bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupled Ferredoxin and Crotonyl Coenzyme A (CoA) Reduction with NADH Catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from
Clostridium kluyveri
Authors: Li Fuli , Hinderberger Julia , Seedorf Henning , Zhang Jin , Buckel Wolfgang , Thauer Rudolf K. 
Published: November 2007

ABSTRACT

Cell extracts of butyrate-forming clostridia have been shown to catalyze acetyl-coenzyme A (acetyl-CoA)- and ferredoxin-dependent formation of H
2
from NADH. It has been proposed that these bacteria contain an NADH:ferredoxin oxidoreductase which is allosterically regulated by acetyl-CoA. We report here that ferredoxin reduction with NADH in cell extracts from
Clostridium kluyveri
is catalyzed by the butyryl-CoA dehydrogenase/Etf complex and that the acetyl-CoA dependence previously observed is due to the fact that the cell extracts catalyze the reduction of acetyl-CoA with NADH via crotonyl-CoA to butyryl-CoA. The cytoplasmic butyryl-CoA dehydrogenase complex was purified and is shown to couple the endergonic reduction of ferredoxin (E
0
′ = −410 mV) with NADH (E
0
′ = −320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (E
0
′ = −10 mV) with NADH. The stoichiometry of the fully coupled reaction is extrapolated to be as follows: 2 NADH + 1 oxidized ferredoxin + 1 crotonyl-CoA = 2 NAD
+
+ 1 ferredoxin reduced by two electrons + 1 butyryl-CoA. The implications of this finding for the energy metabolism of butyrate-forming anaerobes are discussed in the accompanying paper.
Linking Ultrastructure and Function in Four Genera of Anaerobic Ammonium-Oxidizing Bacteria: Cell Plan, Glycogen Storage, and Localization of Cytochrome
c
Proteins
Authors: van Niftrik Laura , Geerts Willie J. C. , van Donselaar Elly G. , Humbel Bruno M. , Webb Richard I. , Fuerst John A. , Verkleij Arie J. , Jetten Mike S. M. , Strous Marc 
Published: November 2007

ABSTRACT

Anaerobic ammonium oxidation (anammox) is an ecologically and industrially important process and is performed by a clade of deeply branching
Planctomycetes
. Anammox bacteria possess an intracytoplasmic membrane-bounded organelle, the anammoxosome. In the present study, the ultrastructures of four different genera of anammox bacteria were compared with transmission electron microscopy and electron tomography. The four anammox genera shared a common cell plan and contained glycogen granules. Differences between the four genera included cell size (from 800 to 1,100 nm in diameter), presence or absence of cytoplasmic particles, and presence or absence of pilus-like appendages. Furthermore, cytochrome
c
proteins were detected exclusively inside the anammoxosome. This detection provides further support for the hypothesis that this organelle is the locus of anammox catabolism.
Role of Hypermutability in the Evolution of the GenusOenococcus
Authors: Marcobal Angela M. , Sela David A. , Wolf Yuri I. , Makarova Kira S. , Mills David A. 
Published: November 2007

ABSTRACTOenococcus oeniis an alcohol-tolerant, acidophilic lactic acid bacterium primarily responsible for malolactic fermentation in wine. A recent comparative genomic analysis ofO. oeniPSU-1 with other sequenced lactic acid bacteria indicates that PSU-1 lacks the mismatch repair (MMR) genesmutSandmutL. Consistent with the lack of MMR, mutation rates forO. oeniPSU-1 and a second oenococcal species,O. kitaharae, were higher than those observed for neighboring taxa,Pediococcus pentosaceusandLeuconostoc mesenteroides. Sequence analysis of therpoBmutations in rifampin-resistant strains from both oenococcal species revealed a high percentage of transition mutations, a result indicative of the lack of MMR. An analysis of common alleles in the two sequencedO. oenistrains, PSU-1 and BAA-1163, also revealed a significantly higher level of transition substitutions than were observed in otherLactobacillalesspecies. These results suggest that the genusOenococcusis hypermutable due to the loss ofmutSandmutL, which occurred with the divergence away from the neighboringLeuconostocbranch. The hypermutable status of the genusOenococcusexplains the observed high level of allelic polymorphism among knownO. oeniisolates and likely contributed to the unique adaptation of this genus to acidic and alcoholic environments.
Vibrio parahaemolyticusScrC Modulates Cyclic Dimeric GMP Regulation of Gene Expression Relevant to Growth on Surfaces
Authors: Ferreira Rosana B. R. , Antunes Luis Caetano M. , Greenberg E. Peter , McCarter Linda L. 
Published: November 2007

ABSTRACTInVibrio parahaemolyticus,scrCparticipates in controlling the decision to be a highly mobile swarmer cell or a more adhesive, biofilm-proficient cell type.scrCmutants display decreased swarming motility over surfaces and enhanced capsular polysaccharide production. ScrC is a cytoplasmic membrane protein that contains both GGDEF and EAL conserved protein domains. These domains have been shown in many organisms to respectively control the formation and degradation of the small signaling nucleotide cyclic dimeric GMP (c-di-GMP). ThescrCgene is part of the three-genescrABCoperon. Here we report that this operon influences the cellular nucleotide pool and that c-di-GMP levels inversely modulate lateral flagellar and capsular polysaccharide gene expression. High concentrations of this nucleotide prevent swarming and promote adhesiveness. Further, we demonstrate that ScrC has intrinsic diguanylate cyclase and phosphodiesterase activities, and these activities are controlled by ScrAB. Specifically, ScrC acts to form c-di-GMP in the absence of ScrA and ScrB; whereas ScrC acts to degrade c-di-GMP in the presence of ScrA and ScrB. ThescrABCoperon is specifically induced by growth on a surface, and the analysis of mutant phenotypes supports a model in which the phosphodiesterase activity of ScrC plays a dominant role during surface translocation and in biofilms.
Characterization of the CopR Regulon ofLactococcus lactisIL1403
Authors: Magnani David , Barré Olivier , Gerber Simon D. , Solioz Marc 
Published: November 2007

ABSTRACTTo identify components of the copper homeostatic mechanism ofLactococcus lactis, we employed two-dimensional gel electrophoresis to detect changes in the proteome in response to copper. Three proteins upregulated by copper were identified: glyoxylase I (YaiA), a nitroreductase (YtjD), and lactate oxidase (LctO). The promoter regions of these genes featurecopboxes of consensus TACAnnTGTA, which are the binding site of CopY-type copper-responsive repressors. A genome-wide search forcopboxes revealed 28 such sequence motifs. They were tested by electrophoretic mobility shift assays for the interaction with purified CopR, the CopY-type repressor ofL. lactis. Seven of thecopboxes interacted with CopR in a copper-sensitive manner. They were present in the promoter region of five genes,lctO, ytjD, copB, ydiD, andyahC; and two polycistronic operons,yahCD-yaiABandcopRZA. Induction of these genes by copper was confirmed by real-time quantitative PCR. ThecopRZAoperon encodes the CopR repressor of the regulon; a copper chaperone, CopZ; and a putative copper ATPase, CopA. When expressed inEscherichia coli, thecopRZAoperon conferred copper resistance, suggesting that it functions in copper export from the cytoplasm. Other member genes of the CopR regulon may similarly be involved in copper metabolism.
Bioinformatics and Experimental Analysis of Proteins of Two-Component Systems in
Myxococcus xanthus
Authors: Shi Xingqi , Wegener-Feldbrügge Sigrun , Huntley Stuart , Hamann Nils , Hedderich Reiner , Søgaard-Andersen Lotte 
Published: November 2007

ABSTRACT

Proteins of two-component systems (TCS) have essential functions in the sensing of external and self-generated signals in bacteria and in the generation of appropriate output responses. Accordingly, in
Myxococcus xanthus
, TCS are important for normal motility and fruiting body formation and sporulation. Here we analyzed the
M. xanthus
genome for the presence and genetic organization of genes encoding TCS. Two hundred seventy-two TCS genes were identified, 251 of which are not part of
che
gene clusters. We report that the TCS genes are unusually organized, with 55% being orphan and 16% in complex gene clusters whereas only 29% display the standard paired gene organization. Hybrid histidine protein kinases and histidine protein kinases predicted to be localized to the cytoplasm are overrepresented among proteins encoded by orphan genes or in complex gene clusters. Similarly, response regulators without output domains are overrepresented among proteins encoded by orphan genes or in complex gene clusters. The most frequently occurring output domains in response regulators are involved in DNA binding and cyclic-di-GMP metabolism. Our analyses suggest that TCS encoded by orphan genes and complex gene clusters are functionally distinct from TCS encoded by paired genes and that the connectivity of the pathways made up of TCS encoded by orphan genes and complex gene clusters is different from that of pathways involving TCS encoded by paired genes. Experimentally, we observed that orphan TCS genes are overrepresented among genes that display altered transcription during fruiting body formation. The systematic analysis of the 25 orphan genes encoding histidine protein kinases that are transcriptionally up-regulated during development showed that 2 such genes are likely essential for viability and identified 7 histidine protein kinases, including 4 not previously characterized that have important function in fruiting body formation or spore germination.
Niche-Specific Features of the Intestinal
Bacteroidales
Authors: Coyne Michael J. , Comstock Laurie E. 
Published: November 2007

ABSTRACT

By analyzing the genomic sequences of 12
Bacteroidales
species, we found that all intestinal species have numerous polysaccharide biosynthesis loci, many with promoters that we demonstrate undergo DNA inversion. This feature is not conserved in the
Bacteroidales
order as a whole, as oral species do not share these genetic features.
Massetolide A Biosynthesis inPseudomonas fluorescens
Authors: de Bruijn I. , de Kock M. J. D. , de Waard P. , van Beek T. A. , Raaijmakers J. M. 
Published: November 2007

ABSTRACTMassetolide A is a cyclic lipopeptide (CLP) antibiotic produced by variousPseudomonasstrains from diverse environments. Cloning, sequencing, site-directed mutagenesis, and complementation showed that massetolide A biosynthesis inP. fluorescensSS101 is governed by three nonribosomal peptide synthetase (NRPS) genes, designatedmassA,massB, andmassC, spanning approximately 30 kb. Prediction of the nature and configuration of the amino acids by in silico analysis of adenylation and condensation domains of the NRPSs was consistent with the chemically determined structure of the peptide moiety of massetolide A. Structural analysis of massetolide A derivatives produced by SS101 indicated that most of the variations in the peptide moiety occur at amino acid positions 4 and 9. Regions flanking themassgenes contained several genes found in otherPseudomonasCLP biosynthesis clusters, which encode LuxR-type transcriptional regulators, ABC transporters, and an RND-like outer membrane protein. In contrast to mostPseudomonasCLP gene clusters known to date, themassgenes are not physically linked but are organized in two separate clusters, withmassAdisconnected frommassBandmassC. Quantitative real-time PCR analysis indicated that transcription ofmassCis strongly reduced whenmassBis mutated, suggesting that these two genes function in an operon, whereas transcription ofmassAis independent ofmassBCand vice versa. Massetolide A is produced in the early exponential growth phase, and biosynthesis appears not to be regulated byN-acylhomoserine lactone-based quorum sensing. Massetolide A production is essential in swarming motility ofP. fluorescensSS101 and plays an important role in biofilm formation.
Do female frogs exploit inadvertent social information to locate breeding aggregations?
Authors: Swanson E.M. , Tekmen S.M. , Bee M.A. 
Published: November 2007

The advertisement calls of male anurans (frogs and toads) are loud and conspicuous signals, and the sound generated by breeding aggregations of males propagates over long distances. As a by-product of communication within an aggregation, the sounds of a frog chorus constitute a form of inadvertent social information that provides potential long-distance cues about the location and timing of breeding. We investigated whether female American toads ( Bufo americanus Holbrook, 1836) and Cope’s gray treefrogs ( Hyla chrysoscelis Cope, 1880) use the sounds of a chorus to locate breeding aggregations in the absence of other sensory cues. Females of both species approached speakers broadcasting recordings of a chorus made from distances of 0, 20, and 40 m, but not from distances of 80 and 160 m. Female toads also exhibited phonotaxis to a completely artificial chorus sound, but female gray treefrogs did not. We found little evidence to suggest that female American toads and Cope’s gray treefrogs differed substantially in their responses to natural chorus sounds despite potential differences in the predictability and duration of breeding seasons in these two species. Our results suggest that the inadvertent social information of a chorus could be used over short distances to locate breeding aggregations.
VARIATION OF THE FUNDAMENTAL CONSTANTS: THEORY AND OBSERVATIONS
Authors: FLAMBAUM V. V. 
Published: November 2007

Review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses (Higgs vacuum) is presented. The results from Big Bang nucleosynthesis, quasar absorption spectra, and Oklo natural nuclear reactor data give us the space-time variation on the Universe lifetime scale. Comparison of different atomic clocks gives us the present time variation. Assuming linear variation with time we can compare different results. The best limit on the variation of the electron-to-proton mass ratio μ = me/Mp and Xe = me/ΛQCD follows from the quasar absorption spectra:1[Formula: see text]. A combination of this result and the atomic clock results2,3 gives the best limt on variation of [Formula: see text]. The Oklo natural reactor gives the best limit on the variation of Xs = ms/ΛQCD where ms is the strange quark mass:4,5[Formula: see text]. Note that the Oklo data can not give us any limit on the variation of α since the effect of α there is much smaller than the effect of Xs and should be neglected. Huge enhancement of the relative variation effects happens in transitions between close atomic, molecular and nuclear energy levels. We suggest several new cases where the levels are very narrow. Large enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance. How changing physical constants and violation of local position invariance may occur? Light scalar fields very naturally appear in modern cosmological models, affecting parameters of the Standard Model (e.g. α). Cosmological variations of these scalar fields should occur because of drastic changes of matter composition in Universe: the latest such event is rather recent (about 5 billion years ago), from matter to dark energy domination. Massive bodies (stars or galaxies) can also affect physical constants. They have large scalar charge S proportional to number of particles which produces a Coulomb-like scalar field U = S/r. This leads to a variation of the fundamental constants proportional to the gravitational potential, e.g. δα/α = kαδ(GM/rc2). We compare different manifestations of this effect. The strongest limits6kα + 0.17ke = (-3.5 ±6) × 10-7 and kα + 0.13kq = (-1 ± 17) × 10-7 are obtained from the measurements of dependence of atomic frequencies on the distance from Sun2,7 (the distance varies due to the ellipticity of the Earth's orbit).
PRECISE VORONOI CELL EXTRACTION OF FREE-FORM PLANAR PIECEWISE C1-CONTINUOUS CLOSED RATIONAL CURVES
Authors: HANNIEL I. , RAMANATHAN M. , ELBER G. , KIM M. -S. 
Published: November 2007

We present an algorithm for generating Voronoi cells for a set of planar piecewise C1-continuous closed rational curves, which is precise up to machine precision. The algorithm starts with the symbolically generated bisectors for pairs of C1-continuous curve segments (C(t),Ci(r)). The bisectors are represented implicitly in the tr-parameter space. Then, they are properly trimmed after being split into monotone pieces. The trimming procedure uses the orientation of the original curves as well as their curvature fields, resulting in a set of trimmed-bisector segments represented as implicit curves in a parameter space. A lower-envelope algorithm is then used in the parameter space of the curve whose Voronoi cell is sought. The lower envelope represents the exact boundary of the Voronoi cell. The algorithm also supports piecewise C1-continuous curves and generates the Voronoi cell of such input curves using additional point/curve bisector segments.
P2Y receptor signaling regulates phenotype and IFN-α secretion of human plasmacytoid dendritic cells
Authors: Shin Amanda , Toy Tracey , Rothenfusser Simon , Robson Neil , Vorac Julia , Dauer Marc , Stuplich Moritz , Endres Stefan , Cebon Jonathan , Maraskovsky Eugene , Schnurr Max 
Published: November 2007

AbstractPlasmacytoid dendritic cells (PDCs) play powerful regulatory roles in innate and adaptive immune responses and are a major source of type I interferon (IFN) following viral infection. During inflammation and mechanical stress, cells release nucleotides into the extracellular space where they act as signaling molecules via G protein–coupled P2Y receptors. We have previously reported on the regulation of myeloid dendritic cell (DC) function by nucleotides. Here, we report that human PDCs express several subtypes of P2Y receptors and mobilize intracellular calcium in response to nucleotide exposure. As a functional consequence, PDCs acquire a mature phenotype that is further enhanced in the context of CD40 ligation. Strikingly, nucleotides strongly inhibit IFN-α secretion induced by influenza virus or CpG-A. This effect is most pronounced for the uridine nucleotides UDP and UTP and the sugar nucleotide UDP-glucose, ligands of P2Y6, P2Y4, and P2Y14, respectively. Nucleotide-induced inhibition of IFN-α production is blocked by suramin, a P2Y receptor antagonist. Pharmacological data point toward a role of protein kinase C in the negative regulation of type I IFN. Manipulating PDC function with P2Y receptor agonists may offer novel therapeutic strategies for autoimmune diseases or cancer.
Dendritic cells loaded with apoptotic antibody-coated tumor cells provide protective immunity against B-cell lymphoma in vivo
Authors: Franki Suzanne N. , Steward Kristopher K. , Betting David J. , Kafi Kamran , Yamada Reiko E. , Timmerman John M. 
Published: November 2007

AbstractThe in vitro priming of tumor-specific T cells by dendritic cells (DCs) phagocytosing killed tumor cells can be augmented in the presence of antitumor monoclonal antibody (mAb). We investigated whether DCs phagocytosing killed lymphoma cells coated with tumor-specific antibody could elicit antitumor immunity in vivo. Irradiated murine 38C13 lymphoma cells were cocultured with bone marrow–derived DCs in the presence or absence of tumor-specific mAb. Mice vaccinated with DCs cocultured with mAb-coated tumor cells were protected from tumor challenge (60% long-term survival), whereas DCs loaded with tumor cells alone were much less effective. The opsonized whole tumor cell–DC vaccine elicited significantly better tumor protection than a traditional lymphoma idiotype (Id) protein vaccine, and in combination with chemotherapy could eradicate preexisting tumor. Moreover, the DC vaccine protected animals from both wild-type and Id-negative variant tumor cells, indicating that Id is not a major target of the induced tumor immunity. Protection was critically dependent upon CD8+ T cells, with lesser contribution by CD4+ T cells. Importantly, opsonized whole tumor cell–DC vaccination did not result in tissue-specific autoimmunity. Since opsonized whole tumor cell–DC and Id vaccines appear to target distinct tumor antigens, optimal antilymphoma immunity might be achieved by combining these approaches.
Angiotensin-converting enzyme (CD143) marks hematopoietic stem cells in human embryonic, fetal, and adult hematopoietic tissues
Authors: Jokubaitis Vanta J. , Sinka Lidia , Driessen Rebecca , Whitty Genevieve , Haylock David N. , Bertoncello Ivan , Smith Ian , Péault Bruno , Tavian Manuela , Simmons Paul J. 
Published: November 2007

AbstractPrevious studies revealed that mAb BB9 reacts with a subset of CD34+ human BM cells with hematopoietic stem cell (HSC) characteristics. Here we map BB9 expression throughout hematopoietic development and show that the earliest definitive HSCs that arise at the ventral wall of the aorta and surrounding endothelial cells are BB9+. Thereafter, BB9 is expressed by primitive hematopoietic cells in fetal liver and in umbilical cord blood (UCB). BB9+CD34+ UCB cells transplanted into nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice contribute 10-fold higher numbers of multilineage blood cells than their CD34+BB9− counterparts and contain a significantly higher incidence of SCID-repopulating cells than the unfractionated CD34+ population. Protein microsequencing of the 160-kDa band corresponding to the BB9 protein established its identity as that of somatic angiotensin-converting enzyme (ACE). Although the role of ACE on human HSCs remains to be determined, these studies designate ACE as a hitherto unrecognized marker of human HSCs throughout hematopoietic ontogeny and adulthood.
Autoantibodies to the C-terminal subunit of RLIP76 induce oxidative stress and endothelial cell apoptosis in immune-mediated vascular diseases and atherosclerosis
Authors: Margutti Paola , Matarrese Paola , Conti Fabrizio , Colasanti Tania , Delunardo Federica , Capozzi Antonella , Garofalo Tina , Profumo Elisabetta , Riganò Rachele , Siracusano Alessandra , Alessandri Cristiano , Salvati Bruno , Valesini Guido , Malorni Walter , Sorice Maurizio , Ortona Elena 
Published: November 2007

AbstractAlthough detection of autoantibodies in the peripheral blood from patients with immune-mediated endothelial dysfunctions has so far failed to provide tools of diagnostic or pathogenetic value, putative bioindicators include anti-endothelial cell antibodies, a heterogeneous family of antibodies that react with autoantigens expressed by endothelial cells. In this study, to identify endothelial autoantigens involved in the autoimmune processes causing endothelial damage, we screened a human microvascular endothelial cell cDNA library with sera from patients with Behçet's disease. We identified antibodies to the C-terminus of Ral binding protein1 (RLIP76), a protein that catalyzes the ATP-dependent transport of glutathione (GSH) conjugates including GSH-4-hydroxy-t-2,3-nonenal, in the serum of a significant percentage of patients with various diseases characterized by immune-mediated endothelial dysfunction, including Behçet disease, systemic sclerosis, systemic lupus erythematosus and carotid atherosclerosis. These autoantibodies increased intracellular levels of 4-hydroxy-t-2,3-nonenal, decreased levels of GSH and activated C-Jun NH2 Kinase signaling (JNK), thus inducing oxidative stress-mediated endothelial cell apoptosis. The dietary antioxidant alpha-tocopherol counteracted endothelial cell demise. These findings suggest that autoantibodies to RLIP76 play a pathogenetic role in immune-mediated vascular diseases and represent a valuable peripheral blood bioindicator of atherosclerosis and immune-mediated vascular diseases.