Search results for: molecular topology

Authors: Beata Lachtara, Renata Szewczyk, Katarzyna Bielinska, Kinga Wieczorek, Jacek Osek

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Listeria monocytogenes is an important human and animal pathogen that causes foodborne outbreaks. The bacteria may be present in different types of food: cheese, raw vegetables, sliced meat products and vacuum-packed sausages, poultry, meat, fish. The most common method, which has been used for the investigation of genetic diversity of L. monocytogenes, is PFGE. This technique is reliable and reproducible and established as gold standard for typing of L. monocytogenes. The aim of the study was characterization by molecular serotyping and PFGE analysis of L. monocytogenes strains isolated from fresh fish and fish products in Poland. A total of 301 samples, including fresh fish (n = 129) and fish products (n = 172) were, collected between January 2014 and March 2016. The bacteria were detected using the ISO 11290-1 standard method. Molecular serotyping was performed with PCR. The isolates were tested with the PFGE method according to the protocol developed by the European Union Reference Laboratory for L. monocytogenes with some modifications. Based on the PFGE profiles, two dendrograms were generated for strains digested separately with two restriction enzymes: AscI and ApaI. Analysis of the fingerprint profiles was performed using Bionumerics software version 6.6 (Applied Maths, Belgium). The 95% of similarity was applied to differentiate the PFGE pulsotypes. The study revealed that 57 of 301 (18.9%) samples were positive for L. monocytogenes. The bacteria were identified in 29 (50.9%) ready-to-eat fish products and in 28 (49.1%) fresh fish. It was found that 40 (70.2%) strains were of serotype 1/2a, 14 (24.6%) 1/2b, two (4.3%) 4b and one (1.8%) 1/2c. Serotypes 1/2a, 1/2b, and 4b were presented with the same frequency in both categories of food, whereas serotype 1/2c was detected only in fresh fish. The PFGE analysis with AscI demonstrated 43 different pulsotypes; among them 33 (76.7%) were represented by only one strain. The remaining 10 profiles contained more than one isolate. Among them 8 pulsotypes comprised of two L. monocytogenes isolates, one profile of three isolates and one restriction type of 5 strains. In case of ApaI typing, the PFGE analysis showed 27 different pulsotypes including 17 (63.0%) types represented by only one strain. Ten (37.0%) clusters contained more than one strain among which four profiles covered two strains; three had three isolates, one with five strains, one with eight strains and one with ten isolates. It was observed that the isolates assigned to the same PFGE type were usually of the same serotype (1/2a or 1/2b). The majority of the clusters had strains of both sources (fresh fish and fish products) isolated at different time. Most of the strains grouped in one cluster of the AscI restriction was assigned to the same groups in ApaI investigation. In conclusion, PFGE used in the study showed a high genetic diversity among L. monocytogenes. The strains were grouped into varied clonal clusters, which may suggest different sources of contamination. The results demonstrated that 1/2a serotype was the most common among isolates from fresh fish and fish products in Poland.

Keywords: Listeria monocytogenes, molecular characteristic, PFGE, serotyping

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Authors: Tushar Bhardwaj

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Internet of Things (IoT) possesses a dynamic network where the network nodes (mobile devices) are added and removed constantly and randomly, hence the traffic distribution in the network is quite variable and irregular. The basic but very important part in any network is route searching. We have many conventional route searching algorithms like link-state, and distance vector algorithms but they are restricted to the static point to point network topology. In this paper we propose a model that uses the Ant Colony Algorithm for route searching. It is dynamic in nature and has positive feedback mechanism that conforms to the route searching. We have also embedded the concept of Non-Deterministic Finite Automata [NDFA] minimization to reduce the network to increase the performance. Results show that Ant Colony Algorithm gives the shortest path from the source to destination node and NDFA minimization reduces the broadcasting storm effectively.

Keywords: routing, ant colony algorithm, NDFA, IoT

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene

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Authors: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

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The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

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Authors: Yasser Gaber, Mohamed Ismail, Serena Bisagni, Mohamad Takwa, Rajni Hatti-Kaul

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Enzymes are safe and selective catalysts. They skillfully catalyze chemical reactions; however, the native form is not usually suitable for industrial applications. Enzymes are therefore engineered by several techniques to meet the required catalytic task. Clopidogrel is recorded among the five best selling pharmaceutical in 2010 under the brand name Plavix. The commonly used route for production of the drug on an industrial scale is the synthesis of the racemic mixture followed by diastereomeric resolution to obtain the pure S isomer. The process consumes a lot of solvents and chemicals. We have evaluated a biocatalytic cleaner approach for asymmetric hydrolysis of racemic clopidogrel. Initial screening of a selected number of hydrolases showed only one enzyme EST to exhibit activity and selectivity towards the desired stereoisomer. As the crude EST is a mixture of several isoenzymes, a homology model of EST-1 was used in molecular dynamic simulations to study the interaction of the enzyme with R and S isomers of clopidogrel. Analysis of the geometric hindrances of the tetrahedral intermediates revealed a potential site for mutagenesis in order to improve the activity and the selectivity. Single point mutation showed dramatic increase in activity and inversion of the enantioselectivity (400 fold change in E value).

Keywords: biocatalysis, biotechnology, enzyme, protein engineering, molecular modeling

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Authors: Margarita S. Tikhonova, Alireza Baniasad, Anton G. Kalmykov, Georgy A. Kalmykov, Ralf Littke

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There is a high complexity in the pore structure of organic-rich rocks caused by the combination of inter-particle porosity from inorganic mineral matter and ultrafine intra-particle porosity from both organic matter and clay minerals. Fluids are retained in that pore space, but there are major uncertainties in how and where the fluids are stored and to what extent they are accessible or trapped in 'closed' pores. A large degree of tortuosity may lead to fractionation of organic matter so that the lighter and flexible compounds would diffuse to the reservoir whereas more complicated compounds may be locked in place. Additionally, parts of hydrocarbons could be bound to solid organic matter –kerogen– and mineral matrix during expulsion and migration. Larger compounds can occupy thin channels so that clogging or oil and gas entrapment will occur. Sequential extraction of applying different solvents is a powerful tool to provide more information about the characteristics of trapped organic matter distribution. The Upper Jurassic – Lower Cretaceous Bazhenov shale is one of the most petroliferous source rock extended in West Siberia, Russia. Concerning the variable mineral composition, pore space distribution and thermal maturation, there are high uncertainties in distribution and composition of organic matter in this formation. In order to address this issue geological and geochemical properties of 30 samples including mineral composition (XRD and XRF), structure and texture (thin-section microscopy), organic matter contents, type and thermal maturity (Rock-Eval) as well as molecular composition (GC-FID and GC-MS) of different extracted materials during sequential extraction were considered. Sequential extraction was performed by a Soxhlet apparatus using different solvents, i.e., n-hexane, chloroform and ethanol-benzene (1:1 v:v) first on core plugs and later on pulverized materials. The results indicate that the studied samples are mainly composed of type II kerogen with TOC contents varied from 5 to 25%. The thermal maturity ranged from immature to late oil window. Whereas clay contents decreased with increasing maturity, the amount of silica increased in the studied samples. According to molecular geochemistry, stored hydrocarbons in open and closed pore space reveal different geochemical fingerprints. The results improve our understanding of hydrocarbon expulsion and migration in the organic-rich Bazhenov shale and therefore better estimation of hydrocarbon potential for this formation.

Keywords: Bazhenov formation, bitumen, molecular geochemistry, sequential extraction

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Authors: S. M. Dankaka, N. Abdullahi

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Context: This research was conducted to isolate and identify phenol-tolerant bacteria from petroleum-contaminated sites in the northwestern part of Nigeria. Research Aim: The aim of this study was to identify bacteria with the ability to tolerate different phenol concentrations. Methodology: Samples were obtained from different petroleum-contaminated sites, and bacteria were cultured, followed by morphological, microscopic, and molecular identification. Isolates were grown on phenol-tolerant nutrient agar. The tolerant ability of the isolates was observed at 500 mg/L, 1000 mg/L, and 1500 mg/L concentrations of phenol. Findings: Two bacteria species (NWPK and NWPKD) were obtained. The total viable counts of phenol-utilizing bacteria from NWPK and NWPKD were 2.71x10⁷ and 4.0x10⁶ cfu/g, respectively. The NWPK showed its capacity to tolerate phenol at 2.3x10⁷, 2.5x10⁷, and 1.0x10⁷ cfu/g of 500, 1000, and 1500 mg/L of phenol concentration, respectively, while NWPKD tolerance ability was 1.5x10⁷, 3.8x10⁷ and 1.0x10⁷ cfu/g of 500, 1000 and 1500 mg/L of phenol respectively. The isolates were identified as Citrobacter and Acinetobacter species, respectively, based on 16S rRNA gene sequence analysis. Conclusion: The study found that these isolates showed the ability to withstand and survive high phenol concentrations in the environment.

Keywords: phenol tolerance, bacteria, petroleum contaminated sites, 16S rRNA

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Authors: M. H. Hussain, I. Musirin, A. F. Abidin, S. R. A. Rahim

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This paper presents the implementation of Artificial Bees Colony (ABC) algorithm in solving Directional OverCurrent Relays (DOCRs) coordination problem for near-end faults occurring in fixed network topology. The coordination optimization of DOCRs is formulated as linear programming (LP) problem. The objective function is introduced to minimize the operating time of the associated relay which depends on the time multiplier setting. The proposed technique is to taken as a technique for comparison purpose in order to highlight its superiority. The proposed algorithms have been tested successfully on 8 bus test system. The simulation results demonstrated that the ABC algorithm which has been proved to have good search ability is capable in dealing with constraint optimization problems.

Keywords: artificial bees colony, directional overcurrent relay coordination problem, relay settings, time multiplier setting

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Authors: B. Wang, W. H. Or, S.C. Lee, Y.C. Leung, B. Organ

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This study presents an investigation of diesel vehicle particulate-phase emissions with neat ultralow sulphur diesel (B0, ULSD) and 5% waste cooking oil-based biodiesel blend (B5) in Hong Kong. A Euro VI light duty diesel vehicle was tested under transient (New European Driving Cycle (NEDC)), steady-state and idling on a chassis dynamometer. Chemical analyses including organic carbon (OC), elemental carbon (EC), as well as 30 polycyclic aromatic hydrocarbons (PAHs) and 10 oxygenated PAHs (oxy-PAHs) were conducted. The OC fuel-based emission factors (EFs) for B0 ranged from 2.86 ± 0.33 to 7.19 ± 1.51 mg/kg, and those for B5 ranged from 4.31 ± 0.64 to 15.36 ± 3.77 mg/kg, respectively. The EFs of EC were low for both fuel blends (0.25 mg/kg or below). With B5, the EFs of total PAHs were decreased as compared to B0. Specifically, B5 reduced total PAH emissions by 50.2%, 30.7%, and 15.2% over NEDC, steady-state and idling, respectively. It was found that when B5 was used, PAHs and oxy-PAHs with lower molecular weight (2 to 3 rings) were reduced whereas PAHs/oxy-PAHs with medium or high molecular weight (4 to 7 rings) were increased. Our study suggests the necessity of taking atmospheric and health factors into account for biodiesel application as an alternative motor fuel.

Keywords: biodiesel, OC/EC, PAHs, vehicular emission

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Authors: Recep Kesli, Huseyin Bilgin, Yasar Unlu, Gokhan Gungor

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Aim: The aim of this study was to compare diagnostic values of two different molecular-based tests (GenoType® HelicoDR ve Seeplex® H. pylori-ClaR- ACE Detection) in detection presence of the H. pylori from gastric biopsy specimens. In addition to this also was aimed to determine resistance ratios of H. pylori strains against to clarytromycine and quinolone isolated from gastric biopsy material cultures by using both the genotypic (GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection) and phenotypic (gradient strip, E-test) methods. Material and methods: A total of 266 patients who admitted to Konya Education and Research Hospital Department of Gastroenterology with dyspeptic complaints, between January 2011-June 2013, were included in the study. Microbiological and histopathological examinations of biopsy specimens taken from antrum and corpus regions were performed. The presence of H. pylori in all the biopsy samples was investigated by five differnt dignostic methods together: culture (C) (Portagerm pylori-PORT PYL, Pylori agar-PYL, GENbox microaer, bioMerieux, France), histology (H) (Giemsa, Hematoxylin and Eosin staining), rapid urease test (RUT) (CLOtest, Cimberly-Clark, USA), and two different molecular tests; GenoType® HelicoDR, Hain, Germany, based on DNA strip assay, and Seeplex ® H. pylori -ClaR- ACE Detection, Seegene, South Korea, based on multiplex PCR. Antimicrobial resistance of H. pylori isolates against clarithromycin and levofloxacin was determined by GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, and gradient strip (E-test, bioMerieux, France) methods. Culture positivity alone or positivities of both histology and RUT together was accepted as the gold standard for H. pylori positivity. Sensitivity and specificity rates of two molecular methods used in the study were calculated by taking the two gold standards previously mentioned. Results: A total of 266 patients between 16-83 years old who 144 (54.1 %) were female, 122 (45.9 %) were male were included in the study. 144 patients were found as culture positive, and 157 were H and RUT were positive together. 179 patients were found as positive with GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection together. Sensitivity and specificity rates of studied five different methods were found as follows: C were 80.9 % and 84.4 %, H + RUT were 88.2 % and 75.4 %, GenoType® HelicoDR were 100 % and 71.3 %, and Seeplex ® H. pylori -ClaR- ACE Detection were, 100 % and 71.3 %. A strong correlation was found between C and H+RUT, C and GenoType® HelicoDR, and C and Seeplex ® H. pylori -ClaR- ACE Detection (r:0.644 and p:0.000, r:0.757 and p:0.000, r:0.757 and p:0.000, respectively). Of all the isolated 144 H. pylori strains 24 (16.6 %) were detected as resistant to claritromycine, and 18 (12.5 %) were levofloxacin. Genotypic claritromycine resistance was detected only in 15 cases with GenoType® HelicoDR, and 6 cases with Seeplex ® H. pylori -ClaR- ACE Detection. Conclusion: In our study, it was concluded that; GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection was found as the most sensitive diagnostic methods when comparing all the investigated other ones (C, H, and RUT).

Keywords: Helicobacter pylori, GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, antimicrobial resistance

Procedia PDF Downloads 137

Authors: Aleksey Fedorov

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Building a scalable platform for quantum computing remains one of the most challenging tasks in quantum science and technologies. However, the implementation of most important quantum operations with qubits (quantum analogues of classical bits), such as multiqubit Toffoli gate, requires either a polynomial number of operation or a linear number of operations with the use of ancilla qubits. Therefore, the reduction of the number of operations in the presence of scalability is a crucial goal in quantum information processing. One of the most elegant ideas in this direction is to use qudits (multilevel systems) instead of qubits and rely on additional levels of qudits instead of ancillas. Although some of the already obtained results demonstrate a reduction of the number of operation, they suffer from high complexity and/or of the absence of scalability. We show a strong reduction of the number of operations for the realization of the Toffoli gate by using qudits for a scalable multi-qudit processor. This is done on the basis of a general relation between the dimensionality of qudits and their topology of connections, that we derived.

Keywords: quantum computing, qudits, Toffoli gates, gate decomposition

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Authors: Nutnicha Wongpadungkiat, Suwit Siriwatanayotin, Aluck Thipayarat, Punchira Vongsawasdi, Chotika Viriyarattanasak

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Chicken products are major export product of Thailand. With a dramatically increasing consumption of chicken product in the world, there are abundant wastes from chicken meat processing industry. Recently, much research in the development of value-added products from chicken meat industry has focused on the production of protein hydrolysate, utilized as food ingredients for human diet and animal feed. The present study aimed to determine the effect of thermal pre-treatment on functional properties of chicken protein hydrolysate. Chicken breasts were heated at 40, 60, 80 and 100ºC prior to hydrolysis by Alcalase at 60ºC, pH 8 for 4 hr. The hydrolysate was freeze-dried, and subsequently used for assessment of its functional properties molecular weight by gel electrophoresis (SDS-PAGE). The obtained results show that increasing the pre-treatment temperature increased oil holding capacity and emulsion stability while decreasing antioxidant activity and water holding capacity. The SDS-PAGE analysis showed the evidence of protein aggregation in the hydrolysate treated at the higher pre-treatment temperature. These results suggest the connection between molecular weight of the hydrolysate and its functional properties.

Keywords: chicken protein hydrolysate, enzymatic hydrolysis, thermal pretreatment, functional properties

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Authors: Nadia Naseem, Farwa Batool, Nasir Mehmood, AbdulHannan Nagi

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Background: The incidence and mortality of breast cancer vary significantly in geographically distinct populations. In Pakistan, breast cancer has shown an increase in incidence in young females and is characterized by more aggressive behavior. The tumor suppressor TP53 gene is a crucial genetic factor that plays a significant role in breast carcinogenesis. This study investigated the TP53 mutations in molecular subtypes of both nodes negative and positive breast cancer in young Pakistani patients. Material and Methods: p53, Estrogen Receptor (ER), Progesterone Receptor (PR), Her-2 neu and Ki 67 expressions were analyzed immunohistochemically in a series of 75 node negative (A) and 75 node positive (B) young (aged: 19-40 years) breast cancer patients diagnosed between 2014 to 2017 at two leading hospitals of Punjab, Pakistan. Tumor tissue specimens and peripheral blood samples were examined for TP53 mutations by direct sequencing of the gene (exons 4-9). The relation of TP53 mutations to these markers and clinicopathological data was investigated. Results: Mean age of the patients was 32.4 + 9.1 SD. Invasive breast carcinoma was the most frequent histological variant (A=92%, B=94.6%). Grade 3 carcinoma was the commonest grade (A=72%, B=81.3%). Triple negative cases (ER-, PR-, Her-2) formed most of the molecular subtypes (A=44%, B=50.6%). A total of 17.2% (A: 6.6%, B: 10.6%) patients showed TP53 mutations. Mutations were significantly more frequent in triple negative cases (A: 74.8%, B: 62.2%) compared to HER2-positive patients (P < 0.0001). In the multivariate analysis of the whole patient group, the independent prognosticator were triple negative cases (P=0.021), TP53 overexpression by IHC (P=0.001) and advanced-stage disease (P=0.007). No statistically significant correlation between TP53 mutations and clinicopathological parameters was found (P < 0.05). Conclusions: It is concluded that TP53 mutations are infrequently present in breast carcinoma of young Pakistani population and there was no significant correlation between p53 mutation and early onset disease. Immunohistochemically detected TP53 expression in our resource-constrained to set up can be beneficial in predicting mutations at the younger age in our population.

Keywords: immunohistochemistry (IHC), invasive breast carcinoma (IBC), Pakistan, TP53

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Authors: Mina Kalantarzadeh, Claire Lockie-Williams, Caroline Howard

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DNA barcoding is increasingly used for identification of medicinal plants worldwide. In the last decade, a large number of DNA barcodes have been generated, and their application in species identification explored. The success of DNA barcoding process relies on the accuracy of the results from polymerase chain reaction (PCR) amplification step which could be negatively affected due to a presence of inhibitors or degraded DNA in herbal samples. An established DNA reference material can be used to support molecular characterisation protocols and prove system suitability, for fast and accurate identification of plant species. The present study describes the use of a novel reference material, the trnH-psbA British Pharmacopoeia Nucleic Acid Reference Material (trnH-psbA BPNARM), which was produced to aid in the identification of Ocimum tenuiflorum L., a widely used herb. During DNA barcoding of O. tenuiflorum, PCR amplifications of isolated DNA produced inconsistent results, suggesting an issue with either the method or DNA quality of the tested samples. The trnH-psbA BPNARM was produced and tested to check for the issues caused during PCR amplification. It was added to the plant material as control DNA before extraction and was co-extracted and amplified by PCR. PCR analyses revealed that the amplification was not as successful as expected which suggested that the amplification is affected by presence of inhibitors co-extracted from plant materials. Various potential issues were assessed during DNA extraction and optimisations were made accordingly. A DNA barcoding protocol for O. tenuiflorum was published in the British Pharmacopoeia 2016, which included the reference sequence. The trnH-psbA BPNARM accelerated degradation test which investigates the stability of the reference material over time demonstrated that it has been stable when stored at 56 °C for a year. Using this protocol and trnH-psbA reference material provides a fast and accurate method for identification of O. tenuiflorum. The optimisations of the DNA extraction using the trnH-psbA BPNARM provided a signposting method which can assist in overcoming common problems encountered when using molecular methods with medicinal plants.

Keywords: degradation, DNA extraction, nucleic acid reference material, trnH-psbA

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Authors: Marianna Maiaru, Gregory M. Odegard, Josh Kemppainen, Ivan Gallegos, Michael Olaya

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Ceramic matrix composites (CMCs) are typically used in applications that require long-term mechanical integrity at elevated temperatures. CMCs are usually fabricated using a polymer precursor that is initially polymerized in situ with fiber reinforcement, followed by a series of cycles of pyrolysis to transform the polymer matrix into a rigid glass or ceramic. The pyrolysis step typically generates volatile gasses, which creates porosity within the polymer matrix phase of the composite. Subsequent cycles of monomer infusion, polymerization, and pyrolysis are often used to reduce the porosity and thus increase the durability of the composite. Because of the significant expense of such iterative processing cycles, new generations of CMCs with improved durability and manufacturability are difficult and expensive to develop using standard Edisonian approaches. The goal of this research is to develop a computational process-modeling-based approach that can be used to design the next generation of CMC materials with optimized material and processing parameters for maximum strength and efficient manufacturing. The process modeling incorporates computational modeling tools, including molecular dynamics (MD), to simulate the material at multiple length scales. Results from MD simulation are used to inform the continuum-level models to link molecular-level characteristics (material structure, temperature) to bulk-level performance (strength, residual stresses). Processing parameters are optimized such that process-induced residual stresses are minimized and laminate strength is maximized. The multiscale process modeling method developed with this research can play a key role in the development of future CMCs for high-temperature and high-strength applications. By combining multiscale computational tools and process modeling, new manufacturing parameters can be established for optimal fabrication and performance of CMCs for a wide range of applications.

Keywords: digital engineering, finite elements, manufacturing, molecular dynamics

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Authors: Belloui Bouzid

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In this paper, broadband design of erbium doped fiber amplifier (EDFA) is demonstrated and proved experimentally. High and broad gain is covered in C and L bands. The used technique combines, in one configuration, two double passes with split band structure for the amplification of two traveled signals one for the C band and the other for L band. This new topology is to investigate the trends of high gain and wide amplification at different status of pumping power, input wavelength, and input signal power. The presented paper is to explore the performance of EDFA gain using what it can be called double pass double branch wide band amplification configuration. The obtained results show high gain and wide broadening range of 44.24 dB and 80 nm amplification respectively.

Keywords: erbium doped fiber amplifier, erbium doped fiber laser, optical amplification, fiber laser

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Authors: Vrushali Guhe, Shailza Singh

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Cutaneous leishmaniasis is neglected tropical disease present worldwide caused by the protozoan parasite Leishmania major, the therapeutic armamentarium for leishmaniasis are showing several limitations as drugs are showing toxic effects with increasing resistance by a parasite. Thus identification of novel therapeutic targets is of paramount importance. Previous studies have shown that autophagy, a cellular process, can either facilitate infection or aid in the elimination of the parasite, depending on the specific parasite species and host background in leishmaniasis. In the present study, our objective was to target the essential autophagy protein ATG8, which plays a crucial role in the survival, infection dynamics, and differentiation of the Leishmania parasite. ATG8 in Leishmania major and its homologue, LC3, in Homo sapiens, act as autophagic markers. Present study manifested the crucial role of ATG8 protein as a potential target for combating Leishmania major infection. Through bioinformatics analysis, we identified non-conserved motifs within the ATG8 protein of Leishmania major, which are not present in LC3 of Homo sapiens. Against these two non-conserved motifs, we generated a peptide library of 60 peptides on the basis of physicochemical properties. These peptides underwent a filtering process based on various parameters, including feasibility of synthesis and purification, compatibility with Selective Reaction Monitoring (SRM)/Multiple reaction monitoring (MRM), hydrophobicity, hydropathy index, average molecular weight (Mw average), monoisotopic molecular weight (Mw monoisotopic), theoretical isoelectric point (pI), and half-life. Further filtering criterion shortlisted three peptides by using molecular docking and molecular dynamics simulations. The direct interaction between ATG8 and the shortlisted peptides was confirmed through Surface Plasmon Resonance (SPR) experiments. Notably, these peptides exhibited the remarkable ability to penetrate the parasite membrane and exert profound effects on Leishmania major. The treatment with these peptides significantly impacted parasite survival, leading to alterations in the cell cycle and morphology. Furthermore, the peptides were found to modulate autophagosome formation, particularly under starved conditions, suggesting their involvement in disrupting the regulation of autophagy within Leishmania major. In vitro, studies demonstrated that the selected peptides effectively reduced the parasite load within infected host cells. Encouragingly, these findings were corroborated by in vivo experiments, which showed a reduction in parasite burden upon peptide administration. Additionally, the peptides were observed to affect the levels of LC3II within host cells. In conclusion, our findings highlight the efficacy of these novel peptides in targeting Leishmania major’s ATG8 and disrupting parasite survival. These results provide valuable insights into the development of innovative therapeutic strategies against leishmaniasis via targeting autophagy protein ATG8 of Leishmania major.

Keywords: ATG8, leishmaniasis, surface plasmon resonance, MD simulation, molecular docking, peptide designing, therapeutics

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Authors: Lutful Karim, Mohammed S. Al-kahtani

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Sensors are being used in various applications such as agriculture, health monitoring, air and water pollution monitoring, traffic monitoring and control and hence, play the vital role in the growth of big data. However, sensors collect redundant data. Thus, aggregating and filtering sensors data are significantly important to design an efficient big data framework. Current researches do not focus on aggregating and filtering data at multiple layers of sensor-based big data framework. Thus, this paper introduces (i) three layers data aggregation and framework for big data and (ii) a priority-based, dynamic data aggregation scheme (PDDA) for the lowest layer at sensors. Simulation results show that the PDDA outperforms existing tree and cluster-based data aggregation scheme in terms of overall network energy consumptions and end-to-end data transmission delay.

Keywords: big data, clustering, tree topology, data aggregation, sensor networks

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Authors: Bilal Ahmad

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Alzheimer’s disease (AD) is one of the most common neurodegenerative illnesses. However, how Gut-microbiota plays a role in the pathogenesis of AD is not well elucidated. The purpose of this literature review is to summarize and understand the current findings that may elucidate the gut microbiota's role in the development of AD. Methods: A literature review of all the relevant papers known to the author was conducted. Relevant articles, abstracts and research papers were collected from well-accepted web sources like PubMed, PMC, and Google Scholar. Results: Recent studies have shown that Gut-microbiota has an important role in the progression of AD via Gut-Microbiota-Brain Axis. The onset of AD supports the ‘Hygiene Hypothesis’, which shows that AD might begin in the Gut, causing dysbiosis, which interferes with the intestinal barrier by releasing pro-inflammatory cytokines and making its way up to the brain via the blood-brain barrier (BBB). Molecular mechanisms lipopolysaccharides and serotonin kynurenine (tryptophan) pathways have a direct association with inflammation, the immune system, neurodegeneration, and AD. Conclusion: The studies helped to analyze the molecular basis of AD, other neurological conditions like depression, autism, and Parkinson's disease and how they are linked to Gut-microbiota. Further, studies to explore the therapeutic effects of probiotics in AD and cognitive enhancement should be warranted to provide significant clinical and practical value.

Keywords: gut-microbiota, Alzheimer’s disease, second brain aging, lipopolysaccharides, short-chain fatty acids

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Authors: Harminder Kaur, Manpreet Kaur, Akanksha Kapila, Reenu

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Schiff base with general formula H₂L was derived from condensation of o-vanillin and 3-nitro-o-phenylenediamine. This Schiff base was used for the synthesis of organotin(IV) complexes with general formula R₂SnL [R=Phenyl or n-octyl] using equimolar quantities. Elemental analysis UV-Vis, FTIR, and multinuclear spectroscopic techniques (¹H, ¹³C, and ¹¹⁹Sn) NMR were carried out for the characterization of the synthesized complexes. These complexes were coloured and soluble in polar solvents. Computational studies have been performed to obtain the details of the geometry and electronic structures of ligand as well as complexes. Geometry of the ligands and complexes have been optimized at the level of Density Functional Theory with B3LYP/6-311G (d,p) and B3LYP/MPW1PW91 respectively followed by vibrational frequency analysis using Gaussian 09. Observed ¹¹⁹Sn NMR chemical shifts of one of the synthesized complexes showed tetrahedral geometry around Tin atom which is also confirmed by DFT. HOMO-LUMO energy distribution was calculated. FTIR, ¹HNMR and ¹³CNMR spectra were also obtained theoretically using DFT. Further IRC calculations were employed to determine the transition state for the reaction and to get the theoretical information about the reaction pathway. Moreover, molecular docking studies can be explored to ensure the anticancer activity of the newly synthesized organotin(IV) complexes.

Keywords: DFT, molecular docking, organotin(IV) complexes, o-vanillin, 3-nitro-o-phenylenediamine

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Authors: G. Baraneedaran, Deepak Singh, Kollipara Tejesh

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The wireless sensors network has been an active research area over the y-ear passed. Due to the limited energy and communication ability of sensor nodes, it seems especially important to design a routing protocol for WSNs so that sensing data can be transmitted to the receiver effectively, an energy-balanced routing method based on forward-aware factor (FAF-EBRM) is proposed in this paper. In FAF-EBRM, the next-hop node is selected according to the awareness of link weight and forward energy density. A spontaneous reconstruction mechanism for Local topology is designed additionally. In this experiment, FAF-EBRM is compared with LEACH and EECU, experimental results show that FAF-EBRM outperforms LEACH and EECU, which balances the energy consumption, prolongs the function lifetime and guarantees high Qos of WSN.

Keywords: energy balance, forward-aware factor (FAF), forward energy density, link weight, network performance

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Authors: R. F. B. Gonçalves, E. N. Iwama, J. A. F. F. Rocco, K. Iha

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Propellants based on Hydroxyl Terminated Polybutadiene/Ammonium Perchlorate (HTPB/AP) are the most commonly used in most of the rocket engines used by the Brazilian Armed Forces. This work aimed at the possibility of extending its useful life (currently in 10 years) by performing kinetic-chemical analyzes of its energetic material via Differential Scanning Calorimetry (DSC) and also performing computer simulation of aging process using the software Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Thermal analysis via DSC was performed in triplicates and in three heating ratios (5 ºC, 10 ºC, and 15 ºC) of rocket motor with 11 years shelf-life, using the Arrhenius equation to obtain its activation energy, using Ozawa and Kissinger kinetic methods, allowing comparison with manufacturing period data (standard motor). In addition, the kinetic parameters of internal pressure of the combustion chamber in 08 rocket engines with 11 years of shelf-life were also acquired, for comparison purposes with the engine start-up data.

Keywords: shelf-life, thermal analysis, Ozawa method, Kissinger method, LAMMPS software, thrust

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Authors: A. Kardi, R. Zagrouba, M. Alqahtani

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The Internet of Everything (IoE) presents today a very attractive and motivating field of research. It is basically based on Wireless Sensor Networks (WSNs) in which the routing task is the major analysis topic. In fact, it directly affects the effectiveness and the lifetime of the network. This paper, developed from recent works and based on extensive researches, proposes a taxonomy of routing protocols in WSNs. Our main contribution is that we propose a classification model based on nine classes namely application type, delivery mode, initiator of communication, network architecture, path establishment (route discovery), network topology (structure), protocol operation, next hop selection and latency-awareness and energy-efficient routing protocols. In order to provide a total classification pattern to serve as reference for network designers, each class is subdivided into possible subclasses, presented, and discussed using different parameters such as purposes and characteristics.

Keywords: routing, sensor, survey, wireless sensor networks, WSNs

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Authors: Shreya Sara Ittycheria, K. C. Sivakumar, Shijulal Nelson Sathi, Priya Srinivas

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hCG, a heterodimer composed of α and β subunits, is a peptide hormone having numerous biological functions. Although hCG is expressed by placenta during pregnancy, ectopic β-hCG secretion is observed in many non-trophoblastic tumors including that of breast. In-vitro and in-vivo studies done in the lab, have proved that BRCA1 defective cancers express β-hCG and when β-hCG is expressed or supplemented, it promotes tumor progression and exhibits resistance to carboplatin and ABT888, in such cancers but not in BRCA1 wild type cancers. In cancer cells, instead of binding to its regular receptor, LH-CGR, β-hCG binds with Transforming Growth Factor Receptor 2 (TGFβRII) and phosphorylates it resulting in faster tumor progression through the Smad signaling pathway. Targeting β-hCG could be a potential therapeutic strategy for managing BRCA1 defective cancers. Here, molecular docking and dynamic simulation studies were done to identify potential small molecule inhibitors against β-hCG as there are currently no such inhibitors reported. The binding sites of TGFβRII on β-hCG were identified from the top 10 predicted complexes from Z Dock. Virtual screening of selected commercially available small molecules from various libraries such as ZINC, NCI and Life Chemicals amounting to a total of 50,025 molecules were done. Four potential small molecule inhibitors were identified, RgcbPs-1, RgcbPs-2, RgcbPs-3 and RgcbPs-4 with binding affinities -60.778 kcal/mol, -45.447 kcal/mol, -65.2268 kcal/mol and -82.040 kcal/mol respectively. Further, 100ns Molecular Dynamics (MD) simulation showed that these molecules form stable complexes with β-hCG. RgcbPs-1 maintains hydrogen bonds with Q54, L52, Q46, C100, G36, C57, C38 residues, RgcbPs-2 maintains hydrogen bonds with A83 residue, RgcbPs-3 maintains hydrogen bonds with C57, Y58, R94, G101 residues and RgcbPs-4 maintains hydrogen bonds with G36, C38, T40, C57, D99, C100, G101 and L104 residues of β-hCG all of which coincide with the TGFβRII binding site on β-hCG. These results show that these two inhibitors could be used either singly or in combination for inhibiting β-hCG from binding to TGFβRII and thereby directly inhibiting the tumorigenesis pathway.

Keywords: β-hCG, breast cancer, dynamic simulations, molecular docking, small molecule inhibitors, virtual screening.

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Authors: Barsha Saha, Shouvik Chakravarty, Sukanta Ray, Kshaunish Das, Nidhan K. Biswas, Srikanta Goswami

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Pancreatic Ductal Adenocarcinoma is a well-recognised cause of cancer death with a five-year survival rate of about 9%, and its incidence in India has been found to be increased manifold in recent years. Due to delayed detection, this highly metastatic disease has a poor prognosis. Several molecular alterations happen during the progression of the disease from pre-cancerous conditions, and many such alterations could be investigated for their biomarker potential. MicroRNAs have been shown to be prognostic for PDAC patients in a variety of studies. We hereby used NGS technologies to evaluate the role of small RNA changes during pancreatic cancer development from chronic pancreatitis. Plasma samples were collected from pancreatic cancer patients (n=16), chronic pancreatitis patients (n=8), and also from normal individuals (n=16). Pancreatic tumour tissue (n=5) and adjacent normal tissue samples (n=5) were also collected. Sequencing of small RNAs was carried out after small RNAs were isolated from plasma samples and tissue samples. We find that certain microRNAs are highly deregulated in pancreatic cancer patients in comparison to normal samples. A combinatorial analysis of plasma and tissue microRNAs and subsequent exploration of their targets and altered molecular pathways could not only identify potential biomarkers for disease diagnosis but also help to understand the underlying mechanism.

Keywords: small RNA sequencing, pancreatic cancer, biomarkers, tissue sample

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Authors: Lynda Golea, Rachid Chebaki

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Schiff bases contain heterocyclic structural units with N and O donor atoms which plays an important role in coordination chemistry. Azomethine groups are a broad class of widely used compounds with applications in many fields, including analytical, inorganic chemistry and biological. Schiff's base is of promising research interest due to the widespread antibacterial resistance in medical science. In addition, the research is essential to generate Schiff base metal complexes with various applications. Schiff complexes have been used as drugs and have antibacterial, antifungal, antiviral, and anti-inflammatory properties. The various donor atoms they contain offer a special ability for metal binding. In this research on the physicochemical properties of azomethine groups, we synthesized and studied the Schiff base compounds by a condensation reaction of tryptamines and acetophenone in ethanol. The structure of the prepared compound was interpreted using 1H NMR, 13C NMR, UV-vis and FT-IR. A computational analysis at the level of DFT with functional B3LYP in conjunction with the base 6-311+G (d, p) was conducted to study its electronic and molecular structure. The biological study was performed on three bacterial strains usually causing infection, including Gram-positive and Gram-negative, for antibacterial activity. Results showed moderate biological activity and proportional activity with increasing concentration.

Keywords: azomethine, HOMO, LUMO, RMN, molecular docking

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Authors: Tatiana N. Astakhova, Alexander E. Saprygin, Tatyana A. Golovko, Alexander N. Savostyanov, Mikhail S. Vlasov, Natalia V. Borisova, Alexandera G. Karpova, Urana N. Kavai-ool, Elena D. Mokur-ool, Nikolay A. Kolchanov, Lubomir I. Aftanas

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The study is dedicated to the research of brain activity in bilingual inhabitants of Siberia. We compared behavioral reactions and event-related potentials in Turkic-speaking inhabitants of Siberia (Tuvinians and Yakuts) and Russians. 63 healthy aboriginals of the Tyva Republic, 29 inhabitants of the Sakha (Yakutia) Republic, and 55 Russians from Novosibirsk participated in the study. All the healthy and right-handed participants, matched on age and sex, were students of different universities. EEG’s were recorded during the solving of linguistic tasks. In these tasks, participants had to find a syntax error in the written sentences. There were four groups of sentences: Russian, English, Tuvinian, and Yakut. All participants completed the tasks in Russian and English. Additionally, Tuvinians and Yakuts completed the tasks in Tuvinian or Yakut respectively. For Russians, EEG's were recorded using 128-channels according to the extended International 10-10 system, and the signals were amplified using “Neuroscan (USA)” amplifiers. For Tuvinians and Yakuts, EEG's were recorded using 64-channels and amplifiers Brain Products, Germany. In all groups, 0.3-100 Hz analog filtering and sampling rate 1000 Hz were used. As parameters of behavioral reactions, response speed and the accuracy of recognition were used. Event-related potentials (ERP) responses P300 and P600 were used as indicators of brain activity. The behavioral reactions showed that in Russians, the response speed for Russian was faster than for English. Also, the accuracy of solving tasks was higher for Russian than for English. The peak P300 in Russians were higher for English, the peak P600 in the left temporal cortex were higher for the Russian language. Both Tuvinians and Yakuts have no difference in accuracy of solving tasks in Russian and in their respective national languages. However, the response speed was faster for tasks in Russian than for tasks in their national language. Tuvinians and Yakuts showed bad accuracy in English, but the response speed was higher for English than for Russian and the national languages. This can be explained by the fact that they did not think carefully and gave a random answer for English. In Tuvinians, The P300 and P600 amplitudes and cortical topology were the same for Russian and Tuvinian and different for English. In Yakuts, the P300 and P600 amplitudes and topology of ERP for Russian were the same as what Russians had for Russian. In Yakuts, brain reactions during Yakut and English comprehension had no difference, and were reflected to foreign language comprehension - while the Russian language comprehension was reflected to native language comprehension. We found out that the Tuvinians recognized both Russian and Tuvinian as native languages, and English as a foreign language. The Yakuts recognized both English and Yakut as a foreign language, and only Russian as a native language. According to the inquirer, both Tuvinians and Yakuts use the national language as a spoken language, whereas they don’t use it for writing. It can well be a reason that Yakuts perceive the Yakut writing language as a foreign language while writing Russian as their native.

Keywords: EEG, ERP, native and foreign languages comprehension, Siberian inhabitants

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Authors: Jessica C. Bannon, Cleso M. Jordao Jr., Mohammad Melebari, Carlos Leon-Velarde, Roger Johnson, Keith Warriner

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There has been an increased incidence of non-O157 Shiga Toxin Escherichia coli (STEC) with six serotypes (Top 6) being implicated in causing haemolytic uremic syndrome (HUS). Beef has been suggested to be a significant vehicle for non-O157 STEC although conclusive evidence has yet to be obtained. The following aimed to determine the prevalence of the Top 6 non-O157 STEC in beef processing using three different diagnostic platforms then characterize the recovered isolates. Hide, carcass and environmental swab samples (n = 60) were collected from a beef processing facility over a 12 month period. Enriched samples were screened using Biocontrol GDS, BAX or PALLgene molecular diagnostic tests. Presumptive non-O157 STEC positive samples were confirmed using conventional PCR and serology. STEC was detected by GDS (55% positive), BAX (85% positive), and PALLgene (93%). However, during confirmation testing only 8 of the 60 samples (13%) were found to harbour STEC. Interestingly, the presence of virulence factors in the recovered isolates was unstable and readily lost during subsequent sub-culturing. There is a low prevalence of Top 6 non-O157 STEC associated with beef although other serotypes are encountered. Yet, the instability of the virulence factors in recovered strains would question their clinical relevance.

Keywords: beef, food microbiology, shiga toxin, STEC

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Authors: Maria Bercea, Bernhard A. Wolf

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The thermodynamic behavior for solutions of poly (methyl methacrylate-ran-t-butyl methacrylate) of variable composition as compared with the corresponding homopolymers was investigated by light scattering measurements carried out for dilute solutions and vapor pressure measurements of concentrated solutions. The complex dependencies of the Flory Huggins interaction parameter on concentration and copolymer composition in solvents of different polarity (toluene and chloroform) can be understood by taking into account the ability of the polymers to rearrange in a response to changes in their molecular surrounding. A recent unified thermodynamic approach was used for modeling the experimental data, being able to describe the behavior of the different solutions by means of two adjustable parameters, one representing the effective number of solvent segments and another one accounting for the interactions between the components. Thus, it was investigated how the solvent quality changes with the composition of the copolymers through the Gibbs energy of mixing as a function of polymer concentration. The largest reduction of the Gibbs energy at a given composition of the system was observed for the best solvent. The present investigation proves that the new unified thermodynamic approach is a general concept applicable to homo- and copolymers, independent of the chain conformation or shape, molecular and chemical architecture of the components and of other dissimilarities, such as electrical charges.

Keywords: random copolymers, Flory Huggins interaction parameter, Gibbs energy of mixing, chemical architecture

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Authors: Mansi Srivastava, Uzma Saqib, Adnan Naim, Anjali Roy, Dongfang Liu, Deepak Bhatnagar, Ravinder Ravinder, Mirza S. Baig

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Macrophages polarize to proinflammatory M1 or anti-inflammatory M2 states with distinct physiological functions. This transition within the M1 to M2 phenotypes decides the nature, duration, and severity of an inflammatory response. However, inspite of a substantial understanding of the fate of these phenotypes, the underlying molecular mechanisms are not well understood. We have investigated the role of Neuronal nitric oxide synthase (NOS1) mediated regulation of Activator protein 1 (AP-1) transcription factor in macrophages as a critical effector of macrophage phenotypic change. Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of jun, Fos, and ATF family proteins. We determined that NOS1-derived nitric oxide (NO) facilitate Fos and jun interaction which induces IL12 & IL23 expression. Pharmacological inhibition of NOS1 inhibits Fos and jun interaction but increases ATF2 and Fos dimerization. Switching of Fos and jun dimer to ATF2 and jun dimerization switches phenotype from IL–12high IL-23high IL-10low to IL–12low IL-23lowIL-10high phenotype, respectively. Together, these findings highlight a key role of the TLR4-NOS1-AP1 signaling axis in regulating macrophage polarization.

Keywords: inflammation, macrophage, lipopolysaccharide (LPS), proinflammatory cytokines, activator protein 1 (AP-1), neuronal nitric oxide synthase (NOS1)

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