bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mlc Is a Transcriptional Activator with a Key Role in Integrating Cyclic AMP Receptor Protein and Integration Host Factor Regulation of Leukotoxin RNA Synthesis in Aggregatibacter actinomycetemcomitans
Authors: Childress Catherine , Feuerbacher Leigh A. , Phillips Linda , Burgum Alex , Kolodrubetz David 
Published: March 2013

ABSTRACT

Aggregatibacter actinomycetemcomitans
, a periodontal pathogen, synthesizes leukotoxin (LtxA), a protein that helps the bacterium evade the host immune response. Transcription of the
ltxA
operon is induced during anaerobic growth. The cyclic AMP (cAMP) receptor protein (CRP) indirectly increases
ltxA
expression, but the intermediary regulator is unknown. Integration host factor (IHF) binds to and represses the leukotoxin promoter, but neither CRP nor IHF is responsible for the anaerobic induction of
ltxA
RNA synthesis. Thus, we have undertaken studies to identify other regulators of leukotoxin transcription and to demonstrate how these proteins work together to modulate leukotoxin synthesis. First, analyses of
ltxA
RNA expression from defined leukotoxin promoter mutations in the chromosome identify positions −69 to −35 as the key control region and indicate that an activator protein modulates leukotoxin transcription. We show that Mlc, which is a repressor in
Escherichia coli
, functions as a direct transcriptional activator in
A. actinomycetemcomitans
; an
mlc
deletion mutant reduces leukotoxin RNA synthesis, and recombinant Mlc protein binds specifically at the −68 to −40 region of the leukotoxin promoter. Furthermore, we show that CRP activates
ltxA
expression indirectly by increasing the levels of Mlc. Analyses of Δ
mlc
, Δ
ihf
, and Δ
ihf
Δ
mlc
strains demonstrate that Mlc can increase RNA polymerase (RNAP) activity directly and that IHF represses
ltxA
RNA synthesis mainly by blocking Mlc binding. Finally, a Δ
ihf
Δ
mlc
mutant still induces
ltxA
during anaerobic growth, indicating that there are additional factors involved in leukotoxin transcriptional regulation. A model for the coordinated regulation of leukotoxin transcription is presented.
Neisseria gonorrhoeae RecQ Helicase HRDC Domains Are Essential for Efficient Binding and Unwinding of the
pilE
Guanine Quartet Structure Required for Pilin Antigenic Variation
Authors: Cahoon Laty A. , Manthei Kelly A. , Rotman Ella , Keck James L. , Seifert H. Steven 
Published: March 2013

ABSTRACT

The strict human pathogen
Neisseria gonorrhoeae
utilizes homologous recombination to antigenically vary the pilus, thus evading the host immune response. High-frequency gene conversion reactions between many silent pilin loci and the expressed pilin locus (
pilE
) allow for numerous pilus variants per strain to be produced from a single strain. For pilin antigenic variation (Av) to occur, a guanine quartet (G4) structure must form upstream of
pilE
. The RecQ helicase is one of several recombination or repair enzymes required for efficient levels of pilin Av, and RecQ family members have been shown to bind to and unwind G4 structures. Additionally, the vast majority of RecQ helicase family members encode one “helicase and RNase D C-terminal” (HRDC) domain, whereas the
N. gonorrhoeae
RecQ helicase gene encodes three HRDC domains, which are critical for pilin Av. Here, we confirm that deletion of RecQ HRDC domains 2 and 3 causes a decrease in the frequency of pilin Av comparable to that obtained with a functional knockout. We demonstrate that the
N. gonorrhoeae
RecQ helicase can bind and unwind the
pilE
G4 structure. Deletion of the RecQ HRDC domains 2 and 3 resulted in a decrease in G4 structure binding and unwinding. These data suggest that the decrease in pilin Av observed in the RecQ HRDC domain 2 and 3 deletion mutant is a result of the enzyme's inability to efficiently bind and unwind the
pilE
G4 structure.
Gap2 Promotes the Formation of a Stable Protein Complex Required for Mature Fap1 Biogenesis
Authors: Echlin Haley , Zhu Fan , Li Yirong , Peng Zhixiang , Ruiz Teresa , Bedwell Gregory J. , Prevelige Peter E. , Wu Hui 
Published: March 2013

ABSTRACT

Serine-rich repeat glycoproteins (SRRPs) are important bacterial adhesins conserved in streptococci and staphylococci. Fap1, a SRRP identified in
Streptococcus parasanguinis
, is the major constituent of bacterial fimbriae and is required for adhesion and biofilm formation. An 11-gene cluster is required for Fap1 glycosylation and secretion; however, the exact mechanism of Fap1 biogenesis remains a mystery. Two glycosylation-associated proteins within this cluster—Gap1 and Gap3—function together in Fap1 biogenesis. Here we report the role of the third glycosylation-associated protein, Gap2. A
gap2
mutant exhibited the same phenotype as the
gap1
and
gap3
mutants in terms of Fap1 biogenesis, fimbrial assembly, and bacterial adhesion, suggesting that the three proteins interact. Indeed, all three proteins interacted with each other independently and together to form a stable protein complex. Mechanistically, Gap2 protected Gap3 from degradation by ClpP protease, and Gap2 required the presence of Gap1 for expression at the wild-type level. Gap2 augmented the function of Gap1 in stabilizing Gap3; this function was conserved in Gap homologs from
Streptococcus agalactiae
. Our studies demonstrate that the three Gap proteins work in concert in Fap1 biogenesis and reveal a new function of Gap2. This insight will help us elucidate the molecular mechanism of SRRP biogenesis in this bacterium and in pathogenic species.
Involvement of Cyclic AMP Receptor Protein in Regulation of the
rmf
Gene Encoding the Ribosome Modulation Factor in Escherichia coli
Authors: Shimada Tomohiro , Yoshida Hideji , Ishihama Akira 
Published: March 2013

ABSTRACT

The decrease in overall translation in stationary-phase
Escherichia coli
is accompanied with the formation of functionally inactive 100S ribosomes mediated by the ribosome modulation factor (RMF). At present, however, little is known regarding the regulation of stationary-phase-coupled RMF expression. In the course of a systematic screening of regulation targets of DNA-binding transcription factors from
E. coli
, we realized that CRP (cyclic AMP [cAMP] receptor protein), the global regulator for carbon source utilization, participates in regulation of some ribosomal protein genes, including the
rmf
gene. In this study, we carried out detailed analysis of the regulation of the RMF gene by cAMP-CRP. The cAMP-dependent binding of CRP to the
rmf
gene promoter was confirmed by gel shift and DNase I footprinting assays. By using a reporter assay system, the expression level of RMF was found to decrease in the
crp
knockout mutant, indicating the involvement of CRP as an activator of the
rmf
promoter. In good agreement with the reduction of
rmf
promoter activity, we observed decreases in RMF production and 100S ribosome dimerization in the absence of CRP. Taken together, we propose that CRP regulates transcription activation of the
rmf
gene for formation of 100S ribosome dimers. Physiological roles of CRP involvement in RMF production are discussed.
Biochemistry and Physiology of the β Class Carbonic Anhydrase (Cpb) from Clostridium perfringens Strain 13
Authors: Kumar R. Siva Sai , Hendrick William , Correll Jared B. , Patterson Andrew D. , Melville Stephen B. , Ferry James G. 
Published: March 2013

ABSTRACT

The carbonic anhydrase (Cpb) from
Clostridium perfringens
strain 13, the only carbonic anhydrase encoded in the genome, was characterized both biochemically and physiologically. Heterologously produced and purified Cpb was shown to belong to the type I subclass of the β class, the first β class enzyme investigated from a strictly anaerobic species of the domain
Bacteria
. Kinetic analyses revealed a two-step, ping-pong, zinc-hydroxide mechanism of catalysis with

K
m

and
k
cat
/

K
m

values of 3.1 mM CO
2
and 4.8 × 10
6
s
−1
M
−1
, respectively. Analyses of a
cpb
deletion mutant of
C. perfringens
strain HN13 showed that Cpb is strictly required for growth when cultured in semidefined medium and an atmosphere without CO
2
. The growth of the mutant was the same as that of the parent wild-type strain when cultured in nutrient-rich media with or without CO
2
in the atmosphere, although elimination of glucose resulted in decreased production of acetate, propionate, and butyrate. The results suggest a role for Cpb in anaplerotic CO
2
fixation reactions by supplying bicarbonate to carboxylases. Potential roles in competitive fitness are discussed.
Cloning and Analysis of the Planosporicin Lantibiotic Biosynthetic Gene Cluster of Planomonospora alba
Authors: Sherwood Emma J. , Hesketh Andrew R. , Bibb Mervyn J. 
Published: March 2013

ABSTRACT

The increasing prevalence of antibiotic resistance in bacterial pathogens has renewed focus on natural products with antimicrobial properties. Lantibiotics are ribosomally synthesized peptide antibiotics that are posttranslationally modified to introduce (methyl)lanthionine bridges. Actinomycetes are renowned for their ability to produce a large variety of antibiotics, many with clinical applications, but are known to make only a few lantibiotics. One such compound is planosporicin produced by
Planomonospora alba
, which inhibits cell wall biosynthesis in Gram-positive pathogens. Planosporicin is a type AI lantibiotic structurally similar to those which bind lipid II, the immediate precursor for cell wall biosynthesis. The gene cluster responsible for planosporicin biosynthesis was identified by genome mining and subsequently isolated from a
P. alba
cosmid library. A minimal cluster of 15 genes sufficient for planosporicin production was defined by heterologous expression in
Nonomuraea
sp. strain ATCC 39727, while deletion of the gene encoding the precursor peptide from
P. alba
, which abolished planosporicin production, was also used to confirm the identity of the gene cluster. Deletion of genes encoding likely biosynthetic enzymes identified through bioinformatic analysis revealed that they, too, are essential for planosporicin production in the native host. Reverse transcription-PCR (RT-PCR) analysis indicated that the planosporicin gene cluster is transcribed in three operons. Expression of one of these,
pspEF
, which encodes an ABC transporter, in
Streptomyces coelicolor
A3(2) conferred some degree of planosporicin resistance on the heterologous host. The inability to delete these genes from
P. alba
suggests that they play an essential role in immunity in the natural producer.
Is the Surgical Safety Checklist successfully conducted? An observational study of social interactions in the operating rooms of a tertiary hospital
Authors: Cullati Stéphane , Le Du Sophie , Raë Anne-Claire , Micallef Martine , Khabiri Ebrahim , Ourahmoune Aimad , Boireaux Armelle , Licker Marc , Chopard Pierre 
Published: March 2013

ObjectivesTo determine whether the items on the Time Out and the Sign Out of the Surgical Safety Checklist are properly checked by operating room (OR) staff and to explore whether the number of checked items is influenced by the severity of the intervention and the use of the checklist as a memory tool during the Time Out and the Sign Out periods.MethodsFrom March to July 2010, data were collected during elective surgery at the Geneva University Hospitals, Switzerland. The main outcome was to assess whether each item of the Time Out and the Sign Out checklists have been checked, that is, ‘confirmed’ by at least one member of the team and ‘validated’ by at least one other member of the team. The secondary outcome was the number of validated items during the Time Out and the Sign Out.ResultsTime Outs (N=80) and Sign Outs (N=81) were conducted quasi systematically (99%). Items were mostly confirmed during the Time Out (range 100–72%) but less often during the Sign Out (range 86–19%). Validation of the items was far from optimal: only 13% of Time Outs and 3% of Sign Outs were properly checked (all items validated). During the Time Out, the validation process was significantly improved among the highest risk interventions (29% validation vs 15% among interventions at lower risk). During the Sign Out, a similar effect was observed (19% and 8%, respectively). A small but significant benefit was observed when using a printed checklist as a memory tool during the Sign Out, the proportion of interventions with almost all validated items being higher compared with those without the memory tool (20% and 0%, respectively).ConclusionsTraining on the proper completion of the checklist must be provided to OR teams. The severity of the interventions influenced the number of items properly checked.
Widening socioeconomic differences in mortality among men aged 65 years and older in Germany
Authors: Kibele Eva U B , Jasilionis Domantas , Shkolnikov Vladimir M 
Published: March 2013

BackgroundAlthough socioeconomic mortality differences in Germany are well documented, trends in group-specific mortality and differences between the eastern and the western parts of the country remain unexplored.MethodsPopulation and death counts by level of lifetime earnings (1995–1996 to 2007–2008) and broad occupational groups (1995–1996 to 2003–2004) for men aged 65 years and older were obtained from the German Federal Pension Fund. Directly standardised mortality rates and life expectancy at age 65 were used as mortality measures.ResultsMortality declined in all socioeconomic groups in eastern and western Germany and these declines tended to be larger in higher status groups. Relative socioeconomic differences in age-standardised mortality rates and in life expectancy at age 65 widened over time. Absolute differences widened over the majority of time periods. The widening was more pronounced in eastern Germany.ConclusionsWidening socioeconomic mortality differences in Germany, especially in eastern Germany, show that population groups did not benefit equally from the improvements in survival. The results suggest that special efforts have to be taken in order to reduce mortality among people with lower socioeconomic status, especially in eastern Germany. Health equity should be considered a priority when planning policies, practices, and changes in the healthcare system and related sectors.
Monitoring the bulk milk antibody response to BVDV: the effects of vaccination and herd infection status
Authors: Booth R. E. , Cranwell M. P. , Brownlie J. 
Published: March 2013

Bovine Viral Diarrhoea Virus (BVDV) is a pestivirus in the flaviviridae family which affects cattle worldwide. Bulk milk (BM) antibody testing is frequently used as a relatively quick method of assessing herd BVDV exposure; however, an understanding of the effects of vaccination and historic infection is essential for test interpretation. This study investigated the trends exhibited by monthly BM antibody analysis in 14 herds split into three categories. Category 1 herds (vaccinating/no persistently infected (PI) animals) began the study with mid‐positive BM antibody titres and experienced an estimated increase of 0.007 optical density (OD) units per month (equating to a rise of 0.35 OD units in 50 months). Category 2 herds (not vaccinating/no PI animals) began the study with mid‐positive BM antibody titres and experienced an estimated decrease of 0.005 OD units per month with antibody levels in one category 2 herd taking 1290 days to decrease from mid‐positive to negative. Category 3 herds (vaccinating/PI animals present) began the study with high BM antibody titres which plateaued within this range throughout the 50‐month observation period. Vaccination was observed to cause transient increases in BM antibody in a number of herds in categories 1 and 3.
Thick-skinned tectonics in the Oriente foreland basin of Ecuador
Authors: Baby P. , Rivadeneira M. , Barragán R. , Christophoul F. 
Published: March 2013

Abstract
The Oriente Basin is part of the retro-arc foreland basin system that developed in the zone of transition between the Central Andes and the Northern Andes since Late Cretaceous times. It is deformed by thick-skinned tectonics related to the inversion of pre-Cretaceous extensional fault systems, which have broken the basin into three tectonic domains during three mean periods of inversion (Late Cretaceous–Palaeocene, Early Eocene and Miocene). The northern part of the present-day Sub-Andean wedge-top corresponded, during the Late Cretaceous, to the forebulge depozone. The NNE–SSW Sacha–Shushufindi Corridor (SSC) extends from the northern region of the Oriente foredeep to the Sub-Andean Cutucú Cordillera. It results from inversion of the Late Triassic–Early Jurassic rifting. The eastern Capiron–Tiputini Inverted System (CTIS) results from the inversion of the normal faults of the Late Jurassic back-arc basin. The Ishpingo–Tambococha–Tiputini (ITT) trend is located in the present-day forebulge depozone of the basin. This position presents favourable conditions for oil biodegradation. Source rocks throughout the Oriente Basin are immature or poorly mature. A large part of oil accumulations must be explained by long-distance migration from the west, before the Eocene uplift of the Cordillera Real, or from the south.
Thick-skinned tectonic style resulting from the inversion of previous structures in the southern Cordillera Oriental (NW Argentine Andes)
Authors: Carrera N. , Muñoz J. A. 
Published: March 2013

Abstract
Structures mapped in the southern Cordillera Oriental of the Andes show an unexpected geometry in an east–west cross-sectional view, with a remarkable predominance of west-directed thrusts. Although some of the Andean structures trend north–south perpendicular to the main east–west direction of Andean shortening, many of them clearly differ from this expected orientation. This peculiar structural style has been largely related to the inversion of the Cretaceous Salta Rift Basin; however, some of these anomalously trending Andean folds and faults do not result from the inversion of Cretaceous faults. This lack of inversion of some Cretaceous structures becomes evident where west-dipping extensional faults rest in the footwall of west-directed thrusts instead of developing east-directed thrusts, as would be expected. Detailed study of several structures and examination of the geometry and facies distribution of several basins highlight not only the role played by the inversion of Cretaceous extensional faults on the geometry of the Andean structures, but also that played by basement anisotropies on the development of both the Cretaceous extensional faults and the Andean contractional structures.
Along-strike extrusion at the transition between thin- and thick-skinned domains in the Pyrenean Orogen (northern Spain)
Authors: Carola E. , Tavani S. , Ferrer O. , Granado P. , Quintà A. , Butillé M. , Muñoz J. A. 
Published: March 2013

Abstract
In the south-verging portion of the western Pyrenean Orogen, a Mesozoic basin and part of the adjacent continental margin were deformed during the Pyrenean collisional stage. The slight obliquity between extensional and compressional trends, and the presence of a Mesozoic Transfer Zone, implied that both extensional domains were exposed along-strike of the belt in the same structural position. These two areas are not only characterized by the widespread reactivation of inherited fault systems but also by different styles of deformation related to the presence or absence of an evaporitic detachment level. To the east, in the Mesozoic basin, a large-displacement south-directed low-dipping thrust detached above Triassic evaporites is present. To the west, in the Mesozoic continental margin, thick-skinned and deeply rooted right-lateral and reverse faults become first-order elements. The presence of a strike-slip component produced the eastwards extrusion of the eastern portion of the Mesozoic continental margin, which imposed an along-strike shortening at the edge of the extruded block. The transitional area from thin- to thick-skinned style of deformation, from a dip-slip to a transpressive framework, and the area accommodating the extrusion are located along a north–south-orientated band representing the southern extension of a Mesozoic Transfer Zone.
Factors controlling selective abandonment and reactivation in thick-skin orogens: a case study in the Magdalena Valley, Colombia
Authors: Caballero Víctor , Parra Mauricio , Mora Andrés , López Cristina , Rojas Luis Ernesto , Quintero Isaid 
Published: March 2013

Abstract
The initial stages of tectonic inversion and the mechanisms of selective reactivation and abandonment of pre-existing normal faults during contractional orogenesis are explored in a partially buried Cenozoic thrust belt in the Andes of Colombia. A multidisciplinary approach that includes subsurface structural mapping, multimethod thermochronometry and detrital zircon U–Pb geochronology reveals the extent of a Palaeogene thrust belt buried underneath the Cenozoic strata of the Middle Magdalena Valley Basin. A less oblique orientation with respect to compressive stress and shorter traces in faults of the Middle Magdalena Valley Basin with respect to faults in the western part of the Eastern Cordillera, apparently acted as deformation inhibitors of the Magdalena faults in advanced Neogene stages of inversion. Protracted Cenozoic eastwards tilting of the Central Cordillera and the tectonic load from the uplifting Eastern Cordillera favoured the accumulation of a thick Cenozoic sedimentary sequence in an, at least episodically, closed basin. All the above-mentioned conditions helped to block deformation in the Magdalena Basin, favouring deformation to be taken up by structures in the western Eastern Cordillera. These relationships underscore the importance of buried structural records in elevated hinterland basins, in which the low-relief stratigraphic cover overlies a complex subsurface record, potentially including large magnitudes of deformation during early orogenesis.

Supplementary material:

Tables and figures on the laboratory methods for the thermochronometrical and geochronometrical analyses are available at
http://www.geolsoc.org.uk/SUP18601
.