DSpace Collection:http://archive.cmb.ac.lk:8080/xmlui/handle/70130/392024-02-25T00:34:00Z2024-02-25T00:34:00ZPredicting the structure and active site of a putative xylanase in Mycobacterium tuberculosis.Madusanka, T.R.M.Perera, Inoka C.http://archive.cmb.ac.lk:8080/xmlui/handle/70130/72112023-10-06T06:14:24Z2023-01-01T00:00:00ZTitle: Predicting the structure and active site of a putative xylanase in Mycobacterium tuberculosis.
Authors: Madusanka, T.R.M.; Perera, Inoka C.
Abstract: Tuberculosis is one of the most common diseases that causes many deaths around the world. As a result of the continuous evolution of Mycobacterium tuberculosis, some novel strains
show high resistance to most anti-TB drug therapies. Antibiotic resistance associated with
Mycobacterium tuberculosis can be resolved by the development of anti-virulence drug
targets. The MarR gene family is one of the major transcriptional regulation families in
Mycobacterium tuberculosis, and this family mainly contributes to controlling several
bacterial responses, such as bacterial virulence. The regulator Rv 3095 which was identified
as a virulence gene regulator, mainly regulates the expression of Rv 3096 gene that codes for
a putative xylanase enzyme. The main objective of this study is to determine the structure
and active site of the putative xylanase enzyme. Molecular docking was conducted to identify
possible antibiotic ligands that can block the active site of putative xylanase enzyme. The
FASTA sequence of Rv 3096 was downloaded from the NCBI database, and the structure of
the protein was predicted by using alpha fold and Robetta fold protein prediction servers. The active site of the Rv 3096 protein was determined by using CoachD active site prediction
server. The molecular docking was done by using PyRx software, and ligand libraries were
downloaded from the Zinc 15 database. The structure of the N-terminal end of the protein
was predicted by both protein prediction servers with high confidence levels. However, both
protein prediction servers were unable to predict the structure of the C-terminal end of the
protein with high confidence levels. The pocket which has the highest C score is considered
an active site of the predicted protein. In the virtual screening, the highest binding affinities to
the active site of the xylanase enzyme were recorded by drug ligands that belong to the
penicillin and doxycycline drug groups.2023-01-01T00:00:00ZEvaluation of in vivo effects of traditional Sri Lankan spice mix on inflammation and the production of reactive oxygen species by peritoneal cellsGunasekara, S.S.Perera, Inoka C.Mapalagamage, M.S.http://archive.cmb.ac.lk:8080/xmlui/handle/70130/72102023-10-06T06:10:57Z2023-01-01T00:00:00ZTitle: Evaluation of in vivo effects of traditional Sri Lankan spice mix on inflammation and the production of reactive oxygen species by peritoneal cells
Authors: Gunasekara, S.S.; Perera, Inoka C.; Mapalagamage, M.S.
Abstract: The traditional Sri Lankan spice mix (TSSM) also known as raw curry powder is prepared by
combining the seeds of coriander (Coriandrum sativum), cumin (Cuminum cyminum), and
fennel (Foeniculum vulgare). Generally, spices contain bioactive compounds like
phytochemicals with therapeutic potential that can boost immunity. As studies on TSSM are
scarce, the potential effects of TSSM on inflammation and the production of reactive oxygen
species (ROS) by peritoneal cells were investigated here. Two groups (test - TSSM; n=4, control – distilled water; n=4) of healthy adult male Wistar rats were orally gavaged daily for
6 weeks during this study. At the end of the 6
th week, the carrageenan-induced rat paw
oedema model was utilized in assessing the anti-inflammatory properties whereas the
Nitroblue tetrazolium (NBT) assay was performed on carrageenan-induced infiltration of
peritoneal cells to determine the effect of TSSM on the ROS production of peritoneal cells. The
assessment of anti-inflammatory properties resulted in different rates of change in hourly
paw volume between the two groups following the carrageenan administration. The mean
peak volume displacement for the test group was observed at the 3
rd hour of carrageenan
treatment and for the control group, it was recorded at the 4
th hour. This manifests better anti inflammatory powers in the test group. Nevertheless, there was no significant difference
between the changes in the volume displacement of the two groups in each hour (p<0.05). The statistical comparison of optical density values of NBT assay at 620 nm revealed no
significant difference (p<0.05) in ROS production of peritoneal cells between the test and
control groups. These results indicate that there is a window for higher concentrations of
TSSM to possess better anti-inflammatory properties that could make TSSM a food adjunct
that acts against hyperinflammation although no significant relationship between the TSSM
and oxidative stress was unveiled2023-01-01T00:00:00ZAntibacterial and anti-inflammatory activities of a polyherbal formulation based on traditional Sri Lankan medicine for diabetic wound healingPeiris, J. A. T. D.Senadeera, S. P. N. N.Weerasekara, K. R.Perera, Inoka C.http://archive.cmb.ac.lk:8080/xmlui/handle/70130/72092023-10-06T05:57:13Z2023-01-01T00:00:00ZTitle: Antibacterial and anti-inflammatory activities of a polyherbal formulation based on traditional Sri Lankan medicine for diabetic wound healing
Authors: Peiris, J. A. T. D.; Senadeera, S. P. N. N.; Weerasekara, K. R.; Perera, Inoka C.
Abstract: Diabetic wounds are a global health issue that has affected many populations worldwide
owing to its severity, slow recovery, and economic burden. Despite the considerable efforts
made in its treatment, they remain a challenge in many nations partly due to its last-resort
treatment of lower-leg amputations, which is burdensome to patients in the long-term. Therefore, the rationale of this study was to explore a topical application prepared in
traditional Sri Lankan medicine as a natural and more cost-effective alternative treatment for
diabetic wounds. The topical application (TA) was prepared into two extracts, TA water and
TA oil, and this study aimed to analyse the wound healing potential of the extracts by means
of their antibacterial and anti-inflammatory activities. The antibacterial activity of both
extracts was determined by performing a disk diffusion assay against four skin pathogens
that inhabit diabetic foot, namely Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus spp., and Escherichia coli with tetracycline antibiotic as the positive control to
obtain the diameter of the zones of inhibition. The anti-inflammatory activity of TA water was
determined using the albumin denaturation method with reference to the known NSAID, Ibuprofen to obtain the percentage inhibition of protein denaturation, which was further
assessed using IC
50 values (GraphPad Prism 9.5.1). The findings indicated that both extracts
possessed sufficient antibacterial potential against all four bacteria. However, in comparison
to tetracycline, the antibacterial activity of the extracts against Pseudomonas aeruginosa was
greater than that of Staphylococcus aureus, Streptococcus spp., and Escherichia coli. Moreover, TA water possessed the highest anti-inflammatory activity at a 0.1 dilution (143.75 mg/ml) of
the concentrated extract (1437.5 mg/ml), which was comparable to that of Ibuprofen (40
mg/ml), and its effectiveness was further confirmed by its IC
50 value (5.14 mg/ml). Therefore, the study concluded that the topical application prepared possesses substantial antibacterial
activity and anti-inflammatory activity validating its potential use in diabetic wound healing2023-01-01T00:00:00ZNest-dwelling Mites of Selected Common Bird Species in Sri LankaKulatunga, Vidyani S.Knee, WaynePerera, Inoka C.Dayawansa, P. Nihalhttp://archive.cmb.ac.lk:8080/xmlui/handle/70130/70752023-05-29T11:57:42Z2023-01-01T00:00:00ZTitle: Nest-dwelling Mites of Selected Common Bird Species in Sri Lanka
Authors: Kulatunga, Vidyani S.; Knee, Wayne; Perera, Inoka C.; Dayawansa, P. Nihal
Abstract: Bird nests primarily function to protect and incubate eggs and nestlings. However, nests are also host to a broad diversity and abundance of arthropod associates, primarily mites (Acari). Our knowledge of nest dwelling mites of common bird species in Sri Lanka is quite limited and necessitates further study. Five different types of nests of selected common bird species (18) in Sri Lanka in urban, suburban, wild, and captive populations were sampled opportunistically using a portable mini vacuum trap. ANOVA: single factor test was used to evaluate statistical significance at p<0.05. A total of 1493 mites were collected from 180 nests. The mites belonging to order Mesostigmata had the highest relative abundance (58.6%) and prevalence (74.4%) of all mite orders collected, followed by the Sarcoptiformes (41.1%, 72.8%), and Trombidiformes (0.3%, 2.2%). Mite diversity of host bird species was measured using the Shannon-Weiner diversity index (H’). Pycnonotus cafer nests had the highest diversity of mites. Cup-shaped nests were host to the highest average abundance value (13.4) of mites, while cavity nests had the lowest value (5.7). Nests from captive populations had the highest average abundance (24.6) of mites and the nests of suburban populations had the lowest value (7.2). These findings can be used as a baseline data set for further detailed research studies on nest-dwelling mites of birds, focusing on avifaunal conservation and the impact on human health by nest-dwelling ectoparasites, built-in human habitations in Sri Lanka.2023-01-01T00:00:00Z