OperomeDB: database of condition specific transcription in prokaryotic genomes and genomic insights of convergent transcription in bacterial genomes

Indiana University-Purdue University Indianapolis (IUPUI)My thesis comprises of two individual projects: 1) we have developed a database for operon prediction using high-throughput sequencing datasets for bacterial genomes. 2) Genomics and mechanistic insights of convergent transcription in bacterial genomes. In the first project we developed a database for the prediction of operons for bacterial genomes using RNA-seq datasets, we predicted operons for bacterial genomes. RNA-seq datasets with different condition for each bacterial genome were taken into account and predicted operons using Rockhopper. We took RNA-seq datasets from NCBI with distinct experimental conditions for each bacterial genome into account and analyzed using tool for operon prediction. Currently our database contains 9 bacterial organisms for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading and querying of data. In our database user can browse through reference genome, genes present in that genome and operons predicted from different RNA-seq datasets. Further in the second project, we studied the genomic and mechanistic insights of convergent transcription in bacterial genomes. We know that convergent gene pairs with overlapping head-to-head configuration are widely spread across both eukaryotic and prokaryotic genomes. They are believed to contribute to the regulation of genes at both transcriptional and post-transcriptional levels, although factors contributing to their abundance across genomes and mechanistic basis for their prevalence are poorly understood. In this study, we explore the role of various factors contributing to convergent overlapping transcription in bacterial genomes. Our analysis shows that the proportion of convergent overlapping gene pairs (COGPs) in a genome is affected due to endospore formation, bacterial habitat, oxygen requirement, GC content and the temperature range. In particular, we show that bacterial genomes thriving in specialized habitats, such as thermophiles, exhibit a high proportion of COGPs. Our results also conclude that the density distribution of COGPs across the genomes is high for shorter overlaps with increased conservation of distances for decreasing overlaps. Our study further reveals that COGPs frequently contain stop codon overlaps with the middle base position exhibiting mismatches between complementary strands. Further, for the functional analysis using cluster of orthologous groups (COGs) annotations suggested that cell motility, cell metabolism, storage and cell signaling are enriched among COGPs, suggesting their role in processes beyond regulation. Our analysis provides genomic insights into this unappreciated regulatory phenomenon, allowing a refined understanding of their contribution to bacterial phenotypes

Genomic and mechanistic insights of convergent transcription in bacterial genomes

Digitized for IUPUI ScholarWorks inclusion in 2021.Convergent gene pairs with overlapping head-to-head configuration are widely spread across both eukaryotic and prokaryotic genomes. They are believed to contribute to the regulation of genes at both transcriptional and post-transcriptional levels, although the factors contributing to their abundance across genomes and mechanistic basis for their prevalence are poorly understood. In this study, we explore the role of various factors contributing to convergent overlapping transcription in bacterial genomes. Our analysis shows that the proportion of convergent overlapping gene pairs (COGPs) in a genome is affected by endospore formation, bacterial habitat and the temperature range. In particular, we show that bacterial genomes thriving in specialized habitats such as thermophiles exhibit a high proportion of COGPs. Our results also show that the density distribution of COGPs across the genomes is high for shorter overlaps with increased conservation of distances for decreasing overlaps. Our study also reveals that COGPs frequently contain stop codon overlaps with the middle base exhibiting mismatches between complementary strands. Functional analysis using COGs (Cluster of Orthologous groups) annotations suggested that cell motility, cell metabolism, storage, and cell signaling are enriched among COGPs suggesting their role in processes beyond regulation. Our analysis provides genomic insights into this unappreciated regulatory phenomenon, allowing a refined understanding of their contribution to bacterial phenotypes

A study of clinical profile of dengue fever in a tertiary care hospital of Jamnagar, Gujarat, India

Background: Dengue is the most rapidly spreading mosquito-borne viral disease of mankind, with a 30-fold increase in global incidence over the last five decades. It is a major public health concern throughout the tropical and subtropical regions of the world. This is a prospective study, objective of which is to study clinical manifestations of all laboratory confirmed dengue cases admitted in the tertiary care hospital, Jamnagar, India.Methods: The study is carried out on 100 cases of dengue fever from January 2014 to November 2015. Patients those who are more or equal 12 year of age and; admitted with fever, headache, myalgia are evaluated with other clinical features and laboratory findings. Other causes of fever like malaria, enteric fever, chikungunya and respiratory infections are excluded by appropriate tests.Results: The most common presentation in our study was dengue fever without any complications (94%) and severe dengue fever (6%). Most common age group was between 20-29 years, mean age being 28.6 years with M: F ratio was 1.94:1. Most common clinical manifestation was fever observed in all patients (100%) followed by headache (98%), myalgia (97%), vomiting (49%). Warning signs present in total 28 patients out of 100.Conclusions: The study draws attention to susceptibility of the male, young adult age group. Fever, headache and myalgia are common presenting complaints.

PERFORMANCE EVALUATION OF CONTROL & SAFETY ROD AND ITS DRIVE MECHANISM OF FAST BREEDER REACTOR DURING SEISMIC EVENT

ABSTRACT Control and safety rods & their drive mechanisms (CSRDM) and diverse safety rods & their drive mechanisms (DSRDM) are the main constituents of the two independent shutdown systems in Prototype Fast Breeder Reactor (PFBR) of 500 MWe. There are nine CSR and three DSR placed within the hexagonal sheaths, which in turn are located in two radial banks of reactor core. This paper deals with the analysis carried out to predict the performance of CSRDM along with CSR. Analysis is carried out for the static and seismic loading under the fuel handling as well as normal operating conditions with the objective of ensuring structural integrity as well as to estimate the drop time during seismic event. The effects of bowing of sub-assemblies corresponding to the end of life situation have been considered. From the analysis, it is found that the drop time of CSR is 0.82 s, which is less than 1 s, and hence there is no concern of reactor shutdown. Further, it is ensured that there is no mechanical interaction of concern between various parts. The induced stresses are found to be very much less than RCC-MR allowable stress intensity. Thus the performance of CSRDM and CSR is demonstrated to be sound during normal as well as seismic events.

ICONE17-75851 DESIGN AND DEVELOPMENT OF DIVERSE SAFETY ROD AND ITS DRIVE MECHANISM FOR PFBR

ABSTRACT Prototype Fast Breeder Reactor (PFBR) is U-PuO 2 fuelled sodium cooled Pool type Fast Reactor and it is currently under advanced stage of construction at Kalpakkam, India. The Fast Breeder Test Reactor (FBTR) which is the only fast reactor currently operational in India is having only one shutdown system. However the IAEA and Atomic Energy Regulatory Board (AERB) Guide Lines call for two independent fast acting diverse shutdown systems for the present generation reactors. Hence PFBR is equipped with two independent, fast acting and diverse shutdown systems. A shutdown system comprises of sensors, logic circuits, drive mechanisms and neutron absorbing rods. The two shutdown systems of PFBR are capable of bringing down the reactor to cold shutdown state independent of the other. The absorber rods of the second shutdown system of PFBR are called as Diverse Safety rods (DSR) and their drive mechanisms are called as Diverse Safety Rod Drive Mechanisms (DSRDM). DSR are normally parked above active core by DSRDM. On receiving scram signal, Electromagnet of DSRDM is de-energised and it facilitates fast shutdown of the reactor by dropping the DSR in to the active core. This paper presents chronological design and development of the prototype DSR and DSRDM starting from the design specifications. Salient design specifications for both DSRDM and DSR are listed initially. The conceptual & detailed design features are explained with the help of figures. Various important design options considered in the initial design stage, choice of final design along with brief explanation for the particular choice are also given for some of the important components. Details on material of construction are given at appropriate places. Details on various analysis such as large displacement analysis for buckling, bending analysis for determining reactive forces and friction in the mechanism, thermal stress analysis of electromagnet during scram, flow induced vibration analysis of DSRDM and DSR and hydraulic analysis for estimating the pressure drop and drop time of DSR are also given. Test plans for design verification, manufacturing and shop testing experience of prototype systems, and criteria for endurance testing in sodium for qualification of DSRDM and DSR for operation in reactor are also briefed

Residual stress measurement round robin on an electron beam welded joint between austenitic stainless steel 316L(N) and ferritic steel P91

This paper is a research output of DMW-Creep project which is part of a national UK programme through the RCUK Energy programme and India's Department of Atomic Energy. The research is focussed on understanding the characteristics of welded joints between austenitic stainless steel and ferritic steel that are widely used in many nuclear power generating plants and petrochemical industries as well as conventional coal and gas-fired power systems. The members of the DMW-Creep project have under- taken parallel round robin activities measuring the residual stresses generated by a dissimilar metal weld (DMW) between AISI 316L(N) austenitic stainless steel and P91 ferritic-martensitic steel. Electron beam (EB) welding was employed to produce a single bead weld on a plate specimen and an additional smoothing pass (known cosmetic pass) was then introduced using a defocused beam. The welding re- sidual stresses have been measured by five experimental methods including (I) neutron diffraction (ND), (II) X-Ray diffraction (XRD), (III) contour method (CM), (IV) incremental deep hole drilling (iDHD) and (V) incremental centre hole drilling (iCHD). The round robin measurements of weld residual stresses are compared in order to characterise surface and sub-surface residual stresses comprehensively

Analysis of a Spanish energy scenario with Generation IV nuclear reactors

The advantages of fast-spectrum reactors consist not only of an efficient use of fuel through the breeding of fissile material and the use of natural or depleted uranium, but also of the potential reduction of the amount of actinides such as americium and neptunium contained in the irradiated fuel. The first aspect means a guaranteed future nuclear fuel supply. The second fact is key for high-level radioactive waste management, because these elements are the main responsible for the radioactivity of the irradiated fuel in the long term. The present study aims to analyze the hypothetical deployment of a Gen-IV Sodium Fast Reactor (SFR) fleet in Spain. A nuclear fleet of fast reactors would enable a fuel cycle strategy different than the open cycle, currently adopted by most of the countries with nuclear power. A transition from the current Gen-II to Gen-IV fleet is envisaged through an intermediate deployment of Gen-III reactors. Fuel reprocessing from the Gen-II and Gen-III Light Water Reactors (LWR) has been considered. In the so-called advanced fuel cycle, the reprocessed fuel used to produce energy will breed new fissile fuel and transmute minor actinides at the same time. A reference case scenario has been postulated and further sensitivity studies have been performed to analyze the impact of the different parameters on the required reactor fleet. The potential capability of Spain to supply the required fleet for the reference scenario using national resources has been verified. Finally, some consequences on irradiated final fuel inventory are assessed. Calculations are performed with the Monte Carlo transport-coupled depletion code SERPENT together with post-processing tools

Effect of Dopants on Zirconia Stabilization—An X-ray Absorption Study: I, Trivalent Dopants

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65562/1/j.1151-2916.1994.tb06964.x.pd