bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interference between
Streptococcus pneumoniae
and
Staphylococcus aureus
: In Vitro Hydrogen Peroxide-Mediated Killing by
Streptococcus pneumoniae
Authors: Regev-Yochay Gili , Trzciński Krzysztof , Thompson Claudette M. , Malley Richard , Lipsitch Marc 
Published: June 2006

ABSTRACT

The bactericidal activity of
Streptococcus pneumoniae
toward
Staphylococcus aureus
is mediated by hydrogen peroxide. Catalase eliminated this activity. Pneumococci grown anaerobically or genetically lacking pyruvate oxidase (SpxB) were not bactericidal, nor were nonpneumococcal streptococci. These results provide a possible mechanistic explanation for the interspecies interference observed in epidemiologic studies.
Cross-Regulation of Biphenyl- and Salicylate-Catabolic Genes by Two Regulatory Systems in
Pseudomonas pseudoalcaligenes
KF707
Authors: Fujihara Hidehiko , Yoshida Hideyuki , Matsunaga Tetsuya , Goto Masatoshi , Furukawa Kensuke 
Published: June 2006

ABSTRACT

Pseudomonas pseudoalcaligenes
KF707 grows on biphenyl and salicylate as sole sources of carbon. The biphenyl-catabolic (
bph
) genes are organized as
bphR1A1A2
(
orf3
)
A3A4BCX0X1X2X3D
, encoding the enzymes for conversion of biphenyl to acetyl coenzyme A. In this study, the salicylate-catabolic (
sal
) gene cluster encoding the enzymes for conversion of salicylate to acetyl coenzyme A were identified 6.6-kb downstream of the
bph
gene cluster along with a second regulatory gene,
bphR2
. Both the
bph
and
sal
genes were cross-regulated positively and/or negatively by the two regulatory proteins, BphR1 and BphR2, in the presence or absence of the effectors. The BphR2 binding sequence exhibits homology with the NahR binding sequences in various naphthalene-degrading bacteria. Based on previous studies and the present study we propose a new regulatory model for biphenyl and salicylate catabolism in strain KF707.
Plasticity of the P
junc
Promoter of ISEc
11
, a New Insertion Sequence of the IS
1111
Family
Authors: Prosseda Gianni , Latella Maria Carmela , Casalino Mariassunta , Nicoletti Mauro , Michienzi Stefano , Colonna Bianca 
Published: June 2006

ABSTRACT

We describe identification and functional characterization of ISEc
11
, a new insertion sequence that is widespread in enteroinvasive
E. coli
(EIEC), in which it is always present on the virulence plasmid (pINV) and very frequently also present on the chromosome. ISEc
11
is flanked by subterminal 13-bp inverted repeats (IRs) and is bounded by 3-bp terminal sequences, and it transposes with target specificity without generating duplication of the target site. ISEc
11
is characterized by an atypical transposase containing the DEDD motif of the Piv/MooV family of DNA recombinases, and it is closely related to the IS
1111
family. Transposition occurs by formation of minicircles through joining of the abutted ends and results in assembly of a junction promoter (P
juncC
) containing a −10 box in the interstitial sequence and a −35 box upstream of the right IR. A natural variant of ISEc
11
(ISEc
11
p), found on EIEC pINV plasmids, contains a perfect duplication of the outermost 39 bp of the right end. Upon circularization, ISEc
11
p forms a junction promoter (P
juncP
) which, despite carrying −10 and −35 boxes identical to those of P
juncC
, exhibits 30-fold-greater strength in vivo. The discovery of only one starting point in primer extension experiments rules out the possibility that there are alternative promoter sites within the 39-bp duplication. Analysis of in vitro-generated transcripts confirmed that at limiting RNA polymerase concentrations, the activity of P
juncP
is 20-fold higher than the activity of P
juncC
. These observations suggest that the 39-bp duplication might host
cis
-acting elements that facilitate the binding of RNA polymerase to the promoter.
Genomic Analysis of Carbon Source Metabolism of
Shewanella oneidensis
MR-1: Predictions versus Experiments
Authors: Serres Margrethe H. , Riley Monica 
Published: June 2006

ABSTRACT

Genomic sequences have been used to find the genetic foundation for carbon source metabolism in
Shewanella oneidensis
MR-1. Annotated
S. oneidensis
MR-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the BioCyc database (
http://www.biocyc.org/
) or in the primary literature. A picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for utilization of up to three-carbon carbohydrates seem to be present. Capacity to utilize amino acids for carbon and energy is also present. A few contradictions emerged in which enzymes appear to be present by annotations but are not active in the cell according to physiological experiments. Annotations are based on close sequence similarity and will not reveal inactivity due to deleterious mutations or due to lack of coordination of regulation and transport. Genes for a few enzymes known by experiment to be active are not found in the genome. This may be due to extensive divergence after duplication or convergence of function in separate lines in evolution rendering activities undetectable by sequence similarity. To minimize false predictions from protein sequences, we have been conservative in predicting pathways. We did not predict any pathway when, although a partial pathway was seen it was composed largely of enzymes already accounted for in any other complete pathway. This is an example of how a biochemically oriented sequence analysis can generate questions and direct further experimental investigation.
Comparison of the RpoH-Dependent Regulon and General Stress Response in
Neisseria gonorrhoeae
Authors: Gunesekere Ishara C. , Kahler Charlene M. , Powell David R. , Snyder Lori A. S. , Saunders Nigel J. , Rood Julian I. , Davies John K. 
Published: June 2006

ABSTRACT

In the gammaproteobacteria the RpoH regulon is often equated with the stress response, as the regulon contains many of the genes that encode what have been termed heat shock proteins that deal with the presence of damaged proteins. However, the betaproteobacteria primarily utilize the HrcA repressor protein to control genes involved in the stress response. We used genome-wide transcriptional profiling to compare the RpoH regulon and stress response of
Neisseria gonorrhoeae
, a member of the betaproteobacteria. To identify the members of the RpoH regulon, a plasmid-borne copy of the
rpoH
gene was overexpressed during exponential-phase growth at 37°C. This resulted in increased expression of 12 genes, many of which encode proteins that are involved in the stress response in other species. The putative promoter regions of many of these up-regulated genes contain a consensus RpoH binding site similar to that of
Escherichia coli
. Thus, it appears that unlike other members of the betaproteobacteria,
N. gonorrhoeae
utilizes RpoH, and not an HrcA homolog, to regulate the stress response. In
N. gonorrhoeae
exposed to 42°C for 10 min, we observed a much broader transcriptional response involving 37 differentially expressed genes. Genes that are apparently not part of the RpoH regulon showed increased transcription during heat shock. A total of 13 genes were also down-regulated. From these results we concluded that although RpoH acts as the major regulator of protein homeostasis,
N. gonorrhoeae
has additional means of responding to temperature stress.
Acyl Carrier Protein Synthases from Gram-Negative, Gram-Positive, and Atypical Bacterial Species: Biochemical and Structural Properties and Physiological Implications
Authors: McAllister Kelly A. , Peery Robert B. , Zhao Genshi 
Published: June 2006

ABSTRACT

Acyl carrier protein (ACP) synthase (AcpS) catalyzes the transfer of the 4′-phosphopantetheine moiety from coenzyme A (CoA) onto a serine residue of apo-ACP, resulting in the conversion of apo-ACP to the functional holo-ACP. The holo form of bacterial ACP plays an essential role in mediating the transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and phospholipids. AcpS is therefore an attractive target for therapeutic intervention. In this study, we have purified and characterized the AcpS enzymes from
Escherichia coli
,
Streptococcus pneumoniae
, and
Mycoplasma pneumoniae
, which exemplify gram-negative, gram-positive, and atypical bacteria, respectively. Our gel filtration column chromatography and cross-linking studies demonstrate that the AcpS enzyme from
M. pneumoniae
, like
E. coli
enzyme, exhibits a homodimeric structure, but the enzyme from
S. pneumoniae
exhibits a trimeric structure. Our biochemical studies show that the AcpS enzymes from
M. pneumoniae
and
S. pneumoniae
can utilize both short- and long-chain acyl CoA derivatives but prefer long-chain CoA derivatives as substrates. On the other hand, the AcpS enzyme from
E. coli
can utilize short-chain CoA derivatives but not the long-chain CoA derivatives tested. Finally, our biochemical studies show that
M. pneumoniae
AcpS is kinetically a very sluggish enzyme compared with those from
E. coli
and
S. pneumoniae
. Together, the results of these studies show that the AcpS enzymes from different bacterial species exhibit different native structures and substrate specificities with regard to the utilization of CoA and its derivatives. These findings suggest that AcpS from different microorganisms plays a different role in cellular physiology.
A Novel Locomotion Interface with Two 6-DOF Parallel Manipulators That Allows Human Walking on Various Virtual Terrains
Authors: Yoon Jungwon , Ryu Jeha 
Published: June 2006

This paper proposes a novel locomotion interface that can generate an infinite floor with various surfaces and can provide a user with proprioceptive feedback about walking. The interface allows users to experience life-like walking in virtual environments with various terrains. The interface consists of two platforms, each consisting of a three-degrees-of-freedom (3-DOF; x, y and yaw) planar device on which a 3-DOF (pitch, roll and z) footpad is mounted. Alternating current servomotors drive the planar devices to generate rapid motions, while pneumatic actuators drive the footpad devices to generate the impedances required for various virtual terrains, in addition to supporting the user’s weight. To simulate natural human walking, the locomotion interface design specifications are based on gait analysis, and each mechanism is optimally designed and manufactured to satisfy these requirements. The locomotion interface allows natural walking (step, 0.8 m; height, 20 cm; load capability, 100 kg; slope, 55°) on various terrains. In addition, a new walking control algorithm is proposed for generating continuous walking on an infinite floor involving various terrains. In this algorithm, each independent platform follows a human foot during the swing phase, while the other platform returns to the home position during the single-limb stance phase. During the double-limb stance phase, the two platforms assume neutral positions to compensate for the offset errors generated by velocity changes. Therefore, this algorithm can satisfy natural walking conditions in any direction. The transition phase between the swing and stance phases is detected using a simple switch sensor system, while human foot motions are sensed using a calibrated magnetic motion tracker attached to the shoe. Actual walking simulations on level ground, slopes, and stairs show that the proposed locomotion interface allows an average person to walk naturally on various virtual terrains in safety, without marked disturbances. This interface has various applications, such as in virtual reality (VR) navigation, rehabilitation, and gait analysis.
Effects of disrupting the polyketide synthase gene WdPKS1 in Wangiella [Exophiala] dermatitidis on melanin production and resistance to killing by antifungal compounds, enzymatic degradation, and extremes in temperature
Authors: Paolo William F , Dadachova Ekaterina , Mandal Piyali , Casadevall Arturo , Szaniszlo Paul J , Nosanchuk Joshua D 
Published: June 2006

Abstract

Background

Wangiella dermatitidis is a human pathogenic fungus that is an etiologic agent of phaeohyphomycosis. W. dermatitidis produces a black pigment that has been identified as a dihydroxynaphthalene melanin and the production of this pigment is associated with its virulence. Cell wall pigmentation in W. dermatitidis depends on the WdPKS1 gene, which encodes a polyketide synthase required for generating the key precursor for dihydroxynaphthalene melanin biosynthesis.

Results
We analyzed the effects of disrupting WdPKS1 on dihydroxynaphthalene melanin production and resistance to antifungal compounds. Transmission electron microscopy revealed that wdpks1 Δ-1 yeast had thinner cell walls that lacked an electron-opaque layer compared to wild-type cells. However, digestion of the wdpks1 Δ-1 yeast revealed small black particles that were consistent with a melanin-like compound, because they were acid-resistant, reacted with melanin-binding antibody, and demonstrated a free radical signature by electron spin resonance analysis. Despite lacking the WdPKS1 gene, the mutant yeast were capable of catalyzing the formation of melanin from L-3,4-dihyroxyphenylalanine. The wdpks1 Δ-1 cells were significantly more susceptible to killing by voriconazole, amphotericin B, NP-1 [a microbicidal peptide], heat and cold, and lysing enzymes than the heavily melanized parental or complemented strains.

Conclusion
In summary, W. dermatitidis makes WdPKS-dependent and -independent melanins, and the WdPKS1- dependent deposition of melanin in the cell wall confers protection against antifungal agents and environmental stresses. The biological role of the WdPKS-independent melanin remains unclear.
Frequency of apnea, bradycardia, and desaturations following first diphtheria-tetanus-pertussis-inactivated polio-Haemophilus influenzae type B immunization in hospitalized preterm infants
Authors: Lee Jackie , Robinson Joan L , Spady Donald W 
Published: June 2006

AbstractBackgroundAdverse cardiorespiratory events including apnea, bradycardia, and desaturations have been described following administration of the first diphtheria-tetanus-pertussis-inactivated polio-Haemophilus influenzaetype B (DTP-IPV-Hib) immunization to preterm infants. The effect of the recent substitution of acellular pertussis vaccine for whole cell pertussis vaccine on the frequency of these events requires further study.MethodsInfants with gestational age of ≤ 32 weeks who received their first DTP-IPV-Hib immunization prior to discharge from two Edmonton Neonatal Intensive Care Units January 1, 1996 to November 30, 2000 were eligible for the study. Each immunized infant was matched by gestational age to one control infant. The number of episodes of apnea, bradycardia, and/or desaturations (ABD) and the treatment required for these episodes in the 72 hours prior to and 72 hours post-immunization (for the immunized cohort) or at the same post-natal age (for controls) was recorded.ResultsThirty-four infants who received DTP-IPV-Hib with whole cell pertussis vaccine, 90 infants who received DTP-IPV-Hib with acellular pertussis vaccine, and 124 control infants were entered in the study. Fifty-six immunized infants (45.1%) and 36 control infants (29.0%) had a resurgence of or increased ABD in the 72 hours post-immunization in the immunized infants and at the same post-natal age in the controls with an adjusted odds ratio for immunized infants of 2.41 (95% CI 1.29,4.51) as compared to control infants. The incidence of an increase in adverse cardiorespiratory events post-immunization was the same in infants receiving whole cell or acellular pertussis vaccine (44.1% versus 45.6%). Eighteen immunized infants (14.5%) and 51 control infants (41.1%) had a reduction in ABD in the 72 hours post- immunization or at the equivalent postnatal age in controls for an odds ratio of 0.175 (95%CI 0.08, 0.39). The need for therapy of ABD in the immunized infants was not statistically different from the control infants. Lower weight at the time of immunization was a risk factor for a resurgence of or increased ABD post-immunization. Birth weight, gestational age, postnatal age or sex were not risk factors.ConclusionThere is an increase in adverse cardiorespiratory events following the first dose of DTP-IPV-Hib in preterm infants. Lower current weight was identified as a risk factor, with the risk being equivalent for whole cell versus acellular pertussis vaccine. Although most of these events are of limited clinical significance, cardiorespiratory monitoring of infants who are sufficiently preterm that they are receiving their first immunization prior to hospital discharge should be considered for 72 hours post-immunization.
Cost-effectiveness of tuberculosis evaluation and treatment of newly-arrived immigrants
Authors: Porco Travis C , Lewis Bryan , Marseille Elliot , Grinsdale Jennifer , Flood Jennifer M , Royce Sarah E 
Published: June 2006

Abstract

Background
Immigrants to the U.S. are required to undergo overseas screening for tuberculosis (TB), but the value of evaluation and treatment following entry to the U.S. is not well understood. We determined the cost-effectiveness of domestic follow-up of immigrants identified as tuberculosis suspects through overseas screening.

Methods
Using a stochastic simulation for tuberculosis reactivation, transmission, and follow-up for a hypothetical cohort of 1000 individuals, we calculated the incremental cost-effectiveness of follow-up and evaluation interventions. We utilized published literature, California Reports of Verified Cases of Tuberculosis (RVCTs), demographic estimates from the California Department of Finance, Medicare reimbursement, and Medi-Cal reimbursement rates. Our target population was legal immigrants to the United States, our time horizon is twenty years, and our perspective was that of all domestic health-care payers. We examined the intervention to offer latent tuberculosis therapy to infected individuals, to increase the yield of domestic evaluation, and to increase the starting and completion rates of LTBI therapy with INH (isoniazid). Our outcome measures were the number of cases averted, the number of deaths averted, the incremental dollar cost (year 2004), and the number of quality-adjusted life-years saved.

Results
Domestic follow-up of B-notification patients, including LTBI treatment for latently infected individuals, is highly cost-effective, and at times, cost-saving. B-notification follow-up in California would reduce the number of new tuberculosis cases by about 6–26 per year (out of a total of approximately 3000). Sensitivity analysis revealed that domestic follow-up remains cost-effective when the hepatitis rates due to INH therapy are over fifteen times our best estimates, when at least 0.4 percent of patients have active disease and when hospitalization of cases detected through domestic follow-up is no less likely than hospitalization of passively detected cases.

Conclusion
While the current immigration screening program is unlikely to result in a large change in case rates, domestic follow-up of B-notification patients, including LTBI treatment, is highly cost-effective. If as many as three percent of screened individuals have active TB, and early detection reduces the rate of hospitalization, net savings may be expected.
Obesity and hypertension in an Iranian cohort study; Iranian women experience higher rates of obesity and hypertension than American women
Authors: Bahrami Hossein , Sadatsafavi Mohsen , Pourshams Akram , Kamangar Farin , Nouraei Mehdi , Semnani Shahriar , Brennan Paul , Boffetta Paolo , Malekzadeh Reza 
Published: June 2006

AbstractBackgroundOnce considered as the main public health problem in developed countries, obesity has become a major problem throughout the world and developing countries, like Iran, are joining the global obesity pandemic. We determined the prevalence of overweight, obesity, and hypertension in a large cohort of Iranians and compared age-adjusted rates with the rates in the US.MethodsGolestan Cohort Study is a population-based study of 8,998 men and women, aged 35-81 years, from urban and rural areas. Anthropometric parameters were measured by interviewers. Prevalence rates were directly adjusted to the 2000 United States standard population.ResultsThe age-adjusted prevalence rates of overweight (BMI ≥ 25 kg/m2) and obesity (BMI ≥ 30 kg/m2) in this Iranian population were 62.2% and 28.0%, respectively. Both overweight and obesity were more common in women than men. Age-adjusted prevalence of overweight was significantly higher in Iranian women compared to the American women (68.6% vs. 61.6%), while the age-adjusted prevalence of obesity is closer in these two populations (34.9% vs. 33.2%). Iranian men—compared to American men—had significantly lower age-adjusted prevalence of overweight (53.7% vs. 68.8%) and obesity (16.2% vs. 27.5%). Age-adjusted prevalence of hypertension was higher in Iranian women than American women (35.7% vs. 30.5%). Diabetes mellitus was reported in 6.2% of participants. Mean waist-to-hip ratio (WHR) among women was 0.96. Smoking rates in men and women were 33.2% and 2.2%, respectively.ConclusionThe prevalence of obesity, overweight, and hypertension in Iran is as high as the US. However, Iranian women are more obese than American women and Iranian men are less obese than their American counterparts. This discrepancy might be due to the low rate of smoking among Iranian women. Iranian women have higher mean WHR than what WHO has defined in 19 other populations.
The Transtheoretical model for fruit, vegetable and fish consumption: associations between intakes, stages of change and stage transition determinants
Authors: De Vet Emely , de Nooijer Jascha , de Vries Nanne K , Brug Johannes 
Published: June 2006

Abstract

Background
Cardiovascular diseases are caused by multiple behavioral factors, including different dietary factors. We examined to what extent fruit, vegetable and fish consumption are related, and whether behavioral determinants vary across these dietary behaviors from a Transtheoretical model perspective.

Methods
Data were collected among 1142 participants (T0; response rate 46%) selected from an Internet panel, who were followed-up one-week later (T1; N = 1055, response rate 92%). Mean age was 35.4 (SD = 11.9) years, 35% was male, and most respondents were of Dutch origin (90%). Of the respondents, 13%, 44% and 43% had a low, medium or high level of education, respectively. Electronic questionnaires assessed fruit, vegetable and fish intake (food frequency questionnaires), stages of change, decisional balance and self-efficacy, for each of these three behaviors.

Results
Stages of change and (changes in) fruit, vegetable and fish intake were only weakly associated; decisional balance and self-efficacy were more strongly associated. Some presumed predictors of stage transitions were similar for fruit, vegetable, and fish intake, i.e., strong pros predicted progress out of precontemplators and low self-efficacy predicted relapse from action/maintenance for all behaviors. However, progress out of contemplation and out of preparation showed different patterns for fruit, vegetable and fish intake.

Conclusion
The weak associations between intakes and potential determinants for fruit, vegetable, and fish consumption do not warrant an integrated dietary change approach targeting the same determinants for each behavior.