Snap Shots of Bacterial Adaptation

Adaptation to changing environmental conditions is necessary for the survival of all living organisms. The research described in this PhD thesis was aimed at understanding adaptive responses mounted by two different bacterial species to challenges that they have to face regularly in their environment. A major part of this PhD thesis focuses on adaptive processes of the soil bacterium Bacillus subtilis when exposed to an environment with low salinity, a condition that occurs upon rain and flooding. This revealed the importance of the so-called Tat pathway for protein transport across the bacterial membrane to prevent oxidative membrane damage. Additionally, it was discovered that a system for iron uptake, which requires the Tat pathway for its assembly, is regulated by a small RNA molecule named S313. More importantly, the studies on the S313 molecule highlighted the global impact that a small regulatory RNA molecule can have on different cellular processes, ranging from iron uptake to the bacterial resistance to antibiotics. Another part of the studies described in this PhD thesis addresses adaptive responses shown by methicillin resistant Staphylococcus aureus (MRSA) upon exposure to the clinically relevant antibiotic ciprofloxacin. This revealed that exposure of clinical MRSA isolates to subinhibitory concentrations of ciprofloxacin may lead both to mutations that cause resistance to antibiotics, and to activation of bacterial viruses (phages) that may transfer the resulting resistance genes into other bacteria. Altogether, this PhD research has put a spotlight on the importance of investigating adaptive responses of bacteria to environmental changes and insults

Spread of Malicious Objects in Computer Network: A Fuzzy Approach

We propose an e-epidemic fuzzy SEIQRS (Susceptible-Exposed-Infectious-Quarantine- Recovered-Susceptible) model for the transmission of malicious codes in a computer network. We have simulated the result for various parameters and analyzed the stability of the model. The efficiency of antivirus software and crashing of the nodes due to attack of malicious code is analyzed. Furthermore, initial simulation results illustrate the behavior of different classes for minimizing the infection in a computer network. It also reflects the positive impact of anti-virus software on malicious code propagation in a computer network. The basic reproduction number R0 f and its formulation is also discussed

Double trouble:Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment

The widely conserved twin-arginine translocases (Tat) allow the transport of fully folded cofactor-containing proteins across biological membranes. In doing so, these translocases serve different biological functions ranging from energy conversion to cell division. In the Gram-positive soil bacterium Bacillus subtilis, the Tat machinery is essential for effective growth in media lacking iron or NaCl. It was previously shown that this phenomenon relates to the Tat-dependent export of the heme-containing peroxidase EfeB, which converts Fe2+ to Fe3+ at the expense of hydrogen peroxide. However, the reasons why the majority of tat mutant bacteria perish upon dilution in NaCl-deprived medium and how, after several hours, a sub-population adapts to this condition was unknown. Here we show that, upon growth in the absence of NaCl, the bacteria face two major problems, namely severe oxidative stress at the membrane and starvation leading to death. The tat mutant cells can overcome these challenges if they are fed with arginine, which implies that severe arginine depletion is a major cause of death and resumed arginine synthesis permits their survival. Altogether, our findings show that the Tat system of B. subtilis is needed to preclude severe oxidative stress and starvation upon sudden drops in the environmental Na+ concentration as caused by flooding or rain

Dengue virus infection during window period of consecutive outbreaks in Nepal and assessment of clinical parameters

Abstract Nepal is an endemic country for dengue infection with rolling of every 3 year’s clear cyclic outbreaks with exponential growth since 2019 outbreak and the virus gearing towards the non-foci temperate hill regions. However, the information regarding circulating serotype and genotype is not frequent. This research discusses on the clinical features, diagnosis, epidemiology, circulating serotype and genotype among 61 dengue suspected cases from different hospitals of Nepal during the window period 2017–2018 between the two outbreaks of 2016 and 2019. E-gene sequences from PCR positive samples were subjected to phylogenetic analysis under time to most recent common ancestor tree using Markov Chain Monte Carlo (MCMC) and BEAST v2.5.1. Both evolution and genotypes were determined based on the phylogenetic tree. Serotyping by Real-time PCR and Nested PCR showed the co-circulation of all the 3 serotypes of dengue in the year 2017 and only DENV-2 in 2018. Genotype V for DENV-1 and Cosmopolitan Genotype IVa for DENV-2 were detected. The detected Genotype V of DENV-1 in Terai was found close to Indian genotype while Cosmopolitan IVa of DENV-2 found spreading to geographically safe hilly region (now gripped to 9 districts) was close to South-East Asia. The genetic drift of DENV-2 is probably due to climate change and rapid viral evolution which could be a representative model for high altitude shift of the infection. Further, the increased primary infection indicates dengue venturing to new populations. Platelets count together with Aspartate transaminase and Aalanine transaminase could serve as important clinical markers to support clinical diagnosis. The study will support future dengue virology and epidemiology in Nepal

A global comparative evaluation of commercial immunochromatographic rapid diagnostic tests for visceral leishmaniasis

Background: Poor access to diagnosis stymies control of visceral leishmaniasis (VL). Antibody-detecting rapid diagnostic tests (RDTs) can be performed in peripheral health settings. However, there are many brands available and published reports of variable accuracy. Methods: Commercial VL RDTs containing bound rK39 or rKE16 antigen were evaluated using archived human sera from confirmed VL cases (n = 750) and endemic non-VL controls (n = 754) in the Indian subcontinent (ISC), Brazil, and East Africa to assess sensitivity and specificity with 95% confidence intervals. A subset of RDTs were also evaluated after 60 days' heat incubation (37°C, 45°C). Interlot and interobserver variability was assessed. Results: All test brands performed well against ISC panels (sensitivity range, 92.8%-100%; specificity range, 96%-100%); however, sensitivity was lower against Brazil and East African panels (61.5%-91% and 36.8%-87.2%, respectively). Specificity was consistently > 95% in Brazil and ranged between 90.8% and 98% in East Africa. Performance of some products was adversely affected by high temperatures. Agreement between lots and readers was good to excellent (κ > 0.73-0.99). Conclusions: Diagnostic accuracy of VL RDTs varies between the major endemic regions. Many tests performed well and showed good heat stability in the ISC; however, reduced sensitivity against Brazilian and East African panels suggests that in these regions, used alone, several RDTs are inadequate for excluding a VL diagnosis. More research is needed to assess ease of use and to compare performance using whole blood instead of serum and in patients coinfected with human immunodeficiency virus