Genotyping SNPs and Indels: A method to improve the scope and sensitivity of High-Resolution melt (HRM) analysis based applications.

High-resolution melt (HRM) analysis is a closed-tube technique for detecting single nucleotide polymorphisms (SNPs). However, it has limited use in high-resolution melting devices, even those with high thermal accuracy (HTA). In addition to the cost of switching to these specialized devices, the presence of nearest neighbour neutral changes (class III, IV SNPs and small indels) made HRM-based assays a challenging task due to reduced sensitivity.

Development of a Low Cost Semiquantitative Polymerase Chain Reaction Assay for Molecular Diagnosis of Williams Syndrome.

Background: Williams Beuren Syndrome (WBS) is a well-recognized and common genetic cause of congenital heart defects, developmental delay, hypercalcemia, and characteristic facial features. It is caused by a 1.5 - 1.

Metals and Metallothionein Expression in Relation to Progression of Chronic Kidney Disease of Unknown Etiology (CKDu) in Sri Lanka.

Chronic kidney disease of unknown etiology was investigated for metal relations in an endemic area by a cross-sectional study with CKD stages G1, G2, G3a, G3b, G4, G5 (ESRD), and endemic and nonendemic controls (EC and NEC) as groups. Subjects with the medical diagnosis were classified into groups by eGFR (SCr, CKD-EPI) and UACR of the study. It determined 24 metals/metalloids in plasma (ICPMS) and metallothionein (MT) mRNA in blood (RT-PCR).

Genotyping Sri Lankan women with polycystic ovary syndrome (PCOS): towards a novel screening tool.

Polycystic ovary syndrome (PCOS) is the multigenic, endocrine disorder of young women. Inheritance of PCOS is likely to be oligogenic and genetic basis remains largely unknown. Screening the candidate genes of PCOS and their SNPs individually is time consuming.

Characterization of a Bacillus megaterium strain with metal bioremediation potential and in silico discovery of novel cadmium binding motifs in the regulator, CadC.

Bioremediation of toxic metal ions using bacterial strains is a promising tool. Metal binding motifs in microbial proteins are involved in the regulation and transport of such toxic metals for metal detoxification. A bacterial strain designated TWSL_4 with metal (Cu, Cd, and Pb) resistance and removal ability was isolated and identified as a Bacillus megaterium strain using 16S rRNA gene analysis.

Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka.

Background: Sri Lanka was certified as a malaria-free nation in 2016; however, imported malaria cases continue to be reported. Evidence-based information on the genetic structure/diversity of the parasite populations is useful to understand the population history, assess the trends in transmission patterns, as well as to predict threatening phenotypes that may be introduced and spread in parasite populations disrupting elimination programmes. This study used a previously developed Plasmodium vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics of P.

Molecular characterization and expression of α-gliadin genes from wheat cultivar Dacke in Bg 250 rice variety.

The main seed storage protein in wheat is gluten. It consists of gliadin and glutenins. Gluten gives high elasticity and extensibility during bread making, facilitating the formation of the dough.

Host genetic polymorphisms and serological response against malaria in a selected population in Sri Lanka.

Background: Antibodies against the merozoite surface protein 1 (MSP1) and the apical membrane antigen 1 (AMA1) of the malaria parasite (Plasmodium vivax) are proven to be important in protection against clinical disease. Differences in the production/maintenance of antibodies may be due to many factors including host genetics. This paper discusses the association of 4 anti-malarial antibodies with selected host genetic markers.

Alterations and Interchange of Morphometric Characters in Different Life Cycle Stages with Reference to Genomic Variations of (Diptera; Culicidae) Sibling Species Complex in Sri Lanka.

The species complex of the mosquito is designated by the sibling species A⁻D, depending on morphological characters of life cycle stages and variations in polytene chromosomes. However, morphological aberrations in the life cycle stages make the identification of sibling species uncertain and imprecise. The objective of the present study is to determine the suitability of morphological variations of sibling species and their genomic variations to identify the sibling species status of an population in Sri Lanka.

Expression, Docking, and Molecular Dynamics of Endo--1,4-xylanase I Gene of in .

It is essential that major carbohydrate polymers in the lignocellulosic biomass are converted into fermentable sugars for the economical production of energy. Xylan, the major component of hemicelluloses, is the second most naturally abundant carbohydrate polymer comprising 20-40% of the total biomass. Endoxylanase (EXN) hydrolyzes xylan into mixtures of xylooligosaccharides.

Trichoderma virens β-glucosidase I (BGLI) gene; expression in Saccharomyces cerevisiae including docking and molecular dynamics studies.

Background: Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose.

A putative nuclear growth factor-like globular nematode specific protein.

Expressed sequence tags (ESTs) are an effective approach for discovery of novel genes. In the current study, approximately 250 ESTs of the cattle parasitic nematode Setaria digitata were examined and a cDNA clone identified whose coding sequence could not be functionally annotated by searching over publicly available genome, protein, EST and STS databases. Here, we report the extensive characterization of this ORF (UP) and its homologues using a bioinformatic approach.

Determination of expression of cyclooxygenase-1 and -2 isozymes in canine tissues and their differential sensitivity to nonsteroidal anti-inflammatory drugs.

Objective: To evaluate cyclooxygenase isozyme distribution in tissues from dogs and determine the differential sensitivity of canine cyclooxygenase (COX)-1 and -2 isozymes to nonsteroidal anti-inflammatory drugs (NSAIDs).

Sample Population: Canine tissue samples (stomach, duodenum, ileum, jejunum, colon, spleen, cerebral cortex, lung, ovary, kidney, and liver) were obtained from 2 dogs for northern and western blot analyses, and blood for whole blood COX assays was obtained from 15 dogs.

Procedure: 11 NSAIDs were evaluated to determine their COX-2 selectivity in whole blood assays.