Roles of transcription factors, RBPA and SIGF, in the mycobacterium tuberculosis

The mechanism of prokaryotic transcription has been characterized primarily in the classic system, Escherichia coli, and cannot be confidently extended to include other prokaryotic species, such as those of the Actinobacteria phylum. Actinobacteria represents a diverse group of Gram-positive species that range from soil dwellers to obligate pathogens, such as Mycobacterium tuberculosis (Tb). These species encode RNA polymerase (RNAP) binding proteins that are not present in model organisms, and therefore present a unique lens through which the basic mechanism of transcription can be further explored outside of model systems. In addition, these mechanisms of transcriptional regulation can be studied in the context of M. Tuberculosis pathogenesis. The model we use for tuberculosis is Mycobacterium Smegmatis, a homologue, which has a faster doubling time and is only Biosafety level 1. Within Actinobacteria, notable conserved RNAP binding proteins include RNA polymerase binding protein A (RbpA) and CarD. RbpA is specific to Actinobacteria, binding the β subunit of RNAP and primary σ factors. CarD binds to the β subunit and associates with DNA. Both proteins are upregulated upon exposure to stress, and have implications in the initiation of rRNA transcription. Each is proposed to stimulate the formation of transcriptionally competent RNAP-holoenzyme open promoter complexes, and CarD is thought to act as a global transcriptional regulator. RbpA and CarD are believed to be essential in M. Tuberculosis and M. Smegmatis. Recent structural analyses of RbpA and CarD suggest the two proteins may share a region of similarity that could compete for binding to the β subunit, and brings into question whether the two proteins are capable of coordinately modulating transcription or antagonize each other's activity. This was investigated through purification of CarD and RbpA and in vitro studies performed with [α-32P] Uridine triphosphate used to measure the level of transcription. These experiments led to the conclusion that RbpA and CarD are able to associate with the same RNAP and have an additive stabilizing action on the polymerase. Whether or not RbpA is an essential protein was also investigated genetically, and by using a Tetracycline on/off system. Sigma factors play an important role in transcription due to their ability to recognize promoter regions and initiate transcription. One connection that we have preliminary data for, through DNA pull downs, is that sigF binds rRNA promoters, and CarD and RbpA are both studied in the context of rRNA transcription. Therefore sigF is another factor that could be regulating rRNA transcription, possibly during stress. SigF is also the sigma factor that responds to oxidative stress, and CarD is involved in oxidative stress. Sigma F is a member of a family of 13 different sigma factors that are preset in M. Tuberculosis. There are two different types of sigma factors: primary, which are essential for normal growth, and alternative, which are typically expressed during differing environmental conditions. Sigma F has been shown to be upregulated during oxidative stress, which is why it was of particular interest to us. To investigate the roles of sig F, we exposed sig F deletion mutants and wild type strains to oxidative stress and measured ribosomal RNA production by reverse transcription quantitative real time PCR. It was concluded that sigF is a probable suppressor of rRNA when exposed to oxidative stress

An Integrated Framework for Treebanks and Multilayer Annotations

Treebank formats and associated software tools are proliferating rapidly, with little consideration for interoperability. We survey a wide variety of treebank structures and operations, and show how they can be mapped onto the annotation graph model, and leading to an integrated framework encompassing tree and non-tree annotations alike. This development opens up new possibilities for managing and exploiting multilayer annotations.Comment: 8 page

The slot car stig: Performance and consistency of a slot car driven by a heuristic algorithm in an embedded microcontroller

We present theory and measured performance of an autonomous slot car driven by a heuristic algorithm on a typical track. The hardware consists of a PIC 8-bit single-chip microcontroller with various sensors driving a standard permanent-magnet (PM) brushed dc (BDC) motor in a mechanically-standard Scalextric platform. We present some interesting results concerning the relative difficulty of apparently-balanced lanes on a track. The car achieves optimum lap times with high consistency. Measured performance agrees with theoretical expectation. The consistency of performance allows the impact of experimental changes to be reliably assessed

Ups and Downs: Does the American Economy Still Promote Upward Mobility?

Examines trends in absolute intragenerational mobility by analyzing short- and long-term income fluctuations from 1967-2004, rates of recovery from declines, recovery time, and rates of gains compared with those of declines

An efficient representation of spatial information for expert reasoning in robotic vehicles

The previous generation of robotic vehicles and drones was designed for a specific task, with limited flexibility in executing their mission. This limited flexibility arises because the robotic vehicles do not possess the intelligence and knowledge upon which to make significant tactical decisions. Current development of robotic vehicles is toward increased intelligence and capabilities, adapting to a changing environment and altering mission objectives. The latest techniques in artificial intelligence (AI) are being employed to increase the robotic vehicle's intelligent decision-making capabilities. This document describes the design of the SARA spatial database tool, which is composed of request parser, reasoning, computations, and database modules that collectively manage and derive information useful for robotic vehicles

Impulse TDR and its application to measurement of antennas

The traditional stimulus signal used in a time-domain reflectometer (TDR) is a voltage step. We propose an alternative technique, whereby an impulse generator is employed in place of the step generator in a TDR. The advantage conferred by “impulse TDR” is that more energy is available at higher frequencies than with conventional step TDR, and so a higher bandwidth and signal-to-noise ratio (SNR) is achieved. The theoretical result is compared with measurement

Cause and Amelioration of MRI-Induced Heating Through Medical Implant Lead Wires

The RF fields present in magnetic resonance imaging (MRI) scanners can induce hazardous heating in patients wearing medical implants. The inherent design and locale of deep brain stimulators (DBS) and spinal cord stimulators (SCS) make them particularly susceptible. We apply antenna concepts and use electromagnetic (EM) simulation to explain the phenomenon and anticipate its sensitivity to lead wire length. We anticipate that a DC resistance of less than 50 Ω/m and an RF impedance of more than 1:23kΩ/m would be required for a safe electrode for SCS use. We investigate the possibility of manipulating wire conductivity and diameter in order to use the skin depth effect to achieve a safe electrode. The effect of the thickness and permittivity of insulation surrounding the wires is explored