bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of a Novel Preribosomal Complex in Trypanosoma brucei Determined by Fluorescence Resonance Energy Transfer
Authors: Wang Lei , Ciganda Martin , Williams Noreen 
Published: December 2012

ABSTRACT

We have previously reported that the trypanosome-specific proteins P34 and P37 form a unique preribosomal complex with ribosomal protein L5 and 5S rRNA in the nucleoplasm. We hypothesize that this novel trimolecular complex is necessary for stabilizing 5S rRNA in
Trypanosoma brucei
and is essential for the survival of the parasite.
In vitro
quantitative analysis of the association between the proteins L5 and P34 is fundamental to our understanding of this novel complex and thus our ability to exploit its unique characteristics. Here we used
in vitro
fluorescence resonance energy transfer (FRET) to analyze the association between L5 and P34. First, we demonstrated that FRET can be used to confirm the association between L5 and P34. We then determined that the binding constant for L5 and P34 is 0.60 ± 0.03 μM, which is in the range of protein-protein binding constants for RNA binding proteins. In addition, we used FRET to identify the critical regions of L5 and P34 involved in the protein-protein association. We found that the N-terminal APK-rich domain and RNA recognition motif (RRM) of P34 and the L18 domain of L5 are important for the association of the two proteins with each other. These results provide us with the framework for the discovery of ways to disrupt this essential complex.
Novel Bilobe Components in Trypanosoma brucei Identified Using Proximity-Dependent Biotinylation
Authors: Morriswood Brooke , Havlicek Katharina , Demmel Lars , Yavuz Sevil , Sealey-Cardona Marco , Vidilaseris Keni , Anrather Dorothea , Kostan Julius , Djinović-Carugo Kristina , Roux Kyle J. , Warren Graham 
Published: December 2012

ABSTRACT

The trypanosomes are a family of parasitic protists of which the African trypanosome,
Trypanosoma brucei
, is the best characterized. The complex and highly ordered cytoskeleton of
T. brucei
has been shown to play vital roles in its biology but remains difficult to study, in large part owing to the intractability of its constituent proteins. Existing methods of protein identification, such as bioinformatic analysis, generation of monoclonal antibody panels, proteomics, affinity purification, and yeast two-hybrid screens, all have drawbacks. Such deficiencies—troublesome proteins and technical limitations—are common not only to
T. brucei
but also to many other protists, many of which are even less well studied. Proximity-dependent biotin identification (BioID) is a recently developed technique that allows forward screens for interaction partners and near neighbors in a native environment with no requirement for solubility in nonionic detergent. As such, it is extremely well suited to the exploration of the cytoskeleton. In this project, BioID was adapted for use in
T. brucei
. The trypanosome bilobe, a discrete cytoskeletal structure with few known protein components, represented an excellent test subject. Use of the bilobe protein TbMORN1 as a probe resulted in the identification of seven new bilobe constituents and two new flagellum attachment zone proteins. This constitutes the first usage of BioID on a largely uncharacterized structure, and demonstrates its utility in identifying new components of such a structure. This remarkable success validates BioID as a new tool for the study of unicellular eukaryotes in particular and the eukaryotic cytoskeleton in general.
Cryptococcus neoformans Growth and Protection from Innate Immunity Are Dependent on Expression of a Virulence-Associated DEAD-Box Protein, Vad1
Authors: Qiu Jin , Olszewski Michal A. , Williamson Peter R. 
Published: December 2012

ABSTRACT

The fungus
Cryptococcus neoformans
has emerged as a major cause of meningoencephalitis worldwide. Host response to the fungus involves both innate and adaptive immunity, but fungal genes that modulate these processes are poorly understood. Previous studies demonstrated attenuated virulence of a mutant of a
v
irulence-
a
ssociated
D
EAD-box protein (
VAD1
) in mice, despite normal growth at host temperatures, suggesting modulation of the immune response. In the present study, the
Δvad1
mutant demonstrated progressive clearance from lung and was unable to induce pathological lesions or to cause extrapulmonary disease, despite retaining its ability to grow in mouse serum and a J774.16 macrophage cell line. Pulmonary clearance occurred with a minimal cellular infiltrate, marked by reduced CD4 cells, CD11b
+
Ly6C
high
monocytes, and F4/80
+
macrophages, but the mutant strain retained recruitment of CD8 cells, compared to infections with wild-type fungi. Adaptive cytokine responses were reduced, including Th1, Th2, and Th17 cytokines; however, early gamma interferon (IFN-γ) and tumor necrosis factor alpha (TNF-α) responses were retained while nonprotective interleukin 4 (IL-4) and IL-5 were diminished. Furthermore, the
Δvad1
mutant was controlled in lungs despite CD4/CD8 cell depletion. These data, along with improved phagocytosis by macrophages and increases in early/innate IL-1α, IFN-γ, and chemokines elicited in the lungs within 3 days of infection with the
Δvad1
mutant, indicate that
VAD1
expression reduces innate recognition of
C. neoformans
, rendering the yeast resistant to elimination by the innate mechanisms of host defense. Thus, our studies define a novel role of the cryptococcal Vad1 protein as a central regulator of cryptococcal virulence and illustrate that Vad1 promotes microbe resistance to innate host defenses.
Tetratricopeptide Repeat Motifs in the World of Bacterial Pathogens: Role in Virulence Mechanisms
Authors: Cerveny Lukas , Straskova Adela , Dankova Vera , Hartlova Anetta , Ceckova Martina , Staud Frantisek , Stulik Jiri 
Published: December 2012

ABSTRACT

The tetratricopeptide repeat (TPR) structural motif is known to occur in a wide variety of proteins present in prokaryotic and eukaryotic organisms. The TPR motif represents an elegant module for the assembly of various multiprotein complexes, and thus, TPR-containing proteins often play roles in vital cell processes. As the TPR profile is well defined, the complete TPR protein repertoire of a bacterium with a known genomic sequence can be predicted. This provides a tremendous opportunity for investigators to identify new TPR-containing proteins and study them in detail. In the past decade, TPR-containing proteins of bacterial pathogens have been reported to be directly related to virulence-associated functions. In this minireview, we summarize the current knowledge of the TPR-containing proteins involved in virulence mechanisms of bacterial pathogens while highlighting the importance of TPR motifs for the proper functioning of class II chaperones of a type III secretion system in the pathogenesis of
Yersinia
,
Pseudomonas
, and
Shigella
.
Estrogenic Modulation of Uropathogenic Escherichia coli Infection Pathogenesis in a Murine Menopause Model
Authors: Wang Caihong , Symington Jane W. , Ma Emily , Cao Bin , Mysorekar Indira U. 
Published: December 2012

ABSTRACT

Recurrent urinary tract infections (UTIs), primarily caused by uropathogenic
Escherichia coli
(UPEC), annually affect over 13 million patients in the United States. Menopausal women are disproportionally susceptible, suggesting estrogen deficiency is a significant risk factor for chronic and recurrent UTI. How estrogen status governs susceptibility to UTIs remains unknown, and whether hormone therapy protects against UTIs remains controversial. Here, we used a mouse model of surgical menopause by ovariectomy and demonstrate a protective role for estrogen in UTI pathogenesis. We found that ovariectomized mice had significantly higher bacteriuria, a more robust inflammatory response, and increased production of the proinflammatory cytokine interleukin-6 (IL-6) upon UPEC infection compared to sham-operated controls. We further show that response of the urothelial stem cell niche to infection, normally activated to restore homeostasis after infection, was aberrant in ovariectomized mice with defective superficial urothelial cell differentiation. Finally, UPEC-infected ovariectomized mice showed a significant increase in quiescent intracellular bacterial reservoirs, which reside in the urothelium and can seed recurrent infections. Importantly, this and other ovariectomy-induced outcomes of UTI were reversible upon estrogen supplementation. Together, our findings establish ovariectomized mice as a model for UTIs in menopausal women and pinpoint specific events during course of infection that are most susceptible to estrogen deficiency. These findings have profound implications for the understanding of the role of estrogen and estrogen therapy in bladder health and pathogen defense mechanisms and open the door for prophylaxis for menopausal women with recurrent UTIs.
Complex T Cell Interactions Contribute to Helicobacter pylori Gastritis in Mice
Authors: Gray Brian M. , Fontaine Clinton A. , Poe Sara A. , Eaton Kathryn A. 
Published: December 2012

ABSTRACTDisease due to the gastric pathogenHelicobacter pylorivaries in severity from asymptomatic to peptic ulcer disease and cancer. Accumulating evidence suggests that one source of this variation is an abnormal host response. The goal of this study was to use a mouse model ofH. pylorigastritis to investigate the roles of regulatory T cells (Treg) as well as proinflammatory T cells (Th1 and Th17) in gastritis, gastric T cell engraftment, and gastric cytokine production. Our results support published data indicating that severe gastritis in T cell recipient mice is due to failure of Treg engraftment, that Treg ameliorate gastritis, and that the proinflammatory response is attributable to interactions between several cell subsets and cytokines. We confirmed that gamma interferon (IFN-γ) is essential for induction of gastritis but showed that IFN-γ-producing CD4 T cells are not necessary. Interleukin 17A (IL-17A) also contributed to gastritis, but to a lesser extent than IFN-γ. Tumor necrosis factor alpha (TNF-α) and IL-17F were also elevated in association with disease. These results indicate that whileH. pylori-specific CD4+T cells and IFN-γ are both essential for induction of gastritis due toH. pylori, IFN-γ production by T cells is not essential. It is likely that other proinflammatory cytokines, such as IL-17F and TNF-α, shown to be elevated in this model, also contribute to the induction of disease. We suggest that gastritis due toH. pyloriis associated with loss of immunoregulation and alteration of several cytokines and cell subsets and cannot be attributed to a single immune pathway.
A tectonic model for hyperextension at magma-poor rifted margins: an example from the West Iberia–Newfoundland conjugate margins
Authors: Pérez-Gussinyé Marta 
Published: December 2012

Abstract

Hyperextended, magma-poor margins are characterized by a wide continent–ocean transition and anomalously small fractions of magmatism during mantle exhumation prior to oceanic spreading. Here, I bring together several aspects of their rift to drift transition and give a coherent picture of their evolution from platform to deep-sea environments. I focus mainly on the West Iberia Margin (WIM)–Newfoundland (NF) conjugates in the North Atlantic Ocean. The architectural evolution of these margins is characterized by upper-crustal faulting and lower-crustal deformation that are tightly coupled, resulting in fault displacement that is accompanied by underlying, equal and coeval crustal thinning. Lower crust deforms first ductilely, but then progressively switches to brittle due to enhanced conductive cooling at very slow extension velocities (<
c.
6 mm a
−1
half-rate). The switch from ductile to progressively brittle lower crust is accompanied by the emergence of a dominant basinwards fault dip and oceanwards younging of fault activity. It is shown that these processes, acting in concert: (1) reconcile the horizontal extension on faults with crustal thinning without the need of lower-crustal flow; (2) explain, within one common Andersonian framework (faults active at 65°–30°), the change in fault geometry from planar to listric to detachment-like with increasing extension; and (3) generate the tectonic asymmetry observed between conjugate pairs. This work also discusses a high-resolution seismic section of the WIM showing that the ‘detachment-like’ fault S is truncated prior to the peridotite ridge where mantle exhumation first takes place. This suggests that serpentinized mantle rises due to its own buoyancy, separating and pulling the thinned crustal blocks apart. Once the crust has been separated, further mantle exhumation takes place by magma-poor extension of the underlying mantle. I show with numerical models that either a small reduction of mantle potential temperature (
c.
25–50 °C), a mantle depletion of more than 10% or very slow half-extension velocities (
c.
6 mm a
−1
) are required to reproduce the small amount of magmatism inferred. Available observations support either a very slow extension velocity or a smaller than normal mantle temperature; however, estimation errors may be large. Ultimately, unravelling which of these factors most contribute to magma-poor mantle exhumation will provide an improved understanding of the mantle lateral homogeneity and the three-dimensional nature of the rifting to drifting process.
Molecular Pathways: Involvement of Immune Pathways in the Therapeutic Response and Outcome in Breast Cancer
Authors: Andre Fabrice , Dieci Maria V. , Dubsky Peter , Sotiriou Christos , Curigliano Giuseppe , Denkert Carsten , Loi Sherene 
Published: December 2012

Abstract
The immune system could mediate the antitumor activity of several anticancer treatments. Several chemotherapy compounds, including anthracyclines and oxaliplatin, induce immunogenic cell death that in turn activates antitumor immune response. Trastuzumab induces antibody-dependant cell-mediated cytotoxicity. On the basis of this background, immune markers have recently been the focus of intense translational research to predict and monitor the efficacy of treatments. Gene expression arrays and immunohistochemistry have assessed immune activation and infiltration by macrophages, natural killer, and T and B lymphocytes. Using these approaches, several retrospective analyses of large trials have shown that activation of immune pathway may predict treatment efficacy and outcome in patients with breast cancers. As examples, intratumoral infiltration by lymphocytes and interferon-response in primary tumor predicted the efficacy of neoadjuvant chemotherapy. Intratumoral infiltration by lymphocytes was associated with good prognosis in patients with triple-negative breast cancer treated with adjuvant chemotherapy. More recently, it has been suggested that lymphocyte infiltration could also predict efficacy of trastuzumab. Finally, small retrospective studies have suggested that postchemotherapy lymphocyte infiltrates could be associated with better outcome in patients who did not reach pathologic complete response. This body of evidence suggests that assessing immune infiltration and activation could be useful in the future to stratify breast cancer patients. In addition, they provide evidence for the development of immunotherapies in breast cancer patients. Clin Cancer Res; 19(1); 28–. ©2012 AACR.
Baseline Characteristics of Patients in the Treatment of Preserved Cardiac Function Heart Failure With an Aldosterone Antagonist Trial
Authors: Shah Sanjiv J. , Heitner John F. , Sweitzer Nancy K. , Anand Inder S. , Kim Hae-Young , Harty Brian , Boineau Robin , Clausell Nadine , Desai Akshay S. , Diaz Rafael , Fleg Jerome L. , Gordeev Ivan , Lewis Eldrin F. , Markov Valetin , O’Meara Eileen , Kobulia Bondo , Shaburishvili Tamaz , Solomon Scott D. , Pitt Bertram , Pfeffer Marc A. , Li Rebecca 
Published: December 2012

Background—
Treatment of Preserved Cardiac Function with an Aldosterone Antagonist (TOPCAT) is an ongoing randomized controlled trial of spironolactone versus placebo for heart failure with preserved ejection fraction (HFpEF). We sought to describe the baseline clinical characteristics of subjects enrolled in TOPCAT relative to other contemporary observational studies and randomized clinical trials of HFpEF.

Methods and Results—

Between August 2006 and January 2012, 3445 patients with symptomatic HFpEF from 270 sites in 6 countries were enrolled in TOPCAT. At the baseline study visit, all subjects provided a detailed medical history and underwent physical examination, electrocardiography, quality of life, and laboratory assessment. Key parameters were compared with other large, contemporary HFpEF studies. The mean age was 68.6±9.6 years with a slight female predominance (52%); mean body mass index was 32 kg/m
2
; and comorbidities were common. History of hypertension (91% prevalence in TOPCAT) exceeded all other major HFpEF clinical trials. However, baseline blood pressure was well controlled (129/76 mm Hg; systolic blood pressure 7–16 mm Hg lower than other similar trials). Other common comorbidities included coronary artery disease (57%), atrial fibrillation (35%), chronic kidney disease (38%) and diabetes mellitus (32%). Self-reported activity levels were low, quality of life scores were comparable with those reported for patients with end-stage renal disease, and the prevalence of moderate or greater depression was 27%.

Conclusions—
TOPCAT subjects share many common characteristics with contemporary HFpEF cohorts. Low activity level, significantly decreased quality of life, and depression were common at baseline in TOPCAT, underscoring the continued unmet need for evidence-based treatment strategies in HFpEF.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00094302.
Zebrafish can hear sound pressure and particle motion in a synthesized sound field
Authors: Bretschneider Franklin , van Veen Herman , Teunis Peter F.M. , Peters Robert C. , van den Berg Albert V. 
Published: December 2012

In order to investigate the hearing capacities of adult zebrafish (Danio rerio), wild type zebrafish were conditioned to both sound pressure and particle motion in a respondent conditioning paradigm. Sound fields were generated by five underwater loudspeakers in a cylindrical tank, which allows separate control of sound pressure and particle motion. Sound stimuli were soft-switched sound pulses having a strength (RMS) of 0.4 to 5 Pa sound pressure (112 to 134 dB re 1 μPa), 6.7 × 10−7 to 6.7 × 10−6 m/s particle velocity or a combination thereof. Frequencies used were 800 Hz or 250 Hz. During the test a fish was placed in the acoustic centre of the tank, confined in a soft nylon mesh fitted with two silver chloride recording electrodes to measure both changes in position and the ventilatory response. Each sound presentation was followed by a brief mechanical jerk of the fish cage (unconditioned stimulus). The startling response to the unconditioned stimulus was thus coupled to the sound signal (conditioned stimulus). Responses were scored as changes in fish position and/or ventilatory rhythm, occurring during or after the sound pulses, but before the unconditioned stimulus. In this way, we found that wildtype zebrafish respond to artificial sounds having either predominantly sound pressure or particle motion. Discrimination of directionally different sounds could not be established. The method is suited well to probe other auditory capabilities, and to test zebrafish mutants lacking one or more otoliths.
Assimilation of Infrared Radiances in the Context of Observing System Simulation Experiments
Authors: Heilliette Sylvain , Rochon Yves J. , Garand Louis , Kaminski Jacek W. 
Published: December 2012

AbstractThe Observing System Simulation Experiment (OSSE) capability developed at Environment Canada allows simulation of all observation types currently used operationally as well as future data types. Its infrastructure, based on the operational global data assimilation system used at the Canadian Meteorological Centre, was recently enhanced to conduct data assimilation experiments for two future satellite missions. This study presents a subcomponent of that system, focusing on the assimilation of infrared radiances from the Atmospheric Infrared Sounder (AIRS) and Infrared Atmospheric Sounding Interferometer (IASI) instruments. The goal is to realistically simulate the radiance observations and to reproduce statistical characteristics of these data seen in the real system, notably background and analysis departures. Care is taken to emulate the operational quality control procedures leading to the assimilation of clear radiances, which implies radiance simulation for all-sky conditions. It is found that the standard deviation of the Gaussian random perturbation applied to the simulated observations should be close to that of the radiometric noise level for sounding channels in the 13.0–14.5-μm region but that it should be significantly higher for water vapor channels in the 5.5–6.7-μm region. The study also allows evaluation of residual biases linked to cloud contamination. For atmospheric window channels, that bias can reach −0.4 K. It reduces rapidly with peak height of the channel response function. This suggests that improvements are needed in low-cloud detection. The realism of the OSSE is further demonstrated through the shown impact consistency of AIRS and IASI radiance assimilation in forecasts up to 5 days from the separate use of simulated and real observations.
Intraseasonal Forecasting of the Asian Summer Monsoon in Four Operational and Research Models*
Authors: Fu Xiouhua , Lee June-Yi , Wang Bin , Wang Wanqiu , Vitart Frederic 
Published: December 2012

Abstract
The boreal summer intraseasonal oscillation (BSISO) is a dominant tropical mode with a period of 30–60 days, which offers an opportunity for intraseasonal forecasting of the Asian summer monsoon. The present study provides a preliminary, yet up-to-date, assessment of the prediction skill of the BSISO in four state-of-the-art models: the ECMWF model, the University of Hawaii (UH) model, the NCEP Climate Forecast System, version 2 (CFSv2), and version 1 for the 2008 summer (CFSv1), which is a common year of two international programs: the Year of Tropical Convection (YOTC) and Asian Monsoon Years (AMY). The mean prediction skill over the global tropics and Southeast Asia for first three models reaches about 1–2 (3) weeks for BSISO-related rainfall (850-hPa zonal wind), measured as the lead time when the spatial anomaly correlation coefficient drops to 0.5. The skill of CFSv1 is consistently lower than the other three. The strengths and weaknesses of the CFSv2, UH, and ECMWF models in forecasting the BSISO for this specific year are further revealed. The ECMWF and UH have relatively better performance for northward-propagating BSISO when the initial convection is near the equator, although they suffer from an early false BSISO onset when initial convection is in the off-equatorial monsoon trough. However, CFSv2 does not have a false onset problem when the initial convection is in monsoon trough, but it does have a problem with very slow northward propagation. After combining the forecasts of CFSv2 and UH into an equal-weighted multimodel ensemble, the resultant skill is slightly better than that of individual models. An empirical model shows a comparable skill with the dynamical models. A combined dynamical–empirical ensemble advances the intraseasonal forecast skill of BSISO-related rainfall to three weeks.