A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana

Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily

Impact of ICT-Usage on SMEs’ Innovations in Western Province of Sri Lanka

Small and Medium Size Enterprises (SMEs) are major sources of employment and value creation, as it plays a key role in Sri Lankan livelihood. It is evident that the SME sector in Sri Lanka does not provide the expected results and this sector lacks innovation. Thus, it is important to identify opportunities to improve the SME’s innovative capacity and business performance. This study was designed to investigate the impact of Information and Communication Technology (ICT) on innovations of SMEs in the Western Province of Sri Lanka, and to identify the existing level of ICT usage among the SMEs in the Western Province of Sri Lanka. This study used a quantitative research method. The population of the study was SMEs with less than 500 employees in the Western Province. The sample frame was derived from the two main listings of organizations: the Ceylon Chamber of Commerce and the Ministry of Industries and Industrial Development Board. Accordingly, 350 respondents were selected by using the simple random sampling method. Data were analyzed using the SPSS statistical tool with descriptive and inferential statistics. This study identified four main types of innovations namely: product, process, market, and organizational, and found that there is a significant effect of ICT usage on SMEs innovations. Future research could be undertaken to examine the mediating effect of ICT-based innovations and ICT usage on business performance. Keywords: Entrepreneur, Innovation, Small and Medium size Enterprises, Information and Communication Technolog

Gender Inequality in Digital Transformation: Evidence from Business Process Management Industry in Sri Lanka

This research examines whether gender inequality exists in Leadership Style, Organizational Culture, and Digital Competence of digital transformation of the Business Process Management (BPM) industry. Data were collected from 507 employees of 40 Sri Lankan BPM companies through a web-based survey. Mann-Whitney U test with descriptive statistics provided evidence to strengthen the findings. The findings confirmed that gender inequality exists in Leadership Style, Organizational Culture, and Digital Competence of digital transformation in the BPM industry in Sri Lanka. This research contributes to "Acker's Theory of Gendered Organizations" by identifying areas that reproduce gender inequality in the new digital economy workplace. This study recommends controlling if not eradicating the gender inequality through proper Human Resource (HR) policies and procedures since it may hinder organizational performance. Digital workplace will improve employee retention, satisfaction, and productivity. Keywords: Business Process Management, Gender Inequality, Leadership Style, Organizational Culture, Digital Competenc

Investigation of Optimum pH and Temperature for In-Vitro Crystallization of Urinary Cystine

Cystinuria contributes in formation of urinary stones. But, it has been reported that cystinuria is diagnosed when someone experiences with cystine stones. Therefore, early diagnosis of this condition is important. Thus, the objective of the study was to determine the optimum pH and temperature for crystallization of urine cystine in-vitro. Cystinuria solutions were prepared with the concentrations of 40, 60, 70, 75, 80, 90, 100 and 120 mg/dL. The pH of each solution was changed with the addition of acetic acid. Then solutions were exposed to temperature +4°C and 37°C, for 15, 30 and 45min. The sediments were observed microscopically for cystine crystals formation. Then acetone was added to cystinuria with the ratio of cystinuria:acetone, 8:1, 4:1, 2:1 and 1.1 and pH was altered with acetic acid and were subjected to +4 °C and 37 °C, for 15, 30 and 45 minutes and sediment was observed for cystine crystals under the microscope. Cystine crystallization had been occurred in the cystinuria of ≥100 mg/dL at pH 5 at 37 ° C and +4 °C, 30min after the addition of acetic acid whereas with the addition of acetone at cystinuria of ≥75mg/dL at pH 5 in both 37°C and at +4°C, 30min after the addition of acetic acid. The number of cystine crystals per High Power Field (HPF) was highest where cystinuria:acetone was 8:1.  The optimum conditions for cystine crystallization is at pH 5, 37 °C and +4 °C, 30min after acidifying with acetic acid at the minimum concentration of 100 mg/dL  of cystinuria. With the addition of acetone, at the ratio of cystinuria:acetone 8:1 with minimum concentration of cystinuria of 75 mg/dL.   KEYWORDS: Cystine, Crystallization, Acetic acid, Acetone, Temperature, p

Occurrence of Urinary Crystals among Urinary Tract Infections Suspected Paediatric Patients, Sri Lanka

Crystalluria has become one of the most vital biomarkers in urinalysis in detecting several disease conditions. It has been reported that urinary tract infections (UTI) may be the presenting sign of Urolithiasis in children. Therefore, the objective of this study was to identify and estimate the different types of crystals in the urine samples collected from UTI suspected children who admitted to the Lady Ridgeway Hospital for children, Sri Lanka. A descriptive cross-sectional study was conducted using 400 children belong to age<12 years suspected with UTI. The participants included 242 males and 158 females. The urine samples were collected prior to start antibiotics. Each sample was examined macroscopically and centrifuged at 2000 rpm for 5 minutes. The urine sediment was examined under the light microscope and different crystal types were identified and counted at x40 magnification. Out of 400 samples 82 samples (82/400) were positive for crystalluria. The crystal types present were uric acid, calcium oxalate, triple phosphate, ammonium biuate and ammonium urate. None of the samples showed abnormal crystal types. The distribution of each crystal type was as follow; uric acid 25/82, calcium oxalate 34/82, triple phosphate 12/82, ammonium biuate 7/82 and ammonium urate 4/82. The quantity of crystals per mL of urine was ranged as follow; uric acid 850-130,000, calcium oxalate 350- >250,000, triple phosphate 650-6,000, ammonium biurate and ammonium urate were presented in clumps. KEYWORDS: Crystalluria, Uric Acid, Calcium Oxalate, Triple Phosphate, Ammonium Biurate, Ammonium Urate, Urolithiasis, Urinary Tract Infections

Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery

<p>Abstract</p> <p>Background</p> <p>There is an important need for the identification of novel serological biomarkers for the early detection of cancer. Current biomarkers suffer from a lack of tissue specificity, rendering them vulnerable to non-disease-specific increases. The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics.</p> <p>Methods</p> <p>Previous studies have focused on either gene or protein expression databases for the identification of candidates. We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies.</p> <p>Results</p> <p>Using colon, lung, pancreatic and prostate cancer as case examples, we identified 48 candidate tissue-specific biomarkers, of which 14 have been previously studied as biomarkers of cancer or benign disease. Twenty-six candidate biomarkers for these four cancer types are proposed.</p> <p>Conclusions</p> <p>We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. Investigation of the 26 candidates in disease states of the organs is warranted.</p

Ecology and Transmission of Buruli Ulcer Disease: A Systematic Review

Buruli ulcer is a neglected emerging disease that has recently been reported in some countries as the second most frequent mycobacterial disease in humans after tuberculosis. Cases have been reported from at least 32 countries in Africa (mainly west), Australia, Southeast Asia, China, Central and South America, and the Western Pacific. Large lesions often result in scarring, contractual deformities, amputations, and disabilities, and in Africa, most cases of the disease occur in children between the ages of 4–15 years. This environmental mycobacterium, Mycobacterium ulcerans, is found in communities associated with rivers, swamps, wetlands, and human-linked changes in the aquatic environment, particularly those created as a result of environmental disturbance such as deforestation, dam construction, and agriculture. Buruli ulcer disease is often referred to as the “mysterious disease” because the mode of transmission remains unclear, although several hypotheses have been proposed. The above review reveals that various routes of transmission may occur, varying amongst epidemiological setting and geographic region, and that there may be some role for living agents as reservoirs and as vectors of M. ulcerans, in particular aquatic insects, adult mosquitoes or other biting arthropods. We discuss traditional and non-traditional methods for indicting the roles of living agents as biologically significant reservoirs and/or vectors of pathogens, and suggest an intellectual framework for establishing criteria for transmission. The application of these criteria to the transmission of M. ulcerans presents a significant challenge

Mycolactone Gene Expression Is Controlled by Strong SigA-Like Promoters with Utility in Studies of Mycobacterium ulcerans and Buruli Ulcer

Mycolactone A/B is a lipophilic macrocyclic polyketide that is the primary virulence factor produced by Mycobacterium ulcerans, a human pathogen and the causative agent of Buruli ulcer. In M. ulcerans strain Agy99 the mycolactone polyketide synthase (PKS) locus spans a 120 kb region of a 174 kb megaplasmid. Here we have identified promoter regions of this PKS locus using GFP reporter assays, in silico analysis, primer extension, and site-directed mutagenesis. Transcription of the large PKS genes mlsA1 (51 kb), mlsA2 (7 kb) and mlsB (42 kb) is driven by a novel and powerful SigA-like promoter sequence situated 533 bp upstream of both the mlsA1 and mlsB initiation codons, which is also functional in Escherichia coli, Mycobacterium smegmatis and Mycobacterium marinum. Promoter regions were also identified upstream of the putative mycolactone accessory genes mup045 and mup053. We transformed M. ulcerans with a GFP-reporter plasmid under the control of the mls promoter to produce a highly green-fluorescent bacterium. The strain remained virulent, producing both GFP and mycolactone and causing ulcerative disease in mice. Mosquitoes have been proposed as a potential vector of M. ulcerans so we utilized M. ulcerans-GFP in microcosm feeding experiments with captured mosquito larvae. M. ulcerans-GFP accumulated within the mouth and midgut of the insect over four instars, whereas the closely related, non-mycolactone-producing species M. marinum harbouring the same GFP reporter system did not. This is the first report to identify M. ulcerans toxin gene promoters, and we have used our findings to develop M. ulcerans-GFP, a strain in which fluorescence and toxin gene expression are linked, thus providing a tool for studying Buruli ulcer pathogenesis and potential transmission to humans

On sacred ground:the political performance of religious responsibility

Parts of this paper were presented at the 2013 Annual Conference of the British Association for South Asian Studies (BASAS); at a ‘Post-War Sri Lanka’ workshop at the London School of Economics; and at a workshop on Muslims in Sri Lanka held at the University of Edinburgh.April 2012: In Dambulla, a bustling market town built around a crossroads on the northern cusp of Sri Lanka's central province, a mosque was attacked by a procession of protestors led by the chief priest of the nearby Buddhist temple. Ostensibly the protest was against the presence of the mosque on the grounds that it had been built in an exclusively Buddhist ‘sacred area’. Beginning with an empirical account of the attack on the Dambulla mosque, this paper argues that the preservation of what is deemed to be ‘sacred’ in Sri Lanka provides an effective idiom through which certain religious figures can intelligibly articulate political claims whilst maintaining critical distance from the dirty world of ‘Politics’. Corollary to this, and drawing on two years of ethnographic fieldwork in Dambulla, the paper explores the various different meanings of politics locally: highlighting the interplay of everyday politicking and high-profile political performance.Economic and Social Research Council (ESRC)