bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale Visualization of a Fibrillar Array in the Cell Wall of Filamentous Cyanobacteria and Its Implications for Gliding Motility
Authors: Read Nicholas , Connell Simon , Adams David G. 
Published: August 2007

ABSTRACTMany filamentous cyanobacteria are motile by gliding, which requires attachment to a surface. There are two main theories to explain the mechanism of gliding. According to the first, the filament is pushed forward by small waves that pass along the cell surface. In the second, gliding is powered by the extrusion of slime through pores surrounding each cell septum. We have previously shown that the cell walls of several motile cyanobacteria possess an array of parallel fibrils between the peptidoglycan and the outer membrane and have speculated that the function of this array may be to generate surface waves to power gliding. Here, we report on a study of the cell surface topography of two morphologically different filamentous cyanobacteria, using field emission gun scanning electron microscopy (FEGSEM) and atomic force microscopy (AFM). FEGSEM and AFM images ofOscillatoriasp. strain A2 confirmed the presence of an array of fibrils, visible as parallel corrugations on the cell surface. These corrugations were also visualized by AFM scanning of fully hydrated filaments under liquid; this has not been achieved before for filamentous bacteria. FEGSEM images ofNostoc punctiformerevealed a highly convoluted, not parallel, fibrillar array. We conclude that an array of parallel fibrils, beneath the outer membrane ofOscillatoria, may function in the generation of thrust in gliding motility. The array of convoluted fibrils inN. punctiformemay have an alternative function, perhaps connected with the increase in outer membrane surface area resulting from the presence of the fibrils.
Contribution of the FtsQ Transmembrane Segment to Localization to the Cell Division Site
Authors: Scheffers Dirk-Jan , Robichon Carine , Haan Gert Jan , den Blaauwen Tanneke , Koningstein Gregory , van Bloois Edwin , Beckwith Jon , Luirink Joen 
Published: August 2007

ABSTRACT

The
Escherichia coli
cell division protein FtsQ is a central component of the divisome. FtsQ is a bitopic membrane protein with a large C-terminal periplasmic domain. In this work we investigated the role of the transmembrane segment (TMS) that anchors FtsQ in the cytoplasmic membrane. A set of TMS mutants was made and analyzed for the ability to complement an
ftsQ
mutant. Study of the various steps involved in FtsQ biogenesis revealed that one mutant (L29/32R;V38P) failed to functionally insert into the membrane, whereas another mutant (L29/32R) was correctly assembled and interacted with FtsB and FtsL but failed to localize efficiently to the cell division site. Our results indicate that the FtsQ TMS plays a role in FtsQ localization to the division site.
Binary Toxin Production in
Clostridium difficile
Is Regulated by CdtR, a LytTR Family Response Regulator
Authors: Carter Glen P. , Lyras Dena , Allen David L. , Mackin Kate E. , Howarth Pauline M. , O'Connor Jennifer R. , Rood Julian I. 
Published: August 2007

ABSTRACT

Clostridium difficile
binary toxin (CDT) is an actin-specific ADP-ribosyltransferase that is produced by various
C. difficile
isolates, including the “hypervirulent” NAP1/027 epidemic strains. In contrast to the two major toxins from
C. difficile
, toxin A and toxin B, little is known about the role of CDT in virulence or how
C. difficile
regulates its production. In this study we have shown that in addition to the
cdtA
and
cdtB
toxin structural genes, a functional
cdt
locus contains a third gene, here designated
cdtR
, which is predicted to encode a response regulator. By introducing functional binary toxin genes into
cdtR
+
and
cdtR
-negative strains of
C. difficile
, it was established that the CdtR protein was required for optimal expression of binary toxin. Significantly increased expression of functional binary toxin was observed in the presence of a functional
cdtR
gene; an internal deletion within
cdtR
resulted in a reduction in binary toxin production to basal levels. Strains that did not carry intact
cdtAB
genes or
cdtAB
pseudogenes also did not have
cdtR
, with the entire
cdt
locus, or CdtLoc, being replaced by a conserved 68-bp sequence. These studies have shown for the first time that binary toxin production is subject to strict regulatory control by the response regulator CdtR, which is a member of the LytTR family of response regulators and is related to the AgrA protein from
Staphylococcus aureus
.
Transducing Particles of
Staphylococcus aureus
Pathogenicity Island SaPI1 Are Comprised of Helper Phage-Encoded Proteins
Authors: Tallent Sandra M. , Langston Timothy B. , Moran Richard G. , Christie Gail E. 
Published: August 2007

ABSTRACT
The relationship between the composition of SaPI1 transducing particles and those of helper phage 80α was investigated by direct comparison of virion proteins. Twelve virion proteins were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry; all were present in both 80α and SaPI1 virions, and all were encoded by 80α. No SaPI1-encoded proteins were detected. This confirms the prediction that SaPI1 is encapsidated in a virion assembled from helper phage-encoded proteins.
Defining the Stressome ofMycobacterium aviumsubsp.paratuberculosisIn Vitro and in Naturally Infected Cows
Authors: Wu Chia-wei , Schmoller Shelly K. , Shin Sung Jae , Talaat Adel M. 
Published: August 2007

ABSTRACTMycobacterium aviumsubsp.paratuberculosiscauses an enteric infection in cattle, with a great impact on the dairy industry in the United States and worldwide. Characterizing the gene expression profile ofM. aviumsubsp.paratuberculosisexposed to different stress conditions, or shed in cow feces, could improve our understanding of the pathogenesis ofM. aviumsubsp.paratuberculosis. In this report, the stress response ofM. aviumsubsp.paratuberculosison a genome-wide level (stressome) was defined for the first time using DNA microarrays. Expression data analysis revealed unique gene groups ofM. aviumsubsp.paratuberculosisthat were regulated under in vitro stressors while additional groups were regulated in the cow samples. Interestingly, acidic pH induced the regulation of a large number of genes (n= 597), suggesting the high sensitivity ofM. aviumsubsp.paratuberculosisto acidic environments. Generally, responses to heat shock, acidity, and oxidative stress were similar inM. aviumsubsp.paratuberculosisandMycobacterium tuberculosis, suggesting common pathways for mycobacterial defense against stressors. Several sigma factors (e.g.,sigHandsigE) were differentially coregulated with a large number of genes depending on the type of each stressor. Subsequently, we analyzed the virulence of sixM. aviumsubsp.paratuberculosismutants with inactivation of differentially regulated genes using a murine model of paratuberculosis. Both bacterial and histopathological examinations indicated the attenuation of all gene mutants, especially those selected based on their expression in the cow samples (e.g.,lipN). Overall, the employed approach profiled mycobacterial genetic networks triggered by variable stressors and identified a novel set of putative virulence genes. A similar approach could be applied to analyze other intracellular pathogens.
The Thiamine Kinase (YcfN) Enzyme Plays a Minor but Significant Role in Cobinamide Salvaging in
Salmonella enterica
Authors: Otte Michele M. , Woodson Jesse D. , Escalante-Semerena Jorge C. 
Published: August 2007

ABSTRACT

Cobinamide (Cbi) salvaging is impaired, but not abolished, in a
Salmonella enterica
strain lacking a functional
cobU
gene. CobU is a bifunctional enzyme (NTP:adenosylcobinamide [NTP:AdoCbi] kinase, GTP:adenosylcobinamide-phosphate [GTP:AdoCbi-P] guanylyltransferase) whose AdoCbi kinase activity is necessary for Cbi salvaging in this bacterium. Inactivation of the
ycfN
gene in a Δ
cobU
strain abrogated Cbi salvaging. Introduction of a plasmid carrying the
ycfN
+
allele into a Δ
cobU
Δ
ycfN
strain substantially restored Cbi salvaging. Mass spectrometry data indicate that when YcfN-enriched cell extracts were incubated with AdoCbi and ATP, the product of the reaction was AdoCbi-P. Results from bioassays confirmed that YcfN converted AdoCbi to AdoCbi-P in an ATP-dependent manner. YcfN is a good example of enzymes that are used by the cell in multiple pathways to ensure the salvaging of valuable precursors.
Short-Tailed Stx Phages Exploit the Conserved YaeT Protein To Disseminate Shiga Toxin Genes among Enterobacteria
Authors: Smith Darren L. , James Chloë E. , Sergeant Martin J. , Yaxian Yan , Saunders Jon R. , McCarthy Alan J. , Allison Heather E. 
Published: August 2007

ABSTRACT

Infection of
Escherichia coli
by Shiga toxin-encoding bacteriophages (Stx phages) was the pivotal event in the evolution of the deadly Shiga toxin-encoding
E. coli
(STEC), of which serotype O157:H7 is the most notorious. The number of different bacterial species and strains reported to produce Shiga toxin is now more than 500, since the first reported STEC infection outbreak in 1982. Clearly, Stx phages are spreading rapidly, but the underlying mechanism for this dissemination has not been explained. Here we show that an essential and highly conserved gene product, YaeT, which has an essential role in the insertion of proteins in the gram-negative bacterial outer membrane, is the surface molecule recognized by the majority (ca. 70%) of Stx phages via conserved tail spike proteins associated with a short-tailed morphology. The
yaeT
gene was initially identified through complementation, and its role was confirmed in phage binding assays with and without anti-YaeT antiserum. Heterologous cloning of
E. coli yaeT
to enable Stx phage adsorption to
Erwinia carotovora
and the phage adsorption patterns of bacterial species possessing natural
yaeT
variants further supported this conclusion. The use of an essential and highly conserved protein by the majority of Stx phages is a strategy that has enabled and promoted the rapid spread of shigatoxigenic potential throughout multiple
E. coli
serogroups and related bacterial species. Infection of commensal bacteria in the mammalian gut has been shown to amplify Shiga toxin production in vivo, and the data from this study provide a platform for the development of a therapeutic strategy to limit this YaeT-mediated infection of the commensal flora.
Maintaining the Transcription Factor SpoIIID Level Late during Sporulation Causes Spore Defects in
Bacillus subtilis
Authors: Wang Lijuan , Perpich John , Driks Adam , Kroos Lee 
Published: August 2007

ABSTRACT

During sporulation of
Bacillus subtilis
, four regulatory proteins act in the order σ
E
, SpoIIID, σ
K
, and GerE to temporally control gene expression in the mother cell. σ
E
and σ
K
work sequentially with core RNA polymerase to transcribe different sets of genes. SpoIIID and GerE are small, sequence-specific DNA-binding proteins that activate or repress transcription of many genes. Previous studies showed that transcriptionally active σ
K
RNA polymerase inhibits early mother cell gene expression, reducing accumulation of SpoIIID late in sporulation. Here, the effects of perturbing the mother cell gene regulatory network by maintaining the SpoIIID level late during sporulation are reported. Persistent expression was obtained by fusing
spoIIID
to the σ
K
-controlled
gerE
promoter on a multicopy plasmid. Fewer heat- and lysozyme-resistant spores were produced by the strain with persistent
spoIIID
expression, but the number of spores resistant to organic solvents was unchanged, as was their germination ability. Transmission electron microscopy showed structural defects in the spore coat. Reporter fusions to σ
K
-dependent promoters showed lower expression of
gerE
and
cotC
and higher expression of
cotD
. Altered expression of
cot
genes, which encode spore coat proteins, may account for the spore structural defects. These results suggest that one role of negative feedback by σ
K
RNA polymerase on early mother cell gene expression is to lower the level of SpoIIID late during sporulation in order to allow normal expression of genes in the σ
K
regulon.
The T4 RI Antiholin Has an N-Terminal Signal Anchor Release Domain That Targets It for Degradation by DegP
Authors: Tran Tram Anh T. , Struck Douglas K. , Young Ry 
Published: August 2007

ABSTRACT

Lysis inhibition (LIN) of T4-infected cells was one of the foundational experimental systems for modern molecular genetics. In LIN, secondary infection of T4-infected cells results in a dramatically protracted infection cycle in which intracellular phage and endolysin accumulation can continue for hours. At the molecular level, this is due to the inhibition of the holin, T, by the antiholin, RI. RI is only 97 residues and contains an N-terminal hydrophobic domain and a C-terminal hydrophilic domain; expression of the latter domain fused to a secretory signal sequence is sufficient to impose LIN, due to its specific interaction with the periplasmic domain of the T holin. Here we show that the N-terminal sequence comprises a signal anchor release (SAR) domain, which causes the secretion of RI in a membrane-tethered form and then its subsequent release into the periplasm, without proteolytic processing. Moreover, the SAR domain confers both functional lability and DegP-mediated proteolytic instability on the released form of RI, although LIN is not affected in a
degP
host. These results are discussed in terms of a model for the activation of RI in the establishment of the LIN state.
Proteins P24 and P41 Function in the Regulation of Terminal-Organelle Development and Gliding Motility in
Mycoplasma pneumoniae
Authors: Hasselbring Benjamin M. , Krause Duncan C. 
Published: August 2007

ABSTRACT

Mycoplasma pneumoniae
is a major cause of bronchitis and atypical pneumonia in humans. This cell wall-less bacterium has a complex terminal organelle that functions in cytadherence and gliding motility. The gliding mechanism is unknown but is coordinated with terminal-organelle development during cell division. Disruption of
M. pneumoniae
open reading frame MPN311 results in loss of protein P41 and downstream gene product P24. P41 localizes to the base of the terminal organelle and is required to anchor the terminal organelle to the cell body, but during cell division, MPN311 insertion mutants also fail to properly regulate nascent terminal-organelle development spatially or gliding activity temporally. We measured gliding velocity and frequency and used fluorescent protein fusions and time-lapse imaging to assess the roles of P41 and P24 individually in terminal-organelle development and gliding function. P41 was necessary for normal gliding velocity and proper spatial positioning of new terminal organelles, while P24 was required for gliding frequency and new terminal-organelle formation at wild-type rates. However, P41 was essential for P24 function, and in the absence of P41, P24 exhibited a dynamic localization pattern. Finally, protein P28 requires P41 for stability, but analysis of a P28
−
mutant established that the MPN311 mutant phenotype was not a function of loss of P28.
Organization of the Aerotaxis Receptor Aer in the Membrane of
Escherichia coli
Authors: Amin Divya N. , Taylor Barry L. , Johnson Mark S. 
Published: August 2007

ABSTRACT

The Aer receptor guides
Escherichia coli
to specific oxygen and energy-generating niches. The input sensor in Aer is a flavin adenine dinucleotide-binding PAS domain, which is separated from a HAMP/signaling output domain by two membrane-spanning segments that flank a short (four-amino-acid) periplasmic loop. In this study, we determined the overall membrane organization of Aer by introducing combinations of residues that allowed us to differentiate intradimeric collisions from interdimeric collisions. Collisions between proximal residues in the membrane anchor were exclusively intra- or interdimeric but, with one exception, not both. Cross-linking profiles were consistent, with a rigid rather than flexible periplasmic loop and a tilted TM2 helix that crossed TM2′ at residue V197C, near the center of the lipid bilayer. The periplasmic loop formed a stable neighborhood that (i) included a maximum of three Aer dimers, (ii) did not swap neighbors over time, and (iii) appeared to be constrained by interactions in the cytosolic signaling domain.
Essential Internal Promoter in the
spoIIIA
Locus of
Bacillus subtilis
Authors: Guillot Chris , Moran Charles P. 
Published: August 2007

ABSTRACT

The
Bacillus subtilis spoIIIA
locus encodes eight proteins, SpoIIIAA to SpoIIIAH, which are expressed in the mother cell during endospore formation and which are essential for the activation of σ
G
in the forespore. Complementation studies indicated that this locus may be transcribed from two promoters, one promoter upstream from the first gene and possibly a second unidentified promoter within the locus. Fragments of the
spoIIIA
locus were expressed at an ectopic site to complement the sporulation-defective phenotype of a
spoIIIAH
deletion, and we determined that complementation required a fragment of DNA that extended into
spoIIIAF
. To confirm that there was a promoter located in
spoIIIAF
, we constructed transcriptional fusions to
lacZ
and found strong sporulation-induced promoter activity. Primer extension assays were used to determine the transcription start site, and point mutations introduced into the −10 and −35 regions of the promoter reduced its activity. This promoter is transcribed by σ
E
-RNA polymerase and is repressed by SpoIIID. Therefore, we concluded that the
spoIIIA
locus is transcribed from two promoters, one at the start of the locus (

P1
spoIIIA

) and the other within the locus (

P2
spoIIIA

). Based on Campbell integrations and reverse transcription-PCR analysis of the

P2
spoIIIA

region, we determined that

P2
spoIIIA

is sufficient for transcription of
spoIIIAG
and
spoIIIAH
. Inactivation of

P2
spoIIIA

blocked spore formation, indicating that

P2
spoIIIA

is essential for expression of
spoIIIAG
and
spoIIIAH
. The

P2
spoIIIA

activity is twice the

P1
spoIIIA

activity; therefore, larger amounts of SpoIIIAG and SpoIIIAH than of proteins encoded at the upstream end of the locus may be required.
Mutations in Type I and Type IV Pilus Biosynthetic Genes Affect Twitching Motility Rates in
Xylella fastidiosa
Authors: De La Fuente Leonardo , Burr Thomas J. , Hoch Harvey C. 
Published: August 2007

ABSTRACT

Xylella fastidiosa
possesses both type I and type IV pili at the same cell pole. By use of a microfluidic device, the speed of twitching movement by wild-type cells on a glass surface against the flow direction of media was measured as 0.86 (standard error [SE], 0.04) μm min
−1
. A type I pilus mutant (
fimA
) moved six times faster (4.85 [SE, 0.27] μm min
−1
) and a
pilY1
mutant moved three times slower (0.28 [SE, 0.03] μm min
−1
) than wild-type cells. Type I pili slow the rate of movement, while the putative type IV pilus protein PilY1 is likely important for attachment to surfaces.
A public-domain image processing tool for automated quantification of fluorescence in situ hybridisation signals
Authors: Konsti J , Lundin J , Jumppanen M , Lundin M , Viitanen A , Isola J 
Published: August 2007

Aims:To develop and evaluate an automated method for quantification ofHER2fluorescence in situ hybridisation (FISH) signals.Methods:Using a popular, open source image manipulation tool, ImageJ, a macro for FISH signal assessment was created. A comparison against traditional manual counting was performed in breast cancer specimens from 42 patients. The tumour specimens were hybridised with probes forHER2and chromosome 17 centromere (CEP17) and selected areas were digitised for image processing. Hybridisation signals were calculated both manually and automatically with the ImageJ custom macro.Results:The correlation coefficient between the automatic and manualHER2/CEP17 ratios was 0.98. The corresponding percentage agreement was 90% and the kappa value was 0.82.Conclusions:This study shows that it is possible to automate the determination ofHER2amplification by the use of open-source software, with results comparable to manual counting. The automated counting decreases the time needed for sample analysis and provides possibilities to enhance inter- and intralaboratory reproducibility of results. The FISH quantification tool (FishJ) is available for download as an ImageJ macro or alternatively it can be utilised through a web interface with an option of uploading FISH images for hybridisation signal counting. Combined with digitisation of FISH samples, the FishJ macro enables gene copy number to be assessed and re-evaluated on any area of a digitised specimen.
Quantification of intrahepatic total hepatitis B virus DNA in chronic hepatitis B patients and its relationship with liver histology
Authors: Bayram A , Erkilic S , Özkur A , Bayram M , Sari I 
Published: August 2007

Aims:This study was conducted to evaluate the relationship between total intrahepatic hepatitis B virus (HBV) DNA levels and liver histology in terms of the degree of histological activity index (HAI) that yields necroinflammation (HAI-NI) and fibrosis (HAI-F) of the liver.Methods:Prospectively, Tru-cut needle biopsy samples were obtained from the livers of 42 patients with chronic hepatitis B. Levels of serum and liver HBV DNA were determined by quantitative real-time PCR. Demographic data of patients, together with hepatitis B serology, alanine aminotransferase levels, and HAI-NI and HAI-F scores, were recorded.Results:Twenty of the patients were hepatitis B e antigen (HBeAg) positive, while 22 patients were positive for antibody to HBeAg (anti-HBe). Serum and liver total HBV DNA levels were found to correlate directly with each other in the two groups (r = 0.669, p = 0.001; and r = 0.880, p<0.001; respectively) and the correlation was more marked in anti-HBe-positive patients. Although serum HBV DNA levels correlated positively with HAI-NI and HAI-F scores in HBeAg-positive and HBeAg-negative patients, total liver HBV DNA levels correlated with HAI-NI and HAI-F scores in anti-HBe-positive patients only.Conclusions:Quantitative measurement of intrahepatic HBV DNA is a valuable marker of the histological status of the liver in anti-HBe-positive patients with chronic hepatitis B, and it may give an insight into the prognosis and the ideal time for the cessation of antiviral treatment.
Mais le Cadi Tranche-t-il?
Authors: Hentati Nejmeddine 
Published: August 2007

AbstractJ. Berque has argued that the main task of the Muslim judge is to encourage agreement between parties to a dispute. In this essay, I test his thesis in the light of information relating to Muslim judges in the Mālikī West between the 3d/9th and 8th/14th centuries. After discussing the relationship between a court judgment, arbitration, and transaction, I analyze the competence and jurisdiction of the judge in an effort to determine whether or not he did in fact settle disputes and enforce his judgments. Jacques Berque estime que l'essentiel du travail du cadi musulman est de favoriser la conclusion d'accords entre les parties en litige. L'objet de cette étude est d'examiner cette thèse à la lumière des données relatives au cadi malikite en Occident musulman médiéval. Dans un premier moment, nous avons évoqué la relation entre qadā' (juridiction), arbitrage et transaction. Dans un second moment, nous avons parlé de la compétence du cadi en matière de jugement et de son exécution pour savoir s'il tranche les litiges et travaille à l'exécution de ses sentences.