bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Functional Analysis of the Gene Cluster for
l
-Arabinose Utilization in
Corynebacterium glutamicum
Authors: Kawaguchi Hideo , Sasaki Miho , Vertès Alain A. , Inui Masayuki , Yukawa Hideaki 
Published: April 2009

ABSTRACT

Corynebacterium glutamicum
ATCC 31831 grew on
l
-arabinose as the sole carbon source at a specific growth rate that was twice that on
d
-glucose. The gene cluster responsible for
l
-arabinose utilization comprised a six-cistron transcriptional unit with a total length of 7.8 kb. Three
l
-arabinose-catabolizing genes,
araA
(encoding
l
-arabinose isomerase),
araB
(
l
-ribulokinase), and
araD
(
l
-ribulose-5-phosphate 4-epimerase), comprised the
araBDA
operon, upstream of which three other genes,
araR
(LacI-type transcriptional regulator),
araE
(
l
-arabinose transporter), and
galM
(putative aldose 1-epimerase), were present in the opposite direction. Inactivation of the
araA
,
araB
, or
araD
gene eliminated growth on
l
-arabinose, and each of the gene products was functionally homologous to its
Escherichia coli
counterpart. Moreover, compared to the wild-type strain, an
araE
disruptant exhibited a >80% decrease in the growth rate at a lower concentration of
l
-arabinose (3.6 g liter
−1
) but not at a higher concentration of
l
-arabinose (40 g liter
−1
). The expression of the
araBDA
operon and the
araE
gene was
l
-arabinose inducible and negatively regulated by the transcriptional regulator AraR. Disruption of
araR
eliminated the repression in the absence of
l
-arabinose. Expression of the regulon was not repressed by
d
-glucose, and simultaneous utilization of
l
-arabinose and
d
-glucose was observed in aerobically growing wild-type and
araR
deletion mutant cells. The regulatory mechanism of the
l
-arabinose regulon is, therefore, distinct from the carbon catabolite repression mechanism in other bacteria.
Identification of a Gene Cluster for the Biosynthesis of a Long, Galactose-Rich Exopolysaccharide in
Lactobacillus rhamnosus
GG and Functional Analysis of the Priming Glycosyltransferase
Authors: Lebeer Sarah , Verhoeven Tine L. A. , Francius Grégory , Schoofs Geert , Lambrichts Ivo , Dufrêne Yves , Vanderleyden Jos , De Keersmaecker Sigrid C. J. 
Published: April 2009

ABSTRACT

Cell surface polysaccharides have an established role as virulence factors in human bacterial pathogens. Less documented are the biosynthesis and biological functions of surface polysaccharides in beneficial bacteria. We identified a gene cluster that encodes the enzymes and regulatory and transporter proteins for the different steps in the biosynthesis of extracellular polysaccharides (EPS) of the well-documented probiotic strain
Lactobacillus rhamnosus
GG. Subsequent mutation of the
welE
gene, encoding the priming glycosyltransferase within this cluster, and comparative phenotypic analyses of wild-type versus mutant strains confirmed the specific function of this gene cluster in the biosynthesis of high-molecular-weight, galactose-rich heteropolymeric EPS molecules. The phenotypic analyses included monomer composition determination, estimation of the polymer length of the isolated EPS molecules, and single-molecule force spectroscopy of the surface polysaccharides. Further characterization of the
welE
mutant also showed that deprivation of these long, galactose-rich EPS molecules results in an increased adherence and biofilm formation capacity of
L. rhamnosus
GG, possibly because of less shielding of adhesins such as fimbria-like structures.
Endoplasmic Reticulum-Associated Secretory Proteins Sec20p, Sec39p, and Dsl1p Are Involved in Peroxisome Biogenesis
Authors: Perry Ryan J. , Mast Fred D. , Rachubinski Richard A. 
Published: April 2009

ABSTRACT

Two pathways have been identified for peroxisome formation: (i) growth and division and (ii) de novo synthesis. Recent experiments determined that peroxisomes originate at the endoplasmic reticulum (ER). Although many proteins have been implicated in the peroxisome biogenic program, no proteins in the eukaryotic secretory pathway have been identified as having roles in peroxisome formation. Using the yeast
Saccharomyces cerevisiae
regulatable
Tet
promoter Hughes clone collection, we found that repression of the ER-associated secretory proteins Sec20p and Sec39p resulted in mislocalization of the peroxisomal matrix protein chimera Pot1p-green fluorescent protein (GFP) to the cytosol. Likewise, the peroxisomal membrane protein chimera Pex3p-GFP localized to tubular-vesicular structures in cells suppressed for Sec20p, Sec39p, and Dsl1p, which form a complex at the ER. Loss of Sec39p attenuated formation of Pex3p-derived peroxisomal structures following galactose induction of Pex3p-GFP expression from the
GAL1
promoter. Expression of Sec20p, Sec39p, and Dsl1p was moderately increased in yeast grown under conditions that proliferate peroxisomes, and Sec20p, Sec39p, and Dsl1p were found to cofractionate with peroxisomes and colocalize with Pex3p-monomeric red fluorescent protein under these conditions. Our results show that
SEC20
,
SEC39
, and
DSL1
are essential secretory genes involved in the early stages of peroxisome assembly, and this work is the first to identify and characterize an ER-associated secretory machinery involved in peroxisome biogenesis.
Role of the AcsF Protein in
Chloroflexus aurantiacus
Authors: Tang Kuo-Hsiang , Wen Jianzhong , Li Xianglu , Blankenship Robert E. 
Published: April 2009

ABSTRACT

The green phototrophic bacteria contain a unique complement of chlorophyll pigments, which self-assemble efficiently into antenna structures known as chlorosomes with little involvement of protein. The few proteins found in chlorosomes have previously been thought to have a primarily structural function. The biosynthetic pathway of the chlorosome pigments, bacteriochlorophylls
c
,
d
, and
e
, is not well understood. In this report, we used spectroscopic, proteomic, and gene expression approaches to investigate the chlorosome proteins of the green filamentous anoxygenic phototrophic bacterium
Chloroflexus aurantiacus
. Surprisingly, Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase, AcsF, was identified under anaerobic growth conditions. The AcsF protein was found in the isolated chlorosome fractions, and the proteomics analysis suggested that significant portions of the AcsF proteins are not accessible to protease digestion. Additionally, quantitative real-time PCR studies showed that the transcript level of the
acsF
gene is not lower in anaerobic growth than in semiaerobic growth. Since the proposed enzymatic activity of AcsF requires molecular oxygen, our studies suggest that the roles of AcsF in
C. aurantiacus
need to be investigated further.
Roles of the Outer Membrane Protein AsmA of
Salmonella enterica
in the Control of
marRAB
Expression and Invasion of Epithelial Cells
Authors: Prieto Ana I. , Hernández Sara B. , Cota Ignacio , Pucciarelli M. Graciela , Orlov Yuri , Ramos-Morales Francisco , García-del Portillo Francisco , Casadesús Josep 
Published: April 2009

ABSTRACT

A genetic screen for suppressors of bile sensitivity in DNA adenine methylase (
dam
) mutants of
Salmonella enterica
serovar Typhimurium yielded insertions in an uncharacterized locus homologous to the
Escherichia coli asmA
gene. Disruption of
asmA
suppressed bile sensitivity also in
phoP
and
wec
mutants of
S. enterica
and increased the MIC of sodium deoxycholate for the parental strain ATCC 14028. Increased levels of
marA
mRNA were found in
asmA
,
asmA dam
,
asmA phoP
, and
asmA wec
strains of
S. enterica
, suggesting that lack of AsmA activates expression of the
marRAB
operon. Hence,
asmA
mutations may enhance bile resistance by inducing gene expression changes in the
marRAB
-controlled Mar regulon. In silico analysis of AsmA structure predicted the existence of one transmembrane domain. Biochemical analysis of subcellular fractions revealed that the
asmA
gene of
S. enterica
encodes a protein of ∼70 kDa located in the outer membrane. Because AsmA is unrelated to known transport and/or efflux systems, we propose that activation of
marRAB
in
asmA
mutants may be a consequence of envelope reorganization. Competitive infection of BALB/c mice with
asmA
+
and
asmA
isogenic strains indicated that lack of AsmA attenuates
Salmonella
virulence by the oral route but not by the intraperitoneal route. Furthermore,
asmA
mutants showed a reduced ability to invade epithelial cells in vitro.
Characterization of the DraT/DraG System for Posttranslational Regulation of Nitrogenase in the Endophytic Betaproteobacterium
Azoarcus
sp. Strain BH72
Authors: Oetjen Janina , Reinhold-Hurek Barbara 
Published: April 2009

ABSTRACT

DraT/DraG-mediated posttranslational regulation of the nitrogenase Fe protein by ADP-ribosylation has been described for a few diazotrophic bacteria belonging to the class
Alphaproteobacteria
. Here we present for the first time the DraT/DraG system of a betaproteobacterium,
Azoarcus
sp. strain BH72, a diazotrophic grass endophyte. Its genome harbors one
draT
ortholog and two physically unlinked genes coding for ADP-ribosylhydrolases. Northern blot analysis revealed cotranscription of
draT
with two genes encoding hypothetical proteins. Furthermore,
draT
and
draG2
were expressed under all studied conditions, whereas
draG1
expression was nitrogen regulated. By using Western blot analysis of deletion mutants and nitrogenase assays in vivo, we demonstrated that DraT is required for the nitrogenase Fe protein modification but not for the physiological inactivation of nitrogenase activity. A second mechanism responsible for nitrogenase inactivation must operate in this bacterium, which is independent of DraT. Fe protein demodification was dependent mainly on DraG1, corroborating the assumption from phylogenetic analysis that DraG2 might be mostly involved in processes other than the posttranslational regulation of nitrogenase. Nitrogenase in vivo reactivation was impaired in a
draG1
mutant and a mutant lacking both
draG
alleles after anaerobiosis shifts and subsequent adjustment to microaerobic conditions, suggesting that modified dinitrogenase reductase was inactive. Our results demonstrate that the DraT/DraG system, despite some differences, is functionally conserved in diazotrophic proteobacteria.
In Vivo Interactions between Toxin-Antitoxin Proteins Epsilon and Zeta of Streptococcal Plasmid pSM19035 in
Saccharomyces cerevisiae
Authors: Zielenkiewicz Urszula , Kowalewska Magdalena , Kaczor Celina , Cegłowski Piotr 
Published: April 2009

ABSTRACT

The widespread prokaryotic toxin-antitoxin (TA) systems involve conditional interaction between two TA proteins. The interaction between the Epsilon and Zeta proteins, constituting the TA system of plasmid pSM19035 from
Streptococcus pyogenes
, was detected in vivo using a yeast two-hybrid system. As we showed using
Saccharomyces cerevisiae
, the Zeta toxin hybrid gene also exerts its toxic effects in a dose-dependent manner in eukaryotic cells. Analysis of mutant proteins in the two-hybrid system demonstrated that the N-terminal part of Zeta and the N-terminal region of Epsilon are involved in the interaction. The N-terminal region of the Zeta protein and its ATP/GTP binding motif were found to be responsible for the toxicity.
Elevated Mutation Frequency in Surviving Populations of Carbon-Starved
rpoS
-Deficient
Pseudomonas putida
Is Caused by Reduced Expression of Superoxide Dismutase and Catalase
Authors: Tarassova Kairi , Tegova Radi , Tover Andres , Teras Riho , Tark Mariliis , Saumaa Signe , Kivisaar Maia 
Published: April 2009

ABSTRACT

RpoS is a bacterial sigma factor of RNA polymerase which is involved in the expression of a large number of genes to facilitate survival under starvation conditions and other stresses. The results of our study demonstrate that the frequency of emergence of base substitution mutants is significantly increased in long-term-starved populations of
rpoS
-deficient
Pseudomonas putida
cells. The increasing effect of the lack of RpoS on the mutation frequency became apparent in both a plasmid-based test system measuring Phe
+
reversion and a chromosomal
rpoB
system detecting rifampin-resistant mutants. The elevated mutation frequency coincided with the death of about 95% of the cells in a population of
rpoS
-deficient
P
.
putida
. Artificial overexpression of superoxide dismutase or catalase in the
rpoS
-deficient strain restored the survival of cells and resulted in a decline in the mutation frequency. This indicated that, compared to wild-type bacteria,
rpoS
-deficient cells are less protected against damage caused by reactive oxygen species. 7,8-Dihydro-8-oxoguanine (GO) is known to be one of the most stable and frequent base modifications caused by oxygen radical attack on DNA. However, the spectrum of base substitution mutations characterized in
rpoS
-deficient
P
.
putida
was different from that in bacteria lacking the GO repair system: it was broader and more similar to that identified in the wild-type strain. Interestingly, the formation of large deletions was also accompanied by a lack of RpoS. Thus, the accumulation of DNA damage other than GO elevates the frequency of mutation in these bacteria. It is known that oxidative damage of proteins and membrane components, but not that of DNA, is a major reason for the death of cells. Since the increased mutation frequency was associated with a decline in the viability of bacteria, we suppose that the elevation of the mutation frequency in the surviving population of carbon-starved
rpoS
-deficient
P
.
putida
may be caused both by oxidative damage of DNA and enzymes involved in DNA replication and repair fidelity.
InEscherichia coli, MreB and FtsZ Direct the Synthesis of Lateral Cell Wall via Independent Pathways That Require PBP 2
Authors: Varma Archana , Young Kevin D. 
Published: April 2009

ABSTRACTInEscherichia coli, the cytoplasmic proteins MreB and FtsZ play crucial roles in ensuring that new muropeptide subunits are inserted into the cell wall in a spatially correct way during elongation and division. In particular, to retain a constant diameter and overall shape, new material must be inserted into the wall uniformly around the cell's perimeter. Current thinking is that MreB accomplishes this feat through intermediary proteins that tether peptidoglycan synthases to the outer face of the inner membrane. We tested this idea inE. coliby using add-carboxypeptidase mutant that accumulates pentapeptides in its peptidoglycan, allowing us to visualize new muropeptide incorporation. Surprisingly, inhibiting MreB with the antibiotic A22 did not result in uneven insertion of new wall, although the cells bulged and lost their rod shapes. Instead, uneven (clustered) incorporation occurred only if MreB and FtsZ were inactivated simultaneously, providing the first evidence inE. colithat FtsZ can direct murein incorporation into the lateral cell wall independently of MreB. Inhibiting penicillin binding protein 2 (PBP 2) alone produced the same clustered phenotype, implying that MreB and FtsZ tether peptidoglycan synthases via a common mechanism that includes PBP 2. However, cell shape was determined only by the presence or absence of MreB and not by the even distribution of new wall material as directed by FtsZ.
A cosimulation methodology for HW/SW validation and performance estimation
Authors: Fummi Franco , Loghi Mirko , Poncino Massimo , Pravadelli Graziano 
Published: April 2009

Cosimulation strategies allow us to simulate and verify HW/SW embedded systems before the real platform is available. In this field, there is a large variety of approaches that rely on different communication mechanisms to implement an efficient interface between the SW and the HW simulators. However, the literature lacks a comprehensive methodology which addresses the need for integrating and synchronizing heterogeneous simulators, like, for example, the SystemC simulation kernel for HW modules and an instruction set simulator for SW applications, without being intrusive for the HW and SW descriptions involved in the simulation. In this context, this article presents, compares, and integrates in a system-level framework two different co-simulation strategies for modeling, analyzing, and validating the performance of a HW/SW embedded system. Moreover, for both of them, a mechanism is proposed to provide an accurate time synchronization of the HW/SW communication. The first strategy is intended to provide an early cosimulation environment where HW/SW interaction can be validated without involving the operating system. The communication is implemented between a single SW task and a SystemC description of an HW module by exploiting the features of the remote debugging interface of a debugger (the GNU GDB), and by modifying the SystemC simulation kernel. On the other hand, the second strategy is intended to be used in further development steps, when the operating system is introduced to validate the cosimulation between HW modules and multitasking SW applications. In this approach, the communication is implemented via interrupts by using the features offered by the operating system.
Experimental results are reported on two different case studies to analyze and compare the effectiveness of both the approaches.
DOLPHIN
Authors: Angiulli Fabrizio , Fassetti Fabio 
Published: April 2009

In this work a novel distance-based outlier detection algorithm, named DOLPHIN, working on disk-resident datasets and whose I/O cost corresponds to the cost of sequentially reading the input dataset file twice, is presented.
It is both theoretically and empirically shown that the main memory usage of DOLPHIN amounts to a small fraction of the dataset and that DOLPHIN has linear time performance with respect to the dataset size. DOLPHIN gains efficiency by naturally merging together in a unified schema three strategies, namely the selection policy of objects to be maintained in main memory, usage of pruning rules, and similarity search techniques. Importantly, similarity search is accomplished by the algorithm without the need of preliminarily indexing the whole dataset, as other methods do.
The algorithm is simple to implement and it can be used with any type of data, belonging to either metric or nonmetric spaces. Moreover, a modification to the basic method allows DOLPHIN to deal with the scenario in which the available buffer of main memory is smaller than its standard requirements. DOLPHIN has been compared with state-of-the-art distance-based outlier detection algorithms, showing that it is much more efficient.
An out-of-core sparse Cholesky solver
Authors: Reid John K. , Scott Jennifer A. 
Published: April 2009

Direct methods for solving large sparse linear systems of equations are popular because of their generality and robustness. Their main weakness is that the memory they require usually increases rapidly with problem size. We discuss the design and development of the first release of a new symmetric direct solver that aims to circumvent this limitation by allowing the system matrix, intermediate data, and the matrix factors to be stored externally. The code, which is written in Fortran and called HSL_MA77, implements a multifrontal algorithm. The first release is for positive-definite systems and performs a Cholesky factorization. Special attention is paid to the use of efficient dense linear algebra kernel codes that handle the full-matrix operations on the frontal matrix and to the input/output operations. The input/output operations are performed using a separate package that provides a virtual-memory system and allows the data to be spread over many files; for very large problems these may be held on more than one device.
Numerical results are presented for a collection of 30 large real-world problems, all of which were solved successfully.
Techniques for Design and Implementation of Secure Reconfigurable PUFs
Authors: Majzoobi Mehrdad , Koushanfar Farinaz , Potkonjak Miodrag 
Published: April 2009

Physically unclonable functions (PUFs) provide a basis for many security and digital rights management protocols. PUF-based security approaches have numerous comparative strengths with respect to traditional cryptography-based techniques, including resilience against physical and side channel attacks and suitability for lightweight protocols. However, classical delay-based PUF structures have a number of drawbacks including susceptibility to guessing, reverse engineering, and emulation attacks, as well as sensitivity to operational and environmental variations.
To address these limitations, we have developed a new set of techniques for FPGA-based PUF design and implementation. We demonstrate how reconfigurability can be exploited to eliminate the stated PUF limitations. We also show how FPGA-based PUFs can be used for privacy protection. Furthermore, reconfigurability enables the introduction of new techniques for PUF testing. The effectiveness of all the proposed techniques is validated using extensive implementations, simulations, and statistical analysis.
Defining defects, errors, and service degradations
Authors: Levine Gertrude Neuman 
Published: April 2009

The study of defects is a principal topic of software systems, af-fecting all phases of a system's lifecycle. Defects are the cause of errors and service degradations. Unresolved errors cause failures. If defects cannot be prevented effectively, then error control me-chanisms must be evaluated.
We introduce a model to distinguish between defects, errors, and service degradations. A two-dimensional classification scheme is developed for defects, defined by the types of process interaction and software corruption that are involved. A third dimension is added to this taxonomy for defects that cause service degradation, based on the deviations in service quality that are tolerated. We investigate the role of service degradation in error prevention.
Memory-level parallelism aware fetch policies for simultaneous multithreading processors
Authors: Eyerman Stijn , Eeckhout Lieven 
Published: April 2009

A thread executing on a simultaneous multithreading (SMT) processor that experiences a long-latency load will eventually stall while holding execution resources. Existing long-latency load aware SMT fetch policies limit the amount of resources allocated by a stalled thread by identifying long-latency loads and preventing the thread from fetching more instructions—and in some implementations, instructions beyond the long-latency load are flushed to release allocated resources.
This article proposes an SMT fetch policy that takes into account the available memory-level parallelism (MLP) in a thread. The key idea proposed in this article is that in case of an isolated long-latency load (i.e., there is no MLP), the thread should be prevented from allocating additional resources. However, in case multiple independent long-latency loads overlap (i.e., there is MLP), the thread should allocate as many resources as needed in order to fully expose the available MLP. MLP-aware fetch policies achieve better performance for MLP-intensive threads on SMT processors, leading to higher overall system throughput and shorter average turnaround time than previously proposed fetch policies.