Background and Objective: In December 2019, patients diagnosed with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China.A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (COVID 19).The article aimed to unmask the genetic stability and nature of the viruses and validated the safety guidelines adopted for the coronaviruses currently causing the global pandemic.Materials and Methods: This study uses in silico approach and bioinformatics tools to validate the stability status and characteristics of the novel SARS-COV 2 coronaviruses by retrieving nucleotide sequences isolated and deposited in the NCBI.Results: The results have revealed that 11 out of 12 isolates studied are genetically and thermally unstable.The aliphatic index ranged from 52.98-112.07 in MT187977.1-MT127116.1,respectively.The instability index among the sequences ranged from 39.58-73.65 in MT187977.1-MT152900.1 isolate, respectively.The G-C contents range from 37.28-49.26% in MN938385.1-MT187977.1,respectively.Phylogenetically, isolates MT127116.1,MT159778.1,MT050414.1 and MT042777.1 showed the same genetic and mutation pathway with an evolutionary distance of 0.4 and 0.8 divergence times relative to the last common ancestor.Conclusion: There is a need for concerted effort in studying and understanding the genetic and thermal stability status and other characteristics of the viruses to be able to find a suitable therapy and drug design for the pandemic and biosecurity of humans against the virus now and in the future.
Background and Objective: Antibiotic resistance is becoming a critical concern for public health that has accelerated the search for new antimicrobial compounds from the natural resources.This study aim to evaluate the antibacterial activities of plant extract (Aloe Vera and Garlic) on multi-drug resistant (MDR) bacteria isolated from polluted water samples of clinical importance by molecular docking and its respective relationship corresponding to the multi-drug efflux pump PBD ID 5YIL protein of E. coli.Methodology: Aloe vera extracted with methanol PBS shown maximum inhibition (28 mm) against MDR strain of Escherichia coli using agar well diffusion.The natural compounds of plant extract responsible for antibacterial activity were screened on the basis of using computational approaches such as molecular docking based validation analysis.The 22 compounds were selected as legend and multi-drug efflux pump (MDEP) transport protein (5 YIL) of E. coli which plays an important role in actively transport of many antibiotics out of the cell was selected as receptors for molecular docking analysis.Results: In silico analysis showed that Aloin compound has strong binding affinity for selected target protein receptors.Hence, results of study showed the ability of Aloin to bind with active sites of MDEP protein targets to disrupt the mechanism of MDR in bacterial cell and allow the drug towards the treatment of diseases.Conclusion: In silico and in vitro methods help us to explore and investigate anti-MDR properties of selected medicinal plants extracts and their overall 22 phytoconstituents.
Background and Objective: An important guideline for preventing amplification bias in Polymerase chain reaction (PCR) based DNA methylation techniques was recently proposed.However, there is no software that facilitates visualizing and applying such recommendations in PCR primers design.The aim of this work was to provide a web tool to facilitate the visualization of critical sequence elements for the design of primers applying the most recent recommendations for PCR-based methylation techniques.Materials and Methods: BiCVisualizer, a script for the visualization of critical sequence elements was designed using Java/html.The amplification specificity of a set of 10 primer pairs designed with the visual assistance of this web-tool was evaluated in silico PCR using BiSearch software.Results: The in silico PCR test showed a mean of 353 matches per primer and strand (range 84-934) using BiSearch.BiSearch did not find non-specific amplification for any primer pair designed using BiCVisualizer.Conclusion: This script was designed to assist the effective design of primers for methylation-sensitive high-resolution melting, the utility of this tool was supported by in silico evaluation.Users requiring visual construct primers can now spend less time in primer design using BiCVisualizer tool.
Background and Objective: Studies on signal peptides remain little and lacking to Cryptosporidium.This study represents the first attempt to investigate selected putative protein sequences of Cryptosporidium parvum in its established genome database for signal peptide.Methodology: Prediction analysis of protein sequences and identification of signal peptides on this parasite were analysed by SignalP 4.1 server.A total of 100 protein sequences were randomly selected and analysed, of which 6 (6%) corresponded to be predicted as signal peptide sequences.Results: Based on the comparison of sequences with database protein sequences in GenBank NCBI, almost all protein sequences were highly conserved with other protein sequences from different species of Cryptosporidium.Considering the secretory proteins in Cryptosporidium, several virulence protein sequences of this parasite may also show presence of N-terminal signal peptide or not.Conclusion: Hence, further studies need to be carried out for identification of N-terminal signal peptide function in Cryptosporidium for facilitating its virulence and pathogenesis pathway.
Background and Objective: Extracts from Colocasia esculenta plant have been found to possess anti-inflammatory properties.2, 3-Dimethylmaleic anhydride (3, 4-Dimethyl-2, 5-furandione) is a recent root stock extract of Colocasia esculenta.This study aimed to look for the possible anti-inflammatory activity of the 2, 3-Dimethylmaleic anhydride by docking study with the target protein, COX-2.Materials and Methods: Crystal structure of COX-2 was retrieved from RCSB protein data bank.The structure of 2, 3-Dimethylmaleic anhydride was retrieved from PubChem compound database in NCBI.Docking study was performed with the help of AutoDock 4.2.6.Results: Docking study showed that 2, 3-Dimethylmaleic anhydride fits into the cyclooxygenase active site of COX-2 with favourable binding energy.Conclusion: NSAIDs best known for their anti-inflammatory properties act by blocking COX enzymes suggest the compound 2, 3-Dimethylmaleic anhydride may possess anti-inflammatory potential bearing a role in alleviating the signs and symptoms of inflammation.
Background and Objective: Precursor microRNA expressions vary depending on their cellular environment and a large amount of genome segments can be folded in similar pseudo precursorʼs microRNA hairpins like structure.Therefore, detection of true precursor microRNA in a genome is challenging task.The computational prediction of precursor MicroRNAs first distinguishes a large amount of similar folded hairpins like structure in genome sequence as a pseudo or true precursor miRNAs.However, researchers need to be improving methods for identification of precursor MicroRNA in a genomic sequence.Materials and Methods: In this computational method, supervised machine learning approach was used as a classifier for classifying the true precursor miRNAs using sequence and secondary structure information.Results: The support vector machine (SVM) classifier achieved accuracy (Q) of 96.28% for predicting true pre-miRNAs.Here, a new precursor miRNA identification tool-PremipreD was developed which performs better in comparison to existing tools, in terms of overall performance and specificity.Conclusion: The PremipreD algorithm reduces the number of false positive prediction rate by using effective Support vector machine methods.
Background and Objective: Singh and Grewalʼs model estimates the population proportion on stratified sampling schemes.The crux of this paper was to develop a new stratified Singh and Grewalʼs model using Geometric Distribution.Materials and Methods: The equilibrium point of the model was investigated and a new stratified sampling and stratified double sampling randomized response model based on Singh and Grewalʼs model using geometric distribution was proposed.Results: This study showed that the proposed method is more efficient than the one recently envisaged by Singh and Grewalʼs model.Numerical illustrations and graphical representations are also given in support of the present study.Conclusion: A new dexterous stratified randomized response model has been proposed and shown theoretically as well as numerically that the proposed model is more efficient than Singh and Grewalʼs randomized response model.
Background and Objective: Elasmobranchs (Sharks, skates, rays) are frequently available marine fishes which serve as an ideal host for the cestode parasites.Paraorygmatobothrium floraformis (Southwell, 1912) Ruhnke, 2011 is a cestode comprising a ubiquitous and specious genus of elasmobranch parasites.This parasite was isolated from the spiral intestine of commercially available elasmobranch fish, Rhizopriondon acutus of the Nellore coast, Bay of Bengal.The main objective of this work is to evaluate the morphological criteria, molecular characterization of Paraorygmatobothrium floraformis using the 28S ribosomal DNA and to determine the phylogenetic position of this species with bioinformatics tools like BLAST and Mega 6. Materials and Methods: The present study is restricted to Nellore Coast, which has a coastline of 169 km.The milk shark, Rhizopriondon acutus was collected from the local fisherman and the nearby Coastal areas of Nellore to examine the cestodes from their spiral intestines.They were preserved in FAA (Formalin-10 mL, Alcohol-85 mL and Acetic acid-5 mL) for further morphological analysis.Also, few parasites were fixed in 95% molecular grade ethanol and placed at low temperature of -20EC for further molecular analysis.Results: The morphological data was taken from the whole mounts.However, the obtained gene sequences of the cestode parasite were submitted to the Genbank.The gene sequence of the parasite was compared with the available gene sequences of other cestode parasite from other elasmobranchs in the Genbank.The pairwise alignment of gene sequences showed 80% similarity with the order Tetraphyllidea and 5-10% mismatches with the sequences of Phyllobothriidea family.Also, the host, Rhizoprionodon acutus and Nellore coast serve as new host record and locality records for Paraorygmatobothrium floraformis (Southwell, 1912) Ruhnke, 2011.Conclusion: Species identification is one of the major difficulties in marine fish parasites.Ribosomal DNA has been widely used for taxonomic studies.The study presents a small molecular phylogenetic analysis of the elasmobranch tapeworms of family phyllobothridea and order Tetraphyllidea.These types of analyses can reveal the relationship between different orders, families and species of the cestode parasites from the marine environment.
Background and Objective: Tuberculosis is a life threatening bacterial disease caused by Mycobacterium tuberculosis (M.tuberculosis) which has affected the population of almost all parts of the world since time immemorial.Although remarkable discovery has been achieved in combating disease control and its propagation but due to emergence of resistant strain of M. tuberculosis exhaustive search for the panacea to counter the bacteria is still on.This study proposes in silico studies of 35 natural compounds against proposed drug target isocitrate dehydrogenase type II (PDBID: 5 KVU) of M. tuberculosis (H37Rv).Almost all available antitubercular drugs in the market now-a-days have some side effects.Hence, there is a strong need of some natural antitubercular compounds that can mitigate the side effects and boost up the overall health of the patients.The aim of the present study was to explore the potential novel natural inhibitor against proposed drug target, isocitrate dehydrogenase II.Materials and Methods: Crystal structure of isocitrate dehydrogenase II was obtained from PDB.All natural compounds used in this study were obtained from Pubchem database and their drug likeliness was also crosschecked.Docking studies were performed with the help of Autodock 4.0.NADP + was used as a reference ligand to compare the docking results with natural compounds.Molecular dynamics study of the docked complex has also been performed to infer the deep insight of the various interactions and stability of the receptor-ligand docked complex.Results: Results showed that molecular docking of isocitrate dehydrogenase II of M. tuberculosis against all 35 natural multi-beneficial compounds, Amentoflavone attained the minimum binding energy, hence amentoflavone is most potential natural compound that may inhibit the proposed enzyme.The molecular dynamics study of the docked receptor ligand complex also showed good congruence to the docking result.Conclusion: Natural compounds showed good binding energies with the receptor protein isocitrate dihydogenase II and amentoflavone, a natural ligand may act as a strong anti-tubercular lead compound against M. tuberculosis.
Background and Objective: The era of high throughput sequencing technology has poured thousands of full genomes sequences in public databases.A remarkable portion of these genomic sequences belongs to the viruses of which viruses infecting archaea are least studied group.Archaeal viruses are morphologically more diverse than bacterial ones and display unique morphotypes.All sequenced archaeal viruses have DNA as their genetic material, which is double stranded in most of the cases.In this study, applied biometric method to understand the local and global feature of nucleotide distribution in all available archaeal genomes on Genbank.ArchaeVir database is dedicated to characterization of archaeal virus genomes with standardized genometrics of Z-curve and cumulative GC and AT skews.Material and Methods: All archaea viruses genomes were downloaded from NCBI.A script was written in MATLAB to calculate and plot the cumulative Z-curve and nucleotide skews.Database was created using MySQL and PHP, AJAX was used to create front end of the database.Results: Genometrics is a biometric analysis of chromosomes which is capable of identifying, at the level of whole genomes, features inherent to chromosome organization and functioning.This database also hosts the basic genomic records like genome length, GC%, total genes and proteins all sequenced viral genomes of archaea.In addition to this, two tools, one for finding the repeats and nucleotide distribution and second for plotting the geometric skew of nucleotide sequence has also been integrated with this database.Conclusion: Genometrics data of archaeal viruses available on the database could be readily accessed by the scientific community for further analysis of local and global features of viral genomes as well as for tutorial purpose.
Background and Objective: Unmanned Aerial Vehicles (UAVs) have found widespread use in many applications due to its mobility and maneuverability.An important aspect in controlling the movement of these vehicles is its state estimation.State estimation is especially challenging for indoor applications, where Global Positioning System (GPS) signals are weak and have low accuracy.Methodology: This research proposed a vision based state estimation that is applicable even for indoor use.It is a low cost, low power and reliable state estimation approach using a monocular camera with a series of fiducial markers.When a marker is captured by the camera, its position and orientation with respect to the cameraʼs coordinate frame is determined based on its homography transformation.The pose of the camera and hence the vehicle, in world coordinate can then be inferred from known markers poses.Results: In this study experimental results showed that the proposed method is suitable for indoor navigation of unmanned aerial vehicles.The reliability of the state estimation was improved by increasing the number of markers captured.Conclusion: The experimental results verified that the vision based state estimation method for indoor UAV navigation a promising solution and had several advantages over traditional other methods.
Background and Objective: Angiogenin is a monomeric protein which has been considered as an important factor in angiogenesis.Recent studies on angiogenin proved that it is an ideal drug target for treating cancer and vascular dysfunctions.The present study aimed to develop a Quantitative Structure Activity Relationship (QSAR) model with small molecules of angiogenin inhibitors.Methodology: The small molecule inhibitors were divided into training and test sets to build the QSAR model.Multiple Linear Regression (MLR) and Partial Least Square (PLS) methods were used to develop QSAR models.Results: In the MLR model, the descriptors generated for the compounds showed multicollinearity and resulted in a mono-parametric equation.The model generated by PLS satisfied both internal and external cross validation parameters.The predicted model showed the positive contribution of ring atoms and donor hydrogen bonds to the activity.Conclusion: As these parameters are reported to be crucial for biological activity of drugs, it can be used to do develop effective small molecule drug candidates for angiogenin.
One of the popular and widely practiced biometric systems is fingerprint. Fingerprint biometric systems are smaller in size, easy to use and has low power. It is available and deployed globally in law enforcement, such as immigration, banking sectors, forensics, health care and many more. This study reviewed fingerprint biometric systems and the methods used in each proposed system. Many studies have been done in the area of feature extraction and matching stages. The current techniques used in these stages are minutiae-based and euclidean distance-based. Application of the fingerprint biometric system in the industries has been accepted widely and used in the Europe and some developed country. Malaysia has also incorporated the use of this system in its administration for controlling the point of entry at the Kuala Lumpur International Airport. Generally, fingerprint biometric systems can be categorized into recognition, security, identification and control systems. Each system has their benefits and drawbacks that complemented each other.
Most developing countries are facing the same problem of increasing population and pollution.This has led to the increase of energy consumption that forces them to seek for alternative energy other than depleting fossil fuel such renewable energy namely solar.Located in South East Asia, Malaysia is confronting with the same situation.In this study, the evaluation of potential of solar energy for three locations in Malaysia including Pontian, Kerteh and Teluk Intan is performed using HOMER software.Based on the results, Pontian generates the highest annual solar electricity generation of 543,509 kWh yearG 1 due to the large size of 400 kW PV panel of the system.However, the cost of energy or also known as COE produced is expensive.On the other hand, with the highest solar radiation received in Kerteh, the PV stand-alone system requires lower size of 350 kW PV panel but at the same time is able to fulfil the demand with the lowest COE of $0.442 kWhG 1 among other locations.
Road transportation system is a complex series of activities.However, this can be broken down into sub-activities for easier understanding to analysis its efficiencies.This study discusses a simple technique of process mapping to develop a simple model for efficiency analysis of road transport specifically container haulage system.Observation was made in the industry, processes are then mapped for model development.Basic variables are then identified after which the model are developed for further analysis of efficiency.
Background: Breast cancer type 1 (BRCA1) gene also known as breast cancer type 1 susceptibility protein homologue plays important role in DNA double-strand break repair, homologous recombination, chromatin remodeling, cell cycle regulation and transcription regulation.Objective: Considering the importance of this protein, the present study was undertaken to analyze BRCA1 gene of different mammalian species by assessing the identity and similarity, phylogenetic relationship, physicochemical properties, predict the motifs, secondary and the tertiary structures.Materials and Methods: Seventeen nucleotide and protein sequences of BRCA1 gene of different mammalian species were retrieved from National Centre for Biotechnology Information (NCBI).Multiple sequence alignment was done using CLUSTAL W software, while identity and similarity was determined by constructing a pair wise comparison.Results: Results obtained at the end of the experiment showed that there was no percentage identity or similarity that was less than 70%.The phylogenetic relationship of BRCA1 gene of the mammalian species clustered into aquatic, herbivores, carnivores and omnivores, respectively.The highest time of divergence (95MYA) of the BRCA1 gene was observed between the BRCA1 gene of killer whale and human, while the least time of divergence (4.6MYA) was observed between the BRCA1 gene of cattle and American buffalo.Physicochemical properties of BRCA1 proteins in the five mammalian species (cattle, sheep, pig, American buffalo and human) were found to be unstable, hydrophilic and intracellular in nature.The following motifs were present at various positions in the BRCA1 gene of the five mammalian species; zinc finger RING, BRCT domain, N-myristoylation site, N-glycosylation, cAMP and cGMP dependent protein kinase phosphorylation site, tyrosine kinase phosphorylation, casein kinase 2 phosphorylation site, protein kinase C phosphorylation site and cell attachment sequence but leucine zipper pattern and microbodies c-terminal motifs were found in only human BRCA1 gene.The BRCA1 secondary structure contained the alpha helix, extended strand and random coil.Conclusion: Based on the results obtained, it can be deduced that BRCA1 gene has identical homologue, functional similarity and highly conserved in these mammalian species.
