bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Map of Growth-Regulated Gene Expression in
Burkholderia pseudomallei
, the Causative Agent of Melioidosis
Authors: Rodrigues Fiona , Sarkar-Tyson Mitali , Harding Sarah V. , Sim Siew Hoon , Chua Hui Hoon , Lin Chi Ho , Han Xu , Karuturi R. Krishna M. , Sung Ken , Yu Kun , Chen Wei , Atkins Timothy P. , Titball Richard W. , Tan Patrick 
Published: November 2006

ABSTRACT

Many microbial pathogens express specific virulence traits at distinct growth phases. To understand the molecular pathways linking bacterial growth to pathogenicity, we have characterized the growth transcriptome of
Burkholderia pseudomallei
, the causative agent of melioidosis. Using a fine-scale sampling approach, we found approximately 17% of all
B. pseudomallei
genes displaying regulated expression during growth in rich medium, occurring as broad waves of functionally coherent gene expression tightly associated with distinct growth phases and transition points. We observed regulation of virulence genes across all growth phases and identified
serC
as a potentially new virulence factor by virtue of its coexpression with other early-phase virulence genes.
serC
-disrupted
B. pseudomallei
strains were serine auxotrophs and in mouse infection assays exhibited a dramatic attenuation of virulence compared to wild-type
B. pseudomallei
. Immunization of mice with
serC
-disrupted
B. pseudomallei
also conferred protection against subsequent challenges with different wild-type
B. pseudomallei
strains. At a genomic level, early-phase genes were preferentially localized on chromosome 1, while stationary-phase genes were significantly biased towards chromosome 2. We detected a significant level of chromosomally clustered gene expression, allowing us to predict ∼100 potential operons in the
B. pseudomallei
genome. We computationally and experimentally validated these operons by showing that genes in these regions are preferentially transcribed in the same 5′→3′ direction, possess significantly shorter intergenic lengths than the overall genome, and are expressed as a common mRNA transcript. The availability of this transcriptome map provides an important resource for understanding the transcriptional architecture of
B. pseudomallei
.
Critical Residues and Novel Effects of Overexpression of the
Streptomyces coelicolor
Developmental Protein BldB: Evidence for a Critical Interacting Partner
Authors: Eccleston Marcus , Willems Andrew , Beveridge Adam , Nodwell Justin R. 
Published: November 2006

ABSTRACT

The
bldB
gene of
Streptomyces coelicolor
encodes the best-characterized member of a family of small proteins that have low isoelectric points but that lack any previously characterized sequence motifs. BldB is dimeric and is required for the efficient production of antibiotics and spore-forming cells, called aerial hyphae, by growing colonies. The mechanism of action of BldB and its relatives is unknown. Here, we have explored amino acids in BldB that either are highly conserved or have been implicated in function genetically. We show that five amino acids are important for its function at physiological expression levels. Mutations in three of these amino acids gave rise to proteins that were either monomeric or unstable in vivo, while two others are not. We find that overexpression of
bldB
in
S. coelicolor
blocks sporulation prior to sporulation-specific septation but permits the formation of aerial hyphae. Vegetative septation was apparently normal in both the
bldB
null mutant and the
bldB
overexpression strain. To our surprise, overexpression of the dimerization-competent but functionally defective alleles caused a dramatic acceleration of sporulation. Our results suggest that BldB makes at least one important contact with another subcellular constituent and that a loss or alteration of this interaction impairs the phenotypic properties of the organism.
YtxR, a Conserved LysR-Like Regulator That Induces Expression of Genes Encoding a Putative ADP-Ribosyltransferase Toxin Homologue inYersinia enterocolitica
Authors: Axler-DiPerte Grace L. , Miller Virginia L. , Darwin Andrew J. 
Published: November 2006

ABSTRACTYersinia enterocoliticacauses human gastroenteritis, and many isolates have been classified as either “American” or “non-American” strains based on their geographic prevalence and virulence properties. In this study we describe identification of a transcriptional regulator that controls expression of theY. enterocolitica ytxABgenes. TheytxABgenes have the potential to encode an ADP-ribosylating toxin with similarity to pertussis toxin. However, aytxABnull mutation did not affect virulence in mice. Nevertheless, theytxABgenes are conserved in manyY. enterocoliticastrains. Interestingly, American and non-American strains have differentytxABalleles encoding proteins that are only 50 to 60% identical. To obtain further insight into theytxABlocus, we investigated whether it is regulated as part of a known or novel regulon. Transposon mutagenesis identified a LysR-like regulator, which we designated YtxR. Expression ofytxRfrom a nonnative promoter increased Φ(ytxA-lacZ) operon fusion expression up to 35-fold. YtxR also activated expression of its own promoter. DNase I footprinting showed that a His6-YtxR fusion protein directly interacted with theytxAandytxRcontrol regions at similar distances upstream of their probable transcription initiation sites, identified by primer extension. Deletion analysis demonstrated that removal of the regions protected by His6-YtxR in vitro eliminated YtxR-dependent induction in vivo. TheytxABlocus is not present in mostYersiniaspecies. In contrast,ytxRis conserved in multipleYersiniaspecies, as well as in the closely related organismsPhotorhabdus luminescensandPhotorhabdus asymbiotica. These observations suggest that YtxR may play a conserved role involving regulation of other genes besidesytxAB.
The ColRS Two-Component System Regulates Membrane Functions and Protects
Pseudomonas putida
against Phenol
Authors: Kivistik Paula Ann , Putrinš Marta , Püvi Külliki , Ilves Heili , Kivisaar Maia , Hõrak Rita 
Published: November 2006

ABSTRACT

As reported, the two-component system ColRS is involved in two completely different processes. It facilitates the root colonization ability of
Pseudomonas fluorescens
and is necessary for the Tn
4652
transposition-dependent accumulation of phenol-utilizing mutants in
Pseudomonas putida
. To determine the role of the ColRS system in
P. putida
, we searched for target genes of response regulator ColR by use of a promoter library. Promoter screening was performed on phenol plates to mimic the conditions under which the effect of ColR on transposition was detected. The library screen revealed the porin-encoding gene
oprQ
and the alginate biosynthesis gene
algD
occurring under negative control of ColR. Binding of ColR to the promoter regions of
oprQ
and
algD
in vitro confirmed its direct involvement in regulation of these genes. Additionally, the porin-encoding gene
ompA
PP0773
and the type I pilus gene
csuB
were also identified in the promoter screen. However, it turned out that
ompA
PP0773
and
csuB
were actually affected by phenol and that the influence of ColR on these promoters was indirect. Namely, our results show that ColR is involved in phenol tolerance of
P. putida
. Phenol MIC measurement demonstrated that a
colR
mutant strain did not tolerate elevated phenol concentrations. Our data suggest that increased phenol susceptibility is also the reason for inhibition of transposition of Tn
4652
in phenol-starving
colR
mutant bacteria. Thus, the current study revealed the role of the ColRS two-component system in regulation of membrane functionality, particularly in phenol tolerance of
P. putida
.
Use of Partial 16S rRNA Gene Sequencing for Identification of
Legionella pneumophila
and Non-
pneumophila Legionella
spp
Authors: Wilson D. A. , Reischl U. , Hall G. S. , Procop G. W. 
Published: November 2006

ABSTRACT

We examined 49
Legionella
species, 26
L. pneumophila
and 23 non-
pneumophila Legionella
spp., using partial 16S rRNA gene sequencing. This approach accurately identified all the
L. pneumophila
isolates, characterized all non-
pneumophila Legionella
isolates as such within this genus, and classified most (20/23; 87%) of the non-
pneumophila Legionella
isolates to the species level.
Analysis of Changes in Recent Tuberculosis Transmission Patterns after a Sharp Increase in Immigration
Authors: Iñigo Jesús , García de Viedma Darío , Arce Araceli , Palenque Elia , Alonso Rodríguez Noelia , Rodríguez Elena , Ruiz Serrano María Jesús , Andrés Sandra , Bouza Emilio , Chaves Fernando 
Published: November 2006

ABSTRACT

We conducted a population-based molecular epidemiological study of tuberculosis (TB) in Madrid, Spain (2002 to 2004), to define transmission patterns and factors associated with clustering. We particularly focused on examining how the increase in TB cases among immigrants in recent years (2.8% in 1997 to 1999 to 36.2% during the current study) was modifying transmission patterns.
Mycobacterium tuberculosis
isolates obtained from patients living in nine districts of Madrid (1,459,232 inhabitants) were genotyped. The TB case rate among foreign-born people was three to four times that of Spanish-born people, and the median time from arrival to the onset of treatment was 22.4 months. During the study period, 227 (36.3%) patients were grouped in 64 clusters, and 115 (50.7%) of them were in 21 clusters with mixed Spanish-born and foreign-born patients. Three of the 21 mixed clusters accounted for 21.1% of clustered patients. Twenty-two of 38 (57.9%) immigrants in mixed clusters were infected with TB strains that had already been identified in the native population in 1997 to 1999, including the three most prevalent strains. Factors identified as independent predictors of clustering were homelessness (odds ratio [OR], 2.3; 95% confidence interval [95% CI], 1.2 to 4.5;
P
= 0.011) and to be born in Spain (OR, 1.8; 95% CI, 1.2 to 2.6;
P
= 0.002). The results indicated that (i) TB transmission was higher in Spanish-born people, associated mainly with homelessness, (ii) that foreign-born people were much less likely to be clustered, suggesting a higher percentage of infection before arriving in Spain, and (iii) that an extensive transmission between Spanish- and foreign-born populations, caused mainly by autochthonous strains, was taking place in Madrid.
Inhibition of Heavy Chain and β2-Microglobulin Synthesis as a Mechanism of Major Histocompatibility Complex Class I Downregulation during Epstein-Barr Virus Replication
Authors: Guerreiro-Cacais Andre Ortlieb , Uzunel Mehmet , Levitskaya Jelena , Levitsky Victor 
Published: November 2006

ABSTRACTThe mechanisms of major histocompatibility complex (MHC) class I downregulation during Epstein-Barr virus (EBV) replication are not well characterized. Here we show that in several cell lines infected with a recombinant EBV strain encoding green fluorescent protein (GFP), the virus lytic cycle coincides with GFP expression, which thus can be used as a marker of virus replication. EBV replication resulted in downregulation of MHC class II and all classical MHC class I alleles independently of viral DNA synthesis or late gene expression. Although assembled MHC class I complexes, the total pool of heavy chains, and β2-microglobulin (β2m) were significantly downregulated, free class I heavy chains were stabilized at the surface of cells replicating EBV. Calnexin expression was increased in GFP+cells, and calnexin and calreticulin accumulated at the cell surface that could contribute to the stabilization of class I heavy chains. Decreased expression levels of another chaperone, ERp57, and TAP2, a transporter associated with antigen processing and presentation, correlated with delayed kinetics of MHC class I maturation. Levels of both class I heavy chain and β2m mRNA were reduced, and metabolic labeling experiments demonstrated a very low rate of class I heavy chain synthesis in lytically infected cells. MHC class I and MHC class II downregulation was mimicked by pharmacological inhibition of protein synthesis in latently infected cells. Our data suggest that although several mechanisms may contribute to MHC class I downregulation in the course of EBV replication, inhibition of MHC class I synthesis plays the primary role in the process.
Creatine intake attenuates corticosteroid-induced impairment of voluntary running in hamsters
Authors: Campos Andrea R. , Serafini Luciano N. , Sobreira Claudia , Menezes Luciana G. , Martinez José A.B. 
Published: November 2006

Myopathy is a well-known side effect of corticosteroid therapy. Creatine monohydrate (Cr) supplementation has been shown to increase fat-free mass and muscular function. This study aimed to investigate if Cr administration could offset the deleterious functional effects of high doses of steroids. Fifty-six male Syrian golden hamsters were randomized among 4 groups: GI (n = 10), subcutaneous (s.c.) and intraperitoneal (i.p.) saline; GII (n = 10), s.c. saline and i.p. Cr (600 mg·kg–1·d–1); GIII (n = 18), s.c. dexamethasone (7.5 mg·kg–1·d–1) and i.p. saline; and GIV (n = 18), s.c. dexamethasone and i.p. Cr. Daily voluntary running was measured using activity wheels for 18 d. At the end of the study, statistically significant differences in running were observed between all groups, except for GI versus GII (GI, 8878 ± 2737 m; GII, 9145 ± 2000 m; GIII, 4289 ± 2623 m; GIV, 6339 ± 2345 m). Dexamethasone led to a significant decrease in cross-sectional area of type II fibers of the medial gastrocnemius. The cross-sectional area of type I fibers was significantly larger in GIV than in GIII. In conclusion, Cr administration attenuated the impairment of daily spontaneous running of hamsters receiving a high dose of corticosteroids. Additional research is needed to clarify the clinical implications of this finding.
Acute effects of exercise timing and breakfast meal glycemic index on exercise-induced fat oxidation
Authors: Bennard Patrick , Doucet Éric 
Published: November 2006

Fat balance is an important determinant of energy balance. Exercise after an overnight fast can significantly increase fat oxidation; however, little information pertaining to the effects of exercise and meal glycemic index on fat oxidation under these conditions is available. The objective of this investigation was to study the acute effects of exercise timing and meal glycemic index (GI) on whole-body fat oxidation. Eight apparently healthy young men completed 4 randomly ordered trials during which measurements were made at rest, during exercise, and for 2 h post-exercise and (or) post-prandial. After an overnight fast, subjects were required to perform 400 kcal (1 kcal = 4.184 kJ) of treadmill exercise (at FATmax) either before consuming a 400 kcal low-GI (Ex-LG) or high-GI (Ex-HG) oatmeal breakfast, or after consuming the low-GI (LG-Ex) or high-GI (HG-Ex) meal. The amount of fat oxidized during exercise was significantly greater during Ex-LG and Ex-HG (17.2 ± 4.0 and 17.5 ± 4.7 g, respectively) than during LG-Ex and HG-Ex (10.9 ± 3.7 and 11.7 ± 3.5 g, respectively) (p < 0.001), as was the amount of fat oxidized during the entire trial (Ex-LG: 23.4 ± 4.7 g; Ex-HG: 23.4 ± 6.5 g; LG-Ex: 18.4 ± 4.7 g; HG-Ex: 19.6 ± 4.9 g) (p < 0.05), even though energy expenditure was not different across experimental conditions. No significant effect of meal GI on the amount of fat oxidized was noted. Total fat oxidized during exercise, and for 2 h after exercise, was greatest when morning exercise was performed in the fasted state, independently of meal GI.
Addition of glutamine to essential amino acids and carbohydrate does not enhance anabolism in young human males following exercise
Authors: Wilkinson Sarah B. , Kim Paul L. , Armstrong David , Phillips Stuart M. 
Published: November 2006

We examined the effect of a post-exercise oral carbohydrate (CHO, 1 g·kg–1·h–1) and essential amino acid (EAA, 9.25 g) solution containing glutamine (0.3 g/kg BW; GLN trial) versus an isoenergetic CHO–EAA solution without glutamine (control, CON trial) on muscle glycogen resynthesis and whole-body protein turnover following 90 min of cycling at 65% VO2 peak. Over the course of 3 h of recovery, muscle biopsies were taken to measure glycogen resynthesis and mixed muscle protein synthesis (MPS), by incorporation of [ring-2H5] phenylalanine. Infusion of [1-13C] leucine was used to measure whole-body protein turnover. Exercise resulted in a significant decrease in muscle glycogen (p < 0.05) with similar declines in each trial. Glycogen resynthesis following 3 h of recovery indicated no difference in total accumulation or rate of repletion. Leucine oxidation increased 2.5 fold (p < 0.05) during exercise, returned to resting levels immediately post-exercise,and was again elevated at 3 h post-exercise (p < 0.05). Leucine flux, an index of whole-body protein breakdown rate, was reduced during exercise, but increased to resting levels immediately post-exercise, and was further increased at 3 h post-exercise (p < 0.05), but only during the CON trial. Exercise resulted in a marked suppression of whole-body protein synthesis (50% of rest; p < 0.05), which was restored post-exercise; however, the addition of glutamine did not affect whole-body protein synthesis post-exercise. The rate of MPS was not different between trials. The addition of glutamine to a CHO + EAA beverage had no effect on post-exercise muscle glycogen resynthesis or muscle protein synthesis, but may suppress a rise in whole-body proteolysis during the later stages of recovery.
Fatigue and muscle–tendon stiffness after stretch–shortening cycle and isometric exercise
Authors: Toumi Hechmi , Poumarat Georges , Best Thomas M. , Martin Alain , Fairclough John , Benjamin Mike 
Published: November 2006

The purpose of the present study was to compare vertical jump performance after 2 different fatigue protocols. In the first protocol, subjects performed consecutive sets of 10 repetitions of stretch–shortening cycle (SSC) contractions. In the second protocol, successive sets of 10 repetitions of isometric contractions were performed for 10 s with the knee at 90° of flexion. The exercises were stopped when the subjects failed to reach 50% of their maximum voluntary isometric contractions. Maximal isometric force and maximal concentric power were assessed by performing supine leg presses, squat jumps, and drop jumps. Surface EMG was used to determine changes in muscle activation before and after fatigue. In both groups, the fatigue exercises reduced voluntary isometric force, maximal concentric power, and drop jump performance. Kinematic data showed a decrease in knee muscle–tendon stiffness accompanied by a lengthened ground contact time. EMG analysis showed that the squat and drop jumps were performed similarly before and after the fatigue exercise for both groups. Although it was expected that the stiffness would decrease more after SSC than after isometric fatigue (as a result of a greater alteration of the reflex sensitivity SSC), our results showed that both protocols had a similar effect on knee muscle stiffness during jumping exercises. Both fatigue protocols induced muscle fatigue, and the decrease in jump performance was linked to a decrease in the strength and stiffness of the knee extensor muscles.
Enriched feather hydrogen isotope values for Wood Thrushes sampled in Georgia, USA, during the breeding season: implications for quantifying dispersal
Authors: Powell L.A. , Hobson K.A. 
Published: November 2006

We used an analysis of deuterium values (δD) of 151 Wood Thrush ( Hylocichla mustelina (J.F. Gmelin, 1789)) feathers collected during the breeding season at the Piedmont National Wildlife Refuge in Georgia, USA, to determine fidelity to the study site. We compared δD values in feathers of birds with known molt locations and birds with unknown molt locations. Mean feather value of δD was –24.8‰ (SD = 10.5‰, range = –48.0‰ to –5.5‰), and we were unable to determine a site-specific signature to assess fidelity of breeders within our sample. We used an information criterion approach to evaluate multiple hypotheses to explain the high variation in δD, and the geographic location of sample sites within the study area was selected as the best model. Feather δD values were higher than expected from mean growing-season rainfall δD values predicted for our study site. We discuss possible explanations for the enriched δD values and postulate that heat stress during molt may have contributed to our results. We suggest that future stable isotope data collection consider the potential for small-scale variation in feather δD values; information on diet gathered simultaneously with feather samples may be valuable for future studies.
Bumblebees avoid flowers containing evidence of past predation events
Authors: Abbott K.R. 
Published: November 2006

Bees are at risk of predation from flower-dwelling ambush predators. Since these predators tend to be cryptic, bees trying to mitigate predation risk may need to make use of indirect cues of the predator’s presence. For example, they may use cues of past predation events as indirect cues of current predation risk. I conducted a series of experiments that examined how bumblebees (genus Bombus Latreille, 1802) respond to cues of past predation events. In two field experiments, I found that wild rose (genus Rosa L.) flowers containing a freshly killed bumblebee, or the scent of a freshly killed bumblebee, received fewer bumblebee visits than control flowers. To test the possibility that bumblebees in the first two experiments were avoiding cues of competition risk rather than cues of predation risk, captive-reared bumblebees were given a choice between two artificial flowers — one containing a freeze-killed bumblebee (relatively more similar to a live foraging bee) and the other containing a crush-killed bumblebee (relatively more similar to a bee killed by a predator). Most bumblebees chose the flower containing the freeze-killed bee, supporting the hypothesis that the bumblebees in the first two experiments were attempting to avoid predation.
The adaptive utility of Richardson’s ground squirrel (Spermophilus richardsonii) short-range ultrasonic alarm signals
Authors: Wilson David R. , Hare James F. 
Published: November 2006

Richardson’s ground squirrels ( Spermophilus richardsonii (Sabine, 1822)) produce audible (ca. 8 kHz) and (or) ultrasonic (ca. 48 kHz) alarm vocalizations that warn conspecifics of impending danger. Audible calls have a larger active space than ultrasonic calls because they travel farther, are louder, and contain frequencies to which conspecific and allospecific recipients are more sensitive. In our first experiment, we presented an alarming stimulus to 103 squirrels to examine the effect of threat proximity on signal type. The ratio of ultrasonic to audible alarm calls increased with increasing distance from the stimulus. We conclude that the size of the active space influences signalling strategy and that squirrels emitting ultrasonic calls can signal conspecifics to the exclusion of distant predators. As recipients of ultrasonic calls must be close to the signaler, one context in which ultrasonic calling may be most adaptive is during natal emergence when juveniles are particularly abundant, highly vulnerable to predation, and clustered in space. In our second experiment, we broadcast ultrasonic alarm signals to emerging juveniles and found that they, like older individuals, responded to calls by increasing vigilance. We discuss the adaptive utility of multiple signalling strategies in light of our findings.