bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Low Vegetation on the Recruitment of Plants in Successional Habitat Types1
Authors: Benitez‐Malvido Julieta 
Published: January 2006

ABSTRACTI assessed the role of low vegetation (plants ca 1 yr old and ≤50 cm tall) as a biotic facilitator or barrier in the recruitment of different growth forms and species in primary forests, secondary forests, and old‐fields (abandoned pastures) in southeastern Mexico. I removed by hand all plants (≤100 cm tall, including roots) and litter from 20, 0.25 m2 plots in each habitat. For 1 yr, I counted the number of plant species (5–50 cm tall) recruited, grouped them into different growth forms, and compared them to undisturbed control plots. Prior to manipulation, the standing density of trees and lianas was highest in primary and secondary forests. Shrubs were more abundant in secondary forests, whereas herbs, epiphytes, and hemi‐epiphytes were more abundant in old‐fields. Herbaceous plants appeared as important components of the community in all habitats. The removal of low vegetation increased total plant recruitment in all habitats. Considering each growth form, the absence of vegetation increased recruitment in primary forests for herbs, in secondary forests for epiphytes and hemi‐epiphytes, in old‐fields for trees, and for lianas in primary forests and old‐fields. In vegetation removal plots, recruitment of species was greater in pastures, lower in secondary forest, and similar in primary forest with respect to control plots. Depending on habitat type, species, and growth form, the presence of low vegetation may act as a recruitment barrier or facilitator for different species, affecting plant community structure, diversity, and composition in different habitats.
Riser-Soil
Interaction: Local Dynamics at TDP and a Discussion on the Eigenvalue and the VIV
Problems
Authors: Pesce Celso
P. , Martins Clóvis de
A. , da Silveira Lauro M. Y. 
Published: January 2006

Abstract
The eigenvalue problem of risers is of utmost importance, particularly if vortex-induced vibration (VIV) is concerned. Design procedures rely on the determination of eigenvalues and eigenmodes. Natural frequencies are not too sensitive to the proper consideration of boundary condition, within a certain extent where dynamics at the touchdown area (TDA) may be modeled as dominated by the dynamics of the suspended part. However, eigenmodes may be strongly affected in this region because, strictly speaking, this is a nonlinear one-side (contact-type) boundary condition. Actually, we shall consider a nonlinear eigenvalue problem. Locally, at TDA, riser flexural rigidity and soil interaction play important roles and may affect the dynamic curvature. Extending and merging former analytical solutions on touchdown point (TDP) dynamics and on the eigenvalue problem, obtained through asymptotic and perturbation methods, the present work critically address soil and bending stiffness effects a little further. As far as linear soil stiffness and planar dynamics hypotheses may be considered valid, it is shown that penetration in the soil is small and that its effect does not change significantly the bending loading that is mainly caused by the cyclic excursion of the TDP and corresponding dynamic tension. A comparison of the analytical results with a full nonlinear time-domain simulation shows a remarkable agreement for a typical steel catenary riser. The WKB approximation for the eigenvalue problem gives good estimates for TDP excursion. As the dynamic tension caused solely by VIV is very small, the merged analytical solution may be used as a first estimate of the curvature variation at TDP in the cases of current perpendicular to the “riser plane.”
Identification and Characterization of RbmA, a Novel Protein Required for the Development of Rugose Colony Morphology and Biofilm Structure in
Vibrio cholerae
Authors: Fong Jiunn C. N. , Karplus Kevin , Schoolnik Gary K. , Yildiz Fitnat H. 
Published: January 2006

ABSTRACT

Phase variation between smooth and rugose colony variants of
Vibrio cholerae
is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. The rugose variant forms corrugated colonies, exhibits increased levels of resistance to osmotic, acid, and oxidative stresses, and has an enhanced capacity to form biofilms. Many of these phenotypes are mediated in part by increased production of an exopolysaccharide termed VPS. In this study, we compared total protein profiles of the smooth and rugose variants using two-dimensional gel electrophoresis and identified one protein that is present at a higher level in the rugose variant. A mutation in the gene encoding this protein, which does not have any known homologs in the protein databases, causes cells to form biofilms that are more fragile and sensitive to sodium dodecyl sulfate than wild-type biofilms. The results indicate that the gene, termed
rbmA
(
r
ugosity and
b
iofilm structure
m
odulator A), is required for rugose colony formation and biofilm structure integrity in
V. cholerae
. Transcription of
rbmA
is positively regulated by the response regulator VpsR but not VpsT.
Bacillus anthracisIsdG, a Heme-Degrading Monooxygenase
Authors: Skaar Eric P. , Gaspar Andrew H. , Schneewind Olaf 
Published: January 2006

ABSTRACTBacillus anthracis, the causative agent of anthrax, utilizes hemin and hemoglobin for growth in culture, suggesting that these host molecules serve as sources for the nutrient iron during bacterial infection. Bioinformatic analyses of theB. anthracisgenome revealed genes with similarity to theiron-regulatedsurfacedeterminant (isd) system responsible for heme uptake inStaphylococcus aureus. We show that the protein product of one of these genes,isdG, binds hemin in a manner resembling the heme binding of known heme oxygenases. Formation of IsdG:hemin complexes in the presence of a suitable electron donor, e.g., ascorbate or cytochrome P450 reductase, promotes catalytic degradation of hemin to biliverdin with concomitant release of iron. IsdG is required forB. anthracisutilization of hemin as a sole iron source, and it is also necessary for bacterial protection against heme-mediated toxicity. These data suggest that IsdG functions as a heme-degrading monooxygenase inB. anthracis.
Regulation and Properties of PstSCAB, a High-Affinity, High-Velocity Phosphate Transport System ofSinorhizobium meliloti
Authors: Yuan Ze-Chun , Zaheer Rahat , Finan Turlough M. 
Published: January 2006

ABSTRACTThe properties and regulation of thepstSCAB-encoded Piuptake system from the alfalfa symbiontSinorhizobium melilotiare reported. We present evidence that thepstSCABgenes and the regulatoryphoUBgenes are transcribed from a single promoter that contains two PhoB binding sites and that transcription requires PhoB.S. melilotistrain 1021 (Rm1021) and its derivatives were found to carry a C deletion frameshift mutation in thepstCgene (designatedpstC1021) that severely impairs activity of the PstSCAB Pitransport system. This mutation is absent in RCR2011, the parent of Rm1021. Correction of thepstC1021mutation in Rm1021 by site-directed mutagenesis revealed that PstSCAB is a Pi-specific, high-affinity (Km, 0.2 μM), high-velocity (Vmax, 70 nmol/min/mg protein) transport system. ThepstC1021allele was shown to generate a partialphoregulon constitutive phenotype, in which transcription is activated by PhoB even under Pi-excess conditions that render PhoB inactive in a wild-type background. The previously reported symbiotic Fix−phenotype ofphoCDETmutants was found to be dependent on thepstC1021mutation, as Rm1021phoCDETmutants formed small white nodules on alfalfa that failed to reduce N2, whereasphoCDETmutant strains with a correctedpstCallele (RmP110) formed pink nodules on alfalfa that fixed N2like the wild type. Alfalfa root nodules formed by the wild-type RCR2011 strain expressed the low-affinityorfA-pit-encoded Piuptake system and neither thepstSCABgenes nor thephoCDETgenes. Thus, metabolism of alfalfa nodule bacteroids is not Pilimited.
Steady-State Kinetic Analysis of Phosphotransacetylase from
Methanosarcina thermophila
Authors: Lawrence Sarah H. , Ferry James G. 
Published: January 2006

ABSTRACT

Phosphotransacetylase (EC 2.3.1.8) catalyzes the reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. A steady-state kinetic analysis of the phosphotransacetylase from
Methanosarcina thermophila
indicated that there is a ternary complex kinetic mechanism rather than a ping-pong kinetic mechanism. Additionally, inhibition patterns of products and a nonreactive substrate analog suggested that the substrates bind to the enzyme in a random order. Dynamic light scattering revealed that the enzyme is dimeric in solution.
Mutations in the
waaR
Gene of
Escherichia coli
Which Disrupt Lipopolysaccharide Outer Core Biosynthesis Affect Cell Surface Retention of Group 2 Capsular Polysaccharides
Authors: Taylor Clare M. , Goldrick Marie , Lord Liz , Roberts Ian S. 
Published: January 2006

ABSTRACT

On the basis of increased resistance to K5 capsule-specific bacteriophage, a
waaR
transposon mutant defective in the biosynthesis of lipopolysaccharide outer core was isolated. In a K1-expressing strain the mutation equally affected sensitivity to K1 capsule-specific bacteriophage, indicating a general effect on group 2 capsules. The
waaR
mutation affected retention on the cell surface of the K5 polysaccharide, with increased polysaccharide accumulating in the culture supernatant. This indicates that interactions between the outer core of lipopolysaccharide and group 2 capsular polysaccharides are important for the stabilization of group 2 capsular polysaccharides on the cell surface.
Comparative Genomic Analysis of 18
Pseudomonas aeruginosa
Bacteriophages
Authors: Kwan Tony , Liu Jing , DuBow Michael , Gros Philippe , Pelletier Jerry 
Published: January 2006

ABSTRACT

A genomic analysis of 18
P. aeruginosa
phages, including nine newly sequenced DNA genomes, indicates a tremendous reservoir of proteome diversity, with 55% of open reading frames (ORFs) being novel. Comparative sequence analysis and ORF map organization revealed that most of the phages analyzed displayed little relationship to each other.
Mammalian Steroid Hormones Are Substrates for the Major RND- and MFS-Type Tripartite Multidrug Efflux Pumps of
Escherichia coli
Authors: Elkins Christopher A. , Mullis Lisa B. 
Published: January 2006

ABSTRACT

A steroid-hormone-dependent growth suppression was observed in
Escherichia coli
efflux-deficient backgrounds containing mutations in the major RND- and MFS-type tripartite multidrug efflux systems, AcrAB-TolC and EmrAB-TolC, respectively. In addition to their previously known natural steroid spectrum, which includes bile acids, both systems were shown to transport the hormones estradiol and progesterone, whereas hydrocortisone served as a substrate of only AcrAB-TolC. Furthermore, at least two other RND-type pumps, YhiV and AcrD, were capable of transporting such hormones when overexpressed on plasmid vectors (with some demonstrable specificity observed with AcrD). When this activity was examined in a wild-type background, cell-associated estradiol levels remained largely unaffected by competition with exogenous bile acids and hydrocortisone, in contrast to progesterone, which produced a significant modulation in estradiol uptake.
TheVibrio harveyiGTPase CgtAVIs Essential and Is Associated with the 50S Ribosomal Subunit
Authors: Sikora A. E. , Zielke R. , Datta K. , Maddock J. R. 
Published: January 2006

ABSTRACTIt was previously reported that unlike the otherobg/cgtAGTPases, theVibrio harveyi cgtAVis not essential. Here we show thatcgtAVwas not disrupted in these studies and is, in fact, essential for viability. Depletion of CgtAVdid not result in cell elongation. CgtAVis associated with the large ribosomal particle. In light of our results, we predict that theV. harveyiCgtAVprotein plays a similar essential role to that seen for Obg/CgtA proteins in other bacteria.
Evidence for Mutagenesis by Nitric Oxide during Nitrate Metabolism in
Escherichia coli
Authors: Weiss Bernard 
Published: January 2006

ABSTRACT

In
Escherichia coli
, nitrosative mutagenesis may occur during nitrate or nitrite respiration. The endogenous nitrosating agent N
2
O
3
(dinitrogen trioxide, nitrous anhydride) may be formed either by the condensation of nitrous acid or by the autooxidation of nitric oxide, both of which are metabolic by-products. The purpose of this study was to determine which of these two agents is more responsible for endogenous nitrosative mutagenesis. An
nfi
(endonuclease V) mutant was grown anaerobically with nitrate or nitrite, conditions under which it has a high frequency of A:T-to-G:C transition mutations because of a defect in the repair of hypoxanthine (nitrosatively deaminated adenine) in DNA. These mutations could be greatly reduced by two means: (i) introduction of an
nirB
mutation, which affects the inducible cytoplasmic nitrite reductase, the major source of nitric oxide during nitrate or nitrite metabolism, or (ii) flushing the anaerobic culture with argon (which should purge it of nitric oxide) before it was exposed to air. The results suggest that nitrosative mutagenesis occurs during a shift from nitrate/nitrite-dependent respiration under hypoxic conditions to aerobic respiration, when accumulated nitric oxide reacts with oxygen to form endogenous nitrosating agents such as N
2
O
3
. In contrast, mutagenesis of nongrowing cells by nitrous acid was unaffected by an
nirB
mutation, suggesting that this mutagenesis is mediated by N
2
O
3
that is formed directly by the condensation of nitrous acid.
Functional and Topological Characterization of Novel Components of the
comB
DNA Transformation Competence System in
Helicobacter pylori
Authors: Karnholz Arno , Hoefler Claudia , Odenbreit Stefan , Fischer Wolfgang , Hofreuter Dirk , Haas Rainer 
Published: January 2006

ABSTRACT

Helicobacter pylori
is one of the most diverse bacterial species known. A rational basis for this genetic variation may be provided by its natural competence for genetic transformation and high-frequency recombination. Many bacterial competence systems have homology with proteins that are involved in the assembly of type IV pili and type II secretion systems. In
H. pylori
, DNA uptake relies on a transport system related to type IV secretion systems (T4SS) designated the
comB
system. The prototype of a T4SS in
Agrobacterium tumefaciens
consists of 11 VirB proteins and VirD4, which form the core unit necessary for the delivery of single proteins or large nucleoprotein complexes into target cells. In the past we identified proteins ComB4 and ComB7 through ComB10 as being involved in the process of DNA uptake in
H. pylori
. In this study we identified and functionally characterized further (T4SS-homologous) components of the
comB
transformation competence system. By combining computer prediction modeling, experimental topology determination, generation of knockout strains, and genetic complementation studies we identified ComB2, ComB3, and ComB6 as essential components of the transformation apparatus, structurally and functionally homologous to VirB2, VirB3, and VirB6, respectively.
comB2
,
comB3
, and
comB4
are organized as a separate operon. Thus, for the
H. pylori comB
system, all T4SS core components have been identified except for homologues to VirB1, VirD4, VirB5, and VirB11.
Polyamine-Mediated Resistance of Uropathogenic
Escherichia coli
to Nitrosative Stress
Authors: Bower Jean M. , Mulvey Matthew A. 
Published: January 2006

ABSTRACT

During the course of a urinary tract infection, substantial levels of nitric oxide and reactive nitrogen intermediates are generated. We have found that many uropathogenic strains of
Escherichia coli
display far greater resistance to nitrosative stress than the K-12 reference strain MG1655. By selecting and screening for uropathogenic
E. coli
transposon mutants that are unable to grow in the presence of acidified nitrite, the
cadC
gene product was identified as a key facilitator of nitrosative stress resistance. Mutation of
cadC
, or its transcriptional targets
cadA
and
cadB
, results in loss of significant production of the polyamine cadaverine and increased sensitivity to acidified nitrite. Exogenous addition of cadaverine or other polyamines rescues growth of
cad
mutants under nitrosative stress. In wild-type cells, the concentration of cadaverine produced per cell is substantially increased by exposure to acidified nitrite. The mechanism behind polyamine-mediated rescue from nitrosative stress is unclear, but it is not attributable solely to chemical quenching of reactive nitrogen species or reduction in mutation frequency.
Effect of Nitrogen Source on Cyanophycin Synthesis in
Synechocystis
sp. Strain PCC 6308
Authors: Kolodny Nancy H. , Bauer Deborah , Bryce Kerstyn , Klucevsek Kristen , Lane Amy , Medeiros Lea , Mercer Wendy , Moin Sogole , Park Deborah , Petersen Juliette , Wright Julie , Yuen Courtney , Wolfson Adele J. , Allen Mary M. 
Published: January 2006

ABSTRACT

Experiments were carried out to examine the effects of nitrogen source on nitrogen incorporation into cyanophycin during nitrogen limitation and repletion, both with or without inhibition of protein synthesis, in cyanobacteria grown on either nitrate or ammonium. The use of nitrate and ammonium,
14
N labeled in the growth medium and
15
N labeled in the repletion medium, allows the determination of the source of nitrogen in cyanophycin using proton nuclear magnetic resonance spectroscopy. The data suggest that nitrogen from both the breakdown of cellular protein (
14
N) and directly from the medium (
15
N) is incorporated into cyanophycin. Nitrogen is incorporated into cyanophycin at different rates and to different extents, depending on the source of nitrogen (ammonium or nitrate) and whether the cells are first starved for nitrogen. These differences appear to be related to the activity of nitrate reductase in cells and to the possible expression of cyanophycin synthetase during nitrogen starvation.
Characterization of
cis-
Acting Sites Controlling Arginine Deiminase Gene Expression in
Streptococcus gordonii
Authors: Zeng Lin , Dong Yiqian , Burne Robert A. 
Published: January 2006

ABSTRACT

The arginine deiminase system (ADS) is responsible for the production of ornithine, CO
2
, ammonia, and ATP from arginine. The ADS of the oral bacterium
Streptococcus gordonii
plays major roles in physiologic homeostasis, acid tolerance, and oral biofilm ecology. To further our understanding of the transcriptional regulation of the ADS (
arc
) operon, the binding of the ArcR transcriptional activator, which governs expression of the ADS in response to arginine, was investigated by DNase I protection and gel mobility shift assays. An ArcR binding sequence was found that was 27 bp in length and had little sequence similarity to binding sites of other arginine metabolism regulators. The presence of arginine at physiologically relevant concentrations enhanced the binding of ArcR to its target. Using
cat
fusions, various deletion and substitution mutations within the putative ArcR footprint were shown to cause dramatic reductions in expression from the
arcA
promoter in vivo, confirming that the 27-bp sequence is required for optimal expression and induction of the ADS by arginine. Mutation of two putative catabolite response elements (CREs) within the
arc
promoter region showed that both CREs contribute to catabolite repression. A thorough understanding of the regulation of the ADS in
S. gordonii
and related organisms is needed to develop ways to exploit arginine catabolism for the control of oral diseases. Identification of the ArcR and CcpA binding sites lays the foundation for a more complete understanding of the complex interactions of multiple regulatory proteins with elements in the
arc
promoter region.
Global transcriptional coactivators CREB-binding protein and p300 are highly essential collectively but not individually in peripheral B cells
Authors: Xu Wu , Fukuyama Tomofusa , Ney Paul A. , Wang Demin , Rehg Jerold , Boyd Kelli , van Deursen Jan M. A. , Brindle Paul K. 
Published: January 2006

AbstractCREB-binding protein (CBP) and its para-log p300 are transcriptional coactivators that physically or functionally interact with over 320 mammalian and viral proteins, including 36 that are essential for B cells in mice. CBP and p300 are generally considered limiting for transcription, yet their roles in adult cell lineages are largely unknown since homozygous null mutations in either gene or compound heterozygosity cause early embryonic lethality in mice. We tested the hypotheses that CBP and p300 are limiting and that each has unique properties in B cells, by using mice with Cre/LoxP conditional knockout alleles for CBP (CBPflox) and p300 (p300flox), which carry CD19Cre that initiates floxed gene recombination at the pro–B-cell stage. CD19Cre-mediated loss of CBP or p300 led to surprisingly modest deficits in B-cell numbers, whereas inactivation of both genes was not tolerated by peripheral B cells. There was a moderate decrease in B-cell receptor (BCR)–responsive gene expression in CBP or p300 homozygous null B cells, suggesting that CBP and p300 are essential for this signaling pathway that is crucial for B-cell homeostasis. These results indicate that individually CBP and p300 are partially limiting beyond the pro-B-cell stage and that other coactivators in B cells cannot replace their combined loss.
Hexa-, Hepta-, and Octacyclic Ladder Polysilanes
Authors: Kyushin Soichiro , Ueta Yoshinori , Tanaka Ryoji , Matsumoto Hideyuki 
Published: January 2006

Abstract
Hexa-, hepta-, and octacyclic ladder polysilanes (5–7) were synthesized, and their structures were determined by X-ray crystallography. These compounds have the double helix structure consisting of two linear polysilane chains. In the UV–visible spectra, the lowest energy absorption maxima of 5–7 shift bathochromically as the number of cyclotetrasilane rings progressively increases.
Cation–π-driven Fluorescence Signalling of Ammonium Cations by Naphthyl-substituted Zn10S16 and Cd10S16 Clusters
Authors: Konishi Katsuaki , Hiratani Takayuki 
Published: January 2006

Abstract
Zn10S16 and Cd10S16 clusters bearing twelve naphthalene units on the surface showed characteristic blue emission in response to the cation–π-mediated intercalative binding of quaternary ammonium cations that allows the formation of ground-state naphthalene aggregates.