Search results for: gene modification

Authors: Reza M. Rudd, Ali Saeedi, Colin Wood

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In this article, the latest advancements made in the applications of polymers in the enhanced hydrocarbon recovery technologies are investigated. For this purpose, different classes of polymers are reviewed and the latest progresses made in making them suitable for application under harsh reservoir conditions are discussed. The main reservoir conditions whose effects are taken into account include the temperature, rock mineralogy and brine salinity and composition. For profile modification and blocking the thief zones, polymers are used in the form of nanocomposite hydrogels. Polymers are also used as thickeners during CO2 flooding. Also, they are used in enhanced gas recovery, to inhibit the mixing of injection gas with the in-situ natural gas. This review covers the main types of polymers, their functions and the challenges in their applications, some of which are mentioned above. Included in this review are also the latest progresses made in the development of new polymeric surfactants used for surfactant flooding.

Keywords: EOR, EGR, polymer flooding, profile modification, mobility control, nanocomposite hydrogels, CO2 flooding, polymeric surfactants

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Authors: N. Slepickova Kasalkova, P. Slepicka, L. Bacakova, V. Svorcik

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Tissue engineering includes combination of materials and techniques used for the improvement, repair or replacement of the tissue. Scaffolds, permanent or temporally material, are used as support for the creation of the "new cell structures". For this important component (scaffold), a variety of materials can be used. The advantage of some polymeric materials is their cytocompatibility and possibility of biodegradation. Poly(L-lactic acid) (PLLA) is a biodegradable,  semi-crystalline thermoplastic polymer. PLLA can be fully degraded into H₂O and CO₂. In this experiment, the effect of the surface modification of biodegradable polymer (performed by plasma treatment) on the various cell types was studied. The surface parameters and changes of the physicochemical properties of modified PLLA substrates were studied by different methods. Surface wettability was determined by goniometry, surface morphology and roughness study were performed with atomic force microscopy and chemical composition was determined using photoelectron spectroscopy. The physicochemical properties were studied in relation to cytocompatibility of human osteoblast (MG 63 cells), rat vascular smooth muscle cells (VSMC), and human stem cells (ASC) of the adipose tissue in vitro. A fluorescence microscopy was chosen to study and compare cell-material interaction. Important parameters of the cytocompatibility like adhesion, proliferation, viability, shape, spreading of the cells were evaluated. It was found that the modification leads to the change of the surface wettability depending on the time of modification. Short time of exposition (10-120 s) can reduce the wettability of the aged samples, exposition longer than 150 s causes to increase of contact angle of the aged PLLA. The surface morphology is significantly influenced by duration of modification, too. The plasma treatment involves the formation of the crystallites, whose number increases with increasing time of modification. On the basis of physicochemical properties evaluation, the cells were cultivated on the selected samples. Cell-material interactions are strongly affected by material chemical structure and surface morphology. It was proved that the plasma treatment of PLLA has a positive effect on the adhesion, spreading, homogeneity of distribution and viability of all cultivated cells. This effect was even more apparent for the VSMCs and ASCs which homogeneously covered almost the whole surface of the substrate after 7 days of cultivation. The viability of these cells was high (more than 98% for VSMCs, 89-96% for ASCs). This experiment is one part of the basic research, which aims to easily create scaffolds for tissue engineering with subsequent use of stem cells and their subsequent "reorientation" towards the bone cells or smooth muscle cells.

Keywords: poly(L-lactic acid), plasma treatment, surface characterization, cytocompatibility, human osteoblast, rat vascular smooth muscle cells, human stem cells

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Authors: Habib Shaban

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Nanocomposites of isotactic polypropylene (iPP) and date wood fiber were prepared after modification of the host matrix by reactive extrusion grafting of maleic anhydride. Chemical and mechanical treatment of date wood flour (WF) was conducted to obtain nanocrystalline cellulose. Layered silicates (clay) were partially intercalated with date wood fiber, and the modified layered silicate was used as filler in the PP matrix via a melt-blending process. The tensile strength of composites prepared from wood fiber modified clay was greater than that of the iPP-clay and iPP-WF composites at a 6% filler concentration, whereas deterioration of mechanical properties was observed when clay and WF were used alone for reinforcement. The dispersion of the filler in the matrix significantly decreased after clay modification with cellulose at higher concentrations, as shown by X-ray diffraction (XRD) data.

Keywords: nanocomposites, isotactic polypropylene, date wood flour, intercalated, melt-blending

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Authors: Hyuk Sang Yoo, Young Ju Son, Wei Mao, Myung Gu Kang, Sol Lee

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Biomedical applications of electrospun nanofibrous meshes have been received tremendous attentions because of their unique structures and versatilities as biomaterials. Incorporation of growth factors in fibrous meshes can be performed by surface-modification and encapsulation. Those growth factors stimulate differentiation and proliferation of specific types of cells and thus lead tissue regenerations of specific cell types. Topographical cues of electrospun nanofibrous meshes also increase differentiation of specific cell types according to alignments of fibrous structures. Wound healing treatments of diabetic ulcers were performed using nanofibrous meshes encapsulating multiple growth factors. Aligned nanofibrous meshes and those with random configuration were compared for differentiating mesenchymal stem cells into neuronal cells. Thus, nanofibrous meshes can be applied to drug delivery carriers and matrix for promoting cellular proliferation.

Keywords: nanofiber, tissue, mesh, drug

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Authors: Mustafa M. Donma, Ayşen Haksayar, Bahadır Batar, Buse Tepe, Birol Topçu, Orkide Donma

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Childhood obesity is an ever-increasing health problem. The Association of obesity with severe chronic diseases such as diabetes and cardiovascular diseases makes the problem life-threatening. Aside from psychological, societal and metabolic factors, genetic polymorphisms have gained importance concerning etiology in recent years. The aim of this study was to evaluate the relationship between rs10455872 gene polymorphism in the Lipoprotein (a) locus and the development of childhood obesity. This was a prospective study carried out according to the Helsinki Declarations. The study protocol was approved by the Institutional Ethics Committee. This study was supported by Tekirdag Namik Kemal University Rectorate, Scientific Research Projects Coordination Unit. Project No: NKUBAP.02.TU.20.278. A total of 180 children (103 obese (OB) and 77 healthy), aged 6-18 years, without any acute or chronic disease, participated in the study. Two different groups were created: OB and healthy control. Each group was divided into two further groups depending on the nature of the polymorphism. Anthropometric measurements were taken during the detailed physical examination. Laboratory tests and TANITA measurements were performed. For the statistical evaluations, SPSS version 28.0 was used. A P-value smaller than 0.05 was the statistical significance degree. The distribution of lipoprotein (a) rs10455872 gene polymorphism did not differ between OB and healthy children. Children with AG genotype in both OB and control groups had lower body mass index (BMI), diagnostic obesity notation model assessment index (DONMA II), body fat ratio (BFR), C-reactive protein (CRP), and metabolic syndrome index (MetS index) values compared to children with normal AA genotype. In the OB group, serum iron, vitamin B12, hemoglobin, MCV, and MCH values were found to be higher in the AG genotype group than those of children with the normal AA genotype. A significant correlation was found between the MetS index and BFR among OB children with normal homozygous genotype. MetS index increased as BFR increased in this group. However, such a correlation was not observed in the OB group with heterozygous AG genotype. To the best of our knowledge, the association of lipoprotein (a) rs10455872 gene polymorphism with the etiology of childhood obesity has not been studied yet. Therefore, this study was the first report suggesting polymorphism with AG genotype as a good risk factor for obesity.

Keywords: child, gene polymorphism, lipoprotein (a), obesity, rs10455872

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Authors: M. Kowalski, M. Brodowski, K. Dziabowska, E. Czaczyk, W. Bialobrzeska, N. Malinowska, S. Zoledowska, R. Bogdanowicz, D. Nidzworski

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Boron-doped-carbon nanowall (BCNW) electrodes are recently in much interest among scientists. BCNWs are good candidates for biosensor purposes as they possess interesting electrochemical characteristics like a wide potential range and the low difference between redox peaks. Moreover, from technical parameters, they are mechanically resistant and very tough. The production process of the microwave plasma-enhanced chemical vapor deposition (MPECVD) allows boron to build into the structure of the diamond being formed. The effect is the formation of flat, long structures with sharp ends. The potential of these electrodes was checked in the biosensing field. The procedure of simple carbon electrodes modification by antibodies was adopted to BCNW for specific antigen recognition. Surface protein D deriving from H. influenzae pathogenic bacteria was chosen as a target analyte. The electrode was first modified with the aminobenzoic acid diazonium salt by electrografting (electrochemical reduction), next anti-protein D antibodies were linked via 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) chemistry, and free sites were blocked by BSA. Cyclic voltammetry measurements confirmed the proper electrode modification. Electrochemical impedance spectroscopy records indicated protein detection. The sensor was proven to detect protein D in femtograms. This work was supported by the National Centre for Research and Development (NCBR) TECHMATSTRATEG 1/347324/12/NCBR/ 2017.

Keywords: anti-protein D antibodies, boron-doped carbon nanowall, impedance spectroscopy, Haemophilus influenzae.

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Authors: Xiaolian Jiang, Dongling Liu, Kun Liu

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Aims: To examine the prevalence of POST-TRAUMATIC STRESS DISORDER (PTSD) symptoms among Tibetan adolescents in heavily-hit disaster area three years after Yushu earthquake, and to explore the interactions of the psycho-social-genetic risk factors. Methods: This was a three-stage study. Firstly, demographic variables，PTSD Checklist-Civilian Version （PCL-C），the Internality、Powerful other、Chance Scale，（IPC），Coping Style Scale（CSS），and the Social Support Appraisal（SSA）were used to explore the psychosocial factors of PTSD symptoms among adolescent survivors. PCL-C was used to examine the PTSD symptoms among 4072 Tibetan adolescents，and the Structured Clinical Interview for DSM-IV Disorders（SCID）was used by psychiatrists to make the diagnosis precisely. Secondly，a case-control trial was used to explore the relationship between PTSD and gene polymorphisms. 287adolescents diagnosed with PTSD were recruited in study group, and 280 adolescents without PTSD in control group. Polymerase chain reaction-restriction fragment length polymorphism technology（PCR-RFLP）was used to test gene polymorphisms. Thirdly，SPSS 22.0 was used to explore the interactions of the psycho-social-genetic risk factors of PTSD on the basis of the above results. Results and conclusions: 1．The prevalence of PTSD was 9.70%. 2．The predictive psychosocial factors of PTSD included earthquake exposure, support from others, imagine, abreact, tolerant, powerful others and family support. 3．Synergistic interactions between A1 gene of DRD2 TaqIA and the external locus of control, negative coping style, severe earthquake exposure were found. Antagonism interactions between A1 gene of DRD2 TaqIA and poor social support was found. Synergistic interactions between A1/A1 genotype and the external locus of control, negative coping style were found. Synergistic interactions between 12 gene of 5-HTTVNTR and the external locus of control, negative coping style, severe earthquake exposure were found. Synergistic interactions between 12/12 genotype and the external locus of control, negative coping style, severe earthquake exposure were also found.

Keywords: adolescents, earthquake, PTSD, risk factors

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Authors: Manasa Perikala, Asha Bhardwaj

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Fluorescent carbon dots (CDs), a young member of Carbon nanomaterial family, has gained a lot of research attention across the globe due to its highly luminescent emission properties, non-toxic behavior, stable emission properties, and zero re-absorption lose. These dots have the potential to replace the use of traditional semiconductor quantum dots in light-emitting devices (LED’s, fiber lasers) and other photonic devices (temperature sensor, UV detector). However, One major drawback of Carbon dots is that, till date, the actual mechanism of photoluminescence (PL) in carbon dots is still an open topic of discussion among various researchers across the globe. PL mechanism of CDs based on wide particle size distribution, the effect of surface groups, hybridization in carbon, and charge transfer mechanisms have been proposed. Although these mechanisms explain PL of CDs to an extent, no universally accepted mechanism to explain complete PL behavior of these dots is put forth. In our work, we report parameters affecting the size and surface of CDs, such as time of the reaction, synthesis temperature and concentration of precursors and their effects on the optical properties of the carbon dots. The effect of auxochromes on the emission properties and re-modification of carbon surface using an external surface functionalizing agent is discussed in detail. All the explanations have been supported by UV-Visible absorption, emission spectroscopies, Fourier transform infrared spectroscopy and Transmission electron microscopy and X-Ray diffraction techniques. Once the origin of PL in CDs is understood, parameters affecting PL centers can be modified to tailor the optical properties of these dots, which can enhance their applications in the fabrication of LED’s and other photonic devices out of these carbon dots.

Keywords: carbon dots, photoluminescence, size effects on emission in CDs, surface modification of carbon dots

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Authors: M. Yusuf

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

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

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Authors: Mai M. Khalaf, Hany M. Abd El-Lateef

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A new good application for the sol gel method is to improve the corrosion inhibition properties of carbon steel by the dip coating method of Nano TiO2 films and its modification with Poly Ethylene Glycol (PEG). The prepared coating samples were investigated by different techniques, X-ray diffraction, Scanning Electron Microscopy (SEM), transmission electron microscopy and Energy Dispersive X-ray Spectroscopy (EDAX). The corrosion inhibition performance of the blank carbon steel and prepared coatings samples were evaluated in 0.5 M H2SO4 by using Electrochemical Impedance Spectroscopy (EIS) and potentiodynamic polarization measurements. The results showed that corrosion resistance of carbon steel increases with increasing the number of coated layers of both nano–TiO2 films and its modification of PEG. SEM-EDAX analyses confirmed that the percentage atomic content of iron for the carbon steel in 0.5 M H2SO4 is 83% and after the deposition of the steel in nano TiO2 sol and that with PEG are 94.3% and 93.7% respectively.

Keywords: dip-coatings, corrosion protection, sol gel, TiO2 films, PEG

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Authors: Jie Lin, Yiwen Pan, Li Zhang, Zhangyong Xia

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Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipids, immune cells, and extracellular matrix in the arterial walls. This pathological process can lead to the formation of plaques that can obstruct blood flow and trigger various cardiovascular diseases such as heart attack and stroke. The underlying molecular mechanisms still remain unclear, although many studies revealed the dysfunction of endothelial cells, recruitment and activation of monocytes and macrophages, and the production of pro-inflammatory cytokines and chemokines in atherosclerosis. This study aimed to identify hub genes involved in the progression of atherosclerosis and to analyze their biological function in silico, thereby enhancing our understanding of the disease’s molecular mechanisms. Through the analysis of microarray data, we examined the gene expression in media and neo-intima from plaques, as well as distant macroscopically intact tissue, across a cohort of 32 hypertensive patients. Initially, 112 differentially expressed genes (DEGs) were identified. Subsequent immune infiltration analysis indicated a predominant presence of 27 immune cell types in the atherosclerosis group, particularly noting an increase in monocytes and macrophages. In the Weighted gene co-expression network analysis (WGCNA), 10 modules with a minimum of 30 genes were defined as key modules, with blue, dark, Oliver green and sky-blue modules being the most significant. These modules corresponded respectively to monocyte, activated B cell, and activated CD4 T cell gene patterns, revealing a strong morphological-genetic correlation. From these three gene patterns (modules morphology), a total of 2509 key genes (Gene Significance >0.2, module membership>0.8) were extracted. Six hub genes (CD36, DPP4, HMOX1, PLA2G7, PLN2, and ACADL) were then identified by intersecting 2509 key genes, 102 DEGs with lipid-related genes from the Genecard database. The bio-functional analysis of six hub genes was estimated by a robust classifier with an area under the curve (AUC) of 0.873 in the ROC plot, indicating excellent efficacy in differentiating between the disease and control group. Moreover, PCA visualization demonstrated clear separation between the groups based on these six hub genes, suggesting their potential utility as classification features in predictive models. Protein-protein interaction (PPI) analysis highlighted DPP4 as the most interconnected gene. Within the constructed key gene-drug network, 462 drugs were predicted, with ursodeoxycholic acid (UDCA) being identified as a potential therapeutic agent for modulating DPP4 expression. In summary, our study identified critical hub genes implicated in the progression of atherosclerosis through comprehensive bioinformatic analyses. These findings not only advance our understanding of the disease but also pave the way for applying similar analytical frameworks and predictive models to other diseases, thereby broadening the potential for clinical applications and therapeutic discoveries.

Keywords: atherosclerosis, hub genes, drug prediction, bioinformatics

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Authors: Ilya B. Tsyrlov, Dmitry Y. Oshchepkov

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A computational search for dioxin response elements (DREs) in genes of proteins comprising the Ah receptor (AhR) cytosolic core complex was performed by highly efficient tool SITECON. Eventually, the following number of new DREs in 5’flanking region was detected by SITECON: one in AHR gene, five in XAP2, eight in HSP90AA1, and three in HSP90AB1 genes. Numerous DREs found in genes of AhR and AhR cytosolic complex members would shed a light on potential mechanisms of expression, the stoichiometry of unliganded AhR core complex, and its degradation vs biosynthesis dynamics resulted from treatment of target cells with the AhR most potent ligand, 2,3,7,8-TCDD. With human viruses, reduced susceptibility to TCDD of geneencoding HIV-1 P247 was justified by the only potential DRE determined in gag gene encoding HIV-1 P24 protein, whereas the regulatory region of CMV genes encoding IE gp/UL37 has five potent DRE, 1.65 kb/UL36 – six DRE, pp65 and pp71 – each has seven DRE, and pp150 – ten DRE. Also, from six to eight DRE were determined with SITECON in the regulatory region of HSV-1 IE genes encoding tegument proteins, UL36 and UL37, and of UL19 gene encoding bindingglycoprotein C (gC). So, TCDD in the low picomolar range may activate in human cells AhR: Arnt transcription pathway that triggers CMV and HSV-1 reactivation by binding to numerous promoter DRE within immediate-early (IE) genes UL37 and UL36, thus committing virus to the lytic cycle.

Keywords: dioxin response elements, Ah receptor, AhR: Arnt transcription pathway, human and viral genes

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Authors: Dibyendu Adak, Saroj Mandal

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The fly ash based geopolymer concrete generally requires heat activation after casting, which has been considered as an important limitation for its practical application. Such limitation can be overcome by a modification in the process at the time of mixing of ingredients (fly and activator fluid) for geopolymer concrete so that curing can be made at ambient temperature. This process modified geopolymer concrete shows an appreciable improvement in structural performance compared to conventional heat cured geopolymer concrete and control cement concrete. The improved durability performance based on water absorption, sulphate test, and RCPT is also noted. The microstructural properties analyzed through Field Emission Scanning Electron Microscope (FESEM) with Energy Dispersive X-ray Spectroscopy (EDS) and X-ray Diffraction (XRD) techniques show the better interaction of fly ash and activator solution at early ages for the process modified geopolymer concrete. This accelerates the transformation of the amorphous phase of fly ash to the crystalline phase.

Keywords: fly ash, geopolymer concrete, process modification, structural properties, durability, micro-structures

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Authors: Neelma Ashraf

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Actinomycetes, particularly genus Streptomyces is of great importance due to their role in the discovery of new natural products, particularly antimicrobial secondary metabolites in the medicinal science and biotechnology industry. Different Streptomyces strains were isolated from Helianthus annuus plants and tested for antibacterial and antifungal activities. The most promising five strains were chosen for further investigation, and growth conditions for antibiotic synthesis were optimised. The supernatants were extracted in different solvents, and the extracted products were analyzed using liquid chromatography-mass spectrometry (LC-MS) and biological testing. From one of the potent strains Streptomyces globusus sp. BR123, a compound lavendamycin was identified using these analytical techniques. In addition, this potent strain also produces a strong antifungal polyene compound with a quasimolecular ion of 2072. Streptomyces sp. BR123 was genome sequenced because of its promising antimicrobial potential in order to identify the gene cluster responsible for analyzed compound “lavendamycin”. The genome analysis yielded candidate genes responsible for the production of this potent compound. The genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 with a GC content of 72.63% and 8103 protein coding genes was attained. Many antimicrobial, antiparasitic, and anticancerous compounds were detected through multiple biosynthetic gene clusters predicted by in-Silico analysis. Though, the novelty of metabolites was determined through the insignificant resemblance with known biosynthetic gene clusters. The current study gives insight into the bioactive potential of Streptomyces sp. isolate BR123 with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study revealed the connection of isolate BR123 with other Streptomyces strains, which could expand the knowledge of this genus and the mechanism involved in the discovery of new antimicrobial metabolites.

Keywords: streptomyces, secondary metabolites, genome, biosynthetic gene clusters, high performance liquid chromatography, mass spectrometry

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Authors: Piotr Kunecki, Magdalena Wdowin

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The fly ash produced as waste in the process of conventional coal combustion was utilized in the hybrid synthesis of zeolites X and A from Faujasite (FAU) and Linde Type A (LTA) frameworks, respectively. The applied synthesis method included modification together with the crystallization stage. The sorbent modification was performed by introducing metals into the zeolite structure in order to create an ability to form stable bonds with elemental mercury (Hg0). The use of waste in the form of fly ash as a source of silicon and aluminum, as well as the proposed method of zeolite synthesis, fits the circular economy idea. The effect of zeolite modification on Hg0 removal from a simulated gas stream was studied empirically using prototype installation designed to test the effectiveness of sorption by solid-state sorbents. Both derived zeolites X and A modified with silver nitrate revealed significant mercury uptake during a 150-minute sorption experiment. The amount of elemental mercury removed in the experiment ranged from 5.69 to 6.01 µg Hg0/1g of sorbent for zeolites X and from 4.47 to 4.86 µg Hg0/1g of sorbent for zeolites A. In order to confirm the effectiveness of the sorbents towards mercury bonding, the possible re-emission effect was tested as well. Derived zeolites X and A did not show mercury re-emission after the sorption process, which confirms the stable bonding of Hg0 in the structure of synthesized zeolites. The proposed hybrid synthesis method possesses the potential to be implemented for both fly ash utilization as well as the time and energy-saving production of aluminosilicate, porous materials with high Hg0 removal efficiency. This research was supported by National Science Centre, Poland, grant no 2021/41/N/ST5/03214.

Keywords: fly ash, synthetic zeolites, elemental mercury removal, sorption, simulated gas stream

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Authors: Berredjem Hajira, Benlaifa Meriem, Becheker Imene, Bardi Rafika, Djebar Med Reda

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Recent acquired or reactivation T.gondii infection is a serious complication in HIV patients. Classical serological diagnosis relies on the detection of anti-Toxoplasma immunoglobulin ; however, serology may be unreliable in HIV immunodeficient patients who fail to produce significant titers of specific antibodies. PCR assays allow a rapid diagnosis of Toxoplasma infection. In this study, we compared the value of the PCR for diagnosing active toxoplasmosis in cerebrospinal fluid and blood samples from HIV patients. Anti-Toxoplasma antibodies IgG and IgM titers were determined by ELISA. In parallel, nested PCR targeting B1 gene and conventional PCR-ELISA targeting P30 gene were used to detect T. gondii DNA in 25 blood samples and 12 cerebrospinal fluid samples from patients in whom toxoplasmic encephalitis was confirmed by clinical investigations. A total of 15 negative controls were used. Serology did not contribute to confirm toxoplasmic infection, as IgG and IgM titers decreased early. Only 8 out 25 blood samples and 5 out 12 cerebrospinal fluid samples PCRs yielded a positive result. 5 patients with confirmed toxoplasmosis had positive PCR results in either blood or cerebrospinal fluid samples. However, conventional nested B1 PCR gave best results than the P30 gene one for the detection of T.gondii DNA in both samples. All samples from control patients were negative. This study demonstrates the unusefulness of the serological tests and the high sensitivity and specificity of PCR in the diagnosis of toxoplasmic encephalitis in HIV patients.

Keywords: cerebrospinal fluid, HIV, Toxoplasmosis, PCR

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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Authors: Amtul Jamil Sami

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Apis mellifera is an insect of immense economic importance lives on rich carbohydrate diet including cellulose, nectar, honey and pollen. The carbohydrate metabolism in A mellifera has not been understood fully, as there are no data available, on the functional expression of cellulase gene. The cellulose hydrolyzing enzyme is required for the digestion of pollen cellulose wall, to release the important nutrients (amino acids, minerals, vitamins etc.) from the pollen. A dissection of Apis genome had revealed that there is one gene present for the expression of endo-beta-1,4-glucanase, for cellulose hydrolysis. In the presented work, functional expression of endo-beta-1,4 glucanase gene is reported. Total soluble proteins of the honey bee were isolated and were tested cellulose hydrolyzing enzyme activity, using carboxy-methyl cellulose, as a substrate. A mellifera proteins were able to hydrolyze carboxy-methyl cellulose, confirming its endo- type mode of action. Endo beta-1,4 glucanase enzyme was only present in the gut tissues, no activity was detected in the salivary glands. The pH optima of the enzyme were in the acidic pH range of 4-5-5-0, indicating its metabolic role in the acidic stomach of A mellifera. The reported enzyme is unique, as endo-beta- 1,4 glucanase was able to generate non reducing sugar, as an end product. The results presented, are supportive to the information that the honey bee is capable of producing its novel endo-beta-1,4 glucanase. Further it could be helpful, in understanding, the carbohydrate metabolism in A mellifera.

Keywords: honey bees, Endo-beta 1, 4- glucanase, Apis mellifera, functional expression

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Authors: Rozeena Baig, R. Rehana Rehman, Rifat Ahmed

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Background: Osteoporosis, characterized by low bone mineral density, poses a global health concern. Diagnosis increases the likelihood of developing osteoporosis, a multifactorial disorder marked by low bone mass, elevating the risk of fractures in the lumbar spine, femoral neck, hip, vertebras, and distal forearm, particularly in postmenopausal women due to bone loss influenced by various pathophysiological factors. Objectives: The aim is to investigate the association of serum cytokine, bone turnover marker, bone mineral density and TLR4 gene polymorphism in pre and post-menopausal women and to find if any of these can be the potential predictor of osteoporosis in postmenopausal women. Material and methods: The study participants consisted of Group A (n=91) healthy pre-menopausal women and Group B (n=102) healthy postmenopausal women having ≥ 5 years’ history of menopause. ELISA was performed for cytokine (TNFα) and bone turnover markers (carboxytelopeptides), respectively. Bone Mineral Density (BMD)was measured through a dual X-ray absorptiometry (DEXA) scan. Toll-like Receptors 4 (TLR4) gene polymorphisms (A896G; Asp299Gly) and (C1196T; Thr399Ile) were investigated by PCR and Sanger sequencing. Results: Statistical analysis reveals a positive correlation of age and BMI with T scores in the premenopausal group, whereas in post-menopausal group found a significant negative correlation between age and T-score at hip (r = - 0.352**), spine (r = - .306**), and femoral neck (r = - 0.344**) and a significant negative correlation of BMI with TNF-α (- 0.316**). No association and significant differences were observed for TLR4 genotype and allele frequencies among studied groups However, both SNPs exhibited significant association with each other. Conclusions: This study concludes that BMI, BMD and TNF-α are the potential predictors of osteoporosis in post-menopausal women. However, CTX and TLR4 gene polymorphism did not appear as potential predictors of bone loss in this study and apparently cannot help in predicting bone loss in post-menopausal women.

Keywords: osteoporosis, post-menopausal, pre-menopausal woemn, genetics mutaiont, TLR4 genepolymorphsum

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Authors: Kohei Yamamoto, Jae-Ho Kim, Susumu Yonezawa

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The surface of polyethylene terephthalate (PET) was modified with fluorine gas at 25 ℃ and 100 Torr for one h. Moreover, the effect of ethanol washing on surface modification was investigated in this study. The surface roughness of the fluorinated and washed PET samples was approximately six times larger than that (0.6 nm) of the untreated thing. The results of Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy showed that the bonds such as -C=O and -C-Hx derived from raw PET decreased and were converted into fluorinated bonds such as -CFx after surface fluorination. Even after washing with ethanol, the fluorinated bonds stably existed on the surface. These fluorinated bonds showed higher electronegativity according to the zeta potential results. The negative surface charges were increased by washing the ethanol, and it caused to increase in the number of polar groups such as -CHF- and -C-Fx. The fluorinated and washed surface of PET could promote the adsorption of Ag+ ions in AgNO₃ solution because of the increased surface roughness and the negatively charged surface.

Keywords: Ag+ ions adsorption, polyethylene terephthalate, surface fluorination, zeta potential

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Authors: Mustafa Malki, Ewan R. Pearson

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Tools utilized by health care practitioners to flag potential adverse drug reactions secondary to drug-drug interactions ignore individual genetic variation, which has the potential to markedly alter the severity of these interactions. To our best knowledge, there have been limited published studies on the impact of genetic variation on drug-drug interactions. Therefore, our aim in this project is the discovery of previously unrecognized, clinically important drug-drug-gene interactions (DDGIs) within the list of most commonly used drug combinations in the UK. The UKBB database was utilized to identify the top most frequently prescribed drug combinations in the UK with at least one route of interaction (over than 200 combinations were identified). We have recognised 37 common and unique interacting genes considering all of our drug combinations. Out of around 600 potential genetic variants found in these 37 genes, 100 variants have met the selection criteria (common variant with minor allele frequency ≥ 5%, independence, and has passed HWE test). The association between these variants and the use of each of our top drug combinations has been tested with a case-control analysis under the log-additive model. As the data is cross-sectional, drug intolerance has been identified from the genotype distribution as presented by the lower percentage of patients carrying the risky allele and on the drug combination compared to those free of these risk factors and vice versa with drug tolerance. In GoDARTs database, the same list of common drug combinations identified by the UKBB was utilized here with the same list of candidate genetic variants but with the addition of 14 new SNPs so that we have a total of 114 variants which have met the selection criteria in GoDARTs. From the list of the top 200 drug combinations, we have selected 28 combinations where the two drugs in each combination are known to be used chronically. For each of our 28 combinations, three drug response phenotypes have been identified (drug stop/switch, dose decrease, or dose increase of any of the two drugs during their interaction). The association between each of the three phenotypes belonging to each of our 28 drug combinations has been tested against our 114 candidate genetic variants. The results show replication of four findings between both databases : (1) Omeprazole +Amitriptyline +rs2246709 (A > G) variant in CYP3A4 gene (p-values and ORs with the UKBB and GoDARTs respectively = 0.048,0.037,0.92,and 0.52 (dose increase phenotype)) (2) Simvastatin + Ranitidine + rs9332197 (T > C) variant in CYP2C9 gene (0.024,0.032,0.81, and 5.75 (drug stop/switch phenotype)) (3) Atorvastatin + Doxazosin + rs9282564 (T > C) variant in ABCB1 gene (0.0015,0.0095,1.58,and 3.14 (drug stop/switch phenotype)) (4) Simvastatin + Nifedipine + rs2257401 (C > G) variant in CYP3A7 gene (0.025,0.019,0.77,and 0.30 (drug stop/switch phenotype)). In addition, some other non-replicated, but interesting, significant findings were detected. Our work also provides a great source of information for researchers interested in DD, DG, or DDG interactions studies as it has highlighted the top common drug combinations in the UK with recognizing 114 significant genetic variants related to drugs' pharmacokinetic.

Keywords: adverse drug reactions, common drug combinations, drug-drug-gene interactions, pharmacogenomics

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Authors: Fitri Rahmi Fadhilah, Edhyana Sahiratmadja, Ani Melani Maskoen, Ratu Safitri, Supartini Syarif, Herman Susanto

Abstract:

Cervical cancer is the second most common cancer in women after breast cancer. In Indonesia, the incidence of cervical cancer cases is estimated at 25-40 per 100,000 women per year. Human papillomavirus (HPV) infection is a major cause of cervical cancer, and HPV-16 is the most common genotype that infects the cervical tissue. The major late protein L1 may be associated with infectivity and pathogenicity and its variation can be used to classify HPV isolates. The aim of this study was to determine the phylogenetic tree of HPV 16 L1 gene from cervical cancer patient isolates in Bandung. After confirming HPV-16 by Linear Array Genotyping Test, L1 gene was amplified using specific primers and subject for sequencing. Phylogenetic analysis revealed that HPV 16 from Bandung was in the subgroup of Asia and East Asia, showing the close host-agent relationship among the Asian type.

Keywords: L1 HPV 16, cervical cancer, bandung, phylogenetic

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

Abstract:

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: Yuxuan Yang, Zhaoping Zhong

Abstract:

Municipal solid waste and sludge are important sources of waste energy and their proper disposal is of great importance. Pyrolysis can fully decompose solid wastes and sludge, and the pyrolysis products (charcoal, oil and gas) have important recovery values. Due to the complex composition of solid wastes and sludge, the pyrolysis process at high temperatures is prone to heavy metal emissions, which are harmful to humans and the environment and reduce the safety of pyrolysis products. In this paper, heavy metal emissions during pyrolysis of municipal sewage sludge, paper mill sludge, municipal domestic waste, and aged refuse at 450-650°C were investigated and the emissions and hazards of heavy metals (Pb, Cr, Cd, Cu and Zn) were effectively reduced by adding modified vermiculite as an additive. The vermiculite was modified by intercalation with cetyltrimethylammonium bromide, which resulted in more than twice the original layer spacing of the vermiculite. Afterward, the interpolated vermiculite was made into vermiculite flakes by exfoliation modification. After that, the expansion rate of vermiculite flakes was increased by Mg2+ modification and thermal activation. The expanded vermiculite flakes were acidified to improve the textural characteristics of the vermiculite. The modified vermiculite was analysed by XRD, FT-IR, BET and SEM to clarify the modification effect. The incorporation of modified vermiculite resulted in more than 80% retention of all heavy metals at 450°C. Cr, Cu and Zn were better retained than Pb and Cd. The incorporation of modified vermiculite effectively reduced the risk of heavy metals, and all risks were low for Pb, Cr, Cu and Zn. The toxicity of all heavy metals was greatly reduced by the incorporation of modified vermiculite and the morphology of heavy metals was transformed from Exchangeable and acid-soluble (F1) and Reducible (F2) to Oxidizable (F3) and Residual (F4). In addition, the increase in temperature favored the stabilization of heavy metal forms. This study provides a new insight into the cleaner use of energy and the safe management of solid waste.

Keywords: heavy metal, pyrolysis, vermiculite, solid waste

Procedia PDF Downloads 48

Authors: D. J. Kalita

Abstract:

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

Procedia PDF Downloads 69

Authors: Navkiran Kaur, Apoorva Mathur, Abhishree Agarwal, Sakshi Gupta, Tuhin Rashmi

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Aim: Breast cancer is the most common cancer in women worldwide, and resistance to the current therapeutics, often concurrently, is an increasing clinical challenge. Glycosylation of proteins is one of the most important post-translational modifications. It is widely known that aberrant glycosylation has been implicated in many different diseases due to changes associated with biological function and protein folding. Alterations in cell surface glycosylation, can promote invasive behavior of tumor cells that ultimately lead to the progression of cancer. In breast cancer, there is an increasing evidence pertaining to the role of glycosylation in tumor formation and metastasis. In the present study, an attempt has been made to study the disease associated sialoglycoproteins in breast cancer by using bioinformatics tools. The sequence will be retrieved from UniProt database. A database in the form of a word document was made by a collection of FASTA sequences of breast cancer gene sequence. Glycosylation was studied using yinOyang tool on ExPASy and Differential genes expression and protein analysis was done in context of breast cancer metastasis. The number of residues predicted O-glc NAc threshold containing 50 aberrant glycosylation sites or more was detected and recorded for individual sequence. We found that the there is a significant change in the expression profiling of glycosylation patterns of various proteins associated with breast cancer. Differential aberrant glycosylated proteins in breast cancer cells with respect to non-neoplastic cells are an important factor for the overall progression and development of cancer.

Keywords: breast cancer, bioinformatics, cancer, metastasis, glycosylation

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Authors: Natesan Balasubramanian, Palpandi Pounpandi, Venkatraman Thamil Priya, Vellasamy Shanmugaiah, Karubbiah Balakrishnan, Mandayam Anandam Thirunarayan

Abstract:

Streptococcus agalactiae is commonly known as Group B Streptococcus (GBS) and it is the most common cause of life-threatening bacterial infection. GBS first considered as a veterinary pathogen causing mastitis in cattle later becomes a human pathogen for severe neonatal infections. In this present study, a total of 20 new clinical isolates of S. agalactiae were collected from male (6) and female patient (14) with different age group. The isolates were from Urinary tract infection (UTI), blood, pus and eye ulcer. All the 20 S. agalactiae isolates has clear hemolysis properties on blood agar medium and were identified by serogrouping and MALTI-TOF-MS analysis. Antibiotic susceptibility/resistance test was performed for 20 S. agalactiae isolates, further phenotypic resistance pattern was observed for tetracycline, vancomycin, ampicillin and penicillin. Genotypically we found two antibiotic resistance genes such as Betalactem antibiotic resistance gene (Tem) (70%) and tetracycline resistance gene Tet(O) 15% in our isolates. Six virulence factors encoding genes were performed by PCR in twenty GBS isolates, cfb gene (100%), followed by, cylE(90.47%), lmp(85.7%), bca(71.42%), rib (38%) and low frequency in bac gene (4.76%) were determined. Most of the S. agalactiae isolates produced strong biofilm in the polystyrene surface (hydrophobic), and low-level biofilm formation was found in glass tube (hydrophilic) surface. lytR is secreted protein and localized in bacterial cell wall, extra cellular membrane, and cytoplasm. In silico docking studies were performed for lytR protein with four antibiofilm compounds, including a peptide (PR39) with the docking study showed peptide has strong interaction followed by ellagic acid and interaction length is 2.95, 2.97 and 2.95 A°. In ligand EGCGO10 and O11 two atoms intract with lytR (Leu271), with binding bond affinity length is 3.24 and 3.14. The aminoacid Leu 271 is act as an impartant aminoacid, since ellagic acid and EGCG interact with same aminoacid.

Keywords: antibiotics, biofilms, clinical isolates, S. agalactiae, virulence

Procedia PDF Downloads 93

Authors: Savjot Kaur, Mridula Mahajan, AJS Bhanwer, Santokh Singh, Kawaljit Matharoo

Abstract:

Background: Disorders of lipid metabolism and genetic predisposition are CAD risk factors. ApoA1 is the apolipoprotein component of anti-atherogenic high density lipoprotein (HDL) particles. The protective action of HDL and ApoA1 is attributed to their central role in reverse cholesterol transport (RCT). Aim: This study was aimed at identifying sequence variations in ApoA1 (-75G>A) and its association with serum ApoA1 levels. Methods: A total of 300 CAD patients and 300 Normal individuals (controls) were analyzed. PCR-RFLP method was used to determine the DNA polymorphism in the ApoA1 gene, PCR products digested with restriction enzyme MspI, followed by Agarose Gel Electrophoresis. Serum apolipoprotein A1 concentration was estimated with immunoturbidimetric method. Results: Deviation from Hardy- Weinberg Equilibrium (HWE) was observed for this gene variant. The A- allele frequency was higher among Coronary Artery disease patients (53.8) compared to controls (45.5), p= 0.004, O.R= 1.38(1.11-1.75). Under recessive model analysis (AA vs. GG+GA) AA genotype of ApoA1 G>A substitution conferred ~1 fold increased risk towards CAD susceptibility (p= 0.002, OR= 1.72(1.2-2.43). With serum ApoA1 levels < 107 A allele frequency was higher among CAD cases (50) as compared to controls (43.4) [p=0.23, OR= 1.2(0.84-2)] and there was zero % occurrence of A allele frequency in individuals with ApoA1 levels > 177. Conclusion: Serum ApoA1 levels were associated with ApoA1 promoter region variation and influence CAD risk. The individuals with the APOA1 -75 A allele confer excess hazard of developing CAD as a result of its effect on low serum concentrations of ApoA1.

Keywords: apolipoprotein A1 (G>A) gene polymorphism, coronary artery disease (CAD), reverse cholesterol transport (RCT)

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Authors: Luvindran Sugumaran, Mohd Nashrul Mohd Zubir, Kazi Md Salim Newaz, Tuan Zaharinie Tuan Zahari, Suazlan Mt Aznam, Aiman Mohd Halil

Abstract:

With the fast growth of integrated circuits and the trend towards making electronic devices smaller, the heat dissipation load of electronic devices has continued to go over the limit. The high heat flux element would not only harm the operation and lifetime of the equipment but would also impede the performance upgrade brought about by the iteration of technological updates, which would have a direct negative impact on the economic and production cost benefits of rising industries. Hence, in high-tech industries like radar, information and communication, electromagnetic power, and aerospace, the development and implementation of effective heat dissipation technologies were urgently required. Pool boiling is favored over other cooling methods because of its capacity to dissipate a high heat flux at a low wall superheat without the usage of mechanical components. Enhancing the pool boiling performance by increasing the heat transfer coefficient via surface modification techniques has received a lot of attention. There are several surface modification methods feasible today, but the stability and durability of surface modification are the greatest priority. Thus, laser machining is an interesting choice for surface modification due to its low production cost, high scalability, and repeatability. In this study, different patterns of laser-processed copper surfaces are fabricated to investigate the nucleate pool boiling heat transfer performance of distilled water. The investigation showed that there is a significant enhancement in the pool boiling heat transfer performance of the laser-processed surface compared to the reference surface due to the notable increase in nucleation frequency and nucleation site density. It was discovered that the heat transfer coefficients increased when both the surface area ratio and the ratio of peak-to-valley height of the microstructure were raised. It is believed that the development of microstructures on the surface as a result of laser processing is the primary factor in the enhancement of heat transfer performance.

Keywords: heat transfer coefficient, laser processing, micro structured surface, pool boiling

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

Abstract:

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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