bluuebunny/crossref_metadata_2025_split huggingface dataset:
INFLUENCE OF POSTHARVEST RIPENING ON CHANGES IN QUALITY AND VOLATILE COMPOUNDS OF “GOLDEN ORANGE” AND “GOLDEN LASA” SCAB‐RESISTANT APPLE CULTIVARS
Authors: RIZZOLO ANNA , GRASSI MAURIZIO , ZERBINI PAOLA ECCHER 
Published: August 2006

ABSTRACT Quality parameters at harvest, and color, ethylene production (EP) and headspace volatile production rates during postharvest ripening at 20C were investigated on two Golden Delicious‐like scab‐resistant apples (Golden Orange [GO] and Golden Lasa [GL]), and on the scab‐susceptible Golden Delicious clone B (G) cultivar. At harvest, quality parameters defined GO and GL apples as less mature than G ones, even if their skin color was yellower. With postharvest ripening, GO and GL apples showed lower EP, lower maximum total volatile production, and their skin color turned as yellow as G ones. When fully mature, GO and GL differed from G apples for organic acid, sugar and volatile compositions, which could explain the different sensory descriptions particular to these cultivars. Canonical discriminant analysis showed that the differences in volatile composition among the three cultivars became greater as the postharvest ripening process went on, and, only when fruits were still immature, could cultivars not be distinguished by using the aroma pattern.
Strangeness at the Gates: The Peculiar Politics of American Immigration
Authors: Ghandnoosh Nazgol , Waldinger Roger 
Published: August 2006

Selecting by Origin: Ethnic Migration in the Liberal State. By Christian Joppke. Cambridge: Harvard University Press, 2005 Impossible Subjects: Illegal Aliens and the Making of Modern America. By Mae Ngai. Princeton: Princeton University Press, 2004 Dividing Lines: The Politics of Immigration Control in America. By Daniel Tichenor. Princeton: Princeton University Press, 2002.
Complete DNA Sequence of a ColBM Plasmid from Avian Pathogenic
Escherichia coli
Suggests that It Evolved from Closely Related ColV Virulence Plasmids
Authors: Johnson Timothy J. , Johnson Sara J. , Nolan Lisa K. 
Published: August 2006

ABSTRACT

Avian pathogenic
Escherichia coli
(APEC), an extraintestinal pathogenic
E. coli
causing colibacillosis in birds, is responsible for significant economic losses for the poultry industry. Recently, we reported that the APEC pathotype was characterized by possession of a set of genes contained within a 94-kb cluster linked to a ColV plasmid, pAPEC-O2-ColV. These included
sitABCD
, genes of the aerobactin operon,
hlyF
,
iss
, genes of the salmochelin operon, and the 5′ end of
cvaB
of the ColV operon. However, the results of gene prevalence studies performed among APEC isolates revealed that these traits were not always linked to ColV plasmids. Here, we present the complete sequence of a 174-kb plasmid, pAPEC-O1-ColBM, which contains a putative virulence cluster similar to that of pAPEC-O2-ColV. These two F-type plasmids share remarkable similarity, except that they encode the production of different colicins; pAPEC-O2-ColV contains an intact ColV operon, and pAPEC-O1-ColBM encodes the colicins B and M. Interestingly, remnants of the ColV operon exist in pAPEC-O1-ColBM, hinting that ColBM-type plasmids may have evolved from ColV plasmids. Among APEC isolates, the prevalence of ColBM sequences helps account for the previously observed differences in prevalence between genes of the “conserved” portion of the putative virulence cluster of pAPEC-O2-ColV and those genes within its “variable” portion. These results, in conjunction with Southern blotting and probing of representative ColBM-positive strains, indicate that this “conserved” cluster of putative virulence genes is primarily linked to F-type virulence plasmids among the APEC isolates studied.
Membrane Vesicles: an Overlooked Component of the Matrices of Biofilms
Authors: Schooling Sarah R. , Beveridge Terry J. 
Published: August 2006

ABSTRACTThe matrix helps define the architecture and infrastructure of biofilms and also contributes to their resilient nature. Although many studies continue to define the properties of both gram-positive and gram-negative bacterial biofilms, there is still much to learn, especially about how structural characteristics help bridge the gap between the chemistry and physical aspects of the matrix. Here, we show that membrane vesicles (MVs), structures derived from the outer membrane of gram-negative bacteria, are a common particulate feature of the matrix ofPseudomonas aeruginosabiofilms. Biofilms grown using different model systems and growth conditions were shown to contain MVs when thin sectioned for transmission electron microscopy, and mechanically disrupted biofilms revealed MVs in association with intercellular material. MVs were also isolated from biofilms by employing techniques for matrix isolation and a modified MV isolation protocol. Together these observations verified the presence and frequency of MVs and indicated that MVs were a definite component of the matrix. Characterization of planktonic and biofilm-derived MVs revealed quantitative and qualitative differences between the two and indicated functional roles, such as proteolytic activity and binding of antibiotics. The ubiquity of MVs was supported by observations of biofilms from a variety of natural environments outside the laboratory and established MVs as common biofilm constituents. MVs appear to be important and relatively unacknowledged particulate components of the matrix of gram-negative or mixed bacterial biofilms.
DksA Is Required for Growth Phase-Dependent Regulation, Growth Rate-Dependent Control, and Stringent Control offisExpression inEscherichia coli
Authors: Mallik Prabhat , Paul Brian J. , Rutherford Steven T. , Gourse Richard L. , Osuna Robert 
Published: August 2006

ABSTRACTDksA is a critical transcription factor inEscherichia colithat binds to RNA polymerase and potentiates control of rRNA promoters and certain amino acid promoters. Given the kinetic similarities between rRNA promoters and thefispromoter (Pfis), we investigated the possibility that DksA might also control transcription from Pfis. We show that the absence ofdksAextends transcription from Pfiswell into the late logarithmic and stationary growth phases, demonstrating the importance of DksA for growth phase-dependent regulation offis. We also show that transcription from Pfisincreases with steady-state growth rate and thatdksAis absolutely required for this regulation. In addition, both DksA and ppGpp are required for inhibition of Pfispromoter activity following amino acid starvation, and these factors act directly and synergistically to negatively control Pfistranscription in vitro. DksA decreases the half-life of the intrinsically short-livedfispromoter-RNA polymerase complex and increases its sensitivity to the concentration of CTP, the predominant initiating nucleotide triphosphate for this promoter. This work extends our understanding of the multiple factors controllingfisexpression and demonstrates the generality of the DksA requirement for regulation of kinetically similar promoters.
N-Acetyl-d-Glucosamine Induces the Expression of Multidrug Exporter Genes,mdtEF, via Catabolite Activation inEscherichia coli
Authors: Hirakawa Hidetada , Inazumi Yoshihiko , Senda Yasuko , Kobayashi Asuka , Hirata Takahiro , Nishino Kunihiko , Yamaguchi Akihito 
Published: August 2006

ABSTRACTThe expression of MdtEF, a multidrug exporter inEscherichia coli, is positively controlled through multiple signaling pathways, but little is known about signals that induce MdtEF expression. In this study, we investigated compounds that induce the expression of themdtEFgenes and found that out of 20 drug exporter genes inE. coli, the expression ofmdtEFis greatly induced byN-acetyl-d-glucosamine (GlcNAc). The induction ofmdtEFby GlcNAc is not mediated by theevgSA,ydeO,gadX, andrpoSsignaling pathways that have been known to regulatemdtEFexpression. On the other hand, deletion of thenagEgene, encoding the phosphotransferase (PTS) system for GlcNAc, prevented induction by GlcNAc. The induction ofmdtEFby GlcNAc was also greatly inhibited by the addition of cyclic AMP (cAMP) and completely abolished upon deletion of the cAMP receptor protein gene (crp). Other PTS sugars, glucose andd-glucosamine, also inducedmdtEFgene expression. These results suggest thatmdtEFexpression is stimulated through catabolite control.
A Functional
dlt
Operon, Encoding Proteins Required for Incorporation of
d
-Alanine in Teichoic Acids in Gram-Positive Bacteria, Confers Resistance to Cationic Antimicrobial Peptides in
Streptococcus pneumoniae
Authors: Kovács Márta , Halfmann Alexander , Fedtke Iris , Heintz Manuel , Peschel Andreas , Vollmer Waldemar , Hakenbeck Regine , Brückner Reinhold 
Published: August 2006

ABSTRACT

Streptococcus pneumoniae
is one of the few species within the group of low-G +C gram-positive bacteria reported to contain no
d
-alanine in teichoic acids, although the
dltABCD
operon encoding proteins responsible for
d
-alanylation is present in the genomes of two
S. pneumoniae
strains, the laboratory strain R6 and the clinical isolate TIGR4. The annotation of
dltA
in R6 predicts a protein,
d
-alanine-
d
-alanyl carrier protein ligase (Dcl), that is shorter at the amino terminus than all other Dcl proteins. Translation of
dltA
could also start upstream of the annotated TTG start codon at a GTG, resulting in the premature termination of
dltA
translation at a stop codon. Applying a novel integrative translation probe plasmid with
Escherichia coli
′
lacZ
as a reporter, we could demonstrate that
dltA
translation starts at the upstream GTG. Consequently,
S. pneumoniae
R6 is a
dltA
mutant, whereas
S. pneumoniae
D39, the parental strain of R6, and Rx, another derivative of D39, contained intact
dltA
genes. Repair of the stop codon in
dltA
of R6 and insertional inactivation of
dltA
in D39 and Rx yielded pairs of
dltA
-deficient and
dltA
-proficient strains. Subsequent phenotypic analysis showed that
dltA
inactivation resulted in enhanced sensitivity to the cationic antimicrobial peptides nisin and gallidermin, a phenotype fully consistent with those of
dltA
mutants of other gram-positive bacteria. In addition, mild alkaline hydrolysis of heat-inactivated whole cells released
d
-alanine from
dltA
-proficient strains, but not from
dltA
mutants. The results of our study suggest that, as in many other low-G+C gram-positive bacteria, teichoic acids of
S. pneumoniae
contain
d
-alanine residues in order to protect this human pathogen against the actions of cationic antimicrobial peptides.
Activity of
Rhodobacter sphaeroides
RpoH
II
, a Second Member of the Heat Shock Sigma Factor Family
Authors: Green Heather A. , Donohue Timothy J. 
Published: August 2006

ABSTRACT

We have identified a second RpoH homolog, RpoH
II
, in the α-proteobacterium
Rhodobacter sphaeroides
. Primary amino acid sequence comparisons demonstrate that
R. sphaeroides
RpoH
II
belongs to a phylogenetically distinct group with RpoH orthologs from α-proteobacteria that contain two
rpoH
genes. Like its previously identified paralog, RpoH
I
, RpoH
II
is able to complement the temperature-sensitive phenotype of an
Escherichia coli
σ
32
(
rpoH
) mutant. In addition, we show that recombinant RpoH
I
and RpoH
II
each transcribe two
E. coli
σ
32
-dependent promoters (
rpoD
P
HS
and
dnaK
P1) when reconstituted with
E. coli
core RNA polymerase. We observed differences, however, in the ability of each sigma factor to recognize six
R. sphaeroides
promoters (
cycA
P1,
groESL
1
,
rpoD
P
HS
,
dnaK
P1,
hslO
, and
ecfE
), all of which resemble the
E. coli
σ
32
promoter consensus. While RpoH
I
reconstituted with
R. sphaeroides
core RNA polymerase transcribed all six promoters, RpoH
II
produced detectable transcripts from only four promoters (
cycA
P1,
groESL
1
,
hslO
, and
ecfE
). These results, in combination with previous work demonstrating that an RpoH
I
mutant mounts a typical heat shock response, suggest that while RpoH
I
and RpoH
II
have redundant roles in response to heat, they may also have roles in response to other environmental stresses.
Two GacA-Dependent Small RNAs Modulate the Quorum-Sensing Response in
Pseudomonas aeruginosa
Authors: Kay Elisabeth , Humair Bérénice , Dénervaud Valérie , Riedel Kathrin , Spahr Stéphanie , Eberl Leo , Valverde Claudio , Haas Dieter 
Published: August 2006

ABSTRACT

In
Pseudomonas aeruginosa
, the GacS/GacA two-component system positively controls the quorum-sensing machinery and the expression of extracellular products via two small regulatory RNAs, RsmY and RsmZ. An
rsmY rsmZ
double mutant and a
gacA
mutant were similarly impaired in the synthesis of the quorum-sensing signal
N
-butanoyl-homoserine lactone, the disulfide bond-forming enzyme DsbA, and the exoproducts hydrogen cyanide, pyocyanin, elastase, chitinase (ChiC), and chitin-binding protein (CbpD). Both mutants showed increased swarming ability, azurin release, and early biofilm development.
Methionine Sulfoxide Reductase inHelicobacter pylori: Interaction with Methionine-Rich Proteins and Stress-Induced Expression
Authors: Alamuri Praveen , Maier Robert J. 
Published: August 2006

ABSTRACTThe reductive repair of oxidized methionine residues performed by methionine sulfoxide reductase is important for the gastric pathogenHelicobacter pylorito maintain persistent stomach colonization. Methionine-containing proteins that are targeted for repair by Msr were identified from whole-cell extracts (after cells were exposed to O2stress) by using a coimmunoprecipitation approach. Proteins identified as Msr-interacting included catalase, GroEL, thioredoxin-1 (Trx1), and site-specific recombinase; with one exception (Trx1, the reductant for Msr) all these proteins have approximately twofold higher methionine (Met) content than other proteins. These Met-rich proteins were purified and were shown to individually form a cross-linked adduct with Msr. Catalase-specific activity in anmsrstrain was one-half that of the parent strain; this difference was only observed under oxidative stress conditions, and the activity was restored to nearly wild-type levels by adding Msr plus dithiothreitol tomsrstrain extracts. In agreement with the cross-linking study, pure Msr used Trx1 but not Trx2 as a reductant. Comparative structure modeling classified theH. pyloriMsr in class II within the MsrB family, like theNeisseriaenzymes. PureH. pylorienzyme reduced only the R isomer of methylp-tolyl-sulfoxide with an apparentKmof 4.1 mM for the substrate. Stress conditions (peroxide, peroxynitrite, and iron starvation) all caused approximately 3- to 3.5-fold transcriptional up-regulation ofmsr. Neither the O2level during growth nor the use of background regulatory mutants had a significant effect onmsrtranscription. Late log and stationary phase cultures had the highest Msr protein levels and specific activity.
Interaction of TonB with the Outer Membrane Receptor FpvA ofPseudomonas aeruginosa
Authors: Adams Hendrik , Zeder-Lutz Gabrielle , Schalk Isabelle , Pattus Franc , Celia Hervé 
Published: August 2006

ABSTRACTPyoverdine-mediated iron uptake by the FpvA receptor in the outer membrane ofPseudomonas aeruginosais dependent on the inner membrane protein TonB1. This energy transducer couples the proton-electrochemical potential of the inner membrane to the transport event. To shed more light upon this process, a recombinant TonB1 protein lacking the N-terminal inner membrane anchor (TonBpp) was constructed. This protein was, after expression inEscherichia coli, purified from the soluble fraction of lysed cells by means of an N-terminal hexahistidine or glutathioneS-transferase (GST) tag. Purified GST-TonBppwas able to capture detergent-solubilized FpvA, regardless of the presence of pyoverdine or pyoverdine-Fe. Targeting of the TonB1 fragment to the periplasm ofP. aeruginosainhibited the transport of ferric pyoverdine by FpvA in vivo, indicating an interference with endogenous TonB1, presumably caused by competition for binding sites at the transporter or by formation of nonfunctional TonB heterodimers. Surface plasmon resonance experiments demonstrated that the FpvA-TonBppinteractions have apparent affinities in the micromolar range. The binding of pyoverdine or ferric pyoverdine to FpvA did not modulate this affinity. Apparently, the presence of either iron or pyoverdine is not essential for the formation of the FpvA-TonB complex in vitro.
Solution Structure of the Conserved Hypothetical Protein Rv2302 from
Mycobacterium tuberculosis
Authors: Buchko Garry W. , Kim Chang-Yub , Terwilliger Thomas C. , Kennedy Michael A. 
Published: August 2006

ABSTRACT

The
Mycobacterium tuberculosis
protein Rv2302 (80 residues; molecular mass of 8.6 kDa) has been characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. While the biochemical function of Rv2302 is still unknown, recent microarray analyses show that Rv2302 is upregulated in response to starvation and overexpression of heat shock proteins and, consequently, may play a role in the biochemical processes associated with these events. Rv2302 is a monomer in solution as shown by size exclusion chromatography and NMR spectroscopy. CD spectroscopy suggests that Rv2302 partially unfolds upon heating and that this unfolding is reversible. Using NMR-based methods, the solution structure of Rv2302 was determined. The protein contains a five-strand, antiparallel β-sheet core with one C-terminal α-helix (A61 to A75) nestled against its side. Hydrophobic interactions between residues in the α-helix and β-strands 3 and 4 hold the α-helix near the β-sheet core. The electrostatic potential on the solvent-accessible surface is primarily negative with the exception of a positive arginine pocket composed of residues R18, R70, and R74. Steady-state {
1
H}-
15
N heteronuclear nuclear Overhauser effects indicate that the protein's core is rigid on the picosecond timescale. The absence of amide cross-peaks for residues G13 to H19 in the
1
H-
15
N heteronuclear single quantum correlation spectrum suggests that this region, a loop between β-strands 1 and 2, undergoes motion on the millisecond to microsecond timescale. Dali searches using the structure closest to the average structure do not identify any high similarities to any other known protein structure, suggesting that the structure of Rv2302 may represent a novel protein fold.
TrzN from
Arthrobacter aurescens
TC1 Is a Zinc Amidohydrolase
Authors: Shapir Nir , Pedersen Charlotte , Gil Omer , Strong Lisa , Seffernick Jennifer , Sadowsky Michael J. , Wackett Lawrence P. 
Published: August 2006

ABSTRACT

TrzN, the broad-specificity triazine hydrolase from
Arthrobacter
and
Nocardioides
spp., is reportedly in the amidohydrolase superfamily of metalloenzymes, but previous studies suggested that a metal was not required for activity. To help resolve that conundrum, a double chaperone expression system was used to produce multimilligram quantities of functionally folded, recombinant TrzN. The TrzN obtained from
Escherichia coli
(
trzN
) cells cultured with increasing zinc in the growth medium showed corresponding increases in specific activity, and enzyme obtained from cells grown with 500 μM zinc showed maximum activity. Recombinant TrzN contained 1 mole of Zn per mole of TrzN subunit. Maximally active TrzN was not affected by supplementation with most metals nor by EDTA, consistent with previous observations (E. Topp, W. M. Mulbry, H. Zhu, S. M. Nour, and D. Cuppels, Appl. Environ. Microbiol. 66:3134-3141, 2000) which had led to the conclusion that TrzN is not a metalloenzyme. Fully active native TrzN showed a loss of greater than 90% of enzyme activity and bound zinc when treated with the metal chelator 8-hydroxyquinoline-5-sulfonic acid. While exogenously added zinc or cobalt restored activity to metal-depleted TrzN, cobalt supported lower activity than did zinc. Iron, manganese, nickel, and copper did not support TrzN activity. Both Zn- and Co-TrzN showed different relative activities with different
s
-triazine substrates. Co-TrzN showed a visible absorption spectrum characteristic of other members of the amidohydrolase superfamily replaced with cobalt.
Rippling Is a Predatory Behavior in
Myxococcus xanthus
Authors: Berleman James E. , Chumley Tatiana , Cheung Patricia , Kirby John R. 
Published: August 2006

ABSTRACT

Cells of
Myxococcus xanthus
will, at times, organize their movement such that macroscopic traveling waves, termed ripples, are formed as groups of cells glide together on a solid surface. The reason for this behavior has long been a mystery, but we demonstrate here that rippling is a feeding behavior which occurs when
M. xanthus
cells make direct contact with either prey or large macromolecules. Rippling has been observed during two fundamentally distinct environmental conditions: (i) starvation-induced fruiting body development and (ii) predation of other organisms. Our results indicate that case (i) does not occur in all wild-type strains and is dependent on the intrinsic level of autolysis. Analysis of predatory rippling indicates that rippling behavior is inducible during predation on proteobacteria, gram-positive bacteria, yeast (such as Saccharomyces cerevisiae), and phage. Predatory efficiency decreases under genetic and physiological conditions in which rippling is inhibited. Rippling will also occur in the presence of purified macromolecules such as peptidoglycan, protein, and nucleic acid but does not occur in the presence of the respective monomeric components and also does not occur when the macromolecules are physically separated from
M. xanthus
cells. We conclude that rippling behavior is a mechanism utilized to efficiently consume nondiffusing growth substrates and that developmental rippling is a result of scavenging lysed cell debris.
Cross-Functionality of Nitrogenase Components NifH1 and VnfH inAnabaena variabilis
Authors: Pratte Brenda S. , Eplin Kim , Thiel Teresa 
Published: August 2006

ABSTRACTAnabaena variabilisfixes nitrogen under aerobic growth conditions in differentiated cells called heterocysts using either a Mo nitrogenase or a V nitrogenase. ThenifH1gene, which encodes the dinitrogenase reductase of the Mo nitrogenase that is expressed only in heterocysts, is cotranscribed withnifD1andnifK1, which together encode the Mo dinitrogenase. These genes were expressed in the presence or absence of molybdate or vanadate. ThevnfHgene, which encodes the dinitrogenase reductase of the V nitrogenase, was located about 23 kb fromvnfDGK, which encodes the V dinitrogenase; however, likevnfDGK,vnfHwas expressed only in the absence of molybdate, with or without vanadate. LikenifH1, thevnfHgene was expressed exclusively in heterocysts under either aerobic or anaerobic growth conditions and thus is under the control of developmental factors. ThevnfHmutant was able to grow diazotrophically using the V nitrogenase, because NifH1, which was also made in cells starved for molybdate, could substitute for VnfH. Under oxic conditions, thenifH1mutant grew in the absence of molybdate but not in its presence, using VnfH, while thenifH1 vnfHdouble mutant did not grow diazotrophically with or without molybdate or vanadate. AnifH1mutant that expressednifDKandvnfHbut notvnfDGKwas able to grow and fix nitrogen normally, indicating that VnfH could substitute for NifH in the Mo nitrogenase and that these dinitrogenase reductases are not involved in determining the metal specificity of the Mo nitrogenase or the V nitrogenase.