Proteome Based Approach Defines Candidates for Designing a Multitope Vaccine against the Nipah Virus

Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-³ and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine.     

A survey on trust based detection and isolation of malicious nodes in ad-hoc and sensor networks

Mobile ad-hoc networks (MANETs) and wireless sensor networks (WSNs) have gained remarkable appreciation and technological development over the last few years. Despite ease of deployment, tremendous applications and significant advantages, security has always been a challenging issue due to the nature of environments in which nodes operate. Nodes’ physical capture, malicious or selfish behavior cannot be detected by traditional security schemes. Trust and reputation based approaches have gained global recognition in providing additional means of security for decision making in sensor and ad-hoc networks. This paper provides an extensive literature review of trust and reputation based models both in sensor and ad-hoc networks. Based on the mechanism of trust establishment, we categorize the stateof-the-art into two groups namely node-centric trust models and system-centric trust models. Based on trust evidence, initialization, computation, propagation and weight assignments, we evaluate the efficacy of the existing schemes. Finally, we conclude our discussion with identification of some unresolved issues in pursuit of trust and reputation management.     

Lipid Droplets and Their Autophagic Turnover via the Raft-Like Vacuolar Microdomains

Although once perceived as inert structures that merely serve for lipid storage, lipid droplets (LDs) have proven to be the dynamic organelles that hold many cellular functions. The LDs’ basic structure of a hydrophobic core consisting of neutral lipids and enclosed in a phospholipid monolayer allows for quick lipid accessibility for intracellular energy and membrane production. Whereas formed at the peripheral and perinuclear endoplasmic reticulum, LDs are degraded either in the cytosol by lipolysis or in the vacuoles/lysosomes by autophagy. Autophagy is a regulated breakdown of dysfunctional, damaged, or surplus cellular components. The selective autophagy of LDs is called lipophagy. Here, we review LDs and their degradation by lipophagy in yeast, which proceeds via the micrometer-scale raft-like lipid domains in the vacuolar membrane. These vacuolar microdomains form during nutrient deprivation and facilitate internalization of LDs via the vacuolar membrane invagination and scission. The resultant intra-vacuolar autophagic bodies with LDs inside are broken down by vacuolar lipases and proteases. This type of lipophagy is called microlipophagy as it resembles microautophagy, the type of autophagy when substrates are sequestered right at the surface of a lytic compartment. Yeast microlipophagy via the raft-like vacuolar microdomains is a great model system to study the role of lipid domains in microautophagic pathways.     

Direct analysis of trace phenolics with a microchip: in-channel sample preconcentration, separation, and electrochemical detection

A micrototal analytical method assembling in-channel preconcentration, separation, and electrochemical detection steps has been developed for trace phenolic compounds. A micellar electrokinetic chromatography separation technique was coupled with two preconcentration steps of field-amplified sample stacking (FASS) and field-amplified sample injection (FASI). An amperometric detection method with a cellulose-dsDNA-modified, screen-printed carbon electrode was applied to detect preconcentrated and separated species at the end of the channel. The microchip was composed of three parallel channels: first, two are for the sample preconcentration using FASS and FASI methods, and the third one is for the separation and electrochemical detection. The modification of the electrode surface improved the detection performance by enhancing the signal-to-noise characteristic without surface fouling of the electrode. The method was examined for the analysis of eight phenolic compounds. Experimental parameters affecting the analytical performance of the method were assessed and optimized. The preconcentration factor was increased by about 5200-fold as compared with a simple capillary zone electrophoretic analysis using the same channel. Reproducible response was observed during multiple injections of samples with a RSD of <8.0%. The calibration plots were shown to be linear (with the correlation coefficient between 0.9913 and 0.9982) over the range of 0.4-600 nM. The sensitivity was between 0.17 +/- 0.001 and 0.48 +/- 0.006 nA/nM, with the detection limit of approximately 100 to approximately 150 pM based on S/N = 3. The applicability of the method to the direct analysis of trace phenolic compounds in water samples was successfully demonstrated.     

Environmental Kuznets Curve hypothesis in Pakistan: Cointegration and Granger causality

The paper is an effort to fill the gap in the energy literature with a comprehensive country study of Pakistan. We investigate the relationship between CO₂ emissions, energy consumption, economic growth and trade openness in Pakistan over the period of 1971–2009. Bounds test for cointegration and Granger causality approach are employed for the empirical analysis. The result suggests that there exists a long-run relationship among the variables and the Environmental Kuznets Curve (EKC) hypothesis is supported. The significant existence of EKC shows the country's effort to condense CO₂ emissions and indicates certain achievement of controlling environmental degradation in Pakistan. Furthermore, we find a one-way causal relationship running from economic growth to CO₂ emissions. Energy consumption increases CO₂ emissions both in the short and long runs. Trade openness reduces CO₂ emissions in the long run but it is insignificant in the short run. In addition, the change of CO₂ emissions from short run to the long span of time is corrected by about 10% yearly.     

Electron-transfer studies with a new flavin adenine dinucleotide dependent glucose dehydrogenase and osmium polymers of different redox potentials

A new extracellular flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase from Glomerella cingulata (GcGDH) was electrochemically studied as a recognition element in glucose biosensors. The redox enzyme was recombinantly produced in Pichia pastoris and homogeneously purified, and its glucose-oxidizing properties on spectrographic graphite electrodes were investigated. Six different Os polymers, the redox potentials of which ranged in a broad potential window between +15 and +489 mV versus the normal hydrogen electrode (NHE), were used to immobilize and "wire" GcGDH to the spectrographic graphite electrode's surface. The GcGDH/Os polymer modified electrodes were evaluated by chronoamperometry using flow injection analysis. The current response was investigated using a stepwisely increased applied potential. It was observed that the ratio of GcGDH/Os polymer and the overall loading of the enzyme electrode significantly affect the performance of the enzyme electrode for glucose oxidation. The best-suited Os polymer [Os(4,4'-dimethyl-2,2'-bipyridine)(2)(PVI)Cl](+) had a potential of +309 mV versus NHE, and the optimum GcGDH/Os polymer ratio was 1:2 yielding a maximum current density of 493 μA·cm(-2) at a 30 mM glucose concentration.     

Fire retardancy of sol–gel derived titania wood-inorganic composites

Sol–gel technology was applied in tailoring novel wood-made-inorganic composites with improved thermal and fire properties. In practice, composites materials were prepared by impregnating pine sapwood wood with nano-scaled precursor solutions derived from titanium(IV) isopropoxide followed by a thermal curing process. Thermal and fire properties were evaluated by thermal analysis and cone calorimetry, whereas flammability was specified by oxygen index (LOI) and UL 94 test. Peak heat release rates were moderately reduced indicating fire retardance potential in terms of flame spread attributed to the appropriate protection layer action of the titania-based depositions. LOI (oxygen index) values of these composites were increased up to 38 vol.% in comparison to 23 vol.% for untreated wood. The flame retardancy performance depends on the fire scenario and is strongly influenced by wood loading and crack-free deposition of the titania layers inside the composite.     

Unsteady natural convection within a differentially heated enclosure of sinusoidal corrugated side walls

Numerically investigation of natural convection within a differentially heated modified square enclosure with sinusoidally corrugated side walls has been performed for different values of Rayleigh number. The fluid inside the enclosure considered is air and is quiescent, initially. The top and bottom surfaces are flat and considered as adiabatic. Results reveal three main stages: an initial stage, a transitory or oscillatory stage and a steady stage for the development of natural convection flow inside the corrugated cavity. The numerical scheme is based on the finite element method adapted to triangular non-uniform mesh element by a non-linear parametric solution algorithm. Investigation has been performed for the Rayleigh number, Ra ranging from 10⁵ to 10⁸ with variation of corrugation amplitude and frequency. Constant physical properties for the fluid medium have been assumed except for the density where Boussinesq’s approximation has been considered. Results have been presented in terms of the isotherms, streamlines, temperature plots, average Nusselt numbers, traveling waves and thermal boundary layer thickness plots, temperature and velocity profiles. The effects of sudden differential heating and its consequent transient behavior on fluid flow and heat transfer characteristics have been observed for the range of governing parameters. The present results show that the transient phenomena are greatly influenced by the variation of the Rayleigh number with corrugation amplitude and frequency.