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Whole-genome sequence analysis through online web interfaces: a review
Gunasekara, A.W.A.C.W.R.,Rajapaksha, L.G.T.G.,Tung, T.L. Korea Genome Organization 2022 Genomics & informatics Vol.20 No.1
The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.
Gunasekara, Buddhika P.,Perera, Kumudu S.,Vidanapathirana, Kamal P.,Vignarooban, K. Techno-Press 2021 Advances in materials research Vol.10 No.2
The prime objective of the present study is to exploit a user friendly, inexpensive all solid state super capacitor using a suitable electrolyte and electrodes. A gel polymer electrolyte (GPE) consisted with polyvinylidene fluoride-co-hexafluopropylene (PVdF), ethylene carbonate (EC), propylene carbonate (PC) and zinc trifluoromethane sulfonate (Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub>-ZnTF) was prepared using solvent casting method and its properties were optimized by varying the composition. The composition of 16 PVdF : 22 ZnTF : 31 EC : 31 PC (weight %) exhibits the optimum room temperature conductivity of 3.09×10<sup>-3</sup> Scm<sup>-1</sup>. It is purely an ionic conductor having a negligible electronic conductivity. In addition, it was possible to obtain a thin, mechanically stable film. The electrodes were prepared using Sri Lankan natural graphite (NG) with a polymer binder. Eventhough there are reports about natural graphite based super capacitors, Sri Lankan natural graphite has not been considered for super capacitors at a large scale. The main reason for turning towards natural graphite is to reap the benefits of low cost as well as the safety. In order to optimize the electrode properties, the ratio between graphite and polymer binder (in weight basis) was changed. The polymer binder used was polytetrafluoroethylene (PTFE). Super capacitor fabricated with the electrode of the composition, NG : PTFE = 90:10 shows the maximum single electrode specific capacitance (2.58 Fg<sup>-1</sup>). The fabricated device retains for continuous charge discharge operation with a minimum performance reduction.
Disinfectant effect of monopersulfate (MPS) compound to white spot syndrome virus (WSSV) of shrimp
( Cwr Gunasekara ),( Seok-ryel Kim ),( Lgtg Rajapaksha ),( Shmp Wimalasena ),( Hnks Pathirana ),( Gee-wook Shin ) 한국어병학회 2020 한국어병학회지 Vol.33 No.2
This study investigated the disinfection effect of monopersulfate (MPS) compound against white spot syndrome virus (WSSV) by bioassay using kuruma shrimp (Marsupenaeus japonicas). A WSSV stock was prepared with muscle homogenate from WSSV-infected whiteleg shrimp (Penaeus vannamei) and its lethal dose 50% endpoint (LD<sub>50</sub>) and infectious dose 50% endpoint (SID<sub>50</sub>) were respectively determined as 10<sup>-5.63</sup> and 10<sup>-6.79</sup> in bioassay using kuruma shrimp, followed by PCR assays. The disinfective effect of MPS compound (1.2 ppm, 2.4 ppm, 4.8 ppm) was performed by bioassay using about 10-fold higher dilution (10<sup>-4</sup>) of WSSV homogenate. The compound resulted in WSSV inactivation by a concentration-dependent manner. In addition, 4.8 ppm of MPS completely prohibited WSSV infection. To our knowledge, this study is the first report about the usefulness of MPS as a disinfectant to WSSV.
Pyrrole Coating with In Situ Polymerization for Piezoresistive Sensor Development - A Review
Dilini Srinika Wijerathne Gunasekara,Xin Niu,Waqar Lqbal,Yin He,Hao Liu 한국고분자학회 2022 Macromolecular Research Vol.30 No.3
Polypyrrole (PPy) is a highly practicing conductive polymer with the potentiality to modify conductivity, sensitivity, and applicability to blend or coated over different materials to offer a wide range of properties, especially for piezoresistive sensors that are highly in demand in smart electronics. The in-situ polymerization is a promising method to prepare PPy coating and composites for cost-effective reliable sensors fabrication that is highly ambitious, for healthcare and rehabilitation purposes with numerous possibilities for modifications. PPy preparation with in-situ polymerization method is still in a great challenge to get desired outcomes so many types of research come out, however not enough records in analysis basis. This research is focused on analyzing different possibilities of PPy with an in-situ polymerization process to get different outcomes related to the change conductivity and sensitivity of PPy coated sensors. As the outcome, this review gives some inspirational ideas to develop high-performance PPy coatings enhancing its conductivity and sensitivity for piezoresistive sensor fabrications.
국내 양식 흰다리새우에서 검출된 노랑머리바이러스(YHV-8)의 유전학적 특성
김석렬,( Gunasekara Cwr ),( Wimalasena Shmp ),신기욱 한국어병학회 2020 한국어병학회지 Vol.33 No.1
This study was performed for screening yellow head virus(YHV) complex in 252 including 235 white leg shrimps (Litopenaeus vannamei) and 17 oriental shrimp (Fenneropenaeus chinensis) collected from 18 farms located in southwestern province of Korea. The virus complex was detected by nested reverse-transcriptase polymerase chain reaction (RT-PCR) assay. In the assay, amplicons were resulted in RNAs exracted from 38 shrimps (21 white leg shrimps and 17 oriental shrimps) obtained from 7 farms. In phylogenetic analysis using sequences of ORF1b gene, all 38 sequences obtained in this study formed an independent lineage with YHV-8 genotype firstly isolated in China, belonged to an YHV-8 clade.
Evaluation of refused tea waste activated carbon for color removal: Equilibrium and kinetic studies
Wijetunga, Somasiri,Gunasekara, Chathurika DFA Techno-Press 2017 Advances in environmental research Vol.6 No.1
New technologies or improvement of the existing technologies are required to enhance the efficiency of removal of pollutants from wastewater. In this study we attempted to produce and test the activated carbon produced from the refused tea waste for the removal of dyes from wastewater. The objectives of this investigation were to produce activated carbon from refused tea waste by chemical activation, evaluate its performance for the removal of color produced from Acid Yellow 36, and the modeling of its dye removal with the kinetic study. The activation was performed in two steps namely carbonization at $375{\pm}25^{\circ}C$ and chemical activation with HCl at $800^{\circ}C$ under the absence of Oxygen. Adsorption isotherms and kinetic studies were performed with a textile dye, Acid Yellow 36, at different concentrations (20-80 mg/L). The maximum dye removal (~90%) observed at 80 mg/L dye concentration and it reduced at low dye concentrations. Maximum adsorption (71.97 mg/g) was recorded at 96 h at $29{\pm}1^{\circ}C$. Low pH increased the dye adsorption (pH=2; 78.27 mg/g) while adsorption reduced at high pH levels indicating that the competition occurs in between OH- ions and AY36 molecules for the adsorption sites in RTAC. The Langmuir isotherm model clearly explained the dye adsorption, favorably, by RTAC. Moreover, kinetic studied performed showed that the pseudo second order kinetic model clearly describes the dye adsorption. Based on the results obtained in this study, it can be concluded that RTAC can be used for the removal of textile dyes.
Matt N. Hicks,Sanjiva Gunasekara,Jose Serate,박진,Pegah Mosharaf,Yue Zhou,이진원,윤환 한국미생물학회 2017 The journal of microbiology Vol.55 No.10
The Escherichia coli cAMP receptor protein (CRP) utilizes the helix-turn-helix motif for DNA binding. The CRP’s recognition helix, termed F-helix, includes a stretch of six amino acids (Arg180, Glu181, Thr182, Val183, Gly184, and Arg185) for direct DNA contacts. Arg180, Glu181 and Arg185 are known as important residues for DNA binding and specificity, but little has been studied for the other residues. Here we show that Gly184 is another F-helix residue critical for the transcriptional activation function of CRP. First, glycine was repeatedly selected at CRP position 184 for its unique ability to provide wild type-level transcriptional activation activity. To dissect the glycine requirement, wild type CRP and mutants G184A, G184F, G184S, and G184Y were purified and their in vitro DNA-binding activity was measured. G184A and G184F displayed reduced DNA binding, which may explain their low transcriptional activation activity. However, G184S and G184Y displayed apparently normal DNA affinity. Therefore, an additional factor is needed to account for the diminished transcriptional activation function in G184S and G184Y, and the best explanation is perturbations in their interaction with RNA polymerase. The fact that glycine is the smallest amino acid could not fully warrant its suitability, as shown in this study. We hypothesize that Gly184 fulfills the dual functions of DNA binding and RNA polymerase interaction by conferring conformational flexibility to the F-helix.
Lan, Pham Thi,Son, Tong Si,Gunasekara, Kavinda,Nhan, Nguyen Thi,Hien, La Phu Korean Society of Surveying 2013 한국측량학회지 Vol.31 No.6
Coastline is the most dynamic part of seascape since its shape is affected by various factors. Coastal zone is an area with immense geological, geomorphological and ecological interest. Monitoring coastal change is very important for safe navigation, coastal resource management. This paper shows a result of monitoring coastal morphological changes using Remote Sensing and GIS. Study was carried out to obtain intensity of erosion, deposition and sand bar movement in the Red River Delta. Satellite images of ALOS/AVNIR-2 and Landsat were used for the monitoring of coastal morphological changes over the period of 1975 to 2009. Band rationing and threshold technique was used for the coastline extraction. Tidal levels at the time of image acquisition varied from -0.89m to 2.87m. Therefore, coastline from another image at a different tidal level in the same year was considered to get the corrected coastline by interpolation technique. A series of points were generated along the coastal line from 1975 image and were established as reference points to see the change in later periods. The changes were measured in Euclidean distances from these reference points. Positive values represented deposition to the sea and negative values are erosion. The result showed that the Red river delta area expanded to the sea 3500m in Red river mouth, and 2873m in Thai Binh river mouth from 1975 to 2009. The erosion process occurred continuously from 1975 up to now with the average magnitude 23.77m/year from 1975 to 1989 and 7.85m/year from 2001 to 2009 in Giao Thuy area. From 1975 to 2009, total 1095.2ha of settlement area was eroded by sea. On the other hand, land expanded to the sea in 4786.24ha of mangrove and 1673.98ha of aquaculture.