bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the Mating-Type (MAT) Locus That Controls Sexual Reproduction of Blastomyces dermatitidis
Authors: Li Wenjun , Sullivan Thomas D. , Walton Eric , Averette Anna Floyd , Sakthikumar Sharadha , Cuomo Christina A. , Klein Bruce S. , Heitman Joseph 
Published: November 2012

ABSTRACTBlastomyces dermatitidisis a dimorphic fungal pathogen that primarily causes blastomycosis in the midwestern and northern United States and Canada. While the genes controlling sexual development have been known for a long time, the genes controlling sexual reproduction ofB. dermatitidis(teleomorph,Ajellomyces dermatitidis) are unknown. We identified the mating-type (MAT) locus in theB. dermatitidisgenome by comparative genomic approaches. TheB. dermatitidis MATlocus resembles those of other dimorphic fungi, containing either an alpha-box (MAT1-1) or an HMG domain (MAT1-2) gene linked to theAPN2,SLA2, andCOX13genes. However, in some strains ofB. dermatitidis, theMATlocus harbors transposable elements (TEs) that make it unusually large compared to theMATlocus of other dimorphic fungi. Based on theMATlocus sequences ofB. dermatitidis, we designed specific primers for PCR determination of the mating type. TwoB. dermatitidisisolates of opposite mating types were cocultured on mating medium. Immature sexual structures were observed starting at 3 weeks of coculture, with coiled-hyphae-containing cleistothecia developing over the next 3 to 6 weeks. Genetic recombination was detected in potential progeny by mating-type determination, PCR-restriction fragment length polymorphism (PCR-RFLP), and random amplification of polymorphic DNA (RAPD) analyses, suggesting that a meiotic sexual cycle might have been completed. The F1 progeny were sexually fertile when tested with strains of the opposite mating type. Our studies provide a model for the evolution of theMATlocus in the dimorphic and closely related fungi and open the door to classic genetic analysis and studies on the possible roles of mating and mating type in infection and virulence.
Candida albicans Induces Arginine Biosynthetic Genes in Response to Host-Derived Reactive Oxygen Species
Authors: Jiménez-López Claudia , Collette John R. , Brothers Kimberly M. , Shepardson Kelly M. , Cramer Robert A. , Wheeler Robert T. , Lorenz Michael C. 
Published: November 2012

ABSTRACT

The interaction of
Candida albicans
with phagocytes of the host's innate immune system is highly dynamic, and its outcome directly impacts the progression of infection. While the switch to hyphal growth within the macrophage is the most obvious physiological response, much of the genetic response reflects nutrient starvation: translational repression and induction of alternative carbon metabolism. Changes in amino acid metabolism are not seen, with the striking exception of arginine biosynthesis, which is upregulated in its entirety during coculture with macrophages. Using single-cell reporters, we showed here that arginine biosynthetic genes are induced specifically in phagocytosed cells. This induction is lower in magnitude than during arginine starvation
in vitro
and is driven not by an arginine deficiency within the phagocyte but instead by exposure to reactive oxygen species (ROS). Curiously, these genes are induced in a narrow window of sublethal ROS concentrations.
C. albicans
cells phagocytosed by primary macrophages deficient in the
gp91

phox

subunit of the phagocyte oxidase do not express the
ARG
pathway, indicating that the induction is dependent on the phagocyte oxidative burst.
C. albicans arg
pathway mutants are retarded in germ tube and hypha formation within macrophages but are not notably more sensitive to ROS. We also find that the
ARG
pathway is regulated not by the general amino acid control response but by transcriptional regulators similar to the
Saccharomyces cerevisiae
ArgR complex. In summary, phagocytosis induces this single amino acid biosynthetic pathway in an ROS-dependent manner.
Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum
Authors: Bauer Ryan , Wilson Jeffrey J. , Philominathan Sagaya Theresa Leena , Davis Dan , Matsushita Osamu , Sakon Joshua 
Published: November 2012

ABSTRACT

Clostridium histolyticum
secretes collagenases, ColG and ColH, that cause extensive tissue destruction in myonecrosis. The C-terminal collagen-binding domain (CBD) of collagenase is required for insoluble collagen fibril binding and subsequent collagenolysis. The high-resolution crystal structures of ColG-CBD (s3b) and ColH-CBD (s3) are reported in this paper. The new X-ray structure of s3 was solved at 2.0-Å resolution (
R
= 17.4%;
R
free
= 23.3%), while the resolution of the previously determined s3b was extended to 1.4 Å (
R
= 17.9%;
R
free
= 21.0%). Despite sharing only 30% sequence identity, the molecules resemble one another closely (root mean square deviation [RMSD] C
α
= 1.5 Å). All but one residue, whose side chain chelates with Ca
2+
, are conserved. The dual Ca
2+
binding site in s3 is completed by an unconserved aspartate. Differential scanning calorimetric measurements showed that s3 gains thermal stability, comparable to s3b, by binding to Ca
2+
(
holo

T
m

= 94.1°C;
apo

T
m

= 70.2°C).
holo
s3 is also stabilized against chemical denaturants urea and guanidine HCl. The three most critical residues for collagen interaction in s3b are conserved in s3. The general shape of the binding pocket is retained by altered loop structures and side chain positions. Small-angle X-ray scattering data revealed that s3 also binds asymmetrically to minicollagen. Besides the calcium-binding sites and the collagen-binding pocket, architecturally important hydrophobic residues and the hydrogen-bonding network around the
cis
-peptide bond are well conserved within the metallopeptidase subfamily M9B. CBDs were previously shown to bind to the extracellular matrix of various tissues. Compactness and extreme stability in physiological Ca
2+
concentration possibly make both CBDs suitable for targeted growth factor delivery.
Genetic Characterization of a Novel Rhizobial Plasmid Conjugation System in Rhizobium leguminosarum bv. viciae Strain VF39SM
Authors: Ding Hao , Yip Cynthia B. , Hynes Michael F. 
Published: November 2012

ABSTRACT

Rhizobium leguminosarum
strain VF39SM contains two plasmids that have previously been shown to be self-transmissible by conjugation. One of these plasmids, pRleVF39b, is shown in this study to carry a set of plasmid transfer genes that differs significantly from conjugation systems previously studied in the rhizobia but is similar to an uncharacterized set of genes found in
R. leguminosarum
bv. trifolii strain WSM2304. The entire sequence of the transfer region on pRleVF39b was determined as part of a genome sequencing project, and the roles of the various genes were examined by mutagenesis. The transfer region contains a complete set of mating pair formation (Mpf) genes, a
traG
gene, and a relaxase gene,
traA
, all of which appear to be necessary for plasmid transfer. Experimental evidence suggested the presence of two putative origins of transfer within the gene cluster. A regulatory gene,
trbR
, was identified in the region between
traA
and
traG
and was mutated. TrbR was shown to function as a repressor of both
trb
gene expression and plasmid transfer.
Pseudomonas syringae pv. tomato DC3000 CmaL (PSPTO4723), a DUF1330 Family Member, Is Needed To Produce
l
-
allo
-Isoleucine, a Precursor for the Phytotoxin Coronatine
Authors: Worley Jay N. , Russell Alistair B. , Wexler Aaron G. , Bronstein Philip A. , Kvitko Brian H. , Krasnoff Stuart B. , Munkvold Kathy R. , Swingle Bryan , Gibson Donna M. , Collmer Alan 
Published: November 2012

ABSTRACT

Pseudomonas syringae
pv. tomato DC3000 produces the phytotoxin coronatine, a major determinant of the leaf chlorosis associated with DC3000 pathogenesis. The DC3000 PSPTO4723 (
cmaL
) gene is located in a genomic region encoding type III effectors; however, it promotes chlorosis in the model plant
Nicotiana benthamiana
in a manner independent of type III secretion. Coronatine is produced by the ligation of two moieties, coronafacic acid (CFA) and coronamic acid (CMA), which are produced by biosynthetic pathways encoded in separate operons. Cross-feeding experiments, performed in
N. benthamiana
with
cfa
,
cma
, and
cmaL
mutants, implicate CmaL in CMA production. Furthermore, analysis of bacterial supernatants under coronatine-inducing conditions revealed that mutants lacking either the
cma
operon or
cmaL
accumulate CFA rather than coronatine, supporting a role for CmaL in the regulation or biosynthesis of CMA. CmaL does not appear to regulate CMA production, since the expression of proteins with known roles in CMA production is unaltered in
cmaL
mutants. Rather, CmaL is needed for the first step in CMA synthesis, as evidenced by the fact that wild-type levels of coronatine production are restored to a Δ
cmaL
mutant when it is supplemented with 50 μg/ml
l
-
allo
-isoleucine, the starting unit for CMA production.
cmaL
is found in all other sequenced
P. syringae
strains with coronatine biosynthesis genes. This characterization of CmaL identifies a critical missing factor in coronatine production and provides a foundation for further investigation of a member of the widespread DUF1330 protein family.
Detoxification of 7-Dehydrocholesterol Fatal to Helicobacter pylori Is a Novel Role of Cholesterol Glucosylation
Authors: Shimomura Hirofumi , Hosoda Kouichi , McGee David J. , Hayashi Shunji , Yokota Kenji , Hirai Yoshikazu 
Published: November 2012

ABSTRACT

The glucosylation of free cholesterol (FC) by
Helicobacter pylori
cells has various biological significances for the survival of this bacterium.
H. pylori
cells with glucosylated FC are capable of evading host immune systems, such as phagocytosis by macrophages and activation of antigen-specific T cells, and surviving in the gastric mucosal tissues for long periods. An additional role of cholesterol glucosylation in the survival of
H. pylori
which is distinct from the role of escaping the host immune system, however, has yet to be identified. This study demonstrated that 7-dehydrocholesterol (7dFC), an FC precursor, is a toxic compound fatal to
H. pylori
cells, but the cell membrane of
H. pylori
is capable of absorbing this toxic sterol via glucosylation. In contrast to the case with 7dFC, no toxicity to
H. pylori
cells was detected from the glucosylated 7dFC. In addition,
cgt
gene mutant
H. pylori
cells that cannot glucosylate cholesterols had higher susceptibility to the toxic action of 7dFC than wild-type
H. pylori
cells. These results indicate that the
cgt
gene product of
H. pylori
serves to detoxify the sterol fatal to this bacterium and to permit this toxic sterol as a cell membrane lipid component. In summary, this study defined a novel role of cholesterol glucosylation in
H. pylori
.
Characterization of BreR Interaction with the Bile Response Promoters
breAB
and
breR
in Vibrio cholerae
Authors: Cerda-Maira Francisca A. , Kovacikova Gabriela , Jude Brooke A. , Skorupski Karen , Taylor Ronald K. 
Published: November 2012

ABSTRACT

The
Vibrio cholerae
BreR protein is a transcriptional repressor of the
breAB
efflux system operon, which encodes proteins involved in bile resistance. In a previous study (F. A. Cerda-Maira, C. S. Ringelberg, and R. K. Taylor, J. Bacteriol.
190:
7441–7452, 2008), we used gel mobility shift assays to determine that BreR binds at two independent binding sites at the
breAB
promoter and a single site at its own promoter. Here it is shown, by DNase I footprinting and site-directed mutagenesis, that BreR is able to bind at a distal and a proximal site in the
breAB
promoter. However, only one of these sites, the proximal 29-bp site, is necessary for BreR-mediated transcriptional repression of
breAB
expression. In addition, it was determined that BreR represses its own expression by recognizing a 28-bp site at the
breR
promoter. These sites comprise regions of dyad symmetry within which residues critical for BreR function could be identified. The BreR consensus sequence AANGTANAC-N
6
-GTNTACNTT overlaps the −35 region at both promoters, implying that the repression of gene expression is achieved by interfering with RNA polymerase binding at these promoters.
Prehospital non-drug assisted intubation for adult trauma patients with a Glasgow Coma Score less than 9
Authors: Evans Christopher Charles Douglas , Brison Robert J , Howes Daniel , Stiell Ian G , Pickett William 
Published: November 2012

ObjectivesPrehospital airway management for adult trauma patients remains controversial. We sought to review the frequency that paramedic non-drug assisted intubation or attempted intubation is performed for trauma patients in Ontario, Canada, and determine its association with mortality.MethodsWe conducted a retrospective cohort study using the Ontario Trauma Registry's Comprehensive Data Set for 2002–2009. Eligible patients were greater than 16 years of age, had an initial Glasgow Coma Score of less than 9 and were cared for by ground-based non-critical care paramedics. The primary outcome was mortality. Outcomes were compared between patients undergoing prehospital intubation versus basic airway management. Logistic regression analyses were used to quantify the association between prehospital intubation and mortality.ResultsOf the 2229 patients included in the analysis, 671 (30.1%) underwent prehospital intubation. Annual rates of prehospital intubation declined from 33.7% to 14.0% (ptrend<0.0001) over the study period. Unadjusted death rates were 66.0% versus 34.8% in the intubation and basic airway groups, respectively (p<0.0001). Intubation in the prehospital setting was associated with a heightened risk of mortality (adjusted OR 2.8, 95% CI 1.1 to 7.6).ConclusionsPrehospital non-drug assisted intubation for trauma is being performed less frequently in Ontario, Canada. Within our study population, paramedic non-drug assisted intubation or attempted intubation was associated with a heightened risk of mortality.
A review of blood component usage in a large UK emergency department after implementation of simple measures
Authors: Kelly Sarah-Louise , Reed Matthew J , Innes Catherine J , Manson Lynn 
Published: November 2012

ObjectivesTo review clinical indications and demographics of transfusion and the patterns of blood component ordering, transfusion, wastage and traceability, before (2007) and after (2011) implementation of simple improvement strategies.MethodsRetrospective case note review of all patients presenting to the Royal Infirmary of Edinburgh (RIE) Emergency Department (ED) for whom a blood component was requested and historic comparison. Improvement measures implemented between 2007 and 2011 included (1) formal staff education, (2) use of e-learning Module One Safe Transfusion Practice (traceability update, Medicines and Healthcare products Regulatory Agency (MHRA) traceability regulations and importance of returning completed blood component tags), (3) an ED resuscitation room blood fridge, (4) introduction of a dedicated ED transfusion consultant and ED transfusion link nurse and (5) the presence of an ED consultant on the Hospital Transfusion Group.ResultsBetween 1st January and 31st December 2011, blood components were requested for 255 patient episodes, totalling 1034 individual units. 687 units (66.4%) of blood component were transfused, 248 components (24.0%) were recycled, 90 components (8.7%) were discarded and nine units (0.9%) were unaccounted for. There was a 64% reduction in blood component ordering (3209 vs 1034 units), a 39% reduction in blood component transfusion (1131 vs 687 units) and a 96% reduction in unaccounted units (214 vs 9 units) between 2007 and 2011. There was a rise in the median age of the patient for whom a transfusion request was made from 63.9 years in 2007 to 67.0 years in 2011.ConclusionsBlood component ordering, usage and traceability within the ED have improved significantly since 2007 following implementation of simple strategies. The age of ED transfusion recipients is increasing.
A novel clinical and imaging based score for predicting outcome prior to endovascular treatment of acute ischemic stroke
Authors: Fargen Kyle M , Chaudry Imran , Turner Raymond D , Bennett Jeffrey A , Turk Aquilla , Mocco J 
Published: November 2012

IntroductionOutcome after stroke intervention remains disappointing, with only 30–50% of patients having a good outcome at 90 days. We sought to identify important outcome prognosticators.MethodsAll consecutive patients that presented with an acute anterior circulation ischemic stroke, with adequate CT perfusion imaging, and that underwent emergency endovascular treatment at two centers between January 1, 2009 and November 2011, were retrospectively reviewed. Investigators estimated the percentage of the total ischemic tissue that had decreased cerebral blood volume (CBV) compared with the total area with elevated time to peak (the penumbra). Multivariate regression analyses were performed to identify variables with prognostic significance and a scoring system was created.Results163 patients underwent endovascular treatment for acute ischemic stroke. Outcome data were available in 147 patients (90.2%). A good outcome (modified Rankin Scale score 0–2) occurred in 64 patients (43.5%). Age, National Institutes of Health Stroke Scale (NIHSS) score and per cent decreased CBV scores were the only variables that predicted prognosis on multivariate analyses. A score was created (NAV score—NIHSS, age, volume) that awards points based on these three factors: 2 points for an NIHSS score of ≥15, 1 point for age ≥70 years, and 1 point for decreased CBV of ≥50%. The NAV score was strongly correlated with overall outcome (p<0.01): scores of 0, 1, 2, 3, and 4 were associated with 84%, 50%, 36%, 25%, and 8% chance of a good outcome at 90 days.ConclusionsWe introduced a simple three factor scoring system to help predict outcome in patients deemed candidates for intra-arterial acute ischemic stroke intervention.
The Kynurenine Pathway in Brain Tumor Pathogenesis
Authors: Adams Seray , Braidy Nady , Bessesde Alban , Brew Bruce J. , Grant Ross , Teo Charlie , Guillemin Gilles J. 
Published: November 2012

AbstractBrain tumors are among the most common and most chemoresistant tumors. Despite treatment with aggressive treatment strategies, the prognosis for patients harboring malignant gliomas remains dismal. The kynurenine pathway (KP) is the principal route of l-tryptophan catabolism leading to the formation of the essential pyridine nucleotide, nicotinamide adenine dinucleotide (NAD+), and important neuroactive metabolites, including the neurotoxin, quinolinic acid (QUIN), the neuroprotective agent, picolinic acid (PIC), the TH17/Treg balance modulator, 3-hydroxyanthranilic acid (3-HAA), and the immunosuppressive agent, l-Kynurenine (KYN). This review provides a new perspective on KP dysregulation in defeating antitumor immune responses, specifically bringing light to the lower segment of the KP, particularly QUIN-induced neurotoxicity and downregulation of the enzyme α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) as a potential mechanism of tumor progression. Given its immunosuppressive effects, 3-HAA produced from the KP may also play a role in suppressing antitumor immunity in human tumors. The enzyme indoleamine 2, 3-dioxygenase (IDO-1) initiates and regulates the first step of the KP in most cells. Mounting evidence directly implicates that the induction and overexpression of IDO-1 in various tumors is a crucial mechanism facilitating tumor immune evasion and persistence. Tryptophan 2, 3-dioxygenase (TDO-2), which initiates the same first step of the KP as IDO-1, has likewise recently been shown to be a mechanism of tumoral immune resistance. Further, it was also recently shown that TDO-2–dependent production of KYN by brain tumors might be a novel mechanism for suppressing antitumor immunity and supporting tumor growth through the activation of the Aryl hydrocarbon receptor (AhR). This newly identified TDO-2-KYN-AhR signaling pathway opens up exciting future research opportunities and may represent a novel therapeutic target in cancer therapy. Our discussion points to a number of KP components, namely TDO-2, IDO-1, and ACMSD, as important therapeutic targets for the treatment of brain cancer. Targeting the KP in brain tumors may represent a viable strategy likely to prevent QUIN-induced neurotoxicity and KYN and 3-HAA–mediated immune suppression. Cancer Res; 72(22); 5649–57. ©2012 AACR.
Angiopoietin-2 Functions as a Tie2 Agonist in Tumor Models, Where It Limits the Effects of VEGF Inhibition
Authors: Daly Christopher , Eichten Alexandra , Castanaro Carla , Pasnikowski Elizabeth , Adler Alexander , Lalani Alshad S. , Papadopoulos Nicholas , Kyle Alastair H. , Minchinton Andrew I. , Yancopoulos George D. , Thurston Gavin 
Published: November 2012

Abstract
The angiopoietins Ang1 (ANGPT1) and Ang2 (ANGPT2) are secreted factors that bind to the endothelial cell–specific receptor tyrosine kinase Tie2 (TEK) and regulate angiogenesis. Ang1 activates Tie2 to promote blood vessel maturation and stabilization. In contrast, Ang2, which is highly expressed by tumor endothelial cells, is thought to inhibit Tie2 activity and destabilize blood vessels, thereby facilitating VEGF-dependent vessel growth. Here, we show that the inhibition of tumor xenograft growth caused by an Ang2-specific antibody (REGN910) is reversed by systemic administration of the Tie2 agonist Ang1. These results indicate that Ang2 blockade inhibits tumor growth by decreasing Tie2 activity, showing that Ang2 is a Tie2 activator. REGN910 treatment of tumors resulted in increased expression of genes that are repressed by Tie2 activation, providing further evidence that REGN910 inhibits Tie2 signaling. Combination treatment with REGN910 plus the VEGF blocker aflibercept reduced tumor vascularity and tumor perfusion more dramatically than either single agent, resulting in more extensive tumor cell death and more potent inhibition of tumor growth. Challenging the prevailing model of Ang2 as a destabilizing factor, our findings indicate that Ang2 plays a protective role in tumor endothelial cells by activating Tie2, thereby limiting the antivascular effects of VEGF inhibition. Thus, blockade of Ang2 might enhance the clinical benefits currently provided by anti-VEGF agents. Cancer Res; 73(1); 108–18. ©2012 AACR.