bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm Growth and Detachment of
Actinobacillus actinomycetemcomitans
Authors: Kaplan Jeffrey B. , Meyenhofer Markus F. , Fine Daniel H. 
Published: January 2003

ABSTRACT

The gram-negative, oral bacterium
Actinobacillus actinomycetemcomitans
has been implicated as the causative agent of several forms of periodontal disease in humans. When cultured in broth, fresh clinical isolates of
A. actinomycetemcomitans
form tenacious biofilms on surfaces such as glass, plastic, and saliva-coated hydroxyapatite, a property that probably plays an important role in the ability of this bacterium to colonize the oral cavity and cause disease. We examined the morphology of
A. actinomycetemcomitans
biofilm colonies grown on glass slides and in polystyrene petri dishes by using light microscopy and scanning and transmission electron microscopy. We found that
A. actinomycetemcomitans
developed asymmetric, lobed biofilm colonies that displayed complex architectural features, including a layer of densely packed cells on the outside of the colony and nonaggregated cells and large, transparent cavities on the inside of the colony. Mature biofilm colonies released single cells or small clusters of cells into the medium. These released cells adhered to the surface of the culture vessel and formed new colonies, enabling the biofilm to spread. We isolated three transposon insertion mutants which produced biofilm colonies that lacked internal, nonaggregated cells and were unable to release cells into the medium. All three transposon insertions mapped to genes required for the synthesis of the O polysaccharide (O-PS) component of lipopolysaccharide. Plasmids carrying the complementary wild-type genes restored the ability of mutant strains to synthesize O-PS and release cells into the medium. Our findings suggest that
A. actinomycetemcomitans
biofilm growth and detachment are discrete processes and that biofilm cell detachment evidently involves the formation of nonaggregated cells inside the biofilm colony that are destined for release from the colony.
cis
Elements Necessary for Developmental Expression of a
Myxococcus xanthus
Gene That Depends on C Signaling
Authors: Viswanathan Poorna , Kroos Lee 
Published: January 2003

ABSTRACT

Cell contact-mediated C signaling coordinates morphogenesis and gene expression during development of
Myxococcus xanthus
. One promoter that depends on C signaling for transcription lies upstream of Ω4403, the site of a Tn
5 lac
insertion in the genome. The Ω4403 promoter has a C-box sequence centered at −49 bp that matches the consensus 5′-CAYYCCY-3′, which is found in several C-signal-dependent promoters. Mutational analysis of the Ω4403 promoter region was performed to test the importance of the C box and to identify other
cis
-acting elements. A 6-bp change in the −10 region eliminated promoter activity, but a 6-bp change in the −35 region decreased activity only about twofold. Certain single-base-pair changes in the C box centered at −49 bp abolished promoter activity, establishing the importance of this sequence element. Single-base-pair changes in a C-box-like sequence centered at −77 bp also abolished promoter activity, but the pattern of mutational effects was different from that for the C box centered at −49 bp. Additional single-base-pair changes indicated that all 10 bp from −79 to −70 bp are important for Ω4403 promoter activity. Mutations at −59, −61, −62, and −63 bp also abolished promoter activity, defining a 5-bp element from −63 to −59 bp. This 5-bp element is separated from the 10-bp element (i.e., −79 to −70 bp) by 6 bp that can be changed without loss of promoter activity. Likewise, the 5 bp between the 5-bp element and the C box can be changed without loss of activity, but deletion of these 5 bp abolished activity, indicating that spacing is important. Sequences similar to the 5- and 10-bp elements, as well as the C box, are present in other C-signal-dependent promoters, suggesting some similarity in the regulatory mechanisms, but there are also indications that these
cis
elements do not function identically in the different promoters.
ldpA
Encodes an Iron-Sulfur Protein Involved in Light-Dependent Modulation of the Circadian Period in the Cyanobacterium
Synechococcus
elongatus
PCC 7942
Authors: Katayama Mitsunori , Kondo Takao , Xiong Jin , Golden Susan S. 
Published: January 2003

ABSTRACT

We generated random transposon insertion mutants to identify genes involved in light input pathways to the circadian clock of the cyanobacterium
Synechococcus
elongatus
PCC 7942. Two mutants, AMC408-M1 and AMC408-M2, were isolated that responded to a 5-h dark pulse differently from the wild-type strain. The two mutants carried independent transposon insertions in an open reading frame here named
ldpA
(for light-dependent period). Although the mutants were isolated by a phase shift screening protocol, the actual defect is a conditional alteration in the circadian period. The mutants retain the wild-type ability to phase shift the circadian gene expression (bioluminescent reporter) rhythm if the timing of administration of the dark pulse is corrected for a 1-h shortening of the circadian period in the mutant. Further analysis indicated that the conditional short-period mutant phenotype results from insensitivity to light gradients that normally modulate the circadian period in
S
.
elongatus
, lengthening the period at low light intensities. The
ldpA
gene encodes a polypeptide that predicts a 7Fe-8S cluster-binding motif expected to be involved in redox reactions. We suggest that the LdpA protein modulates the circadian clock as an indirect function of light intensity by sensing changes in cellular physiology.
Peptidoglycan Synthesis in the Absence of Class A Penicillin-Binding Proteins in
Bacillus subtilis
Authors: McPherson Derrell C. , Popham David L. 
Published: January 2003

ABSTRACT

Penicillin-binding proteins (PBPs) catalyze the final, essential reactions of peptidoglycan synthesis. Three classes of PBPs catalyze either trans-, endo-, or carboxypeptidase activities on the peptidoglycan peptide side chains. Only the class A high-molecular-weight PBPs have clearly demonstrated glycosyltransferase activities that polymerize the glycan strands, and in some species these proteins have been shown to be essential. The
Bacillus subtilis
genome sequence contains four genes encoding class A PBPs and no other genes with similarity to their glycosyltransferase domain. A strain lacking all four class A PBPs has been constructed and produces a peptidoglycan wall with only small structural differences from that of the wild type. The growth rate of the quadruple mutant is much lower than those of strains lacking only three of the class A PBPs, and increases in cell length and frequencies of wall abnormalities were noticeable. The viability and wall production of the quadruple-mutant strain indicate that a novel enzyme can perform the glycosyltransferase activity required for peptidoglycan synthesis. This activity was demonstrated in vitro and shown to be sensitive to the glycosyltransferase inhibitor moenomycin. In contrast, the quadruple-mutant strain was resistant to moenomycin in vivo. Exposure of the wild-type strain to moenomycin resulted in production of a phenotype similar to that of the quadruple mutant.
Identification of Genes Required for Synthesis of the Adhesive Holdfast in
Caulobacter crescentus
Authors: Smith Chris S. , Hinz Aaron , Bodenmiller Diane , Larson David E. , Brun Yves V. 
Published: January 2003

ABSTRACT

Adhesion to both abiotic and biotic surfaces by the gram-negative prothescate bacterium
Caulobacter crescentus
is mediated by a polar organelle called the “holdfast,” which enables the bacterium to form stable monolayer biofilms. The holdfast, a complex polysaccharide composed in part of
N
-acetylglucosamine, localizes to the tip of the stalk (a thin cylindrical extension of the cell wall and membranes). We report here the isolation of adhesion mutants with transposon insertions in an uncharacterized gene cluster involved in holdfast biogenesis (
hfs
) as well as in previously identified polar development genes (
podJ
and
pleC
), and the holdfast attachment genes (
hfa
). Clean deletions of three of the four genes in the
hfs
gene cluster (
hfsDAB
) resulted in a severe holdfast biogenesis phenotype. These mutants do not bind to surfaces or to a fluorescently labeled lectin, specific for
N
-acetylglucosamine. Transmission electron microscopy indicated that the
hfsDAB
mutants fail to synthesize a holdfast at the stalk tip. The predicted
hfs
gene products have significant sequence similarity to proteins necessary for exopolysaccharide export in gram-negative bacteria. HfsA has sequence similarity to GumC from
Xanthomonas campestris
, which is involved in exopolysaccharide export in the periplasm. HfsD has sequence similarity to Wza from
Escherichia coli
, an outer membrane protein involved in secretion of polysaccharide through the outer membrane. HfsB is a novel protein involved in holdfast biogenesis. These data suggest that the
hfs
genes play an important role in holdfast export.
Proteomic Analysis of the Spore Coats of
Bacillus subtilis
and
Bacillus anthracis
Authors: Lai Erh-Min , Phadke Nikhil D. , Kachman Maureen T. , Giorno Rebecca , Vazquez Santiago , Vazquez Jenny A. , Maddock Janine R. , Driks Adam 
Published: January 2003

ABSTRACT

The outermost proteinaceous layer of bacterial spores, called the coat, is critical for spore survival, germination, and, for pathogenic spores, disease. To identify novel spore coat proteins, we have carried out a preliminary proteomic analysis of
Bacillus subtilis
and
Bacillus anthracis
spores, using a combination of standard sodium dodecyl sulfate-polyacrylamide gel electrophoresis separation and improved two-dimensional electrophoretic separations, followed by matrix-assisted laser desorption ionization-time of flight and/or dual mass spectrometry. We identified 38
B
.
subtilis
spore proteins, 12 of which are known coat proteins. We propose that, of the novel proteins, YtaA, YvdP, and YnzH are bona fide coat proteins, and we have renamed them CotI, CotQ, and CotU, respectively. In addition, we initiated a study of coat proteins in
B
.
anthracis
and identified 11 spore proteins, 6 of which are candidate coat or exosporium proteins. We also queried the unfinished
B
.
anthracis
genome for potential coat proteins. Our analysis suggests that the
B
.
subtilis
and
B
.
anthracis
coats have roughly similar numbers of proteins and that a core group of coat protein species is shared between these organisms, including the major morphogenetic proteins. Nonetheless, a significant number of coat proteins are probably unique to each species. These results should accelerate efforts to develop
B
.
anthracis
detection methods and understand the ecological role of the coat.
Differentiation and Anaerobiosis in Standing Liquid Cultures of
Streptomyces coelicolor
Authors: van Keulen Geertje , Jonkers Henk M. , Claessen Dennis , Dijkhuizen Lubbert , Wösten Han A. B. 
Published: January 2003

ABSTRACT

Streptomyces coelicolor
differentiates on solid agar media by forming aerial hyphae that septate into spores. We here show that differentiation also occurs in standing liquid minimal media. After a period of submerged growth, hyphae migrate to the air interface, where they become fixed by a rigid reflecting film. Colonies that result from these hyphae form sporulating aerial hyphae. In addition, submerged hyphae in the liquid minimal medium may attach to the surface. Liquid standing cultures easily become anoxic only 1 to 2 mm below the surface. Yet, biomass increases, implying the existence of metabolic pathways supporting anaerobic growth.
2-Aminopurine Allows Interspecies Recombination by a Reversible Inactivation of the
Escherichia coli
Mismatch Repair System
Authors: Matic Ivan , Babic Ana , Radman Miroslav 
Published: January 2003

ABSTRACT

2-Aminopurine treatment of
Escherichia coli
induces a reversible phenotype of DNA mismatch repair deficiency. This transient phenotype results in a 300-fold increase in the frequency of interspecies conjugational recombination with a
Salmonella enterica
serovar Typhimurium Hfr donor. This method can be used for the generation of biodiversity by allowing recombination between diverged genes and genomes.
Identification and Characterization of the
gerH
Operon of
Bacillus anthracis
Endospores: a Differential Role for Purine Nucleosides in Germination
Authors: Weiner Matthew A. , Read Timothy D. , Hanna Philip C. 
Published: January 2003

ABSTRACT

We identified a tri-cistronic operon,
gerH
, in
Bacillus anthracis
that is important for endospore germination triggered by two distinct germination response pathways termed inosine-His and purine-Ala. Together, the two pathways allow
B
.
anthracis
endospores a broader recognition of purines and amino acids that may be important for host-mediated germination.
The Periplasmic Protein MppA Requires an Additional Mutated Locus To Repress
marA
Expression in
Escherichia coli
Authors: Bina Xiaowen , Perreten Vincent , Levy Stuart B. 
Published: January 2003

ABSTRACT

Escherichia coli
strain TP985, which has an insertional mutation in the gene for the periplasmic murein tripeptide binding protein MppA, was previously reported to overproduce MarA and exhibit a multiple-antibiotic resistance (Mar) phenotype (H. Li and J. T. Park, J. Bacteriol.
181:
4842-4847, 1999). We found that TP985 contained a previously unrecognized
marR
mutation which was responsible for the Mar phenotype. Transduction of the
mppA
mutation from TP985 to another wild-type strain did not affect antibiotic susceptibility. Overproduction of MppA repressed
marA
transcription in TP985 but not in other
mppA
or
marR
mutants. Therefore, TP985 contains an additional unknown mutation(s) that facilitates the repression of
marA
expression by MppA.
Overrepresentation of a Gene Family Encoding Extracytoplasmic Solute Receptors in
Bordetella
Authors: Antoine Rudy , Jacob-Dubuisson Françoise , Drobecq Hervé , Willery Eve , Lesjean Sarah , Locht Camille 
Published: January 2003

ABSTRACT

A family of genes that are likely to encode extracytoplasmic solute receptors is strongly overrepresented in several β-proteobacteria, including
Bordetella pertussis
. This gene family, of which members have been called
bug
genes, contains some examples that are contained within polycistronic operons coding for tripartite uptake transporters of the TTT family, while the vast majority are “orphan” genes. Proteomic and functional analyses demonstrated that several of these genes are expressed in
B. pertussis
, and one is involved in citrate uptake. The
bug
genes probably form an ancient family that has been subjected to a large expansion in a restricted phylogenic group.
Corrected Sequence of the Bacteriophage P22 Genome
Authors: Pedulla Marisa L. , Ford Michael E. , Karthikeyan Tharun , Houtz Jennifer M. , Hendrix Roger W. , Hatfull Graham F. , Poteete Anthony R. , Gilcrease Eddie B. , Winn-Stapley Danella A. , Casjens Sherwood R. 
Published: January 2003

ABSTRACT
We report the first accurate genome sequence for bacteriophage P22, correcting a 0.14% error rate in previously determined sequences. DNA sequencing technology is now good enough that genomes of important model systems like P22 can be sequenced with essentially 100% accuracy with minimal investment of time and resources.
Prokaryotic Utilization of the Twin-Arginine Translocation Pathway: a Genomic Survey
Authors: Dilks Kieran , Rose R. Wesley , Hartmann Enno , Pohlschröder Mechthild 
Published: January 2003

ABSTRACT
The twin-arginine translocation (Tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. However, the extent to which this pathway is used among the prokaryotes is not known. By using a genomic approach, a comprehensive list of putative Tat substrates for 84 diverse prokaryotes was established. Strikingly, the results indicate that the Tat pathway is utilized to highly varying extents. Furthermore, while many prokaryotes use this pathway predominantly for the secretion of redox proteins, analyses of the predicted substrates suggest that certain bacteria and archaea secrete mainly nonredox proteins via the Tat pathway. While no correlation was observed between the number of Tat machinery components encoded by an organism and the number of predicted Tat substrates, it was noted that the composition of this machinery was specific to phylogenetic taxa.
Acute disseminated encephalomyelitis
Authors: Garg R K 
Published: February 2003

Abstract
Acute disseminated encephalomyelitis (ADEM) is an acute demyelinating disorder of the central nervous system, and is characterised by multifocal white matter involvement. Diffuse neurological signs along with multifocal lesions in brain and spinal cord characterise the disease. Possibly, a T cell mediated autoimmune response to myelin basic protein, triggered by an infection or vaccination, underlies its pathogenesis. ADEM is a monophasic illness with favourable long term prognosis. The differentiation of ADEM from a first attack of multiple sclerosis has prognostic and therapeutic implications; this distinction is often difficult. Most patients with ADEM improve with methylprednisolone. If that fails immunoglobulins, plasmapheresis, or cytotoxic drugs can be given. Recent literature suggests that a significant proportion of patients with ADEM will later develop multiple sclerosis; however, follow up experience from developing countries does not support this view.
Hereditary haemorrhagic telangiectasia (Osler-Weber-Rendu syndrome): a view from the 21st century
Authors: Begbie M E , Wallace G M F , Shovlin C L 
Published: February 2003

Abstract
Hereditary haemorrhagic telangiectasia (HHT) affects one in 5−8000, and no longer can be viewed as solely causing anaemia (due to nasal and gastrointestinal bleeding) and characteristic mucocutaneous telangiectasia. Arteriovenous malformations commonly occur, and in the pulmonary and cerebral circulations demand knowledge of risks and benefits of asymptomatic screening and treatment. HHT is inherited as an autosomal dominant trait and there is no age cut off when apparently unaffected offspring of an individual with HHT can be told they are unaffected. This review focuses on the evolving evidence base for HHT management, issues regarding pregnancy and prothrombotic treatments, and discusses the molecular and cellular changes that underlie this disease.
Evaluation and treatment of dyspepsia
Authors: Jones M P 
Published: February 2003

Abstract
Dyspepsia is a common symptom. Dyspeptic symptoms may be caused by a variety of conditions such as peptic ulcer disease, gastro-oesophageal reflux, and malignancy. Most often, however, no cause is identified and dyspepsia is deemed to be functional. While symptom severity does influence frequency of consultation, dyspeptic consulters also differ from non-consulters with respect to symptom perception and anxiety. This highlights the importance of understanding the patient’s agenda early in the course of evaluation. Patients over the age of 55 years or with alarm symptoms should be referred for prompt endoscopy. In the absence of other clinically apparent aetiologies, uninvestigated dyspeptics can be either tested and treated for Helicobacter pylori or empirically treated with proton pump inhibitors. Uninvestigated dyspeptics failing empiric therapy should be referred for evaluation that includes endoscopy. Further therapy with prokinetics, tricyclic antidepressants, fundal relaxants, antidepressants, or psychotherapy is guided by predominant symptoms and assessment of possible psychiatric factors.
Evolution of diabetes medical nutrition therapy
Authors: Franz M J , Warshaw H , Daly A E , Green-Pastors J , Arnold M S , Bantle J 
Published: February 2003

Abstract
Research supports the importance of medical nutrition therapy in achieving diabetes treatment goals. For persons requiring insulin therapy, the first priority is to integrate an insulin regimen into the patient’s lifestyle. For type 2 diabetes, the priority is to focus on lifestyle strategies (that is, nutrition and exercise) that will improve metabolic outcomes at diagnosis and as the disease progresses. Patients with diabetes need nutrition recommendations that are supported by scientific evidence and that can be easily understood and translated into everyday life. To achieve positive outcomes, a coordinated team effort that provides continued education and support is essential.
HIV viral suppression in the era of antiretroviral therapy
Authors: Thaker H K , Snow M H 
Published: February 2003

Abstract
Altogether 42 million people worldwide have been infected with HIV, and 12 million have died over the last 20 years. Effective antiretroviral therapy has lead to sustained HIV viral suppression and immunological recovery in patients who have been infected with the virus. The incidence of AIDS has declined in the Western world with the introduction of effective antiretroviral therapy. Questions on When to start treatment?, What to start with?, How to monitor patients?, remain heavily debated. Adherence to antiretroviral treatment remains the cornerstone of effective treatment, and failure to adhere is the strongest predictor of virological failure. Long term therapy can lead to metabolic complications. Resource poor countries are dealing with difficult issues such as mother to child prevention of HIV transmission. Other treatment options are now available, with the recent introduction of fusion inhibitors, second generation non-nucleoside reverse transcriptase inhibitors, and nucleotide reverse transcriptase inhibitors to clinical practice.
Total arterial revascularisation as a primary strategy for coronary artery bypass grafting
Authors: Naik M J , Abu-Omar Y , Alvi A , Wright N , Henderson A , Channon K , Forfar J C , Taggart D P 
Published: February 2003

Abstract

Background
Bilateral internal thoracic arteries confer improved survival benefit after coronary artery bypass grafting (CABG). Despite increasing evidence, the use of arterial conduits has not been accepted as a primary practice in most of the centres in the UK for various reasons. A series of patients has been analysed to assess the feasibility of total arterial revascularisation as a primary strategy in patients requiring first time CABG.

Methods
Altogether 245 patients undergoing first time CABG by one surgeon, from June 1999 to October 2000, were studied. Group 1 consisted of 165 patients undergoing total arterial revascularisation (using bilateral internal thoracic and radial arteries) and group 2 consisted of 80 patients undergoing conventional CABG (using one internal thoracic artery and supplemental veins). Thirty day mortality and early morbidity with particular reference to resternotomy for bleeding, cerebrovascular accidents, renal failure, and sternal dehiscence were the main outcome measures.

Results
Patients in group 1 were younger (mean (SD) 60 (10) v 65 (9) years; p&lt;0.001), had lower Parsonnet scores (mean (SD) 5 (5) v 11 (7); p&lt;0.001), and better left ventricular function. Both groups received a similar number of grafts. The percentage of patients undergoing total arterial revascularisation rose from 44% in the first three months to over 75% in the three latter three month periods. Overall 30 day mortality was 1.3%, one patient (0.6%) in group 1 and two patients (2.5%) in group 2. There was a similar incidence of postoperative complications and length of median postoperative stay in both groups.

Conclusion
Total arterial revascularisation can be adopted as a primary strategy in most patients undergoing CABG with no increase in mortality or morbidity.