COVID-19 Pandemic: lessons learnt and the way forward

Although the scientific community had been predicting and preparing for a pandemic for the last 10 years, many policy makers did not envision that a virus could cause such devastation to human life, economies and to the social structure. COVID-19 has taught us many bitter lessons and while moving forward it is important to understand that this current pandemic is yet to end. However, COVID-19 is unlikely to be the last pandemic that we face, Due to certain human activities such as urbanization, deforestation, increased human and animal interactions and climate change, we will see more pandemics emerging in the coming years. Preparedness and anticipation of such an event is the only way forward

Development of a Simple Conductivity Meter to Test Soil Electrical Conductivity at the Field Level

Soil salinity is one of the most common problems in agricultural fields. Saline soils reduce crop yield. The most common method for testing soil salinity is the test of Electrical Conductivity (EC) of a given soil solution by using a soil conductivity meter. Many farmers are unaware of their soil salinity because soil testing facilities are not available at the field level in Sri Lanka. Therefore, a requirement for a simple conductivity meter that can be used in the field is high. Thus, in this study, the aim is to develop a simple soil electrical conductivity meter by using a D400 transistor, 50K volume control, and an LED. The developed simple soil electrical conductivity meter was calibrated using standard KCl s Soil salinity is one of the most common problems in agricultural fields. Saline soils reduce crop yield. The most common method for testing soil salinity is the test of Electrical Conductivity (EC) of a given soil solution by using a soil conductivity meter. Many farmers are unaware of their soil salinity because soil testing facilities are not available at the field level in Sri Lanka. Therefore, the requirement for a simple conductivity meter that can be used in the field is high. Thus, in this study, the aim is to develop a simple soil electrical conductivity meter by using a D400 transistor, 50K volume control, and an LED. The developed simple soil electrical conductivity meter was calibrated using standard KCl solutions with conductivities of 0.2 ms/m and 0.4 ms/m respectively. Finally, the EC of eighteen soil samples around Sri Lanka was tested using a laboratory soil conductivity meter (Spectrum Tech. ECTestr 11+) and the developed simple conductivity meter. Our results indicate that this simple conductivity meter works well with Sri Lankan soil and could be promoted among farmers to test and increase awareness about soil salinity. olutions with the conductivities of 0.2 ms/m and 0.4 ms/m respectively. Finally, the EC of eighteen soil samples around Sri Lanka was tested using a laboratory soil conductivity meter (Spectrum Tech. ECTestr 11+) and the developed simple conductivity meter. Our results indicate that this simple conductivity meter works well with Sri Lankan soil and could be promoted among farmers to test and increase awareness about soil salinity

Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population

Background: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population. Methods: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n = 112) and colonic tissue (n = 36) in 112 individuals. The cohort comprised of individuals with CRC (n = 24), premalignant lesions (n = 10), healthy individuals (n = 50) and in those with diabetes (n = 28). Results: Overall, the relative abundances of genus Fusobacterium (p < 0.001), Acinetobacter (p < 0.001), Escherichia-Shigella (p < 0.05) were significantly higher in gut tissue, while Romboutsia (p < 0.01) and Prevotella (p < 0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p < 0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p < 0.01) in stool samples in healthy individuals compared to those with CRC and diabetes. Conclusion: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population

Developing an Algorithm to Improve Positioning Accuracy of Low-Cost Global Navigation Satellite System Modules

Global Navigation Satellite System (GNSS) technology is the most widely used technique for obtaining positioning and navigation information for various applications. However, GNSS is not an error free technology. Differential GNSS techniques are used to mitigate these errors and different commercial brands of GNSS receivers have been developed to avoid some errors where quality and &nbsp;performance depends heavily on the price tag of such advance GNSS receivers due to the fact that technological capabilities adopted and&nbsp; embedded in each single GNSS receiver. There are user cases where the few or more those capabilities has to keep leave behind thereby compromise the cost to benefit ratio. As an alternative to above problem, some low-cost GNSS modules are now available in the market which has quite low position accuracy but can be developed to address unique requirements of some user cases. In practical situations, Real-Time-Kinematic (RTK) positioning systems cannot be used everywhere due to its technical limitations and GNSS receivers use different levels of techniques such as moving baseline system or Satellite Based Augmentation System (SBAS). Further, heading information is also a very important parameter in marine industry for obtaining the vessel’s orientation. This research attempts to assess the capability of u-blox NEO M8N GNSS module for hydrographic surveys by developing a moving baseline GNSS configuration and simple Kalman filter based algorithm. The developed prototype was tested in both static and kinematic observations. The prototype achieved 0.5-2.5 meters of position accuracy at the 95% confidence level in static observations, while it archived around 3 meters of positioning accuracy in kinematic observations. This is a sufficient accuracy for Order 1a, Order 1b and Order 2 standards of hydrographic surveys according to the IHO S-44 guidelines

Screening of five Sri Lankan endemic plants for anti-cancer effects on breast cancer stem cells isolated from MCF-7 and MDA-MB-231 cell lines

Purpose: To screen selected endemic plants grown in Sri Lanka on breast cancer stem cells (bCSCs) for their anti-cancer propertiesMethods: Breast-CSCs expressing CD24-/CD44+ surface markers were isolated from MDA-MB-231 cells by magnetic-assisted cell sorting method and validated using flow cytometry. A panel of forty extracts from barks and leaves of Doona nervosa, Garcinia quaesita, Garcinia zeylanica, Memecylon rostratum and Schumacheria castaneifolia were obtained by sequential solvent extraction and tested on bCSC-mammospheres derived from MDA-MB-231 and MCF-7 cells and normal mammary epithelial (MCF-10A) cells. Proliferation and cell stemness were analyzed using WST-1 cell proliferation assay and alkaline phosphatase assay.Results: Hexane and chloroform extracts of G. zeylanica and G. quaesita barks showed dosedependent reduction in proliferation and stemness in both bCSCs tested with less effect on MCF-10A cells. Hexane, chloroform and ethyl acetate extracts of S. castaneifolia bark selectively inhibited mammospheres of triple negative bCSCs cells.Conclusion: This study demonstrates that the non-polar extracts of G. zeylanica and G. quaesita, S. castaneifolia barks inhibit the proliferation of bCSCs of triple negative and estrogen-progesterone positive breast cancers. Findings of the present study may useful for developing a future anti-cancer therapeutics which can target bCSCs.Keywords: Cancer stem cells, Garcinia zeylanica, Garcinia quaesita, Schumacheria castaneifolia, Mammosphere

Viral load, clinical disease severity and cellular immune responses in primary varicella zoster virus infection in Sri Lanka

Background In Sri Lanka, varicella zoster virus (VZV) is typically acquired during adulthood with significant associated disease morbidity and mortality. T cells are believed to be important in the control of VZV replication and in the prevention of reactivation. The relationship between viral load, disease severity and cellular immune responses in primary VZV infection has not been well studied. Methodology We used IFNγ ELISpot assays and MHC class II tetramers based on VZV gE and IE63 epitopes, together with quantitative real time PCR assays to compare the frequency and phenotype of specific T cells with virological and clinical outcomes in 34 adult Sri Lankan individuals with primary VZV infection. Principal Findings Viral loads were found to be significantly higher in patients with moderate to severe infection compared to those with mild infection (p<0.001) and were significantly higher in those over 25 years of age (P<0.01). A significant inverse correlation was seen between the viral loads and the ex vivo IFNγ ELISpot responses of patients (P<0.001, r = −0.85). VZV-specific CD4+ T cells expressed markers of intermediate differentiation and activation. Conclusions Overall, these data show that increased clinical severity in Sri Lankan adults with primary VZV infection associates with higher viral load and reduced viral specific T cell responses

Dengue NS1 interaction with lipids alters its pathogenic effects on monocyte derived macrophages

Background: While dengue NS1 antigen has been shown to be associated with disease pathogenesis in some studies, it has not been linked in other studies, with the reasons remaining unclear. NS1 antigen levels in acute dengue are often associated with increased disease severity, but there has been a wide variation in results based on past dengue infection and infecting dengue virus (DENV) serotype. As NS1 engages with many host lipids, we hypothesize that the type of NS1-lipid interactions alters its pathogenicity. Methods: Primary human monocyte derived macrophages (MDMs) were co-cultured with NS1 alone or with HDL, LDL, LPS and/or platelet activating factor (PAF) from individuals with a history of past dengue fever (DF = 8) or dengue haemorrhagic fever (DHF = 8). IL-1β levels were measured in culture supernatants, and gene expression analysis carried out in MDMs. Monocyte subpopulations were assessed by flow cytometry. Hierarchical cluster analysis with Euclidean distance calculations were used to differentiate clusters. Differentially expressed variables were extracted and a classifier model was developed to differentiate between past DF and DHF. Results: Significantly higher levels of IL-1β were seen in culture supernatants when NS1 was co-cultured with LDL (p = 0.01, median = 45.69 pg/ml), but lower levels when NS1 was co-cultured with HDL (p = 0.05, median = 4.617 pg/ml). MDMs of those with past DHF produced higher levels of IL-1β when NS1 was co-cultured with PAF (p = 0.02). MDMs of individuals with past DHF, were significantly more likely to down-regulate RPLP2 gene expression when macrophages were co-cultured with either PAF alone, or NS1 combined with PAF, or NS1 combined with LDL. When NS1 was co-cultured with PAF, HDL or LDL two clusters were detected based on IL10 expression, but these did not differentiate those with past DF or DHF. Conclusions: As RPLP2 is important in DENV replication, regulating cellular stress responses and immune responses and IL-10 is associated with severe disease, it would be important to further explore how differential expression of RPLP2 and IL-10 could lead to disease pathogenesis based on NS1 and lipid interactions