specifically, we examine enzyme kinetics and binding features of this enzyme to determine the nature of interaction with ligands/inhibitors and understand the molecular mechanism of catalysis. This research will provide more insight into the targetability of the C. diff FDTS enzyme for novel antibiotic drugs.

Keywords: flavin-dependent thymidylate synthase, FDTS, clostridioides difficile, C. diff, antibiotic resistance, DNA synthesis, enzyme kinetics, binding features

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Authors: Bindu I. Somarajan, Viney Gupta, Gagandeep Kaur Walia, Jasbir Kaur, Sunil Kumar, Shikha Gupta, Abadh K. Chaurasia, Dinesh Gupa, Abhinav Kaushik, Aditi Mehta, Vipin Gupta, Arundhati Sharma

Abstract:

Background: Juvenile onset primary open angle glaucoma (JOAG), affects individuals under the age of 40 years. Studies on a few families of JOAG, that led to the discovery of the Myocilin gene, reported the disease to have an autosomal dominant pattern of inheritance. However, sporadic forms of JOAG been seen to be more common in some populations. Most pathological homozygous mutations in the CYP1B1 gene associated with JOAG have been seen among sporadic cases. Given the higher prevalence of sporadic JOAG cases in our population, we aimed to look for common mutations E229K and R368H, the two most common variants in the CYP1B1 gene associated with glaucoma. Objective: To determine the frequency and evaluate genotype phenotype correlation of CYP1B1 E229K and R368H mutations in a cohort of 120 sporadic Juvenile open angle glaucoma patients.Methods: Unrelated JOAG patients whose first degree relatives had been examined and found to be unaffected were included in the study. The patients and their parents were screened for E229K and R368H mutations. The phenotypic characteristics were compared between probands with and with out these mutations by SPSS v16. Results: Out of 120 JOAG patients included in the study, the E229K mutation was seen in 9 probands (7.5%) and R368H in 7 (5.8%). The average age of onset of the disease (p=0.3) and the highest untreated IOP (p=0.4) among those carrying mutations was not significantly different from those who did not have these mutations. The proportion of probands with angle dysgenesis among those with E229K and R368H mutations was 70% (11 out of 16) in comparison to 65% (67 out of 104) of those who did not harbour these mutations (p=0.56). Similarly the probands with moderate to high myopia among those with E229K and R368H mutations was 20% (3 out of 16) in comparison to 18% (18 out of 104) of those who did not harbour these mutations(p=0.59). Conclusion: The frequency of E229K and R368H mutations of the CYP1B1 gene is low even among sporadic JOAG patients. Moreover there is no clinical correlation between the presence of these mutations and disease severity

Keywords: CYP1B1, gene, IOP, JOAG, mutation

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Authors: Murali Aarthy, Sanjeev Kumar Singh

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High risk human papillomaviruses are highly associated with the carcinoma of the cervix and the other genital tumors. Cervical cancer develops through the multistep process in which increasingly severe premalignant dysplastic lesions called cervical intraepithelial neoplastic progress to invasive cancer. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers drives the cells into S-phase creating an environment conducive for viral genome replication and cell proliferation. The replication of the virus occurs in the terminally differentiating epithelium and requires the activation of cellular DNA replication proteins. To date, no suitable drug molecule is available to treat HPV infection whereas identification of potential drug targets and development of novel anti-HPV chemotherapies with unique mode of actions are expected. Hence, our present study aimed to identify the potential inhibitors analogous to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems. A 3D similarity search on the natural small molecule library from natural product database using EGCG identified 11 potential hits based on their similarity score. The structure based docking strategies were implemented in the potential hits and the key interacting residues of protein with compounds were identified through simulation studies and binding free energy calculations. The conformational changes between the apoprotein and the complex were analyzed with the simulation and the results demonstrated that the dynamical and structural effects observed in the protein were induced by the compounds and indicated the dominance to the oncoprotein. Overall, our study provides the basis for the structural insights of the identified potential hits and EGCG and hence, the analogous compounds identified can be potent inhibitors against the HPV 16 E7 oncoprotein.

Keywords: EGCG, oncoprotein, molecular dynamics simulation, analogues

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Authors: Memoona Ramzan, Bushra Tabassum, Anwar Khan, Muhammad Tariq, Mudassar Fareed Awan, Idrees Ahmad Nasir, Zahida Qamar, Naila Shahid, Tayyab Husnain

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Biological control is a novel approach being used in crop protection nowadays. Bacteria like Bacillus and Pseudomonas are reported for this purpose and few of their products are commercially available too. Rhizosphere and phyllosphere of healthy cotton plants were used as a source to isolate bacteria capable of exhibiting properties worthy for selection as biocontrol agent. For this purpose all isolated strains were screened for the activities like phosphate solubilization, Indole acetic acid (IAA) production and biocontrol against fungi. Two strains S1HL3 and S1HL4 showed phosphate solubilization and IAA production simultaneously while two other JS2HR4 and JS3HR2 were good inhibitors of fungal pathogens. Through biochemical and molecular characterization these bacteria were identified as P. aeruginosa, Burkholderia and Bacillus respectively. In green house trials of these isolates against Cotton leaf curl virus (CLCuV), seven treatments including individual bacterial isolate and consortia were included. Treated plants were healthy as compared to control plants in which upto 74% CLCuV symptomatic plants exist. Maximum inhibition of CLCuV was observed in T7 treated plants where viral load was only 0.4% as compared to control where viral load was upto 74%. This treatment consortium included Bacillus and Pseudomonas isolates; S1HL3, S1HL4, JS2HR4 and JS3HR2. Principal Component Biplot depicted highly significant correlation between percentage viral load and the disease incidence.

Keywords: cotton leaf curl virus, biological control, bacillus, pseudomonas

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Authors: Anika Chebrolu

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Mono-targeted drugs can be of limited efficacy against complex diseases. Recently, multi-target drug design has been approached as a promising tool to fight against these challenging diseases. However, the scope of current computational approaches for multi-target drug design is limited. DeepLig presents a de-novo drug discovery platform that uses reinforcement learning to generate and optimize novel, potent, and multitargeted drug candidates against protein targets. DeepLig’s model consists of two networks in interplay: a generative network and a predictive network. The generative network, a Stack- Augmented Recurrent Neural Network, utilizes a stack memory unit to remember and recognize molecular patterns when generating novel ligands from scratch. The generative network passes each newly created ligand to the predictive network, which then uses multiple Graph Attention Networks simultaneously to forecast the average binding affinity of the generated ligand towards multiple target proteins. With each iteration, given feedback from the predictive network, the generative network learns to optimize itself to create molecules with a higher average binding affinity towards multiple proteins. DeepLig was evaluated based on its ability to generate multi-target ligands against two distinct proteins, multi-target ligands against three distinct proteins, and multi-target ligands against two distinct binding pockets on the same protein. With each test case, DeepLig was able to create a library of valid, synthetically accessible, and novel molecules with optimal and equipotent binding energies. We propose that DeepLig provides an effective approach to design multi-targeted drug therapies that can potentially show higher success rates during in-vitro trials.

Keywords: drug design, multitargeticity, de-novo, reinforcement learning

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Authors: Mohammadjavad Mehrabanpour, Maryam Ranjbar Bushehri, Dorsa Mehrabanpour

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Respiratory diseases are the most important problems in the country’s poultry industry, particularly when it comes to broiler flocks. Ornithobacterium rhinotracheale (ORT) is a species that causes poor performance in growth rate, egg production, and mortality. This pathogen causes a respiratory infection including pulmonary alveolar inflammation, and pneumonia of birds throughout the world. Newcastle disease (ND) is a highly contagious disease in poultry, and also, it causes considerable losses to the poultry industry. The aim of this study was to evaluate the simultaneous occurrence of ORT and ND and NDV isolation by inoculation in embryonated eggs and confirmed by RT-PCR in broiler chicken flocks in Fars province. In this study, 318 blood and 85 tissue samples (brain, trachea, liver, and cecal tonsils) were collected from 15 broiler chicken farms. Survey serum antibody titers against ORT by using a commercial enzyme-linked immunosorbent assay (ELISA) kit performed. Evaluation of antibody titer against ND virus is performed by hemagglutination inhibition test. Virus isolation with chick embryo eggs 9-11 and RT-PCR method were carried out. A total of 318 serum samples, 135 samples (42.5%) were positive for antibodies to ORT and titer of HI antibodies against NDV in 122 serum samples (38/4%) were 7-10 (log2) and 61 serum samples (19/2%) had occurrence antibody titer against Newcastle virus and ORT. Results of the present study indicated that 20 tissue samples were positive in embryonated egg and in rapid hemagglutination (HA) test. HI test with specific ND positive serum confirmed that 6 of 20 samples. PCR confirmed that all six samples were positive and PCR products of samples indicated 535-base pair fragments in electrophrosis. Due to the great economic importance of these two diseases in the poultry industry, it is necessary to design and implement a comprehensive plan for prevention and control of these diseases.

Keywords: ELISA, Ornithobacterium rhinotracheale, newcastle disease, seroprevalence

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Authors: M. Umar Dahot, G. S. Mangrio

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In this study Agro-industrial waste was used as a carbon source, which is a low cost substrate. Along with this, various sugars and molasses of 2.5% and 5% were investigated as substrate/carbon source for the growth of A.niger and Pectinase production. Different nitrogen sources were also used. An overview of results obtained show that 5% sucrose, 5% molasses and 0.4% (NH4)2SO4 were found the best carbon and nitrogen sources for the production of pectinase by A. niger. The maximum production of pectinase (26.87units/ml) was observed at pH 6.0 after 72 hrs incubation. The optimum temperature for the maximum production of pectinase was achieved at 35ºC when maximum production of pectinase was obtained as 28.25Units/ml.Pectinase enzyme was purified with ammonium sulphate precipitation and dialyzed sample was finally applied on gel filtration chromatography (Sephadex G-100) and Ion Exchange DEAE A-50. The enzyme was purified 2.5 fold by gel chromatography on Sephadex G-100 and Four fractions were obtained, Fraction 1, 2, 4 showed single band while Fraction -3 showed multiple bands on SDS Page electrophoresis. Fraction -3 was pooled, dialyzed and separated on Sephdex A-50 and two fractions 3a and 3b showed single band. The molecular weights of the purified fractions were detected in the range of 33000 ± 2000 and 38000± 2000 Daltons. The purified enzyme was specifically most active with pure pectin, while pectin, Lemon pectin and orange peel given lower activity as compared to (control). The optimum pH and temperature for pectinase activity was found between pH 5.0 and 6.0 and 40°- 50°C, respectively. The enzyme was stable over the pH range 3.0-8.0. The thermostability of was determined and it was observed that the pectinase activity is heat stable and retains activity more than 40% when incubated at 90°C for 10 minutes. The pectinase activity of F3a and F3b was increased with different metal ions. The Pectinase activity was stimulated in the presence of CaCl2 up to 10-30%. ZnSO4, MnSO4 and Mg SO4 showed higher activity in fractions F3a and F3b, which indicates that the pectinase belongs to metalo-enzymes. It is concluded that A. niger is capable to produce pH stable and thermostable pectinase, which can be used for industrial purposes.

Keywords: pectinase, a. niger, production, purification, characterization

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