bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shuttle Vector-Based Transformation System for
Pyrococcus furiosus
Authors: Waege Ingrid , Schmid Georg , Thumann Sybille , Thomm Michael , Hausner Winfried 
Published: April 2010

ABSTRACT

Pyrococcus furiosus
is a model organism for analyses of molecular biology and biochemistry of archaea, but so far no useful genetic tools for this species have been described. We report here a genetic transformation system for
P. furiosus
based on the shuttle vector system pYS2 from
Pyrococcus abyssi
. In the redesigned vector, the
pyrE
gene from
Sulfolobus
was replaced as a selectable marker by the 3-hydroxy-3-methylglutaryl coenzyme A reductase gene (HMG-CoA) conferring resistance of transformants to the antibiotic simvastatin. Use of this modified plasmid resulted in the overexpression of the HMG-CoA reductase in
P. furiosus
, allowing the selection of strains by growth in the presence of simvastatin. The modified shuttle vector replicated in
P. furio
s
us
, but the copy number was only one to two per chromosome. This system was used for overexpression of His
6
-tagged subunit D of the RNA polymerase (RNAP) in
Pyrococcus
cells. Functional RNAP was purified from transformed cells in two steps by Ni-NTA and gel filtration chromatography. Our data provide evidence that expression of transformed genes can be controlled from a regulated gluconeogenetic promoter.
Antibiofilm Activity of the Marine Bacterium
Pseudoalteromonas
sp. Strain 3J6
Authors: Dheilly Alexandra , Soum-Soutéra Emmanuelle , Klein Géraldine L. , Bazire Alexis , Compère Chantal , Haras Dominique , Dufour Alain 
Published: April 2010

ABSTRACT

Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions,
Pseudoalteromonas
sp. strain 3J6 formed mixed biofilms with
Bacillus
sp. strain 4J6 but was largely predominant over
Paracoccus
sp. strain 4M6 and
Vibrio
sp. strain D01. The supernatant of
Pseudoalteromonas
sp. 3J6 liquid culture (SN
3J6
) was devoid of antibacterial activity against free-living
Paracoccus
sp. 4M6 and
Vibrio
sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN
3J6
were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN
3J6
had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other
Pseudoalteromonas
strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN
3J6
also impaired biofilm formation by three strains belonging to the human-pathogenic species
Pseudomonas aeruginosa
,
Salmonella enterica
, and
Escherichia coli
. Such an antibiofilm activity is original and opens up a variety of applications for
Pseudoalteromonas
sp. 3J6 and/or its active exoproducts in biofilm prevention strategies.
Role of Extracellular DNA in Initial Bacterial Adhesion and Surface Aggregation
Authors: Das Theerthankar , Sharma Prashant K. , Busscher Henk J. , van der Mei Henny C. , Krom Bastiaan P. 
Published: April 2010

ABSTRACT
Extracellular DNA (eDNA) is an important component of the biofilm matrix. We show that removal of eDNA from Gram-positive bacteria reduces initial adhesion to and aggregation of bacteria on surfaces. Thermodynamic analyses indicated that eDNA introduces favorable acid-base interactions, explaining the effect of eDNA on aggregation and adhesion to the surface.
Molecular Pathogenesis of Infections Caused byLegionella pneumophila
Authors: Newton Hayley J. , Ang Desmond K. Y. , van Driel Ian R. , Hartland Elizabeth L. 
Published: April 2010

SUMMARYThe genusLegionellacontains more than 50 species, of which at least 24 have been associated with human infection. The best-characterized member of the genus,Legionella pneumophila, is the major causative agent of Legionnaires' disease, a severe form of acute pneumonia.L. pneumophilais an intracellular pathogen, and as part of its pathogenesis, the bacteria avoid phagolysosome fusion and replicate within alveolar macrophages and epithelial cells in a vacuole that exhibits many characteristics of the endoplasmic reticulum (ER). The formation of the unusualL. pneumophilavacuole is a feature of its interaction with the host, yet the mechanisms by which the bacteria avoid classical endosome fusion and recruit markers of the ER are incompletely understood. Here we review the factors that contribute to the ability ofL. pneumophilato infect and replicate in human cells and amoebae with an emphasis on proteins that are secreted by the bacteria into theLegionellavacuole and/or the host cell. Many of these factors undermine eukaryotic trafficking and signaling pathways by acting as functional and, in some cases, structural mimics of eukaryotic proteins. We discuss the consequences of this mimicry for the biology of the infected cell and also for immune responses toL. pneumophilainfection.
Cardiac Involvement with Parasitic Infections
Authors: Hidron Alicia , Vogenthaler Nicholas , Santos-Preciado José I. , Rodriguez-Morales Alfonso J. , Franco-Paredes Carlos , Rassi Anis 
Published: April 2010

SUMMARYParasitic infections previously seen only in developing tropical settings can be currently diagnosed worldwide due to travel and population migration. Some parasites may directly or indirectly affect various anatomical structures of the heart, with infections manifested as myocarditis, pericarditis, pancarditis, or pulmonary hypertension. Thus, it has become quite relevant for clinicians in developed settings to consider parasitic infections in the differential diagnosis of myocardial and pericardial disease anywhere around the globe. Chagas' disease is by far the most important parasitic infection of the heart and one that it is currently considered a global parasitic infection due to the growing migration of populations from areas where these infections are highly endemic to settings where they are not endemic. Current advances in the treatment of African trypanosomiasis offer hope to prevent not only the neurological complications but also the frequently identified cardiac manifestations of this life-threatening parasitic infection. The lack of effective vaccines, optimal chemoprophylaxis, or evidence-based pharmacological therapies to control many of the parasitic diseases of the heart, in particular Chagas' disease, makes this disease one of the most important public health challenges of our time.
Clinical and Laboratory Update on Blastomycosis
Authors: Saccente Michael , Woods Gail L. 
Published: April 2010

SUMMARYBlastomycosis is endemic in regions of North America that border the Great Lakes and the St. Lawrence River, as well as in the Mississippi River and Ohio River basins. Men are affected more often than women and children because men are more likely to participate in activities that put them at risk for exposure toBlastomyces dermatitidis. Human infection occurs when soil containing microfoci of mycelia is disturbed and airborne conidia are inhaled. If natural defenses in the alveoli fail to contain the infection, lymphohematogenous dissemination ensues. Normal host responses generate a characteristic pyogranulomatous reaction. The most common sites of clinical disease are the lung and skin; osseous, genitourinary, and central nervous system manifestations follow in decreasing order of frequency. Blastomycosis is one of the great mimickers in medicine; verrucous cutaneous blastomycosis resembles malignancy, and mass-like lung opacities due toB. dermatitidisoften are confused with cancer. Blastomycosis may be clinically indistinguishable from tuberculosis. Diagnosis is based on culture and direct visualization of round, multinucleated yeast forms that produce daughter cells from a single broad-based bud. Although a long course of amphotericin B is usually curative, itraconazole is also highly effective and is the mainstay of therapy for most patients with blastomycosis.
A Global Perspective on Hantavirus Ecology, Epidemiology, and Disease
Authors: Jonsson Colleen B. , Figueiredo Luiz Tadeu Moraes , Vapalahti Olli 
Published: April 2010

SUMMARYHantaviruses are enzootic viruses that maintain persistent infections in their rodent hosts without apparent disease symptoms. The spillover of these viruses to humans can lead to one of two serious illnesses, hantavirus pulmonary syndrome and hemorrhagic fever with renal syndrome. In recent years, there has been an improved understanding of the epidemiology, pathogenesis, and natural history of these viruses following an increase in the number of outbreaks in the Americas. In this review, current concepts regarding the ecology of and disease associated with these serious human pathogens are presented. Priorities for future research suggest an integration of the ecology and evolution of these and other host-virus ecosystems through modeling and hypothesis-driven research with the risk of emergence, host switching/spillover, and disease transmission to humans.
Candida
Infections of the Genitourinary Tract
Authors: Achkar Jacqueline M. , Fries Bettina C. 
Published: April 2010

SUMMARY

All humans are colonized with
Candida
species, mostly
Candida albicans
, yet some develop diseases due to
Candida
, among which genitourinary manifestations are extremely common. The forms of genitourinary candidiasis are distinct from each other and affect different populations. While vulvovaginal candidiasis affects mostly healthy women, candiduria occurs typically in elderly, hospitalized, or immunocompromised patients and in neonates. Despite its high incidence and clinical relevance, genitourinary candidiasis is understudied, and therefore, important questions about pathogenesis and treatment guidelines remain to be resolved. In this review, we summarize the current knowledge about genitourinary candidiasis.
Sequential XylS-CTD Binding to the Pm Promoter Induces DNA Bending Prior to Activation
Authors: Domínguez-Cuevas Patricia , Ramos Juan-Luís , Marqués Silvia 
Published: April 2010

ABSTRACTXylS protein, a member of the AraC family of transcriptional regulators, comprises a C-terminal domain (CTD) involved in DNA binding and an N-terminal domain required for effector binding and protein dimerization. In the absence of benzoate effectors, the N-terminal domain behaves as an intramolecular repressor of the DNA binding domain. To date, the poor solubility properties of the full-length protein have restricted XylS analysis to genetic approachesin vivo. To characterize the molecular consequences of XylS binding to its operator, we used a recombinant XylS-CTD variant devoid of the N-terminal domain. The resulting protein was soluble and monomeric in solution and activated transcription from its cognate promoter in an effector-independent manner. XylS binding sites in the Pm promoter present an intrinsic curvature of 35° centered at position −42 within the proximal site. Gel retardation and DNase footprint analysis showed XylS-CTD binding to Pm occurred sequentially: first a XylS-CTD monomer binds to the proximal site overlapping the RNA polymerase binding sequence to form complex I. This first event increased Pm bending to 50° and was followed by the binding of the second monomer, which further increased the observed global curvature to 98°. This generated a concomitant shift in the bending center to a region centered at position −51 when the two sites were occupied (complex II). We propose a model in which DNA structure and binding sequences strongly influence XylS binding events previous to transcription activation.
Mixed Infections and
In Vivo
Evolution in the Human Fungal Pathogen Cryptococcus neoformans
Authors: Desnos-Ollivier Marie , Patel Sweta , Spaulding Adam R. , Charlier Caroline , Garcia-Hermoso Dea , Nielsen Kirsten , Dromer Françoise 
Published: April 2010

ABSTRACT

Koch’s postulates are criteria establishing a causal relationship between a microbe and a disease that lead to the assumption that diseases are caused by a single strain or its evolved forms.
Cryptococcus neoformans
is a life-threatening human fungal pathogen responsible for an estimated 1 million cases of cryptococcosis/year, predominantly meningoencephalitis. To assess the molecular diversity of clinical isolates and gain knowledge of
C. neoformans
biology in the host, we analyzed clinical cultures collected during the prospective CryptoA/D study. Using molecular analysis of unpurified isolates, we demonstrated that mixed infections in humans are more common than previously thought, occurring in almost 20% of patients diagnosed with cryptococcosis. These mixed infections are composed of different mating types, serotypes, and/or genotypes. We also identified genetically related haploid and diploid strains in the same patients. Experimental infections and quantitative PCR show that these ploidy changes can result from endoreplication (duplication of DNA content) and that shuttling between haploid and diploid states can occur, suggesting
in vivo
evolution. Thus, the concept of one strain/one infection does not hold true for
C. neoformans
and may apply to other environmentally acquired fungal pathogens. Furthermore, the possibility of mixed and/or evolving infections should be taken into account when developing therapeutic strategies against these pathogens.

IMPORTANCE
Cryptococcus  neoformans
is a life-threatening human fungal pathogen that is present in the environment and is responsible for an estimated 1 million cases of cryptococcosis/year, predominantly meningoencephalitis in HIV-infected patients. To assess the molecular diversity of clinical isolates and gain knowledge of
C. neoformans
biology in the host, we analyzed clinical cultures collected during a prospective study on cryptococcosis. Using molecular analysis of unpurified isolates, we uncovered an unexpectedly high frequency (almost 20%) of mixed infections. We further demonstrated that these mixed infections could result from infestation by multiple strains acquired from the environment. We also made the serendipitous discovery of
in vivo
evolution leading to endoreplication of the yeasts within the host. Thus, the concept of one strain causing one infection does not hold true for
C. neoformans
and potentially for other environmentally acquired fungal pathogens. The possibility of mixed and/or evolving infections should be taken into account when developing therapeutic strategies against these pathogens.
Investigation of a possible submarine landslide at the Var delta front (Nice continental slope, southeast France)
Authors: Sultan N. , Savoye B. , Jouet G. , Leynaud D. , Cochonat P. , Henry P. , Stegmann S. , Kopf A. 
Published: April 2010

The Var prodelta progrades across a straight, narrow shelf (less than 2 km wide) with a very steep continental slope reaching locally more than 30°. Historically, the Var delta front is sadly famous for the 1979 catastrophic submarine landslide that resulted in several casualties and infrastructural damage. Geotechnical and geophysical investigations carried out in late 2007 to the east of the 1979 landslide scar provide evidence for the possible occurrence of a new important sedimentary collapse and submarine landslide. Geophysical data acquired in the area show the presence of several seafloor morphological steps rooted to shallow subsurface seismic reflections. Moreover, in situ piezocone measurements demonstrate the presence of several shear zones at the border of the shelf break at different depths below the seafloor. The aim of this technical note is to present and discuss acquired geotechnical and geophysical data in terms of failure mechanisms and submarine landslides. Both geophysical and geotechnical data suggest the start-up of a progressive failure mechanism and reveal the possible occurrence of a submarine landslide and the urgent need for mitigation procedures.
Geometric algorithms for optimal airspace design and air traffic controller workload balancing
Authors: Basu Amitabh , Mitchell Joseph S. B. , Sabhnani Girish Kumar 
Published: April 2010

The National Airspace System (NAS) is designed to accommodate a large number of flights over North America. For purposes of workload limitations for air traffic controllers, the airspace is partitioned into approximately 600 sectors; each sector is observed by one or more controllers. In order to satisfy workload limitations for controllers, it is important that sectors be designed carefully according to the traffic patterns of flights, so that no sector becomes overloaded. We formulate and study the airspace sectorization problem from an algorithmic point-of-view, modeling the problem of optimal sectorization as a geometric partition problem with constraints. The novelty of the problem is that it partitions data consisting of trajectories of moving points, rather than static point set partitioning that is commonly studied. First, we formulate and solve the 1D version of the problem, showing how to partition a line into “sectors” (intervals) according to historical trajectory data. Then, we apply the 1D solution framework to design a 2D sectorization heuristic based on binary space partitions. We also devise partitions based on balanced “pie partitions” of a convex polygon.
We evaluate our 2D algorithms experimentally, applying our algorithms to actual historical flight track data for the NAS. We compare the workload balance of our methods to that of the existing set of sectors for the NAS and find that our resectorization yields competitive and improved workload balancing. In particular, our methods yield an improvement by a factor between 2 and 3 over the current sectorization in terms of the time-average and the worst-case workloads of the maximum workload sector. An even better improvement is seen in the standard deviations (over all sectors) of both time-average and worst-case workloads.
Crosstalk between Mast Cells and Pancreatic Cancer Cells Contributes to Pancreatic Tumor Progression
Authors: Strouch Matthew J. , Cheon Eric C. , Salabat Mohammad R. , Krantz Seth B. , Gounaris Elias , Melstrom Laleh G. , Dangi-Garimella Surabhi , Wang Edward , Munshi Hidayatullah G. , Khazaie Khashayarsha , Bentrem David J. 
Published: April 2010

Abstract
Purpose: To assess the clinical and pathologic significance of mast cell infiltration in human pancreatic cancer and evaluate crosstalk between mast cells and cancer cells in vitro.
Experimental Design: Immunohistochemistry for tryptase was done on 53 pancreatic cancer specimens. Mast cell counts were correlated with clinical variables and survival. Serum tryptase activity from patients with cancer was compared with patients with benign pancreatic disease. In vitro, the effect of pancreatic cancer–conditioned medium on mast cell migration was assessed. The effect of conditioned medium from the human mast cell line, LAD-2, on cancer and normal ductal cell proliferation was assessed by thymidine incorporation. Matrigel invasion assays were used to evaluate the effect of mast cell–conditioned medium on cancer cell invasion in the presence and absence of a matrix metalloproteinase inhibitor, GM6001.
Results: Mast cell infiltration was significantly increased in pancreatic cancer compared with normal pancreatic tissue (11.4 ± 6.7 versus 2.0 ± 1.4, P &lt; 0.001). Increased infiltrating mast cells correlated with higher grade tumors (P &lt; 0.0001) and worse survival. Patients with pancreatic cancer had elevated serum tryptase activity (P &lt; 0.05). In vitro, AsPC1 and PANC-1 cells induced mast cell migration. Mast cell–conditioned medium induced pancreatic cancer cell migration, proliferation, and invasion but had no effect on normal ductal cells. Furthermore, the effect of mast cells on cancer cell invasion was, in large part, matrix metalloproteinase–dependent.
Conclusions: Tumor-infiltrating mast cells are associated with worse prognosis in pancreatic cancer. In vitro, the interaction between mast cells and pancreatic cancer cells promotes tumor growth and invasion. Clin Cancer Res; 16(8); 2257–65. ©2010 AACR.
The EPHB6 Receptor Tyrosine Kinase Is a Metastasis Suppressor That Is Frequently Silenced by Promoter DNA Hypermethylation in Non–Small Cell Lung Cancer
Authors: Yu Jun , Bulk Etmar , Ji Ping , Hascher Antje , Tang Moying , Metzger Ralf , Marra Alessandro , Serve Hubert , Berdel Wolfgang E. , Wiewroth Rainer , Koschmieder Steffen , Müller-Tidow Carsten 
Published: April 2010

Abstract
Purpose: Loss of EPHB6 receptor tyrosine kinase expression in early-stage non–small cell lung carcinoma (NSCLC) is associated with the subsequent development of distant metastasis. Here, we analyzed the regulation and function of EPHB6 in lung cancer metastasis.
Experimental Design: The expression levels of EPHB6 were compared among normal lung tissue (n = 9), NSCLC without metastasis (n = 39), and NSCLC with metastasis (n = 39) according to the history of the patients. In addition, EPHB6 expression levels of matched tumor-normal pairs from 24 NSCLC patients were analyzed. The promoter DNA methylation status and its association with the expression levels of EPHB6 were determined among 14 pairs of tumor-normal samples. Metastatic potential of EPHB6 was assessed in vitro and in vivo in a metastasis mouse model. Overexpression and RNA interference (RNAi) approaches were used for analysis of the biological functions of EPHB6.
Results: EPHB6 mRNA and protein levels were significantly reduced in NSCLC tumors compared with matched normal lung tissue. Decreased EPHB6 expression levels were associated with an increased risk for metastasis development in NSCLC patients. Loss of expression correlated with EPHB6 hypermethylation. EPHB6 expression was induced by 5-aza-2'-deoxycytidine treatment in an NSCLC cell line. Restoration of EPHB6 expression in lung adenocarcinoma cells increased adhesion and decreased migration. Reexpression of EPHB6 in lung cancer cells almost entirely abolished metastasis formation in non obese diabetic (NOD)/severe combined immunodeficient mice.
Conclusions: Taken together, these analyses show that EPHB6 is a metastasis inhibitory gene that is frequently silenced by hypermethylation of its promoter in NSCLC. Clin Cancer Res; 16(8); 2275–83. ©2010 AACR.