bluuebunny/crossref_metadata_2025 huggingface dataset:
φ29 Family of Phages
Authors: Meijer Wilfried J. J. , Horcajadas José A. , Salas Margarita
Published: January 2003

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

Degradation 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

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

A 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

The 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.
ROBUSTNESS OF ADAPTATION IN CONTROLLED SELF-ADJUSTING CHAOTIC SYSTEMS
Authors: MELBY PAUL , WEBER NICHOLAS , HÜBLER ALFRED
Published: January 2003

It was recently shown that self-adjusting systems adapt to the edge of chaos. We study the robustness of that adaptation with respect to a controlling force. We first use numerical simulations in a modified logistic map. With these, we find that, if the controlling force has a target value of the parameter that leads to periodic dynamics, the control is successful, even for very small controlling forces. We also find, however, that if the target value for the parameter leads to chaotic dynamics, the parameter resists the control and adaptation to the edge of chaos is still observed. When the controlling force is very strong, adaptation to the edge of chaos is weaker, but still present in the system. We also perform experiments with a self-adjusting Chua circuit and find the same behavior. We quantify these results with a measurement of the robustness of the adaptation as a function of the strength of the controlling force. The control used can be expressed either as a parametric control or as an additive, closed-loop control.
COMPUTER INVESTIGATION INTO THE ANATOMICAL LOCATION OF THE AXES OF ROTATION IN THE KNEE
Authors: MARTELLI S. , VISANI A.
Published: January 2003

The purpose of this paper was to investigate the anatomical location of the main axes of rotation of the knee, that is the axes of flexion-extension and longitudinal rotation. We compared 4 hypotheses on the correlation between the axis of flexion-extension and the femoral anatomy and 4 hypotheses on the correlation between the axis of longitudinal rotation and the tibial anatomy in 6 normal human knees. The methods used for the study were:. digitization by an electrogoniometer; computer reconstruction of motion and bone geometry, and an original geometrical interpolation to identify axes location. Our results suggest that: (a) the axis of flexion-extension lies in a cone spanned by the transepicondylar line and the so called FFc line;19(b) the axis of longitudinal rotation can be represented by a line parallel to the tibial anatomical axis intersecting the flexion axis in a fixed point of the medial compartment.
HISTORY DEPENDENCE OF SKELETAL MUSCLE FORCE PRODUCTION: A FORGOTTEN PROPERTY
Authors: HERZOG W. , RASSIER D. E.
Published: January 2003

Steady-state force enhancement following active muscle stretching has been observed for well over fifty years, and is a widely accepted property of skeletal muscle contraction. Force enhancement has typically been associated with instability of sarcomere length on the descending limb of the force-length relationship. Here, we demonstrate that the sarcomere length non-uniformity paradigm, based on instability, cannot explain much of the newly discovered results. We provide evidence that force enhancement can occur on the stable ascending limb of the force-length relationship, that force enhancement can exceed the isometric tetanic plateau forces, that it is associated with an increased passive force, and that it occurs for perfectly stable sarcomere lengths on the descending limb of the force-length relationship. Combining all the results, we conclude that force enhancement has at least two components, an active and a passive component, that contribute towards the total force enhancement to varying degrees, depending on the contractile history of muscle contraction.
ON THE COMPLEXITY OF BIOMECHANICAL MODELS USED FOR NEUROPROSTHESES DEVELOPMENT
Authors: RIENER ROBERT , FUHR THOMAS , SCHNEIDER JOHANNES
Published: January 2003

The use of mathematical models has the potential to enhance the development of lower extremity neuroprostheses (NP) based on Functional Electrical Simulation (FES). The choice of model complexity is not trivial when building a model for FES control design. On the one hand, a comprehensive model might be useful to account for the many different biomechanical and neurophysiological effects that can be observed during FES-induced movements. On the other hand, too complex models are difficult to be utilized in and identified for NP applications. In this paper we discuss the disadvantages of too complex models, and propose potential simplifications on the basis of existing models that are commonly used to describe muscle activation, muscle contraction and body-segmental motion. The obtained model approach is simple enough to be identified, and sufficiently comprehensive to describe most of the relevant effects that occur during FES-induced locomotion.
Invited Commentary on Training for approval under Section 12(2). Ethics and implications of assessments
Authors: Zigmond Tony
Published: January 2003

Now that training under Section 12 (Section 20 in Scotland) of the Mental Health Act 1983 is mandatory under the NHS Executive Guidelines HSG (96) 3 (1996) both prior to and while maintaining approval, discussion of the educational objectives and how to achieve them is overdue. The article by Brown & Humphreys (2003, this issue) is a welcome introduction to the debate. Given that psychiatrists may move between different legal jurisdictions and that there is a constant stream of new and relevant case law (not to mention that we may soon have a new Mental Health Act), it is clearly important that training is about principles, issues and asking questions rather than a didactic teaching of facts. One must consider what are the relevant issues.
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

The 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.
Local structure in molecular complexes probed by multiple-scattering XAS
Authors: Di Cicco Andrea
Published: January 2003

The GNXAS (n-body distribution function X-ray absorption spectroscopy) method for multiple-scattering (MS) data analysis of EXAFS (extended X-ray absorption fine structure) data and the results recently obtained on molecular complexes relevant to biological matter are briefly reviewed and discussed. Practical MS calculations for important molecular fragments like Fe—O—O and Fe—C—N—Cu are presented in detail showing the potential of the techniques for measuring bond-angle distributions. The optimal conditions for obtaining accurate structural refinements using EXAFS measurements and modern data-analysis schemes are discussed as well as the current perspectives in the exploitation of the technique.
New developments in the theory and interpretation of X-ray spectra based on fast parallel calculations
Authors: Rehr J. J. , Ankudinov A. L.
Published: January 2003

There has been dramatic progress over the past decade both in theory and inab initiocalculations of X-ray absorption fine structure. Significant progress has also been made in understanding X-ray absorption near-edge structure (XANES). This contribution briefly reviews the developments in this field leading up to the current state. One of the key advances has been the development of severalab initiocodes such asFEFF, which permit an interpretation of the spectra in terms of geometrical and electronic properties of a material. Despite this progress, XANES calculations have remained challenging both to compute and to interpret. However, recent advances based on parallel Lanczos multiple-scattering algorithms have led to speed increases of typically two orders of magnitude, making fast calculations practicable. Improvements in the interpretation of near-edge structure have also been made. It is suggested that these developments can be advantageous in structural biology,e.g.in post-genomics studies of metalloproteins.
An overview of the CCP4 project in protein crystallography: an example of a collaborative project
Authors: Winn M. D.
Published: January 2003

The Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. CCP4 now distributes a large software suite and is active in developing new software. Equally importantly, CCP4 provides a focus for the whole protein crystallography communityviameetings, workshops, email lists and various publications. In this article, an overview is given of CCP4 activities and their administration. The emphasis is on generic features of the collaboration rather than details specific to protein crystallography. The CCP4 model has inspired similar developments in NMR, and it is hoped that the biological XAS community may pursue similar collaboration.
X-ray absorption spectroscopy of low-molar-mass metallic complexes in pharmacy
Authors: Nicolis Ioannis , Curis Emmanuel , Deschamps Patrick , Bénazeth Simone
Published: January 2003

X-ray absorption spectroscopy provides valuable information on metallic speciation and so has a wide range of applications in bioinorganic systems. In this paper, low-molar-mass metallic complexes as used in pharmaceutical science are focused on. The results of structural studies on metal-based drugs applied as disease treatments, nutritional supplements or tools for diagnostic methods are presented. Then metal speciation (spatial and chemical distribution) in biological samples through micro-XANES imaging experiments are dealt with. Problems arising from the analysis of noisy data collected from these diluted samples are discussed.
A structural genomics initiative on yeast proteins
Authors: Quevillon-Cheruel Sophie , Collinet Bruno , Zhou Cong-Zhao , Minard Philippe , Blondeau Karine , Henkes Gilles , Aufrère Robert , Coutant Jérôme , Guittet Eric , Lewit-Bentley Anita , Leulliot Nicolas , Ascone Isabella , Sorel Isabelle , Savarin Philippe , de La Sierra Gallay Ines Li , de la Torre Françoise , Poupon Anne , Fourme Roger , Janin Joël , van Tilbeurgh Herman
Published: January 2003

A canonical structural genomics programme is being conducted at the Paris-Sud campus area on baker's yeast proteins. Experimental strategies, first results and identified bottlenecks are presented. The actual or potential contributions to the structural genomics of several experimental structure-determination methods are discussed.
Introductory overview: X-ray absorption spectroscopy and structural genomics
Authors: Ascone Isabella , Fourme Roger , Hasnain S. Samar
Published: January 2003

A special issue of the journal is presented, dedicated to biological applications of X-ray absorption spectroscopy (BioXAS) and examining the role of this technique in post-genomic biology. The issue confirms that BioXAS has come of age and it can be expected to make a significant contribution in the structural genomics effort on metalloproteins, which are estimated to make up about 30% of proteins coded by genomes.
Isolation and Structure of Higher Diamondoids, Nanometer-Sized Diamond Molecules
Authors: Dahl J. E. , Liu S. G. , Carlson R. M. K.
Published: January 2003

We exploited the exceptional thermal stability and diverse molecular shapes of higher diamondoids (C
22
and higher polymantanes) to isolate them from petroleum. Molecules containing 4 to 11 diamond-crystal cages were isolated and crystallized, and we obtained single-crystal x-ray structures for representatives from three families. Rigidity, strength, remarkable assortments of three- dimensional shapes, including resolvable chiral forms, and multiple, readily derivatizable attachment sites make them valuable nanometer-size molecular building blocks.
Dependence of Upper Critical Field and Pairing Strength on Doping in Cuprates
Authors: Wang Yayu , Ono S. , Onose Y. , Gu G. , Ando Yoichi , Tokura Y. , Uchida S. , Ong N. P.
Published: January 2003

We have determined the upper critical field
H
c2
as a function of hole concentration in bismuth-based cuprates by measuring the voltage induced by vortex flow in a driving temperature gradient (the Nernst effect), in magnetic fields up to 45 tesla. We found that
H
c2
decreased steeply as doping increased, in both single and bilayer cuprates. This relationship implies that the Cooper pairing potential displays a trend opposite to that of the superfluid density versus doping. The coherence length of the pairs ξ
0
closely tracks the gap measured by photoemission. We discuss implications for understanding the doping dependence of the critical temperature
T
c0
.
The Pull of Weird Horizons
Authors: Zajc W. A.
Published: January 2003

Strange Matters
. Undiscovered Ideas at the Frontiers of Space and Time. Tom Siegfried. Joseph Henry Press (National Academy Press), Washington, DC, 2002. 317 pp. $24.95, C$34.95. ISBN 0-309-08407-5.

In this discussion of "dark matter" and the reconciliation of Einstein's theory of gravity with quantum mechanics, science journalist Siegfried blends accounts of active research with summaries of the historical paths that have led to it.
Genetic Evidence for Local Retention of Pelagic Larvae in a Caribbean Reef Fish
Authors: Taylor Michael S. , Hellberg Michael E.
Published: January 2003

The pelagic larvae of many marine organisms can potentially disperse across hundreds of kilometers, but whether oceanographic or behavioral mechanisms can constrain dispersal over periods sufficient for the evolution of genetic differentiation remains unclear. Here, we concurrently examine larval duration and genetic population differentiation in a cleaner goby,
Elacatinus evelynae
, a member of the most species-rich genus of Caribbean reef fishes. Despite evidence for extended pelagic duration (21 days), populations of
E. evelynae
show strong genetic differentiation: among color forms (1.36 to 3.04% divergent at mitochondrial cytochrome b) and among island populations within color forms (Φ
ST
up to 70%). These results suggest that marine populations can remain demographically closed for thousands of generations despite extended larval duration, and that recognition cues such as color may promote speciation when geographic barriers are transient or weak.
Features of
Rhodobacter sphaeroides
CcmFH
Authors: Rios-Velazquez Carlos , Coller Ryan , Donohue Timothy J.
Published: January 2003

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

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

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

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

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

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

Virus 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.
Genome of the Extremely Radiation-Resistant Bacterium
Deinococcus radiodurans
Viewed from the Perspective of Comparative Genomics
Authors: Makarova Kira S. , Aravind L. , Wolf Yuri I. , Tatusov Roman L. , Minton Kenneth W. , Koonin Eugene V. , Daly Michael J.
Published: January 2003

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.
Cytokinesis in Prokaryotes and Eukaryotes: Common Principles and Different Solutions
Authors: Nanninga Nanne
Published: January 2003

Cytokinesis requires duplication of cellular structures followed by bipolarization of the predivisional cell. As a common principle, this applies to prokaryotes as well as eukaryotes. With respect to eukaryotes, the discussion has focused mainly on Saccharomyces cerevisiae and on Schizosaccharomyces pombe. Escherichia coli and to a lesser extent Bacillus subtilis have been used as prokaryotic examples. To establish a bipolar cell, duplication of a eukaryotic origin of DNA replication as well as its genome is not sufficient. Duplication of the microtubule-organizing center is required as a prelude to mitosis, and it is here that the dynamic cytoskeleton with all its associated proteins comes to the fore. In prokaryotes, a cytoskeleton that pervades the cytoplasm appears to be absent. DNA replication and the concomitant DNA segregation seem to occur without help from extensive cytosolic supramacromolecular assemblies but with help from the elongating cellular envelope. Prokaryotic cytokinesis proceeds through a contracting ring, which has a roughly 100-fold-smaller circumference than its eukaryotic counterpart. Although the ring contains proteins that can be considered as predecessors of actin, tubulin, and microtubule-associated proteins, its macromolecular composition is essentially different.
Cytoskeleton of Apicomplexan Parasites
Authors: Morrissette Naomi S. , Sibley L. David
Published: January 2003

The Apicomplexa are a phylum of diverse obligate intracellular parasites including Plasmodium spp., the cause of malaria; Toxoplasma gondii and Cryptosporidium parvum, opportunistic pathogens of immunocompromised individuals; and Eimeria spp. and Theileria spp., parasites of considerable agricultural importance. These protozoan parasites share distinctive morphological features, cytoskeletal organization, and modes of replication, motility, and invasion. This review summarizes our current understanding of the cytoskeletal elements, the properties of cytoskeletal proteins, and the role of the cytoskeleton in polarity, motility, invasion, and replication. We discuss the unusual properties of actin and myosin in the Apicomplexa, the highly stereotyped microtubule populations in apicomplexans, and a network of recently discovered novel intermediate filament-like elements in these parasites.
INTRA-, EXTRA- AND INTERMUSCULAR MYOFASCIAL FORCE TRANSMISION OF SYNERGISTS AND ANTAGONISTS: EFFECTS OF MUSCLE LENGTH AS WELL AS RELATIVE POSITION
Authors: HUIJING PETER A.
Published: January 2003

The concepts of intramuscular myofascial force transmission is reintroduced and reviewed on the basis of experiments involving tenotomy and aponeurotomy of dissected rat EDL muscle studied in situ. Results from experiments with measurements of force of EDL muscle, of which the muscle belly was not dissected (i.e. the muscle is surrounded by its natural connective tissue milieu) are discussed. In such experiments, force was measured at proximal as well as distal EDL tendons. Examples of experimental evidence for both extramuscular and intermuscular myofascial force transmission within the rat anterior crural compartment are presented. Evidence is presented also for differential effects of proximal and distal lengthening on myofascial force transmission from EDL, even for the case in which symmetric length changes were imposed on the muscle. It is shown that myofascial force transmission effects are not limited to synergists located within one compartment, but do also play a very substantial role in the interaction between antagonist muscles in neighbouring anterior crural and peroneal compartments.
DYNAMIC MECHANICAL PROPERTIES OF ARTERIAL AND VENOUS GRAFTS USED IN CORONARY BYPASS SURGERY
Authors: MAVRILAS DIMOSTHENIS , TSAPIKOUNI THEODORA , MIKROULIS DIMITRIOS , BITZIKAS GRIGORIOS , DIDILIS VASSILIOS , TSAKIRIDIS KOSMAS , KONSTANTINOU FOTIS , BOUGIOUKAS GEORGIOS
Published: January 2003

In this work we studied the frequency dependence of the dynamic mechanical characteristic s of saphenous vein (SV) and internal mammary artery (IMA) grafts. Rectangular longitudinal strips from 14 patients were tested under cyclic uniaxial tensile loading in the frequency range of 0.1–20 Hz, at 37°C in wet conditions. The dynamic mechanical parameters (the storage modulus ES and the hysteresis ratio h (loading/loop area)) together with the collagen phase modulus EH were computed as a function of frequency. The results showed that in all graft types ES and EH varied with frequency in the range 0.5–10 Hz, presenting a maximum in the neighboring of 1 Hz. The hysteresis ratio h was increased in the frequency range 1–20 Hz. It seems from the results that the physical resonance frequency of the components of the tissue responsible for their elastic behavior may lay in the range around 1 Hz, while that for the viscous behavior in the range of 20 Hz or more. Early clinical outcomes of both grafting were studied in parallel. In a one-year postoperative period the follow-up (clinical examination, electrocardiography, echocardiography and stress test) did not reveal any sign of graft occlusion or severe stenosis except one perioperative infraction but without any correlation to the graft quality.
A Randomized, Controlled Double‐blind Trial of Usual‐dose versus High‐dose Albuterol via Continuous Nebulization in Patients with Acute Bronchospasm
Authors: Stein John , Levitt M. Andrew
Published: January 2003

Objective: Continuous nebulization is becoming more popular in the management of acute bronchospasm in the emergency department (ED). Controversy still exists as to the optimal dose of albuterol for such exacerbations. The present study hypothesis was that there is no difference between continuous nebulization of albuterol at 7.5 mg/hr (usual dose) and 15 mg/hr (high dose) in peak flow improvement up to three hours. Methods: This was a randomized, controlled, double‐blind trial, set in an urban county teaching ED. One hundred twenty‐seven patients with acute bronchospasm and an initial peak flow (PF) less than 75% predicted were enrolled. Patients were randomized to usual‐dose (UD) or high‐dose (HD) groups along with a standard treatment protocol. Primary end‐points were analyzed using repeated‐measures analysis of variance (ANOVA), and 95% confidence intervals (95% CIs) are given for such variables. Results: Sixty‐seven patients were randomized to the HD albuterol group, and 63 completed the study. Sixty patients were randomized to the UD group, and 55 completed the study. Repeated‐measures ANOVA found no difference in systolic blood pressure, diastolic blood pressure, pulse, respiratory rate, Borg dyspnea scale score, and peak flow over time between the groups. The mean (±SD) peak flow improvement at one hour was UD 51 (±49) L/min vs. HD 45 (±50) L/min, mean difference 6.8 L/min (95% CI = ‐11 to 24.9 L/min). Adjusting for baseline, the percentage increase in peak flow at one hour was UD 44% (±60%) vs. HD 30% (±40%), mean difference 14% (95% CI = ‐4.4% to 32.4%). Time to disposition showed a mean of 188 (±129) minutes for UD and 230 (±183) minutes for HD, mean difference 42 minutes (95% CI = ‐170 to 101 min). One patient in the HD group was intubated. Admission rate was UD 70.9% vs. HD 65%, mean difference 5.9% (95% CI = ‐10.9% to 22.7%). Conclusions: In treating acute, moderately‐severe bronchospastic ED patients with peak flow less than 75% of predicted with albuterol by continuous nebulization, 15 mg/hr appears to offer no advantage over 7.5 mg/hr in peak flow improvement or length of stay in the ED.
Predictors of Emergency Medical Services Utilization by Elders
Authors: Shah Manish N. , Glushak Cai , Karrison Theodore G. , Mulliken Robert , Walter James , Friedmann Peter D. , Hayley Deon Cox , Chin Marshall H.
Published: January 2003

Objective: Elders (age ≥ 65 years) frequently use emergency medical services (EMS) for care. Understanding reasons for EMS use by elders may allow better management of EMS demand. To the best of the authors' knowledge, no studies have identified patient characteristics associated with EMS use by elders. This study aimed to identify patient attributes associated with elder EMS users. Methods: This was a prospective cohort study of non‐institutionalized elders presenting to an urban university hospital emergency department. Nine hundred thirty elder patients completed the survey. The authors asked patients about access to care, health beliefs, and reasons for requesting EMS assistance. Univariate and logistic regression were used to identify predictors of EMS use. Results: The sample had a mean age of 76 years; 37% were male; 79% were African American. Thirty percent arrived via EMS. Sixty‐five percent of those transported and 46% of those not transported by EMS were admitted to the hospital (p < 0.001). Reported reasons for using EMS transport included immobility (33%), illness (22%), request by others (21%), instruction from health care providers (10%), and lack of transportation (10%). Logistic regression identified symptom onset within four hours of seeking care (OR = 3.1), age ≥ 85 years (OR = 1.63), increased deficiencies in activities of daily living (OR = 1.40 per deficiency), worse physical functioning (OR = 1.14/10 points), and worse social functioning (OR = 1.06/10 points) as factors associated with EMS use. Conclusions: Elders report using EMS because of immobility, perceived medical needs, or requests by others. Similarly, the presence of acute illness symptoms, older age, and poor social and physical function, rather than health beliefs, predict EMS use among elders. These factors must be considered when managing the demand for EMS services.
Patient Safety: A Curriculum for Teaching Patient Safety in Emergency Medicine
Authors: Cosby Karen S. , Croskerry Pat
Published: January 2003

The last decade has witnessed a growing awareness of medical error and the inadequacies of our health care delivery systems. The Harvard Practice Study and subsequent Institute of Medicine Reports brought national attention to long‐overlooked problems with health care quality and patient safety. The Committee on Quality of Health Care in America challenged professional societies to develop curriculums on patient safety and adopt patient safety teaching into their training and certification requirements. The Patient Safety Task Force of the Society for Academic Emergency Medicine (SAEM) was charged with that mission. The curriculum presented here offers an approach to teaching patient safety in emergency medicine.
Emergency Department Services for Patients with Alcohol Problems: Research Directions
Authors: Hungerford Daniel W. , Pollock Daniel A.
Published: January 2003

This report summarizes recommendations on research directions developed from the conference “Alcohol Problems among Emergency Department Patients: Research on Identification and Intervention.” The conference was developed in order to evaluate the existing state of the art research on emergency department interventions for alcohol problems, and offer further recommendations for research.
Emergency Bedside Ultrasound to Detect Pneumothorax
Authors: Chan Stewart Siu Wa
Published: January 2003

A relatively new application of emergency ultrasound is its use in the diagnosis of pneumothorax. In patients with major trauma, early detection and treatment of pneumothorax are vital. Chest radiography in these patients is limited to anteroposterior (AP) supine films, in which radiographic features of pneumothorax may be quite subtle. Hence, rapid and accurate bedside ultrasonography can expedite resuscitation. Sonographic features of pneumothorax have been identified in a number of studies. The technique involves identification of the pleural line and observation for features such as “lung sliding” and comet‐tail artifacts, which are absent in pneumothorax. Based on a review of the literature, the author describes these features and discusses the utility of emergency ultrasound in detecting pneumothorax.
XAS of dilute biological samples
Authors: Ranieri-Raggi Maria , Raggi Antonio , Martini Daniela , Benvenuti Manuela , Mangani Stefano
Published: January 2003

The experimental setup of beamline ID26 at ESRF (Grenoble) has been successfully exploited to obtain high-quality XAS (X-ray absorption spectroscopy) data from a biological sample where the metal concentration is about 100 µM. The sample consists of the adenosine monophosphate deaminase (AMPD) histidine proline rich glycoprotein (HPRG) complex that contains 3–4 Zn(II) ions per dimer of approximately 320 kDa molecular weight. The experiment shows that third-generation X-ray sources equipped with insertion devices and appropriate optics and detectors allow the investigation of complex biological systems where the metal concentration is intrinsically low. The availability of such experimental setups makes possible a completely new set of experiments in biological XAS.
XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysis
Authors: Strange Richard W. , Eady Robert R. , Lawson David , Hasnain S. Samar
Published: January 2003

This paper reports a three-dimensional EXAFS refinement of the Mo coordination sphere of the FeMoco cluster of the dithionite-reduced MoFe protein fromKlebsiella pneumoniaenitrogenase (Kp1) using the 1.6 Å-resolution crystallographic coordinates. At this resolution, the positions of the heavy (Fe and S) atoms of the cluster are well determined and there is excellent agreement between the crystallographic and EXAFS models. However, the lighter homocitrate and histidine ligands are poorly determined in the crystal structure, and it is shown that the application of EXAFS-derived distance restraints during the early stages of crystallographic refinement provides a means of substantially improving (by ∼0.1 Å) the final crystallographic model. The consistency of the EXAFS analysis with the crystallographic information in this case justifies applications of EXAFS to cases where protein crystal structures are absent. Thus, the VFe protein of V-nitrogenase has been shown by EXAFS to possess a V-atom site catalytically similar to the well characterized MoFe-nitrogenases, with V replacing Mo.