bluuebunny/crossref_metadata_2025_split huggingface dataset:
The β-Barrel Outer Membrane Protein Assembly Complex ofNeisseria meningitidis
Authors: Volokhina Elena B. , Beckers Frank , Tommassen Jan , Bos Martine P. 
Published: September 2009

ABSTRACTThe evolutionarily conserved protein Omp85 is required for outer membrane protein (OMP) assembly in gram-negative bacteria and in mitochondria. ItsEscherichia colihomolog, designated BamA, functions with four accessory lipoproteins, BamB, BamC, BamD, and BamE, together forming the β-barrel assembly machinery (Bam). Here, we addressed the composition of this machinery and the function of its components inNeisseria meningitidis, a model organism for outer membrane biogenesis studies. Analysis of genome sequences revealed homologs of BamC, BamD (previously described as ComL), and BamE and a second BamE homolog, Mlp. No homolog of BamB was found. As inE. coli, ComL/BamD appeared essential for viability and for OMP assembly, and it could not be replaced by itsE. colihomolog. BamE was not essential but was found to contribute to the efficiency of OMP assembly and to the maintenance of OM integrity. AbamCmutant showed only marginal OMP assembly defects, but the impossibility of creating abamC bamEdouble mutant further indicated the function of BamC in OMP assembly. Anmlpmutant was unaffected in OMP assembly. The results of copurification assays demonstrated the association of BamC, ComL, and BamE with Omp85. Semi-native gel electrophoresis identified the RmpM protein as an additional component of the Omp85 complex, which was confirmed in copurification assays. RmpM was not required for OMP folding but stabilized OMP complexes. Thus, the Bam complex inN. meningitidisconsists of Omp85/BamA plus RmpM, BamC, ComL/BamD, and BamE, of which ComL/BamD and BamE appear to be the most important accessory components for OMP assembly.
The Response Regulator SprE (RssB) Modulates Polyadenylation and mRNA Stability inEscherichia coli
Authors: Carabetta Valerie J. , Mohanty Bijoy K. , Kushner Sidney R. , Silhavy Thomas J. 
Published: September 2009

ABSTRACTInEscherichia coli, the adaptor protein SprE (RssB) controls the stability of the alternate sigma factor RpoS (σ38and σS). When nutrients are abundant, SprE binds RpoS and delivers it to ClpXP for degradation, but when carbon sources are depleted, this process is inhibited. It also has been noted that overproduction of SprE is toxic. Here we show that null mutations inpcnB, encoding poly(A) polymerase I (PAP I), and inhfq, encoding the RNA chaperone Hfq, suppress this toxicity. Since PAP I, in conjunction with Hfq, is responsible for targeting RNAs, including mRNAs, for degradation by adding poly(A) tails onto their 3′ ends, these data indicate that SprE helps modulate the polyadenylation pathway inE. coli. Indeed, in exponentially growing cells,sprEdeletion mutants exhibit significantly reduced levels of polyadenylation and increased stability of specific mRNAs, similar to what is observed in a PAP I-deficient strain. In stationary phase, we show that SprE changes the intracellular localization of PAP I. Taken together, we propose that SprE plays a multifunctional role in controlling the transcriptome, regulating what is made via its effects on RpoS, and modulating what is degraded via its effects on polyadenylation and turnover of specific mRNAs.
Tryptophan Inhibits
Proteus vulgaris
TnaC Leader Peptide Elongation, Activating
tna
Operon Expression
Authors: Cruz-Vera Luis R. , Yang Rui , Yanofsky Charles 
Published: September 2009

ABSTRACT

Expression of the
tna
operon of
Escherichia coli
and of
Proteus vulgaris
is induced by
l
-tryptophan. In
E. coli
, tryptophan action is dependent on the presence of several critical residues (underlined) in the newly synthesized TnaC leader peptide,
W
FNI
D
XX
L/I
XXXX
P
. These residues are conserved in TnaC of
P. vulgaris
and of other bacterial species. TnaC of
P. vulgaris
has one additional feature, distinguishing it from TnaC of
E. coli
; it contains two C-terminal lysine residues following the conserved proline residue. In the present study, we investigated
l
-tryptophan induction of the
P. vulgaris tna
operon, transferred on a plasmid into
E. coli
. Induction was shown to be
l
-tryptophan dependent; however, the range of induction was less than that observed for the
E. coli tna
operon. We compared the genetic organization of both operons and predicted similar folding patterns for their respective leader mRNA segments. However, additional analyses revealed that
l
-tryptophan action in the
P. vulgaris tna
operon involves inhibition of TnaC elongation, following addition of proline, rather than inhibition of leader peptide termination. Our findings also establish that the conserved residues in TnaC of
P. vulgaris
are essential for
l
-tryptophan induction, and for inhibition of peptide elongation. TnaC synthesis is thus an excellent model system for studies of regulation of both peptide termination and peptide elongation, and for studies of ribosome recognition of the features of a nascent peptide.
Complete Genome Sequence of
Lactobacillus johnsonii
FI9785, a Competitive Exclusion Agent against Pathogens in Poultry
Authors: Wegmann Udo , Overweg Karin , Horn Nikki , Goesmann Alexander , Narbad Arjan , Gasson Michael J. , Shearman Claire 
Published: September 2009

ABSTRACT

Lactobacillus johnsonii
is a member of the acidophilus group of lactobacilli. Because of their probiotic properties, including attachment to epithelial cells, immunomodulation, and competitive exclusion of pathogens, representatives of this group are being intensively studied. Here we report the complete annotated genome sequence of
Lactobacillus johnsonii
FI9785, a strain which prevents the colonization of specific-pathogen-free chicks by
Clostridium perfringens
.
Complete Genome Sequence of
Robiginitalea biformata
HTCC2501
Authors: Oh Hyun-Myung , Giovannoni Stephen J. , Lee Kiyoung , Ferriera Steve , Johnson Justin , Cho Jang-Cheon 
Published: September 2009

ABSTRACT

Robiginitalea biformata
HTCC2501, isolated from the Sargasso Sea by dilution-to-extinction culturing, has been known as an aerobic chemoheterotroph with carotenoid pigments and dimorphic growth phases. Here, we announce the complete sequence of the
R. biformata
HTCC2501 genome, which contains genes for carotenoid biosynthesis and several macromolecule-degrading enzymes.
MULTIDIMENSIONAL INDEPENDENT COMPONENT ANALYSIS FOR STATISTICAL ESTIMATIONS OF INDETERMINACIES IN ELECTROCARDIOGRAMS
Authors: CHAWLA M. P. S. 
Published: September 2009

Independent component analysis (ICA) is a technique capable of separating independent components (ICs) from complex electrocardiogram (ECG) signals. The basic intention behind using multidimensional independent component analysis (MICA) is to find stable higher dimensional source signal subspaces. This study highlights the ability of ICA for parametrization of ECG signals to reduce the amount of redundant ECG data if any in a data set. The aim of this paper is to justify the underlying theory of the use of ICA and how it can be extended to for MICA separation of the ECG signals for combinational leads to attain most useful diagnostic information, which was not discussed in other some similar previous publications in this field. It is also investigated that the value of kurtosis coefficients for the ICs, which represents the noise component, can be further reduced using parametrized multidimensional independent component analysis (PMICA) technique. The indeterminacies available in the ECG data are also analyzed using modified version of Jade algorithm for PMICA and parametrized standard independent component analysis (PSICA). For the ECG data set, Jade algorithm is applied first to find smaller subspaces for MICA analysis and can therefore be regarded as a basis algorithm for PMICA analysis. The simulation results are obtained in Matlab environment to indicate that, ICA can definitely improve signal–noise ratio (SNR) in minimizing the reconstruction errors. The future scope of MICA expected by author is that, by reconsidering the notion of ICA, a more general perspective can be envisioned: i.e. modified multidimensional independent component analysis (MMICA). It would be based on a morphological geometric parametrization (MGP) which would further reduce the indeterminacies involved in matrix-based modeling (MBM).
Anti-CD3 antibodies modulate anti–factor VIII immune responses in hemophilia A mice after factor VIII plasmid-mediated gene therapy
Authors: Peng Baowei , Ye Peiqing , Rawlings David J. , Ochs Hans D. , Miao Carol H. 
Published: September 2009

AbstractOne major obstacle in gene therapy is the generation of immune responses directed against transgene product. Five consecutive anti-CD3 treatments concomitant with factor VIII (FVIII) plasmid injection prevented the formation of inhibitory antibodies against FVIII and achieved persistent, therapeutic levels of FVIII gene expression in treated hemophilia A mice. Repeated plasmid gene transfer is applicable in tolerized mice without eliciting immune responses. Anti-CD3 treatment significantly depleted both CD4+ and CD8+ T cells, whereas increased transforming growth factor-β levels in plasma and the frequency of both CD4+CD25+FoxP3+ and CD4+CD25−Foxp3+ regulatory T cells in the initial few weeks after treatment. Although prior depletion of CD4+CD25+ cells did not abrogate tolerance induction, adoptive transfer of CD4+ cells from tolerized mice at 6 weeks after treatment protected recipient mice from anti-FVIII immune responses. Anti-CD3–treated mice mounted immune responses against both T-dependent and T-independent neo-antigens, indicating that anti-CD3 did not hamper the immune systems in the long term. Concomitant FVIII plasmid + anti-CD3 treatment induced long-term tolerance specific to FVIII via a mechanism involving the increase in transforming growth factor-β levels and the generation of adaptive FVIII-specific CD4+Foxp3+ regulatory T cells at the periphery. Furthermore, anti-CD3 can reduce the titers of preexisting anti-FVIII inhibitory antibodies in hemophilia A mice.
Control of CD56 expression and tumor cell cytotoxicity in human Vγ2Vδ2 T cells
Authors: Urban Elizabeth M , Li Haishan , Armstrong Cheryl , Focaccetti Chiara , Cairo Cristiana , Pauza C David 
Published: September 2009

AbstractBackgroundIn lymphocyte subsets, expression of CD56 (neural cell adhesion molecule-1) correlates with cytotoxic effector activity. For cells bearing the Vγ2Vδ2 T cell receptor, isoprenoid pyrophosphate stimulation leads to uniform activation and proliferation, but only a fraction of cells express CD56 and display potent cytotoxic activity against tumor cells. Our goal was to show whether CD56 expression was regulated stochastically, similar to conventional activation antigens, or whether CD56 defined a lineage of cells committed to the cytotoxic phenotype.ResultsTracking individual cell clones defined by their Vγ2 chain CDR3 region sequences, we found that CD56 was expressed on precursor cytotoxic T cells already present in the population irrespective of their capacity to proliferate after antigen stimulation. Public T cell receptor sequences found in the CD56+ subset from one individual might appear in the CD56- subset of another donor. The commitment of individual clones to CD56+ or CD56- lineages was stable for each donor over a 1 year interval.ConclusionThe ability to express CD56 was not predicted by TCR sequence or by the strength of signal received by the TCR. For γδ T cells, cytotoxic effector function is acquired when cytotoxic precursors within the population are stimulated to proliferate and express CD56. Expression of CD56 defines a committed lineage to the cytotoxic phenotype.
Antimicrobial resistance profiling and molecular subtyping of Campylobacterspp. from processed turkey
Authors: Lutgen Ellen M , McEvoy John M , Sherwood Julie S , Logue Catherine M 
Published: September 2009

Abstract

Background

Campylobacter is a major cause of human disease worldwide and poultry are identified as a significant source of this pathogen. Most disease in humans is associated with the consumption of contaminated poultry or cross-contamination with other foods. The primary drugs of choice for treatment of human campylobacteriosis include erythromycin and ciprofloxacin. In this study, we investigated the prevalence of resistance to erythromycin and ciprofloxacin in Campylobacter isolates recovered from turkey carcasses at two processing plants in the Upper Midwest US. Further analysis of a subset of isolates was carried out to assess resistance and genotype profiles.

Results

Campylobacter isolates from plant A (n = 439; including 196 C. coli and 217 C. jejuni) and plant B (n = 362, including 281 C. coli and 62 C. jejuni) were tested for susceptibility to ciprofloxacin and erythromycin using agar dilution. C. coli were more frequently resistant than C. jejuni in both plants, including resistance to ciprofloxacin (28% of C. jejuni and 63% of C. coli, plant B; and 11% of C. coli, plant A). Erythromycin resistance was low among C. jejuni (0% plant A and 0.3% plant B) compared to C. coli (41%, plant A and 17%, plant B). One hundred resistant and susceptible isolates were selected for additional antimicrobial susceptibility testing, restriction fragment length polymorphism analysis of the flaA gene (fla typing), and pulsed-field gel electrophoresis (PFGE). Fla-PFGE types obtained (n = 37) were associated with a specific plant with the exception of one type that was isolated from both plants. C. coli isolates (n = 65) were grouped into 20 types, while C. jejuni isolates (n = 35) were grouped into 17 types. Most isolates with identical fla-PFGE patterns shared identical or very similar antimicrobial resistance profiles. PFGE alone and composite analysis using fla-PFGE with resistance profiles separated C. jejuni and C. coli into distinct groups.

Conclusion
Ciprofloxacin and erythromycin resistance in Campylobacter recovered from processed turkey occurred more frequently among C. coli than C. jejuni. Fla-PFGE types were associated with a particular species, antimicrobial resistance profiles, and a specific plant. Molecular subtyping in this study provided more information about the relationships among antimicrobial-resistant Campylobacter at the processing level.
Association analyses of the INSIG2polymorphism in the obesity and cholesterol levels of Korean populations
Authors: Cha Seongwon , Koo Imhoi , Choi Sun Mi , Park Byung Lae , Kim Kil Soo , Kim Jae-Ryong , Shin Hyoung Doo , Kim Jong Yeol 
Published: September 2009

Abstract

Background
While INSIG2 has been reported to be associated with BMI in many populations, conflicting results have prevented consensus over its role. In analyses of mice and cell cultures the gene has been found to be involved in the regulation of cholesterol synthesis; however, no relationship has been found with cholesterol metabolism in human epidemiological research. Therefore, this study attempts to assess the effect of rs7566605 near INSIG2 on both obesity- and cholesterol-related traits in Koreans.

Methods
The rs7566605 polymorphism was genotyped with 2,364 Koreans, and associations with obesity- and cholesterol-related traits were analyzed statistically via an ANOVA or T-test.

Results
Replication of an association with BMI, WHR, fat mass, fat percent, and abdominal fat area failed, and the C allele of rs7566605 was not associated significantly with total cholesterol, HDL cholesterol, or triglyceride. However, it was found in a meta-analysis of a dominant model that the C allele of rs7566605 appeared to affect the level of the total cholesterol, especially in female subjects.

Conclusion
We failed to show associations of rs7566605 with cholesterol- and obesity-related phenotypes, although we newly suggest the possible involvement of INSIG2 with the plasma level of the total cholesterol in women.
Development of a theoretical framework for analyzing cerebrospinal fluid dynamics
Authors: Cohen Benjamin , Voorhees Abram , Vedel Søren , Wei Timothy 
Published: September 2009

Abstract

Background
To date hydrocephalus researchers acknowledge the need for rigorous but utilitarian fluid mechanics understanding and methodologies in studying normal and hydrocephalic intracranial dynamics. Pressure volume models and electric circuit analogs introduced pressure into volume conservation; but control volume analysis enforces independent conditions on pressure and volume. Previously, utilization of clinical measurements has been limited to understanding of the relative amplitude and timing of flow, volume and pressure waveforms; qualitative approaches without a clear framework for meaningful quantitative comparison.

Methods
Control volume analysis is presented to introduce the reader to the theoretical background of this foundational fluid mechanics technique for application to general control volumes. This approach is able to directly incorporate the diverse measurements obtained by clinicians to better elucidate intracranial dynamics and progression to disorder.

Results
Several examples of meaningful intracranial control volumes and the particular measurement sets needed for the analysis are discussed.

Conclusion
Control volume analysis provides a framework to guide the type and location of measurements and also a way to interpret the resulting data within a fundamental fluid physics analysis.
The capacity for multistability in small gene regulatory networks
Authors: Siegal-Gaskins Dan , Grotewold Erich , Smith Gregory D 
Published: September 2009

Abstract

Background
Recent years have seen a dramatic increase in the use of mathematical modeling to gain insight into gene regulatory network behavior across many different organisms. In particular, there has been considerable interest in using mathematical tools to understand how multistable regulatory networks may contribute to developmental processes such as cell fate determination. Indeed, such a network may subserve the formation of unicellular leaf hairs (trichomes) in the model plant Arabidopsis thaliana.

Results
In order to investigate the capacity of small gene regulatory networks to generate multiple equilibria, we present a chemical reaction network (CRN)-based modeling formalism and describe a number of methods for CRN analysis in a parameter-free context. These methods are compared and applied to a full set of one-component subnetworks, as well as a large random sample from 40,680 similarly constructed two-component subnetworks. We find that positive feedback and cooperativity mediated by transcription factor (TF) dimerization is a requirement for one-component subnetwork bistability. For subnetworks with two components, the presence of these processes increases the probability that a randomly sampled subnetwork will exhibit multiple equilibria, although we find several examples of bistable two-component subnetworks that do not involve cooperative TF-promoter binding. In the specific case of epidermal differentiation in Arabidopsis, dimerization of the GL3-GL1 complex and cooperative sequential binding of GL3-GL1 to the CPC promoter are each independently sufficient for bistability.

Conclusion
Computational methods utilizing CRN-specific theorems to rule out bistability in small gene regulatory networks are far superior to techniques generally applicable to deterministic ODE systems. Using these methods to conduct an unbiased survey of parameter-free deterministic models of small networks, and the Arabidopsis epidermal cell differentiation subnetwork in particular, we illustrate how future experimental research may be guided by network structure analysis.
Tyrosine Kinase Inhibitor Enhances the Bioavailability of Oral Irinotecan in Pediatric Patients With Refractory Solid Tumors
Authors: Furman Wayne L. , Navid Fariba , Daw Najat C. , McCarville M. Beth , McGregor Lisa M. , Spunt Sheri L. , Rodriguez-Galindo Carlos , Panetta John C. , Crews Kristine R. , Wu Jianrong , Gajjar Amar J. , Houghton Peter J. , Santana Victor M. , Stewart Clinton F. 
Published: September 2009

Purpose To assess the maximum-tolerated dosages (MTDs), and dose-limiting toxicities (DLTs) of the epidermal growth factor receptor inhibitor gefitinib and of intravenous (IV) irinotecan when administered together in children with refractory solid tumors. To assess the effect of gefitinib on the pharmacokinetics of IV irinotecan and on the bioavailability of a single oral dose of irinotecan. Patients and Methods IV irinotecan (15 or 20 mg/m2) was given daily for 5 days of 2 consecutive weeks. Oral gefitinib (150 or 112.5 mg/m2) was concomitantly given daily for 12 or 21 days. A single oral dose of irinotecan was given on day 9 of course 2 to allow pharmacokinetic analysis. Results The study enrolled 29 patients with recurrent solid tumors. The 21-day regimen of oral gefitinib with irinotecan was not tolerated. Diarrhea was the most common DLT. The MTD of the combination regimen was 15 mg/m2/d of IV irinotecan for 5 days of 2 consecutive weeks and 112.5 mg/m2/d of gefitinib given for 12 days. Gefitinib increased the bioavailability of oral irinotecan by four-fold over that observed in historical controls (median, 0.09 v 0.42; P < .000001), reducing the apparent clearance (an inverse measure of exposure) of irinotecan and SN-38 by 37% and 38%, respectively (P < .0001). A partial response was observed in a patient with refractory Ewing sarcoma. Conclusion IV irinotecan given with 12 days of oral gefitinib is well tolerated in children. We observed one partial response. Gefitinib significantly enhances the bioavailability of oral irinotecan. This combination warrants further investigation, particularly with orally administered irinotecan.
Effect of Exercise on Postmenopausal Sex Hormone Levels and Role of Body Fat: A Randomized Controlled Trial
Authors: Monninkhof Evelyn M. , Velthuis Miranda J. , Peeters Petra H.M. , Twisk Jos W.R. , Schuit Albertine J. 
Published: September 2009

PurposeTo examine the effects of a 1-year exercise intervention on sex hormone levels in postmenopausal women and whether any effects are mediated by changes in body fat composition.MethodsWe randomly assigned 189 sedentary postmenopausal women (age 50 to 69 years, body mass index of 22 to 40 kg/m2) to an exercise intervention (n = 96) or a control group (n = 93). The intervention combined aerobic and strength training and comprised supervised group sessions and home-based exercises (a total of 2.5 h/wk). Between-group differences in sex hormone levels (at baseline and 4 and 12 months) were examined with generalized estimating equations.ResultsIn total, 183 women (97%) completed the study. Overall, the exercise intervention did not result in favorable effects on sex hormone levels. Among women who lost more than 2% body fat, declines in all estrogens were not significantly different between exercisers and controls. Androgen levels decreased significantly in the exercise group who lost body fat compared with their peers in the control group. Furthermore, this study confirmed that fat loss was significantly associated with declines in postmenopausal estrogen levels. Although not significant, a similar trend was observed for the androgens.ConclusionThis study confirms that fat loss is associated with changes in postmenopausal sex hormone levels and suggests that exercise may be effective in inducing favorable changes in these hormones.