Search results for: molecular topology

Authors: Felicia Segeth, Florian G. Klein, Lea Berger, Andreas Kolk, Per S. Holm

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The entry of oncolytic viruses (OVs) into clinical application opens groundbreaking changes in current and future treatment regimens. However, despite their potent anti-cancer activity in vitro, clinical studies revealed limitations of OVs as monotherapy. The same applies to CDK 4/6 inhibitors (CDK4/6i) targeting cell cycle as well as bromodomain and extra-terminal domain inhibitors (BETi) targeting gene expression. In this study, the anti-tumoral effect of XVir-N-31, an YB-1 dependent oncolytic adenovirus, was evaluated in combination with Ribociclib, a CDK4/6i, and JQ1, a BETi. The head and neck squamous cell carcinoma (HNSCC) cell lines Fadu, SAS, and Cal-33 were used. DNA replication and gene expression of XVir-N-31 was measured by RT-qPCR, protein expression by western blotting, and cell lysis by SRB assays. Treatment with CDK4/6i and BETi increased viral gene expression, viral DNA replication, and viral particle formation. The data show that the combination of oncolytic adenovirus XVir-N-31 with CDK4/6i & BETi acts highly synergistic in cancer cell lysis. Furthermore, additional molecular analyses on this subject demonstrate that the positive transcription elongation factor P-TEFb plays a decisive role in this regard, indicating an influence of the combinational therapy on gene transcription control. The combination of CDK4/6i & BETi and XVir-N-31 is an attractive strategy to achieve substantial cancer cell killing and is highly suitable for clinical testing.

Keywords: adenovirus, BET, CDK4/6, HNSCC, P-TEFb, YB-1

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Authors: Abdollah Sobhani, Hossein Vaseghi-Dodaran

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Proteomics is defined as the study of the component of a cell, tissue and biological fluid. This technique has the potential to identify protein biomarkers of a disease states. In this study which was performed on bovine ovarian follicular cysts (BOFC), eight proteins are over expressed in BOFC that these proteins could be useful biomarkers for BOFC. The difference between serum proteome pattern cows affected by postpartum endometritis with healthy cows revealed that concentrations orosomucoid was decreased in endometritis. The comparison proteome of brucella abortus between laboratory adapted strains and clinical isolates could be useful to better understand this disease and vaccine development. Proteomics experiments identified new proteins and pathways that may be important in future hypothesis-driven studies of glucocorticoid-induced immunosuppression. Understanding the molecular mechanisms of effective parameters on male fertility is essential for obtaining high reproductive efficiency by decreasing cost and time. The investigations on proteome of high fertility spermatozoa indicated that expression of some proteins such as casein kinase 2 (CKII) prime poly peptide and tyrosine kinase in high fertility spermatozoa was higher compared to low fertility spermatozoa. Also, some evidence has indicated that variation in protein types and amounts in seminal fluid regulates fertility indexes in dairy bull. In conclusion, proteomics is a useful technique for discovering drugs, vaccine development, and diagnosis disease by biomarkers and improvement of reproduction efficiency.

Keywords: proteomics, reproduction, biomarker, immunity

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Authors: Sirikwan Ponprateep, Anchalee Tassanakajon, Vichien Rimphanitchayakit

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A Kazal-type serine proteinase inhibitor, SPIPm2, was abundantly expressed in the hemocytes and secreted into shrimp plasma has anti-viral property against white spot syndrome virus (WSSV). To discover the molecular mechanism of antiviral activity, the binding assay showed that SPIPm2 bind to the components of viral particle and shrimp hemocyte. From our previous report, viral target protein of SPIPm2 was identified, namely WSV477 using yeast two-hybrid screening. WSV477 is an early gene product of WSSV and involved in viral propagation. In this study, the co-immunoprecipitation technique and Tandem Mass Spectrometry (LC-MS/MS) was used to identify the target protein of SPIPm2 from shrimp hemocyte. The target protein of SPIPm2 was cyclophilin A. In vertebrate, cyclophilin A or peptidylprolyl isomerase A was reported to be the immune suppressor interacted with cyclosporin A involved in immune defense response. The recombinant cyclophilin A from Penaeus monodon (rPmCypA) was produced in E.coli system and purified using Ni-NTA column to confirm the protein-protein interaction. In vitro pull-down assay showed the interaction between rSPIPm2 and rPmCypA. To study the biological function of these proteins, the expression analysis of immune gene in shrimp defense pathways will be investigated after rPmCypA administration.

Keywords: cyclophilin A, protein-protein interaction, Kazal-type serine proteinase inhibitor, Penaeus monodon

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Authors: Yash M. Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan

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The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species.

Keywords: cross-amplification, microsatellite markers, observed heterozygosity, population genetic, simple sequence repeats

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Authors: Vemula Amalakrishna, S. Pushpavanam

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Change and motion characterize and persistently reshape the world around us, on scales from molecular to global. The subtle interplay between change (Reaction) and motion (Diffusion) gives rise to an astonishing intricate spatial or temporal pattern. These pattern formation in nature has been intellectually appealing for many scientists since antiquity. Periodic precipitation patterns, also known as Liesegang patterns (LP), are one of the stimulating examples of such self-assembling reaction-diffusion (RD) systems. LP formation has a great potential in micro and nanotechnology. So far, the research on LPs has been concentrated mostly on how these patterns are forming, retrieving information to build a universal mathematical model for them. Researchers have developed various theoretical models to comprehensively construct the geometrical diversity of LPs. To the best of our knowledge, simulation studies of LPs assume an arbitrary value of RD parameters to explain experimental observation qualitatively. In this work, existing models were studied to understand the mechanism behind this phenomenon and challenges pertaining to models were understood and explained. These models are not computationally effective due to the presence of discontinuous precipitation rate in RD equations. To overcome the computational challenges, smoothened Heaviside functions have been introduced, which downsizes the computational time as well. Experiments were performed using a conventional LP system (AgNO₃-K₂Cr₂O₇) to understand the effects of different gels and temperatures on formed LPs. The model is extended for real parameter values to compare the simulated results with experimental data for both 1-D (Cartesian test tubes) and 2-D(cylindrical and Petri dish).

Keywords: reaction-diffusion, spatio-temporal patterns, nucleation and growth, supersaturation

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Authors: Reza Talebi

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Wheat (Triticum aestivum) is one of the most important food staples in Iran. Understanding genetic variability among the landrace wheat germplasm is important for breeding. Landraces endemic to Iran are a genetic resource that is distinct from other wheat germplasm. In this study, 60 Iranian landrace wheat accessions were characterized AFLP and ISSR markers. Twelve AFLP primer pairs detected 128 polymorphic bands among the sixty genotypes. The mean polymorphism rate based on AFLP data was 31%; however, a wide polymorphism range among primer pairs was observed (22–40%). Polymorphic information content (PIC value) calculated to assess the informativeness of each marker ranged from 0.28 to 0.4, with a mean of 0.37. According to AFLP molecular data, cluster analysis grouped the genotypes in five distinct clusters. .ISSR markers generated 68 bands (average of 6 bands per primer), which 31 were polymorphic (45%) across the 60 wheat genotypes. Polymorphism information content (PIC) value for ISSR markers was calculated in the range of 0.14 to 0.48 with an average of 0.33. Based on data achieved by ISSR-PCR, cluster analysis grouped the genotypes in three distinct clusters. Both AFLP and ISSR markers able to showed that high level of genetic diversity in Iranian landrace wheat accessions has maintained a relatively constant level of genetic diversity during last years.

Keywords: wheat, genetic diversity, AFLP, ISSR

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Authors: Rahul Shrivastava, Manish Tripathi, Mohmmad Yasir, Shailesh Singh

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Life style changes and depletion in atmospheric ozone layer in recent decades lead to increase in skin cancer including both melanoma and nonmelanomas. Natural products which were obtained from different plant species have the potential of anti skin cancer activity. In regard of this, present study focuses the potential effect of Glycosmis pentaphylla against anti skin cancer activity. Different Phytochemical constituents which were present in the roots of Glycosmis pentaphylla were identified and were used as ligands after sketching of their structures with the help of ACD/Chemsketch. These ligands are screened for their anticancer potential with proteins which are involved in skin cancer effects with the help of pyrx software. After performing docking studies, results reveal that Noracronycine secondary metabolite of Glycosmis pentaphylla shows strong affinity of their binding energy with Ribosomal S6 Kinase 2 (2QR8) protein. Ribosomal S6 Kinase 2 (2QR8) has an important role in the cell proliferation and transformation mediated through by N-terminal kinase domain and was induced by the tumour promoters such as epidermal growth factor. It also plays a key role in the neoplastic transformation of human skin cells and in skin cancer growth. Noracronycine interact with THR-493 and MET-496 residue of Ribosomal S6 Kinase 2 protein with binding energy ΔG = -8.68 kcal/mole. Thus on the basis of this study we can say that Noracronycine which present in roots of Glycosmis pentaphylla can be used as lead compound against skin cancer.

Keywords: glycosmis pentaphylla, pyrx, ribosomal s6 kinase, skin cancer

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Authors: Angelica Salmeron Alcocer, Deifilia Ahuatzi Chacon, Felipe Rodriguez Casasola

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Polycyclic aromatic hydrocarbons (PAHs) are produced naturally (forest fires, volcanic eruptions) and human activity (burning fossil fuels). Concern for PAHs is due to their toxic, mutagenic and carcinogenic effects and so pose a potential risk to human health and ecology. Therefore these are considered the most toxic components of oil, they are highly hydrophobic, making them easily depositable on the floor, air and water. One method of removing PAHs of contaminated soil used surfactants such as Tween 80, which it has been reported as less toxic and also increases the solubility of the PAH compared to other surfactants, fluoranthene is a PAH with molecular formula C16H10, its name derives from the fluorescence which presents to UV light. In this paper, a study of the fluoranthene removal solubilized with Tween 80 in synthetic wastewater using a microbial community (isolated from soil of coffee plantations in the state of Veracruz, Mexico) and Fenton oxidation method was performed. The microbial community was able to use both tween 80 and fluoranthene as carbon sources for growth, when the biological treatment in batch culture was applied, 100% of fluoranthene was mineralized, this only occurred at an initial concentration of 100 ppm, but by increasing the initial concentration of fluoranthene the removal efficiencies decay and degradation time increases due to the accumulation of byproducts more toxic or less biodegradable, however when the Fenton oxidation was previously applied to the biological treatment, it was observed that removal of fluoranthene improved because it is consumed approximately 2.4 times faster.

Keywords: fluoranthene, polycyclic aromatic hydrocarbons, biological treatment, fenton oxidation

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Authors: Nesrine Lenchi, Salima Kebbouche-Gana, Laddada Belaid, Mohamed Lamine Khelfaoui, Mohamed Lamine Gana

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Saline lakes are extreme hypersaline environments that are considered five to ten times saltier than seawater (150 – 300 g L-1 salt concentration). Hypersaline regions differ from each other in terms of salt concentration, chemical composition and geographical location, which determine the nature of inhabitant microorganisms. In order to explore the diversity of moderate and extreme halophiles Bacteria in Chott Tinsilt (East of Algeria), an isolation program was performed. In the first time, water samples were collected from the saltern during pre-salt harvesting phase. Salinity, pH and temperature of the sampling site were determined in situ. Chemical analysis of water sample indicated that Na +and Cl- were the most abundant ions. Isolates were obtained by plating out the samples in complex and synthetic media. In this study, seven halophiles cultures of Bacteria were isolated. Isolates were studied for Gram’s reaction, cell morphology and pigmentation. Enzymatic assays (oxidase, catalase, nitrate reductase and urease), and optimization of growth conditions were done. The results indicated that the salinity optima varied from 50 to 250 g L-1, whereas the optimum of temperature range from 25°C to 35°C. Molecular identification of the isolates was performed by sequencing the 16S rRNA gene. The results showed that these cultured isolates included members belonging to the Halomonas, Staphylococcus, Salinivibrio, Idiomarina, Halobacillus Thalassobacillus and Planococcus genera and what may represent a new bacterial genus.

Keywords: bacteria, Chott, halophilic, 16S rRNA

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Authors: Nidhi S. Chandra, Veena Agrawal, Debprasad Chattopadhyay

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Background: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in developing countries. It spreads feco orally mainly due to contamination of drinking water by sewage. There is limited data on the genotypic comparison of HEV isolates from sewage water and humans. The aim of this study was to identify genotype and conduct phylogenetic analysis of HEV isolates from sewage water and humans. Materials and Methods: 14 sewage water and 60 serum samples from acute sporadic hepatitis E cases (negative for hepatitis A, B, C) were tested for HEV-RNA by nested polymerase chain reaction (RTnPCR) using primers designed with in RdRp (RNA dependent RNA polymerase) region of open reading frame-1 (ORF-1). Sequencing was done by ABI prism 310. The sequences (343 nucleotides) were compared with each other and were aligned with previously reported HEV sequences obtained from GeneBank, using Clustal W software. A Phylogenetic tree was constructed by using PHYLIP version 3.67 software. Results: HEV-RNA was detected in 49/ 60 (81.67%) serum and 5/14 (35.71%) sewage samples. The sequences obtained from 17 serums and 2 sewage specimens belonged to genotype I with 85% similarity and clustering with previously reported human HEV sequences from India. HEV isolates from human and sewage in North West India are genetically closely related to each other. Conclusion: These finding suggest that sewage acts as reservoir of HEV. Therefore it is important that measures are taken for proper waste disposal and treatment of drinking water to prevent outbreaks and epidemics due to HEV.

Keywords: hepatitis E virus, nested polymerase chain reaction, open reading frame-1, nucleotidies

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Authors: Maninderjeet K. Grewal, Sakshi Bhatnor, Renu Chadha

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The composition of pharmaceutical entities and the molecular interactions can be altered to optimize drug properties such as solubility and bioavailability by the crystal engineering technique. The present work has emphasized on the preparation, characterization, and biopharmaceutical evaluation of co-crystal of BCS Class II anti-osteoarthritis drug, Oxaprozin (OXA) with aspartic acid (ASPA) as co-former. The co-crystals were prepared through the mechanochemical solvent drop grinding method. Characterization of the prepared co-crystal (OXA-ASPA) was done by using analytical tools such as differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), powder X-ray diffraction (PXRD). DSC thermogram of OXA-ASPA cocrystal showed a single sharp melting endotherm at 235 ºC, which was between the melting peaks of the drug and the counter molecules suggesting the formation of a new phase which is a co-crystal that was further confirmed by using other analytical techniques. FT-IR analysis of OXA-ASPA cocrystal showed a shift in a hydroxyl, carbonyl, and amine peaks as compared to pure drugs indicating all these functional groups are participating in cocrystal formation. The appearance of new peaks in the PXRD pattern of cocrystals in comparison to individual components showed that a new crystalline entity has been formed. The Crystal structure of cocrystal was determined using material studio software (Biovia) from PXRD. The equilibrium solubility study of OXA-ASPA showed improvement in solubility as compared to pure drug. Therefore, it was envisioned to prepare the co-crystal of oxaprozin with a suitable conformer to modulate its physiochemical properties and consequently, the biopharmaceutical parameters.

Keywords: cocrystals, coformer, oxaprozin, solubility

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Authors: Mallikarjunachari Gangapuram

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The design of stimuli-responsive hydrogel nanocomposite thin films is gaining significant attention in these days due to its wide variety of applications. Soft microrobots, drug delivery, biosensors, regenerative medicine, bacterial adhesion, energy storage and wound dressing are few advanced applications in different fields. In this research work, the nanomechanical properties of composite thin films of 20 microns were tuned by applying homogeneous external DC, and AC magnetic fields of magnitudes 0.05 T and 0.1 T. Polyvinyl alcohol (PVA) used as a matrix material and elliptical hematite nanoparticles (ratio of the length of the major axis to the length of the minor axis is 140.59 ± 1.072 nm/52.84 ± 1.072 nm) used as filler materials to prepare the nanocomposite thin films. Both quasi-static nanoindentation, Nano Dynamic Mechanical Analysis (Nano-DMA) tests were performed to characterize the viscoelastic properties of PVA, PVA+Hematite (0.1% wt, 2% wt and 4% wt) nanocomposites. Different properties such as storage modulus, loss modulus, hardness, and Er/H were carefully analyzed. The increase in storage modulus, hardness, Er/H and a decrease in loss modulus were observed with increasing concentration and DC magnetic field followed by AC magnetic field. Contact angle and ATR-FTIR experiments were conducted to understand the molecular mechanisms such as hydrogen bond formation, crosslinking density, and particle-particle interactions. This systematic study is helpful in design and modeling of magnetic responsive hydrogel nanocomposite thin films for biomedical applications.

Keywords: hematite, hydrogel, nanoindentation, nano-DMA

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Authors: Y. V. S. Annapurna, V. V. Lakshmi

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Urinary tract infection (UTI) is one of the most common infectious diseases at the community level with a high rate of morbidity . This is further augmented by increase in the number of resistant and multi resistant strains of bacteria particularly by those producing Extended spectrum of beta lactamases. The present study was aimed at analysis of antibiograms of E.coli and Klebsiella sp causing urinary tract infections. Between November 2011 and April 2013, a total of 1120 urine samples were analyzed,. Antibiotic sensitivity testing was done with 542(48%) isolates of E.coli and 446(39%) of Klebsiella sp using the standard disc diffusion method against eleven commonly used antibiotics .Organisms showed high susceptibility to Amikacin and Netilimicin and low susceptibility to Cephalosporins. MAR index was calculated for the multidrug resistant strains. Maximum MAR index detected among the isolates was 0.9. Phenotypic identification for ESBL production was confirmed by double disk synergy test (DDST) according to CLSI guidelines. Plasmid profile of the isolates was carried out using alkaline hydrolysis method. Agarose-gel electrophoresis showed presence of high-molecular weight plasmid DNA among the ESBL strains. This study emphasizes the importance of indiscriminate use of antibiotics which if discontinued, in turn would prevent further development of bacterial drug resistance. For this, a proper knowledge of susceptibility pattern of uropathogens is necessary before prescribing empirical antibiotic therapy and it should be made mandatory.

Keywords: escherichia coli, extended spectrum of beta lactamase, Klebsiella spp, Uropathogens

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Authors: Ogbonnaya O. Iroanya, Samson T. Fakorede, Osamudiamen J. Edosa, Hadiat A. Azeez

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The human mitochondrial DNA (mtDNA) is about 17 kbp circular DNA fragments found within the mitochondria together with smaller fragments of 1200 bp known as the control region. Knowledge of variation within populations has been employed in forensic and molecular anthropology studies. The study was aimed at investigating the polymorphic nature of the two hypervariable segments (HVS) of the mtDNA, i.e., HVS1 and HVS2, and to determine the haplogroup distribution among individuals resident in Lagos, Southwestern Nigeria. Peripheral blood samples were obtained from sixty individuals who are not related maternally, followed by DNA extraction and amplification of the extracted DNA using primers specific for the regions under investigation. DNA amplicons were sequenced, and sequenced data were aligned and compared to the revised Cambridge Reference Sequence (rCRS) GenBank Accession number: NC_012920.1) using BioEdit software. Results obtained showed 61 and 52 polymorphic nucleotide positions for HVS1 and HVS2, respectively. While a total of three indels mutation were recorded for HVS1, there were seven for HVS2. Also, transition mutations predominate nucleotide change observed in the study. Genetic diversity (GD) values for HVS1 and HVS2 were estimated to be 84.21 and 90.4%, respectively, while random match probability was 0.17% for HVS1 and 0.89% for HVS2. The study also revealed mixed haplogroups specific to the African (L1-L3) and the Eurasians (U and H) lineages. New polymorphic sites obtained from the study are promising for human identification purposes.

Keywords: hypervariable region, indels, mitochondrial DNA, polymorphism, random match probability

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Authors: Yung-Feng Yen, I-an Jen, Yi-Ming Arthur Chen

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The molecular mimicry between human immunodeficiency virus (HIV) protein and red blood cell (RBC) antigens could induce the production of anti-RBC autoantibodies. However, the association between HIV infection and subsequent development of autoimmune hemolytic anemia (AIHA) remains unclear. This nationwide population-based cohort study aimed to determine the association between incident AIHA and HIV in Taiwan. From 2000–2012, we identified adult people living with HIV/AIDS (PLWHA) from the Taiwan centers for disease control HIV Surveillance System. HIV-infected individuals were defined by positive HIV-1 western blot. Age- and sex-matched controls without HIV infection were selected from the Taiwan National Health Insurance Research Database for comparison. All patients were followed until Dec. 31, 2012, and observed for occurrence of AIHA. Of 171,468 subjects (19,052 PLWHA, 152,416 controls), 30 (0.02%) had incident AIHA during a mean follow-up of 5.45 years, including 23 (0.12%) PLWHA and 7 (0.01%) controls. After adjusting for potential confounders, HIV infection was found to be an independent risk factor of incident AIHA (adjusted hazard ratio [AHR], 20.9; 95% confidence interval [CI], 8.34-52.3). Moreover, PLWHA receiving HAART were more likely to develop AIHA than those not receiving HAART (AHR, 10.8; 95% CI, 2.90-40.1). Additionally, the risk of AIHA was significantly increased in those taking efavirenz (AHR, 3.15; 95% CI, 1.18-8.43) or atazanavir (AHR, 6.58; 95% CI, 1.88-22.9) component of the HAART. In conclusion, HIV infection is an independent risk factor for incident AIHA. Clinicians need to be aware of the higher risk of AIHA in PLWHA.

Keywords: autoimmune disease , hemolytic anemia, HIV, highly active antiretroviral treatment

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Authors: Mohammed N. Al Kindi, Mazin Al Khabouri, Khalsa Al Lamki, Tommasso Pappuci, Giovani Romeo, Nadia Al Wardy

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Hereditary hearing loss is a heterogeneous group of complex disorders with an overall incidence of one in every five hundred newborns presented as syndromic and non-syndromic forms. Cadherin-related 23 (CDH23) is one of the listed deafness causative genes. CDH23 is found to be expressed in the stereocilia of hair cells and the retina photoreceptor cells. Defective CDH23 has been associated mostly with prelingual severe-to-profound sensorineural hearing loss (SNHL) in either syndromic (USH1D) or non-syndromic SNHL (DFNB12). An Omani family diagnosed clinically with severe-profound sensorineural hearing loss was genetically analysed by whole exome sequencing technique. A novel homozygous missense variant, c.A7451C (p.D2484A), in exon 53 of CDH23 was detected. One hundred and thirty control samples were analysed where all were negative for the detected variant. The variant was analysed in silico for pathogenicity verification using several mutation prediction software. The variant proved to be a pathogenic mutation and is reported for the first time in Oman and worldwide. It is concluded that in silico mutation prediction analysis might be used as a useful molecular diagnostics tool benefiting both genetic counseling and mutation verification. The aspartic acid 2484 alanine missense substitution might be the main disease-causing mutation that damages CDH23 function and could be used as a genetic hearing loss marker for this particular Omani family.

Keywords: Cdh23, d2484a, in silico, Oman

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Authors: Nafiseh Noormohammadi, Ahmad Sobhani Najafabadi

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Hypericins (hypericin and pseudohypericin) are natural napthodianthrone derivatives produced by Hypericum perforatum (St. John’s Wort), which have many medicinal properties such as antitumor, antineoplastic, antiviral, and antidepressant activities. Production and accumulation of hypericin in the plant are influenced by both genetic and environmental conditions. Despite the existence of different high-throughput data on the plant, genetic dimensions of hypericin biosynthesis have not yet been completely understood. In this research, 21 high-quality RNA-seq data on different parts of the plant were integrated into metabolic data to reconstruct a coexpression network. Results showed that a cluster of 30 transcripts was correlated with total hypericin. The identified transcripts were divided into three main groups based on their functions, including hypericin biosynthesis genes, transporters, detoxification genes, and transcription factors (TFs). In the biosynthetic group, different isoforms of polyketide synthase (PKSs) and phenolic oxidative coupling proteins (POCPs) were identified. Phylogenetic analysis of protein sequences integrated into gene expression analysis showed that some of the POCPs seem to be very important in the biosynthetic pathway of hypericin. In the TFs group, six TFs were correlated with total hypericin. qPCR analysis of these six TFs confirmed that three of them were highly correlated. The identified genes in this research are a rich resource for further studies on the molecular breeding of H. perforatum in order to obtain varieties with high hypericin production.

Keywords: hypericin, St. John’s Wort, data mining, transcription factors, secondary metabolites

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Authors: Andres Piña, Amy Meléndez, Pablo Cano, Tomas Cahuich

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The purpose of this project is to propose a quick and environmentally friendly alternative to measure the quality of oils used in food industry. There is evidence that repeated and indiscriminate use of oils in food processing cause physicochemical changes with formation of potentially toxic compounds that can affect the health of consumers and cause organoleptic changes. In order to assess the quality of oils, non-destructive optical techniques such as Interferometry offer a rapid alternative to the use of reagents, using only the interaction of light on the oil. Through this project, we used interferograms of samples of oil placed under different heating conditions to establish the changes in their quality. These interferograms were obtained by means of a Mach-Zehnder Interferometer using a beam of light from a HeNe laser of 10mW at 632.8nm. Each interferogram was captured, analyzed and measured full width at half-maximum (FWHM) using the software from Amcap and ImageJ. The total of FWHMs was organized in three groups. It was observed that the average obtained from each of the FWHMs of group A shows a behavior that is almost linear, therefore it is probable that the exposure time is not relevant when the oil is kept under constant temperature. Group B exhibits a slight exponential model when temperature raises between 373 K and 393 K. Results of the t-Student show a probability of 95% (0.05) of the existence of variation in the molecular composition of both samples. Furthermore, we found a correlation between the Iodine Indexes (Physicochemical Analysis) and the Interferograms (Optical Analysis) of group C. Based on these results, this project highlights the importance of the quality of the oils used in food industry and shows how Interferometry can be a useful tool for this purpose.

Keywords: food industry, interferometric, oils, quality control

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Authors: Sabir Khan, Sajjad Hussain, Ademar Wong, Maria Del Pilar Taboada Sotomayor

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The present work aims to develop magnetic molecularly imprinted polymers (MMIPs) for determination of a selected pesticide (ametryne) using high-performance liquid chromatography (HPLC). Computational simulation can assist the choice of the most suitable monomer for the synthesis of polymers. The (MMIPs) were polymerized at the surface of Fe3O4@SiO2 magnetic nanoparticles (MNPs) using 2-vinylpyradine as functional monomer, ethylene-glycol-dimethacrylate (EGDMA) is a cross-linking agent and 2,2-Azobisisobutyronitrile (AIBN) used as radical initiator. Magnetic non-molecularly imprinted polymer (MNIPs) was also prepared under the same conditions without analyte. The MMIPs were characterized by scanning electron microscopy (SEM), Brunauer, Emmett and Teller (BET) and Fourier transform infrared spectroscopy (FTIR). Pseudo first-order and pseudo second order model were applied to study kinetics of adsorption and it was found that adsorption process followed the pseudo-first-order kinetic model. Adsorption equilibrium data was fitted to Freundlich and Langmuir isotherms and the sorption equilibrium process was well described by Langmuir isotherm mode. The selectivity coefficients (α) of MMIPs for ametryne with respect to atrazine, ciprofloxacin and folic acid were 4.28, 12.32 and 14.53 respectively. The spiked recoveries ranged between 91.33 and 106.80% were obtained. The results showed high affinity and selectivity of MMIPs for pesticide ametryne in the food samples.

Keywords: molecularly imprinted polymer, pesticides, magnetic nanoparticles, adsorption

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Authors: Jerry John T. M., Sylas V. P., Shijo Joy

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Hydrogen is the most essential gas that can be used for many purposes. During the production of hydrogen using raw materials like Soil and leftover cooked rice water (kanjivellam), the major by-product formed is water. Soil is collected from three different places in kottayam district: Kallara, Meenachilar, and Athirampuzha. Collected samples are mixed with rice water and tested for traces of hydrogen using a biohydrogen sensor after 72 hours. The result was the presence of hydrogen in all the 3 samples. After streaking, PCR and gel electrophoresis detected the bacteria which produced the hydrogen. RGCB Thiruvananthapuram conducted the sequencing of the PCR resultant. And identified the bacterial strains. Five variants of Bacillus bacteria ( (1) Bacillus cereus strain JTM GenBank: OP278839.1 (2) Bacillus toyonensis strain JTM2 GenBank: OP278841.1 (3) Bacillus anthracis strain JTM_SR2989-3-R_H08 GenBank: OP278960.1 (4) Bacillus thuringiensis strain JRY1 GenBank: OP278976.1 (5) Bacillus anthracis strain JTM_SR2989-3-F_H07 GenBank: OP278959.1 ) are identified and successfully registered in NCBI Gen bank. These Bacillus bacteria are major types of Rhizobacteria that can form spores and can survive in the soil for a long time period under harsh environmental conditions. Also, plant growth is enhanced by PGPR (Plant growth promoting rhizobacteria) through the induction of systemic resistance, antibiosis, and competitive omission. The molecular sequencing was submitted to the NCBI Gen Bank, and the accession numbers were allotted for the bacterial cultures.

Keywords: bio hydrogen production, bacterial bio hydrogen production, plant related to bacillus bacteria., bacillus bacteria study

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

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

Keywords: tephritid, Anastrepha fraterculus, COI, numts

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Authors: Nesrine Benarous, Hassiba Bougueria, Nabila Moussa Slimane, Aouatef Cherouana

Abstract:

Crystal polymorphism is important for the synthesis of more potent and bioactive pharmaceutical compounds, including their different properties, such as packing arrangement and conformation. In fact, polymorphism plays a vital role in drug development. Different parameters affect the crystallization and give their degree of freedom. Severalproperties affected polymorphism, like kinetics, thermodynamics, spectroscopy, and mechanical property. Various techniques are used for characterizing polymorphs, are crystallography, morphology, phase transitions, molecular motion, and chemical environment. In this work, crystal structures of two polymorphs (I and II) of the Schiff base (SB) title compound were prepared by condensation reaction. The crystal structures of both polymorphs were determined by single X-ray analysis. The two polymorphs crystallize in two different space groups: P21/c for I and Pbca for II. The dihedral angles between the two phenyl rings are 4.81º for I and 82.27º for II. Both crystal structures are built on the basis of moderate and weak hydrogen bonds, 𝜋-stacking, and halogen⋯halogeninteractions. On the other hand, Hirshfeld surface (HS) analysis indicates that the most important contributions to the crystal packing for the two polymorphs are from Cl⋯H/H⋯Cl, H⋯H, and N⋯H/H⋯N contacts. These are followed by C⋯H/H⋯C for compound I and C⋯C and by C⋯H/H⋯C contacts for compound II. Afterwards, the in vitro antibacterial activity revealed that the SB have been found effective against G- bacteria Klebsiella pneumonia andG+ bacteria Staphylococcus aureuswith MIC value of14.37μg/mL. Moreover, the SBexhibited moderate toxicity against Brine Shrimp with LC50 value of 44.19μg/mL.

Keywords: polymorph, crystal structure, hirshfeld surface analysis, in vitro antibacterial activity, toxicity

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Authors: Kanchan Yadav, Ai-Chuan Chou, Rajesh Kumar Ulaganathan, Hua-De Gao, Hsien-Ming Lee, Chien-Yuan Pan, Yit-Tsong Chen

Abstract:

Optogenetics is an innovative technology now widely adopted by researchers in different fields of the biological sciences. However, due to the weak tissue penetration capability of the short wavelengths used to activate light-sensitive proteins, an invasive light guide has been used in animal studies for photoexcitation of target tissues. Upconverting nanoparticles (UCNPs), which transform near-infrared (NIR) light to short-wavelength emissions, can help address this issue. To improve optogenetic performance, we enhance the target selectivity for optogenetic controls by specifically conjugating the UCNPs with light-sensitive proteins at a molecular level, which shortens the distance as well as enhances the efficiency of energy transfer. We tagged V5 and Lumio epitopes to the extracellular N-terminal of channelrhodopsin-2 with an mCherry conjugated at the intracellular C-terminal (VL-ChR2m) and then bound NeutrAvidin-functionalized UCNPs (NAv-UCNPs) to the VL-ChR2m via a biotinylated antibody against V5 (bV5-Ab). We observed an apparent energy transfer from the excited UCNP (donor) to the bound VL-ChR2m (receptor) by measuring emission-intensity changes at the donor-receptor complex. The successful patch-clamp electrophysiological test and an intracellular Ca2+ elevation observed in the designed UCNP-ChR2 system under optogenetic manipulation confirmed the practical employment of UCNP-assisted NIR-optogenetic functionality. This work represents a significant step toward improving therapeutic optogenetics.

Keywords: Channelrhodopsin-2, near infrared, optogenetics, upconverting nanoparticles

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Authors: Dhruv Mehta, Alexander van Zuijlen, Hester Bijl

Abstract:

Large Eddy Simulation (LES) numerically resolves the large energy-containing eddies of a turbulent flow, while modelling the small dissipative eddies. On a wind farm, these large scales carry the energy wind turbines extracts and are also responsible for transporting the turbines’ wakes, which may interact with downstream turbines and certainly with the atmospheric boundary layer (ABL). In this situation, it is important to conserve the energy that these wake’s carry and which could be altered artificially through numerical dissipation brought about by the schemes used for the spatial discretisation and temporal integration. Numerical dissipation has been reported to cause the premature recovery of turbine wakes, leading to an over prediction in the power produced by wind farms.An energy-conserving scheme is free from numerical dissipation and ensures that the energy of the wakes is increased or decreased only by the action of molecular viscosity or the action of wind turbines (body forces). The aim is to create an LES package with energy-conserving schemes to simulate wind turbine wakes correctly to gain insight into power-production, wake meandering etc. Such knowledge will be useful in designing more efficient wind farms with minimal wake interaction, which if unchecked could lead to major losses in energy production per unit area of the wind farm. For their research, the authors intend to use the Energy-Conserving Navier-Stokes code developed by the Energy Research Centre of the Netherlands.

Keywords: energy-conserving schemes, modelling turbulence, Large Eddy Simulation, atmospheric boundary layer

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Authors: Seokyoon Moon, Yun-Ho Ahn, Heejoong Kim, Sujin Hong, Yunseok Lee, Youngjune Park

Abstract:

Gas hydrate is a non-stoichiometric crystalline compound consisting of host water-framework and low molecular weight guest molecules. Small gaseous molecules such as CH₄, CO₂, and N₂ can be captured in the host water framework lattices of the gas hydrate with specific temperature and pressure conditions. The three well-known crystal structures of structure I (sI), structure II (sII), and structure H (sH) are determined by the size and shape of guest molecules. In this study, we measured the phase equilibria of binary (2,2-dimethyl-1-propanol + CO₂, CH₄, N₂) hydrates to explore their fundamental thermodynamic characteristics. We identified the structure of the binary gas hydrate by employing synchrotron high-resolution powder diffraction (HRPD), and the guest distributions in the lattice of gas hydrate were investigated via dispersive Raman and ¹³C solid-state nuclear magnetic resonance (NMR) spectroscopies. The end-to-end distance of 2,2-dimethyl-1-propanol was calculated to be 7.76 Å, which seems difficult to be enclathrated in large cages of sI or sII. However, due to the flexibility of the host water framework, binary hydrates of sI or sII types can be formed with the help of small gas molecule. Also, the synchrotron HRPD patterns revealed that the binary hydrate structure highly depends on the type of help gases; a cubic Fd3m sII hydrate was formed with CH₄ or N₂, and a cubic Pm3n sI hydrate was formed with CO₂. Interestingly, dispersive Raman and ¹³C NMR spectra showed that the unique tuning phenomenon occurred in binary (2,2-dimethyl-1-propanol + CO₂) hydrate. By optimizing the composition of NPA, we can achieve both thermodynamic stability and high CO₂ storage capacity for the practical application to CO₂ capture.

Keywords: clathrate, gas hydrate, neopentyl alcohol, CO₂, tuning phenomenon

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Authors: Zhang Lei, Zhao Qingrong, Wang Chen, Zhang Sufang, Zhang Hanguo

Abstract:

Larch is the main afforestation and timber tree species in Northeast China, and drought is one of the main factors limiting the growth of Larch and other organisms in Northeast China. In order to further explore the mechanism of Larch drought resistance, PEG was used to simulate drought stress. The full-length sequencing of Larch embryogenic callus under PEG simulated drought stress was carried out by combining Illumina-Hiseq and SMRT-seq. A total of 20.3Gb clean reads and 786492 CCS reads were obtained from the second and third generation sequencing. The de-redundant transcript sequences were predicted by lncRNA, 2083 lncRNAs were obtained, and the target genes were predicted, and a total of 2712 target genes were obtained. The de-redundant transcripts were further screened, and 1654 differentially expressed genes (DEGs )were obtained. Among them, different DEGs respond to drought stress in different ways, such as oxidation-reduction process, starch and sucrose metabolism, plant hormone pathway, carbon metabolism, lignin catabolic/biosynthetic process and so on. This study provides basic full-length sequencing data for the study of Larch drought resistance, and excavates a large number of DEGs in response to drought stress, which helps us to further understand the function of Larch drought resistance genes and provides a reference for in-depth analysis of the molecular mechanism of Larch drought resistance.

Keywords: larch, drought stress, full-length transcriptome sequencing, differentially expressed genes

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Authors: Somit Dutta, Pallab Kar, Arnab Kumar Chakraborty, Arnab Sen, Tapas Kumar Chaudhuri

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In the present study three species of Clerodendrum; Clerodendrum indicum, Volkameria inermis and Clerodendrum colebrookianum were used to investigate the possible activity against oxidative stress. A detailed in-vivo and in-vitro antioxidant profiling, directly associated with inflammation-related carcinogenesis, has been executed with a motive to evaluate the free radical scavenging activity of Clerodendrum extract. Measurement of cell viability and ROS generation in HEK-293 (Human Embryonic Kidney Cell Line) cells was also estimated. The immune cell proliferative properties (MTT) and in-vitro assay for evaluation of their antioxidant activities including hydroxyl radical, nitric oxide, singlet oxygen, peroxinitrate and hydrogen peroxide, etc. were investigated. GC-MS and FTIR analyses have been performed to identify the active biological compounds. These active biological compounds were further studied to assess their potential medicinal properties, aided by molecular docking and interaction analysis between the active compounds and different proteins related to oxidative stress leading to progression of carcinogenesis. The research article clearly demonstrates the role of ROS in various phases of carcinogenesis. Therefore, the antioxidant and free radical scavenging capacity of all the Clerodendrum species might prove beneficial for the immune system. It might be concluded that this plant species offers great promise for cancer prevention and therapy due to the presence of several bioactive compounds and potent antioxidant capacity of C. colebrookianum.

Keywords: antioxidant, cancer, oxidative stress, reactive oxygen species (ROS)

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

Abstract:

The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, sport performance, Slovakia

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

Abstract:

Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: Pawit Tangviroon, Apichit Svang-Ariyaskul

Abstract:

As the limited availability of petroleum-based fuel has been a major concern, biodiesel is one of the most attractive alternative fuels because it is renewable and it also has advantages over the conventional petroleum-base diesel. At Present, productions of biodiesel generally perform by transesterification of vegetable oils with low molecular weight alcohol, mainly methanol, using chemical catalysts. Methanol is petrochemical product that makes biodiesel producing from methanol to be not pure renewable energy source. Therefore, ethanol as a product produced by fermentation processes. It appears as a potential feed stock that makes biodiesel to be pure renewable alternative fuel. The research is conducted based on two biodiesel production processes by reacting soybean oils with methanol and ethanol. Life cycle assessment was carried out in order to evaluate the environmental impacts and to identify the process alternative. Nine mid-point impact categories are investigated. The results indicate that better performance on Abiotic Depletion Potential (ADP) and Acidification Potential (AP) are observed in biodiesel production from methanol when compared with biodiesel production from ethanol due to less energy consumption during the production processes. Except for ADP and AP, using methanol as feed stock does not show any advantages over biodiesel from ethanol. The single score method is also included in this study in order to identify the best option between two processes of biodiesel production. The global normalization and weighting factor based on eco-taxes are used and it shows that producing biodiesel form ethanol has less environmental load compare to biodiesel from methanol.

Keywords: biodiesel, ethanol, life cycle assessment, methanol, soybean oil

Procedia PDF Downloads 186