Search results for: plasma-assisted molecular beam epitaxy

Authors: Joshua N. Edokpayi, John O. Odiyo, Titus A. M. Msagati, Elizabeth O. Popoola

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Polycyclic aromatic hydrocarbons (PAHs) are very toxic and persistent environmental contaminants. This study was undertaken to assess the concentrations and possible sources of 16 PAHs classified by the United State Environmental Protection Agency as priority pollutants in Mvudi and Nzhelele Rivers and sediments. Effluents from Thohoyandou wastewater treatment plant and Siloam waste stabilization ponds were also investigated. Diagnostic ratios were used to evaluate the possible sources of PAHs. PAHs in the water samples were extracted using 1:1 dichloromethane and n-hexane mixtures, while those in the sediment samples were extracted with 1:1 acetone and dichloromethane using ultrasonication method. The extracts were purified using SPE technique and reconstituted in n-hexane before analyses with GC-TOF-MS. The results obtained indicate the prevalence of high molecular weight PAHs in all the samples. PAHs concentrations in water and sediment samples from all the sampling sites were in the range of 13.174-26.382 mg/L and 27.10-55.93 mg/kg, respectively. Combustion of biomass was identified as the major possible source of PAHs. Effluents from wastewater treatment facilities were also considered as major anthropogenic contributions to the levels of PAHs determined in both river waters and sediments. Mvudi and Nzhelele Rivers show moderate to high contamination level of PAHs.

Keywords: polycyclic aromatic hydrocarbon, rivers, sediments, wastewater effluents

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Authors: Joseph E. Estevez, Mahdi Ghazizadeh, James G. Ryan, Ajit D. Kelkar

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Radiation shielding is an obstacle in long duration space exploration. Boron Nitride Nanotubes (BNNTs) have attracted attention as an additive to radiation shielding material due to B10’s large neutron capture cross section. The B10 has an effective neutron capture cross section suitable for low energy neutrons ranging from 10-5 to 104 eV and hydrogen is effective at slowing down high energy neutrons. Hydrogenated BNNTs are potentially an ideal nanofiller for radiation shielding composites. We use Molecular Dynamics (MD) Simulation via Material Studios Accelrys 6.0 to model the Young’s Modulus of Hydrogenated BNNTs. An extrapolation technique was employed to determine the Young’s Modulus due to the deformation of the nanostructure at its theoretical density. A linear regression was used to extrapolate the data to the theoretical density of 2.62g/cm3. Simulation data shows that the hydrogenated BNNTs will experience a 11% decrease in the Young’s Modulus for (6,6) BNNTs and 8.5% decrease for (8,8) BNNTs compared to non-hydrogenated BNNT’s. Hydrogenated BNNTs are a viable option as a nanofiller for radiation shielding nanocomposite materials for long range and long duration space exploration.

Keywords: boron nitride nanotube, radiation shielding, young modulus, atomistic modeling

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Authors: Kalaumari Mayoral-Peña, Ana I. Montejano-Montelongo, Josué Reyes-Muñoz, Gonzalo A. Ortiz-Mancilla, Mayrin Rodríguez-Cruz, Víctor Hernández-Villalobos, Jesús A. Guzmán-López, Santiago García-Jacobo, Iván Licona-Vázquez, Grisel Fierros-Romero, Rosario Flores-Vallejo

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The group B-lactamic antibiotics include some of the most frequently used small drug molecules against bacterial infections. Nevertheless, an alarming decrease in their efficacy has been reported due to the emergence of antibiotic-resistant bacteria. Infections caused by bacteria expressing extended Spectrum B-lactamases (ESBLs) are difficult to treat and account for higher morbidity and mortality rates, delayed recovery, and high economic burden. According to the Global Report on Antimicrobial Resistance Surveillance, it is estimated that mortality due to resistant bacteria will ascend to 10 million cases per year worldwide. These facts highlight the importance of developing low-cost and readily accessible detection methods of drug-resistant ESBLs bacteria to prevent their spread and promote accurate and fast diagnosis. Bacterial detection is commonly done using molecular diagnostic techniques, where PCR stands out for its high performance. However, this technique requires specialized equipment not available everywhere, is time-consuming, and has a high cost. Loop-Mediated Isothermal Amplification (LAMP) is an alternative technique that works at a constant temperature, significantly decreasing the equipment cost. It yields double-stranded DNA of several lengths with repetitions of the target DNA sequence as a product. Although positive and negative results from LAMP can be discriminated by colorimetry, fluorescence, and turbidity, there is still a large room for improvement in the point-of-care implementation. DNA origami is a technique that allows the formation of 3D nanometric structures by folding a large single-stranded DNA (scaffold) into a determined shape with the help of short DNA sequences (staples), which hybridize with the scaffold. This research aimed to generate DNA origami structures using LAMP products as scaffolds to improve the sensitivity to detect ESBLs in point-of-care diagnosis. For this study, the coding sequence of the CTM-X-15 ESBL of E. coli was used to generate the LAMP products. The set of LAMP primers were designed using PrimerExplorerV5. As a result, a target sequence of 200 nucleotides from CTM-X-15 ESBL was obtained. Afterward, eight different DNA origami structures were designed using the target sequence in the SDCadnano and analyzed with CanDo to evaluate the stability of the 3D structures. The designs were constructed minimizing the total number of staples to reduce costs and complexity for point-of-care applications. After analyzing the DNA origami designs, two structures were selected. The first one was a zig-zag flat structure, while the second one was a wall-like shape. Given the sequence repetitions in the scaffold sequence, both were able to be assembled with only 6 different staples each one, ranging between 18 to 80 nucleotides. Simulations of both structures were performed using scaffolds of different sizes yielding stable structures in all the cases. The generation of the LAMP products were tested by colorimetry and electrophoresis. The formation of the DNA structures was analyzed using electrophoresis and colorimetry. The modeling of novel detection methods through bioinformatics tools allows reliable control and prediction of results. To our knowledge, this is the first study that uses LAMP products and DNA-origami in combination to delect ESBL-producing bacterial strains, which represent a promising methodology for diagnosis in the point-of-care.

Keywords: beta-lactamases, antibiotic resistance, DNA origami, isothermal amplification, LAMP technique, molecular diagnosis

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Authors: Kave Moloudi, Heidi Abrahamse, Blassan P. George

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Radiotherapy (RT) and photodynamic therapy (PDT) are both forms of cancer treatment that aim to kill cancer cells while minimizing damage to healthy tissue. The similarity between RT and PDT lies in their mechanism of action. Both treatments use energy to damage cancer cells. RT uses high-energy radiation to damage the DNA of cancer cells, while PDT uses light energy to activate a photosensitizing agent, which produces reactive oxygen species (ROS) that damage the cancer cells. Both treatments require careful planning and monitoring to ensure the correct dose is delivered to the tumor while minimizing damage to surrounding healthy tissue. They are also often used in combination with other treatments, such as surgery or chemotherapy, to improve overall outcomes. However, there are also significant differences between RT and PDT. For example, RT is a non-invasive treatment that can be delivered externally or internally, while PDT requires the injection of a photosensitizing agent and the use of a specialized light source to activate it. Additionally, the side effects and risks associated with each treatment can vary. In this review, we focus on generalizing the 6Rs of radiobiology in PDT, which can open a window for the clinical application of Radio-photodynamic therapy with minimum side effects. Furthermore, this review can open new insight to work on and design new radio-photosensitizer agents in Radio-photodynamic therapy.

Keywords: radiobiology, photodynamic therapy, radiotherapy, 6Rs in radiobiology, ROS, DNA damages, cellular and molecular mechanism, clinical application.

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Authors: Nour El Houda Bensiradj, Nafila Zouaghi, Taha Bensiradj

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The pollution of water resources is characterized by the presence of microorganisms, chemicals, or industrial waste. Generally, this waste generates effluents containing large quantities of heavy metals, making the water unsuitable for consumption and causing the death of aquatic life and associated biodiversity. Currently, it is very important to assess the impact of heavy metals in water pollution as well as the processes for treating and reducing them. Among the methods of water treatment and disinfection, we mention the complexation of metal ions using ligands which serve to precipitate and subsequently eliminate these ions. In this context, we are interested in the study of complexes containing heavy metals such as zinc, nickel, and cadmium, which are present in several industrial discharges and are discharged into water sources. We will use the ligands of triethanolamine (TEA) and nitrilotriacetic acid (NTA). The theoretical study is based on molecular modeling, using the density functional theory (DFT) implemented in the Gaussian 09 program. The geometric and energetic properties of the above complexes will be calculated. Spectral properties such as infrared, as well as reactivity descriptors, and thermodynamic properties such as enthalpy and free enthalpy will also be determined.

Keywords: heavy metals, NTA, TEA, DFT, IR, reactivity descriptors

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Authors: Haolun Sun, Ping Wang, Mei Wu, Meng Zhang, Bin Hou, Ling Yang, Xiaohua Ma, Yue Hao

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Gallium nitride (GaN) is an attractive material for next-generation power devices. It is noted that the performance of GaN-based high electron mobility transistors (HEMTs) is always limited by the self-heating effect. In response to the problem, integrating devices with polycrystalline diamond (PCD) has been demonstrated to be an efficient way to alleviate the self-heating issue of the GaN-based HEMTs. Among all the heat-spreading schemes, using PCD to cap the epitaxial layer before the HEMTs process is one of the most effective schemes. Now, the mainstream method of fabricating the PCD-capped HEMTs is to deposit the diamond heat-spreading layer on the AlGaN surface, which is covered by a thin nucleation dielectric/passivation layer. To achieve the pattern etching of the diamond heat spreader and device preparation, we selected SiN as the hard mask for diamond etching, which was deposited by plasma-enhanced chemical vapor deposition (PECVD). The conventional diamond etching method first uses F-based etching to remove the SiN from the special window region, followed by using O₂/Ar plasma to etch the diamond. However, the results of the scanning electron microscope (SEM) and focused ion beam microscopy (FIB) show that there are lots of diamond pillars on the etched diamond surface. Through our study, we found that it was caused by the high roughness of the diamond surface and the existence of the overlap between the diamond grains, which makes the etching of the SiN hard mask insufficient and leaves micro-masks on the diamond surface. Thus, a cyclic etching method was proposed to solve the problem of the residual SiN, which was left in the F-based etching. We used F-based etching during the first step to remove the SiN hard mask in the specific region; then, the O₂/Ar plasma was introduced to etch the diamond in the corresponding region. These two etching steps were set as one cycle. After the first cycle, we further used cyclic etching to clear the pillars, in which the F-based etching was used to remove the residual SiN, and then the O₂/Ar plasma was used to etch the diamond. Whether to take the next cyclic etching depends on whether there are still SiN micro-masks left. By using this method, we eventually achieved the self-terminated etching of the diamond and the smooth surface after the etching. These results demonstrate that the cyclic etching method can be successfully applied to the integrated preparation of polycrystalline diamond thin films and GaN HEMTs.

Keywords: AlGaN/GaN heterojunction, O₂/Ar plasma, cyclic etching, polycrystalline diamond

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Authors: Randa M. Mostafa, Y. Moustafa

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During our daily life, we are continuously exposed to the extremely low frequency electromagnetic fields (ELF-EMFs) generated by electric appliances. The possible relation between exposure to (ELF-MFs) and adverse health effects has attracted and passed through long debate sessions. Extremely low frequency is a term used to describe radiation frequencies below 300 Hertz (Hz).It is very important for public health because of the widespread use of electrical power at 50-60 Hz in most countries. This study set out to investigate the impact of chronic exposure of male rats to 50- Hz, 1 mTesla (ELF-EMF) of over periods of 1, 2, and 4 weeks on concentration of serum FSH, LH, and testosterone hormones. 60 male albino rats were divided into 6 groups and were continuously exposed to 50-Hz, 1 m Tesla (ELF-EMF) generated by magnetic field chamber for periods of 1, 2, and 4 weeks. For each experimental point, sham treated group was used as a control. Assay of serum testosterone LH, and FSHwere performed. Serum testosterone showed no significant changes. FSH showed significant increase than sham exposed group after 1 week of field exposure. LH showed significant increase than sham exposed group only after 4 weeks of field exposure. A future detailed molecular studies must be carried out to figure out and may be able to explain the possible interactions between ELF-EMF and hypothalamic-pituitary gonadal axis.

Keywords: extremely low frequency electromagnetic fields, testosterone, follicular stimulating hormone, LH

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Authors: Ashish Kumar Pathak, Ritika Sharma, Vishal Nath, Sudhir Pratap Singh, Rakesh Tuli

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Litchi is a sub-tropical fruit crop with genotypes bearing delicious juicy fruits with variable seed size (bold to rudimentary size). Small seed size is a desirable trait in litchi, as it increases consumer acceptance and fruit processing. The biochemical activities in mid- stage ovules (e.g. 16, 20, 24 and 28 days after anthesis) determine the fate of seed and fruit development in litchi. Comprehensive ovule-specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to gain molecular insight on determinants of seed fates in litchi fruits. The transcriptomic data was de-novo assembled in 1,39,608 trinity transcripts, out of which 6,325 trinity transcripts were differentially expressed between the two contrasting genotypes. Differential transcriptional pattern was found among ovule development stages in contrasting litchi genotypes. The putative genes for salicylic acid, jasmonic acid and brassinosteroid pathway were down-regulated in ovules of small-seeded litchi. Embryogenesis, cell expansion, seed size and stress related trinity transcripts exhibited altered expression in small-seeded genotype. The putative regulators of seed maturation and seed storage were down-regulated in small-seed genotype.

Keywords: Litchi, seed, transcriptome, defence

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Authors: Kesavan Markkandan, Ha Young Park, Seung-Il Yoo, Sin-Gi Park, Junhyung Park

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For genetic identification of crop cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, PCR based, co-dominant and relatively abundant. However, new InDels need to be developed for genetic studies of new varieties due to the difference of allele frequencies in InDels among the population groups. These new varieties are evolved with low levels of genetic diversity in specific genome loci with high recombination rate. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a variation block (VB), where the genomes split by all assumed recombination sites. Firstly, VBs in crop cultivars were mined for transferability to VB-specific InDel markers. Secondly, putative InDels in the VB regions were identified for the development of barcode system by analyzing particular cultivar’s whole genome data. Thirdly, common VB-specific InDels from all cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the selected markers was assessed with other cultivars, and the barcode system that allows a clear distinction among those cultivars is described. The same approach can be applicable for other commercial crops. Hence, VB-based genetic identification not only minimize the molecular markers but also useful for assessing cultivars and for marker-assisted breeding in other crop species.

Keywords: variation block, polymorphism, InDel marker, genetic identification

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Authors: Chen-Fu Wang, Lin-Ya Kung

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For traditional painting materials, the artisan used to combine the pigments with different binders to create colors. As time goes by, the materials used for painting evolved from natural to chemical materials. The vast variety of ingredients used in chemical materials has complicated restoration work; it makes conservation work more difficult. Conservation work also becomes harder when the materials cannot be easily identified; therefore, it is essential that we take a more scientific approach to assist in conservation work. Paintings materials are high molecular weight polymer, and their analysis is very complicated as well other contamination such as smoke and dirt can also interfere with the analysis of the material. The current methods of composition analysis of painting materials include Fourier transform infrared spectroscopy (FT-IR), mass spectrometer, Raman spectroscopy, X-ray diffraction spectroscopy (XRD), each of which has its own limitation. In this study, FT-IR was used to analyze the components of the paint coating. We have taken the most commonly seen materials as samples and deteriorated it. The aged information was then used for the database to exam the temple painting materials. By observing the FT-IR changes over time, we can tell all of the painting materials will be deteriorated by the UV light, but only the speed of its degradation had some difference. From the deterioration experiment, the acrylic resin resists better than the others. After collecting the painting materials aging information on FT-IR, we performed some test on the paintings on the temples. It was found that most of the artisan used tune-oil for painting materials, and some other paintings used chemical materials. This method is now working successfully on identifying the painting materials. However, the method is destructive and high cost. In the future, we will work on the how to know the painting materials more efficiently.

Keywords: temple painting, painting material, conservation, FT-IR

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Authors: Tobias Schmithuesen, Johannes Henrich Schleifenbaum

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The additive manufacturing process laser powder bed fusion offers many advantages over conventional manufacturing processes. For example, almost any complex part can be produced, such as topologically optimized lightweight parts, which would be inconceivable with conventional manufacturing processes. A major challenge posed by the LPBF process, however, is, in most cases, the need to use and remove support structures on critically inclined part surfaces (α < 45 ° regarding substrate plate). These are mainly used for dimensionally accurate mapping of part contours and to reduce distortion by absorbing process-related internal stresses. Furthermore, they serve to transfer the process heat to the substrate plate and are, therefore, indispensable for the LPBF process. A major challenge for the economical use of the LPBF process in industrial process chains is currently still the high manual effort involved in removing support structures. According to the state of the art (SoA), the parts are usually treated by simple hand tools (e.g., pliers, chisels) or by machining (e.g., milling, turning). New automatable approaches are the removal of support structures by means of wet chemical ablation and thermal deburring. According to the state of the art, the support structures are essentially adapted to the LPBF process and not to potential post-processing steps. The aim of this study is the determination of support structure designs that are adapted to the mentioned post-processing approaches. In the first step, the essential boundary conditions for complete removal by means of the respective approaches are identified. Afterward, a representative demonstrator part with various macroscopic support structure designs will be LPBF-manufactured and tested with regard to a complete powder and support removability. Finally, based on the results, potentially suitable support structure designs for the respective approaches will be derived. The investigations are carried out on the example of the aluminum alloy AlSi10Mg.

Keywords: additive manufacturing, laser powder bed fusion, laser beam melting, selective laser melting, post processing, tool-free, wet chemical ablation, thermal deburring, aluminum alloy, AlSi10Mg

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Authors: S. M. Anisuzzaman, Sariah Abang, Awang Bono, D. Krishnaiah, N. M. Ismail, G. B. Sandrison

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Wax and asphaltene are high molecular weighted compounds that contribute to the stability of crude oil at a dispersed state. Transportation of crude oil along pipelines from the oil rig to the refineries causes fluctuation of temperature which will lead to the coagulation of wax and flocculation of asphaltenes. This paper focuses on the prevention of wax and asphaltene precipitate deposition on the inner surface of the pipelines by using a wax inhibitor and an asphaltene dispersant. The novelty of this prevention method is the combination of three substances; a wax inhibitor dissolved in a wax inhibitor solvent and an asphaltene solvent, namely, ethylene-vinyl acetate (EVA) copolymer dissolved in methylcyclohexane (MCH) and toluene (TOL) to inhibit the precipitation and deposition of wax and asphaltene. The objective of this paper was to optimize the percentage composition of each component in this inhibitor which can maximize the viscosity reduction of crude oil. The optimization was divided into two stages which are the laboratory experimental stage in which the viscosity of crude oil samples containing inhibitor of different component compositions is tested at decreasing temperatures and the data optimization stage using response surface methodology (RSM) to design an optimizing model. The results of experiment proved that the combination of 50% EVA + 25% MCH + 25% TOL gave a maximum viscosity reduction of 67% while the RSM model proved that the combination of 57% EVA + 20.5% MCH + 22.5% TOL gave a maximum viscosity reduction of up to 61%.

Keywords: asphaltene, ethylene-vinyl acetate, methylcyclohexane, toluene, wax

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Authors: Abdullah Mohammad, Abdullah Alshemali, Esmaeil Alsaleh

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The chemical composition of desalinated water is modified to make it more acceptable to the end-user. Sometimes, this modification is approached by mixing with brackish water that is known to contain a variety of minerals. Expectedly, besides minerals, brackish water indigenous bacterial communities access the final mixture hence reaching the end consumer. The current project examined the safety of using brackish water as an ingredient in potable water. Pseudomonas aeruginosa strains were detected in potable and brackish water samples collected from storage facilities in residential areas as well as from main water distribution and storage tanks. The application of molecular and biochemical fingerprinting methods, including phylogeny, RFLP (restriction fragment length polymorphism), MLST (multilocus sequence typing) and substrate specificity testing, suggested that the potable water P. aeruginosa strains were most probably originated from brackish water. Additionally, all the sixty-four isolates showed multi-drug resistance (MDR) phenotype and harboured the three genes responsible for biofilm formation. These virulence factors represent serious health hazards compelling the scientific community to revise the WHO (World Health Organization) and USEP (US Environmental Protection Agency) A potable water quality guidelines, particularly those related to the types of bacterial genera that evade the current water quality guidelines.

Keywords: potable water, brackish water, pseudomonas aeroginosa, multidrug resistance

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Authors: Devesh Motwani, Amey Kashyap

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Interest in cost effective drilling has increased substantially in the past years. Economics associated with drilling fluids is needed to be considered seriously for lesser cost per foot in planning and drilling of a wellbore and the various environmental concerns imposed by international communities related with the constituents of the drilling fluid. Viscofier such as Guar Gum is a high molecular weight polysaccharide from Guar plants, is used to increase viscosity in water-based and brine-based drilling fluids thus enabling more efficient cleaning of the bore. Other applications of this Viscofier are to reduce fluid loss by giving a better colloidal solution, decrease fluid friction and so minimising power requirements and used in hydraulic fracturing to increase the recovery of oil and gas. Guar gum is also used as a surfactant, synthetic polymer and defoamer. This paper presents experimental results to verifying the properties of guar gum as a viscofier and filtrate retainer as well as observing the impact of different quantities of guar gum and Carboxymethyl cellulose (CMC) in a standard sample of water based bentonite mud solution. This is in attempt to make a drilling fluid which contains half of the quantity of drilling mud used and yet is equally viscous to the standardised mud sample. Thus we can see that mud economics will be greatly affected by this approach. However guar gum is thermally stable till 60-65°C thus limited to be used in drilling shallow wells and for a wider thermal range, suitable chrome free additives are required.

Keywords: economics, guargum, viscofier, CMC, thermal stability

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Authors: Ifigeneia V. Mavragani, Zacharenia Nikitaki, George Kalantzis, George Iliakis, Alexandros G. Georgakilas

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Complex DNA damage consisting of a combination of DNA lesions, such as Double Strand Breaks (DSBs) and non-DSB base lesions occurring in a small volume is considered as one of the most important biological endpoints regarding ionizing radiation (IR) exposure. Strong theoretical (Monte Carlo simulations) and experimental evidence suggests an increment of the complexity of DNA damage and therefore repair resistance with increasing linear energy transfer (LET). Experimental detection of complex (clustered) DNA damage is often associated with technical deficiencies limiting its measurement, especially in cellular or tissue systems. Our groups have recently made significant improvements towards the identification of key parameters relating to the efficient detection of complex DSBs and non-DSBs in human cellular systems exposed to IR of varying quality (γ-, X-rays 0.3-1 keV/μm, α-particles 116 keV/μm and 36Ar ions 270 keV/μm). The induction and processing of DSB and non-DSB-oxidative clusters were measured using adaptations of immunofluorescence (γH2AX or 53PB1 foci staining as DSB probes and human repair enzymes OGG1 or APE1 as probes for oxidized purines and abasic sites respectively). In the current study, Relative Biological Effectiveness (RBE) values for DSB and non-DSB induction have been measured in different human normal (FEP18-11-T1) and cancerous cell lines (MCF7, HepG2, A549, MO59K/J). The experimental results are compared to simulation data obtained using a validated microdosimetric fast Monte Carlo DNA Damage Simulation code (MCDS). Moreover, this simulation approach is implemented in two realistic clinical cases, i.e. prostate cancer treatment using X-rays generated by a linear accelerator and a pediatric osteosarcoma case using a 200.6 MeV proton pencil beam. RBE values for complex DNA damage induction are calculated for the tumor areas. These results reveal a disparity between theory and experiment and underline the necessity for implementing highly precise and more efficient experimental and simulation approaches.

Keywords: complex DNA damage, DNA damage simulation, protons, radiotherapy

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Authors: Yina A. Cifuentes Triana, Andrés M. Pinzón Velásco, Marío E. Velásquez Lozano

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In this work the sequencing and genome characterization of a natural isolate of Saccharomyces cerevisiae yeast (strain 202-3), identified with potential for the production of second generation ethanol from sugarcane bagasse hydrolysates is presented. This strain was selected because its capability to consume xylose during the fermentation of sugarcane bagasse hydrolysates, taking into account that many strains of S. cerevisiae are incapable of processing this sugar. This advantage and other prominent positive aspects during fermentation profiles evaluated in bagasse hydrolysates made the strain 202-3 a candidate strain to improve the production of second-generation ethanol, which was proposed as a first step to study the strain at the genomic level. The molecular characterization was carried out by genome sequencing with the Illumina HiSeq 2000 platform paired end; the assembly was performed with different programs, finally choosing the assembler ABYSS with kmer 89. Gene prediction was developed with the approach of hidden Markov models with Augustus. The genes identified were scored based on similarity with public databases of nucleotide and protein. Records were organized from ontological functions at different hierarchical levels, which identified central metabolic functions and roles of the S. cerevisiae strain 202-3, highlighting the presence of four possible new proteins, two of them probably associated with the positive consumption of xylose.

Keywords: cellulosic ethanol, Saccharomyces cerevisiae, genome sequencing, xylose consumption

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Authors: Stephen Eyije Abechi, Casimir Emmanuel Gimba, Zaharaddeen Nasiru Garba, Sani Shamsudeen, David Ebuka Authur

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The mechanisms of corrosion inhibition of mild steel in acid medium using Acalypha chamaedrifolia leaves extract as potential green inhibitor were investigated. Gravimetric (weight loss) technique was used for the corrosion studies. Mild steel coupons of 2cm × 1cm × 0.27 cm dimensions were exposed for varying durations of between 24 to 120 hours, in 1M HCl medium containing a varying concentrations of the leaves extract (0.25g/L, - 1.25g/L). The results show that corrosion rates dropped from a value of 0.49 mgcm-2hr-1 for the uninhibited medium to a value of 0.15 mgcm-2hr-1 for the inhibited medium of 1M HCl in 0.25 g/l of the extract. Values of corrosion inhibition efficiencies of 70.38-85.11% were observed as the concentration of the inhibitor were increased from 0.25g/L, - 1.25g/L. Corrosion Inhibition was found to increase with increase in immersion time and temperature. The magnitude of the Ea indicates that the interaction between the metal surface and the inhibitor was chemisorptions. The Adsorption process fit into the Langmuir isotherm model with a correlation coefficient of 0.97. Evidence from molecular dynamics model shows that Methyl stearate (Line 5) and (3Z, 13Z)-2-methyloctadeca-3,13-dien-1-ol (line 11) were found to have the highest binding energy of -197.69 ± 3.12 and-194.56 ± 10.04 in kcal/mol respectively. The binding energy of these compounds indicates that they would be a very good corrosion inhibitor for mild steel and other Fe related materials.

Keywords: binding energy, corrosion, inhibitor, Langmuir isotherm, mild steel.

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Authors: Geun-Yeon Kim, S. P. Praveen Kumar, Kwon-Hee Lee

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A steering knuckle arm is the component that connects the steering system and suspension system. The structural performances such as stiffness, strength, and durability are considered in its design process. The former study suggested the lightweight design of a knuckle arm considering the structural performances and using the metamodel-based optimization. The six shape design variables were defined, and the optimum design was calculated by applying the kriging interpolation method. The finite element method was utilized to predict the structural responses. The suggested knuckle was made of the aluminum Al6082, and its weight was reduced about 60% in comparison with the base steel knuckle, satisfying the design requirements. Then, we investigated its manufacturability by performing foraging analysis. The forging was done as hot process, and the product was made through two-step forging. As a final step of its developing process, the durability is investigated by using the flexible dynamic analysis software, LS-DYNA and the pre and post processor, eta/VPG. Generally, a car make does not provide all the information with the part manufacturer. Thus, the part manufacturer has a limit in predicting the durability performance with the unit of full car. The eta/VPG has the libraries of suspension, tire, and road, which are commonly used parts. That makes a full car modeling. First, the full car is modeled by referencing the following information; Overall Length: 3,595mm, Overall Width: 1,595mm, CVW (Curve Vehicle Weight): 910kg, Front Suspension: MacPherson Strut, Rear Suspension: Torsion Beam Axle, Tire: 235/65R17. Second, the road is selected as the cobblestone. The road condition of the cobblestone is almost 10 times more severe than that of usual paved road. Third, the dynamic finite element analysis using the LS-DYNA is performed to predict the durability performance of the suggested knuckle arm. The life of the suggested knuckle arm is calculated as 350,000km, which satisfies the design requirement set up by the part manufacturer. In this study, the overall design process of a knuckle arm is suggested, and it can be seen that the developed knuckle arm satisfies the design requirement of the durability with the unit of full car. The VPG analysis is successfully performed even though it does not an exact prediction since the full car model is very rough one. Thus, this approach can be used effectively when the detail to full car is not given.

Keywords: knuckle arm, structural optimization, Metamodel, forging, durability, VPG (Virtual Proving Ground)

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Authors: Samantha Shallop, Hakinya Karra, Tytus Bernas, Gladys Shaw, Gretchen Neigh, Jeffrey Dupree, Mathula Thangarajh

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Abnormal neuronal homeostasis is considered a structural correlate of cognitive deficits in Duchenne Muscular Dystrophy. Neurons are highly polarized cells with multiple dendrites but a single axon. Trafficking of cellular organelles are highly regulated, with the cargo in the somatodendritic region of the neuron not permitted to enter the axonal compartment. We investigated the molecular mechanisms that regular organelle trafficking in neurons using a multimodal approach, including high-resolution structural illumination, proteomics, immunohistochemistry, and computational modeling. We investigated the expression of ankyrin-G, the master regulator controlling neuronal polarity. The expression of ankyrin G and the morphology of the axon initial segment was profoundly abnormal in the CA1 hippocampal neurons in the mdx52 animal model of DMD. Ankyrin-G colocalized with kinesin KIF5a, the anterograde protein transporter, with higher levels in older mdx52 mice than younger mdx52 mice. These results suggest that the functional trafficking from the somatodendritic compartment is abnormal. Our data suggests that dystrophin deficiency compromised neuronal homeostasis via ankyrin-G-based mechanisms.

Keywords: neurons, axonal transport, duchenne muscular dystrophy, organelle transport

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Authors: Carlos F. Sanz-Navarro, Sonia Fereres

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Binary and ternary mixtures of molten salts are excellent thermal energy storage systems and have been widely used in commercial tanks both in nuclear and solar thermal applications. However, the energy density of the commercially used mixtures is still insufficient, and therefore, new systems based on latent heat storage (or phase change materials, PCM) are currently being investigated. In order to shed some light on the macroscopic physical properties of the molten salt phases, knowledge of the microscopic structure and dynamics is required. Several molecular dynamics (MD) simulations have been performed to model the thermal behavior of (Li,K)2CO3 mixtures. Up to this date, this particular molten salt mixture has not been extensively studied but it is of fundamental interest for understanding the behavior of other commercial salts. Molten salt diffusivities, the internal electrical ion mobility, and the physical properties of the solid-liquid phase transition have been calculated and compared to available data from literature. The effect of anion polarization and the application of a strong external electric field have also been investigated. The influence of electrical ion mobility on local composition is explained through the Chemla effect, well known in electrochemistry. These results open a new way to design optimal high temperature energy storage materials.

Keywords: atomistic simulations, thermal storage, latent heat, molten salt, ion mobility

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Authors: Melliti Rihab, Zaeid Sonia, Khechine Wiem, Daldoul Amira

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Introduction: Lung cancer is the leading cause of cancer death. Its incidence is increasing, and its prognosis remains pejorative. We present the clinical, pathological, and therapeutic characteristics of bronchopulmonary cancer (BPC) in Tunisia. Methods: Retrospective study including patients followed in the oncology department of the University Hospital of Monastir between April 2014 and December 2021 suffering from lung cancer. Results: These are 117 patients, including 86.3% men and 13.7% women (sex ratio 6.3). The average age was 64 years ± 9 (37-83), with 95.7% being over 50 years old. Patients were smokers in 82% of cases. The clinical signs were dominated by chest pain (27.5%) and dyspnea in 21.1% of cases. In 6 patients, an episode of COVID-19 infection revealed the diagnosis. Half of the patients had a PS between 0 and 1. Small cell lung cancer was present in 18 patients (15.4%). The majority of non small cell lung cancer was of the adenocarcinoma type (68.7%). The diagnosis was late (stage IV) in 62.4% of cases. BPC was metastatic to bone (52%), contralateral lung (25.9%), and brain (27.3%). Patients were oligometastatic in 26% of cases. Surgery and radiotherapy were performed respectively in 14.5% and 23.1% of cases. Three-quarters of the patients had had nutrition (75.2%). The ROS1 mutation was present in 1 patient. PDL-1 expression was >40% in 2 patients. Survival was mean eight months ± 7.4. Conclusion: Lung cancer is diagnosed at a late stage in Tunisia. The lack of molecular study for non-small cell PBC and the lack of marketing authorization for tyrosine kinase inhibitors in Tunisia make the management incomplete.

Keywords: SCLC, NCSLC, ROS1, PDL1

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Authors: Yen-Ni Teng, Hsing-Yi Chen, Hsien-An Pan, Yung-Ming Lin, Hany A. Omar, Jui-Hsiang Hung

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Leucine-rich repeats and WD repeat domain containing 1 (LRWD1) is highly expressed in the testes of healthy males. On the other hand, LRWD1 is significantly down-regulated in the testicular tissues of patients with severe spermatogenic defects. In our study, the downregulation of LRWD1 expression by shRNA caused a significant reduction of cell growth and mitosis and a noteworthy increase in the cell microtubule atrophy rate. Here, we used EMBOSS CpG plot analysis to explore the promoter region of LRWD1 gene. We found that CpG islands are located between positions -253 to +5 nucleotides upstream from the LRWD1 transcription start site. Luciferase reporter assay revealed that the hypermethylation of the LRWD1 promoter reduced the transcription activity in cells. In addition, quantitative methylation-specific PCR and immunostaining showed that the methylation inhibitor, 5-Aza-2'-deoxycytidine, increased LRWD1 promoter activity, LRWD1 mRNA, protein expression and cell viability. Whereas, the methylation activator, S-adenosylmethionine, caused opposite effects. The overexpression of p53 and Nrf2 in NT2/D1 cells increased LRWD1 promoter activity while 5-fluorodeoxyuridine decreased it. In conclusion, this study highlights evidence that the methylation status of LRWD1 promoter is associated with LRWD1 expression. Since the expression level of LRWD1 plays an important role in spermatogenesis, the methylation status of LRWD1 may serve as a novel molecular diagnostic or therapeutic approach in male's infertility.

Keywords: LRWD1, DNA methylation, p53, Nrf2

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Authors: Tripti Mishra, Shipra Shukla, Sanjeev Meena, , Ruchi Singh, Mahesh Pal, D. K. Upreti, Dipak Datta

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Roccella montagnei belongs to lichen family Roccelleceae growing luxuriantly along the coastal regions of India. As Roccella has been shown to be bioactive, we prepared methanolic extract and assessed its anticancer potential. The methanolic extract showed significant in vitro cytotoxic activity against four human cancer cell lines such as Colon (DLD-1, SW-620), Breast (MCF-7), Head and Neck (FaDu). This prompted us to isolate bioactive compounds through column chromatography. Two compounds Roccellic acid and Everninic acid have been isolated, out of which Everninic acid is reported for the first time. Both the compounds have been tested for in vitro cytotoxic activity in which Roccellic acid showed strong anticancer activity as compared to the Everninic acid. CDK-10 (Cyclin-dependent kinase) contributes to proliferation of cancer cells, and aberrant activity of these kinases has been reported in a wide variety of human cancers. These kinases, therefore, constitute biomarkers of proliferation and attractive pharmacological targets for the development of anticancer therapeutics. Therefore both the isolated compounds were tested for in silico molecular docking study against CDK-10 isomer enzyme to support the cytotoxic activity.

Keywords: cytotoxic activity, everninic acid, roccellic acid, R. montagnei

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Authors: Nwadike Emmanuel Chinagoron, Achebe Chukwunonso, Ezeliora Chukwuemeka Daniel, Azaka Onyemazuwa Andrew

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In this research work, the process of biodiesel production in a pilot plant was studied using cow tallow as raw material, methanol as the solvent and potassium hydroxide as catalysts. The biodiesel quality was determined by characterization. The tallow used in the production had a molecular weight of 860g. Its oil had a density value of 0.8g/ml, iodine value of 63.45, viscosity at 300C was 9.83pas, acid value was 1.96, free fatty acid (FFA) of 0.98%, saponification value of 82.75mleq/kg, specific gravity of 0.898, flash point of 1100C, cloud point of 950C and Calorific value also called Higher Heating Value (HHV) of 38.365MJ/Kg. The produced biodiesel had a density of 0.82g/ml, iodine value of 126.9, viscosity of 4.32pas at 300C, acid value of 0.561, FFA of 0.2805%, saponification value of 137.45 mleq/kg.Flash point, cloud point and centane number of the biodiesel produced are 1390C, 980C and 57.5 respectively, with fat content, protein content, ash content, moisture content, fiber content and carbohydrate content values of 10%, 2.8%, 5%, 5%, 20%, and 37.2% respectively. The biodiesel higher heating values (calorific values) when estimated from viscosity, density and flash points were 41.4MJ/Kg, 63.8MJ/Kg, and 34.6MJ/Kg respectively. The biodiesel was blended with conventional diesel. The blend B-10 had values of 1320C and 960C for flash and cloud points, with Calorific value (or HHV) of 34.6 MJ/Kg (when estimated from its Flash point) and fat content, protein content, ash content, moisture content, fiber content and carbohydrate content values of 5%, 2.1%,10%, 5%, 15%, and 62.9% respectively.

Keywords: biodiesel, characterization, cow-tallow, cetane rating

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Authors: Reza Ferdousi, Reza Safdari, Yadollah Omidi

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Drug-drug interactions (DDIs) are main cause of the adverse drug reactions and nature of the functional and molecular complexity of drugs behavior in human body make them hard to prevent and treat. With the aid of new technologies derived from mathematical and computational science the DDIs problems can be addressed with minimum cost and efforts. Market basket analysis is known as powerful method to identify co-occurrence of thing to discover patterns and frequency of the elements. In this research, we used market basket analysis to identify important bio-elements in DDIs occurrence. For this, we collected all known DDIs from DrugBank. The obtained data were analyzed by market basket analysis method. We investigated all drug-enzyme, drug-carrier, drug-transporter and drug-target associations. To determine the importance of the extracted bio-elements, extracted rules were evaluated in terms of confidence and support. Market basket analysis of the over 45,000 known DDIs reveals more than 300 important rules that can be used to identify DDIs, CYP 450 family were the most frequent shared bio-elements. We applied extracted rules over 2,000,000 unknown drug pairs that lead to discovery of more than 200,000 potential DDIs. Analysis of the underlying reason behind the DDI phenomena can help to predict and prevent DDI occurrence. Ranking of the extracted rules based on strangeness of them can be a supportive tool to predict the outcome of an unknown DDI.

Keywords: drug-drug interaction, market basket analysis, rule discovery, important bio-elements

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Authors: Chih-Chung Huang, Po-Hsun Peng

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Ultrasound transient elastography has become a valuable tool for many clinical diagnoses, such as liver diseases and breast cancer. The pathological tissue can be distinguished by elastography due to its stiffness is different from surrounding normal tissues. An ultrafast frame rate of ultrasound imaging is needed for transient elastography modality. The elastography obtained in the ultrafast system suffers from a low quality for resolution, and affects the robustness of the transient elastography. In order to overcome these problems, a coherent plane wave compounding technique has been proposed for conventional ultrasound system which the operating frequency is around 3-15 MHz. The purpose of this study is to develop a novel beamforming technique for high frequency ultrasound coherent plane-wave compounding imaging and the simulated results will provide the standards for hardware developments. Plane-wave compounding imaging produces a series of low-resolution images, which fires whole elements of an array transducer in one shot with different inclination angles and receives the echoes by conventional beamforming, and compounds them coherently. Simulations of plane-wave compounding image and focused transmit image were performed using Field II. All images were produced by point spread functions (PSFs) and cyst phantoms with a 64-element linear array working at 35MHz center frequency, 55% bandwidth, and pitch of 0.05 mm. The F number is 1.55 in all the simulations. The simulated results of PSFs and cyst phantom which were obtained using single, 17, 43 angles plane wave transmission (angle of each plane wave is separated by 0.75 degree), and focused transmission. The resolution and contrast of image were improved with the number of angles of firing plane wave. The lateral resolutions for different methods were measured by -10 dB lateral beam width. Comparison of the plane-wave compounding image and focused transmit image, both images exhibited the same lateral resolution of 70 um as 37 angles were performed. The lateral resolution can reach 55 um as the plane-wave was compounded 47 angles. All the results show the potential of using high-frequency plane-wave compound imaging for realizing the elastic properties of the microstructure tissue, such as eye, skin and vessel walls in the future.

Keywords: plane wave imaging, high frequency ultrasound, elastography, beamforming

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Authors: Adinarayana Gorajana, Venkata Srikanth Meka, Sanjay Garg, Lim Sue May

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This study was designed to evaluate and enhance the solubility of poorly soluble drug, docetaxel through solid dispersion (SD) technique prepared using freeze drying method. Docetaxel solid dispersions were formulated with Soluplus in different weight ratios. Freeze drying method was used to prepare the solid dispersions. Solubility of the solid dispersions were evaluated respectively and the optimized of drug-solubilizers ratio systems were characterized with different analytical methods like Differential scanning calorimeter (DSC), Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) to confirm the formation of complexes between drug and solubilizers. The solubility data revealed an overall improvement in solubility for all SD formulations. The ternary combination 1:5:2 gave the highest increase in solubility that is approximately 3 folds from the pure drug, suggesting the optimum drug-solubilizers ratio system. This data corresponds with the DSC and SEM analyses, which demonstrates presence of drug in amorphous state and the dispersion in the solubilizers in molecular level. The solubility of the poorly soluble drug, docetaxel was enhanced through preparation of solid dispersion formulations employing freeze drying method. Solid dispersion with multiple carrier system shows better solubility compared to single carrier system.

Keywords: docetaxel, freeze drying, soluplus, solid dispersion technique

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Authors: Vinicius Buccelli Ribeiro, Maria Teresa Destro, Mariza Landgraf

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Bacteriophages are one of the most abundant replicating entities on Earth and can be found everywhere in which their hosts live and there are reports regarding isolation from different niches such as soil and foods. Since studies are moving forward with regard to biotechnology area, different research projects are being performed focusing on the phage technology and its use by the food industry. This study aimed to evaluate a cocktail (LP501) of phages isolated in Brazil for its lytic potential against Listeria monocytogenes. Three bacteriophages (LP05, LP12 and LP20) were isolated from soil samples and all of them showed 100% lysis against a panel of 10 L. monocytogenes strains representing different serotypes of this pathogen. A mix of L. monocytogenes 1/2a and 4b were inoculated in soft cheeses (approximately 105 cfu/cm2) with the phage cocktail added thereafter (1 x 109 PFU/cm2). Samples were analyzed immediately and then stored at 10°C for ten days. At 30 min post-infection, the cocktail reduced L. monocytogenes counts approximately 1.5 logs, compared to controls without bacteriophage. The treatment produced a statistically significant decrease in the counts of viable cells (p < 0.05) and in all assays performed we observed a decrease of up to 4 logs of L. monocytogenes. This study will make available to the international community behavioral and molecular data regarding bacteriophages present in soil samples in Brazil. Furthermore, there is the possibility to apply this new cocktail of phages in different food products to combat L. monocytogenes.

Keywords: bacteriophages, biocontrol, listeria monocytogenes, soft cheese

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Authors: Prasanthi Malapati, R. Reshma, Vijay Soni, Perumal Yogeeswari, Dharmarajan Sriram

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In the present study, we attempted to develop Mycobacterium tuberculosis (Mtb) inhibitors by exploring the pharmaceutically underexploited enzyme targets which are majorly involved in cell wall biosynthesis of mycobacteria. For this purpose, glutamate racemase (coded by MurI gene) was selected. This enzyme racemize L-glutamate to D-glutamate required for the construction of peptidoglycan in the bacterial cell wall synthesis process. Furthermore this enzyme is neither expressed nor its product, D-glutamate is normally found in mammals, and hence designing inhibitors against this enzyme will not affect the host system as well act as potential antitubercular drugs. A library of BITS in house compounds were screened against Mtb MurI enzyme. Based on docking score, interactions and synthetic feasibility one hit lead was identified. Further optimization of lead was attempted and its derivatives were synthesized. Forty eight derivatives of 2-phenylbenzo[d]oxazole and 2-phenylbenzo[d]thiazole were synthesized and evaluated for Mtb MurI inhibition study, in vitro activities against Mtb, cytotoxicity against RAW 264.7 cell line. Chemical derivatization of the lead resulted in compounds NR-1213 AND NR-1124 as the potent M. tuberculosis glutamate racemase inhibitors with IC50 of 4-5µM which are remarkable and were found to be non-cytotoxic. Molecular dynamics, dormant models and cardiotoxicity studies of the most active molecules are in process.

Keywords: cell wall biosynthesis, dormancy, glutamate racemase, tuberculosis

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Authors: Brian Wartell, Michel Boufadel

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Contaminants such as polycyclic aromatic hydrocarbons (PAHs) are compounds present in crude and petroleum oils and are known to be toxic and often carcinogenic. Therefore, a major effort is placed on tracking their subsurface soil concentrations following an oil spill. The PAHs can persist for years in the subsurface especially if there is a lack of oxygen. Both aerobic and anaerobic biodegradation of PAHs encounter the difficulties of both nutrient transport and bioavailability (proximal access) to the organisms of the contaminants. A technology, known as electrokinetics (EK or EK-BIO for ‘electrokinetic bioremediation’) has been found to transport efficiently nutrients or other chemicals in the subsurface. Experiments were conducted to demonstrate migration patterns in both sands and clay for both ionic and nonionic compounds and aerobic biodegradation studies were conducted with soil spiked with Polycyclic Aromatic Hydrocarbons yielding interesting results. In one set of experiment, Self-designed electrokinetic setups were constructed to examine the differences in electromigration and electroosmotic rates. Anionic and non-ionic dyes were used to visualize these phenomena, respectively. In another experiment, a silt-clay soil was spiked with three low-molecular-weight compounds (fluorene, phenanthrene, fluoranthene) and placed within self-designed electrokinetic setups and monitored for aerobic degradation. Plans for additional studies are in progress including the transport of peroxide through anaerobic sands.

Keywords: bioavailability, bioremediation, electrokinetics, subsurface transport

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