Search results for: stranded gas liquefaction

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

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Authors: Nishal Parbhoo, John B. Dewar, Samantha Gildenhuys

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Rotavirus is the major cause of severe gastroenteritis worldwide in children aged 5 and younger. Death rates are high particularly in developing countries. The mature rotavirus is a non-enveloped triple-layered nucleocapsid containing 11 double-stranded RNA segments. Here a global view on the sequence and structure of the three main capsid proteins, VP7, VP6, and VP2 is taken by generating a consensus sequence for each of these rotavirus proteins, for each species obtained from published data of representative rotavirus genotypes from across the world and across species. The degree of conservation between species was represented on homology models for each of the proteins. VP7 shows the highest level of variation with 14 - 45 amino acids showing conservation of less than 60%. These changes are localized to the outer surface which is exposed to antibodies alluding to a possible mechanism in evading the immune system. The middle layer, VP6 shows lower variability with only 14-32 sites having lower than 70% conservation. The inner structural layer made up of VP2 showed the lowest variability with only 1-16 sites having less than 70% conservation across species. The results correlate with proteins’ multiple structural roles. Although the nucleotide sequences vary due to an error-prone replication and lack of proofreading, the corresponding amino acid sequence of VP2, 6 and 7 remains conserved. Sequence conservation maintained for the virus results in stable protein structures, fit for function. This can be exploited in drug design, molecular studies and biotechnological applications.

Keywords: amino acid sequence conservation, capsid protein, protein structure, vaccine candidate

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Authors: Toake Endoh

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Cross-border migration of people is a critical driver for sustainable economic development in the Asia-Pacific region. Meanwhile, the region is susceptible to mega-scale natural disasters, such as tsunami, earthquakes, and typhoons. When migrants are stranded in a foreign country by a disaster, who should be responsible for their safety and security? What legal or moral foundation is there to advocate for the protection and assistance of “migrants at risk (M@R)”? How can the states practice “good governance” in their response to displacement of the foreign migrants? This paper inquires how to protect foreign migrants displaced by a natural disaster under international law and proposes protective actions to be taken by of migrant-receiver governments. First, the paper discusses the theoretical foundation for protection of M@R and argues that the nation-states are charged of responsibility to protect at-risk foreigners as “internally displaced persons” in the light of the United Nations’ Guiding Principles of Internal Displacement (1998). Second, through the case study of the Kobe Earthquake in Japan (1995), the Tsunami in Thailand (2004), and the Hurricane Katrina in the U.S. (2005), the paper evaluates how effectively (or poorly) institutions and state actors addressed the specific vulnerability felt by M@R in these crises.

Keywords: internal displaced persons, natural disaster, international migration, responsibility to protect

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Authors: Ergun Sakalar, Kubra Bilgic

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In the last decades, real-time PCR has become a reliable tool preferred to use in many laboratories for pathogen detection. This technique allows for monitoring target amplification via fluorescent molecules besides admit of quantitative analysis by enabling of convert outcomes of thermal cycling to digital data. Sensitivity and traceability of real-time PCR are based on measuring of fluorescence that appears only when fluorescent reporter dye bound to specific target DNA.The fluorescent reporter systems developed for this purpose are divided into two groups. The first group consists of intercalator fluorescence dyes such as SYBR Green, EvaGreen which binds to double-stranded DNA. On the other hand, the second group includes fluorophore-labeled oligonucleotide probes that are separated into three subgroups due to differences in mechanism of action; initial primer-probes such as Cyclicons, Angler®, Amplifluor®, LUX™, Scorpions, and the second one hydrolysis probes like TaqMan, Snake assay, finally hybridization probes, for instance, Molecular Beacons, Hybprobe/FRET, HyBeacon™, MGB-Eclipse, ResonSense®, Yin-Yang, MGB-Pleiades. In addition nucleic acid analogues, an increase of probe affinity to target site is also employed with fluorescence-labeled probes. Consequently, abundant real-time PCR detection chemistries are chosen by researcher according to the field of application, mechanism of action, advantages, and proper structures of primer/probes.

Keywords: fluorescent dye, food safety, molecular probes, nucleic acid analogues

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Authors: Jae Young Song, In-Ohk Ouh, Seyeon Park, Byeong Sul Kang, Soo Dong Cho, In-Soo Cho

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Canine parvovirus (CPV) is a major pathogen of diarrhea disease in dogs. CPV type 2 has three of antigenic variants such as 2a, 2b, and 2c. CPV constructs a small non-enveloped, icosahedral capsid that contains single-stranded DNA. It has capsids that two largely overlapping virion proteins (VP), VP1 (82 kDa), and VP2 (65 kDa). Baculoviruses are insect pathogens that regulate insect populations in nature and are being successfully used to control insect pests. The proteins produced in the baculovirus-expression system are used for instance for functional studies, vaccine preparations, or diagnostics. The vaccines produced by baculovirus-expression system showed elicitation of antibodies. The recombinant baculovirus infected SF9 cells showed broken shape. The recombinant VP2 proteins from cell pellet or supernatant were confirmed by western blotting. The result showed that the recombinant VP2 protein bands were appeared at 65 kDa molecular weight in both cell pellet and supernatant of infected SF9 cell. These results indicated that the recombinant baculovirus infected SF9 cell express the recombinant VP2 protein successfully. In addition, the expressed recombinant VP2 protein is secreted from cell to supernatant. The baculovirus expression system can be used to produce the VP2 protein of CPV 2c. In addition, the secretion property of the expression of VP2 protein may decrease the cost of production, because it can be skipped the cell breaking step. The produced VP2 protein could be used for vaccine and the agent of diagnostic tests. This study provides the foundation of the production of CPV 2c vaccine and the diagnostic agent.

Keywords: baculovirus, canine parvovirus 2c, dog, Korea

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Authors: Siti Aishah Hasbullah

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Studies on identification of pork content in food have grown rapidly to meet the Halal food standard in Malaysia. The used mitochondria DNA (mtDNA) approaches for the identification of pig species is thought to be the most precise marker due to the mtDNA genes are present in thousands of copies per cell, the large variability of mtDNA. The standard method commonly used for DNA detection is based on polymerase chain reaction (PCR) method combined with gel electrophoresis but has major drawback. Its major drawbacks are laborious, need longer time and toxic to handle. Therefore, the need for simplicity and fast assay of DNA is vital and has triggered us to develop DNA biosensors for porcine DNA detection. Therefore, the aim of this project is to develop electrochemical DNA biosensor based on ruthenium (II) complex, [Ru(bpy)2(p-PIP)]2+ as DNA hybridization label. The interaction of DNA and [Ru(bpy)2(p-HPIP)]2+ will be studied by electrochemical transduction using Gold Screen-Printed Electrode (GSPE) modified with gold nanoparticles (AuNPs) and succinimide acrylic microspheres. The electrochemical detection by redox active ruthenium (II) complex was measured by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The results indicate that the interaction of [Ru(bpy)2(PIP)]2+ with hybridization complementary DNA has higher response compared to single-stranded and mismatch complementary DNA. Under optimized condition, this porcine DNA biosensor incorporated modified GSPE shows good linear range towards porcine DNA.

Keywords: gold, screen printed electrode, ruthenium, porcine DNA

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Authors: Waleed S. Alwaneen

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In many countries, cow dung is used as farm manure and for biogas production. Several bacterial strains associated with cow dung such as Campylobacter, Salmonella sp. and Escherichia coli cause serious human diseases. The objective of the present study was to investigate the use of insect larvae including fruit beetle, waxworms and tiger worms to improve the breakdown of agricultural wastes and reduce their pathogen loads. Fresh cow faeces were collected from a cattle farm and distributed into plastic boxes (100 g/box). Each box was provided with 10 larvae of fruit beetle, Waxworms and Tiger worms, respectively. There were 3 replicates in each treatment including the control. Bacteria were isolated weekly from both control and cow faeces to which larvae were added to determine the bacterial populations. Results revealed that the bacterial load was higher in the cow faeces treated with fruit beetles than in the control, while the bacterial load was lower in the cow faeces treated with waxworms and tiger worms than in the control. The activities of the fruit beetle larvae led to the cow faeces being liquefied which provided a more conducive growing media for bacteria. Therefore, higher bacterial load in the cow faeces treated with fruit beetle might be attributed to the liquefaction of cow faeces.

Keywords: fruit beetle, waxworms, tiger worms, waste conditioning, composting

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Authors: R. Ziaie Moayed, M. Hamidzadeh

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The use of waste rubber chips not only can be of great importance in terms of the environment, but also can be used to increase the shear strength of soils. The purpose of this study was to evaluate the variation of the internal friction angle of liquefiable sandy soil using waste rubber chips. For this purpose, the geotechnical properties of unmodified and modified soil samples by waste lining rubber chips have been evaluated and analyzed by performing the triaxial consolidated drained test. In order to prepare the laboratory specimens, the sandy soil in part of Rudsar shores in Gilan province, north of Iran with high liquefaction potential has been replaced by two percent of waste rubber chips. Samples have been compressed until reaching the two levels of density of 15.5 and 16.7 kN/m³. Also, in order to find the optimal length of chips in sandy soil, the rectangular rubber chips with the widths of 0.5 and 1 cm and the lengths of 0.5, 1, and 2 cm were used. The results showed that the addition of rubber chips to liquefiable sandy soil greatly increases the shear resistance of these soils. Also, it can be seen that decreasing the width and increasing the length-to-width ratio of rubber chips has a direct impact on the shear strength of the modified soil samples with rubber chips.

Keywords: improvement, shear strength, internal friction angle, sandy soil, rubber chip

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Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

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The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

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Authors: Arab M., Ait Abdallah M., Zeraoulia N., Boumaza H., Aoutia M., Griene L., Ait Abdelkader B.,

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breast and ovarian cancer are respectively the first and fourth leading causes of cancer among women in Algeria. A family story of cancer in the most important risk factor, and in most cases of families with breast and /or ovarian cancer, the pattern of cancer family can be attributed to mutation in BRCA1/2genes. objectibes: the aim of our study in to investigate the spectrum of BRCA1/2 germiline mutation in familial breast and /or ovarian cancer and to determine the prevalence and the nature of BRCA1/2mutation in Algeria methods: we deremined the prevalence of BRCA1/2 mutation within a cohort of 161 probands selected according the eisinger score double stranded sanger sequencing of all coding exons of BRCA1/2including flanking intronic region were performed results: we identified a total of 23 distinct deleterious mutations (class5) 12 differents mutations in BRCA1(52%) and 11 in BRCA2(48%). 78% (18/23) were protein truncating and 22%(5/23) missens mutations.3 novel deleterious mutations have been identified, which have not been described in public mutation database. one new mutation were found in two unrelated patients. the overall mutation detection rate in our study is 28,5%(46/161).more over, an UVS c7783 located in BRCA2 is found in two unrelated probands and segregate in the 02 families/ conclusion: our results sugget of large spectrum of BRCA1/2 mutation in Algerian breast/ovarian cancer family. The nature and prevalence of BRCA1/2mutation in algerian families are ongoing in a larger study, 80 probands are to day under investigation. This study which may therefore identify the genetic particularity of Algerian breast /ovarian cancer.

Keywords: BRCA1/2 mutations, hereditary breast cancer, algerian women, prvalence

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure conformed by stacked planes of four base paired guanines (G-quartet). The guanine rich DNA sequences are present in many sites of genomic DNA and can potentially lead to the formation of G-quadruplexes, especially at the 3'-terminus of the human telomeric DNA with many TTAGGG repeats. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to regulate oncogene expression making the G-quadruplex an attractive target for anticancer therapy. Clearly, the G-quadruplex structured in the telomeric DNA is of fundamental importance for rational drug design. In this context, we investigate two G-quadruplex structures, the first follows from the sequence TTAGGG(TTAGGG)3TT (HUT1), and the second from AAAGGG(TTAGGG)3AA (HUT2), both in a K+ solution. We determine the free energy surfaces of the HUT1 and HUT2 structures and investigate their conformations using replica-exchange metadynamics simulations. The carbonyl-carbonyl distances belonging to different guanines residues are selected as the main collective variables to determine the free energy surfaces. The surfaces exhibit two main local minima, compatible with experiments on the conformational transformations of HUT1 and HUT2 under substitution of the K+ ions by the Na+ ions. The conformational transitions are not observed in short MD simulations without the use of the metadynamics approach. The results of this work should be of help to understand the formation and stability of human telomeric G-quadruplex in environments including the presence of K+ and Na+ ions.

Keywords: g-quadruplex, metadynamics, molecular dynamics, replica-exchange

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Authors: Akhtar Naveed, Kanwal Shahla, Khan HMS, Rasool Fatima, Ijaz Shakeel

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The focus of the study was to design, develop and characterize in vivo, a stable Emulgel formulation containing Anacardium occidentale L.(cashew extract) as an active ingredient. The formulation was prepared and kept at 8ºC, 25 ºC, 40ºC and 40ºC±RH for a period of 28 days. During this time period, stability, pH values, conductivity, organoleptic features (color, liquefaction, phase separation) were conducted at the intervals of day 1st, 2nd, 3rd , 7th, 14th and 28th days. In In vivo studies, the test formulation (5% Anacardium occidentale L, extract) and a base formulation (without cashew extract) were prepared and both were applied on cheek areas of healthy human female volunteers, after the skin sensitivity test of each volunteer, for a study period of 8 weeks after getting consent from them. Various parameters of skin like Melanin level, Erythema level, and skin elasticity were measured at regular time intervals. Results of the study were analyzed by statistical techniques i.e. Two Way ANOVA and paired sample t-test. The result showed significant results as the p ≤ 0.05. Findings of paired sample t-test explained that test formulation have profound effects on skin parameters when compared with control formulation.

Keywords: Anacardium occientale L., anti-oxidant, cashew nut, emulgel

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Authors: Muhammad Yousaf Ali, Shahid Mansoor, Javeria Qazi, Imran Amin, Musarrat Shaheen

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Cotton leaf curl disease (CLCuD) is the major threat to the cotton crop and is transmitted by whitefly (Bemisia tabaci). Since multiple begomoviruses and associated satellites are involved in CLCuD, approaches based on the concept of broad-spectrum resistance are essential for effective disease control. Gro-El and G5 are two proteins from whitefly endosymbiont and M13 bacteriophage origin, respectively. Gro-El encapsulates the virus particle when it enters the whitefly and protects the virus from the immune system of the whitefly as well as prevents viral expression in it. This characteristic of Gro-El can be exploited to get resistance against viruses if expressed in plants. G5 is a single-stranded DNA binding protein, expression of which in transgenic plants will stop viral expression on its binding with ssDNA. The use of tissue-specific promoters is more efficient than constitutive promoters. Transgenics of Nicotiana benthamiana for Gro-El under constitutive promoter and Gro-El under phloem specific promoter were made. In comparison to non-transgenic plants, transgenic plants with Gro-El under NSP promoter showed promising results when challenged against cotton leaf curl Multan virus (CLCuMuV) along with cotton leaf curl Multan beta satellite (CLCuMB), cotton leaf curl Khokhran virus (CLCuKoV) along with cotton leaf curl Multan beta satellite (CLCuMB) and Pedilenthus leaf curl virus (PedLCV) along with Tobacco leaf curl beta satellite (TbLCB).

Keywords: cotton leaf curl disease, whitefly, endosymbionts, transgenic, resistance

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Authors: Chang Hsueh-Sheng, Chen Tzu-Ling

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Earthquake is an unpredictable natural disaster and intensive earthquakes have caused serious impacts on social-economic system, environmental and social resilience. Conventional ways to mitigate earthquake disaster are to enhance building codes and advance structural engineering measures. However, earthquake-induced ground damage such as liquefaction, land subsidence, landslide happen on places nearby earthquake prone or poor soil condition areas. Therefore, this study uses spatial statistical analysis to explore the spatial pattern of damaged buildings. Afterwards, principle components analysis (PCA) is applied to categorize the similar features in different kinds of clustered patterns. The results show that serious landslide prone area, close to fault, vegetated ground surface and mudslide prone area are common in those highly damaged buildings. In addition, the oldest building might not be directly referred to the most vulnerable one. In fact, it seems that buildings built between 1974 and 1989 become more fragile during the earthquake. The incorporation of both spatial statistical analyses and PCA can provide more accurate information to subsidize retrofit programs to enhance earthquake resistance in particular areas.

Keywords: earthquake disaster, spatial statistic analysis, principle components analysis (pca), clustered patterns

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Authors: K. P. Shinde, M. V. Tien, H. Lin, H.-R. Park, S.-C.Yu, K. C. Chung, D.-H. Kim

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Magnetic refrigeration provides an attractive alternative cooling technology due to its potential advantages such as high cooling efficiency, environmental friendliness, low noise, and compactness over the conventional cooling techniques based on gas compression. Magnetocaloric effect (MCE) occurs by changes in entropy (ΔS) and temperature (ΔT) under external magnetic fields. We have been focused on identifying materials with large MCE in two temperature regimes, not only room temperature but also at cryogenic temperature for specific technological applications, such as space science and liquefaction of hydrogen in fuel industry. To date, the commonly used materials for cryogenic refrigeration are based on hydrated salts. In the present work, we report giant MCE in rare earth Ho2O3 nanopowder at cryogenic temperature. HoN nanoparticles with average size of 30 nm were prepared by using plasma arc discharge method with gas composition of N2/H2 (80%/20%). The prepared HoN was sintered in air atmosphere at 1200 oC for 24 hrs to convert it into oxide. Structural and morphological properties were studied by XRD and SEM. XRD confirms the pure phase and cubic crystal structure of Ho2O3 without any impurity within error range. It has been discovered that Holmium oxide exhibits giant MCE at low temperature without magnetic hysteresis loss with the second-order antiferromagnetic phase transition with Néels temperature around 2 K. The maximum entropy change was found to be 25.2 J/kgK at an applied field of 6 T.

Keywords: magnetocaloric effect, Ho₂O₃, magnetic entropy change, nanopowder

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Authors: Adel M. Zakri, Mohammed A. Al-Saleh, Judith. K. Brown, Ali M. Idris

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Betasatellites are small circular single stranded DNA molecules found associated with begomoviruses on field symptomatic plants. Their genome size is about half that of the helper begomovirus, ranging between 1.3 and 1.4 kb. The helper begomoviruses are usually members of the family Geminiviridae. Okra leaves showing vein thickening were collected from okra plants growing in Jazan, Saudi Arabia. Total DNA was extracted from leaves and used as a template to amplify circular DNA using rolling circle amplification (RCA) technology. Products were digested with PstI to linearize the helper viral genome(s), and associated DNA satellite(s), yielding a 2.8kbp and 1.4kbp fragment, respectively. The linearized fragments were cloned into the pGEM-5Zf (+) vector and subjected to DNA sequencing. The 2.8 kb fragment was identified as Cotton leaf curl Gezira virus genome, at 2780bp, an isolate closely related to strains reported previously from Saudi Arabia. A clone obtained from the 1.4 kb fragments he 1.4kb was blasted to GeneBank database found to be a betasatellite. The genome of betasatellite was 1357-bp in size. It was found to be a recombinant containing one fragment (877-bp) that shared 91% nt identity with Cotton leaf curl Gezira betasatellite [KM279620], and a smaller fragment [133--bp) that shared 86% nt identity with Tomato leaf curl Sudan virus [JX483708]. This satellite is thus a recombinant between a malvaceous-infecting satellite and a solanaceous-infecting begomovirus.

Keywords: begomovirus, betasatellites, cotton leaf curl Gezira virus, okra plants

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Authors: N. V. Nikhil, S. R. Lee, Do Won Park

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Korean peninsula receives about two third of the annual rainfall during summer season. The extreme rainfall pattern due to typhoon and heavy rainfall results in severe mountain disasters among which 55% of them are debris flows, a major natural hazard especially when occurring around major settlement areas. The basic mechanism underlined for this kind of failure is the unsaturated shallow slope failure by reduction of matric suction due to infiltration of water and liquefaction of the failed mass due to generation of positive pore water pressure leading to abrupt loss of strength and commencement of flow. However only an empirical model cannot simulate this complex mechanism. Hence, we have employed an empirical-physical based approach for hazard analysis of debris flow using TRIGRS, a debris flow initiation criteria and DAN3D in mountain Woonmyun, South Korea. Debris flow initiation criteria is required to discern the potential landslides which can transform into debris flow. DAN-3D, being a new model, does not have the calibrated values of rheology parameters for Korean conditions. Thus, in our analysis we have used the recent 2011 debris flow event in mountain Woonmyun san for calibration of both TRIGRS model and DAN-3D, thereafter identifying and predicting the debris flow initiation points, path, run out velocity, and area of spreading for future extreme rainfall based scenarios.

Keywords: debris flow, DAN-3D, extreme rainfall, hazard analysis

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Authors: Emil F. Khisamutdinov

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Development of functional materials undergoing structural transformations in response to an external stimulus such as environmental changes (pH, temperature, etc.), the presence of particular proteins, or short oligonucleotides are of great interest for a variety of applications ranging from medicine to electronics. The dynamic operations of most nucleic acid (NA) devices, including circuits, nano-machines, and biosensors, rely on networks of NA strand displacement processes in which an external or stimulus strand displaces a target strand from a DNA or RNA duplex. The rate of strand displacement can be greatly increased by the use of “toeholds,” single-stranded regions of the target complex to which the invading strand can bind to initiate the reaction, forming additional base pairs that provide a thermodynamic driving force for transformation. Herein, we developed a highly robust nanoparticle shape transition, sequentially transforming DNA polygons from one shape to another using the toehold-mediated DNA strand displacement technique. The shape transformation was confirmed by agarose gel electrophoresis and atomic force microscopy. Furthermore, we demonstrate that our approach is applicable for RNA shape transformation from triangle to square, which can be detected by fluorescence emission from malachite green binding RNA aptamer. Using gel-shift and fluorescence assays, we demonstrated efficient transformation occurs at isothermal conditions (37°C) that can be implemented within living cells as reporter molecules. This work is intended to provide a simple, cost-effective, and straightforward model for the development of biosensors and regulatory devices in nucleic acid nanotechnology.

Keywords: RNA nanotechnology, bionanotechnology, toehold mediated DNA switch, RNA split fluorogenic aptamers

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Authors: Praveen Huded, Suresh Dash

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Pile foundations are one of the most preferred deep foundation system for high rise or heavily loaded structures. In many instances, the failure of the pile founded structures in liquefiable soils had been observed even in many recent earthquakes. Recent centrifuge and shake table experiments on two layered soil system have credibly shown that failure of pile foundation can occur because of buckling, as the pile behaves as an unsupported slender structural element once the surrounding soil liquefies. However the buckling capacity depends on largely on the depth of soil liquefied and its residual strength. Hence it is essential to check the pile against the possible buckling failure. Beam on non-linear Winkler Foundation is one of the efficient method to model the pile-soil behavior in liquefiable soil. The pile-soil interaction is modelled through p-y springs, different author have proposed different types of p-y curves for the liquefiable soil. In the present paper the influence two such p-y curves on the buckling capacity of pile foundation is studied considering initial geometric and non-linear behavior of pile foundation. The proposed method is validated against experimental results. Significant difference in the buckling capacity is observed for the two p-y curves used in the analysis. A parametric study is conducted to understand the influence of pile diameter, pile flexural rigidity, different initial geometric imperfections, and different soil relative densities on buckling capacity of pile foundation.

Keywords: Pile foundation , Liquefaction, Buckling load, non-linear py curve, Opensees

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Authors: Vasudha Thapa, Kiran Chappa

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There is a pressing need to prepare cities in the developing countries of the global south such as India against the chaos created by COVID 19 pandemic and future disaster risks. This pandemic posed the nation with an unprecedented challenge of dealing with a wave of stranded migrant workers. These workers comprise the most vulnerable section of the society in case of any pandemic or disaster risks. The COVID 19 pandemic exposed the vulnerability of migrant workers in the urban form and the need for capacity-building strategies against future pandemics. This paper highlights the challenges of these migrant workers in the case of Mumbai city in lockdown, post lockdown, and the current uncertain scenarios. The paper deals with a thorough investigation of the existing and the recent policies and strategies taken by the Urban Local Bodies (ULBs), state, and central government to assist these migrants in the city during this mayhem of uncertainties. The paper looks further deep into the challenges and opportunities presented in the current scenario through the assessment of existing data and response to policy measures taken by the government organizations. The ULBs are at the forefront in the response to any disaster risk, hence the paper assesses the capacity gaps of the Urban local bodies in mitigating the risks posed by any pandemic-like situation. The study further recommends capacity-building strategies at various levels of governance and uniform policy measures to assist the migrant population of the city.

Keywords: urban resilience, covid 19, migrant population, India, capacity building, governance

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Authors: Narayan Gurung, Fawu Wang, Ranjan Kumar Dahal

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Nepal is highly prone to earthquakes and has witnessed at least one major earthquake in 80 to 90 years interval. The Gorkha earthquake, that measured 7.8 RS in magnitude and struck Nepal on 25th April 2015, after 81 years since Mw 8.3 Nepal Bihar earthquake in 1934, was the largest earthquake after Mw 8.3 Nepal Bihar earthquake. In this paper, an attempt has been made to highlight the lessons learnt from the MwW 7.8 Gorkha (Nepal) earthquake. Several types of damage patterns in buildings were observed for reinforced concrete buildings, as well as for unreinforced masonry and adobe houses in the earthquake of 25 April 2015. Many field visits in the affected areas were conducted, and thus, associated failure and damage patterns were identified and analyzed. Damage patterns in non-engineered buildings, middle and high-rise buildings, commercial complexes, administrative buildings, schools and other critical facilities are also included from the affected districts. For most buildings, the construction and structural deficiencies have been identified as the major causes of failure; however, topography, local soil amplification, foundation settlement, liquefaction associated damages and buildings built in hazard-prone areas were also significantly observed for the failure or damages to buildings and hence are reported. Finally, the lessons learnt from Mw 7.8 Gorkha (Nepal) earthquake are presented in order to mitigate impacts of future earthquakes in Nepal.

Keywords: Gorkha earthquake, reinforced concrete structure, Nepal, lesson learnt

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: A. Banerjee, C. Grazon, B. Nadal, T. Pons, Y. Krishnan, B. Dubertret

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Quantum Dots (QDs) have emerged as novel fluorescent probes for biomedical applications. The photophysical properties of QDs such as broad absorption, narrow emission spectrum, reduced blinking, and enhanced photostability make them advantageous over organic fluorophores. However, for some biological applications, QDs need to be first targeted to specific intracellular locations. It parallel, base pairing properties and biocompatibility of DNA has been extensively used for biosensing, targetting and intracellular delivery of numerous bioactive agents. The combination of the photophysical properties of QDs and targettability of DNA has yielded fluorescent, stable and targetable nanosensors. QD-DNA conjugates have used in drug delivery, siRNA, intracellular pH sensing and several other applications; and continue to be an active area of research. In this project, a novel method to synthesise QD-DNA conjugates and their applications in bioimaging are investigated. QDs are first solubilized in water using a thiol based amphiphilic co-polymer and, then conjugated to amine functionalized DNA using a heterobifunctional linker. The conjugates are purified by size exclusion chromatography and characterized by UV-Vis absorption and fluorescence spectroscopy, electrophoresis and microscopy. Parameters that influence the conjugation yield such as reducing agents, the excess of salt and pH have been investigated in detail. In optimized reaction conditions, up to 12 single-stranded DNA (15 mer length) can be conjugated per QD. After conjugation, the QDs retain their colloidal stability and high quantum yield; and the DNA is available for hybridization. The reaction has also been successfully tested on QDs emitting different colors and on Gold nanoparticles and therefore highly generalizable. After extensive characterization and robust synthesis of QD-DNA conjugates in vitro, the physical properties of these conjugates in cellular milieu are being invistigated. Modification of QD surface with DNA appears to remarkably alter the fate of QD inside cells and can have potential implications in therapeutic applications.

Keywords: bioimaging, cellular targeting, drug delivery, photostability

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Authors: Raj Banerjee, Y. M. Parulekar, Aniruddha Sengupta, J. Chattopadhyay

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This study proposes a Discrete Element Method (DEM) simulation using a commercial software PFC 2D (2019) for quantitatively simulating the monotonic and cyclic behaviour of sand using irregular shapes of sand grains. A preliminary analysis of the number of particles for optimal Representative Element Volume (REV) simulation of dimension 35mm x 35mm x 70mm using the scaled Grain Size Distribution (GSD) of sand is carried out. Subsequently, the effect of particle shape on the performance of sand during monotonic and cyclic bi-axial tests is assessed using numerical simulation. The validation of the numerical simulation for one case is carried out using the test results from the literature. Further numerical studies are performed in which the particles in REV are simulated by mixing round discs with irregular clumps (100% round disc, 75% round disc 25% irregular clump, 50% round disc 50% irregular clump, 25% round disc 75% irregular clump, 100% irregular clump) in different proportions using Dry Deposition (DD) method. The macro response for monotonic loading shows that irregular sand has a higher strength than round particles and that the Mohr-Coulomb failure envelope depends on the shape of the grains. During cyclic loading, it is observed that the liquefaction resistance curve (Cyclic Stress Ratio (CSR)-Number of cycles (N)) of sand is dependent on the combination of particle shapes with different proportions.

Keywords: biaxial test, particle shape, monotonic, cyclic

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Authors: Badr Eddine Lebrouhi, Melissa Lopez Viveros, Silvia De Los Santos, Kolthoum Missaoui, Pamela Ramirez Vidal

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Since the Paris Climate Agreement, numerous countries, including France, have committed to achieving carbon neutrality by 2050 by enhancing renewable energy capacity and decarbonizing various sectors, including aviation. In this way, the Occitanie region aspires to become a renewable energy pioneer and has focused on Toulouse's Blagnac airport—a prominent hub characterized by high-energy demands. As part of a holistic strategy to reduce the airport's energy dependency, green hydrogen has emerged as a promising alternative fuel, offering the potential to significantly enhance aviation's environmental sustainability. This study assesses the technical and economic aspects of green hydrogen production, particularly its potential to replace fossil kerosene in aviation at Toulouse-Blagnac airport. It analyzes future liquid hydrogen fuel demand, calculates energy requirements for electrolysis and liquefaction, considers diverse renewable energy scenarios, and assesses the Levelized Cost of Hydrogen (LCOH) for economic viability. The research also projects LCOH evolution from 2023 to 2050, offering a comprehensive view of green hydrogen's feasibility as a sustainable aviation fuel, aligning with the region's renewable energy and sustainable aviation objectives.

Keywords: Toulouse-Blagnac Airport, green hydrogen, aviation decarbonization, electrolysis, renewable energy, technical-economic feasibility

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Authors: Q. Toufeeq, R. Kauser, U. R. Jamil, N. Sohaib

Abstract:

Foundation design of a structure needs soil investigation to avoid failures due to settlements. This soil investigation is expensive and time-consuming. Developments of new residential societies involve huge leveling of large sites that is accompanied by heavy land filling. Poor practices of land fill for deep depths cause differential settlements and consolidations of underneath soil that sometimes result in the collapse of structures. The extent of filling remains unknown to the individual developer unless soil investigation is carried out. Soil investigation cannot be performed on each available site due to involved costs. However, fair estimate of bearing capacity can be made if such tests are already done in the surrounding areas. The geotechnical guidance maps can provide a fair assessment of soil properties. Previously, GIS-based approaches have been used to develop maps using extrapolation and interpolations techniques for bearing capacities, underground recharge, soil classification, geological hazards, landslide hazards, socio-economic, and soil liquefaction mapping. Standard penetration test (SPT) data of surrounding sites were already available. Google Earth is used for digitization of collected data. Few points were considered for data calibration and validation. Resultant Geographic information system (GIS)-based guidance maps are helpful to anticipate the bearing capacity in the real estate industry.

Keywords: bearing capacity, soil classification, geographical information system, inverse distance weighted, radial basis function

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

Abstract:

The DNA G-quadruplex is a four-stranded DNA structure formed by stacked planes of four base paired guanines (G-quartet). Guanine rich DNA sequences appear in many sites of genomic DNA and can potential form G-quadruplexes, such as those occurring at 3'-terminus of the human telomeric DNA. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to down regulate oncogene expression making G-quadruplex an attractive target for anticancer therapy. Many G-quadruplex ligands have been proposed with a planar core to facilitate the pi–pi stacking and electrostatic interactions with the G-quartets. However, many drug candidates are impossibilitated to discriminate a G-quadruplex from a double helix DNA structure. In this context, it is important to investigate the site topology for the interaction of a G-quadruplex with a ligand. In this work, we determine the free energy surface of a G-quadruplex-ligand to study the binding modes of the G-quadruplex (TG4T) with the daunomycin (DM) drug. The complex TG4T-DM is studied using classical molecular dynamics in combination with metadynamics simulations. The metadynamics simulations permit an enhanced sampling of the conformational space with a modest computational cost and obtain free energy surfaces in terms of the collective variables (CV). The free energy surfaces of TG4T-DM exhibit other local minima, indicating the presence of additional binding modes of daunomycin that are not observed in short MD simulations without the metadynamics approach. The results are compared with similar calculations on a different structure (the mutated mu-G4T-DM where the 5' thymines on TG4T-DM have been deleted). The results should be of help to design new G-quadruplex drugs, and understand the differences in the recognition topology sites of the duplex and quadruplex DNA structures in their interaction with ligands.

Keywords: g-quadruplex, cancer, molecular dynamics, metadynamics

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Authors: Abbas Pourreza

Abstract:

MicroRNAs (miRNAs) are small single-stranded non-coding RNAs. They are almost 18-25 nucleotides long and very conservative through evolution. They are involved in adjusting the expression of numerous genes due to the existence of a complementary region, generally in the 3' untranslated regions (UTR) of target genes, against particular mRNAs in the cell. Also, miRNAs have been proven to be involved in cell development, differentiation, proliferation, and apoptosis. More than 2000 miRNAs have been recognized in human cells, and these miRNAs adjust approximately one-third of all genes in human cells. Dysregulation of miRNA originated from abnormal DNA methylation patterns of the locus, cause to down-regulated or overexpression of miRNAs, and it may affect tumor formation or development of it. Breast cancer (BC) is the most commonly identified cancer, the most prevalent cancer (23%), and the second-leading (14%) mortality in all types of cancer in females. BC can be classified based on the status (+/−) of the hormone receptors, including estrogen receptor (ER), progesterone receptor (PR), and the Receptor tyrosine-protein kinase erbB-2 (ERBB2 or HER2). Currently, there are four main molecular subtypes of BC: luminal A, approximately 50–60 % of BCs; luminal B, 10–20 %; HER2 positive, 15–20 %, and 10–20 % considered Basal (triple-negative breast cancer (TNBC)) subtype. Aberrant expression of miR-145, miR-21, miR-10b, miR-125a, and miR-206 was detected by Stem-loop real-time RT-PCR in BC cases. Breast tumor formation and development may result from down-regulation of a tumor suppressor miRNA such as miR-145, miR-125a, and miR-206 and/or overexpression of an oncogenic miRNA such as miR-21 and miR-10b. MiR-125a, miR-206, miR-145, miR-21, and miR-10b are hugely predicted to be new tumor markers for the diagnosis and prognosis of BC. MiR-21 and miR-125a could play a part in the treatment of HER-2-positive breast cancer cells, while miR-145 and miR-206 could speed up the evolution of cure techniques for TNBC. To conclude, miRNAs will be presented as hopeful molecules to be used in the primary diagnosis, prognosis, and treatment of BC and battle as opposed to its developed drug resistance.

Keywords: breast cancer, HER2 positive, miRNA, TNBC

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Authors: Sima Parvizi Omran, Rezvan Tavakoli, Mahnaz Safari, Mohammadreza Aghasadeghi, Abolfazl Fateh, Pooneh Rahimi

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Background: SARS-CoV-2, a single-stranded RNA betacoronavirus causes the global outbreak of coronavirus disease 2019 (COVID-19). Several clinical and scientific concerns are raised by this pandemic. Genetic factors can contribute to pathogenesis and disease susceptibility. There are single nucleotide polymorphisms (SNPs) in many of the genes in the immune system that affect the expression of specific genes or functions of some proteins related to immune responses against viral infections. In this study, we analyzed the impact of polymorphism in the interferon alpha and beta receptor subunit 2 (IFNAR2) and dipeptidyl peptidase 9 (Dpp9) genes and clinical parameters on the susceptibility and resistance to Coronavirus disease (COVID-19). Methods: A total of 330- SARS-CoV-2 positive patients (188 survivors and 142 nonsurvivors) were included in this study. All single-nucleotide polymorphisms (SNPs) on IFNAR2 (rs2236757) and Dpp9 (rs2109069) were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: In survivor patients, the frequency of the favourable genotypes of IFNAR2 SNP (rs2236757 GC) was significantly higher than in nonsurvivor patients, and also Dpp9 (rs2109069 AT) genotypes were associated with the severity of COVID-19 infection. Conclusions: This study demonstrated that the severity of COVID- 19 patients was strongly associated with clinical parameters and unfavourable IFNAR2, Dpp9 SNP genotypes. In order to establish the relationship between host genetic factors and the severity of COVID-19 infection, further studies are needed in multiple parts of the world.

Keywords: SARS-CoV-2, COVID-19, interferon alpha and beta receptor subunit 2, dipeptidyl peptidase 9, single-nucleotide polymorphisms

Procedia PDF Downloads 126

Authors: Genevieve D. Fernandes, Nisha P. Naik

Abstract:

All through the ages in all human civilizations, men have been engaged in construction activity, not only to build their dwellings and house their activities, but also roads, bridges to facilitate means of transport, and communication etc. The main concern in this activity was to ensure safety and reduce the collapse of the buildings and other structures. But even after taking all precautions, it is impossible to guarantee safety and collapse because of several unforeseen reasons like faulty constructions, design errors, overloading, soil liquefaction, gas explosion, material degradation, terrorist attacks and economic factors also contributing to the collapse. It is also uneconomical to design the structure for unforeseen events unless they have a reasonable chance of occurrence. In order to ensure safety and prevent collapse, many guidelines have been framed by local bodies and government authorities in many countries like the United States Department of Defence (DOD), United States General Service Administration (GSA) and Euro-Codes in European Nations. Some other practices are followed to incorporate redundancies in the structure like detailing, ductile designs, tying of elements at particular locations, and provision of hinges and interconnections. It is also to be admitted that a full-proof safe design structure for accidental events cannot be prepared and implemented as it is uneconomical and the chances of such occurrences are less. This paper reviews past case studies of the collapse of structures with the aim of developing an understanding of the collapse mechanism. This study will definitely help to bring about a detailed improvement in the design to maximise the quality of the construction at a minimal cost.

Keywords: unforeseen factors, progressive collapse, collapse resisting mechanisms, column removal scenario

Procedia PDF Downloads 86