Department of Plant Science

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C), and a previously published linkage map to produce a highly contiguous assembly composed of 7,378 contigs (contig N50 = 1.8 mb) assigned to 4,120 scaffolds (scaffold N50 = 44.975 mb). 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologs were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitome assembly was also produced. Self-vs-self synteny ana...

Despite the availability of highly efficacious vaccines, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lacks effective drug treatment, which results in a high rate of mortality. To address this therapeutic shortcoming, we applied a systems biology approach to the study of patients hospitalized with severe COVID. We show that, at the time of hospital admission, patients who were equivalent on the clinical ordinal scale displayed significant differential monocyte epigenetic and transcriptomic attributes between those who would survive and those who would succumb to COVID-19. We identified messenger RNA metabolism, RNA splicing, and interferon signaling pathways as key host responses overactivated by patients who would not survive. Those pathways are prime drug targets to reduce mortality of critically ill patients with COVID-19, leading us to identify tacrolimus, zotatifin, and nintedanib as three strong candidates for treat...

Propagation of bryophytes using in vitro culture techniques would be useful in many ways, particularly in ex situ conservation which is a novel approach to Sri Lanka. The aim of the reported study was to develop an in vitro propagation protocol for thalloid liverwort Riccia sorocarpa Bisch. Establishment of initial axenic culture was successful from the newly grown gametophyte (immature thalli tips of 5 mm length). The best surface sterilization was achieved by dipping thalli tips in 5% Clorox TM (5.25% active NaOCl) for 2 minutes followed by washing with 700 ppm fungicide Bullet 50 TM (Carbendazim 50%) and bactericide, Ampicillin Sodium TM (250 ppm) and three rinses with sterile distilled water. With the optimized surface sterilization procedure, percentage of survival of the tested propagules was observed to be 66%. For in vitro regeneration, both direct regeneration method and callus induction method were used. In the first approach, surface sterilized immature thalli tips were placed on the nutrient medium under aseptic conditions, and incubated under continuous light conditions provided by white florescence light of 1210 Lux at 24 °C. Several media were tested and quarter strength Murashige and Skoog (1/4 × MS) medium containing mineral salts and vitamins, 100 mgdm-3 inositol, with 0.7% (w/v) agar was observed to be the best medium for regeneration of gametophytic thalli to be morphologically similar to the plants grown under natural conditions. Under the direct regeneration method regeneration was found to be 90 %. In the second approach, callus induction was achieved from the surface sterilized thalli tips on MS medium supplemented with 1.0 mgdm-3 NAA and 1.0 mgdm-3 BAP. From the green, compact calli that developed after 14 days, shoots could be induced in MS supplemented with 0.5mgdm-3 NAA+ 1.0 mgdm-3 BAP. Rhizoid induction was achieved in MS medium without sucrose after 7 days. Percentage of regeneration of plants via callus induction method was 100%. Thalli obtained through callus showed optimum growth in 1/4×MS medium. In vitro culture of the thalloid liverwort R. sorocarpa Bisch. was successful. The plants regenerated by this method can be reintroduced to their natural habitats or may be cryopreserved as means of conservation.

Amaryllidaceae alkaloids (AAs) are plant specialized metabolites with therapeutic properties exclusively produced by the Amaryllidaceae plant family. The two most studied representatives of the family are galanthamine, an acetylcholinesterase inhibitor used as a treatment of Alzheimer’s disease, and lycorine, displaying potent in vitro and in vivo cytotoxic and antiviral properties. Unfortunately, the variable level of AAs’ production in planta restricts most of the pharmaceutical applications. Several biotechnological alternatives, such as in vitro culture or synthetic biology, are being developed to enhance the production and fulfil the increasing demand for these AAs plant-derived drugs. In this review, current biotechnological approaches to produce different types of bioactive AAs are discussed.

BackgroundSri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. As it was felt that more patients appeared to develop complications and severe dengue, we compared clinical features of patients with acute dengue, with the previous circulating serotype (DENV1) and also sequenced the new virus, to determine the lineage of the virus.Methodology/Principal findingsWe studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. 65 (82.3%) of those with DENV1 and 86 (92.4%) of those with DENV2 were experiencing a secondary infection. The risk of developing dengue haemorrhagic fever (DHF) was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection dev...

BackgroundSri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. As it was felt that more patients appeared to develop complications and severe dengue, we compared clinical features of patients with acute dengue, with the previous circulating serotype (DENV1) and also sequenced the new virus, to determine the lineage of the virus.Methodology/Principal findingsWe studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. 65 (82.3%) of those with DENV1 and 86 (92.4%) of those with DENV2 were experiencing a secondary infection. The risk of developing dengue haemorrhagic fever (DHF) was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection dev...

Transgenic mosquitoes developed by genetic manipulation, offer a promising strategy for the sustainable and effective control of mosquito-borne diseases. This strategy relies on the mass release of transgenic mosquitoes into the wild, where their transgene is expected to persist in the natural environment, either permanently or transiently, within the mosquito population. In such circumstances, the fitness of transgenic mosquitoes is an important factor in determining their survival in the wild. The impact of transgene expression, insertional mutagenesis, inbreeding depression related to laboratory adaptation, and the hitchhiking effect involved in developing homozygous mosquito lines can all have an effect on the fitness of transgenic mosquitoes. Therefore, real-time estimation of transgene-associated fitness cost is imperative for modeling and planning transgenic mosquito release programs. This can be achieved by directly comparing fitness parameters in individuals homozygous or h...

Tuberculosis (TB) is a prevalent infectious disease in Sri Lanka with an estimated incidence of 65/100,000 new cases every year. Early and accurate diagnosis is critical for the care of TB patients and for controlling transmission. Interferon-γ release assays (IGRAs) have emerged as an immunodiagnostic tool to detect TB infection. T-spot.TB blood test is a commercially available IGRA which measures the number of IFN-γ-secreting T cells via an enzyme-linked immunoSpot (ELISPOT) assay. This study was conducted, recruiting 24 patients with suspected pulmonary TB to evaluate diagnostic performance of T-spot assay against TB infection. Microbiological examinations of three sputum smears, one sputum culture and TB PCR were performed for each patient. Of the 24 patients, 14 confirmed TB, 3 non-TB and 7 were indeterminate from the T-SPOT.TB test. Out of the indeterminate test results (ITRs) 71.43% were above 50 years, indicating a declining immune response with age. When excluding ITRs, the...