Search results for: molecular virology and microbiology
1903 Magneto-Transport of Single Molecular Transistor Using Anderson-Holstein-Caldeira-Leggett Model
Authors: Manasa Kalla, Narasimha Raju Chebrolu, Ashok Chatterjee
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We have studied the quantum transport properties of a single molecular transistor in the presence of an external magnetic field using the Keldysh Green function technique. We also used the Anderson-Holstein-Caldeira-Leggett Model to describe the single molecular transistor that consists of a molecular quantum dot (QD) coupled to two metallic leads and placed on a substrate that acts as a heat bath. The phonons are eliminated by the Lang-Firsov transformation and the effective Hamiltonian is used to study the effect of an external magnetic field on the spectral density function, Tunneling Current, Differential Conductance and Spin polarization. A peak in the spectral function corresponds to a possible excitation. In the presence of a magnetic field, the spin-up and spin-down states are degenerate and this degeneracy is lifted by the magnetic field leading to the splitting of the central peak of the spectral function. The tunneling current decreases with increasing magnetic field. We have observed that even the differential conductance peak in the zero magnetic field curve is split in the presence electron-phonon interaction. As the magnetic field is increased, each peak splits into two peaks. And each peak indicates the existence of an energy level. Thus the number of energy levels for transport in the bias window increases with the magnetic field. In the presence of the electron-phonon interaction, Differential Conductance in general gets reduced and decreases faster with the magnetic field. As magnetic field strength increases, the spin polarization of the current is increasing. Our results show that a strongly interacting QD coupled to metallic leads in the presence of external magnetic field parallel to the plane of QD acts as a spin filter at zero temperature.Keywords: Anderson-Holstein model, Caldeira-Leggett model, spin-polarization, quantum dots
Procedia PDF Downloads 1741902 Multiscale Process Modeling Analysis for the Prediction of Composite Strength Allowables
Authors: Marianna Maiaru, Gregory M. Odegard
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During the processing of high-performance thermoset polymer matrix composites, chemical reactions occur during elevated pressure and temperature cycles, causing the constituent monomers to crosslink and form a molecular network that gradually can sustain stress. As the crosslinking process progresses, the material naturally experiences a gradual shrinkage due to the increase in covalent bonds in the network. Once the cured composite completes the cure cycle and is brought to room temperature, the thermal expansion mismatch of the fibers and matrix cause additional residual stresses to form. These compounded residual stresses can compromise the reliability of the composite material and affect the composite strength. Composite process modeling is greatly complicated by the multiscale nature of the composite architecture. At the molecular level, the degree of cure controls the local shrinkage and thermal-mechanical properties of the thermoset. At the microscopic level, the local fiber architecture and packing affect the magnitudes and locations of residual stress concentrations. At the macroscopic level, the layup sequence controls the nature of crack initiation and propagation due to residual stresses. The goal of this research is use molecular dynamics (MD) and finite element analysis (FEA) to predict the residual stresses in composite laminates and the corresponding effect on composite failure. MD is used to predict the polymer shrinkage and thermomechanical properties as a function of degree of cure. This information is used as input into FEA to predict the residual stresses on the microscopic level resulting from the complete cure process. Virtual testing is subsequently conducted to predict strength allowables. Experimental characterization is used to validate the modeling.Keywords: molecular dynamics, finite element analysis, processing modeling, multiscale modeling
Procedia PDF Downloads 851901 Effect of Iron Contents on Rheological Properties of Syndiotactic Polypropylene/iron Composites
Authors: Naveed Ahmad, Farooq Ahmad, Abdul Aal
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The effect of iron contents on the rheological behavior of sPP/iron composites in the melt phase was investigated using a series of syndiotactic polypropylene/iron (sPP/iron) composite samples. Using the Advanced Rheometric Expansion System, studies with small amplitude oscillatory shear were conducted (ARES). It was discovered that the plateau modulus rose along with the iron loading. Also it was found that both entanglement molecular weight and packing length decrease with increase in iron loading.. This finding demonstrates how iron content in polymer/iron composites affects chain parameters and dimensions, which in turn affects the entire chain dynamics.Keywords: plateau modulus, packing lenght, polymer/iron composites, rheology, entanglement molecular weight
Procedia PDF Downloads 1511900 Impact of Wastewater from Outfalls of River Ganga on Germination Percentage and Growth Parameters of Bitter Gourd (Momordica charantia L.) with Antioxidant Activity Study
Authors: Sayanti Kar, Amitava Ghosh, Pritam Aitch, Gupinath Bhandari
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An extensive seasonal analysis of wastewater had been done from outfalls of river Ganga in Howrah, Hooghly, 24 PGS (N) District, West Bengal, India during 2017. The morphological parameters of Bitter gourd (Momordica charantia L.) were estimated under wastewater treatment. An approach to study the activity within the range of low molecular weight peptide 3-0.5 kDa were taken through its extraction and purification by ion exchange resin column, cation, and anion exchanger. HPLC analysis had been done for both in wastewater treated and untreated plants. The antioxidant activity by using DPPH and germination percentage in control and treated plants were also determined in relation to wastewater effect. The inhibition of growth and its parameters were maximum in pre-monsoon in comparing to post-monsoon and monsoon season. The study also helped to explore the effect of wastewater on the peptidome of Bitter gourd (Momordica charantia L.). Some of these low molecular weight peptide(s) (3-0.5 kDa) also inhibited during wastewater treatment. Expression of particular peptide(s) or absence of some peptide(s) in chromatogram indicated the adverse effects on plants which may be the indication of stressful condition. Pre monsoon waste water was found to create more impact than other two.Keywords: bitter gourd (Momordica charantia l.), low molecular weight peptide, river ganga, waste water
Procedia PDF Downloads 1191899 Biosensor Design through Molecular Dynamics Simulation
Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang
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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structure-process-property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.Keywords: biosensor, DNA, biomarker, molecular dynamics simulation
Procedia PDF Downloads 4551898 Molecular Detection of Viruses Causing Hemorrhagic Fevers in Rodents in the South-West of Korea
Authors: Sehrish Jalal, Choon-Mee Kim, Dong-Min Kim
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Background: Many pathogens causing hemorrhagic fevers of medical and veterinary importance have been identified and isolated from rodents in the Republic of Korea (ROK). Objective: We investigated the prevalence of emerging viruses causing hemorrhagic fevers, such as hemorrhagic fever with renal syndrome (HFRS), severe fever with thrombocytopenia syndrome (SFTS) and flaviviruses, from wild rodents. Methods: Striped field mice, Apodemus agrarius, (n=39) were captured during 2014-2015 in the south-west of ROK. Using molecular methods, lung samples were evaluated for SFTS virus, HFRS virus and flavivirus, and seropositivity was evaluated in the blood. Results: A high positive rate of Hantavirus (46.2%) was detected in A.agrarius lungs by reverse transcription-nested polymerase chain reaction (RT-N-PCR). The monthly prevalence of HFRS virus was 16.7% in October, 86.7% in November and 25% in August of the following year (p < 0.001). Moreover, 17.9% of blood samples were serologically positive for Hantavirus antibodies. The most prevalent strain in A. agrarius was Hantaan virus. All samples were positive for neither SFTS nor flavivirus. Conclusion: Hantan virus was detected in 86.7% of A. agrarius in November (autumn), and thus, virus shedding from A. agrarius can increase the risk of humans contracting HFRS. These findings may help to predict and prevent disease outbreaks in ROK.Keywords: hemorrhagic fever virus, molecular diagnostic technique, rodents, Korea
Procedia PDF Downloads 1481897 PYURF and ZED9 Have a Prominent Role in Association with Molecular Pathways in Bortezomib in Myeloma Cells in Acute Myeloid Leukemia
Authors: Atena Sadat Hosseini, Mohammadhossein Habibi
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Acute myeloid leukemia (AML) is the most typically diagnosed leukemia. In older adults, AML imposes a dismal outcome. AML originates with a dominant mutation, then adds collaborative, transformative mutations leading to myeloid transformation and clinical/biological heterogeneity. Several chemotherapeutic drugs are used for this cancer. These drugs are naturally associated with several side effects, and finding a more accurate molecular mechanism of these drugs can have a significant impact on the selection and better candidate of drugs for treatment. In this study, we evaluated bortezomibin myeloma cells using bioinformatics analysis and evaluation of RNA-Seq data. Then investigated the molecular pathways proteins- proteins interactions associated with this chemotherapy drug. A total of 658upregulated genes and 548 downregulated genes were sorted.AUF1 (hnRNP D0) binds and destabilizes mRNA, degradation of GLI2 by the proteasome, the role of GTSE1 in G2/M progression after G2 checkpoint, TCF dependent signaling in response to WNT demonstrated in upregulated genes. Besides insulin resistance, AKT phosphorylates targets in the nucleus, cytosine methylation, Longevity regulating pathway, and Signal Transduction of S1P Receptor were related to low expression genes. With respect to this results, HIST2H2AA3, RP11-96O20.4, ZED9, PRDX1, and DOK2, according to node degrees and betweenness elements candidates from upregulated genes. in the opposite side, PYURF, NRSN1, FGF23, UPK3BL, and STAG3 were a prominent role in downregulated genes. Sum up, Using in silico analysis in the present study, we conducted a precise study ofbortezomib molecular mechanisms in myeloma cells. so that we could take further evaluation to discovermolecular cancer therapy. Naturally, more additional experimental and clinical procedures are needed in this survey.Keywords: myeloma cells, acute myeloid leukemia, bioinformatics analysis, bortezomib
Procedia PDF Downloads 911896 Pathological and Molecular Diagnosis of Caseous Lymphadenitis in Chinkara Deer (Gazella Bennettii), in Pakistan
Authors: Mudassar Iqbal, Riaz Hussain, Khalid Mehmood, Farah Ali, Fazal Mahmood, Abdul Ghaffar
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Corynebacterium pseudotuberculosis is an important cause of caseous lymphadenitis (CL), a complex, chronic devastating and destructive disease of small ruminants. In present study, postmortem examination of Chinkara deer (n=25) was conducted in year 2014. Pus samples suggestive of CL were collected from the superficial lymph nodes, liver, spleen and lungs during necropsy and subjected to standard microbiological procedures for isolation and molecular analysis of bacterial pathogens. Pus samples collected from carcasses (25) presenting clinical lesions of C. pseudotuberculosis infection was identified in 19 (76%) carcasses on the basis of culture characteristics. The frequency of C. pseudotuberculosis bacterium was higher in older animals as compared to young animals. Grossly, multiple tubercles of variable size having caseous material were observed in liver, lungs, spleen and lymph nodes. Histopathologically, tissue sections from all the visceral organs were extensively plugged with abscess. In present study specific prolineiminopeptidase (PIP) gene of the C. pseudotuberculosis was amplified by the Polymerase chain reaction technique (PCR) in 17(25) cases. The efficient and reliable molecular analysis along with necropsy findings in present study can be used as valuable approach for diagnosis of caseous lymphadenitis in small ruminants.Keywords: Chinkara deer, Corynebacterium pseudotuberculosis, Caseous lymphadenitis, PCR
Procedia PDF Downloads 4751895 Assessment of DNA Degradation Using Comet Assay: A Versatile Technique for Forensic Application
Authors: Ritesh K. Shukla
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Degradation of biological samples in terms of macromolecules (DNA, RNA, and protein) are the major challenges in the forensic investigation which misleads the result interpretation. Currently, there are no precise methods available to circumvent this problem. Therefore, at the preliminary level, some methods are urgently needed to solve this issue. In this order, Comet assay is one of the most versatile, rapid and sensitive molecular biology technique to assess the DNA degradation. This technique helps to assess DNA degradation even at very low amount of sample. Moreover, the expedient part of this method does not require any additional process of DNA extraction and isolation during DNA degradation assessment. Samples directly embedded on agarose pre-coated microscopic slide and electrophoresis perform on the same slide after lysis step. After electrophoresis microscopic slide stained by DNA binding dye and observed under fluorescent microscope equipped with Komet software. With the help of this technique extent of DNA degradation can be assessed which can help to screen the sample before DNA fingerprinting, whether it is appropriate for DNA analysis or not. This technique not only helps to assess degradation of DNA but many other challenges in forensic investigation such as time since deposition estimation of biological fluids, repair of genetic material from degraded biological sample and early time since death estimation could also be resolved. With the help of this study, an attempt was made to explore the application of well-known molecular biology technique that is Comet assay in the field of forensic science. This assay will open avenue in the field of forensic research and development.Keywords: comet assay, DNA degradation, forensic, molecular biology
Procedia PDF Downloads 1491894 Molecular Identification and Genotyping of Human Brucella Strains Isolated in Kuwait
Authors: Abu Salim Mustafa
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Brucellosis is a zoonotic disease endemic in Kuwait. Human brucellosis can be caused by several Brucella species with Brucella melitensis causing the most severe and Brucella abortus the least severe disease. Furthermore, relapses are common after successful chemotherapy of patients. The classical biochemical methods of culture and serology for identification of Brucellae provide information about the species and serotypes only. However, to differentiate between relapse and reinfection/epidemiological investigations, the identification of genotypes using molecular methods is essential. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-16] were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. The 16S rRNA gene sequencing suggested that all the strains were B. melitensis and real-time PCR confirmed their species identity as B. melitensis. The ERIC-PCR band profiles produced a dendrogram of 75 branches suggesting each strain to be of a unique type. The cluster classification, based on ~ 80% similarity, divided all the ERIC genotypes into two clusters, A and B. Cluster A consisted of 9 ERIC genotypes (A1-A9) corresponding to 9 individual strains. Cluster B comprised of 13 ERIC genotypes (B1-B13) with B5 forming the largest cluster of 51 strains. MLVA-16 identified all isolates as B. melitensis and divided them into 71 MLVA-types. The cluster analysis of MLVA-16-types suggested that most of the strains in Kuwait originated from the East Mediterranean Region, a few from the African group and one new genotype closely matched with the West Mediterranean region. In conclusion, this work demonstrates that B. melitensis, the most pathogenic species of Brucella, is prevalent in Kuwait. Furthermore, MLVA-16 is the best molecular method, which can identify the Brucella species and genotypes as well as determine their origin in the global context. Supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.Keywords: Brucella, ERIC-PCR, MLVA-16, RT-PCR, 16S rRNA gene sequencing
Procedia PDF Downloads 3841893 Aqueous Hydrogen Sulphide in Slit-Shaped Silica Nano-Pores: Confinement Effects on Solubility, Structural and Dynamical Properties
Authors: Sakiru Badmos, David R. Cole, Alberto Striolo
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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations
Procedia PDF Downloads 1551892 Assessing the Material Determinants of Cavity Polariton Relaxation using Angle-Resolved Photoluminescence Excitation Spectroscopy
Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury
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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling
Procedia PDF Downloads 651891 Effect of Hydroxyl Functionalization on the Mechanical and Fracture Behaviour of Monolayer Graphene
Authors: Akarsh Verma, Avinash Parashar
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The aim of this article is to study the effects of hydroxyl functional group on the mechanical strength and fracture toughness of graphene. This functional group forms the backbone of intrinsic atomic structure of graphene oxide (GO). Molecular dynamics-based simulations were performed in conjunction with reactive force field (ReaxFF) parameters to capture the mode-I fracture toughness of hydroxyl functionalised graphene. Moreover, these simulations helped in concluding that spatial distribution and concentration of hydroxyl functional group significantly affects the fracture morphology of graphene nanosheet. In contrast to literature investigations, atomistic simulations predicted a transition in the failure morphology of hydroxyl functionalised graphene from brittle to ductile as a function of its spatial distribution on graphene sheet.Keywords: graphene, graphene oxide, ReaxFF, molecular dynamics
Procedia PDF Downloads 1721890 DNA-Polycation Condensation by Coarse-Grained Molecular Dynamics
Authors: Titus A. Beu
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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.
Procedia PDF Downloads 1141889 Phylogenetic Analysis Based On the Internal Transcribed Spacer-2 (ITS2) Sequences of Diadegma semiclausum (Hymenoptera: Ichneumonidae) Populations Reveals Significant Adaptive Evolution
Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan
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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection
Procedia PDF Downloads 4091888 Physicochemical and Microbiological Assessment of Source and Stored Domestic Water from Three Local Governments in Ile-Ife, Nigeria
Authors: Mary A. Bisi-Johnson, Kehinde A. Adediran, Saheed A. Akinola, Hamzat A. Oyelade
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Some of the main problems man contends with are the quantity (source and amount) and quality of water in Nigeria. Scarcity leads to water being obtained from various sources and microbiological contaminations of the water may thus occur between the collection point and the point of usage. Thus, this study aims to assess the general and microbiological quality of domestic water sources and household stored water used within selected areas in Ile-Ife, South-Western part of Nigeria for microbial contaminants. Physicochemical and microbiological examination were carried out on 45 source and stored water samples collected from well and spring in three different local government areas i.e. Ife east, Ife-south, and Ife-north. Physicochemical analysis included pH value, temperature, total dissolved solid, dissolved oxygen, and biochemical oxygen demand. Microbiology involved most probable number analysis, total coliform, heterotrophic plate, faecal coliform, and streptococcus count. The result of the physicochemical analysis of samples showed anomalies compared to acceptable standards with the pH value of 7.20-8.60 for stored and 6.50-7.80 for source samples as the total dissolved solids (TDS of stored 20-70mg/L, source 352-691mg/L), dissolved oxygen (DO of stored 1.60-9.60mg/L, source 1.60-4.80mg/L), biochemical oxygen demand (BOD stored 0.80-3.60mg/L, source 0.60-5.40mg/L). General microbiological quality indicated that both stored and source samples with the exception of a sample were not within acceptable range as indicated by analysis of the MPN/100ml which ranges (stored 290-1100mg/L, source 9-1100mg/L). Apart from high counts, most samples did not meet the World Health Organization standard for drinking water with the presence of some pathogenic bacteria and fungi such as Salmonella and Aspergillus spp. To annul these constraints, standard treatment methods should be adopted to make water free from contaminants. This will help identify common and likely water related infection origin within the communities and thus help guide in terms of interventions required to prevent the general populace from such infections.Keywords: domestic, microbiology, physicochemical, quality, water
Procedia PDF Downloads 3541887 DNA Based Identification of Insect Vectors for Zoonotic Diseases From District Faisalabad, Pakistan
Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas
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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1
Procedia PDF Downloads 1611886 Molecular Epidemiology of Egyptian Biomphalaria Snail: The Identification of Species, Diagnostic of the Parasite in Snails and Host Parasite Relationship
Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din
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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis
Procedia PDF Downloads 1921885 Investigation of Genetic Variation among Anemone narcissiflora L. Population Using PCR-RAPD Molecular Marker
Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian
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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR
Procedia PDF Downloads 4711884 Docking and Dynamic Molecular Study of Isoniazid Derivatives as Anti-Tuberculosis Drug Candidate
Authors: Richa Mardianingrum, Srie R. N. Endah
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In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide
Procedia PDF Downloads 1751883 Molecular Epidemiologic Distribution of HDV Genotypes among Different Ethnic Groups in Iran: A Systematic Review
Authors: Khabat Barkhordari
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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.Keywords: HDV, genotype, epidemiology, distribution
Procedia PDF Downloads 2641882 Ab Initio Spectroscopic Study of the Electronic Properties of the (Bana)+ Molecular Ion
Authors: Tahani H. Alluhaybi, Leila Mejrissi
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In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy
Procedia PDF Downloads 1011881 Thiazolo[5,4-D]Thiazole-Core Organic Chromophore with Furan Spacer for Organic Solar Cells
Authors: M. Nazim, S. Ameen, H. K. Seo, H. S. Shin
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Energy is the basis of life and strong attention has been growing for the cost-effective energy production. Recently, solution-processed small molecule organic solar cells (SMOSCs) have grown much attention due to the wages such as well-defined molecular structures, definite molecular weight, easy synthesis and easy purification techniques. In particular, the size of donor (D) and acceptor (A) unit is a crucial factor for the exciton-diffusion towards D-A interface and then charge-separation for the effective charge-transport to the electrodes. Furan-bridged materials are more electron-rich, high fluorescence, with better molecular-packing, and greater rigidity and greater solubility than their thiophene-counterparts In this work, a furan-bridged thiazolo[5,4-d]thiazole based organic small molecule (RFTzR) was formulated and applied for BHJ organic solar cells (OSCs). The introduction of furan spacer with two terminal alkyl units improved its absorption and solubility in the common organic solvents, significantly. RFTzR exhibited a HOMO and LUMO energy levels of -5.36 eV and -3.14 eV, respectively. The fabricated solar cell devices of RFTzR (donor) with PC60BM (acceptor) as photoactive materials showed high performance of 2.72% (RFTzR:PC60BM, 2:1, w/w) ratio with open-circuit voltage of 0.756 V and high photocurrent density of 10.13 mA/cm².Keywords: chromophore, organic solar cells, photoactive materials, small molecule
Procedia PDF Downloads 1581880 Typification and Determination of Antibiotic Susceptibility Profiles with E Test Methods of Anaerobic Gram Negative Bacilli Isolated from Various Clinical Specimen
Authors: Cengiz Demir, Recep Keşli, Gülşah Aşık
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Objective: This study was carried out with the purpose of defining by using the E test method and determining the antibiotic resistance profiles of Gram-negative anaerobic bacilli isolated from various clinical specimens obtained from patients with suspected anaerobic infections and referred to Medical Microbiology Laboratory of Afyon Kocatepe University, ANS Application and Research Hospital. Methods: Two hundred and seventy eight clinical specimens were examined for isolation of the anaerobic bacteria in Medical Microbiology Laboratory between the 1st November 2014 and 30th October 2015. Specimens were cultivated by using Scheadler agar that 5% defibrinated sheep blood added, and Scheadler broth. The isolated anaerobic Gram-negative bacilli were identified conventional methods and Vitek 2 (ANC ID Card, bioMerieux, France) cards. Antibiotic resistance rates against to penicillin G, clindamycin, cefoxitin, metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem were determined with E-test method for each isolate. Results: Of the isolated twenty-eight anaerobic gram negative bacilli fourteen were identified as the B. fragilis group, 9 were Prevotella group, and 5 were Fusobacterium group. The highest resistance rate was found against penicillin (78.5%) and resistance rates against clindamycin and cefoxitin were found as 17.8% and 21.4%, respectively. Against to the; metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem, no resistance was found. Conclusion: Since high rate resistance has been detected against to penicillin in the study penicillin should not be preferred in empirical treatment. Cefoxitin can be preferred in empirical treatment; however, carrying out the antibiotic sensitivity testing will be more proper and beneficial. No resistance was observed against carbapenem group antibiotics and metronidazole; so that reason, these antibiotics should be reserved for treatment of infectious caused by resistant strains in the future.Keywords: anaerobic gram-negative bacilli, anaerobe, antibiotics and resistance profiles, e-test method
Procedia PDF Downloads 2961879 Analysis of Some Produced Inhibitors for Corrosion of J55 Steel in NaCl Solution Saturated with CO₂
Authors: Ambrish Singh
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The corrosion inhibition performance of pyran (AP) and benzimidazole (BI) derivatives on J55 steel in 3.5% NaCl solution saturated with CO₂ was investigated by electrochemical, weight loss, surface characterization, and theoretical studies. The electrochemical studies included electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), electrochemical frequency modulation (EFM), and electrochemical frequency modulation trend (EFMT). Surface characterization was done using contact angle, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques. DFT and molecular dynamics (MD) studies were done using Gaussian and Materials Studio softwares. All the studies suggested the good inhibition by the synthesized inhibitors on J55 steel in 3.5% NaCl solution saturated with CO₂ due to the formation of a protective film on the surface. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface.Keywords: corrosion, inhibitor, EFM, AFM, DFT, MD
Procedia PDF Downloads 961878 The Rational Design of Original Anticancer Agents Using Computational Approach
Authors: Majid Farsadrooh, Mehran Feizi-Dehnayebi
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Serum albumin is the most abundant protein that is present in the circulatory system of a wide variety of organisms. Although it is a significant macromolecule, it can contribute to osmotic blood pressure and also, plays a superior role in drug disposition and efficiency. Molecular docking simulation can improve in silico drug design and discovery procedures to propound a lead compound and develop it from the discovery step to the clinic. In this study, the molecular docking simulation was applied to select a lead molecule through an investigation of the interaction of the two anticancer drugs (Alitretinoin and Abemaciclib) with Human Serum Albumin (HSA). Then, a series of new compounds (a-e) were suggested using lead molecule modification. Density functional theory (DFT) including MEP map and HOMO-LUMO analysis were used for the newly proposed compounds to predict the reactivity zones on the molecules, stability, and chemical reactivity. DFT calculation illustrated that these new compounds were stable. The estimated binding free energy (ΔG) values for a-e compounds were obtained as -5.78, -5.81, -5.95, -5,98, and -6.11 kcal/mol, respectively. Finally, the pharmaceutical properties and toxicity of these new compounds were estimated through OSIRIS DataWarrior software. The results indicated no risk of tumorigenic, irritant, or reproductive effects and mutagenicity for compounds d and e. As a result, compounds d and e, could be selected for further study as potential therapeutic candidates. Moreover, employing molecular docking simulation with the prediction of pharmaceutical properties helps to discover new potential drug compounds.Keywords: drug design, anticancer, computational studies, DFT analysis
Procedia PDF Downloads 691877 The Molecular Bases of Δβ T-Cell Mediated Antigen Recognition
Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras
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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology
Procedia PDF Downloads 4201876 Profile of Cross-Reactivity Allergens Highlighted by Multiplex Technology “Alex Microchip Technique” in the Diagnosis of Type I Hypersensitivity
Authors: Gadiri Sabiha
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Introduction: Current allergy diagnostic tools using Multiplex technology have made it possible to increase the efficiency of the search for specific IgE. This opportunity is provided by the newly developed “Alex Biochip”, consisting of a panel of 282 allergens in native and molecular form, a CCD inhibitor, and the potential for detecting cross-reactive allergens. We evaluated the performance of this technology in detecting cross-reactivity in previously explored patients. Material/Method: The sera of 39 patients presenting sensitization and polysensitization profiles were explored. The search for specific IgE is carried out by the Alex ® IgE Biochip, and the results are analyzed by nature and by molecular family of allergens using specific software. Results/Discussion: The analysis gave a particular profile of cross-reactivity allergens: 33% for the Ole e1 family, 31% for NPC2, 26% for storage proteins, 20% for Tropomyosin, 10% for LTPs, 10% for Arginine Kinase and 10% for Uteroglobin CCDs were absent in all patients. The “Ole e1” allergen is responsible for a pollen-pollen cross allergy. The storage proteins found and LTP are not species-specific, causing cross-pollen-food allergy. The nDer p2 of the NPC2 family is responsible for cross-reactivity between mite species. Conclusion: The cross-reactivities responsible for mixed syndromes at diagnosis in our patients were dominated by pollen-pollen and pollen-food syndromes. They allow the identification of severity factors linked to the prognosis and the best-adapted immunotherapy.Keywords: specific IgE, allergy, cross reactivity, molecular allergens
Procedia PDF Downloads 621875 Influence of Molecular and Supramolecular Structure on Thermally Stimulated Short-Circuit Currents in Polyvinylidene Fluoride Films
Authors: Temnov D., Volgina E., Gerasimov D.
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Relaxation processes in polyvinylidene fluoride (PVDF) films were studied by the method of thermally stimulated fractional polarization currents (TSTF). The films were obtained by extrusion of a polymer melt followed by isometric annealing. PVDF granules of the Kynar-720 brand (Atofina Chemicals, USA) with a molecular weight of Mw=190,000 g•mol-1 were used for the manufacture of films. The annealing temperature was varied in the range from 120 °C to 170 °C in increments of 10 °C. The dependences of the degree of crystallinity of films (χ) and the intensity of thermally stimulated depolarization currents on the annealing temperature (Toc) are investigated. The TSTF spectra were obtained at the TSC II facility (Setaram, France). Measurements were carried out in a helium atmosphere, and the values of currents were determined by a Keithley electrometer. The annealed PVDF films were polarized at an electric field strength of 100 V/mm at a temperature of 31°C, after which they were cooled to 26°C, at which they were kept for 1 minute. During depolarization, the external field was removed, and the short-circuit sample was cooled to 0°C. The thermally stimulated short-circuit current was recorded during linear heating. Relaxation processes in PVDF films were studied in the temperature range from 0 – 70 °C. It is shown that the intensity curve of the peaks of TST FP has a course that is the reverse of the dependence of the degree of crystallinity on the annealing temperature. This allows us to conclude that the relaxation processes occurring in PVDF in the 35°C region are associated with the amorphous part of the structure of PVDF films between the layers of the spherulite crystalline phase.Keywords: molecular and supramolecular structure, thermally stimulated currents, polyvinylidene fluoride films, relaxation processes
Procedia PDF Downloads 421874 Isolation and Molecular Identification of Two Fungal Strains Capable of Degrading hydrocarbon Contaminants on Saudi Arabian Environment
Authors: Amr A. EL Hanafy, Yasir Anwar, Saleh A. Mohamed, Saleh Mohamed Saleh Al-Garni, Jamal S. M. Sabir , Osama A. H. Abu Zinadah, Mohamed Morsi Ahmed
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In the vicinity of the red sea about 15 fungi species were isolated from oil contaminated sites. On the basis of aptitude to degrade the crude oil and DCPIP assay, two fungal isolates were selected amongst 15 oil degrading strains. Analysis of ITS-1, ITS-2 and amplicon pyrosequencing studies of fungal diversity revealed that these strains belong to Penicillium and Aspergillus species. Two strains that proved to be the most efficient in degrading crude oil was Aspergillus niger (54 %) and Penicillium commune (48 %) Subsequent to two weeks of cultivation in BHS medium the degradation rate were recorded by using spectrophotometer and GC-MS. Hence, it is cleared that these fungal strains has the capability of degradation and can be utilized for cleaning the Saudi Arabian environment.Keywords: fungal strains, hydrocarbon contaminants, molecular identification, biodegradation, GC-MS
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