bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parameterized evaluation of macromolecules and lipids in proton MR spectroscopy of brain diseases
Authors: Seeger Uwe , Klose Uwe , Mader Irina , Grodd Wolfgang , Nägele Thomas 
Published: January 2003

AbstractShort echo time (TE) proton MR spectra of the brain include signals of several metabolites as well as macromolecules. In various pathologies, such as brain tumors and multiple sclerosis (MS), the presence of mobile lipids or pathologically altered macromolecules may provide useful additional diagnostic information. A reliable quantitation of these resonances, however, is often not possible due to the lack of adequate prior knowledge. Furthermore, even if advanced fitting procedures are used, a reliable evaluation of metabolites in the presence of pathological lipids or macromolecules often fails if the latter are omitted in the spectral evaluation. In this study, a method is presented for the simultaneous evaluation of all visible components, including metabolites, lipids, and macromolecules, by the use of the fitting procedure LCModel. A standard basis set of brain metabolites was extended by inclusion of parameterized components for macromolecules and lipids that were derived from metabolite‐nulled in vivo spectra of normal brain and high‐grade gliomas, respectively. The improved spectral quantitation is demonstrated in glial brain tumors and MS lesions as well as in normal brain. It is pointed out that both macromolecules and lipids must be included to provide a proper spectral evaluation. Magn Reson Med 49:19–28, 2003. © 2003 Wiley‐Liss, Inc.
Sonography in the diagnosis of carpal tunnel syndrome: A critical review of the literature
Authors: Beekman Roy , Visser Leo H. 
Published: January 2003

AbstractAdvances in ultrasound technology have made it possible to gain higher spatial resolution and even depict nerves with excellent visual quality. In this article, the literature concerning sonography in the diagnosis of carpal tunnel syndrome (CTS) is critically reviewed. We searched Medline for studies on sonography in the diagnosis of CTS and used the reference lists of the articles found. A total of seven studies on the diagnostic capabilities of sonography was found. There were considerable differences in study design. A reliable diagnosis of CTS could be made sonographically, mainly based on an increase in cross‐sectional area of the median nerve at the level of the pisiform or hamate bone. However, most studies could not compare the diagnostic capabilities of sonography to those of electrodiagnostic studies, because the latter was applied as the gold standard. Several other reports on the possible extra value of sonography in CTS are mentioned (mass lesions, anatomical variants, rheumatological diseases, renal dialysis–related amyloidosis, surgery, corticosteroid injection). It is probable that sonography will not replace electrodiagnostic studies, but may serve as an additional investigation. To gain further insight into the possible additional value of sonography, it is necessary to examine subcategories of CTS patients in which electrodiagnostic studies are equivocal. © 2002 Wiley Periodicals, Inc. Muscle Nerve 27: 26–33, 2003
tmRNA Is Required for Correct Timing of DNA Replication in
Caulobacter crescentus
Authors: Keiler Kenneth C. , Shapiro Lucy 
Published: January 2003

ABSTRACT

SsrA, or tmRNA, is a small RNA that interacts with selected translating ribosomes to target the nascent polypeptides for degradation. Here we report that SsrA activity is required for normal timing of the G
1
-to-S transition in
Caulobacter crescentus
. A deletion of the
ssrA
gene, or of the gene encoding SmpB, a protein required for SsrA activity, results in a specific delay in the cell cycle during the G
1
-to-S transition. The
ssrA
deletion phenotype is not due to accumulation of stalled ribosomes, because the deletion is not complemented by a mutated version of SsrA that releases ribosomes but does not target proteins for degradation. Degradation of the CtrA response regulator normally coincides with initiation of DNA replication, but in strains lacking SsrA activity there is a 40-min delay between the degradation of CtrA and replication initiation. This uncoupling of initiation of replication from CtrA degradation indicates that there is an SsrA-dependent pathway required for correct timing of DNA replication.
φ29 Family of Phages
Authors: Meijer Wilfried J. J. , Horcajadas José A. , Salas Margarita 
Published: January 2003

SUMMARY
Continuous research spanning more than three decades has made the Bacillus bacteriophage φ29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage φ29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5′ ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to φ29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5′ ends. These φ29-like phages can be divided into three groups. The first group includes, in addition to φ29, phages PZA, φ15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of φ29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of φ29-like phages, which is included in this review.
AspergillusEnzymes Involved in Degradation of Plant Cell Wall Polysaccharides
Authors: de Vries Ronald P. , Visser Jaap 
Published: January 2003

SUMMARYDegradation of plant cell wall polysaccharides is of major importance in the food and feed, beverage, textile, and paper and pulp industries, as well as in several other industrial production processes. Enzymatic degradation of these polymers has received attention for many years and is becoming a more and more attractive alternative to chemical and mechanical processes. Over the past 15 years, much progress has been made in elucidating the structural characteristics of these polysaccharides and in characterizing the enzymes involved in their degradation and the genes of biotechnologically relevant microorganisms encoding these enzymes. The members of the fungal genus Aspergillus are commonly used for the production of polysaccharide-degrading enzymes. This genus produces a wide spectrum of cell wall-degrading enzymes, allowing not only complete degradation of the polysaccharides but also tailored modifications by using specific enzymes purified from these fungi. This review summarizes our current knowledge of the cell wall polysaccharide-degrading enzymes from aspergilli and the genes by which they are encoded.
Biodegradation of Aromatic Compounds by
Escherichia coli
Authors: Dı́az Eduardo , Ferrández Abel , Prieto Marı́a A. , Garcı́a José L. 
Published: January 2003

SUMMARY
Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications.
Actin-Based Motility of Intracellular Microbial Pathogens
Authors: Goldberg Marcia B. 
Published: January 2003

SUMMARYA diverse group of intracellular microorganisms, including Listeria monocytogenes, Shigella spp., Rickettsia spp., and vaccinia virus, utilize actin-based motility to move within and spread between mammalian host cells. These organisms have in common a pathogenic life cycle that involves a stage within the cytoplasm of mammalian host cells. Within the cytoplasm of host cells, these organisms activate components of the cellular actin assembly machinery to induce the formation of actin tails on the microbial surface. The assembly of these actin tails provides force that propels the organisms through the cell cytoplasm to the cell periphery or into adjacent cells. Each of these organisms utilizes preexisting mammalian pathways of actin rearrangement to induce its own actin-based motility. Particularly remarkable is that while all of these microbes use the same or overlapping pathways, each intercepts the pathway at a different step. In addition, the microbial molecules involved are each distinctly different from the others. Taken together, these observations suggest that each of these microbes separately and convergently evolved a mechanism to utilize the cellular actin assembly machinery. The current understanding of the molecular mechanisms of microbial actin-based motility is the subject of this review.
Molecular Biologist's Guide to Proteomics
Authors: Graves Paul R. , Haystead Timothy A. J. 
Published: January 2003

SUMMARYThe emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems.
Transactivation Functions of the N-Terminal Domains of Nuclear Hormone Receptors: Protein Folding and Coactivator Interactions
Authors: Kumar Raj , Thompson E. Brad 
Published: January 2003

AbstractThe N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.
Features of
Rhodobacter sphaeroides
CcmFH
Authors: Rios-Velazquez Carlos , Coller Ryan , Donohue Timothy J. 
Published: January 2003

ABSTRACT

In this study, the in vivo function and properties of two cytochrome
c
maturation proteins, CcmF and CcmH from
Rhodobacter sphaeroides
, were analyzed. Strains lacking CcmH or both CcmF and CcmH are unable to grow under anaerobic conditions where
c
-type cytochromes are required, demonstrating their critical role in the assembly of these electron carriers. Consistent with this observation, strains lacking both CcmF and CcmH are deficient in
c
-type cytochromes when assayed under permissive growth conditions. In contrast, under permissive growth conditions, strains lacking only CcmH contain several soluble and membrane-bound
c
-type cytochromes, albeit at reduced levels, suggesting that this bacterium has a CcmH-independent route for their maturation. In addition, the function of CcmH that is needed to support anaerobic growth can be replaced by adding cysteine or cystine to growth media. The ability of exogenous thiol compounds to replace CcmH provides the first physiological evidence for a role of this protein in thiol chemistry during
c
-type cytochrome maturation. The properties of
R. sphaeroides
cells containing translational fusions between CcmF and CcmH and either
Escherichia coli
alkaline phosphatase or β-galactosidase suggest that they are each integral cytoplasmic membrane proteins with their presumed catalytic domains facing the periplasm. Analysis of CcmH shows that it is synthesized as a higher-molecular-weight precursor protein with an N-terminal signal sequence.
Transcriptional Analysis of the
sfa
Determinant Revealing Multiple mRNA Processing Events in the Biogenesis of S Fimbriae in Pathogenic
Escherichia coli
Authors: Balsalobre Carlos , Morschhäuser Joachim , Jass Jana , Hacker Jörg , Uhlin Bernt Eric 
Published: January 2003

ABSTRACT

Among the virulence factors present in pathogenic extraintestinal
Escherichia coli
strains, expression of fimbrial adhesins is necessary for attachment to the host tissues and subsequent colonization. Occurrence of the
sfa
determinant coding for the S fimbriae is widespread among the uropathogens and meningitis isolates. The
sfa
operon consists of nine genes. In the biogenesis of S fimbriae, the proteins encoded by the
sfa
genes are presumably required in a specific stoichiometry. In the present work we studied how differential expression of the
sfa
operon genes occurs. Our findings indicate that a number of endoribonucleolytic cleavages occur in the mRNA from the
sfa
operon, and we detected the presence of different distinct transcriptional products, including
sfaBA
,
sfaA
,
sfaADE
, and
sfaGSH
. The
sfaGSH
transcript represents the three distal genes of the
sfa
operon, which code for the minor subunits of the S fimbriae. Analysis of the proteins in S fimbriae suggested that expression of the
sfaGSH
transcript provides equimolar amounts of the minor subunits. Furthermore, we showed that in the generation of the major
sfaA
transcript, the processing included RNase E endoribonuceolytic cleavage of the precursor
sfaBA
transcript. We suggest that posttranscriptional mRNA processing events result in differential gene expression important to achieve the stoichiometry necessary for fimbrial adhesin biogenesis.
Novel Methylotrophy Genes of
Methylobacterium extorquens
AM1 Identified by using Transposon Mutagenesis Including a Putative Dihydromethanopterin Reductase
Authors: Marx Christopher J. , O'Brien Brooke N. , Breezee Jennifer , Lidstrom Mary E. 
Published: January 2003

ABSTRACT

Ten novel methylotrophy genes of the facultative methylotroph
Methylobacterium extorquens
AM1 were identified from a transposon mutagenesis screen. One of these genes encodes a product having identity with dihydrofolate reductase (DHFR). This mutant has a C
1
-defective and methanol-sensitive phenotype that has previously only been observed for strains defective in tetrahydromethanopterin (H
4
MPT)-dependent formaldehyde oxidation. These results suggest that this gene,
dmrA
, may encode dihydromethanopterin reductase, an activity analogous to that of DHFR that is required for the final step of H
4
MPT biosynthesis.
Experimental Verification of a Sequence-Based Prediction: F
1
F
0
-Type ATPase of
Vibrio cholerae
Transports Protons, Not Na
+
Ions
Authors: Dzioba Judith , Häse Claudia C. , Gosink Khoosheh , Galperin Michael Y. , Dibrov Pavel 
Published: January 2003

ABSTRACT

The membrane energetics of the intestinal pathogen
Vibrio cholerae
involves both H
+
and Na
+
as coupling ions. The sequence of the c subunit of
V. cholerae
F
0
F
1
ATPase suggested that this enzyme is H
+
specific, in contrast to the results of previous studies on the Na
+
-dependent ATP synthesis in closely related
Vibrio
spp. Measurements of the pH gradient and membrane potential in membrane vesicles isolated from wild-type and Δ
atpE
mutant
V. cholerae
show that the F
1
F
0
ATPase of
V. cholerae
is an H
+
, not Na
+
, pump, confirming the bioinformatics assignments that were based on the Na
+
-binding model of S. Rahlfs and V. Müller (FEBS Lett.
404:
269-271, 1999). Application of this model to the AtpE sequences from other bacteria and archaea indicates that Na
+
-specific F
1
F
0
ATPases are present in a number of important bacterial pathogens.
Identification of MpaA, an Amidase in
Escherichia coli
That Hydrolyzes the γ-
d
-Glutamyl-
meso-
Diaminopimelate Bond in Murein Peptides
Authors: Uehara Tsuyoshi , Park James T. 
Published: January 2003

ABSTRACT

MpaA amidase was identified in
Escherichia coli
by its amino acid sequence homology with the ENP1 endopeptidase from
Bacillus sphaericus
. The enzymatic activity of MpaA, i.e., hydrolysis of the γ-
d
-glutamyl-diaminopimelic acid bond in the murein tripeptide
l
-alanyl-γ-
d
-glutamyl-
meso
-diaminopimelic acid, was demonstrated in the cell extract of a strain expressing
mpaA
from a multicopy plasmid. An
mpaA mpl
(murein peptide ligase) double mutant accumulated large amounts of murein tripeptide in its cytoplasm, consistent with the premise that MpaA degrades the tripeptide if its recycling via the peptidoglycan biosynthetic pathway is blocked.
Polar Targeting of DivIVA in
Bacillus subtilis
Is Not Directly Dependent on FtsZ or PBP 2B
Authors: Hamoen Leendert W. , Errington Jeffery 
Published: January 2003

ABSTRACT

DivIVA is involved in
Bacillus subtilis
cell division and is located at the cell poles. Previous experiments suggested that the cell division proteins FtsZ and PBP 2B are required for polar targeting of DivIVA. By using outgrowing spores, we show that DivIVA accumulates at the cell poles independent of the presence of FtsZ or PBP 2B.
Molecular Pathways in Virus-Induced Cytokine Production
Authors: Mogensen Trine H. , Paludan Søren R. 
Published: January 2003

SUMMARYVirus infections induce a proinflammatory response including expression of cytokines and chemokines. The subsequent leukocyte recruitment and antiviral effector functions contribute to the first line of defense against viruses. The molecular virus-cell interactions initiating these events have been studied intensively, and it appears that viral surface glycoproteins, double-stranded RNA, and intracellular viral proteins all have the capacity to activate signal transduction pathways leading to the expression of cytokines and chemokines. The signaling pathways activated by viral infections include the major proinflammatory pathways, with the transcription factor NF-κB having received special attention. These transcription factors in turn promote the expression of specific inducible host proteins and participate in the expression of some viral genes. Here we review the current knowledge of virus-induced signal transduction by seven human pathogenic viruses and the most widely used experimental models for viral infections. The molecular mechanisms of virus-induced expression of cytokines and chemokines is also analyzed.