Search results for: pyruvic acid

Authors: Meiling Yu, Nadia Rouatbi, Khuloud T. Al-Jamal

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Background: Treatment of neurological disorders with modern medical and surgical approaches remains difficult. Gene therapy, allowing the delivery of genetic materials that encodes potential therapeutic molecules, represents an attractive option. The treatment of brain diseases with gene therapy requires the gene-editing tool to be delivered efficiently to the central nervous system. In this study, we explored the efficiency of different delivery routes, namely intravenous (i.v.), intra-cranial (i.c.), and intra-nasal (i.n.), to deliver stable nucleic acid-lipid particles (SNALPs) containing gene-editing tools namely Cas9 mRNA and sgRNA encoding for GFP as a reporter protein. We hypothesise that SNALPs can reach the brain and perform gene-editing to different extents depending on the administration route. Intranasal administration (i.n.) offers an attractive and non-invasive way to access the brain circumventing the blood–brain barrier. Successful delivery of gene-editing tools to the brain offers a great opportunity for therapeutic target validation and nucleic acids therapeutics delivery to improve treatment options for a range of neurodegenerative diseases. In this study, we utilised Rosa26-Cas9 knock-in mice, expressing GFP, to study brain distribution and gene-editing efficiency of SNALPs after i.v.; i.c. and i.n. routes of administration. Methods: Single guide RNA (sgRNA) against GFP has been designed and validated by in vitro nuclease assay. SNALPs were formulated and characterised using dynamic light scattering. The encapsulation efficiency of nucleic acids (NA) was measured by RiboGreen™ assay. SNALPs were incubated in serum to assess their ability to protect NA from degradation. Rosa26-Cas9 knock-in mice were i.v., i.n., or i.c. administered with SNALPs to test in vivo gene-editing (GFP knockout) efficiency. SNALPs were given as three doses of 0.64 mg/kg sgGFP following i.v. and i.n. or a single dose of 0.25 mg/kg sgGFP following i.c.. knockout efficiency was assessed after seven days using Sanger Sequencing and Inference of CRISPR Edits (ICE) analysis. In vivo, the biodistribution of DiR labelled SNALPs (SNALPs-DiR) was assessed at 24h post-administration using IVIS Lumina Series III. Results: Serum-stable SNALPs produced were 130-140 nm in diameter with ~90% nucleic acid loading efficiency. SNALPs could reach and stay in the brain for up to 24h following i.v.; i.n. and i.c. administration. Decreasing GFP expression (around 50% after i.v. and i.c. and 20% following i.n.) was confirmed by optical imaging. Despite the small number of mice used, ICE analysis confirmed GFP knockout in mice brains. Additional studies are currently taking place to increase mice numbers. Conclusion: Results confirmed efficient gene knockout achieved by SNALPs in Rosa26-Cas9 knock-in mice expressing GFP following different routes of administrations in the following order i.v.= i.c.> i.n. Each of the administration routes has its pros and cons. The next stages of the project involve assessing gene-editing efficiency in wild-type mice and replacing GFP as a model target with therapeutic target genes implicated in Motor Neuron Disease pathology.

Keywords: CRISPR, nanoparticles, brain diseases, administration routes

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Authors: Abdulrahman T. Essa, Ahmed Aied, Omar Hamid, Felicity R. A. J. Rose, Kevin M. Shakesheff

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Biodegradable poly(ester amide)s are promising polymers for biomedical applications such as drug delivery and tissue engineering because of their optimized chemical and physical properties. In this study, we developed a biodegradable polyester amide elastomer poly(serinol sebacate) (PSS) composed of crosslinked networks based on serinol and sebacic acid. The synthesized polymers were characterized to evaluate their chemical structures, mechanical properties, degradation behaviors and in vitro cytocompatibility. Analysis of proton nuclear magnetic resonance and Fourier transform infrared spectroscopy revealed the structure of the polymer. The PSS exhibit excellent solubility in a variety of solvents such as methanol, dimethyl sulfoxide and dimethylformamide. More importantly, the mechanical properties of PSS could be tuned by changing the curing conditions. In addition, the 3T3 fibroblast cells cultured on the PSS demonstrated good cell attachment and high viability.

Keywords: biodegradable, biomaterial, elastomer, mechanical properties, poly(serinol sebacate)

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Authors: Weijie Gu, Sergio Martinez, Hoai Nguyen, Hongtao Xu, Piet Herdewijn, Steven De Jonghe, Kalyan Das

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Nucleotide analogs are used for treating viral infections such as HIV, hepatitis B, hepatitis C, influenza, and SARS-CoV-2. To become polymerase substrates, a nucleotide analog must be phosphorylated by cellular kinases, which are rate-limiting. The goal of this study is to develop dNTP/NTP analogs directly from nucleotides. Tenofovir (TFV) analogs were synthesized by conjugating with natural or unnatural amino acids. It demonstrates that some conjugates act as dNTP analogs, and HIV-1 reverse transcriptase (RT) catalytically incorporates the TFV part as the chain terminator. X-ray structures in complex with HIV-1 RT/dsDNA showed binding of the conjugates at the polymerase active site, however, in different modes in the presence of Mg²⁺ vs. Mn²⁺ ions. The adaptability of the compounds is seemingly essential for catalytic incorporation of TFV by RT. 4d with a carboxyl sidechain demonstrated the highest incorporation. 4e showed weak incorporation and rather behaved as a dNTP-competitive inhibitor. This result advocates the feasibility of designing NTP/dNTP analogs by chemical substitutions to nucleotide analogs.

Keywords: dNTP analogs, nucleotide analogs, polymerase, tenofovir, X-ray structure

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Authors: Rekia. Cherbi, Mokhtar. Saidi, Mohamed. Yousfi, Zhor. Rahmani

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Lawsonia alba (Henna) is widely used in folkloric medicinal for a treatment of various skin diseases such as Eczema (atopic dermatitis), boils and sores. The aim of the present study is to determine the antioxidant activity, total phenolics, flavonoids, and condensed tannins content of extracts from the seeds of Lawsonia. alba grown in Algeria and selected from three different regions (Adrar, Biskra, and Ouargla). Total phenolics content ranged from 68,42 ± 0,54 to 88,31 ± 0,78mg gallic acid equivalents (GAE)/g dry weight, the flavonoids content varied from 1,13 ± 0,0035 to 1,367 ± 0,002mg quercetin equivalents (Q)/ g dry weight and condensed tannins (14,47 ± 0,138 to 25,50 ± 0,076 mg catechin equivalents (CE)/g dry weight). The antioxidant activities of the extracts were evaluated by DPPH assay. The results showed that all extracts from the seeds of Lawsonia. alba seem to be good trappers of radicals, the IC50 values of the extracts ranged between 0,00826 and 0,01 g/l.

Keywords: antioxidant activity, Lawsonia. alba, phenolic compounds, seeds

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Authors: Min-Hwa Lim, Mi-Jeong Park, Ho-Young Jung

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Imidazolium-brominated polyphenylene oxide (Im-bPPO) is based on the functionalization of bromomethylated poly(2,6-dimethyl-1,4-phenylene oxide) (BPPO) using 1-Methylimdazole. For the purpose of long cycle life of vanadium redox battery (VRB), the chemical stability of Im-bPPO, sPPO (sulfonated 2,6-dimethyl-1,4-phenylene oxide) and Fumatech membranes were evaluated firstly in the 0.1M vanadium (V) solution dissolved in 3M sulfuric acid (H2SO4) for 72h, and UV analyses of the degradation products proved that ether bond in PPO backbone was vulnerable to be attacked by vanadium (V) ion. It was found that the membranes had slightly weight loss after soaking in 2 ml distilled water included in STS pressure vessel for 1 day at 200◦C. ATR-FT-IR data indicated before and after the degradation of the membranes. Further evaluation on the degradation mechanism of the menbranes were carried out in Fenton’s reagent solution for 72 h at 50 ◦C and analyses of the membranes before and after degradation confirmed the weight loss of the membranes. The Fumatech membranes exhibited better performance than AEM and CEM, but Nafion 212 still suffers chemical degradation.

Keywords: vanadium redox flow battery, ion exchange membrane, permeability, degradation, chemical stability

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Authors: Delele Worku Ayele, Bing-Joe Hwang

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A method that does not employ hot injection techniques has been developed for the size-tunable synthesis of high-quality CdSe quantum dots (QDs) with a zinc blende structure. In this environmentally benign synthetic route, which uses relatively less toxic precursors, solvents, and capping ligands, CdSe QDs that absorb visible light are obtained. The size of the as-prepared CdSe QDs and, thus, their optical properties can be manipulated by changing the microwave reaction conditions. The QDs are characterized by XRD, TEM, UV-vis, FTIR, time-resolved fluorescence spectroscopy, and fluorescence spectrophotometry. In this approach, the reaction is conducted in open air and at a much lower temperature than in hot injection techniques. The use of microwaves in this process allows for a highly reproducible and effective synthesis protocol that is fully adaptable for mass production and can be easily employed to synthesize a variety of semiconductor QDs with the desired properties. The possible application of the as-prepared CdSe QDs has been also assessed using deposition on TiO2 films.

Keywords: average life time, CdSe QDs, microwave (MW), mass production oleic acid, Na2SeSO3

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Authors: Richa Bhardwaj

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Tecomella undulata (Sm.) Seem is a monotypic genus belonging to family Bignoniaceae. The plant holds tremendous potential of medicinal value and has been traditionally used in various ailments like syphilis, leukoderma, blood disorders to name a few. The plant has gained prominence due to the presence of some prominent secondary metabolites. The present study focuses on the GC-MS analysis of leaf extracts of T. undulata which revealed the presence of certain bioactive compounds like stigmasterol, sitosterol, thiazoline, phytol, pthalic acid, methyl alpha ketopalmitate and so forth. A total of about 20 bioactive compounds were identified from the leaf extract spectra. Antimicrobial activity of the leaf extract was assayed against pathogenic bacteria and fungi. The alkaloids from leaf extracts showed antimicrobial activity against E.coli and B.subtilis. The flavonoids from leaves showed positive activity against Penicillium species and Candida albicans. The study thus infers that the presence of bioactive components may be the principle behind the antimicrobial property of different plant parts and therefore Tecomella forms a potential plant for herbal drug formulation.

Keywords: Tecomella undulata, bioactive compounds, GC-MS, antimicrobial activity

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Authors: Benyoucef Amel, Benmechernene Zineb, Kihal Mebrouk

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One strain (V1) of Leuconostoc mesonteroides was isolated from goat’s milk collected from El Bayadh which is located in the west of Algeria and was characterized by phenotypic and biochemical methods. This strain was tested for their antimicrobial activity against indicator bacteria (Staphylococcus aureus ATCC 43300, Listeria innocua ATCC 33090, Listeria ivanovii ATCC 19119) and was evaluated for certain properties relevant to probiotic including acid resistance (pH 2 ; 3and 4), bile tolerance at 0.5%, 1% and 2%, pepsin resistance 3mg/ml at pH 2 and 3, hemolytic activity and antibiotics sensitivity. Our results revealed the strain V1 showed antagonistic activity against Staphylococcus aureus, Listeria innocua and Listeria ivanovii, due to a production of proteinous nature substances. The strain was resistant to pH 3 and 4, bile salts at 0.5%, 1% and 2% and pepsin at pH 3; and was γ-hemolytic and susceptible to four antibiotics: Chloramphenicol, pristinamycin, Clindamycin and Lincomycin. These results may be considered the strain V1 as suitable probiotic candidate.

Keywords: antimicrobial, goat‘s milk, Leuconostoc, probiotic

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Authors: Parcha Sreenivasa Rao, P. Lakshmi

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Diabetes Mellitus is metabolic disorder, characterized by high glucose levels in the blood due to one of the reason i.e., the death of β cells. The lack of β cells leads to the reduced insulin levels. The β cell death generally occurs due to apoptosis induced by the several cytokines. IL-1β, IFN- ϒ and TNF –α cytokines that are generally cause apoptosis to the β cell. The nutrient based apoptosis is generally seen with high glucose and free fatty acids. It is also noted that the β cell death triggered by Fas ligand and its receptor Fas at the surface of the activated CD8+ T- lymphocytes. Reports also reveal that the β cell apoptosis is under control of the transcription factors NF-kB and STAT- 1. The arresting or opposing of the β cell apoptosis can be overcome by the different growth factors like GLP-1, growth hormone, prolactin, VEGF, Dipeptidyl peptidase-4, Vildagliptin, suberoylanilidehydroxamic acid, trichistatin-A, XIAP, Bcl-2, FGF-21. Present investigation explains antiapoptotic property of the β cells derived from the mesenchymal stem cells of umbilical cord.

Keywords: stem cells, umblical cord, diabetes, apoptosis

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Authors: Ramim Tanver Rahman, Muhammad Mahbub Sobhan, M. A. Alim

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This study reports on processing of biscuits using skinned, treated and dried cassava flour. Five samples of biscuits S2, S3, S4, S5, and S6 containing 8, 16, 24, 32, and 40% cassava flour with wheat flour and a control sample (S1) containing no cassava flour were processed. The weights of all the biscuit samples were higher than that of control biscuit. The biscuit containing cassava flour was lower width than the control biscuit. The spread ratio of biscuits with 16% cassava flour was higher than other combinations of cassava flour. No remarkable changes in moisture content, peroxide value, fatty acid value, texture, and flavor were observed up to 4 months of storage in ambient conditions (27° to 35°C). A decreasing trend in color, flavor, texture and overall acceptability was observed with the increased incorporation of cassava flour. The sample S1 (no cassava flour) secured the highest overall acceptability and sample S6 (40% cassava flour) obtained the lowest overall acceptability. It is recommended that good quality cassava flour fortified biscuits may be processed in industrial-scale substituting the wheat flour by cassava flour up to 24% levels.

Keywords: cassava flour, wheat flour, shelf life, spread ratio, storage, biscuit

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

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In Arabidopsis, several genes encoding proteins with ankyrin repeats and trans-membrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrin repeats and trans-membrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number of trans-membrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: alternative splicing, ankyrin repeats, trans-membrane domains, arabidopsis

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Authors: S. K. Thind, Neha Gupta

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Glycine betaine (N, N’, N’’– trimethyl glycine), (GB) as aqueous solution (100 mM) containing 0.1% TWEEN-20 (Ploythylene glycol sorbitan monolaurate) was sprayed on selected nineteen wheat genotypes at maximum tillering and anthesis stages. Water-deficit conditions resulted in lipid peroxidation. GB applications reduced lipid peroxidation in all wheat genotypes at both the stages. Catalase (CAT) activity was recorded more in control than under stressed conditions in selected wheat genotypes at both the stages; GB had no effect. The ascorbic acid content in leaves of selected genotypes increased under water deficit. A genotypic variability in Ascorbate peroxidase (APx) activity was recorded and GB treatment decreased it. Superoxide dismutase (SOD) activity was increased significantly under water-deficit at both stages in all genotypes. In present study, prolonged water-deficit conditions caused CAT deficiency/suppression which was compensated by APX and SOD; and GB exogenous application mitigated negative effect of water-deficit stress on lipid peroxidation.

Keywords: glycine-betaine, lipid peroxidation, ROS, water deficit stress

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Authors: Reza Pashaei, Reda Dzingelevičienė

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An efficient, reliable, and sensitive multiclass analytical method has been expanded to simultaneously determine 15 human pharmaceutical residues in fish and shrimp tissue samples by ultra-high-performance liquid chromatography-tandem mass spectrometry. The investigated compounds comprise ten classes, namely analgesic, antibacterial, anticonvulsant, cardiovascular, fluoroquinolones, macrolides, nonsteroidal anti-inflammatory, penicillins, stimulant, and sulfonamide. A simple liquid extraction procedure based on 0.1% formic acid in methanol was developed. Chromatographic conditions were optimized, and mobile phase namely 0.1 % ammonium acetate (A), and acetonitrile (B): 0 – 2 min, 15% B; 2 – 5 min, linear to 95% B; 5 – 10 min, 95% B; and 10 – 12 min was obtained. Limits of detection and quantification ranged from 0.017 to 1.371 μg/kg and 0.051 to 4.113 μg/kg, respectively. Finally, amoxicillin, azithromycin, caffeine, carbamazepine, ciprofloxacin, clarithromycin, diclofenac, erythromycin, furosemide, ibuprofen, ketoprofen, naproxen, sulfamethoxazole, tetracycline, and triclosan were quantifiable in fish and shrimp samples.

Keywords: fish, liquid chromatography, mass spectrometry, pharmaceuticals, shrimp, solid-phase extraction

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Authors: Ali Bahri Lubis

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The study of dioxygenase enzymatic mechanism on tryptophan oxidation has been a wide interest since the reaction is rate-limiting step of kynurenine pathway. In this research, observation of tryptophan oxidation through h-IDO enzyme along with synthesis of enzyme products was conducted in order to comprehend how the enzyme works on distinct substrates. UV-vis spectrophotometry, LC-MS, H-NMR and HSQC measurement were carried out to characterise enzyme product. It is found that while tryptophan was oxidised to form Nformylkynurenine (NFK) as a major product and hydroxypyrroloindole amine carboxylic acid (HPIC) in cis and trans confirmed in HSQC, N-methyl tryptophan substrate was converted to NFK and trans HPIC only. Other intriguing results showed that 5-hydroxy- tryptophan and Stryptophan was degraded to become NFK and epoxide cyclic respectively. The formation of NFK was considered through dioxygenation pathway, however HPIC was formed via monooxygenation. The epoxide cyclic—considered as intermediate compound in the mechanism— from S-tryptophan was not able to cleave the epoxide ring since bond energy of epoxide was probably much stronger. This validates the enzymatic mechanism where the intermediate compound in the enzymatic mechanism is epoxide cyclic.

Keywords: tryptophan oxidation, heme-dioxygenases, N-formylkynurenine, hydroxypyrrroloindoleamine, monooxidation

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Authors: B. Benalioua, I. Benyamina, A. Bentouami, B. Boury

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The objective of this study is based on the synthesis of a new photocatalyst based on TiO2 and its application in the photo-degradation of an acid dye under the visible light. The material obtained was characterized by different techniques like diffuse reflectance UV–Vis spectroscopy (DRS), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The photocatalytic efficiency of the Bi, N co-doped TiO2 treated at 600°C for 1 h was tested on the Indigo Carmine under the irradiation of visible light and compared with that of the commercial titanium oxide TiO2-P25 (Degussa). The XRD characterization of the material Bi -N- TiO2 (600°C) revealed the presence of the anatase phase and the absence of the rutile phase in comparison of the TiO2 P25 diffractogram. Characterization by UV- visible diffuse reflection (DRS) material showed that the Bi-N-TiO2 exhibits redshift (move visible) relative to commercial titanium oxide TiO2-P25, this property promises a photocatalytic activity of Bi-N-TiO2 under visible light. Indeed, the efficiency of photocatalytic Bi-N-TiO2 as a visible light is shown by a complete discoloration of indigo carmine solution of 16 mg/L after 40 minutes, whereas with the P25-TiO2 discoloration is achieved after 90 minutes.

Keywords: POA, heterogeneous photocatalysis, TiO2, co-doping

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Authors: Priya Arora, Ashutosh Mishra

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Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

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Authors: Peter O. Osifo, Hein W. J. P. Neomagus

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In this study, a predicted pH model was used to determine adsorption equilibrium properties of copper, lead, zinc and cadmium. Chitosan was prepared from the exoskeleton of Cape rock-lobsters, collected from the surroundings of Cape Town, South Africa. The beads were cross-linked with gluteraldehyde to restore its chemical stability in acid media. The chitosan beads were characterized; the beads water contents and pKa varied in the range of 90-96% and 4.3-6.0 respectively and the degree of crosslinking for the beads was 18%. A pH-model, which described the reversibility of the metal adsorbed onto the beads, was used to predict the equilibrium properties of copper, lead, zinc and cadmium adsorption onto the cross-linked beads. The model accounts for the effect of pH and the important model parameters; the equilibrium adsorption constant (Kads) and to a lesser extent the adsorbent adsorption capacity (qmax). The adsorption equilibrium constant for copper, lead, zinc and cadmium were found to be 2.58×10-3, 2.22×0-3, 9.55×0-3, and 4.79×0-3, respectively. The adsorbent maximum capacity was determined to be 4.2 mmol/g.

Keywords: chitosan beads, adsorption, heavy metals, waste water

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Authors: Trenten Theis, Trevor Daubert, Kennedy Kluthe, Austin Nuxoll

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Staphylococcus aureus is a gram-positive bacterium responsible for an estimated 23,000 deaths in the United States and 25,000 deaths in the European Union annually. Recurring S. aureus bacteremia is associated with biofilm-mediated infections and can occur in 5 - 20% of cases, even with the use of antibiotics. Despite these infections being caused by drug-susceptible pathogens, they are surprisingly difficult to eradicate. One potential explanation for this is the presence of persister cells—a dormant type of cell that shows a high tolerance to antibiotic treatment. Recent studies have shown a connection between low intracellular ATP and persister cell formation. Specifically, this decrease in ATP, and therefore increase in persister cell formation, is due to an interrupted tricarboxylic acid (TCA) cycle. However, S. aureus persister cells’ role in pathogenesis remains unclear. Initial studies have shown that a fumC (TCA cycle gene) knockout survives challenge from aspects of the innate immune system better than wild-type S. aureus. Specifically, challenges from two antimicrobial peptides--LL-37 and hBD-3—show a log increase in survival of the fumC::N∑ strain compared to wild type S. aureus after 18 hours. Furthermore, preliminary studies show that the fumC knockout has a log more survival within a macrophage. These data lead us to hypothesize that the fumC knockout is better suited to other aspects of the innate immune system compared to wild-type S. aureus. To further investigate the mechanism for increased survival of fumC::N∑ within a macrophage, we tested bacterial growth in the presence of reactive oxygen species (ROS), reactive nitrogen species (RNS), and a low pH. Preliminary results suggest that the fumC knockout has increased growth compared to wild-type S. aureus in the presence of all three antimicrobial factors; however, no difference was observed in any single factor alone. To investigate survival within a host, a nine-day biofilm-associated catheter infection was performed on 6–8-week-old male and female C57Bl/6 mice. Although both sexes struggled to clear the infection, female mice were trending toward more frequently clearing the HG003 wild-type infection compared to the fumC::N∑ infection. One possible reason for the inability to reduce the bacterial burden is that biofilms are largely composed of persister cells. To test this hypothesis further, flow cytometry in conjunction with a persister cell marker was used to measure persister cells within a biofilm. Cap5A (a known persister cell marker) expression was found to be increased in a maturing biofilm, with the lowest levels of expression seen in immature biofilms and the highest expression exhibited by the 48-hour biofilm. Additionally, bacterial cells in a biofilm state closely resemble persister cells and exhibit reduced membrane potential compared to cells in planktonic culture, further suggesting biofilms are largely made up of persister cells. These data may provide an explanation as to why infections caused by antibiotic-susceptible strains remain difficult to treat.

Keywords: antibiotic tolerance, Staphylococcus aureus, host-pathogen interactions, microbial pathogenesis

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Authors: Alexander Hudson, Shaogang Gong

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Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive, time-consuming analytical methods to visualise detailed protein conformation. In this study, we demonstrate that it is possible to make accurate (≥80%) predictions of protein class and architecture from structures determined at low (>3A) resolution, using a deep convolutional neural network trained on high-resolution (≤3A) structures represented as 2D matrices. Thus, we provide proof of concept for high-speed, low-cost protein structure classification at low resolution, and a basis for extension to prediction of function. We investigate the impact of the input representation on classification performance, showing that side-chain information may not be necessary for fine-grained structure predictions. Finally, we confirm that high resolution, low-resolution and NMR-determined structures inhabit a common feature space, and thus provide a theoretical foundation for boosting with single-image super-resolution.

Keywords: transfer learning, protein distance maps, protein structure classification, neural networks

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Authors: Lav Kesharwani, Nalini Shankar, A. K. Gupta

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A serial number is a unique code assigned for identification of a single unit. Serial number are present on many objects. In an attempt to hide the identity of the numbered item, the numbers are often obliterated or removed by mechanical methods. The present work was carried out with an objective to develop less toxic, less time consuming, more result oriented chemical etching reagent for restoration of serial number on the copper metal plate. Around nine different reagents were prepared using different combination of reagent along with standard reagent and it was applied over 50 erased samples of copper metal and compared it with the standard reagent for restoration of erased marks. After experiment, it was found that the prepared Etching reagent no. 3 (10 g FeCl3 + 20 ml glacial acetic acid + 100 ml distilled H2O) showed the best result for restoration of erased serial number on the copper metal plate .The reagent was also less toxic and less time consuming as compared to standard reagent (19 g FeCl3 + 6 ml cans. HCl + 100 ml distilled H2O).

Keywords: serial number restoration, copper plate, obliteration, chemical method

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Authors: Benedict O. Ayomanor, Cookey Iyen, Ifeoma S. Iyen

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Rice hull (RH) biomass product gives feasible silica for exact temperature and period. The minimal fabrication price turns its best feasible produce to metallurgical grade silicon (MG-Si). In this work, to avoid ecological worries extending from CO₂ release to oil leakage on water and land, or nuclear left-over pollution, all finally add to the immense topics of ecological squalor; high purity silicon > 98.5% emerge set from rice hull ash (RHA) by solid-liquid removal. The RHA derived was purified by nitric and hydrochloric acid solutions. Leached RHA sieved, washed in distilled water, and desiccated at 1010ºC for 4h. Extra cleansing was achieved by carefully mixing the SiO₂ ash through Mg dust at a proportion of 0.9g SiO₂ to 0.9g Mg, galvanised at 1010ºC to formula magnesium silicide. The solid produced was categorised by X-ray fluorescence (XRF), X-ray diffractometer (XRD), and Fourier transformation infrared (FTIR) spectroscopy. Elemental analysis using XRF found the percentage of silicon in the material is approximately 98.6%, main impurities are Mg (0.95%), Ca (0.09%), Fe (0.3%), K (0.25%), and Al (0.40%).

Keywords: siliceous, leached, biomass, solid-liquid extraction

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Authors: Olufunke O. Ezekiel, Adenike O. Ogunshe, Omotola F. Olagunju, Arinola O. Falola

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Studies were conducted on fermentation of tamarind seed for production of food condiment. Fermentation followed the conventional traditional method of fermented locust bean (iru) production and was carried out over a period of three days (72 hours). Samples were withdrawn and analysed for proximate composition, pH, titratable acidity, tannin content, phytic acid content and trypsin inhibitor activity using standard methods. Effects of fermentation on proximate composition, anti-nutritional factors and sensory properties of the seed were evaluated. All data were analysed using ANOVA and means separated using Duncan multiple range test. Microbiological analysis to identify and characterize the microflora responsible for the fermentation of the seed was also carried out. Fermentation had significant effect on the proximate composition on the fermented seeds. As fermentation progressed, there was significant reduction in the anti-nutrient contents. Organisms isolated from the fermenting tamarind seeds were identified as non-pathogenic and common with fermented legumes.

Keywords: condiment, fermentation, legume, tamarind seed

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Authors: Ewa Brychcy, Natalia Ulbin-Figlewicz, Dominika Kulig, Żaneta Król, Andrzej Jarmoluk

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Acidic electrolyzed water (AEW) is an alternative with environmentally friendly broad spectrum microbial decontamination. It is produced by membrane electrolysis of a dilute NaCl solution in water ionizers. The aim of the study was to evaluate the effectiveness of low-concentrated AEW in reducing selected foodborne pathogens and to examine its bactericidal effect on cellular structures of Escherichia coli. E. coli and S. aureus cells were undetectable after 10 minutes of contact with electrolyzed salt solutions. Non-electrolyzed solutions did not inhibit the growth of bacteria. AE water was found to destroy the cellular structures of the E. coli. The use of more concentrated salt solutions and prolonged electrolysis time from 5 to 10 minutes resulted in a greater changes of rods shape as compared to the control and non-electrolyzed NaCl solutions. This research showed that low-concentrated acid electrolyzed water is an effective method to significantly reduce pathogenic microorganisms and indicated its potential application for decontamination of meat.

Keywords: acidic electrolyzed water, foodborne pathogens, meat decontamination, membrane electrolysis

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Authors: N. Marzban, J. K. Heydarzadeh M. Pourmohammadbagher, M. H. Hatami, A. Samia

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A nano-alumina-zirconia composite catalyst was synthesized by a simple aqueous sol-gel method using AlCl₃.6H₂O and ZrCl₄ as precursors. Thermal decomposition of the precursor and subsequent formation of γ-Al₂O₃ and t-Zr were investigated by thermal analysis. XRD analysis showed that γ-Al₂O₃ and t-ZrO₂ phases were formed at 700 °C. FT-IR analysis also indicated that the phase transition to γ-Al₂O₃ occurred in corroboration with X-ray studies. TEM analysis of the calcined powder revealed that spherical particles were in the range of 8-12 nm. The nano-alumina-zirconia composite particles were mesoporous and uniformly distributed in their crystalline phase. In order to measure the catalytic activity, esterification reaction was carried out. Biodiesel, as a renewable fuel, was formed in a continuous packed column reactor. Free fatty acid (FFA) was esterified with ethanol in a heterogeneous catalytic reactor. It was found that the synthesized γ-Al₂O₃/ZrO₂ composite had the potential to be used as a heterogeneous base catalyst for biodiesel production processes.

Keywords: nano alumina-zirconia, composite catalyst, thin film, biodiesel

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Authors: Afiqah Shafify Amran, Siti Aisyah Shamsudin, Nurul Yuziana Mohd Yusof

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Cadmium Sulphide (CdS) from group II-IV quantum dots with good optical properties was successfully synthesized by using the simple colloidal method. Capping them with ligand Polyethylinamine (PEI) alters the surface defect of CdS while, thioglycolic acid (TGA) was added to the reaction as a stabilizer. Due to their cytotoxicity, we decided to conjugate them with the protein cage nanoparticles. In this research, we used capsid of Cowpea Chlorotic Mottle Virus (CCMV) to package the CdS because they have the potential to serve in drug delivery, cell targeting and imaging. Adding Sodium Hydroxide (NaOH) changes the pH of the systems hence the isoelectric charge is adjusted. We have characterized and studied the morphology and the optical properties of CdS and CdS-CCMV by transmitted electron microscopic (TEM), UV-Vis spectroscopy, photoluminescence spectroscopy, UV lamp and Fourier transform infrared spectroscopy (FTIR), respectively. The results obtained suggest that the protein cage nanoparticles do not affect the optical properties of CdS.

Keywords: cadmium sulphide, cowpea chlorotic mottle virus, protein cage nanoparticles, quantum dots

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Authors: Abdelsabour G. A. Khaled, Ahmed W. A. Abdalla And Sabry Y. M. Mahmoud

Abstract:

Banana plants showing typical mosaic and yellow stripes on leaves as symptoms were collected from Assiut Governorate in Egypt. The causal agent was identified as Cucumber mosaic virus (CMV) on the basis of symptoms, transmission, serology, transmission electron microscopy and reverse transcription polymerase chain reaction (RT-PCR). Coat protein (CP) gene was amplified using gene specific primers for coat protein (CP), followed by cloning into desired cloning vector for sequencing. In this study the CMV was transmitted into propagation host either by aphid or mechanically. The transmission was confirmed through Direct Antigen Coating Enzyme Linked Immuno Sorbent Assay (DAC-ELISA). Analysis of the 120 deduced amino acid sequence of the coat protein gene revealed that the EG-A strain of CMV shared from 97.50 to 98.33% with those strains belonging to subgroup IA. The cluster analysis grouped the Egyptian isolate with strains Fny and Ri8 belonging sub-group IA. It appears that there occurs a high incidence of CMV infecting banana belonging to IA subgroup in most parts of Egypt.

Keywords: banana, CMV, transmission, CP gene, RT-PCR

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Authors: Luguang Qi, Chuang Xie

Abstract:

In recent years, there has been an increase in the number of reports on cocrystal polymorphism and stoichiomorphism. However, the research on the factors that influence these phenomena is limited. Herein, picolinamide (PAM), nicotinamide (NAM), and isonicotinamide (INA) were selected as co-formers to form multicomponent solids with 4-chloro-3-sulfamoylbenzoic acid (CSBA). Six new cocrystal forms of CSBA were discovered, and their crystal structures were determined. It was found that PAM and NAM can only form one cocrystal with CSBA, while INA can form up to four cocrystals, including both cocrystal polymorphism and stoichiomorphism. Molecular electrostatic potential analysis and crystal structure analysis showed that the functional group position of PAM limited the diversity of cocrystal synthons, while the lattice energy limited the diversity of cocrystal synthons when NAM acted as a co-former. Only INA was not subject to these restrictions when forming cocrystals. Finally, the influence of solvents on cocrystals was illustrated by determining the ternary phase diagrams. The mechanism of two similar solvents, ethyl acetate, and acetone, controlling the crystallization of cocrystal polymorphism was analyzed by molecular simulations.

Keywords: cocrystal polymorphism, cocrystal stoichiomorphism, phase diagram, molecular simulation

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Authors: Elham Rezaee, Sayyed Abbas Tabatabai

Abstract:

Dual inhibition of COX-2 and sEH enzymes represents one of the distinct pharmaceutical approaches for the treatment of inflammation, pain, cancers, and other diseases. The discovery of these inhibitors for treatment is a great deal of attention because of some advantages such as increased efficacy, a promising safety profile, ease of formulation, and better target engagement. In this research, based on the structure-activity relationship of COX-2 and sEH inhibitors, some amide derivatives with oxadiazole and dihydropyrimidinone rings against sEH and COX-2 enzymes were developed. The designed compounds showed high affinity to the active site of both enzymes in docking studies and were synthesized in good yield and characterized by IR, Mass, 1HNMR, and 13CNMR. All of the novel compounds exhibited considerable in-vitro sEH and COX-2 inhibitory activities in comparison with 12-(3-Adamantan-1-yl-ureido)- dodecanoic acid and celecoxib (a potent urea-based sEH inhibitor and selective nonsteroidal anti-inflammatory drug, respectively). Ethyl 6-methyl-4-(4-(4-(methylsulfonyl)benzamido)phenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate was found to be the most selective COX-2 inhibitor (COX-2/COX-1 ratio: 683) with IC50 value of 2.1 nM targeting sEH enzyme.

Keywords: COX-2, dual inhibitors, sEH, synthesis

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Authors: Patricia O. Carvalho, Marcia C. F. Messias, Laura Credidio, Carlos A. R. Martinez

Abstract:

Lipidomic strategy can provide important information regarding cancer pathogenesis mechanisms and could reveal new biomarkers to enable early diagnosis of rectal adenocarcinoma (RAC). This study set out to evaluate lipoperoxidation biomarkers, and lipidomic signature by gas chromatography (GC) and electrospray ionization-qToF-mass spectrometry (ESI-qToF-MS) combined with multivariate data analysis in plasma from 23 RAC patients (early- or advanced-stages cancer) and 18 healthy controls. The most abundant ions identified in the RAC patients were those of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) while those of lisophosphatidylcholine (LPC), identified as LPC (16:1), LPC (18:1) and LPC (18:2), were down-regulated. LPC plasmalogen containing palmitoleic acid (LPC (P-16:1)), with highest VIP score, showed a low tendency in the cancer patients. Malondialdehyde plasma levels were higher in patients with advanced cancer (III/IV stages) than in the early stages groups and the healthy group (p<0.05). No differences in F2-isoprostane levels were observed between these groups. This study shows that the reduction in plasma levels of LPC plasmalogens associated to an increase in MDA levels may indicate increased oxidative stress in these patients and identify the metabolite LPC (P-16:1) as new biomarkers for RAC.

Keywords: biomarkers, lipidomic, plasmalogen, rectal adenocarcinoma

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Authors: Saha Saradindu, Das Payel, Somdeb BoseDasgupta

Abstract:

Tuberculosis caused by Mycobacteria tuberculosis is a dreadful disease and more so with the advent of extreme and total drug-resistant species. Mycobacterial pathogenesis is an ever-changing paradigm from phagosome maturation block to phagosomal escape into macrophage cytosol and finally acid tolerance and survival inside the lysosome. Mycobacteria are adept at subverting the host immune response by highjacking host cell signaling and secreting virulence factors. One such virulence factor is a ser/thr kinase; Protein kinase G (PknG), which is known to prevent phagosome maturation. The host substrates of PknG, allowing successful pathogenesis still remain an enigma. Hence we carried out a comparative phosphoproteomic screen and identified a number of substrates phosphorylated by PknG. We characterized some of these substrates in vivo and in vitro and observed that PknG mediated phosphorylation of these substrates leads to reduced TNFa production as well as decreased response to TNFa induced macrophage necroptosis, thus enabling mycobacterial survival and proliferation.

Keywords: mycobacteria, Protein kinase G, phosphoproteomics, necroptosis

Procedia PDF Downloads 146