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Bacterial Systems (bacterial + system)

Distribution by Scientific Domains

Life Sciences	50%
Chemistry	50%

Selected Abstracts

DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial Systems

BIOTECHNOLOGY PROGRESS, Issue 5 2004
Yandi Dharmadi
DNA microarrays are currently used to study the transcriptional response of many organisms to genetic and environmental perturbations. Although there is much room for improvement of this technology, its potential has been clearly demonstrated in the past 5 years. The general consensus is that the bottleneck is now located in the processing and analysis of transcriptome data and its use for purposes other than the quantification of changes in gene expression levels. In this article we discuss technological aspects of DNA microarrays, statistical and biological issues pertinent to the design of microarray experiments, and statistical tools for microarray data analysis. A review on applications of DNA microarrays in the study of bacterial systems is presented. Special attention is given to studies in the following areas: (1) bacterial response to environmental changes; (2) gene identification, genome organization, and transcriptional regulation; and (3) genetic and metabolic engineering. Soon, the use of DNA microarray technologies in conjunction with other genome/system-wide analyses (e.g., proteomics, metabolomics, fluxomics, phenomics, etc.) will provide a better assessment of genotype-phenotype relationships in bacteria, which serve as a basis for understanding similar processes in more complex organisms. [source]

Cloning, expression and characterization of the pig liver GDP-mannose pyrophosphorylase

FEBS JOURNAL, Issue 23 2000
Evidence that GDP-mannose, GDP-Glc pyrophosphorylases are different proteins
GDP-Man, the mannosyl donor for most Man-containing polymers is formed by the transfer of Man-1- P to GTP to form GDP-Man and PPi. This reaction is catalyzed by the widespread and essential enzyme, GDP-Man pyrophosphorylase (GMPP). The pig liver GMPP consists of an , subunit (43 kDa) and a , subunit (37 kDa). Purified pig GMPP catalyzes the synthesis of GDP-Glc (from Glc-1- P and GTP) and GDP-Man (from Man-1- P and GTP), but has higher activity for the formation of GDP-Glc than for synthesis of GDP-Man. In the present study, we report the cloning of the cDNA for the , subunit of GMPP, and its expression in a bacterial system resulting in the formation of active enzyme. The full length cDNA encoding the , subunit was isolated from a porcine cDNA library, and its predicted gene product showed high amino-acid sequence homology to GMPPs from other species. The gene was expressed in Escherichia coli cells, and a 37-kDa protein was over-produced in these cells. This gene product reacted strongly with antibody reactive to the native , subunit of pig GMPP. Most interestingly, this recombinant protein had high activity for synthesizing GDP-Man (from Man-1- P and GTP), but very low activity for the formation of GDP-Glc (from Glc-1- P and GTP). Other properties of the recombinant protein were also analyzed. This study suggests that the , subunit is the GMPP, whereas the , subunit, or a combination of both subunits, may have the GDP-Glc pyrophosphorylase activity. [source]

Crystallization and preliminary X-ray analysis of a rat aldose reductase-like protein (AKR1B14)

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009
Roland Chung
Mouse vas deferens protein/aldo-keto reductase 1B7 (AKR1B7) is involved in the detoxification of isocaproaldehyde, a steroidogenesis byproduct, and of 4-hydroxynonenal formed by lipid peroxidation. The rat orthologue of AKR1B7 has recently been named AKR1B14 in the AKR superfamily. Recombinant AKR1B14 was expressed in a bacterial system and purified to homogeneity. The purified protein was crystallized from polyethylene glycol solutions using the hanging-drop vapour-diffusion method and an X-ray diffraction data set was collected to 1.86,Å resolution. The crystals belonged to space group P21, with unit-cell parameters a = 50.66, b = 69.14, c = 72.27,Å, , = 96.4°. This is the first crystallization report of a rodent AKR1B7 orthologue. [source]

Complex responses to culture conditions in Pseudomonas syringae pv. tomato DC3000 continuous cultures: The role of iron in cell growth and virulence factor induction

BIOTECHNOLOGY & BIOENGINEERING, Issue 5 2010
Beum Jun Kim
Abstract The growth of a model plant pathogen, Pseudomonas syringae pv. tomato DC3000, was investigated using a chemostat culture system to examine environmentally regulated responses. Using minimal medium with iron as the limiting nutrient, four different types of responses were obtained in a customized continuous culture system: (1) stable steady state, (2) damped oscillation, (3) normal washout due to high dilution rates exceeding the maximum growth rate, and (4) washout at low dilution rates due to negative growth rates. The type of response was determined by a combination of initial cell mass and dilution rate. Stable steady states were obtained with dilution rates ranging from 0.059 to 0.086,h,1 with an initial cell mass of less than 0.6,OD600. Damped oscillations and negative growth rates are unusual observations for bacterial systems. We have observed these responses at values of initial cell mass of 0.9,OD600 or higher, or at low dilution rates (<0.05,h,1) irrespectively of initial cell mass. This response suggests complex dynamics including the possibility of multiple steady states. Iron, which was reported earlier as a growth limiting nutrient in a widely used minimal medium, enhances both growth and virulence factor induction in iron-supplemented cultures compared to unsupplemented controls. Intracellular iron concentration is correlated to the early induction (6,h) of virulence factors in both batch and chemostat cultures. A reduction in aconitase activity (a TCA cycle enzyme) and ATP levels in iron-limited chemostat cultures was observed compared to iron-supplemented chemostat cultures, indicating that iron affects central metabolic pathways. We conclude that DC3000 cultures are particularly dependent on the environment and iron is likely a key nutrient in determining physiology. Biotechnol. Bioeng. 2010;105: 955,964. © 2009 Wiley Periodicals, Inc. [source]

DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial Systems

Purification, crystallization and preliminary crystallographic analysis of the Hermes transposase

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2005
Zhanita N. Perez
DNA transposition is the movement of a defined segment of DNA from one location to another. Although the enzymes that catalyze transposition in bacterial systems have been well characterized, much less is known about the families of transposase enzymes that function in higher organisms. Active transposons have been identified in many insect species, providing tools for gene identification and offering the possibility of altering the genotypes of natural insect populations. One of these active transposons is Hermes, a 2749-base-pair element from Musca domestica that encodes its own transposase. An N-terminally deleted version of the Hermes transposase (residues 79,612) has been overexpressed and purified, and crystals that diffract to 2.1,Å resolution have been obtained at 277,K by the hanging-drop method. [source]