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Title: Identification and characterization of transcription networks in environmentally significant species

Abstract

Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.

Authors:
;
Publication Date:
Research Org.:
Health Research Inc., Rensselaer, NY 12144
Sponsoring Org.:
USDOE Office of Science (SC); US - Atomic Energy Commission
OSTI Identifier:
860762
Report Number(s):
DOE/ER/63204-1
TRN: US200710%%173
DOE Contract Number:
FG02-01ER63204
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ABUNDANCE; ALGORITHMS; ESCHERICHIA COLI; FUNCTIONALS; GENES; MOLECULAR BIOLOGY; REGULATIONS; RHODOPSEUDOMONAS; SPECIFICITY; TRANSCRIPTION; TRANSCRIPTION FACTORS; bioinformatics; transcription regulation

Citation Formats

Lawrence, Charles E., and McCue, Lee Ann. Identification and characterization of transcription networks in environmentally significant species. United States: N. p., 2005. Web. doi:10.2172/860762.
Lawrence, Charles E., & McCue, Lee Ann. Identification and characterization of transcription networks in environmentally significant species. United States. doi:10.2172/860762.
Lawrence, Charles E., and McCue, Lee Ann. Wed . "Identification and characterization of transcription networks in environmentally significant species". United States. doi:10.2172/860762. https://www.osti.gov/servlets/purl/860762.
@article{osti_860762,
title = {Identification and characterization of transcription networks in environmentally significant species},
author = {Lawrence, Charles E. and McCue, Lee Ann},
abstractNote = {Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.},
doi = {10.2172/860762},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Nov 30 00:00:00 EST 2005},
month = {Wed Nov 30 00:00:00 EST 2005}
}

Technical Report:

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  • A quality assurance program for trace analyses of environmentally significant species has begun. In the first stage, methods to analyze environmental samples for a variety of components have been developed and documented. Techniques include visual inspection, gravimetric analysis, ion chromatography (IC), inductively coupled plasma (ICP) emission spectrometry, ICP-mass spectrometry (ICP/MS), atomic absorption (AA) (flame, furnace, and mercury cold vapor techniques), gas chromatography (GC), potentiometry, and visible spectrophotometry. Industrial sites are analyzed for contamination by methylene dianiline (MDA). Precious metal waste sludges are analyzed for cyanide, halogens, mercury, and precious metals. Paint samples are analyzed for volatile organic compounds by GCmore » and gravimetric analysis. Polychlorinated biphenyls (PCBs) also are determined in oil samples. In the second stage of quality assurance, methods are validated by accuracy and precision studies and by determination of detection limits and ranges. Improved methods provide additional information about key substances targeted by EPA. Furthermore, quality assurance data on IC and GC analyses are presented. IC methods simultaneously determine five anions in one run and four cations in another. Results on EPA-sponsored round robin tests indicate that IC can accurately determine the concentrations of anions and cations. Spiked samples analyzed by both GC and IC methods gave recoveries very close to 100%.« less
  • A quality assurance program for trace analyses of environmentally significant species has begun. In the first stage, methods to analyze environmental samples for a variety of components have been developed and documented. Techniques include visual inspection, gravimetric analysis, ion chromatography (IC), inductively coupled plasma (ICP) emission spectrometry, ICP-mass spectrometry (ICP/MS), atomic absorption (AA) (flame, furnace, and mercury cold vapor techniques), gas chromatography (GC), potentiometry, and visible spectrophotometry. Industrial sites are analyzed for contamination by methylene dianiline (MDA). Precious metal waste sludges are analyzed for cyanide, halogens, mercury, and precious metals. Paint samples are analyzed for volatile organic compounds by GCmore » and gravimetric analysis. Polychlorinated biphenyls (PCBs) also are determined in oil samples. In the second stage of quality assurance, methods are validated by accuracy and precision studies and by determination of detection limits and ranges. Improved methods provide additional information about key substances targeted by EPA. Furthermore, quality assurance data on IC and GC analyses are presented. IC methods simultaneously determine five anions in one run and four cations in another. Results on EPA-sponsored round robin tests indicate that IC can accurately determine the concentrations of anions and cations. Spiked samples analyzed by both GC and IC methods gave recoveries very close to 100%.« less
  • We have completed our characterization of both the transcriptional regulatory network and post-transcriptional regulatory motifs in Shewanella.
  • Several bench-scale column tests (resin bed volume less than or equal to 75 mL) have been conducted with SuperLig 639 resin and simulated Hanford waste supernates. Rhenium (surrogate for technetium in actual waste samples) breakthrough profiles were determined for three simulant compositions which are representative of the basic waste categories requiring treatment in the Hanford River Protection Project Waste Treatment Plant. Considerable loading performance variability was observed between the three waste types, although the resin is effective at rhenium removal from each solution. Careful and frequent analysis during elution studies conducted at the conclusion of the column loading tests confirmedmore » that sodium nitrate and sodium perrhenate ion pairs are primary sorbing species on SuperLig 639 resin. Furthermore, it was discovered that potassium nitrate and potassium perrhenate salts are significant competitors for sorption sites on the resin. Successive desorption profiles were identified for all four salt species during elution tests. Integration of the desorption profiles revealed that the resin is selective for removal of the potassium salts over the sodium salts.« less
  • Technetium, as pertechnetate (TcO4 -), is a mobile species in the environment. This characteristic, along with its long half-life, (99Tc, t1/2 = 213,000 a) makes technetium a major contributor to the long-term hazard associated with low level waste (LLW) disposal. Technetium partitioning from the nuclear waste at DOE sites will be required so that the LLW forms meet DOE performance assessment criteria. Technetium separations assume that technetium exists as TcO4 - in the waste. However, years of thermal, chemical, and radiolytic digestion in the presence of organic material, has transformed much of the TcO4 - into unidentified, stable, reduced, technetiummore » complexes. To successfully partition technetium from tank wastes, it will be necessary to either remove these technetium species with a new process, or reoxidize them to TcO4 - so that conventional pertechnetate separation schemes will be successful.« less