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Item Potential of Inhibiting the Receptor Binding Mechanism of SARS-COV-2 using Phytochemicals contained in Paspanguwa Water Extract: Molecular Docking and Dynamic Studies(Asian Journal of Chemistry, 2024-11-30) JAYAWARDENA, P.A.S.N.P.; SOORIYAWANSHA, A.M.S.C.; KUMARATHUNGA, P.G.J.D.; DANANJAYA, P.D.H.; KADIGAMUWA, C.C.; DAHANAYAKE, J.N.This study is focused on the SARS-CoV-2 virus by in silico screening of phytochemicals contained in ‘Paspanguwa’ water extract, targeting ACE2 receptors using molecular docking. Phytochemicals of the five herbal ingredients contained in ‘Paspanguwa’ were extracted into water and were identified based on the literature reviews. Ligands geometries were optimized using Avogadro software and transformed to PDBQT format files by detecting torsion root using AutoDock Tools 1.5.6. SWISS-MODEL server was used to model the structure of the ACE2 receptor based on the UniProt ID Q9BYF1. The stereochemical quality of the protein model was assessed using SAVES v 6.0 and ProSA servers. Finally, potential ligands were docked to the ACE2 receptor protein by considering all variants of this virus and their interactions with the ACE2 receptor. The highest binding energy (BE) (-10.42 kcal/mol) was given by carpesterol phytochemical with allosteric site-2 and allosteric site-3 in the ACE2 receptor and this complex was subjected to molecular dynamic (MD) analysis using a CHARMM36 force field. According to the radius of gyration (Rg), root mean square deviation (RMSD) and root mean square fluctuation (RMSF) results, the studied protein-ligand complex was stable throughout the simulation time.Item Influence of pumpkin seed powder on the characteristic properties of whole wheat cake(Elsevier eBooks, 2024) De, Suprakash; Bharti, D.; Pradhan, B. K.; Behera, H.; Kim, N. M.; Wickramarachchi, S.; Sarkar, P.; Pal, K.Pumpkin seeds are a good source of unsaturated fatty acids, dietary fibers, and minerals. It can be used as a food supplement as the nutritional value of the seeds is relatively high. This study incorporates PSP (pumpkin seed powder) in varying amounts (0%, 5%, 10%, 15%, and 20%) in cake samples. Afterward, their effects on physicochemical, thermal, mechanical, and electrical characteristics were observed. Adding PSP to the cake recipe significantly increased the porosity of the cake by only up to 10% PSP incorporation. The PSP improved the hardness and other textural properties of the cake samples. Also, we can deduce that the water retention capacity of the cake samples increased with the addition of PSP, which increased the moisture content of the cake samples. From the results, we can observe that the browning of the cake increased with the incorporation of PSP in the cake samples. From all the characteristics, we can conclude that the cake sample with 10% PSP had the best texture. This means that PSP can be incorporated into cake samples only up to 10% without compromising the texture and taste.Item Effect of pumpkin seed powder on the properties of cake batter prepared with whole wheat flour(Elsevier eBooks, 2024) De, Suprakash; Bharti, D.; Pradhan, B. K.; Behera, H.; Kim, N. M.; Wickramarachchi, S.; Pal, K.; Sarkar, P.Nutrition plays a crucial role in overall health. Recently, different fruit and vegetable seeds have been incorporated into various food products to increase their nutritional values. Due to its higher nutritional content, the research community has recently explored pumpkin seed powder (PSP) as an ingredient in different bakery products. In the current study the batter composition prepared by whole wheat flour at varying PSP concentrations (5%, 10%, 15%, and 20% w/w) has been studied. The obtained results from the current study suggested that incorporating PSP significantly alters the color, texture, and microstructure of the prepared batter samples. Also, the water retention and air incorporation capacity of the batter samples showed a significant increase after the PSP incorporation. From the 2,2-diphenyl-1-picryl-hydrazyl-hydrate scavenging assay, the antioxidant properties of the prepared batter samples were analyzed. The results suggested an increased antioxidant activity after PSP addition. Though PSP adds to the nutritional value, adding PSP greater than 10% adversely affects the texture of the batters. With 10% of PSP replacement the prepared batter showed a balanced textural property in our study.Item Long-term exposure to environmentally relevant Bisphenol-A levels affects growth, swimming, condition factor, sex ratio and histology of juvenile zebrafish(Scientific Reports, 2024) Pathirajage, K. S.; Rajapaksa, G.Bisphenol A (BPA) is an environmental estrogen which perturbs hormone signaling pathways adversely affecting aquatic organisms. To evaluate the impact of developmental exposure to long term yet environmentally relevant low doses of BPA, wild-type juvenile zebrafish of 35 days post fertilization were treated with BPA (1 and 10 μg/L), treatment control (0.5% v/v methanol) and control for 60 days. Both BPA treatments led to significantly increased morality overtime. Length increment and specific growth rates became significantly high in BPA exposed zebrafish overtime. Obesogenic property of BPA was not evident with longexposure to low BPA doses. A significantly high and BPA dosedependent female-biased sex ratios were observed following the juvenile exposure. Significantly low swimming speed was recorded in the fish of both BPA-treated tanks than that of control. Condition factor was significantly low in BPA exposed fish indicating the poor-wellness. There were numerous histopathological alterations of gonads, liver and kidney indicating impacts of juvenile exposure in zebrafish. Altered growth, swimming, mortality, feminization and histopathological changes in zebrafish induced by BPA indicate the risks associated with developmental exposures. The findings call for more comprehensive studies to comprehend the ecological risks imposed by low concentrations of environmental estrogens in urban aquatic ecosystems.Item Inadequacy of Zernike Polynomials for Accounting the Variability of Wavefront Measurements(Postgraduate Institute of Science Research Congress, Sri Lanka., 2024) Lakshmi, M.P.D.S.; Karunarathna, S.P.D.S.S.K.; De Silva, T.M.M.Wavefront measurements have been crucial in vision science and ophthalmology, especially for wavefront-driven corrections like laser refractive surgeries and customized contact lens design. However, the accuracy of these corrections hinges on precise measurements. In clinical practice, multiple measurements are taken from a patient’s eye during each session to avoid ambiguous conclusions from a single measurement. Despite these efforts, variations in measurements occur due to aberrometer misalignments, pupil size, lens position, and eye accommodation. These variations directly impact custom vision corrections, leading to errors. However, comprehensive studies on these dynamics are lacking, but understanding them is crucial in vision science. Previous studies have found that the variability in repeated measurements is significant, as indicated by changes in Zernike coefficients. However, these studies have only examined this variability through the Zernike coefficients themselves. In contrast, this study uniquely investigated their variability using the raw local slope data from wavefront measurements. The least squares estimation was implemented to analyse data from patients with astigmatism, myopia, keratoconus, and keratoplasty. Further, measurement noise was simulated using normally distributed random numbers, with signal-to-noise ratios (SNR) varied between 20 dB and 80 dB. The SNRs for individual Zernike coefficients have been determined. The results from patients showed that most Zernike coefficients had SNRs above 10, indicating minimal measurement variation impact. A few Zernike modes had SNRs below 2 for some patients. The study concludes that it is crucial to balance the addition of more Zernike modes with measurement variability to avoid introducing errors in custom vision corrections. Moreover, the results challenge the existing findings and suggest opportunities for deeper analysis and new insights.Item Bioaccumulation and health risks of chromium and cadmium in Basella alba with emphasis on Urea, muriate of potash and triple super phosphate mixtures(National Science Foundation of Sri Lanka, 2024) Amarasena, M. D. M. C. K.; Wijeyaratne, W. M. D. N.Basella alba is a commonly consumed green leafy vegetable in South Asian countries and it is considered as an economical source of essential vitamins and dietary fibers. Urea, muriate of potash (MOP) and triple super phosphate (TSP) mixture is the most commonly used inexpensive fertilizer mixture in the commercial cultivation of B. alba. This study was conducted to assess the effect of using a mixture of Urea-MOP-TSP on the bioaccumulation potential of cadmium (Cd) and chromium (Cr) by the leaves of B. alba. Pots treated with the Urea-MOP-TSP mixture and compost were maintained in a greenhouse with controlled light and temperature settings. The concentrations of Cd and Cr in the root zone soil, roots and leaves of B. alba were analyzed using an Atomic Absorption Spectrophotometer after acid digestion. The health risk of consuming B. alba was evaluated using the daily intake of metals, health risk index and cancer risk index. The results showed that Cd and Cr can bioaccumulate in the leaves of B. alba. The bioaccumulation potential of Cr was higher than that of Cd. Although the daily intake of Cd and Cr from B. alba were below the maximum values stipulated by the WHO, the cancer risk index indicated potential cancer risks based on Cd intake due to consumption of B. alba cultivated using the Urea-MOP-TSP mixture. Furthermore, the health risks associated with the hyper-accumulation of Cd and Cr in the edible parts of B. alba cultivated using compost were significantly less compared to that of the plants treated with the Urea-MOP-TSP mixture. Therefore, if B. alba is cultivated using chemical fertilizer, it is recommended to regularly monitor the concentrations of Cd and Cr in the cultivation soil, chemical fertilizer and in the edible parts of B. alba to prevent the excessive buildup of Cd and Cr along the food chain. In addition, it is recommended to identify the potential microbial assemblages that can be inoculated to the cultivation soil to reduce the bioavailability of Cd and Cr.Item Morpho-molecular genetic diversity and population structure analysis to enrich core collections in tea [Camellia sinensis (L.) O. Kuntze] germplasm of Sri Lanka and India(Genetic Resources and Crop Evolution, 2023) Kottawa-Arachchi, J. D.; Ranatunga, M. A. B.; Sharma, R. K.; Chaudhary, H. K.; Attanayake, R. N.; Amarakoon, A. M. T.; Gunasekare, M. T. K.; Sharma, B.; Kumar, N.; Sood, V. K.Despite tea [Camellia sinensis (L.) O. Kuntze] is one of the top non-alcoholic beverages consumed around the world; its genetic and phenotypic diversity is less understood compared to other plantation crops. The study’s aims were to undertake phenotypic and genotypic characterization of Sri Lankan and Indian tea germplasm and to identify diverse accessions to accelerate tea breeding programmes in both countries. A total of 171 tea accessions, comprising 94 Sri Lankan and 77 Indian accessions were used. All the accessions were subjected to phenotyping and genotyping using 28 polymorphic simple sequence repeat (SSR) markers. Based on 16 morphological characters, the first three principal components explained 57.61% and 58.43% of the total variability of Sri Lankan and Indian accessions, respectively. Young shoot pubescence, young shoot pigmentation, serration of leaf margin, and mature leaf colour contributed positively to the grouping of accessions. Based on Neighbor-joining analysis, all Sri Lankan accessions grouped in a single cluster, whereas Indian accessions grouped in two distinct clusters. The Gower’s distance method was the most appropriate than other methods for developing core subsets. Among 21 Sri Lankan core accessions selected, 11 accessions belong to introductions, five TRI-developed cultivars and five estate selections. Among 18 Indian core accessions selected, 11 belong to China types, two Assam types and five Indian recommended cultivars. The current study is the first study to compare tea germplasm of both countries and the results are useful for tea crop improvement programme, conservation and utilization of tea germplasm in India and Sri Lanka in the future.Item Chemometric assessment of bioaccumulation and contamination pathways for toxic metals in diet and environment: implications for chronic kidney disease of unknown etiology (CKDu) in Sri Lankan agricultural regions(Environmental Monitoring and Assessment, 2024) Perera, R.A.; Perera, R.T.; Liyanage, U.P.; Premaratne, J.; Liyanage, J. A.Prolonged consumption of foods containing toxic metals can elevate the risk of noncommunicable diseases, including chronic kidney disease of uncertain etiology (CKDu). Despite the increasing number of CKDu cases in Maradankulama and Mahakanadrawa Grama Niladhari Divisions (GN) in Sri Lanka, no prior studies have examined the accumulation of heavy metal(loid)s and their potential association with CKDu prevalence. Furthermore, there is an absence of comprehensive analyses using chemometric techniques such as PCA and hierarchical studies regarding CKDu and heavy metal contamination in Sri Lanka. This study aims to provide initial insights into the accumulation and potential pathways of toxic metals in staple foods within local diets and their subsequent presence in the agricultural environment of examined GNs. Cr, Cd, As, and Ni concentrations in analyzed foods were within permissible limits (MPLs), whereas Pb levels exceeded MPLs in rice (Oryza sativa), gotukola (Centella asiatica), lime (Citrus crenatifolia), and inland fish (Etroplus suratensis). High target hazard quotient (THQt) values in polished rice suggest possible health risks with prolonged intake. Hierarchical analysis suggested a common source of Pb accumulation. PCA and hierarchical clustering revealed the intricate connection between As and Cd, with their concurrent clustering in samples suggesting a potential common origin. This indicates that while individual concentrations comply with acceptable standards, the potential synergistic effects of Cd and As accumulation might pose elevated health risks. Further, the gut tissues of inland fish exhibited pronounced metal concentrations and significant (p < 0.05) positive correlations with toxic metals in the tank sediments suggesting a diet-based bioaccumulation pathway through sediments.Item Synthesis of TIO2-(B) nanobelts for acetone sensing(Sensors, 2023) Kumarage, G. W. C.; Panamaldeniya, S. A.; Maddumage, D. C.; Moumen, A.; Maraloiu, V. A.; Mihalcea, C. G.; Negrea, R. F.; Dassanayake, B. S.; Gunawardhana, N.; Zappa, D.; Galstyan, V.; Comini, E.Titanium dioxide nanobelts were prepared via the alkali-hydrothermal method for application in chemical gas sensing. The formation process of TiO2-(B) nanobelts and their sensing properties were investigated in detail. FE-SEM was used to study the surface of the obtained structures. The TEM and XRD analyses show that the prepared TiO2 nanobelts are in the monoclinic phase. Furthermore, TEM shows the formation of porous-like morphology due to crystal defects in the TiO2-(B) nanobelts. The gas-sensing performance of the structure toward various concentrations of hydrogen, ethanol, acetone, nitrogen dioxide, and methane gases was studied at a temperature range between 100 and 500 °C. The fabricated sensor shows a high response toward acetone at a relatively low working temperature (150 °C), which is important for the development of low-power-consumption functional devices. Moreover, the obtained results indicate that monoclinic TiO2-B is a promising material for applications in chemo-resistive gas detectors.Item Species identification and pollination biology of an economically important true halophyte, Salicornia brachiata Roxb.(Aquatic Botany, 2024) Siridewa, K.; De Silva, W.; Ratnayake, R.; Wijesundara, S.; Perera, D.; Attanayake, R. N.Members of the genus Salicornia have gained a global attraction due to their ability to thrive under high saline conditions and as potential candidates in saline agriculture. However, it has been a taxonomically challenging genus for decades since the members show plastic responses to extreme environmental conditions and due to incongruences between morphological and molecular identification methods. While only a handful of commercially grown Salicornia species are fully described, most of the species including S. brachiata, a native species in the Indian sub-continent, Myanmar, and Sri Lanka are poorly described. With the potentials in adapting S. brachiata in saline agriculture, the aim of this study was to establish a morphology and DNA barcodebased species delineation system and to study pollination biology for future crop improvement projects. Tentatively identified S. brachiata plant samples were collected from two populations in Sri Lanka and completely described. GenBank lacked authenticated barcode data for S. brachiata except for one chloroplast genome to which the matK sequence obtained in the present study matched with 100 % identity. For the first time, well defined sequences of three barcode regions, ITS, ETS and matK, of S. brachiata were made available for accurate species identification. Reproductive dynamics in different parts of the inflorescence was studied. A facultative xenogamous mating system was recorded for the first time in the genus and while the lower florets in the cladode showed a preference towards outcrossing, the upper florets displayed adaptations for selfing. Data could be effectively utilized in future Salicornia breeding programs.