bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT 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

summaryClimate Change and Hunger: Africa’s Smallholder Farmers Struggle to AdaptFarmers 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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTYersinia 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.