Bioinformatics and Statistical Methods for Identifying Enrichment of Functional Gene Classes in Telomeric Regions of Chromosomes

It has been noted that the telomeric regions of Saccharomyces cerevisiae has fewer essential genes than expected from random shuffling. Further the general effect of single gene silencing of non-essential genes in the telomeric regions with an average has less effect on viability than for non-essential genes in other chromosomal regions. It has also been suggested that the genes in the telomeric regions are less stable with higher mutation and recombination rates. And this could be an evolutionary positive property for adaption of genes with changing environment, provided that there are back up systems for the genes. In this work, we took a look at some different statistical properties of the telomeres and the genes in the telomeric regions. Some of the studied properties are: How dense the code is in the telomeric region compared to the rest of the genome? What length distribution do the genes have in the telomeric region in comparison to the general length distribution? What GO-annotated classes are over-represented in telomeres? Can we find protein sequence clusters that are over-represented in the telomeres? We have found fairly a lot of interesting properties and at least partly our results also support the earlier suggestions. Finally, for the future, we suggest that comparison of our different finding corresponding telomeric statistical properties in Saccharomyces cerevisiae should be performed with other yeast species, like Schizosaccharomyces pombe, which is evolutionary distant enough to be genomically fairly reshuffled. As usual, in multivariate statistics, the statistical properties are correlated (Length correlates to viability, function, etc.) and causality is hard to deduce, but may be easier to understand using more organisms. The main findings of the thesis were that, there is less code in the extreme telomeric region. In percentage, long essential genes in the telomeric region are very few. The numbers of genes in the long non-essential gene category are larger but also quite few compared to elsewhere. And of those that reside in the telomeric region, there are many genes related to metal ion transport, disaccharide and oligosaccharide metabolic and catabolic process. The pipeline of methods used in the present research also identifies some gene function related to helicase activity that has been pointed out in earlier research

Starvation induces changes in abundance and small RNA cargo of extracellular vesicles released from Plasmodium falciparum infected red blood cells

The lethal malaria parasite Plasmodium falciparum needs to constantly respond and adapt to changes within the human host in order to survive and transmit. One such change is composed of nutritional limitation, which is augmented with increased parasite loads and intimately linked to severe disease development. Extracellular vesicles released from infected red blood cells have been proposed as important mediators of disease pathogenesis and intercellular communication but whether important for the parasite response to nutritional availability is unknown. Therefore, we investigated the abundance and small RNA cargo of extracellular vesicles released upon short-term nutritional starvation of P. falciparum in vitro cultures. We show that primarily ring-stage parasite cultures respond to glucose and amino acid deprivation with an increased release of extracellular vesicles. Small RNA sequencing of these extracellular vesicles further revealed human miRNAs and parasitic tRNA fragments as the main constituent biotypes. Short-term starvations led to alterations in the transcriptomic profile, most notably in terms of the over-represented biotypes. These data suggest a potential role for extracellular vesicles released from P. falciparum infected red blood cells in the response to nutritional perturbations, their potential as prognostic biomarkers and point towards an evolutionary conserved role among protozoan parasites

Remedy of contamination of multidrug resistant Salmonella and Escherichia coli from betel leaves (Piper betle) keeping them fresh for long time

Objective: The present study was carried out to identify the associated Salmonella and Escherichia coli in betel leaves (Piper betle), and to develop an effective method to remove those microbes. Materials and methods: Betel leaves were collected from local and whole sale markets, and borouj (cultivation place). Salmonella and E. coli were isolated and identified by cultural, morphological, and biochemical tests followed by confirmation by polymerase chain reaction (PCR) targeting the genus specific 16S rRNA genes. Antibiogram of the isolated bacteria was performed by disc diffusion method. Different concentrations of Salmosan-A Soln were used to remediate the contaminating bacteria keeping the quality of betel leaves for longer periods. Results: Total Salmonella counts in the betel leaves were 3.9×105, 4.9×106, 3.5×104, 1.1×103 and 1.5×103 CFU/mL, while E. coli counts were 5.5×107, 6.3×107, 4.4×105, 3.3×103 and 3.1×103 CFU/mL in the betel leaves collected from K.R. market, Kewatkhali Bazaar, whole sale market, borouj in Kushtia and borouj in Natore, respectively. Antibiogram study revealed that the isolated bacteria were sensitive to doxycyclline, ciprofloxacin, chloramphenicol and cefotaxime. Application of 0.3% Salmosan-A Soln was found to be the most effective and suitable, where [J Adv Vet Anim Res 2018; 5(1.000): 73-80

Surveillance, epidemiological, and virological detection of highly pathogenic H5N1 avian influenza viruses in duck and poultry from Bangladesh

Avian influenza viruses (AIVs) continue to pose a global threat. Waterfowl are the main reservoir and are responsible for the spillover of AIVs to other hosts. This study was conducted as part of routine surveillance activities in Bangladesh and it reports on the serological and molecular detection of H5N1 AIV subtype. A total of 2169 cloacal and 2191 oropharyngeal swabs as well as 1725 sera samples were collected from live birds including duck and chicken in different locations in Bangladesh between the years of 2013 and 2014. Samples were tested using virus isolation, serological tests and molecular methods of RT-PCR. Influenza A viruses were detected using reverse transcription PCR targeting the virus matrix (M) gene in 41/4360 (0.94%) samples including both cloacal and oropharyngeal swab samples, 31 of which were subtyped as H5N1 using subtype-specific primers. Twenty-one live H5N1 virus isolates were recovered from those 31 samples. Screening of 1,868 blood samples collected from the same birds using H5-specific ELISA identified 545/1603 (34%) positive samples. Disconcertingly, an analysis of 221 serum samples collected from vaccinated layer chicken in four districts revealed that only 18 samples (8.1%) were seropositive for anti H5 antibodies, compared to unvaccinated birds (n=105), where 8 samples (7.6%) were seropositive. Our result indicates that the vaccination program as currently implemented should be reviewed and updated. In addition, surveillance programs are crucial for monitoring the efficacy of the current poultry vaccinations programs, and to monitor the circulating AIV strains and emergence of AIV subtypes in Bangladesh