bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation of Structure and Protein-Protein Interactions Mediated by the Secreted Mycobacterial Proteins EsxA, EsxB, and EspA
Authors: Callahan Brian , Nguyen Kiet , Collins Alissa , Valdes Kayla , Caplow Michael , Crossman David K. , Steyn Adrie J. C. , Eisele Leslie , Derbyshire Keith M. 
Published: October 2009

ABSTRACTMycobacterium tuberculosisEsxA and EsxB proteins are founding members of the WXG100 (WXG) protein family, characterized by their small size (∼100 amino acids) and conserved WXG amino acid motif.M. tuberculosiscontains 11 tandem pairs of WXG genes; each gene pair is thought to be coexpressed to form a heterodimer. The precise role of these proteins in the biology ofM. tuberculosisis unknown, but several of the heterodimers are secreted, which is important for virulence. However, WXG proteins are not simply virulence factors, since nonpathogenic mycobacteria also express and secrete these proteins. Here we show that three WXG heterodimers have structures and properties similar to those of theM. tuberculosisEsxBA (MtbEsxBA) heterodimer, regardless of their host species and apparent biological function. Biophysical studies indicate that the WXG proteins fromM. tuberculosis(EsxG and EsxH),Mycobacterium smegmatis(EsxA and EsxB), andCorynebacterium diphtheriae(EsxA and EsxB) are heterodimers and fold into a predominately α-helical structure. An in vivo protein-protein interaction assay was modified to identify proteins that interact specifically with the native WXG100 heterodimer. MtbEsxA and MtbEsxB were fused into a single polypeptide, MtbEsxBA, to create a biomimetic bait for the native heterodimer. The MtbEsxBA bait showed specific association with severalesx-1-encoded proteins and EspA, a virulence protein secreted by ESX-1. The MtbEsxBA fusion peptide was also utilized to identify residues in both EsxA and EsxB that are important for establishing protein interactions with Rv3871 and EspA. Together, the results are consistent with a model in which WXG proteins perform similar biological roles in virulent and nonvirulent species.
Structure and Regulation of thegabGene Cluster, Involved in the γ-Aminobutyric Acid Shunt, Are Controlled by a σ54Factor inBacillus thuringiensis
Authors: Zhu Li , Peng Qi , Song Fuping , Jiang Yanan , Sun Changpo , Zhang Jie , Huang Dafang 
Published: October 2009

ABSTRACTThe structure and regulation of thegabgene cluster, involved in γ-aminobutyric acid (GABA) shunt, were studied by characterizinggabTandgabDgenes cloned fromBacillus thuringiensis. Deletions of thegabTandgabDgenes inB. thuringiensisstrain HD-73 did not affect the growth of mutant strains in rich culture media, but the growth of agabTdeletion mutant strain was reduced in basic media (containing 0.2% GABA). Genome analysis indicates that the structure of thegabgene cluster inB. thuringiensisHD-73 is different from that inEscherichia coliandBacillus subtilisbut is common in strains of theBacillus cereusgroup. This suggests that the gene cluster involved in GABA shunt is specific to theB. cereusgroup. Based on reverse transcription-PCR and transcriptional fusion analysis, we confirmed that thegabTandgabDgenes belong to different transcriptional units, while thegabDandgabRgenes form an operon. We also demonstrated that thegabRgene plays a positive regulatory role ingabDandgabTexpression. The GabR protein may be a σ54-dependent transcriptional activator, according to a conserved domain search in the NCBI database, and it is highly conserved in theB. cereusgroup. The −24/−12 consensus sequence of a promoter upstream fromgabTsuggests that the promoter can be recognized by a σ54factor. Further analysis of the genetic complementation studies also suggests that the expression of thegabTgene is controlled by a σ54factor. Thus, the expression of thegabcluster is regulated by a σ54factor by way of the transcription activator GabR.
Appendage-Mediated Surface Adherence of
Sulfolobus solfataricus
Authors: Zolghadr Behnam , Klingl Andreas , Koerdt Andrea , Driessen Arnold J. M. , Rachel Reinhard , Albers Sonja-Verena 
Published: October 2009

ABSTRACT

Attachment of microorganisms to surfaces is a prerequisite for colonization and biofilm formation. The hyperthermophilic crenarchaeote
Sulfolobus solfataricus
was able to attach to a variety of surfaces, such as glass, mica, pyrite, and carbon-coated gold grids. Deletion mutant analysis showed that for initial attachment the presence of flagella and pili is essential. Attached cells produced extracellular polysaccharides containing mannose, galactose, and
N
-acetylglucosamine. Genes possibly involved in the production of the extracellular polysaccharides were identified.
Metabolic Control of Virulence Genes inBrucella abortus: HutC CoordinatesvirBExpression and the Histidine Utilization Pathway by Direct Binding to Both Promoters
Authors: Sieira Rodrigo , Arocena Gastón M. , Bukata Lucas , Comerci Diego J. , Ugalde Rodolfo A. 
Published: October 2009

ABSTRACTType IV secretion systems (T4SS) are multicomponent machineries involved in the translocation of effector molecules across the bacterial cell envelope. ThevirBoperon ofBrucella abortuscodes for a T4SS that is essential for virulence and intracellular multiplication of the bacterium in the host. Previous studies showed that thevirBoperon ofB. abortusis tightly regulated within the host cells. In order to identify factors implicated in the control ofvirBexpression, we searched for proteins ofBrucellathat directly bind to thevirBpromoter (PvirB). Using different procedures, we isolated a 27-kDa protein that binds specifically to PvirB. This protein was identified as HutC, the transcriptional repressor of the histidine utilization (hut) genes. Analyses ofvirBandhutpromoter activity revealed that HutC exerts two different roles: it acts as a coactivator of transcription of thevirBoperon, whereas it represses thehutgenes. Such activities were observed both intracellularly and in bacteria incubated under conditions that resemble the intracellular environment. Electrophoresis mobility shift assays (EMSA) and DNase I footprinting experiments revealed the structure, affinity, and localization of the HutC-binding sites and supported the regulatory role of HutC in bothhutandvirBpromoters. Taken together, these results indicate thatBrucellacoopted the function of HutC to coordinate the Hut pathway with transcriptional regulation of thevirBgenes, probably as a way to sense its own metabolic state and develop adaptive responses to overcome intracellular host defenses.
Accumulation of Intermediates of the Carbon-Phosphorus Lyase Pathway for Phosphonate Degradation in
phn
Mutants of
Escherichia coli
Authors: Hove-Jensen Bjarne , Rosenkrantz Tina J. , Zechel David L. , Willemoës Martin 
Published: October 2009

ABSTRACT

The catabolism of phosphonic acids occurs in
Escherichia coli
by the carbon-phosphorus lyase pathway, which is governed by the 14-cistron
phn
operon. Here, several compounds are shown to accumulate in strains of
E. coli
with genetic blocks in various
phn
cistrons when the strains are fed with phosphonate.
Control of Thioredoxin Reductase Gene (
trxB
) Transcription by SarA in
Staphylococcus aureus
Authors: Ballal Anand , Manna Adhar C. 
Published: October 2009

ABSTRACT

Thioredoxin reductase (encoded by
trxB
) protects
Staphylococcus aureus
against oxygen or disulfide stress and is indispensable for growth. Among the different
sarA
family mutants analyzed, transcription of
trxB
was markedly elevated in the
sarA
mutant under conditions of aerobic as well as microaerophilic growth, indicating that SarA acts as a negative regulator of
trxB
expression. Gel shift analysis showed that purified SarA protein binds directly to the
trxB
promoter region DNA
in vitro
. DNA binding of SarA was essential for repression of
trxB
transcription
in vivo
in
S. aureus
. Northern blot analysis and DNA binding studies of the purified wild-type SarA and the mutant SarAC9G with oxidizing agents indicated that oxidation of Cys-9 reduced the binding of SarA to the
trxB
promoter DNA. Oxidizing agents, in particular diamide, could further enhance transcription of the
trxB
gene in the
sarA
mutant, suggesting the presence of a SarA-independent mode of
trxB
induction. Analysis of two oxidative stress-responsive
sarA
regulatory target genes,
trxB
and
sodM
, with various mutant
sarA
constructs showed a differential ability of the SarA to regulate expression of the two above-mentioned genes
in vivo
. The overall data demonstrate the important role played by SarA in modulating expression of genes involved in oxidative stress resistance in
S. aureus
.
Identification and Characterization of Noncoding Small RNAs inStreptococcus pneumoniaeSerotype 2 Strain D39
Authors: Tsui Ho-Ching Tiffany , Mukherjee Dhriti , Ray Valerie A. , Sham Lok-To , Feig Andrew L. , Winkler Malcolm E. 
Published: October 2009

ABSTRACTWe report a search for small RNAs (sRNAs) in the low-GC, Gram-positive human pathogenStreptococcus pneumoniae. Based on bioinformatic analyses by Livny et al. (J. Livny, A. Brencic, S. Lory, and M. K. Waldor, Nucleic Acids Res.34:3484-3493, 2006), we tested 40 candidates by Northern blotting and confirmed the expression of nine new and one previously reported (CcnA) sRNAs in strain D39. CcnA is one of five redundant sRNAs reported by Halfmann et al. (A. Halfmann, M. Kovacs, R. Hakenbeck, and R. Bruckner, Mol. Microbiol.66:110-126, 2007) that are positively controlled by the CiaR response regulator. We characterized 3 of these 14 sRNAs: Spd-sr17 (144 nucleotides [nt]; decreased in stationary phase), Spd-sr37 (80 nt; strongly expressed in all growth phases), and CcnA (93 nt; induced by competence stimulatory peptide). Spd-sr17 and CcnA likely fold into structures containing single-stranded regions between hairpin structures, whereas Spd-sr37 forms a base-paired structure. Primer extension mapping and ectopic expression in deletion/insertion mutants confirmed the independent expression of the three sRNAs. Microarray analyses indicated that insertion/deletion mutants inspd-sr37andccnAexerted strongcis-acting effects on the transcription of adjacent genes, indicating that these sRNA regions are also cotranscribed in operons. Deletion or overexpression of the three sRNAs did not cause changes in growth, certain stress responses, global transcription, or virulence. Constitutive ectopic expression of CcnA reversed some phenotypes of D39 ΔciaRmutants, but attempts to link CcnA to -E tocomCas a target were inconclusive inciaR+strains. These results show thatS. pneumoniae, which lacks known RNA chaperones, expresses numerous sRNAs, but three of these sRNAs do not strongly affect common phenotypes or transcription patterns.
Mismatch Correction Modulates Mutation Frequency and Pilus Phase and Antigenic Variation in
Neisseria gonorrhoeae
Authors: Criss Alison K. , Bonney Kevin M. , Chang Rhoda A. , Duffin Paul M. , LeCuyer Brian E. , Seifert H. Steven 
Published: October 2009

ABSTRACT

The mismatch correction (MMC) system repairs DNA mismatches and single nucleotide insertions or deletions postreplication. To test the functions of MMC in the obligate human pathogen
Neisseria gonorrhoeae
, homologues of the core MMC genes
mutS
and
mutL
were inactivated in strain FA1090. No
mutH
homologue was found in the FA1090 genome, suggesting that gonococcal MMC is not methyl directed. MMC mutants were compared to a mutant in
uvrD
, the helicase that functions with MMC in
Escherichia coli
. Inactivation of MMC or
uvrD
increased spontaneous resistance to rifampin and nalidixic acid, and MMC/
uvrD
double mutants exhibited higher mutation frequencies than any single mutant. Loss of MMC marginally enhanced the transformation efficiency of DNA carrying a single nucleotide mismatch but not that of DNA with a 1-kb insertion. Unlike the exquisite UV sensitivity of the
uvrD
mutant, inactivating MMC did not affect survival after UV irradiation. MMC and
uvrD
mutants exhibited increased PilC-dependent pilus phase variation.
mutS-
deficient gonococci underwent an increased frequency of pilin antigenic variation, whereas
uvrD
had no effect. Recombination tracts in the
mutS
pilin variants were longer than in parental gonococci but utilized the same donor
pilS
loci. These results show that gonococcal MMC repairs mismatches and small insertion/deletions in DNA and also affects the recombination events underlying pilin antigenic variation. The differential effects of MMC and
uvrD
in gonococci unexpectedly reveal that MMC can function independently of
uvrD
in this human-specific pathogen.
Response of the Oxygen Sensor NreB to Air
In Vivo
: Fe-S-Containing NreB and Apo-NreB in Aerobically and Anaerobically Growing
Staphylococcus carnosus
Authors: Reinhart F. , Huber A. , Thiele R. , Unden G. 
Published: October 2009

ABSTRACT

The sensor kinase NreB from
Staphylococcus carnosus
contains an O
2
-sensitive [4Fe-4S]
2+
cluster which is converted by O
2
to a [2Fe-2S]
2+
cluster, followed by complete degradation and formation of Fe-S-less apo-NreB. NreB·[2Fe-2S]
2+
and apoNreB are devoid of kinase activity. NreB contains four Cys residues which ligate the Fe-S clusters. The accessibility of the Cys residues to alkylating agents was tested and used to differentiate Fe-S-containing and Fe-S-less NreB. In a two-step labeling procedure, accessible Cys residues in the native protein were first labeled by iodoacetate. In the second step, Cys residues not labeled in the first step were alkylated with the fluorescent monobromobimane (mBBr) after denaturing of the protein. In purified (aerobic) apoNreB, most (96%) of the Cys residues were alkylated in the first step, but in anaerobic (Fe-S-containing) NreB only a small portion (23%) were alkylated. In anaerobic bacteria, a very small portion of the Cys residues of NreB (9%) were accessible to alkylation in the native state, whereas most (89%) of the Cys residues from aerobic bacteria were accessible. The change in accessibility allowed determination of the half-time (6 min) for the conversion of NreB·[4Fe-4S]
2+
to apoNreB after the addition of air
in vitro
. Overall, in anaerobic bacteria most of the NreB exists as NreB·[4Fe-4S]
2+
, whereas in aerobic bacteria the (Fe-S-less) apoNreB is predominant and represents the physiological form. The number of accessible Cys residues was also determined by iodoacetate alkylation followed by mass spectrometry of Cys-containing peptides. The pattern of mass increases confirmed the results from the two-step labeling experiments.
Complete Genome Sequence of
Anaplasma marginale
subsp.
centrale
Authors: Herndon David R. , Palmer Guy H. , Shkap Varda , Knowles Donald P. , Brayton Kelly A. 
Published: October 2009

ABSTRACT

Anaplasma marginale
subsp.
centrale
is a naturally attenuated subtype that has been used as a vaccine for a century. We sequenced the genome of this organism and compared it to those of virulent
senso stricto A. marginale
strains. The comparison markedly narrows the number of outer membrane protein candidates for development of a safer inactivated vaccine and provides insight into the diversity among strains of
senso lato A. marginale
.
Does physical activity reduce seniors' need for healthcare?: a study of 24 281 Canadians
Authors: Woolcott John C , Ashe Maureen C , Miller William C , Shi Peilin , Marra Carlo A ,   PACC Research Team
Published: October 2009

ObjectivesPhysical inactivity has been associated with significant increases in disease morbidity and mortality. This study assessed the association between physical activity and (1) health resource use and (2) health resource use costs.Design and ParticipantsThe responses from 24 281 respondents >65 years to the Canadian Community Health Survey Cycle 1.1 were used to find activity levels and determine health resource use and costs. Logistic regression models were used to assess risks of hospitalisation.ResultsPhysical inactivity was associated with statistically significant increases to hospitalisations, lengths of stay and healthcare visits (p<0.01). Average healthcare costs (based on the 2007 value of the Canadian dollar) for the physically inactive were $C1214.15 higher than the healthcare costs of the physically active ($C2005.27 vs $C791.12, p<0.01).ConclusionAmong those >65 years, physical activity is strongly associated with reduced health resource use and costs.
Biological markers of cardiac damage are not related to measures of cardiac systolic and diastolic function using cardiovascular magnetic resonance and echocardiography after an acute bout of prolonged endurance exercise
Authors: Wilson M , O'Hanlon R , Prasad S , Oxborough D , Godfrey R , Alpendurada F , Smith G , Wong J , Basavarajaiah S , Sharma S , Nevill A , Gaze David , George K , Whyte G 
Published: October 2009

ObjectivesSeventeen male participants (mean (SD) (range): age 33.5 (6.5) years (46–26 years), body mass 80 (9.2) kg (100–63 kg), height 1.81 (0.06) m (1.93– 1.70 m)) ran a marathon to investigate the relationship between systolic function (using cardiac magnetic resonance (CMR)) and diastolic function (using echocardiography) against biomarkers of cardiac damage.MethodsEchocardiographic and cardiac troponin I (cTnI)/N-terminal pro-B-type natriuretic peptide (NTproBNP) data were collected 24 h premarathon, immediately postmarathon and 6 h postmarathon. CMR data were collected 24 h premarathon and at 6 h postmarathon.ResultsBody mass was significantly reduced postmarathon (80 (9.2) vs 78.8 (8.6) kg; p<0.001). There was a significant E/A reduction postmarathon (1.11 (0.34) vs 1.72 (0.44); p<0.05) that remained depressed 6 h postmarathon (1.49 (0.43); p<0.05). CMR demonstrated left ventricular end-diastolic and end-systolic volumes were reduced postmarathon, with a preserved stroke volume. Left ventricular ejection fraction 6 h postmarathon significantly increased (64.4% (4.2%) vs 67.4% (5%); p<0.05). There were significant elevations in cTnI (0.00 vs 0.04 (0.03) μg/l; p<0.05) and NTproBNP (37.4 (24.15) ng/l vs 59.34 (43.3) ng/l; p<0.05) immediately postmarathon. Eight runners had cTnI elevations immediately postmarathon above acute myocardial infarction cutoff levels (≥0.03 μg/l). No correlations between cTnI/NTproBNP and measures of diastolic function (E, A, E/A, isovolumic relaxation time, E deceleration time and E/E′) or measures of systolic function (stroke volume or ejection fraction) were observed immediately postmarathon or 6 h postmarathon.ConclusionsBiomarkers of cardiac damage after prolonged exercise are not associated with either systolic or diastolic functional measures.
Some sex hormone profiles are consistent over time in normal menstruating women: implications for sports injury epidemiology
Authors: Shultz S J , Wideman L , Montgomery M M , Levine B J 
Published: October 2009

PurposeIt is unclear whether sex hormone profiles obtained in two consecutive months are consistent within women. Month-to-month consistency in daily, nadir, peak and mean hormone concentrations during the early follicular and luteal phases in recreationally active, young eumenorrheic women was prospectively examined.Methods60 healthy, non-smoking women who reported normal and consistent menstrual cycles lasting 26–32 days for the past 6 months were followed prospectively to obtain serum samples for the first 6 days of menses and for 8 days after a positive ovulation test over two consecutive months. Month-to-month consistency of daily concentrations of oestradiol (pg/ml), progesterone (ng/ml), testosterone (ng/dl), sex hormone-binding globulin (nmol/l) and free androgen index were determined using linear mixed models. Month-to-month consistency in nadir, peak and mean concentrations were then assessed using intraclass correlation coefficients and SEM to more precisely examine intraindividual consistency.ResultsLinear mixed models revealed stable hormone concentrations across cycles and cycles by day. Reliability estimates for nadir, peak, mean menses and mean postovulatory concentrations range from 0.56 to 0.86 for oestradiol, 0.44 to 0.91 for progesterone, 0.60 to 0.86 for testosterone, 0.88 to 0.97 for sex hormone-binding globulin and 0.78 to 0.91 for free androgen index.ConclusionsHormone profiles were reproducible over two consecutive months. To reduce month-to-month intraindividual variations and improve measurement consistency, it is recommended that multiple samples be taken over consecutive days as opposed to a single sample.
Identifying pesticide use patterns among flower growers to assess occupational exposure to mixtures
Authors: Schilmann Astrid , Lacasaña Marina , Blanco-Muñoz Julia , Aguilar-Garduño Clemente , Salinas-Rodríguez Aarón , Flores-Aldana Mario , Cebrián Mariano E 
Published: October 2009

ObjectivesExposure assessment to a single pesticide does not capture the complexity of the occupational exposure. Recently, pesticide use patterns analysis has emerged as an alternative to study these exposures. The aim of this study is to identify the pesticide use pattern among flower growers in Mexico participating in the study on the endocrine and reproductive effects associated with pesticide exposure.MethodsA cross-sectional study was carried out to gather retrospective information on pesticide use applying a questionnaire to the person in charge of the participating flower growing farms. Information about seasonal frequency of pesticide use (rainy and dry) for the years 2004 and 2005 was obtained. Principal components analysis was performed.ResultsComplete information was obtained for 88 farms and 23 pesticides were included in the analysis. Six principal components were selected, which explained more than 70% of the data variability. The identified pesticide use patterns during both years were: 1. fungicides benomyl, carbendazim, thiophanate and metalaxyl (both seasons), including triadimephon during the rainy season, chlorotalonyl and insecticide permethrin during the dry season; 2. insecticides oxamyl, biphenthrin and fungicide iprodione (both seasons), including insecticide methomyl during the dry season; 3. fungicide mancozeb and herbicide glyphosate (only during the rainy season); 4. insecticides metamidophos and parathion (both seasons); 5. insecticides omethoate and methomyl (only rainy season); and 6. insecticides abamectin and carbofuran (only dry season). Some pesticides do not show a clear pattern of seasonal use during the studied years.ConclusionsThe principal component analysis is useful to summarise a large set of exposure variables into smaller groups of exposure patterns, identifying the mixtures of pesticides in the occupational environment that may have an interactive effect on a particular health effect.
Diagnostic strategies using physical examination are minimally useful in defining carpal tunnel syndrome in population-based research studies: Table 1
Authors: Descatha A , Dale A-M , Franzblau A , Coomes J , Evanoff B 
Published: October 2009

ObjectiveWe evaluated the utility of physical examination manoeuvres in the prediction of carpal tunnel syndrome (CTS) in a population-based research study.MethodsWe studied a cohort of 1108 newly employed workers in several industries. Each worker completed a symptom questionnaire, a structured physical examination and nerve conduction study. For each hand, our CTS case definition required both median nerve conduction abnormality and symptoms classified as “classic” or “probable” on a hand diagram. We calculated the positive predictive values and likelihood ratios for physical examination manoeuvres in subjects with and without symptoms.ResultsThe prevalence of CTS in our cohort was 1.2% for the right hand and 1.0% for the left hand. The likelihood ratios of a positive test for physical provocative tests ranged from 2.0 to 3.3, and those of a negative test from 0.3 to 0.9. The post-test probability of positive testing was <50% for all strategies tested.ConclusionOur study found that physical examination, alone or in combination with symptoms, was not predictive of CTS in a working population. We suggest using specific symptoms as a first-level screening tool, and nerve conduction study as a confirmatory test, as a case definition strategy in research settings.