bluuebunny/crossref_metadata_2025_split huggingface dataset:
Operation of the CO Dehydrogenase/Acetyl Coenzyme A Pathway in both Acetate Oxidation and Acetate Formation by the Syntrophically Acetate-Oxidizing Bacterium
Thermacetogenium phaeum
Authors: Hattori Satoshi , Galushko Alexander S. , Kamagata Yoichi , Schink Bernhard 
Published: May 2005

ABSTRACT

Thermacetogenium phaeum
is a homoacetogenic bacterium that can grow on various substrates, such as pyruvate, methanol, or H
2
/CO
2
. It can also grow on acetate if cocultured with the hydrogen-consuming methanogenic partner
Methanothermobacter thermautotrophicus
. Enzyme activities of the CO dehydrogenase/acetyl coenzyme A (CoA) pathway (CO dehydrogenase, formate dehydrogenase, formyl tetrahydrofolate synthase, methylene tetrahydrofolate dehydrogenase) were detected in cell extracts of pure cultures and of syntrophic cocultures. Mixed cell suspensions of
T. phaeum
and
M. thermautotrophicus
oxidized acetate rapidly and produced acetate after addition of H
2
/CO
2
after a short time lag. CO dehydrogenase activity staining after native polyacrylamide gel electrophoresis exhibited three oxygen-labile bands which were identical in pure culture and coculture. Protein profiles of
T. phaeum
cells after sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the strain exhibited basically the same protein patterns in both pure and syntrophic culture. These results indicate that
T. phaeum
operates the CO dehydrogenase/acetyl-CoA pathway reversibly both in acetate oxidation and in reductive acetogenesis by using the same biochemical apparatus, although it has to couple this pathway to ATP synthesis in different ways.
Biofilm Formation and Sloughing inSerratia marcescensAre Controlled by Quorum Sensing and Nutrient Cues
Authors: Rice S. A. , Koh K. S. , Queck S. Y. , Labbate M. , Lam K. W. , Kjelleberg S. 
Published: May 2005

ABSTRACTWe describe here a role for quorum sensing in the detachment, or sloughing, ofSerratia marcescensfilamentous biofilms, and we show that nutrient conditions affect the biofilm morphotype. Under reduced carbon or nitrogen conditions,S. marcescensformed a classical biofilm consisting of microcolonies. The filamentous biofilm could be converted to a microcolony-type biofilm by switching the medium after establishment of the biofilm. Similarly, when initially grown as a microcolony biofilm,S. marcescenscould be converted back to a filamentous biofilm by increasing the nutrient composition. Under high-nutrient conditions, anN-acyl homoserine lactone quorum-sensing mutant formed biofilms that were indistinguishable from the wild-type biofilms. Similarly, other quorum-sensing-dependent behaviors, such as swarming motility, could be rendered quorum sensing independent by manipulating the growth medium. Quorum sensing was also found to be involved in the sloughing of the filamentous biofilm. The biofilm formed by the bacterium consistently sloughed from the substratum after approximately 75 to 80 h of development. The quorum-sensing mutant, when supplemented with exogenous signal, formed a wild-type filamentous biofilm and sloughed at the same time as the wild type, and this was independent of surfactant production. When we removed the signal from the quorum-sensing mutant prior to the time of sloughing, the biofilm did not undergo significant detachment. Together, the data suggest that biofilm formation byS. marcescensis a dynamic process that is controlled by both nutrient cues and the quorum-sensing system.
Solution Structure of the Carbon Storage Regulator Protein CsrA from
Escherichia coli
Authors: Gutiérrez Pablo , Li Yan , Osborne Michael J. , Pomerantseva Ekaterina , Liu Qian , Gehring Kalle 
Published: May 2005

ABSTRACT
The carbon storage regulator A (CsrA) is a protein responsible for the repression of a variety of stationary-phase genes in bacteria. In this work, we describe the nuclear magnetic resonance (NMR)-based structure of the CsrA dimer and its RNA-binding properties. CsrA is a dimer of two identical subunits, each composed of five strands, a small α-helix and a flexible C terminus. NMR titration experiments suggest that the β1-β2 and β3-β4 loops and the C-terminal helix are important elements in RNA binding. Even though the β3-β4 loop contains a highly conserved RNA-binding motif, GxxG, typical of KH domains, our structure excludes CsrA from being a member of this protein family, as previously suggested. A mechanism for the recognition of mRNAs downregulated by CsrA is proposed.
Genetic Dissection of the Sporulation Protein SpoIIE and Its Role in Asymmetric Division inBacillus subtilis
Authors: Carniol Karen , Ben-Yehuda Sigal , King Nicole , Losick Richard 
Published: May 2005

ABSTRACTSpoIIE is a dual-function protein inBacillus subtilisthat contributes to the switch from medial to polar cell division during sporulation and is responsible for activating the cell-specific transcription factor σF. SpoIIE consists of an N-terminal domain with 10 membrane-spanning segments (region I), a C-terminal phosphatase domain (region III), and a central domain (region II) of uncertain function. To investigate the role of SpoIIE in polar division, we took advantage of a system for efficiently producing polar septa during growth in a SpoIIE-dependent manner using cells engineered to produce the sporulation protein in response to an inducer. The results show that regions II and III play a critical role in polar septum formation and that specific amino acid substitutions in those regions affect the abilities of SpoIIE both to promote polar division and to localize to the division machinery. Additionally, we show that neither the phosphatase function of SpoIIE nor the N-terminal, membrane-spanning region is needed for the switch to asymmetric division.
The Linear Double-Stranded DNA of Phage Bam35 Enters Lysogenic Host Cells, but the Late Phage Functions Are Suppressed
Authors: Gaidelytė Aušra , Jaatinen Silja T. , Daugelavičius Rimantas , Bamford Jaana K. H. , Bamford Dennis H. 
Published: May 2005

ABSTRACT

Bam35, a temperate double-stranded DNA bacteriophage with a 15-kb linear genome, infects gram-positive
Bacillus thuringiensis
cells. Bam35 morphology and genome organization resemble those of PRD1, a lytic phage infecting gram-negative bacteria. Bam35 and PRD1 have an outer protein coat surrounding a membrane that encloses the viral DNA. We used electrochemical methods to investigate physiological changes of the lysogenic and nonlysogenic hosts during Bam35 DNA entry and host cell lysis. During viral DNA entry, there was an early temporal decrease of membrane voltage associated with K
+
efflux that took place when either lysogenic or nonlysogenic hosts were infected. Approximately 40 min postinfection, a second strong K
+
efflux was registered that was proposed to be associated with the insertion of holin molecules into the plasma membrane. This phenomenon occurred only when nonlysogenic cells were infected. Lysogenic hosts rarely were observed entering the lytic cycle as demonstrated by thin-section electron microscopy.
Gyrase Inhibitors and Thymine Starvation Disrupt the Normal Pattern of Plasmid RK2 Localization in
Escherichia coli
Authors: Johnson Erik P. , Yao Shiyin , Helinski Donald R. 
Published: May 2005

ABSTRACT

Multicopy plasmids in
Escherichia coli
are not randomly distributed throughout the cell but exist as defined clusters that are localized at the mid-cell, or at the 1/4 and 3/4 cell length positions. To explore the factors that contribute to plasmid clustering and localization,
E. coli
cells carrying a plasmid RK2 derivative that can be tagged with a green fluorescent protein-LacI fusion protein were subjected to various conditions that interfere with plasmid superhelicity and/or DNA replication. The various treatments included thymine starvation and the addition of the gyrase inhibitors nalidixic acid and novobiocin. In each case, localization of plasmid clusters at the preferred positions was disrupted but the plasmids remained in clusters, suggesting that normal plasmid superhelicity and DNA synthesis in elongating cells are not required for the clustering of individual plasmid molecules. It was also observed that the inhibition of DNA replication by these treatments produced filaments in which the plasmid clusters were confined to one or two nucleoid bodies, which were located near the midline of the filament and were not evenly spaced throughout the filament, as is found in cells treated with cephalexin. Finally, the enhanced yellow fluorescent protein-RarA fusion protein was used to localize the replication complex in individual
E. coli
cells. Novobiocin and nalidixic acid treatment both resulted in rapid loss of RarA foci. Under these conditions the RK2 plasmid clusters were not disassembled, suggesting that a completely intact replication complex is not required for plasmid clustering.
Severity of the Streptomycin Resistance and Streptomycin Dependence Phenotypes of Ribosomal Protein S12 of
Thermus thermophilus
Depends on the Identity of Highly Conserved Amino Acid Residues
Authors: Carr Jennifer F. , Gregory Steven T. , Dahlberg Albert E. 
Published: May 2005

ABSTRACT

The structural basis for the streptomycin dependence phenotype of ribosomal protein S12 mutants is poorly understood. Here we describe the application of site-directed mutagenesis and gene replacement of
Thermus thermophilus rpsL
to assess the importance of side chain identity and tertiary interactions as phenotypic determinants of drug-dependent mutants.
Virulence and the Environment: a Novel Role for
Vibrio cholerae
Toxin-Coregulated Pili in Biofilm Formation on Chitin
Authors: Reguera Gemma , Kolter Roberto 
Published: May 2005

ABSTRACT

The toxin-coregulated pilus (TCP) of
Vibrio cholerae
is required for intestinal colonization and cholera toxin acquisition. Here we report that TCP mediates bacterial interactions required for biofilm differentiation on chitinaceous surfaces. We also show that undifferentiated TCP
−
biofilms have reduced ecological fitness and, thus, that chitin colonization may represent an ecological setting outside the host in which selection for a host colonization factor may take place.
TheSalmonellaTranslocated Effector SopA Is Targeted to the Mitochondria of Infected Cells
Authors: Layton Abigail N. , Brown Philip J. , Galyov Edouard E. 
Published: May 2005

ABSTRACTThis study investigates theSalmonellaeffector protein SopA. We show that inSalmonella entericaserovar Dublin-infected cells, SopA1-347fused to two carboxy-terminal hemagglutinin tags partially colocalized with mitochondria. Transfection of eukaryotic cells with a panel of constructs encoding truncated versions of SopA identified that amino acids 100 to 347 were sufficient to target SopA to the mitochondria.
Purification and Properties of the
Klebsiella aerogenes
UreE Metal-Binding Domain, a Functional Metallochaperone of Urease
Authors: Mulrooney Scott B. , Ward Sarah K. , Hausinger Robert P. 
Published: May 2005

ABSTRACT

Klebsiella aerogenes
UreE, a metallochaperone that delivers nickel ions during urease activation, consists of distinct “peptide-binding” and “metal-binding” domains and a His-rich C terminus. Deletion analyses revealed that the metal-binding domain alone is sufficient to facilitate urease activation. This domain was purified and shown to exhibit metal-binding properties similar to those of UreE lacking only the His-rich tail.
An Adenylyl Cyclase, CyaB, Acts as an Osmosensor in
Myxococcus xanthus
Authors: Kimura Yoshio , Ohtani Mika , Takegawa Kaoru 
Published: May 2005

ABSTRACT

We have previously reported that a receptor-type adenylyl cyclase (CyaA) of
Myxococcus xanthus
undergoes an osmosensor mainly during spore germination (Y. Kimura et al., J. Bacteriol. 184:3578-3585, 2002). In the present study, we cloned another receptor-type adenylyl cyclase gene (
cyaB
) and characterized the function of the
cyaB
-encoded protein. Disruption of
cyaB
generates a mutant that showed growth retardation at high ionic (NaCl) or high nonionic (sucrose) osmolarity. When vegetative cells were stimulated with 0.15 M NaCl, the increases in intracellular cyclic AMP levels of
cyaB
mutant cells were lower than those of wild-type cells. Under nonionic osmostress, the
cyaB
mutant exhibited reduced spore germination; however, the germination rate of the
cyaB
mutant was significantly higher than that of the
cyaA
mutant.
Localization of Chaperones DnaK and GroEL in Bacterial Inclusion Bodies
Authors: Carrió M. Mar , Villaverde Antonio 
Published: May 2005

ABSTRACT

By immunostaining and transmission electron microscopy, chaperones DnaK and GroEL have been identified at the solvent-exposed surface of bacterial inclusion bodies and entrapped within these aggregates, respectively. Functional implications of this distinct localization are discussed in the context of
Escherichia coli
protein quality control.
Expression of granulocyte colony stimulating factor receptor in human colorectal cancer
Authors: Yang X , Liu F , Xu Z , Chen C , Wu X , Li G , Li J 
Published: May 2005

Abstract

Aims
To discover if human colorectal cancer expresses granulocyte colony stimulating factor receptor (G-CSFR) and if granulocyte colony stimulating factor (G-CSF) plays an important part in the development and progression of human colorectal cancer.

Methods
Forty two specimens of colorectal cancer and normal colorectal mucosa were investigated, taken from the colon or rectum in group of colorectal cancer patients. Immunohistochemistry and reverse transcription polymerase chain reaction (RT-PCR) technique were used to show G-CSFR expression. The relation between expression of G-CSFR and clinical or pathological factors was analysed.

Results
Immucohistochemical analyses showed that G-CSFR was expressed in the human colorectal cancer (25 of 42, 59.52%) and seemed to be up-regulated compared with the normal mucosa (14 of 42, 33.33%, p&lt;0.001). In pronounced contrast with mostly strongly positive tumours, corresponding normal colorectal mucosa was negative or weakly positive. A significant correlation was found between G-CSFR expression and tumour stage (p = 0.001), tumour differentiation (p&lt;0.001), but there was no significant relation between the expression of G-CSFR and the age, sex, and tumour size (p = 0.346, p = 0.686, p = 0.459). In RT-PCR, 21 of all 42 tumours had G-CSFR mRNA expression, while only 11 of 42 normal colorectal mucosa had such expression.

Conclusions
These data show that G-CSFR is commonly expressed in human colorectal cancers, thus supporting a possible role for G-CSF in colorectal cancer physiology.
Epistaxis: an update on current management
Authors: Pope L E R , Hobbs C G L 
Published: May 2005

AbstractEpistaxis is one of the commonest ENT emergencies. Although most patients can be treated within an accident and emergency setting, some are complex and may require specialist intervention. There are multiple risk factors for the development of epistaxis and it can affect any age group, but it is the elderly population with their associated morbidity who often require more intensive treatment and subsequent admission. Treatment strategies have been broadly similar for decades. However, with the evolution of endoscopic technology, new ways of actively managing epistaxis are now available. Recent evidence suggests that this, combined with the use of stepwise management plans, should limit patient complications and the need for admission. This review discusses the various treatment options and integrates the traditional methods with modern techniques.
Do consultants differ? Inferences drawn from hospital in-patient enquiry (HIPE) discharge coding at an Irish teaching hospital
Authors: Moloney E D , Smith D , Bennett K , O’Riordan D , Silke B 
Published: May 2005

Abstract

Objective
To find out if there was a difference between hospital consultants, all trained in acute general medicine, in length of stay (LOS), re-admission rates, resource utilisation, and diagnostic coding, among patients admitted as emergencies to St James’ Hospital (SJH) Dublin.

Methods
A retrospective analysis was performed of data on discharges from hospital, recorded in the hospital in-patient enquiry (HIPE) system, relating to 9204 episodes among 6968 emergency medical patients admitted to SJH between 1 January 2002 and 31 October 2003. For comparative analysis, four physician groups were defined consisting of gastroenterology (GI, n = 4), respiratory (n = 3), general internal medicine (GIM, n = 2), or specialty (n = 5).

Results
GIM consultants had the shortest LOS (median 5 days); GIM and respiratory consultants were less likely to have long stay patients (&gt; 30 days, p&lt;0.0001). Patients re-admitted under the same consultant had a longer LOS than those re-admitted under a different consultant (p&lt;0.0001). Endoscopy and GI radiology investigations were used most by GI consultants, computed tomography of the thorax by respiratory, ECHO by respiratory and specialty, and computed tomography of brain by GIM and specialty consultants. GI diagnostic codings were more frequent with GI consultants (p&lt;0.0001), respiratory diagnoses and malignancy with respiratory (p&lt;0.0001 for both), diabetes and hypertension with specialty (p = 0.0017), and heart failure more with GIM consultants (p = 0.001).

Conclusions
This study found that the HIPE database was very powerful in predicting differences between hospital consultants in LOS, re-admission rates, resource utilisation, and disease coding. It would be of interest to examine the extent to which protocols and guidelines could reduce such variations.
Device based treatment of heart failure
Authors: Patwala A Y , Wright D J 
Published: May 2005

Abstract
As the population ages and survival from ischaemic heart disease improves, the incidence and prevalence of congestive cardiac failure has increased dramatically. Medical treatments including ACE inhibitors, β blockers, and aldosterone antagonists have improved the outlook for most patients. However, despite optimal medical treatment there is a significant group of patients who continue to suffer poor morbidity and mortality. Device based treatment consisting of implantable cardioverter defibrillators (ICD) and cardiac resynchronisation therapy (CRT) devices offer new modes of treatment to patients with symptomatic heart failure despite optimal medical therapy. ICDs have been shown to reduce mortality in patients with severe heart failure while CRT leads to an improvement in functional class, quality of life scores, physiological measures such as peak vo 2, and reduce hospitalisations. Combination devices, which provide both ICD and CRT functions, have now been seen to provide synergistic benefits in selected patients.
Multiple sclerosis: diagnosis and the management of acute relapses
Authors: Leary S M , Porter B , Thompson A J 
Published: May 2005

Abstract
Multiple sclerosis is an inflammatory demyelinating disease of the central nervous system that may result in a wide range of neurological symptoms and accumulating disability. Its course is unpredictable resulting in a changing pattern of clinical need. Diagnostic criteria for multiple sclerosis require objective evidence for dissemination in space and time. The diagnostic and management process should follow good practice guidelines with the person at the centre of the process. Appropriate support and information should be available from the time of diagnosis. Continuing education is key in enabling the person to actively participate in their management. In the event of an acute relapse the person should have direct access to the most appropriate local service. Provided medical causes have been excluded, corticosteroid treatment to hasten the recovery from the relapse should be considered. Management of an acute relapse should be comprehensive addressing any medical, functional, or psychosocial sequelae.
Diaspora, a large family of Ty3-gypsy retrotransposons in Glycine max, is an envelope-less member of an endogenous plant retrovirus lineage
Authors: Yano Sho T , Panbehi Bahman , Das Arpita , Laten Howard M 
Published: May 2005

Abstract
Background
The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful colonizers of the chromosomes of higher plants and examinations of their function, evolution, and dispersal are essential to understanding the evolution of eukaryotic genomes. In soybean, several families of retrotransposons have been identified, including at least two that, by virtue of the presence of an envelope-like gene, may constitute endogenous retroviruses. However, most elements are highly degenerate and are often sequestered in regions of the genome that sequencing projects initially shun. In addition, finding potentially functional copies from genomic DNA is rare. This study provides a mechanism to surmount these issues to generate a consensus sequence that can then be functionally and phylogenetically evaluated.

Results
Diaspora is a multicopy member of the Ty3-gypsy-like family of LTR retrotransposons and comprises at least 0.5% of the soybean genome. Although the Diaspora family is highly degenerate, and with the exception of this report, is not represented in the Genbank nr database, a full-length consensus sequence was generated from short overlapping sequences using a combination of experimental and in silico methods. Diaspora is 11,737 bp in length and contains a single 1892-codon ORF that encodes a gag-pol polyprotein. Phylogenetic analysis indicates that it is closely related to Athila and Calypso retroelements from Arabidopsis and soybean, respectively. These in turn form the framework of an endogenous retrovirus lineage whose members possess an envelope-like gene. Diaspora appears to lack any trace of this coding region.

Conclusion
A combination of empirical sequencing and retrieval of unannotated Genome Survey Sequence database entries was successfully used to construct a full-length representative of the Diaspora family in Glycine max. Diaspora is presently the only fully characterized member of a lineage of putative plant endogenous retroviruses that contains virtually no trace of an extra coding region. The loss of an envelope-like coding domain suggests that non-infectious retrotransposons could swiftly evolve from infectious retroviruses, possibly by anomalous splicing of genomic RNA.