Functional, and phylogenetic analysis of maleylacetate reductase of Pseudomonas sp strain PNPG3: An in-silico approach

Shrinking freshwater ecosystems are under tremendous pollution threat due to anthropocentric activities. Para nitrophenol (PNP), a well-documented priority pollutant extensively used in dyes, petrochemical, pharmaceutical, explosives, pesticides, leather industries, and agrochemicals, is responsible for contaminating aquatic ecosystems globally. It is highly toxic and has carcinogenic and mutagenic effects on living organisms like humans and several animal models. Bioremediation approaches mainly involving bacteria are considered the best, most eco-friendly, cost-effective, green, and clean method for effective removal PNP from its contaminated sites. This manuscript highlights the structural and functional analysis of a lower pathway enzyme involved in PNP degradation, maleylacetate reductase (MR), from Pseudomonas sp strain PNPG3, which was recently isolated from a freshwater ecosystem. This enzyme plays a role in converting maleylacetate to 3-oxoadipate. Despite its crucial functional role, no model is available for this protein in the protein database (PDB). Therefore, attempts were made for the computational investigation of physicochemical, functional, and structural properties, including secondary, and tertiary structure prediction, model quality analysis, and phylogenetic assessment using several standard bioinformatics tools. This enzyme has a molecular weight of about ~37.6 kDa, is acidic and thermostable, belonging to a member of iron-containing alcohol dehydrogenase. Moreover, this study will benefit the scientific community in deciphering the prediction of the function of similar proteins of interest

Microbial biodegradation of nitrophenols and their derivatives: A Review

Today, nitrophenols (NPs) represent chemicals highly in demand not only due to their function in synthetic chemistry but also due to their huge applications in several industries. Such diverse requirements and applications has resulted in a widespread abundance of these chemicals. Improper application and waste disposal practice results in the continuous discharge of these compounds into the environment and causes pollution threat to soil, groundwater, river water, etc. These xenobiotic chemicals are hazardous, toxic, carcinogenic, and mutagenic which results in serious health problems. The Nitro group present in the phenol makes them recalcitrant which causes the persistence of these chemicals in the environment. Although several chemicals, electrochemical, physical, and physicochemical methods have been proposed, bioremediation approaches mainly involving bacteria are considered best. To date, very few successful attempts (related to microbe-assisted bioremediation) have been carried out with environmental habitats for the removal of NPs (both in-situ and ex-situ attempts). So, as far as the effectiveness of the bioremediation process for NP decontamination is concerned, we are far away. More explorative studies using efficient aerobic-anaerobic NP degrading bacterial consortium (or combination of microbes- plant systems) and advanced techniques including omics approaches and nanotechnologies may help towards developing better practicable bioremediation approaches, in the future. This review article focuses on the list of nitrophenol degrading microorganisms, biodegradation pathways of NPs, bioremediation by immobilized cell technique, and the advantages and disadvantages of bioremediation. This article will increase our knowledge of the biodegradation of NPs

Pre-emptive Dynamic Source Routing: A Repaired Backup Approach and Stability Based DSR with Multiple Routes

DSR algorithm finds out the best path for communicating between two nodes in a highly dynamic environment. Since, the environment changes frequently, the probability of established path breakage is also high. Again, as the breakage possibility increases, a new route has to be discovered every time .In order to avoid path discovery every time, we propose the modification of the existing DSR algorithm. In this paper we propose an enhancement of the DSR protocol based on a backup route(second best route) which will be provided by the destination node to the source node along with the best route during the process of path discovery. During the path maintenance process, in case any intermediate node identifies that the signal strength falls below a threshold i.e. the established route is about to break, the intermediate node sends a caution message to the source node. The source node switches the communication through the backup path , apprehending that the established route is about to break. As the communication through the backup route takes place, the previous route is repaired, if possible and acts as the new backup route. This process of toggling between backup route and established route reduces the call for path discovery to some extent. The stability in consideration of failure of common link and nodes in the back up repaired algorithm has been investigated with new algorithm for stable route selection

Identification of Serotype in Culture Negative Pneumococcal Meningitis Using Sequential Multiplex PCR: Implication for Surveillance and Vaccine Design

BACKGROUND: PCR-based serotyping of Streptococcus pneumoniae has been proposed as a simpler approach than conventional methods, but has not been applied to strains in Asia where serotypes are diverse and different from other part of the world. Furthermore, PCR has not been used to determine serotype distribution in culture-negative meningitis cases. METHODOLOGY: Thirty six serotype-specific primers, 7 newly designed and 29 previously published, were arranged in 7 multiplex PCR sets, each in new hierarchies designed for overall serotype distribution in Bangladesh, and specifically for meningitis and non-meningitis isolates. Culture-negative CSF specimens were then tested directly for serotype-specific sequences using the meningitis-specific set of primers. PCR-based serotyping of 367 strains of 56 known serotypes showed 100% concordance with quellung reaction test. The first 7 multiplex reactions revealed the serotype of 40% of all, and 31% and 48% non-meningitis and meningitis isolates, respectively. By redesigning the multiplex scheme specifically for non-meningitis or meningitis, the quellung reaction of 43% and 48% of respective isolates could be identified. Direct examination of 127 culture-negative CSF specimens, using the meningitis-specific set of primers, yielded serotype for 51 additional cases. CONCLUSIONS: This PCR approach, could improve ascertainment of pneumococcal serotype distributions, especially for meningitis in settings with high prior use of antibiotics

Investigating the impact of land-use land-cover change on Indian summer monsoon daily rainfall and temperature during 1951–2005 using a regional climate model

Daily moderate rainfall events, which constitute a major portion of seasonal summer monsoon rainfall over central India, have decreased significantly during the period 1951 through 2005. On the other hand, mean and extreme near-surface daily temperature during the monsoon season have increased by a maximum of 1–1.5 °C. Using simulations made with a high-resolution regional climate model (RegCM4) and prescribed land cover of years 1950 and 2005, it is demonstrated that part of the changes in moderate rainfall events and temperature have been caused by land-use/land-cover change (LULCC), which is mostly anthropogenic. Model simulations show that the increase in seasonal mean and extreme temperature over central India coincides with the region of decrease in forest and increase in crop cover. Our results also show that LULCC alone causes warming in the extremes of daily mean and maximum temperatures by a maximum of 1–1.2 °C, which is comparable with the observed increasing trend in the extremes. Decrease in forest cover and simultaneous increase in crops not only reduces the evapotranspiration over land and large-scale convective instability, but also contributes toward decrease in moisture convergence through reduced surface roughness. These factors act together in reducing significantly the moderate rainfall events and the amount of rainfall in that category over central India. Additionally, the model simulations are repeated by removing the warming trend in sea surface temperatures over the Indian Ocean. As a result, enhanced warming at the surface and greater decrease in moderate rainfall events over central India compared to the earlier set of simulations are noticed. Results from these additional experiments corroborate our initial findings and confirm the contribution of LULCC in the decrease in moderate rainfall events and increase in daily mean and extreme temperature over India. Therefore, this study demonstrates the important implications of LULCC over India during the monsoon season. Although, the regional climate model helps in better resolving land–atmosphere feedbacks over the Indian region, the inferences do depend on the fidelity of the model in capturing the features of Indian monsoon realistically. It is proposed that similar studies using a suite of climate models will further enrich our understanding about the role of LULCC in the Indian monsoon climate

Experimental and numerical investigation of capillary flow in SU8 and PDMS microchannels with integrated pillars

Microfluidic channels with integrated pillars are fabricated on SU8 and PDMS substrates to understand the capillary flow. Microscope in conjunction with highspeed camera is used to capture the meniscus front movement through these channels for ethanol and isopropyl alcohol, respectively. In parallel, numerical simulations are conducted, using volume of fluid method, to predict the capillary flow through the microchannels with different pillar diameter to height ratio, ranging from 2.19 to 8.75 and pillar diameter to pitch ratio, ranging from 1.44 to 2.6. The pillar size (diameter, pitch and height) and the physical properties of the fluid (surface tension and viscosity) are found to have significant influence on the capillary phenomena in the microchannel. The meniscus displacement is non-uniform due to the presence of pillars and the non-uniformity in meniscus displacement is observed to increase with decrease in pitch to diameter ratio. The surface area to volume ratio is observed to play major roles in the velocity of the capillary meniscus of the devices. The filling speed is observed to change more dramatically under different pillar heights upto 120 mu m and the change is slow with further increase in the pillar height. The details pertaining to the fluid distribution (meniscus front shapes) are obtained from the numerical results as well as from experiments. Numerical predictions for meniscus front shapes agree well with the experimental observations for both SU8 and PDMS microchannels. It is observed that the filling time obtained experimentally matches very well with the simulated filling time. The presence of pillars creates uniform meniscus front in the microchannel for both ethanol and isopropyl alcohol. Generalized plots in terms of dimensionless variables are also presented to predict the performance parameters for the design of these microfluidic devices. The flow is observed to have a very low Capillary number, which signifies the relative importance of surface tension to viscous effects in the present study