bluuebunny/crossref_metadata_2025 huggingface dataset:
Population decline is accompanied by loss of genetic diversity in the Lesser Grey Shrike Lanius minor
Authors: KVIST LAURA , GIRALT DAVID , VALERA FRANCISCO , HOI HERBERT , KRISTIN ANTON , DARCHIASHVILI GIORGI , LOVASZI PETER
Published: December 2010

The Lesser Grey Shrike has suffered successive declines in population size and a marked contraction of its breeding range since the early 20th century, largely because of long‐term agricultural intensification. This has resulted in a severely fragmented distribution in Western Europe, with isolated breeding nuclei in Spain, France and Italy and a more continuous distribution in Eastern Europe and Asia. Using a combination of nuclear and mitochondrial markers, we assessed the genetic structure and diversity of Lesser Grey Shrike populations from Western Europe, Central Europe and Asia. There was significant genetic differentiation among three major regional groups, one European and two Asian. Genetic diversity measures were lowest in the smallest and most marginal Spanish population. Limited genetic diversity, combined with rapid population decline, suggests the Spanish population may face extinction in the near future.
Pharmacological characterization of the cytoprotective effects of polyunsaturated fatty acids in insulin‐secreting BRIN‐BD11 cells
Authors: Dhayal Shalinee , Morgan Noel G
Published: December 2010

BACKGROUND AND PURPOSE Free fatty acids are important metabolic fuels for mammalian cells but, recently, it has become clear that they can also fulfil signalling functions, which are independent of their metabolic fate. We are investigating the ability of unsaturated free fatty acids to exert a cytoprotective response during exposure of insulin‐secreting cells to toxic stimuli. The majority of earlier studies have focussed on monounsaturated fatty acids but this has now been extended to define the structural requirements of the cytoprotective effects of polyunsaturated species.

EXPERIMENTAL APPROACH Clonal rat insulin‐secreting cell lines, BRIN‐BD11 or INS‐1, were exposed to fatty acids or their derivatives complexed with BSA and the viability of the cells was analysed by flow cytometry after staining with propidium iodide.

KEY RESULTS A variety of polyunsaturated fatty acids with chain lengths between C18–C22 attenuated the cytotoxic actions of the saturated fatty acid, palmitate (C16:0) in BRIN‐BD11 and INS‐1 cells. These effects were dose‐dependent and displayed potencies that were much higher than those achieved with monounsaturated fatty acids. Methyl esters of the polyunsaturates were also effective. The cytoprotective responses were not altered by incubation of cells with inhibitors of cyclooxygenase or lipoxygenase enzymes although they were antagonized dose‐dependently by arachidonyltrifluoromethylketone (AACOCF3).

CONCLUSIONS AND IMPLICATIONS The results are consistent with the involvement of a specific fatty acid binding site having loose, but defined, structural criteria, in mediating the cytoprotective effects of unsaturated fatty acids. AACOCF3 may be of value in defining this site in molecular terms.
Sildenafil, a phosphodiesterase type 5 inhibitor, attenuates diabetic nephropathy in non‐insulin‐dependent Otsuka Long‐Evans Tokushima Fatty rats
Authors: Kuno Yoshihiro , Iyoda Masayuki , Shibata Takanori , Hirai Yuki , Akizawa Tadao
Published: December 2010

BACKGROUND It is well established that the pathogenesis of diabetic nephropathy is associated with abnormalities of renal nitric oxide (NO) generation. Many of the biological actions of NO are mediated by cGMP, which is rapidly degraded by phosphodiesterases. In this study, we evaluated the renoprotective effects of sildenafil (SIL), an inhibitor of phosphodiesterase‐5, in type 2 diabetic rats.

METHODS Male Otsuka Long‐Evans Tokushima Fatty (OLETF) rats, a non‐insulin‐dependent diabetes model, and Long‐Evans Tokushima Otsuka rats, a non‐diabetic control, were treated with either SIL (2.5 mg·kg−1 in drinking water) or undosed water for 28 weeks, starting at 30 weeks of age.

RESULTS Sildenafil treatment significantly decreased albuminuria, attenuated glomerular hyperfiltration and resulted in a decrease in glomerular hypertrophy, in addition to a reduced glomerulosclerosis score and a dramatic decrease in the number of glomerular and tubulointerstitial proliferating cell nuclear antigen‐positive cells in OLETF rats. This was accompanied by a significant reduction in renal cortical mRNA levels of collagen types I and III. The increased mRNA levels of matrix metalloproteinase (MMP)‐2, MMP‐9, tissue inhibitors of MMPs (TIMP)‐1 and TIMP‐2 in the OLETF rats were significantly or partially attenuated by SIL treatment.

CONCLUSIONS This study suggests that SIL attenuated diabetic nephropathy due to its potent antiproliferative effects and its regulatory effects on extracellular matrix. This latter effect is thought to be a result of its ability to affect the balance between MMPs and their inhibitors.
Pathology Without Crisis? The Strange Demise of the Anglo-Liberal Growth Model
Authors: Hay Colin
Published: December 2010

In the wake of the deepest and longest recession the UK has experienced since the 1930s, this article examines the origins, sustenance and puncturing of the growth dynamic the UK economy enjoyed between 1992 and 2007. In so doing it seeks to gauge the interventions made to attempt to shore up the growth model and the prospects for the resumption of growth. It argues that the Anglo-liberal growth model is, indeed, fatally flawed and that, in the absence of a new growth model, it is difficult to see how sustained economic growth can be achieved. Yet it also argues that, at present, no alternative growth model is on offer and that it is wrong to infer the likelihood of a paradigm shift in economic thinking from the ‘inter-paradigm’ borrowing used to shore up the old growth model in the midst of the recession. If crises are judged as much by the transformations to which they give rise as by the accumulation of pathologies out of which they crystallize, then what we have experienced to date is not so much a crisis as a catastrophic equilibrium. Though the symptoms to which it has given rise are pregnant with the possibility of crisis, the crisis itself is yet to come.
New Modes of Governance, Political Accountability and Public Reason
Authors: Weale Albert
Published: December 2010

New modes of governance are said to create problems of political accountability. To understand this claim, we need a theory of accountability. Electoral accountability provides authorization and sanction, but it neglects the problems entailed in the requirement to provide explanation and justification. Political accountability in this discursive sense can be understood through the idea of public reason, where this is defined in terms of substantive rationality and an orientation to the public interest. This conceptualization leads in turn to the requirement of replicability and openness in public reasoning. The problem of accountability is one of securing the conditions under which the institutions within which policy deliberation takes place can merit the confidence of citizens in these terms, and the Commission White Paper on European governance is used to illustrate the application of these tests.
Blood transfusions recruit the microcirculation during cardiac surgery
Authors: Yuruk Koray , Almac Emre , Bezemer Rick , Goedhart Peter , de Mol Bas , Ince Can
Published: December 2010

BACKGROUND: Perioperative red blood cell transfusions are commonly used in patients undergoing cardiac surgery to correct anemia caused by blood loss and hemodilution associated with cardiopulmonary bypass circulation. The aim of this investigation was to test the hypothesis that blood transfusion has beneficial effects on sublingual microcirculatory density, perfusion, and oxygenation. To this end, sidestream dark field (SDF) imaging and spectrophotometry were applied sublingually before and after blood transfusion during cardiac surgery.

STUDY DESIGN AND METHODS: Twenty‐four adult patients undergoing on‐pump cardiac surgery, including coronary artery bypass grafting, cardiac‐valve surgery, or a combination of these two procedures, were included consecutively in this prospective, observational study. Sublingual microcirculatory density and perfusion were assessed using SDF imaging in 12 patients (Group A). Sublingual reflectance spectrophotometry was applied in 12 patients (Group B) to monitor microcirculatory oxygenation and hemoglobin (Hb) concentration.

RESULTS: Blood transfusion caused an increase in systemic Hb concentration (p < 0.01) and hematocrit (p < 0.01). At the microcirculatory level, blood transfusion resulted in increased microcirculatory density (from 10.5 ± 1.2 to 12.9 ± 1.2 mm capillary/mm2 tissue, p < 0.01) as shown using SDF imaging. In concert with the SDF measurements, spectrophotometry showed that microcirculatory Hb content increased from 61.4 ± 5.9 to 70.0 ± 4.7 AU (p < 0.01) and that microcirculatory Hb oxygen saturation increased from 65.6 ± 8.3% to 68.6 ± 8.4% (p = 0.06).

CONCLUSION: In this study we have shown that blood transfusion: 1) improves the systemic circulation and oxygen‐carrying capacity, 2) improves sublingual microcirculatory density but not perfusion velocity, and 3) improves microcirculatory oxygen saturation.
The Colorado Patient‐Centered Interprofessional Evidence‐Based Practice Model: A Framework for Transformation
Authors: Goode Colleen J. , Fink Regina M. , Krugman Mary , Oman Kathleen S. , Traditi Lisa K.
Published: December 2010

Background: Evidence‐based practice (EBP) models provide a framework to guide organizations and their clinicians to implement evidence‐based policies, protocols, and guidelines. A historical review of evidence‐based models is presented. The revised Colorado Patient‐Centered Interprofessional EBP Model supports use of research evidence and nonresearch evidence and adopts a patient‐centered approach to EBP.

Aim: The purpose of this article is to present a framework that can be used to transform an organization and foster the use of evidence by interdisciplinary team members.

Approach: An evidence‐based intervention to decrease catheter associated urinary tract infections (CAUTI) is presented to show how the model is operationalized. The EBP model is supported by the five steps that clinicians should use as they identify a clinical problem, gather the evidence, and move the evidence into practice. Ideas for dissemination of new models to clinicians throughout the organization are presented.
Climate Change and Hunger: Africa’s Smallholder Farmers Struggle to Adapt  Changement climatique et famine : les petits exploitants africains peinent à s’ajuster  Klimawandel und Hunger: Kleinbauern in Afrika haben Schwierigkeiten bei der Anpassung
Authors: Ringler Claudia
Published: December 2010

summary

Climate Change and Hunger: Africa’s Smallholder Farmers Struggle to Adapt

Farmers in Sub‐Saharan Africa are already feeling the effects of climate change, but many have done little or nothing in response. Researchers from the International Food Policy Research Institute (IFPRI) and their partners studied the perceptions of climate change among smallholder farmers in Ethiopia, Kenya and South Africa. They found that a lack of access to credit, markets, information, risk‐sharing tools, and property rights has limited the ability of many farm households to adapt to the negative effects of climate change. This article discusses on‐the‐ground findings in the context of computer model projections that show a decline in future yields of staple crops under most climate change scenarios. It concludes that adaptation to rising temperatures and changing weather patterns is crucial to the food security of millions of people. Without significant investment in agricultural technology and rural development, however, many farmers in Sub‐Saharan Africa will be unable to meet the challenges of the coming decades. As a result, calorie availability would drop dramatically and millions more children will be malnourished in 2050. Some of this funding could be secured if agricultural mitigation activities, which have important synergies with adaptation in the region, could be included in global carbon markets. But the political will and resources to support ‘charismatic carbon’– that is, lower entry barriers for pro‐poor adaptation and mitigation – have yet to be realised.
Seasoned Equity Offers: The Effect of Insider Ownership and Float
Authors: Intintoli Vincent J. , Kahle Kathleen M.
Published: December 2010

Seasoned equity offering (SEO) underpricing has increased dramatically since the early 1980s. While previous research has examined the determinants of SEO underpricing, these studies have not explored the effect of insider ownership on discounts. We find that this effect is twofold. First, higher insider ownership reduces float, thereby increasing price pressure and SEO underpricing. This effect is greatest in firms with low liquidity. Second, the greater the percentage of secondary shares offered, the lower the underpricing, suggesting that manager's pressure banks to reduce underpricing when their personal wealth is at stake. However, we find that this negative relation is mitigated if the firm employs a prestigious underwriter.
Coupled Surge-Heave-Pitch Dynamic Modeling of Spar-Moonpool-Riser Interaction
Authors: Spanos Pol D. , Nava Vincenzo , Arena Felice
Published: December 2010

Due to the rather intense ongoing development of deep water gas and oil fields, the technical community has devoted considerable attention to the dynamic behavior of Spar floating systems. Spar dynamics exhibits a highly nonlinear behavior due to the presence of various components such as mooring lines, moonpool, and risers. Certain studies have focused on the reduction of the heave response of single-degree-of-freedom Spar models due to the oscillations of water entrapped in the moonpool through the partially closed bottom plates. In this paper, a novel coupled six-degree-of-freedom analytical model of a Spar system comprising top tensioned risers is proposed. The model accounts for the interactions among the Spar hull kinematics (heave, surge, and pitch), the riser kinematics (heave and surge), and the moonpool. This model involves six coupled differential equations comprising nonlinearities associated not only with stiffness and damping but also with inertia terms. A dynamic analysis is performed by subjecting the model to JONSWAP ocean wave spectrum compatible extreme forces (corresponding to the 100 year wave) and to moments applied to the center of gravity computed by means of a standard motion simulation program. Both numerical and analytical techniques (statistical linearization including inertia terms) are used for the determination of the response of the proposed dynamic model, both in the time and the frequency domains. Related parameter study results are reported, including ones pertaining to the dependence of the Spar system motion on the degree of opening of the bottom plates.
Plastic Collapse Loads of Cracked Square Hollow Section T-, Y-, and K-joints
Authors: Lie S. T. , Yang Z. M.
Published: December 2010

This paper concerns on the development of numerical models for cracked square hollow sections (SHSs) T-, Y-, and K-joints. Based on these numerical models, the plastic collapse loads Pc are calculated using nonlinear finite element method and through twice-elastic compliance criterion. It is found that the numerical plastic collapse loads Pc are slightly conservative compared with the ones calculated using formulae proposed by BS7910 [British Standards, 2005, “Guide on Methods for Assessing the Acceptability of Flaws in Metallic Structures,” BS 7910-Amendment 1] and are in close agreement with the experimental tests data. Therefore, the proposed numerical model is robust and it can be used to calculate the plastic collapse loads Pc of the cracked (SHS) T-, Y-, and K-joints.
Microdialysis Technique to Quantify Drug Concentration in Human Intervertebral Disks
Authors: Han Hyun Kyu , Buckley Jenni , Kursa Kathy , O’Neill Conor , Lotz Jeffrey
Published: December 2010

No dependable method has yet been established to find time-dependent concentrations of substances injected into the intervertebral disk. This study investigated the feasibility of microdialysis in the measurement of local concentrations of a low-molecular weight drug in the human lumbar disk. A quasi-static experiment and a dynamic computer finite element simulation were used to study the spread of lidocaine in the lumbar disk. Fresh-frozen cadaveric lumbar motion segments were immersed in a 0.1% lidocaine HCl solution for 6 days prior to continuous microdialysis sampling for 30 min at the posterolateral annulus. Samples were collected every 10 min, for a total of three samples per probe. To maintain quasi-static conditions, where the output of lidocaine was equal to the diffusion rate, the microdialysis flow rate was set to 0.6 μl/min. The finite element model treated the disk as poroelastic tissue under compressive load and introduced 1 ml of 4% lidocaine into the nucleus pulposus. Higher microdialysis flow rates suffered from significant losses during consecutive recoveries. Relative recovery in the annulus at 0.6 μl/min was found to be 53.3%±16.2% of the initial solution. This was determined to be a result of low diffusivity of lidocaine through tissue. The FEA model predicted low diffusivity of lidocaine and slow transport to the posterolateral annulus if no fissures were present in the annulus. The results from in vitro experiments and computer simulations showed that while microdialysis can take reliable concentration measurements in the posterolateral annulus, probe placement near a fissure is critical if a measurement is to be made immediately following injection of a drug into the nucleus.
Diversity and Activity of Free-Living Nitrogen-Fixing Bacteria and Total Bacteria in Organic and Conventionally Managed Soils
Authors: Orr Caroline H. , James Angela , Leifert Carlo , Cooper Julia M. , Cummings Stephen P.
Published: December 2010

Agricultural soils are heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, the molecular ecology of the total bacterial and free-living nitrogen-fixing communities in soils from the Nafferton Factorial Systems Comparison (NFSC) study in northeast England were examined. The field experiment was factorial in design, with organic versus conventional crop rotation, crop protection, and fertility management factors. Soils were sampled on three dates (March, June, and September) in 2007. Total RNA was extracted from all soil samples and reverse transcribed. Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were used to analyze
nifH
and 16S rRNA genes in order to study free-living diazotrophs and the total bacterial community, respectively. Crop rotation was shown to have a significant effect on total bacterial diversity (and that of free-living N fixers) (
P
≤ 0.001). On all three dates,
nifH
activity was higher in the conventional crop rotation. In contrast, qPCR analysis of free-living N fixers indicated significantly higher levels of activity in conventionally fertilized plots in June (
P
= 0.0324) and in plots with organic crop protection in September (
P
= 0.0143). To our knowledge, the effects of organic and conventional farming systems on free-living diazotrophs have never been studied. An increased understanding of the impacts of management practices on free-living N fixers could allow modifications in soil management practices to optimize the activity of these organisms.
Cofactor Trapping, a New Method To Produce Flavin Mononucleotide
Authors: Krauss Ulrich , Svensson Vera , Wirtz Astrid , Knieps-Grünhagen Esther , Jaeger Karl-Erich
Published: December 2010

We have purified flavin mononucleotide (FMN) from a flavoprotein-overexpressing
Escherichia coli
strain by cofactor trapping. This approach uses an overexpressed flavoprotein to trap FMN, which is thus removed from the cascade regulating FMN production in
E. coli
. This, in turn, allows the isolation of highly pure FMN.
Assessment of the Diversity of Dairy
Lactococcus lactis
subsp.
lactis
Isolates by an Integrated Approach Combining Phenotypic, Genomic, and Transcriptomic Analyses
Authors: Tan-a-ram Punthip , Cardoso Tamara , Daveran-Mingot Marie-Line , Kanchanatawee Sunthorn , Loubière Pascal , Girbal Laurence , Cocaign-Bousquet Muriel
Published: December 2010

The intrasubspecies diversity of six strains of
Lactococcus lactis
subsp.
lactis
was investigated at the genomic level and in terms of phenotypic and transcriptomic profiles in an ultrafiltration cheese model. The six strains were isolated from various sources, but all exhibited a dairy phenotype (growth in ultrafiltration cheese model and high acidification rate). The six strains exhibited similar behaviors in terms of growth during cheese ripening, while different acidification capabilities were detected. Even if all strains displayed large genomic similarities, sharing a large core genome of almost 2,000 genes, the expression of this core genome directly in the cheese matrix revealed major strain-specific differences that potentially could account for the observed different acidification capabilities. This work demonstrated that significant transcriptomic polymorphisms exist even among
Lactococcus lactis
subsp.
lactis
strains with the same dairy origin.
Genomic Diversity of
Lactobacillus salivarius
Authors: Raftis Emma J. , Salvetti Elisa , Torriani Sandra , Felis Giovanna E. , O'Toole Paul W.
Published: December 2010

Strains of
Lactobacillus salivarius
are increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity of
L. salivarius
has been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals.
L. salivarius
displays a high level of genomic diversity, and while selection of
L. salivarius
strains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits.
Enhancement of the Initial Rate of Ethanol Fermentation Due to Dysfunction of Yeast Stress Response Components Msn2p and/or Msn4p
Authors: Watanabe Daisuke , Wu Hong , Noguchi Chiemi , Zhou Yan , Akao Takeshi , Shimoi Hitoshi
Published: December 2010

Sake yeasts (strains of
Saccharomyces cerevisiae
) produce high concentrations of ethanol in sake fermentation. To investigate the molecular mechanisms underlying this brewing property, we compared gene expression of sake and laboratory yeasts in sake mash. DNA microarray and reporter gene analyses revealed defects of sake yeasts in environmental stress responses mediated by transcription factors Msn2p and/or Msn4p (Msn2/4p) and stress response elements (STRE). Furthermore, we found that dysfunction of
MSN2
and/or
MSN4
contributes to the higher initial rate of ethanol fermentation in both sake and laboratory yeasts. These results provide novel insights into yeast stress responses as major impediments of effective ethanol fermentation.
Population Structure and Evolution of Pathogenicity ofYersinia pseudotuberculosis
Authors: Ch'ng Shear Lane , Octavia Sophie , Xia Qiuyu , Duong An , Tanaka Mark M. , Fukushima Hiroshi , Lan Ruiting
Published: December 2010

Yersinia pseudotuberculosisis an enteric human pathogen but is widespread in the environment. Pathogenicity is determined by a number of virulence factors, including the virulence plasmid pYV, the high-pathogenicity island (HPI), and theY. pseudotuberculosis-derived mitogen (YPM), a superantigen. The presence of the 3 virulence factors varies amongY. pseudotuberculosisisolates. We developed a multilocus sequence typing (MLST) scheme to address the population structure ofY. pseudotuberculosisand the evolution of its pathogenicity. The seven housekeeping genes selected for MLST weremdh,recA,sucA,fumC,aroC,pgi, andgyrB. An MLST analysis of 83 isolates ofY. pseudotuberculosis, representing 19 different serotypes and six different genetic groups, identified 61 sequence types (STs) and 12 clonal complexes. Out of 26 allelic changes that occurred in the 12 clonal complexes, 13 were mutational events while 13 were recombinational events, indicating that recombination and mutation contributed equally to the diversification of the clonal complexes. The isolates were separated into 2 distinctive clusters, A and B. Cluster A is the major cluster, with 53 STs (includingY. pestisstrains), and is distributed worldwide, while cluster B is restricted to the Far East. The YPM gene is widely distributed on the phylogenetic tree, withypmAin cluster A andypmBin cluster B. pYV is present in cluster A only but is sporadically absent in some cluster A isolates. In contrast, an HPI is present only in a limited number of lineages and must be gained by lateral transfer. Three STs carry all 3 virulence factors and can be regarded as high-pathogenicity clones. Isolates from the same ST may not carry all 3 virulence factors, indicating frequent gain or loss of these factors. The differences in pathogenicity amongY. pseudotuberculosisstrains are likely due to the variable presence and instability of the virulence factors.
Effect of a New Probiotic
Saccharomyces cerevisiae
Strain on Survival of
Escherichia coli
O157:H7 in a Dynamic Gastrointestinal Model
Authors: Etienne-Mesmin Lucie , Livrelli Valérie , Privat Maud , Denis Sylvain , Cardot Jean-Michel , Alric Monique , Blanquet-Diot Stéphanie
Published: December 2010

Survival of
Escherichia coli
O157:H7 was investigated using a dynamic gastrointestinal model. A high bacterial mortality was observed in the stomach and duodenum. In contrast, bacteria grew in the distal parts of the small intestine. The coadministration of
Saccharomyces cerevisiae
CNCM I-3856 led to a significant reduction of bacterial resumption, maybe through ethanol production.
Anaplerotic Role for Cytosolic Malic Enzyme in Engineered
Saccharomyces cerevisiae
Strains
Authors: Zelle Rintze M. , Harrison Jacob C. , Pronk Jack T. , van Maris Antonius J. A.
Published: December 2010

Malic enzyme catalyzes the reversible oxidative decarboxylation of malate to pyruvate and CO
2
. The
Saccharomyces cerevisiae MAE1
gene encodes a mitochondrial malic enzyme whose proposed physiological roles are related to the oxidative, malate-decarboxylating reaction. Hitherto, the inability of pyruvate carboxylase-negative (Pyc
−
)
S. cerevisiae
strains to grow on glucose suggested that Mae1p cannot act as a pyruvate-carboxylating, anaplerotic enzyme. In this study, relocation of malic enzyme to the cytosol and creation of thermodynamically favorable conditions for pyruvate carboxylation by metabolic engineering, process design, and adaptive evolution, enabled malic enzyme to act as the sole anaplerotic enzyme in
S. cerevisiae
. The
Escherichia coli
NADH-dependent
sfcA
malic enzyme was expressed in a Pyc
−
S. cerevisiae
background. When
PDC2
, a transcriptional regulator of pyruvate decarboxylase genes, was deleted to increase intracellular pyruvate levels and cells were grown under a CO
2
atmosphere to favor carboxylation, adaptive evolution yielded a strain that grew on glucose (specific growth rate, 0.06 ± 0.01 h
−1
). Growth of the evolved strain was enabled by a single point mutation (Asp336Gly) that switched the cofactor preference of
E. coli
malic enzyme from NADH to NADPH. Consistently, cytosolic relocalization of the native Mae1p, which can use both NADH and NADPH, in a
pyc1,2Δ pdc2
Δ strain grown under a CO
2
atmosphere, also enabled slow-growth on glucose. Although growth rates of these strains are still low, the higher ATP efficiency of carboxylation via malic enzyme, compared to the pyruvate carboxylase pathway, may contribute to metabolic engineering of
S. cerevisiae
for anaerobic, high-yield C
4
-dicarboxylic acid production.
Microbial Communities and Electrochemical Performance of Titanium-Based Anodic Electrodes in a Microbial Fuel Cell
Authors: Michaelidou Urania , ter Heijne Annemiek , Euverink Gerrit Jan W. , Hamelers Hubertus V. M. , Stams Alfons J. M. , Geelhoed Jeanine S.
Published: December 2010

Four types of titanium (Ti)-based electrodes were tested in the same microbial fuel cell (MFC) anodic compartment. Their electrochemical performances and the dominant microbial communities of the electrode biofilms were compared. The electrodes were identical in shape, macroscopic surface area, and core material but differed in either surface coating (Pt- or Ta-coated metal composites) or surface texture (smooth or rough). The MFC was inoculated with electrochemically active, neutrophilic microorganisms that had been enriched in the anodic compartments of acetate-fed MFCs over a period of 4 years. The original inoculum consisted of bioreactor sludge samples amended with
Geobacter sulfurreducens
strain PCA. Overall, the Pt- and Ta-coated Ti bioanodes (electrode-biofilm association) showed higher current production than the uncoated Ti bioanodes. Analyses of extracted DNA of the anodic liquid and the Pt- and Ta-coated Ti electrode biofilms indicated differences in the dominant bacterial communities. Biofilm formation on the uncoated electrodes was poor and insufficient for further analyses. Bioanode samples from the Pt- and Ta-coated Ti electrodes incubated with Fe(III) and acetate showed several Fe(III)-reducing bacteria, of which selected species were dominant, on the surface of the electrodes. In contrast, nitrate-enriched samples showed less diversity, and the enriched strains were not dominant on the electrode surface. Isolated Fe(III)-reducing strains were phylogenetically related, but not all identical, to
Geobacter sulfurreducens
strain PCA. Other bacterial species were also detected in the system, such as a
Propionicimonas
-related species that was dominant in the anodic liquid and
Pseudomonas
-,
Clostridium
-,
Desulfovibrio
-,
Azospira
-, and
Aeromonas
-related species.
Candida albicans Hap43 Is a Repressor Induced under Low-Iron Conditions and Is Essential for Iron-Responsive Transcriptional Regulation and Virulence
Authors: Hsu Po-Chen , Yang Cheng-Yao , Lan Chung-Yu
Published: December 2010

Candida albicans
is an opportunistic fungal pathogen that exists as normal flora in healthy human bodies but causes life-threatening infections in immunocompromised patients. In addition to innate and adaptive immunities, hosts also resist microbial infections by developing a mechanism of “natural resistance” that maintains a low level of free iron to restrict the growth of invading pathogens.
C. albicans
must overcome this iron-deprived environment to cause infections. There are three types of iron-responsive transcriptional regulators in fungi; Aft1/Aft2 activators in yeast, GATA-type repressors in many fungi, and HapX/Php4 in
Schizosaccharomyces pombe
and
Aspergillus
species. In this study, we characterized the iron-responsive regulator Hap43, which is the
C. albicans
homolog of HapX/Php4 and is repressed by the GATA-type repressor Sfu1 under iron-sufficient conditions. We provide evidence that Hap43 is essential for the growth of
C. albicans
under low-iron conditions and for
C. albicans
virulence in a mouse model of infection. Hap43 was not required for iron acquisition under low-iron conditions. Instead, it was responsible for repression of genes that encode iron-dependent proteins involved in mitochondrial respiration and iron-sulfur cluster assembly. We also demonstrated that Hap43 executes its function by becoming a transcriptional repressor and accumulating in the nucleus in response to iron deprivation. Finally, we found a connection between Hap43 and the global corepressor Tup1 in low-iron-induced flavinogenesis. Taken together, our data suggest a complex interplay among Hap43, Sfu1, and Tup1 to coordinately regulate iron acquisition, iron utilization, and other iron-responsive metabolic activities.
The Aspergillus nidulans
nucA
EndoG
Homologue Is Not Involved in Cell Death
Authors: de Castro Pimentel Figueiredo Bárbara , de Castro Patrícia Alves , Dinamarco Taísa Magnani , Goldman Maria Helena S. , Goldman Gustavo Henrique
Published: December 2010

Upon apoptosis induction, translocation of mammalian mitochondrial endonuclease G (EndoG) to the nucleus coincides with large-scale DNA fragmentation. Here, we describe for the first time a homologue of EndoG in filamentous fungi by investigating if the
Aspergillus nidulans
homologue of the EndoG gene, named
nucA
EndoG
, is being activated during farnesol-induced cell death. Our results suggest that NucA is not involved in cell death, but it plays a role in the DNA-damaging response in
A. nidulans
.
Staphylococcus aureus
ClpC Divergently Regulates Capsule via
sae
and
codY
in Strain Newman but Activates Capsule via
codY
in Strain UAMS-1 and in Strain Newman with Repaired
saeS
Authors: Luong Thanh T. , Sau Keya , Roux Christelle , Sau Subrata , Dunman Paul M. , Lee Chia Y.
Published: December 2010

ClpC is an ATPase chaperone found in most Gram-positive low-GC bacteria. It has been recently reported that ClpC affected virulence gene expression in
Staphylococcus aureus
. Here we report that ClpC regulates transcription of the
cap
operon and accumulation of capsule, a major virulence factor for
S. aureus
. As virulence genes are regulated by a complex regulatory network in
S. aureus
, we have used capsule as a model to understand this regulation. By microarray analyses of strain Newman, we found that ClpC strongly activates transcription of the
sae
operon, whose products are known to negatively regulate capsule synthesis in this strain. Further studies indicated that ClpC repressed capsule production by activating the
sae
operon in strain Newman. Interestingly, the
clpC
gene cloned into a multiple-copy plasmid vector exhibited an activation phenotype, suggesting that ClpC overexpression has a net positive effect. In the absence of
sae
function, by either deletion or correction of a native mutation within
saeS
, we found that ClpC had a positive effect on capsule production. Indeed, in the UAMS-1 strain, which does not have the
saeS
mutation, ClpC functioned as an activator of capsule production. Our microarray analyses of strain Newman also revealed that CodY, a repressor of capsule production, was repressed by ClpC. Using genetic approaches, we showed that CodY functioned downstream of ClpC, leading to capsule activation both in Newman and in UAMS-1. Thus, ClpC functions in two opposite pathways in capsule regulation in strain Newman but functions as a positive activator in strain UAMS-1.
Constitutive Expression of the Maltoporin LamB in the Absence of OmpR Damages the Cell Envelope
Authors: Reimann Sylvia A. , Wolfe Alan J.
Published: December 2010

Cells experience multiple environmental stimuli simultaneously. To survive, they must respond accordingly. Unfortunately, the proper response to one stress easily could make the cell more susceptible to a second coexistent stress. To deal with such a problem, a cell must possess a mechanism that balances the need to respond simultaneously to both stresses. Our recent studies ofompR malT(Con) double mutants show that elevated expression of LamB, the outer membrane porin responsible for maltose uptake, causes cell death when the osmoregulator OmpR is disabled. To obtain insight into the nature of the death experienced byompR malT(Con) mutants, we described the death process. On the basis of microscopic and biochemical approaches, we conclude that death results from a loss of membrane integrity. On the basis of an unbiased genome-wide search for suppressor mutations, we conclude that this loss of membrane integrity results from a LamB-induced envelope stress that the cells do not sufficiently perceive and thus do not adequately accommodate. Finally, we conclude that this envelope stress involves an imbalance in the lipopolysaccharide/porin composition of the outer membrane and an increased requirement for inorganic phosphate.
Bacillus anthracis sinLocus and Regulation of Secreted Proteases
Authors: Pflughoeft Kathryn J. , Sumby Paul , Koehler Theresa M.
Published: December 2010

Bacillus anthracisshares many regulatory loci with the nonpathogenicBacillusspeciesBacillus subtilis. One such locus issinIR, which inB. subtiliscontrols sporulation, biofilm formation, motility, and competency. AsB. anthracisis not known to be motile, to be naturally competent, or to readily form biofilms, we hypothesized that theB. anthracis sinIRregulon is distinct from that ofB. subtilis. A genome-wide expression microarray analysis ofB. anthracisparental andsinRmutant strains indicated limited convergence of theB. anthracisandB. subtilisSinR regulons. TheB. anthracisregulon includes homologues of someB. subtilisSinR-regulated genes, including the signal peptidase genesipWnear thesinIRlocus and the sporulation genespoIIE. TheB. anthracisSinR protein also negatively regulates transcription of genes adjacent to thesinIRlocus that are unique to theBacillus cereusgroup species. These includecalYandinhA1, structural genes for the metalloproteases camelysin and immune inhibitor A1 (InhA1), which have been suggested to be associated with virulence inB. cereusandB. anthracis, respectively. Electrophoretic mobility shift assays revealed direct binding ofB. anthracisSinR to promoter DNA from strongly regulated genes, such ascalYandsipW, but not to the weakly regulatedinhA1gene. Assessment of camelysin and InhA1 levels in culture supernates fromsinR-,inhA1-, andcalY-null mutants showed that the concentration of InhA1 in the culture supernatant is inversely proportional to the concentration of camelysin. Our data are consistent with a model in which InhA1 protease levels are controlled at the transcriptional level by SinR and at the posttranslational level by camelysin.
The SMC-Like Protein Complex SbcCD Enhances DNA Polymerase IV-Dependent Spontaneous Mutation inEscherichia coli
Authors: Storvik Kimberly A. M. , Foster Patricia L.
Published: December 2010

InEscherichia coli, RpoS, the general stress response sigma factor, regulates the activity of the specialized DNA polymerase DNA polymerase IV (Pol IV) both in stationary-phase and in exponential-phase cells. Because during exponential phasedinB, the gene encoding Pol IV, is transcribed independently of RpoS, RpoS must regulate Pol IV activity in growing cells indirectly via one or more intermediate factors. The results presented here show that one of these intermediate factors is SbcCD, an SMC-like protein and an ATP-dependent nuclease. By initiating or participating in double-strand break repair, SbcCD may provide DNA substrates for Pol IV polymerase activity.
Flavobacterium johnsoniae sprB
Is Part of an Operon Spanning the Additional Gliding Motility Genes
sprC
,
sprD
, and
sprF
Authors: Rhodes Ryan G. , Nelson Shawn S. , Pochiraju Soumya , McBride Mark J.
Published: December 2010

Cells of
Flavobacterium johnsoniae
move rapidly over surfaces by a process known as gliding motility. Gld proteins are thought to comprise the gliding motor that propels cell surface adhesins, such as the 669-kDa SprB. A novel protein secretion apparatus called the Por secretion system (PorSS) is required for assembly of SprB on the cell surface. Genetic and molecular analyses revealed that
sprB
is part of a seven-gene operon spanning 29.3 kbp of DNA. In addition to
sprB
, three other genes of this operon (
sprC
,
sprD
, and
sprF
) are involved in gliding. Mutations in
sprB
,
sprC
,
sprD
, and
sprF
resulted in cells that failed to form spreading colonies on agar but that exhibited some motility on glass in wet mounts. SprF exhibits some similarity to
Porphyromonas gingivalis
PorP, which is required for secretion of gingipain protease virulence factors via the
P. gingivalis
PorSS.
F. johnsoniae sprF
mutants produced SprB protein but were defective in localization of SprB to the cell surface, suggesting a role for SprF in secretion of SprB. The
F. johnsoniae
PorSS is involved in secretion of extracellular chitinase in addition to its role in secretion of SprB. SprF was not needed for chitinase secretion and may be specifically required for SprB secretion by the PorSS. Cells with nonpolar mutations in
sprC
or
sprD
produced and secreted SprB and propelled it rapidly along the cell surface. Multiple paralogs of
sprB
,
sprC
,
sprD
, and
sprF
are present in the genome, which may explain why mutations in
sprB
,
sprC
,
sprD
, and
sprF
do not result in complete loss of motility and suggests the possibility that semiredundant SprB-like adhesins may allow movement of cells over different surfaces.
Genome Sequence of an
Erwinia amylovora
Strain with Pathogenicity Restricted to
Rubus
Plants
Authors: Powney Rachel , Smits Theo H. M. , Sawbridge Tim , Frey Beatrice , Blom Jochen , Frey Jürg E. , Plummer Kim M. , Beer Steven V. , Luck Joanne , Duffy Brion , Rodoni Brendan
Published: December 2010

Here, we present the genome of a strain of
Erwinia amylovora
, the fire blight pathogen, with pathogenicity restricted to
Rubus
spp. Comparative genomics of ATCC BAA-2158 with
E. amylovora
strains from non-
Rubus
hosts identified significant genetic differences but support the inclusion of this strain within the species
E. amylovora.
Genome Sequence of
Leuconostoc gelidum
KCTC 3527, Isolated from Kimchi
Authors: Kim Dae-Soo , Choi Sang-Haeng , Kim Dong-Wook , Kim Ryong Nam , Nam Seong-Hyeuk , Kang Aram , Kim Aeri , Park Hong-Seog
Published: December 2010

Leuconostoc gelidum
KCTC 3527 is found mainly in vegetables and plays an important role in vegetable fermentation, including that of Korean traditional kimchi. Here we announce the draft genome sequence of
Leuconostoc gelidum
KCTC 3527, isolated from Korean traditional kimchi, and describe major findings from its annotation.
An efficient synthesis of 2-arylbenzothiazoles using silica sulfuric acid, oxalic acid and aluminum chloride hydrate as heterogeneous and homogeneous catalyst systems
Authors: Maleki Behrooz
Published: December 2010

A convenient method for the synthesis of 2-arylbenzothiazoles from condensation of aromatic/heteroaromatic aldehydes with 2-aminothiophenol has been developed using inexpensive, green and reusable solid acids – silica sulfuric acid (SSA), oxalic acid or AlCl3·6H2O as efficient catalysts. The reactions occurred under mild conditions to afford the corresponding 2-arylbenzothiazoles in good to excellent yields.
Should medicine assist a teenager to achieve a pregnancy?
Authors: Habiba Marwan
Published: December 2010

This article discusses a scenario of a teenager seeking medical assistance for infertility. Despite its apparent simplicity, the case poses a significant challenge to healthcare professionals. It requires consideration of maternal and child welfare and examination of the legitimate limits of doctors' role vis-à-vis the policy objective of reducing teenage pregnancy rate. The negative stereotypic representation of teenage pregnancy is an important confounding factor.
Choice is not the issue. The misrepresentation of healthcare in bioethical discourse
Authors: Agledahl Kari Milch , Førde Reidun , Wifstad Åge
Published: December 2010

The principle of respect for autonomy has shaped much of the bioethics' discourse over the last 50 years, and is now most commonly used in the meaning of respecting autonomous choice. This is probably related to the influential concept of informed consent, which originated in research ethics and was soon also applied to the field of clinical medicine. But while available choices in medical research are well defined, this is rarely the case in healthcare. Consideration of ordinary medical practice reveals that the focus on patient choice does not properly grasp the moral aspects involved in healthcare. Medical decisions are often portrayed as if doctors and patients in confidence confront specific decisions about examinations or treatment, yet the reality often involves many different participants, with decisions being made over time and space. Indeed, most of the decisions are never even presented to patients, as it would be unethical to suggest something that is not medically justifiable. The options patients do confront are somewhat arbitrarily constructed within the narrow framework of both what is deemed to be medically appropriate and how the healthcare system is organised practically. While the autonomy discourse has proven valuable, a failure to distinguish between the fields of medical research and clinical medicine has generated a focus on patient choice that does not reflect what is really at stake in healthcare settings. This is alarming, because the current discourse misrepresents medical practice in a way that actually contributes to bioethical self-delusion.
What sort of bioethical values are the evidence-based medicine and the GRADE approaches willing to deal with?
Authors: Watine Joseph
Published: December 2010

The concept of evidence-based medicine (EBM) has been invented by physicians mostly from English Canada, mostly from McMaster University, Ontario, Canada. The term EBM first appeared in the biomedical literature in 1991 in an article written by a prominent member of this group—Gordon Guyatt from McMaster University. The inventors of EBM have also created the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) working group, which is a prominent international organisation whose main purpose is to develop evidence-based clinical practice guidelines (CPGs). CPGs that are based on the GRADE approach are becoming increasingly adopted worldwide, in particular by many professional or governmental organisations. This group of thinkers being thus identified, we have retrieved and read many of their publications in order to try and understand how they intend to incorporate bioethical values into their concept. The author of this little essay did also spend a few years on the internet as an active member of the GRADE group discussion list. The observations thus gathered suggest that although some of the inventors of EBM, at least Gordon Guyatt, wish to incorporate core principles of biomedical ethics into their concept (ie, non-malevolence, beneficence and maybe to a lesser extent respect for autonomy, and justice), some clarifications are still necessary in order to better understand how they intend to more explicitly incorporate bioethical values into their concept and, perhaps more importantly, into evidence-based CPGs.