bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sulfate-Driven Elemental Sparing Is Regulated at the Transcriptional and Posttranscriptional Levels in a Filamentous Cyanobacterium
Authors: Gutu Andrian , Alvey Richard M. , Bashour Sami , Zingg Daniel , Kehoe David M. 
Published: January 2011

ABSTRACT

Sulfur is an essential nutrient that can exist at growth-limiting concentrations in freshwater environments. The freshwater cyanobacterium
Fremyella diplosiphon
(also known as
Tolypothrix
sp. PCC 7601) is capable of remodeling the composition of its light-harvesting antennae, or phycobilisomes, in response to changes in the sulfur levels in its environment. Depletion of sulfur causes these cells to cease the accumulation of two forms of a major phycobilisome protein called phycocyanin and initiate the production of a third form of phycocyanin, which possesses a minimal number of sulfur-containing amino acids. Since phycobilisomes make up approximately 50% of the total protein in these cells, this elemental sparing response has the potential to significantly influence the fitness of this species under low-sulfur conditions. This response is specific for sulfate and occurs over the physiological range of sulfate concentrations likely to be encountered by this organism in its natural environment.
F. diplosiphon
has two separate sulfur deprivation responses, with low sulfate levels activating the phycobilisome remodeling response and low sulfur levels activating the chlorosis or bleaching response. The phycobilisome remodeling response results from changes in RNA abundance that are regulated at both the transcriptional and posttranscriptional levels. The potential of this response, and the more general bleaching response of cyanobacteria, to provide sulfur-containing amino acids during periods of sulfur deprivation is examined.
Two DNA Translocases Synergistically Affect Chromosome Dimer Resolution inBacillus subtilis
Authors: Kaimer Christine , Schenk Katrin , Graumann Peter L. 
Published: January 2011

ABSTRACTInBacillus subtilis, chromosome dimers that block complete segregation of sister chromosomes arise in about 15% of exponentially growing cells. Two dedicated recombinases, RipX and CodV, catalyze the resolution of dimers by site-specific recombination at thedifsite, which is located close to the terminus region on the chromosome. We show that the two DNA translocases inB. subtilis, SftA and SpoIIIE, synergistically affect dimer resolution, presumably by positioning thedifsites in close proximity, before or after completion of cell division, respectively. Furthermore, we observed that both recombinases, RipX and CodV, assemble on the chromosome at thedifsite throughout the cell cycle. The preassembly of recombinases probably ensures that dimer resolution can occur rapidly within a short time window around cell division.
Core and Panmetabolism in
Escherichia coli
Authors: Vieira Gilles , Sabarly Victor , Bourguignon Pierre-Yves , Durot Maxime , Le Fèvre François , Mornico Damien , Vallenet David , Bouvet Odile , Denamur Erick , Schachter Vincent , Médigue Claudine 
Published: January 2011

ABSTRACT

Escherichia coli
exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of
E. coli
strains remains, however, largely unknown. Following a previous study of
E. coli
genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genome-scale metabolic networks of 29
E. coli
strains (8 commensal and 21 pathogenic strains, including 6
Shigella
strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming
E. coli
panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the
E. coli
pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow
E. coli
phylogeny rather than pathogenic phenotypes, except for
Shigella
networks, which were significantly more distant from the others. This suggests that most metabolic changes in non-
Shigella
strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.
Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose bySulfolobus acidocaldarius
Authors: Joshua Chijioke J. , Dahl Robert , Benke Peter I. , Keasling Jay D. 
Published: January 2011

ABSTRACTSulfolobus acidocaldariusutilizes glucose and xylose as sole carbon sources, but its ability to metabolize these sugars simultaneously is not known. We report the absence of diauxie during growth ofS. acidocaldariuson glucose and xylose as co-carbon sources. The presence of glucose did not repress xylose utilization. The organism utilized a mixture of 1 g/liter of each sugar simultaneously with a specific growth rate of 0.079 h−1and showed no preference for the order in which it utilized each sugar. The organism grew faster on 2 g/liter xylose (0.074 h−1) as the sole carbon source than on an equal amount of glucose (0.022 h−1). When grown on a mixture of the two carbon sources, the growth rate of the organism increased from 0.052 h−1to 0.085 h−1as the ratio of xylose to glucose increased from 0.25 to 4.S. acidocaldariusappeared to utilize a mixture of glucose and xylose at a rate roughly proportional to their concentrations in the medium, resulting in complete utilization of both sugars at about the same time. Gene expression in cells grown on xylose alone was very similar to that in cells grown on a mixture of xylose and glucose and substantially different from that in cells grown on glucose alone. The mechanism by which the organism utilized a mixture of sugars has yet to be elucidated.
The
Escherichia coli
K-12 MntR Miniregulon Includes
dps
, Which Encodes the Major Stationary-Phase DNA-Binding Protein
Authors: Yamamoto Kaneyoshi , Ishihama Akira , Busby Stephen J. W. , Grainger David C. 
Published: January 2011

ABSTRACT

Escherichia coli
MntR protein is the Mn
2+
-responsive transcriptional repressor of the MntH manganese transporter. We have used chromatin immunoprecipitation to determine the distribution of Mn
2+
-MntR across the entire
E. coli
chromosome
in vivo
, and we report that MntR binds to only four targets, adjacent to the
mntH
,
mntR
,
yebN
, and
dps
genes. Unexpectedly, we found that
dps
expression is directly repressed by Mn
2+
-MntR.
Effects of Metal on the Biochemical Properties of
Helicobacter pylori
HypB, a Maturation Factor of [NiFe]-Hydrogenase and Urease
Authors: Sydor Andrew M. , Liu Jenny , Zamble Deborah B. 
Published: January 2011

ABSTRACT

The biosyntheses of the [NiFe]-hydrogenase and urease enzymes in
Helicobacter pylori
require several accessory proteins for proper construction of the nickel-containing metallocenters. The hydrogenase accessory proteins HypA and HypB, a GTPase, have been implicated in the nickel delivery steps of both enzymes. In this study, the metal-binding properties of
H. pylori
HypB were characterized, and the effects of metal binding on the biochemical behavior of the protein were examined. The protein can bind stoichiometric amounts of Zn(II) or Ni(II), each with nanomolar affinity. Mutation of Cys106 and His107, which are located between two major GTPase motifs, results in undetectable Ni(II) binding, and the Zn(II) affinity is weakened by 2 orders of magnitude. These two residues are also required for the metal-dependent dimerization observed in the presence of Ni(II) but not Zn(II). The addition of metals to the protein has distinct impacts on GTPase activity, with zinc significantly reducing GTP hydrolysis to below detectable levels and nickel only slightly altering the
k
cat
and

K
m

of the reaction. The regulation of HypB activities by metal binding may contribute to the maturation of the nickel-containing enzymes.
The Sporulation Protein SirA Inhibits the Binding of DnaA to the Origin of Replication by Contacting a Patch of Clustered Amino Acids
Authors: Rahn-Lee Lilah , Merrikh Houra , Grossman Alan D. , Losick Richard 
Published: January 2011

ABSTRACT

Bacteria regulate the frequency and timing of DNA replication initiation by controlling the activity of the replication initiator protein DnaA. SirA is a recently discovered regulator of DnaA in
Bacillus subtilis
whose synthesis is turned on at the start of sporulation. Here, we demonstrate that SirA contacts DnaA at a patch of 3 residues located on the surface of domain I of the replication initiator protein, corresponding to the binding site used by two unrelated regulators of DnaA found in other bacteria. We show that the interaction of SirA with domain I inhibits the ability of DnaA to bind to the origin of replication. DnaA mutants containing amino acid substitutions of the 3 residues are functional in replication initiation but are immune to inhibition by SirA.
Structural and Mechanical Properties ofKlebsiella pneumoniaeType 3 Fimbriae
Authors: Chen Feng-Jung , Chan Chia-Han , Huang Ying-Jung , Liu Kuo-Liang , Peng Hwei-Ling , Chang Hwan-You , Liou Gunn-Guang , Yew Tri-Rung , Liu Cheng-Hsien , Hsu Ken Y. , Hsu Long 
Published: January 2011

ABSTRACTThis study investigated the structural and mechanical properties ofKlebsiella pneumoniaetype 3 fimbriae, which constitute a known virulence factor for the bacterium. Transmission electron microscopy and optical tweezers were used to understand the ability of the bacterium to survive flushes. An individualK. pneumoniaetype 3 fimbria exhibited a helix-like structure with a pitch of 4.1 nm and a three-phase force-extension curve. The fimbria was first nonlinearly stretched with increasing force. Then, it started to uncoil and extended several micrometers at a fixed force of 66 ± 4 pN (n= 22). Finally, the extension of the fimbria shifted to the third phase, with a characteristic force of 102 ± 9 pN (n= 14) at the inflection point. Compared with the P fimbriae and type 1 fimbriae of uropathogenicEscherichia coli,K. pneumoniaetype 3 fimbriae have a larger pitch in the helix-like structure and stronger uncoiling and characteristic forces.
Gene Expression Profiling of
Corynebacterium glutamicum
during Anaerobic Nitrate Respiration: Induction of the SOS Response for Cell Survival
Authors: Nishimura Taku , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki 
Published: January 2011

ABSTRACT

The gene expression profile of
Corynebacterium glutamicum
under anaerobic nitrate respiration revealed marked differences in the expression levels of a number of genes involved in a variety of cellular functions, including carbon metabolism and respiratory electron transport chain, compared to the profile under aerobic conditions using DNA microarrays. Many SOS genes were upregulated by the shift from aerobic to anaerobic nitrate respiration. An elongated cell morphology, similar to that induced by the DivS-mediated suppression of cell division upon cell exposure to the DNA-damaging reagent mitomycin C, was observed in cells subjected to anaerobic nitrate respiration. None of these transcriptional and morphological differences were observed in a
recA
mutant strain lacking a functional RecA regulator of the SOS response. The
recA
mutant cells additionally showed significantly reduced viability compared to wild-type cells similarly grown under anaerobic nitrate respiration. These results suggest a role for the RecA-mediated SOS response in the ability of cells to survive any DNA damage that may result from anaerobic nitrate respiration in
C. glutamicum
.
Genetic Analysis of the Protein Shell of the Microcompartments Involved in Coenzyme B12-Dependent 1,2-Propanediol Degradation bySalmonella
Authors: Cheng Shouqiang , Sinha Sharmistha , Fan Chenguang , Liu Yu , Bobik Thomas A. 
Published: January 2011

ABSTRACTHundreds of bacterial species use microcompartments (MCPs) to optimize metabolic pathways that have toxic or volatile intermediates. MCPs consist of a protein shell encapsulating specific metabolic enzymes. InSalmonella, an MCP is used for 1,2-propanediol utilization (Pdu MCP). The shell of this MCP is composed of eight different types of polypeptides, but their specific functions are uncertain. Here, we individually deleted the eight genes encoding the shell proteins of the Pdu MCP. The effects of each mutation on 1,2-PD degradation and MCP structure were determined by electron microscopy and growth studies. Deletion of thepduBB′,pduJ, orpduNgene severely impaired MCP formation, and the observed defects were consistent with roles as facet, edge, or vertex protein, respectively. Metabolite measurements showed thatpduA,pduBB′,pduJ, orpduNdeletion mutants accumulated propionaldehyde to toxic levels during 1,2-PD catabolism, indicating that the integrity of the shell was disrupted. Deletion of thepduK,pduT, orpduUgene did not substantially affect MCP structure or propionaldehyde accumulation, suggesting they are nonessential to MCP formation. However, thepduUorpduTdeletion mutants grew more slowly than the wild type on 1,2-PD at saturating B12, indicating that they are needed for maximal activity of the 1,2-PD degradative enzymes encased within the MCP shell. Considering recent crystallography studies, this suggests that PduT and PduU may mediate the transport of enzyme substrates/cofactors across the MCP shell. Interestingly, apduKdeletion caused MCP aggregation, suggesting a role in the spatial organization of MCP within the cytoplasm or perhaps in segregation at cell division.
The HIF-1–Inducible Lysyl Oxidase Activates HIF-1 via the Akt Pathway in a Positive Regulation Loop and Synergizes with HIF-1 in Promoting Tumor Cell Growth
Authors: Pez Floriane , Dayan Frédéric , Durivault Jérome , Kaniewski Bastien , Aimond Géraldine , Le Provost Gabrielle S. , Deux Blandine , Clézardin Philippe , Sommer Pascal , Pouysségur Jacques , Reynaud Caroline 
Published: January 2011

AbstractAdaptation to hypoxia is a driving force for tumor progression that leads to therapy resistance and poor clinical outcome. Hypoxic responses are mainly mediated by hypoxia-inducible transcription factor-1 (HIF-1). One critical HIF-1 target mediating tumor progression is lysyl oxidase (LOX), which catalyzes cross-linking of collagens and elastin in the extracellular matrix, thereby regulating tissue tensile strength. Paradoxically, LOX has been reported to be both upregulated and downregulated in cancer cells, especially in colorectal cancer. Thus, we hypothesized that LOX might regulate expression of HIF-1 to create a self-timing regulatory circuit. Using human colorectal carcinoma cell lines in which HIF-1 and LOX expression could be modulated, we showed that LOX induction enhanced HIF-1 expression, whereas LOX silencing reduced it. Mechanistic investigations revealed that LOX activated the PI3K (phosphoinositide 3-kinase)–Akt signaling pathway, thereby upregulating HIF-1α protein synthesis in a manner requiring LOX-mediated hydrogen peroxide production. Consistent with these results, cancer cell proliferation was stimulated by secreted and active LOX in an HIF-1α–dependent fashion. Furthermore, nude mice xenograft assays established that HIF-1 potentiated LOX action on tumor growth in vivo. Taken together, these findings provide compelling evidence that LOX and HIF-1 act in synergy to foster tumor formation, and they suggest that HIF-1/LOX mutual regulation is a pivotal mechanism in the adaptation of tumor cells to hypoxia. Cancer Res; 71(5); 1647–57. ©2011 AACR.
Eddy and Wind-Forced Heat Transports in the Gulf of Mexico
Authors: Chang Y-L. , Oey L-Y. 
Published: January 2011

Abstract
The Gulf of Mexico (GOM) receives heat from the Caribbean Sea via the Yucatan–Loop Current (LC) system, and the corresponding ocean heat content (OHC) is important to weather and climate of the continental United States. However, the mechanisms that affect this heat influx and how it is distributed in the Gulf have not been studied. Using the Princeton Ocean Model, the authors show that a steady, uniform westward wind in the Gulf increases (∼100 KJ cm−2) the upper OHC (temperature T &gt; 18°C) of the Gulf. This is because wind increases the water exchange between the Gulf and the Caribbean Sea, and the heat input into the Gulf is also increased, by about 50 TW. The westward heat transport to the western Gulf is ∼30 TW, and a substantial portion of this is due to wind-induced shelf currents, which converge to produce downwelling near the western coast. Finally, eddies are effective transporters of heat across the central Gulf. Wind forces larger LC and rings with deeper isotherms. This and downfront-wind mixing on the southern side of anticyclonic rings, northward spread of near-zero potential vorticity waters, and downwelling on the northern shelf break result in wide and deep eddies that transport large OHCs across the Gulf.
L’application de la spiritualité bénédictine au loisir des personnes âgées : un modèle théorique du bonheur spirituel
Authors: Ouellette Pierre , Snyder Patrick , Carette Raymond 
Published: January 2011

Le but de cette réflexion théologique est de montrer, à l’aide d’un modèle théorique, comment l’application de la spiritualité bénédictine au loisir des personnes âgées peut favoriser le bonheur spirituel. L’analyse s’est articulée notamment autour d’un syllogisme. Le cœur de la spiritualité bénédictine est la contemplation. Or, les personnes âgées sont tout naturellement disposées à la réminiscence, à l’introspection et à la contemplation. Donc, la spiritualité bénédictine convient particulièrement au loisir des personnes âgées. Quatre valeurs bénédictines ont été retenues, à savoir la fraternité, la modération, l’hospitalité et l’humilité. Dans le modèle, la spiritualité bénédictine est reliée à la contemplation, à l’union avec Dieu et au bonheur spirituel. Par ailleurs, la spiritualité bénédictine, le loisir contemplatif et les personnes âgées sont interreliés; en plus, les personnes âgées et le loisir contemplatif sont directement reliés à la contemplation. Bref, il s’agissait de jeter un regard bénédictin sur le loisir, le vieillissement et le bonheur. The purpose of this theological reflection is the application of Benedictine spirituality to the leisure of older people. Based on a syllogism, it presupposes that the heart of Benedictine spirituality is contemplation. Hence, older people are predisposed to reminiscence, introspection and contemplation. Therefore, Benedictine spirituality is particularly appropriate for the leisure of older people. Four Benedictine values were selected namely fraternity, moderation, hospitality and humility. Also in a proposed theoretical model, Benedictine spirituality is related to contemplation, union with God and spiritual happiness. Furthermore, Benedictine spirituality, contemplative leisure and older people are all interrelated while older people and contemplation are directly related to contemplation. Essentially, this paper aimed at providing a monastic outlook on happiness, aging and contemplative leisure.
Expectations about and impact of the Liverpool Care Pathway for the dying patient in an Italian hospital
Authors: Di Leo Silvia , Beccaro Monica , Finelli Stefania , Borreani Claudia , Costantini Massimo 
Published: January 2011

This study is aimed at exploring the expectations about and the impact on healthcare staff of the Liverpool Care Pathway for the dying patient (LCP) in an Italian hospital. Qualitative information was derived from four focus group (FG) meetings that were carried out separately by profession and scheduled before the beginning and after the end of the implementation process of the Italian version of LCP for hospitals (LCP-I). Interview topics concerned end-of-life care related problems and expectations about the impact of the LCP-I programme. Tape recordings of the FGs were transcribed verbatim, and transcripts analysed independently by two research psychologists using thematic analysis. Five major topics were identified: managing pain and discontinuing inappropriate treatments, communicating with patients, communicating with relatives, communicating between professionals and practical issues. As compared with those reported in the initial FGs, responses from the final FGs highlighted that physicians felt more confident with pain management and with discontinuing inappropriate treatment, and were more inclined to recognize the value of the nurses’ work. Nurses underlined advantages in using pro re nata medication, but stressed lack of personnel and time as obstacles in consistent improvement of end-of-life care. All participants seemed to acquire greater awareness of their difficulties in communication and, paradoxically, became more uncertain of their ability to liaise with dying patients and their families. LCP-I implementation may improve both knowledge about physical symptom management and professional awareness of the problems related to emotional and informative support in end-of-life care.
Proteinase-activated receptor 2 activation promotes an anti-inflammatory and alternatively activated phenotype in LPS-stimulated murine macrophages
Authors: Nhu Quan M , Shirey Kari Ann , Pennini Meghan E , Stiltz Jennifer , Vogel Stefanie N 
Published: January 2011

Proteinase-activated receptor 2 (PAR2), a 7-transmembrane G protein-coupled receptor, contributes to inflammation either positively or negatively in different experimental systems. Previously, we reported that concurrent activation of PAR2 and TLRs in human lung and colonic epithelial cells resulted in a synergistic increase in NF-κB-mediated gene expression, but a down-regulation of IRF-3-mediated gene expression. In this study, the effect of PAR2 activation on LPS-induced TLR4 signaling was examined in primary murine macrophages. The PAR2 activation of wild-type macrophages enhanced LPS-induced expression of the anti-inflammatory cytokine, IL-10, while suppressing gene expression of pro-inflammatory cytokines, TNF-α, IL-6, and IL-12. Similar PAR2-mediated effects on LPS-stimulated IL-10 and IL-12 mRNA were also observed in vivo. In contrast, [Formula: see text] macrophages exhibited diminished LPS-induced IL-10 mRNA and protein expression and downstream STAT3 activation, but increased KC mRNA and protein. PAR2 activation also enhanced both rIL-4- and LPS-induced secretion of IL-4 and IL-13, and mRNA expression of alternatively activated macrophage (AA-Mϕ) markers, e.g. arginase-1, mannose receptor, Ym-1. Thus, in the context of a potent inflammatory stimulus like LPS, PAR2 activation acts to re-establish tissue homeostasis by dampening the production of inflammatory mediators and causing the differentiation of macrophages that may contribute to the development of a Th2 response.