bluuebunny/crossref_metadata_2025 huggingface dataset:
Hippea jasoniae sp. nov. and Hippea alviniae sp. nov., thermoacidophilic members of the class

Deltaproteobacteria

isolated from deep-sea hydrothermal vent deposits
Authors: Flores Gilberto E. , Hunter Ryan C. , Liu Yitai , Mets Anchelique , Schouten Stefan , Reysenbach Anna-Louise
Published: July 2011

Thirteen novel, obligately anaerobic, thermoacidophilic bacteria were isolated from deep-sea hydrothermal vent sites. Four of the strains, designated EP5-rT, KM1, Mar08-272rT and Mar08-368r, were selected for metabolic and physiological characterization. With the exception of strain EP5-rT, all strains were short rods that grew between 40 and 72 °C, with optimal growth at 60–65 °C. Strain EP5-rT was more ovoid in shape and grew between 45 and 75 °C, with optimum growth at 60 °C. The pH range for growth of all the isolates was between pH 3.5 and 5.5 (optimum pH 4.5 to 5.0). Strain Mar08-272rT could only grow up to pH 5.0. Elemental sulfur was required for heterotrophic growth on acetate, succinate, Casamino acids and yeast extract. Strains EP5-rT, Mar08-272rT and Mar08-368r could also use fumarate, while strains EP5-rT, KM1 and Mar08-272rT could also use propionate. All isolates were able to grow chemolithotrophically on H2, CO2, sulfur and vitamins. Phylogenetic analysis of 16S rRNA gene sequences placed all isolates within the family

Desulfurellaceae

of the class

Deltaproteobacteria

, with the closest cultured relative being

Hippea maritima

MH2
T (~95–98 % gene sequence similarity). Phylogenetic analysis also identified several isolates with at least one intervening sequence within the 16S rRNA gene. The genomic DNA G+C contents of strains EP5-rT, KM1, Mar08-272rT and Mar08-368r were 37.1, 42.0, 35.6 and 37.9 mol%, respectively. The new isolates differed most significantly from

H. maritima

MH2
T in their phylogenetic placement and in that they were obligate thermoacidophiles. Based on these phylogenetic and phenotypic properties, the following two novel species are proposed: Hippea jasoniae sp. nov. (type strain Mar08-272rT = DSM 24585T = OCM 985T) and Hippea alviniae sp. nov. (type strain EP5-rT = DSM 24586T = OCM 986T).
Molecular Analysis of the Metabolic Rates of Discrete Subsurface Populations of Sulfate Reducers
Authors: Miletto M. , Williams K. H. , N'Guessan A. L. , Lovley D. R.
Published: July 2011

Elucidating the
in situ
metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of
dsrAB
sequences prior to the addition of acetate indicated that
Desulfobacteraceae
,
Desulfobulbaceae
, and
Syntrophaceae
-related sulfate reducers were the most abundant. Quantifying
dsrB
transcripts of the individual populations suggested that
Desulfobacteraceae
initially had higher
dsrB
transcripts per cell than
Desulfobulbaceae
or
Syntrophaceae
populations and that the activity of
Desulfobacteraceae
increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast,
dsrB
transcript abundance in
Desulfobulbaceae
and
Syntrophaceae
remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the
Desulfobacteraceae
was consistent with the finding that
Desulfobacteraceae
became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in
dsrB
transcript abundance in the
Desulfobacteraceae
. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.
Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus
Authors: Zarzycki Jan , Fuchs Georg
Published: July 2011

Chloroflexus aurantiacus
is a facultative autotrophic green nonsulfur bacterium that grows phototrophically in thermal springs and forms microbial mats with cyanobacteria. Cyanobacteria produce glycolate during the day (photorespiration) and excrete fermentation products at night.
C. aurantiacus
uses the 3-hydroxypropionate bi-cycle for autotrophic carbon fixation. This pathway was thought to be also suited for the coassimilation of various organic substrates such as glycolate, acetate, propionate, 3-hydroxypropionate, lactate, butyrate, or succinate. To test this possibility, we added these compounds at a 5 mM concentration to autotrophically pregrown cells. Although the provided amounts of H
2
and CO
2
allowed continuing photoautotrophic growth, cells immediately consumed most substrates at rates equaling the rate of autotrophic carbon fixation. Using [
14
C]acetate, half of the labeled organic carbon was incorporated into cell mass. Our data suggest that
C. aurantiacus
uses the 3-hydroxypropionate bi-cycle, together with the glyoxylate cycle, to channel organic substrates into the central carbon metabolism. Enzyme activities of the 3-hydroxypropionate bi-cycle were marginally affected when cells were grown heterotrophically with such organic substrates. The 3-hydroxypropionate bi-cycle in
Chloroflexi
is unique and was likely fostered in an environment in which traces of organic compounds can be coassimilated. Other bacteria living under oligotrophic conditions acquired genes of a rudimentary 3-hydroxypropionate bi-cycle, possibly for the same purpose. Examples are
Chloroherpeton thalassium
,
Erythrobacter
sp. strain NAP-1,
Nitrococcus mobilis
, and marine gammaproteobacteria of the OM60/NOR5 clade such as
Congregibacter litoralis
.
Trophic Links between the Acetogen Clostridium glycolicum KHa and the Fermentative Anaerobe Bacteroides xylanolyticus KHb, Isolated from Hawaiian Forest Soil
Authors: Hunger Sindy , Gößner Anita S. , Drake Harold L.
Published: July 2011

Isolate KH was obtained from Hawaiian forest soil and found to be composed of two functionally linked anaerobes, KHa and KHb. Gene analyses (16S rRNA,
fhs
,
cooS
) identified KHa as an acetogenic strain of
Clostridium glycolicum
and KHb as
Bacteroides xylanolyticus
. KHb fermented xylan and other saccharides that KHa could not utilize and formed products (e.g., ethanol and H
2
) that supported the acetogenic growth of KHa.
Vacuolar Protein Sorting Protein 13A, TtVPS13A, Localizes to the Tetrahymena thermophila Phagosome Membrane and Is Required for Efficient Phagocytosis
Authors: Samaranayake Haresha S. , Cowan Ann E. , Klobutcher Lawrence A.
Published: July 2011

Vacuolar protein sorting 13 (VPS13) proteins have been studied in a number of organisms, and mutations in
VPS13
genes have been implicated in two human genetic disorders, but the function of these proteins is poorly understood. The TtVPS13A protein was previously identified in a mass spectrometry analysis of the
Tetrahymena thermophila
phagosome proteome (M. E. Jacobs et al., Eukaryot. Cell 5:1990–2000, 2006), suggesting that it is involved in phagocytosis. In this study, we analyzed the structure of the macronuclear
TtVPS13A
gene, which was found to be composed of 17 exons spanning 12.5 kb and was predicted to encode a protein of 3,475 amino acids (aa). A strain expressing a TtVPS13A-green fluorescent protein (GFP) fusion protein was constructed, and the protein was found to associate with the phagosome membrane during the entire cycle of phagocytosis. In addition,
Tetrahymena
cells with a
TtVPS13A
knockout mutation displayed impaired phagocytosis. Specifically, they grew slowly under conditions where phagocytosis is essential, they formed few phagosomes, and the digestion of phagosomal contents was delayed compared to wild-type cells. Overall, these results provide evidence that the TtVPS13A protein is required for efficient phagocytosis.
Identification of Rgg Binding Sites in the Streptococcus pyogenes Chromosome
Authors: Anbalagan Srivishnupriya , McShan W. Michael , Dunman Paul M. , Chaussee Michael S.
Published: July 2011

Streptococcus pyogenes
Rgg is a regulatory protein that controls the transcription of 588 genes in strain NZ131 during the post-exponential phase of growth, including the virulence-associated genes encoding the extracellular SpeB protease, pullulanase A (PulA), and two extracellular nucleases (SdaB and Spd-3). Rgg binds to DNA proximally to the
speB
promoter (P
speB
) to activate transcription; however, it is not known if Rgg binds to the promoters of other genes to influence expression, or if the perturbation of other global regulons accounts for the genome-wide changes in expression associated with the mutant. To address this issue, chromatin immunoprecipitation followed by DNA microarray analysis (ChIP-chip) was used to identify the DNA binding sites of Rgg. Rgg bound to 65 sites in the chromosome. Thirty-five were within noncoding DNA, and 43% of these were adjacent to genes previously identified as regulated by Rgg. Electrophoretic mobility shift assays were used to assess the binding of Rgg to a subset of sites bound
in vivo
, including the noncoding DNA upstream of
speB
, the genes encoding PulA, Spd-3, and a transcriptional regulator (SPY49_1113), and prophage-associated genes encoding a putative integrase (SPY49_0746) and a surface antigen (SPY49_0396). Rgg bound to all target DNAs
in vitro
, consistent with the
in vivo
results. Finally, analyses with a transcriptional reporter system showed that the DNA bound by Rgg contained an active promoter that was regulated by Rgg. Overall, the results indicate that Rgg binds specifically to multiple sites in the chromosome, including prophage DNA, to influence gene expression.
Changes in myofilament proteins, but not Ca2+ regulation, are associated with a high-fat diet-induced improvement in contractile function in heart failure
Authors: Cheng Y. , Li W. , McElfresh T. A. , Chen X. , Berthiaume J. M. , Castel L. , Yu X. , Van Wagoner D. R. , Chandler M. P.
Published: July 2011

Pathological conditions such as diabetes, insulin resistance, and obesity are characterized by elevated plasma and myocardial lipid levels and have been reported to exacerbate the progression of heart failure (HF). Alterations in cardiomyocyte Ca2+ regulatory properties and myofilament proteins have also been implicated in contractile dysfunction in HF. However, our prior studies reported that high saturated fat (SAT) feeding improves in vivo myocardial contractile function, thereby exerting a cardioprotective effect in HF. Therefore, we hypothesized that SAT feeding improves contractile function by altering Ca2+ regulatory properties and myofilament protein expression in HF. Male Wistar rats underwent coronary artery ligation (HF) or sham surgery (SH) and were fed normal chow (SHNC and HFNC groups) or a SAT diet (SHSAT and HFSAT groups) for 8 wk. Contractile properties were measured in vivo [echocardiography and left ventricular (LV) cannulation] and in isolated LV cardiomyocytes. In vivo measures of contractility (peak LV +dP/d t and −dP/d t) were depressed in the HFNC versus SHNC group but improved in the HFSAT group. Isolated cardiomyocytes from both HF groups were hypertrophied and had decreased percent cell shortening and a prolonged time to half-decay of the Ca2+ transient versus the SH group; however, SAT feeding reduced in vivo myocyte hypertrophy in the HFSAT group only. The peak velocity of cell shortening was reduced in the HFNC group but not the HFSAT group and was positively correlated with in vivo contractile function (peak LV +dP/d t). The HFNC group demonstrated a myosin heavy chain (MHC) isoform switch from fast MHC-α to slow MHC-β, which was prevented in the HFSAT group. Alterations in Ca2+ transients, L-type Ca2+ currents, and protein expression of sarco(endo)plasmic reticulum Ca2+-ATPase and phosphorylated phospholamban could not account for the changes in the in vivo contractile properties. In conclusion, the cardioprotective effects associated with SAT feeding in HF may occur at the level of the isolated cardiomyocyte, specifically involving changes in myofilament function but not sarcoplasmic reticulum Ca2+ regulatory properties.
Data Impediments to Empirical Work on Health Insurance Markets
Authors: Dafny Leemore , Dranove David , Limbrock Frank , Scott Morton Fiona
Published: July 2011

We compare four datasets that researchers might use to study competition in the health insurance industry. We show that the two datasets most commonly used to estimate market concentration differ considerably from each other (both in levels and in changes over time), and reflect implausibly high volatility in market shares. By comparison, market share volatility is much lower in a private dataset gathered by a leading investment bank, and in state-level hospital discharge data. We also demonstrate that the outcome of regressions using these data vary considerably by the source used. We conclude that researchers should be cautious about using available data and recommend a new source be developed for public use.
Prescription for Education: Development, Evaluation, and Implementation of a Successful Interprofessional Education Program for Adults with Inflammatory Arthritis
Authors: KENNEDY CAROL A. , BEATON DORCAS E. , WARMINGTON KELLY , SHUPAK RACHEL , JONES CAROLINE , HOGG-JOHNSON SHEILAH
Published: July 2011

Objective.

To assess the feasibility of recruitment and standardize care delivery for an interprofessional program for inflammatory arthritis education (Prescription for Education, or RxEd), and to explore outcomes relevant to arthritis patient education.

Methods.

A patient-based needs assessment and ongoing patient feedback guided program development. An interprofessional team was involved in developing program content and delivering and adapting the program to patient needs. A quasiexperimental, waitlisted control with crossover design was used to evaluate the program. Data were collected at baseline, immediately following intervention, at 6 months (when the crossover control group received intervention), and at 1 year. Self-report measures included demographics, disorder-related data, Arthritis Self-efficacy Scale, arthritis knowledge, coping efficacy, and illness intrusiveness. Analysis included baseline comparisons and longitudinal trends; direct between-group comparison at 6 months; and generalized estimating equations (GEE) analysis to evaluate the main effect of the intervention on the primary outcome (arthritis self-efficacy) and secondary outcomes.

Results.

Program modifications based on patient input made recruitment possible. Forty-two persons participated (including 19 controls), with 93% followup at 1 year. Comparison of change shows moderate effect sizes (standardized effect size 0.5 to 0.7). GEE analysis showed significant main effect, before to after the program, in both groups for primary outcome (arthritis self-efficacy) and most secondary outcomes.

Conclusion.

Program feasibility was dependent on patient feedback. Our pilot study provides evidence that the RxEd program is feasible and improves arthritis self-efficacy and other outcomes.
Cytomegalovirus-Specific T Cell Immunity Is Maintained in Immunosenescent Rhesus Macaques
Authors: Čičin-Šain Luka , Sylwester Andrew W. , Hagen Shoko I. , Siess Don C. , Currier Noreen , Legasse Alfred W. , Fischer Miranda B. , Koudelka Caroline W. , Axthelm Michael K. , Nikolich-Žugich Janko , Picker Louis J.
Published: July 2011

Although CMV infection is largely benign in immunocompetent people, the specific T cell responses associated with control of this persistent virus are enormous and must be maintained for life. These responses may increase with advanced age and have been linked to an “immune risk profile” that is associated with poor immune responsiveness and increased mortality in aged individuals. Based on this association, it has been suggested that CMV-specific T cell responses might become dysfunctional with age and thereby contribute to the development of immune senescence by homeostatic disruption of other T cell populations, diminished control of CMV replication, and/or excess chronic inflammation. In this study, we use the rhesus macaque (RM) model of aging to ask whether the quantity and quality of CMV-specific T cell responses differ between healthy adult RMs and elderly RMs that manifest hallmarks of immune aging. We demonstrate that the size of the CD4+ and CD8+ CMV-specific T cell pools are similar in adult versus old RMs and show essentially identical phenotypic and functional characteristics, including a dominant effector memory phenotype, identical patterns of IFN-γ, TNF-α, and IL-2 production and cytotoxic degranulation, and comparable functional avidities of optimal epitope-specific CD8+ T cells. Most importantly, the response to and protection against an in vivo CMV challenge were identical in adult and aged RMs. These data indicate that CMV-specific T cell immunity is well maintained in old RMs and argue against a primary role for progressive dysfunction of these responses in the development of immune senescence.
Multiple toe transfer and sensory free flap use after a traumatic amputation of multiple digits. Surgery done in a single setting: A case study
Authors: Galpern David W , Tsai Tsu‐Min
Published: July 2011

Crush avulsion injuries to the hand with concomitant traumatic amputation of multiple digits can be a devastating injury to the patient. These injuries have multiple issues occurring under emergency conditions. When feasible, replantation of the multiple digits is optimal, but in many cases, it is not possible. Because of the crushing force on the digits, they are not viable candidates for replantation. The usual course of treatment for these patients is a two stage procedure, usually involving a groin flap. Here, we present the case of a patient who had a left hand skin avulsion of the whole palm and P1 of index, long, ring and small fingers. The left index finger had a complete amputation at the P2 level, the long, ring and small fingers all had complete amputations at the P1 level. This injury was dealt with by a left foot second and third toe transplant, a sensory free flap from the left big toe and a fourth toe microvascular free transfer to the left hand. The remainder of the defect was managed with a 10 × 14 cm reversed radial forearm flap and a combination of full and split thickness skin grafts. The procedure was performed in a single operation, obviating the need for a second surgery. This procedure optimized the patient's outcome during a single setting, making it an ideal choice in an emergency setting. © 2011 Wiley‐Liss, Inc. Microsurgery, 2011.
Appendage expression driven by the
Hoxd
Global Control Region is an ancient gnathostome feature
Authors: Schneider Igor , Aneas Ivy , Gehrke Andrew R. , Dahn Randall D. , Nobrega Marcelo A. , Shubin Neil H.
Published: July 2011

The evolutionary transition of the fins of fish into tetrapod limbs involved genetic changes to developmental systems that resulted in novel skeletal patterns and functions. Approaches to understanding this issue have entailed the search for antecedents of limb structure in fossils, genes, and embryos. Comparative genetic analyses have produced ambiguous results: although studies of posterior
Hox
genes from homology group 13 (Hoxa-13 and
Hoxd
-13) reveal similarities in gene expression between the distal segments of fins and limbs, this functional homology has not been supported by genomic comparisons of the activity of their
cis
-regulatory elements, namely the
Hoxd
Global Control Region. Here, we show that
cis
-regulatory elements driving
Hoxd
gene expression in distal limbs are present in fish. Using an interspecies transgenesis approach, we find functional conservation between gnathostome
Hoxd
enhancers, demonstrating that orthologous sequences from tetrapods, zebrafish and skate can drive reporter gene expression in mouse limbs and zebrafish fins. Our results support the notion that some of the novelties associated with tetrapod limbs arose by modification of deeply conserved
cis
- and
trans
-acting mechanisms of
Hox
regulation in gnathostomes.
Green light-emitting diodes based on a hybrid TiO2 nanoparticle-conducting polymer blend
Authors: Nguyen Phuong Hoai Nam , Nguyen Nang Dinh
Published: July 2011

The energy transfer in a blend of conducting polymers, poly[9-vinylcarbarzole] (PVK) and poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV), was investigated. Energy transfer from PVK to MEH-PPV leads to enhanced emission of MEH-PPV. Photoluminescence (PL) of the nanocomposite of TiO
2 and the blended polymer films was enhanced as the relative content of TiO
2 was increased, and, in particular, the most improved PL was observed for the optimal ratio of TiO
2 and these films emitted green light. These results provide further insight into the photophysics of conjugated polymers and the improvement of the current–voltage (I–V) characteristics of the devices based on blended conducting polymer systems.
β-Adrenergic receptors in the insular cortex are differentially involved in aversive vs. incidental context memory formation
Authors: Miranda María Isabel , Sabath Elizabeth , Nuñez-Jaramillo Luis , Purón-Sierra Liliana
Published: July 2011

The goal of this research was to determine the effects of β-adrenergic antagonism in the IC before or after inhibitory avoidance (IA) training or context pre-exposure in a latent inhibition protocol. Pretraining intra-IC infusion of the β-adrenergic antagonist propranolol disrupted subsequent IA retention and impaired latent inhibition of IA, but had no effect on formation of memory for an inert context (termed incidental memory). These results indicate that IC β-adrenergic receptors are necessary for memory acquisition of an aversive, but not an inconsequential, context. Nevertheless, subsequent association of a familiar and hitherto inconsequential context with an unconditioned stimulus (US) does require activation of these receptors during its initial acquisition.
Transcriptomic Response of Listeria monocytogenes during the Transition to the Long-Term-Survival Phase
Authors: Wen Jia , Deng Xiangyu , Li Zengxin , Dudley Edward G. , Anantheswaran Ramaswamy C. , Knabel Stephen J. , Zhang Wei
Published: July 2011

Listeria monocytogenes
can change its cellular morphology from bacilli to cocci during the transition to the long-term-survival (LTS) phase. The LTS cells demonstrated increased baro- and thermotolerance compared to their vegetative counterparts. So far, the underlying mechanisms that trigger this morphological and physiological transition remain largely unknown. In this study, we compared the transcriptomic profiles of
L. monocytogenes
serotype 4b strain F2365 at different growth stages in tryptic soy broth with yeast extract (TSBYE) using a whole-genome DNA chip approach. We identified a total of 225 differentially expressed genes (≥4-fold;
P
< 0.05) during the transition to the LTS phase in TSBYE. Genes related to cell envelope structure, energy metabolism, and transport were most significantly upregulated in the LTS phase. The upregulation of compatible solute transporters may lead to the accumulation of cellular solutes, lowering intracellular water activity and thus increasing bacterial stress resistance during the transition to the LTS phase. The downregulation of genes associated with protein synthesis may indicate a status of metabolic dormancy of the LTS cells. The transcriptomic profiles of resuscitated LTS cells in fresh TSBYE resembled those of log-phase cells (
r
=0.94), as the LTS cells rapidly resume metabolic activities and transit back to log phase with decreased baro- and thermotolerance.
Scaffoldin Modules Serving as “Cargo” Domains To Promote the Secretion of Heterologous Cellulosomal Cellulases by Clostridium acetobutylicum
Authors: Chanal Angélique , Mingardon Florence , Bauzan Marielle , Tardif Chantal , Fierobe Henri-Pierre
Published: July 2011

The secretion of large heterologous cellulases by
Clostridium acetobutylicum
was formerly shown to be deleterious. To circumvent this issue, various scaffoldins' modules were grafted at their N termini. Family 3a cellulose binding module combined with an X2 module(s) was found to trigger the secretion of
Clostridium cellulolyticum
cellulases by the solventogenic bacterium.
Potential of
pmoA
Amplicon Pyrosequencing for Methanotroph Diversity Studies
Authors: Lüke Claudia , Frenzel Peter
Published: July 2011

We analyzed the potential of
pmoA
amplicon pyrosequencing compared to that of Sanger sequencing with paddy soils as a model environment. We defined operational taxonomic unit (OTU) cutoff values of 7% and 18%, reflecting methanotrophic species and major phylogenetic
pmoA
lineages, respectively. Major lineages were already well covered by clone libraries; nevertheless, pyrosequencing provided a higher level of diversity at the species level.
New Nystatin-Related Antifungal Polyene Macrolides with Altered Polyol Region Generated via Biosynthetic Engineering of Streptomyces noursei
Authors: Brautaset Trygve , Sletta Håvard , Degnes Kristin F. , Sekurova Olga N. , Bakke Ingrid , Volokhan Olga , Andreassen Trygve , Ellingsen Trond E. , Zotchev Sergey B.
Published: July 2011

Polyene macrolide antibiotics, including nystatin and amphotericin B, possess fungicidal activity and are being used as antifungal agents to treat both superficial and invasive fungal infections. Due to their toxicity, however, their clinical applications are relatively limited, and new-generation polyene macrolides with an improved therapeutic index are highly desirable. We subjected the polyol region of the heptaene nystatin analogue S44HP to biosynthetic engineering designed to remove and introduce hydroxyl groups in the C-9-C-10 region. This modification strategy involved inactivation of the P450 monooxygenase NysL and the dehydratase domain in module 15 (DH15) of the nystatin polyketide synthase. Subsequently, these modifications were combined with replacement of the exocyclic C-16 carboxyl with the methyl group through inactivation of the P450 monooxygenase NysN. Four new polyene macrolides with up to three chemical modifications were generated, produced at relatively high yields (up to 0.51 g/liter), purified, structurally characterized, and subjected to
in vitro
assays for antifungal and hemolytic activities. Introduction of a C-9 hydroxyl by DH15 inactivation also blocked NysL-catalyzed C-10 hydroxylation, and these modifications caused a drastic decrease in both antifungal and hemolytic activities of the resulting analogues. In contrast, single removal of the C-10 hydroxyl group by NysL inactivation had only a marginal effect on these activities. Results from the extended antifungal assays strongly suggested that the 9-hydroxy-10-deoxy S44HP analogues became fungistatic rather than fungicidal antibiotics.
Ligand Responses of Vfr, the Virulence Factor Regulator from Pseudomonas aeruginosa
Authors: Serate Jose , Roberts Gary P. , Berg Otto , Youn Hwan
Published: July 2011

Vfr, a transcription factor homologous to the
Escherichia coli
cyclic AMP (cAMP) receptor protein (CRP), regulates many aspects of virulence in
Pseudomonas aeruginosa
. Vfr, like CRP, binds to cAMP and then recognizes its target DNA and activates transcription. Here we report that Vfr has important functional differences from CRP in terms of ligand sensing and response. First, Vfr has a significantly higher cAMP affinity than does CRP, which might explain the mysteriously unidirectional functional complementation between the two proteins (S. E. H. West et al., J. Bacteriol. 176:7532–7542, 1994). Second, Vfr is activated by both cAMP and cGMP, while CRP is specific to cAMP. Mutagenic analyses show that Thr133 (analogous to Ser128 of CRP) is the key residue for both of these distinct Vfr properties. On the other hand, substitutions that cause cAMP-independent activity in Vfr are similar to those seen in CRP, suggesting that a common cAMP activation mechanism is present. In the course of these analyses, we found a remarkable class of Vfr variants that have completely reversed the regulatory logic of the protein: they are active in DNA binding without cAMP and are strongly inhibited by cAMP. The physiological impact of Vfr's ligand sensing and response is discussed, as is a plausible basis for the fundamental change in protein allostery in the novel group of Vfr variants.
Staphylococcus lugdunensis IsdG Liberates Iron from Host Heme
Authors: Haley Kathryn P. , Janson Eric M. , Heilbronner Simon , Foster Timothy J. , Skaar Eric P.
Published: July 2011

Staphylococcus lugdunensisis often found as part of the normal flora of human skin but has the potential to cause serious infections even in healthy individuals. It remains unclear what factors enableS. lugdunensisto transition from a skin commensal to an invasive pathogen. Analysis of the complete genome reveals a putative iron-regulated surface determinant (Isd) system encoded withinS. lugdunensis. In other bacteria, the Isd system permits the utilization of host heme as a source of nutrient iron to facilitate bacterial growth during infection. In this study, we establish thatS. lugdunensisexpresses an iron-regulated IsdG-family heme oxygenase that binds and degrades heme. Heme degradation by IsdG results in the release of free iron and the production of the chromophore staphylobilin. IsdG-mediated heme catabolism enables the use of heme as a sole source of iron, establishing IsdG as a pathophysiologically relevant heme oxygenase inS. lugdunensis. Together these findings offer insight into howS. lugdunensisfulfills its nutritional requirements while invading host tissues and establish theS. lugdunensisIsd system as being involved in heme-iron utilization.
Role of pagL and lpxO in Bordetella bronchiseptica Lipid A Biosynthesis
Authors: MacArthur I. , Jones J. W. , Goodlett D. R. , Ernst R. K. , Preston A.
Published: July 2011

PagL and LpxO are enzymes that modify lipid A. PagL is a 3-O deacylase that removes the primary acyl chain from the 3 position, and LpxO is an oxygenase that 2-hydroxylates specific acyl chains in the lipid A.pagLandlpxOhomologues have been identified in the genome ofBordetella bronchiseptica, but in the current structure forB. bronchisepticalipid A the 3 position is acylated and 2-OH acylation is not reported. We have investigated the role ofB. bronchiseptica pagLandlpxOin lipid A biosynthesis. We report a different structure for wild-type (WT)B. bronchisepticalipid A, including the presence of 2-OH-myristate, the presence of which is dependent onlpxO. We also demonstrate that the 3 position is not acylated in the major WT lipid A structures but that mutation ofpagLresults in the presence of 3-OH-decanoic acid at this position, suggesting that lipid A containing this acylation is synthesized but that PagL removes most of it from the mature lipid A. These data refine the structure ofB. bronchisepticalipid A and demonstrate thatpagLandlpxOare involved in its biosynthesis.
The Residue Threonine 82 of DevR (DosR) Is Essential for DevR Activation and Function in Mycobacterium tuberculosis Despite Its Atypical Location
Authors: Gautam Uma Shankar , Sikri Kriti , Tyagi Jaya Sivaswami
Published: July 2011

The DevR (DosR) response regulator initiates the bacterial adaptive response to a variety of signals, including hypoxia in
in vitro
models of dormancy. Its receiver domain works as a phosphorylation-mediated switch to activate the DNA binding property of its output domain. Receiver domains are characterized by the presence of several highly conserved residues, and these sequence features correlate with structure and hence function. In response regulators, interaction of phosphorylated aspartic acid at the active site with the conserved threonine is believed to be crucial for phosphorylation-mediated conformational change. DevR contains all the conserved residues, but the structure of its receiver domain in the unphosphorylated protein is strikingly different, and key threonine (T82), tyrosine (Y101), and lysine (K104) residues are placed uncharacteristically far from the D54 phosphorylation site. In view of the atypical location of T82 in DevR, the present study aimed to examine the importance of this residue in the activation mechanism.
Mycobacterium tuberculosis
expressing a DevR T82A mutant protein is defective in autoregulation and supports hypoxic induction of the DevR regulon only very weakly. These defects are ascribed to slow and partial phosphorylation and the failure of T82A mutant protein to bind cooperatively with DNA. Our results indicate that the T82 residue is crucial in implementing conformational changes in DevR that are essential for cooperative binding and for subsequent gene activation. We propose that the function of the T82 residue in the activation mechanism of DevR is conserved in spite of the unusual architecture of its receiver domain.
The 5.5 Protein of Phage T7 Inhibits H-NS through Interactions with the Central Oligomerization Domain
Authors: Ali Sabrina S. , Beckett Emily , Bae Sandy Jeehoon , Navarre William Wiley
Published: July 2011

The 5.5 protein (T7p32) of coliphage T7 (5.5
T7
) was shown to bind and inhibit gene silencing by the nucleoid-associated protein H-NS, but the mechanism by which it acts was not understood. The 5.5
T7
protein is insoluble when expressed in
Escherichia coli
, but we find that 5.5
T7
can be isolated in a soluble form when coexpressed with a truncated version of H-NS followed by subsequent disruption of the complex during anion-exchange chromatography. Association studies reveal that 5.5
T7
binds a region of H-NS (residues 60 to 80) recently found to contain a distinct domain necessary for higher-order H-NS oligomerization. Accordingly, we find that purified 5.5
T7
can disrupt higher-order H-NS-DNA complexes
in vitro
but does not abolish DNA binding by H-NS
per se
. Homologues of the 5.5
T7
protein are found exclusively among members of the
Autographivirinae
that infect enteric bacteria, and despite fairly low sequence conservation, the H-NS binding properties of these proteins are largely conserved. Unexpectedly, we find that the 5.5
T7
protein copurifies with heterogeneous low-molecular-weight RNA, likely tRNA, through several chromatography steps and that this interaction does not require the DNA binding domain of H-NS. The 5.5 proteins utilize a previously undescribed mechanism of H-NS antagonism that further highlights the critical importance that higher-order oligomerization plays in H-NS-mediated gene repression.
Ectoine and Hydroxyectoine as Protectants against Osmotic and Cold Stress: Uptake through the SigB-Controlled Betaine-Choline- Carnitine Transporter-Type Carrier EctT from Virgibacillus pantothenticus
Authors: Kuhlmann Anne U. , Hoffmann Tamara , Bursy Jan , Jebbar Mohamed , Bremer Erhard
Published: July 2011

Virgibacillus pantothenticushas been shown to synthesize the compatible solute ectoine in response to high salinity or low growth temperature. We found that exogenously provided ectoine and hydroxyectoine also serve as protectants against these challenges. Transport studies with [14C]ectoine revealed that both types of stress induced a high-affinity ectoine uptake activity inV. pantothenticus. By using anEscherichia colimutant defective in osmoprotectant uptake systems, a functional complementation approach for osmostress resistance in the presence of ectoine was employed to retrieve a gene encoding an ectoine transporter fromV. pantothenticus.The cloned gene (ectT) encodes a protein (EctT) that is a member of the BCCT (betaine-choline-carnitine-transporter) family of carriers. Osmoprotection assays demonstrated that the EctT carrier mediates the preferential import of ectoine and hydroxyectoine but also possesses minor uptake activities for the compatible solutes proline and glycine betaine. Northern blot analysis with RNA isolated fromV. pantothenticusrevealed that a rise in the external osmolality or a reduction in growth temperature strongly increased the transcription of theectTgene. Primer extension analysis demonstrated thatectTwas transcribed under these conditions from a SigB-type promoter. SigB is the master regulator of the general stress regulon of bacilli and provides protection to cells against various challenges, including high salinity and low temperature. Both the synthesis of ectoine and the EctT-mediated uptake of ectoine and hydroxyectoine are triggered by the same environmental cues, high salinity and cold stress, and thereby provide, in a concerted fashion, the protection ofV. pantothenticusagainst these challenges.
Transformation Frequency of a mariner-Based Transposon in Rickettsia rickettsii
Authors: Clark Tina R. , Lackey Amanda M. , Kleba Betsy , Driskell Lonnie O. , Lutter Erika I. , Martens Craig , Wood David O. , Hackstadt Ted
Published: July 2011

Transformation frequencies of a
mariner
-based transposon system in
Rickettsia rickettsii
were determined using a plaque assay system for enumeration and isolation of mutants. Sequence analysis of insertion sites in both
R. rickettsii
and
R. prowazekii
indicated that insertions were random. Transposon mutagenesis provides a useful tool for rickettsial research.
Characterization of Components of the Staphylococcus aureus mRNA Degradosome Holoenzyme-Like Complex
Authors: Roux Christelle M. , DeMuth Jonathon P. , Dunman Paul M.
Published: July 2011

Bacterial two-hybrid analysis identified theStaphylococcus aureusRNA degradosome-like complex to include RNase J1, RNase J2, RNase Y, polynucleotide phosphorylase (PNPase), enolase, phosphofructokinase, and a DEAD box RNA helicase. Results also revealed that the recently recognized RNase RnpA interacts with theS. aureusdegradosome and that this interaction is conserved in other Gram-positive organisms.
Optimizing Chemotherapy-Free Survival for the ER/HER2-Positive Metastatic Breast Cancer Patient
Authors: Glück Stefan , Arteaga Carlos L. , Osborne C. Kent
Published: July 2011

The recent incremental advances made in the treatment of metastatic breast cancer have elicited potential for survival extension in this treatable, yet incurable, population of breast cancer patients. Clinicians have focused on targeted therapies, which aim at signaling receptors such as the human epidermal receptor superfamily, the estrogen receptor, VEGF, the insulin-like growth factor receptor, the hepatocyte growth factor receptor (cMET), phosphoinositide 3-kinase, mTOR, and many others. Clin Cancer Res; 17(17); 5559–61. ©2011 AACR.
Exon 11 Skipping of E-Cadherin RNA Downregulates Its Expression in Head and Neck Cancer Cells
Authors: Sharma Sanjai , Liao Wei , Zhou Xiaofeng , Wong David T.W. , Lichtenstein Alan
Published: July 2011

E-cadherin is an important tumor suppressor gene whose expression is lost when cells acquire a metastatic phenotype. We analyzed the role of E-cadherin missplicing as a mechanism of its downregulation by analyzing a misspliced E-cadherin transcript that lacks exon 11 of this gene. This results in a frameshift and a premature termination codon that targets this transcript for degradation. Tumor tissues, including breast (20%, n = 9), prostate (30%, n = 9) and head and neck (75%, n = 8) cancer, express the exon 11-skipped transcripts (vs. nonmalignant controls) and its levels inversely correlate with E-cadherin expression. This is a novel mechanism of E-cadherin downregulation by missplicing in tumor cells, which is observed in highly prevalent human tumors. In the head and neck cancer model, nontumorigenic keratinocytes express exon 11–skipped splice product two- to sixfold lower than the head and neck tumor cell lines. Mechanistic studies reveal that SFRS2 (SC35), a splicing factor, as one of the regulators that increases missplicing and downregulates E-cadherin expression. Furthermore, this splicing factor was found to be overexpressed in 5 of 7 head and neck cell lines and primary head and neck tumors. Also, methylation of E-cadherin gene acts as a regulator of this aberrant splicing process. In 2 head and neck cell lines, wild-type transcript expression increased 16- to 25-folds, whereas the percentage of exon 11-skipped transcripts in both the cell lines decreased five- to 30-folds when cells were treated with a hypomethylating agent, azacytidine. Our findings reveal that promoter methylation and an upregulated splicing factor (SFRS2) are involved in the E-cadherin missplicing in tumors. Mol Cancer Ther; 10(9); 1751–9. ©2011 AACR.
Long Pentraxin-3 Inhibits FGF8b-Dependent Angiogenesis and Growth of Steroid Hormone–Regulated Tumors
Authors: Leali Daria , Alessi Patrizia , Coltrini Daniela , Ronca Roberto , Corsini Michela , Nardo Giorgia , Indraccolo Stefano , Presta Marco
Published: July 2011

Fibroblast growth factor-8b (FGF8b) exerts nonredundant autocrine/paracrine functions in steroid hormone–regulated tumors. Previous observations had shown that the soluble pattern recognition receptor long pentraxin-3 (PTX3) is a natural selective antagonist for a restricted number of FGF family members, inhibiting FGF2 but not FGF1 and FGF4 activity. Here, we assessed the capacity of PTX3 to antagonize FGF8b and to inhibit the vascularization and growth of steroid hormone–regulated tumors. Surface plasmon resonance analysis shows that PTX3 binds FGF8b with high affinity (Kd = 30–90 nmol/L). As a consequence, PTX3 prevents the binding of FGF8b to its receptors, inhibits FGF8b-driven ERK1/2 activation, cell proliferation, and chemotaxis in endothelial cells, and suppresses FGF8b-induced neovascularization in vivo. Also, PTX3 inhibits dihydrotestosterone (DHT)- and FGF8b-driven proliferation of androgen-regulated Shionogi 115 (S115) mouse breast tumor cells. Furthermore, DHT-treated, PTX3 overexpressing hPTX3_S115 cell transfectants show a reduced proliferation rate in vitro and a limited angiogenic activity in the chick embryo chorioallantoic membrane and murine s.c. Matrigel plug assays. Accordingly, hPTX3_S115 cells show a dramatic decrease of their tumorigenic activity when grafted in immunodeficient male mice. These results identify PTX3 as a novel FGF8b antagonist endowed with antiangiogenic and antineoplastic activity with possible implications for the therapy of hormonal tumors. Mol Cancer Ther; 10(9); 1600–10. ©2011 AACR.
Potent, Selective Inhibitors of Fibroblast Growth Factor Receptor Define Fibroblast Growth Factor Dependence in Preclinical Cancer Models
Authors: Squires Matthew , Ward George , Saxty Gordan , Berdini Valerio , Cleasby Anne , King Peter , Angibaud Patrick , Perera Tim , Fazal Lynsey , Ross Douglas , Jones Charlotte Griffiths , Madin Andrew , Benning Rajdeep K. , Vickerstaffe Emma , O'Brien Alistair , Frederickson Martyn , Reader Michael , Hamlett Christopher , Batey Michael A. , Rich Sharna , Carr Maria , Miller Darcey , Feltell Ruth , Thiru Abarna , Bethell Susanne , Devine Lindsay A. , Graham Brent L. , Pike Andrew , Cosme Jose , Lewis Edward J. , Freyne Eddy , Lyons John , Irving Julie , Murray Christopher , Newell David R. , Thompson Neil T.
Published: July 2011

We describe here the identification and characterization of 2 novel inhibitors of the fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases. The compounds exhibit selective inhibition of FGFR over the closely related VEGFR2 receptor in cell lines and in vivo. The pharmacologic profile of these inhibitors was defined using a panel of human tumor cell lines characterized for specific mutations, amplifications, or translocations known to activate one of the four FGFR receptor isoforms. This pharmacology defines a profile for inhibitors that are likely to be of use in clinical settings in disease types where FGFR is shown to play an important role. Mol Cancer Ther; 10(9); 1542–52. ©2011 AACR.
Risk Factors of Caries Progression in a Hispanic School-aged Population
Authors: Fontana M. , Santiago E. , Eckert G.J. , Ferreira-Zandona A.G.
Published: July 2011

The purpose of this Institutional Review Board-approved study was to identify risk factors of caries lesion progression in children enrolled in rural schools in Puerto Rico. A convenience sample of 408 children (5-13 yrs old) was examined at baseline and at 12 and 24 mos with the International Caries Detection and Assessment System (ICDAS). A total of 395 caregivers completed a 25-item questionnaire including socio-demographic, dietary, protective factors, disease experience, and access to care. Caries progression was significant (89% and 91% at 12 and 24 mos, respectively). Multiple-variable models for predicting children with lesion progression and numbers of lesions progressing were calculated for 2 outcome variables (any-progression vs. progression-toward-cavitation). Models developed had areas under the receiver operating characteristic (ROC) curve ranging between 0.70 and 0.79 and were very similar regardless of the outcome (progression criteria), prediction time (12-24 mos), or inclusion (or not) of previous caries experience. Significant predictors of disease progression collected through a parent-completed questionnaire included questions related to caries experience in the child or caregiver, and the caregiver’s rating of the child’s oral health.
Psychologists’ research activities and professional information-seeking behaviour: Empirical analyses with reference to the theory of the Intellectual and Social Organization of the Sciences
Authors: Krampen Günter , Fell Clemens , Schui Gabriel
Published: July 2011

Five facets of professional information-seeking behaviour were analysed in a sample of 298 psychology researchers from the German-speaking countries. In an online survey data were gathered on (1) information-processing behaviour during research project development, research implementation, results publication, use of citation databases, and preferred publication language, (2) scientists’ functional dependence, strategic dependence, technical uncertainty, and strategic uncertainty with reference to the theory of the Intellectual and Social Organization of the Sciences, (3) scientists’ engagement in Big vs Little Science and (4) in psychological subdisciplines, and (5) scientists’ personal characteristics (age, job position, sex, information competence, cognitive style). Empirical results refer to (1) the construction of economical psychometric Scales on Perceived Mutual Dependence and Task Uncertainty in the Sciences (S-DUS) and (2) the prediction of information behaviour by the DUS-scales, research engagement in Big vs Little Sciences and in subdisciplines, as well as age in hierarchical regression analyses. The paper discusses the broad usability of the S-DUS and the result that different facets of scientists’ information behaviour require differential predictors.
Gender Differences in Prison-Based Drug Treatment Participation
Authors: Belenko Steven , Houser Kimberly A.
Published: July 2011

Prisons inmates have high rates of substance abuse and associated social and health problems, and a concomitant high need for drug treatment while incarcerated. Female inmates have an even greater treatment need, yet most inmates do not participate in treatment while incarcerated. Using data from a nationally representative sample of prison inmates, this article examines the impact of gender on prison treatment participation and gender differences in the factors associated with clinical treatment participation. Females were significantly more likely to participate in prison drug treatment than males, controlling for other factors. For both males and females, severity of drug problems predicted participation in treatment. For males but not females, race was associated with prison treatment participation, and among those with drug abuse or dependence, females with co-occurring mental health problems were more likely to participate in treatment. Implications for prison assessment and treatment policies, and future research, are discussed.