bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Matroid Method in Kinematic Analysis of Parallel Axes Epicyclic Gear Trains
Authors: Talpasanu Ilie , Yih T. C. , Simionescu P. A. 
Published: November 2006

Abstract
A novel method for kinematic analysis of parallel-axes epicyclic gear trains is presented, called the incidence and transfer method, which uses the incidence matrices associated with the edge-oriented graph associated to the mechanism and the transfer joints (teeth contact joints). Relative to such joints, a set of independent equations can be generated for calculating the angular positions, velocities, and accelerations. Complete kinematic equations are obtained in matrix form using a base of circuits from a cycle matroid. The analysis uses the relationships between the number of mobile links, number of joints, and number of circuits in the base of circuits, together with the Latin matrix (whose entries are function of the absolute values of the partial gear ratios of the transmission). Calculating the rank of the Latin matrix can identify singularities, like groups of gears that rotate as a whole. Relationships between the output and input angular velocities and accelerations are then determined in a matrix-based approach without using any derivative operations. The proposed method has general applicability and can be employed for systems with any number of gears and degrees of freedom, as illustrated by the numerical examples presented.
Role of Branched-Chain Fatty Acids in pH Stress Tolerance in
Listeria monocytogenes
Authors: Giotis Efstathios S. , McDowell David A. , Blair Ian S. , Wilkinson Brian J. 
Published: November 2006

ABSTRACT

In alkaline conditions,
Listeria monocytogenes
cells develop higher proportions of branched-chain fatty acids (FAs), including more anteiso forms. In acid conditions, the opposite occurs. Reduced growth of pH-sensitive mutants at adverse pH (5.0/9.0) was alleviated by the addition of 2-methylbutyrate (an anteiso-FA precursor), suggesting that anteiso-FAs are important in adaptation to adverse pH. The balance between anteiso- and iso-FAs may be more important than changes in the amounts and/or degrees of saturation of FAs in pH adaptation.
Role of Zearalenone Lactonase in Protection of
Gliocladium roseum
from Fungitoxic Effects of the Mycotoxin Zearalenone
Authors: Utermark Jan , Karlovsky Petr 
Published: November 2006

ABSTRACT

Zearalenone is a mycotoxin with estrogenic effects on mammals that is produced by several species of
Fusarium
. We found that zearalenone and its derivatives inhibit the growth of filamentous fungi on solid media at concentrations of ≤10 μg/ml. The fungitoxic effect declined in the order zearalenone > α-zearalenol > β-zearalenol. The mycoparasitic fungus
Gliocladium roseum
produces a zearalenone-specific lactonase which catalyzes the hydrolysis of zearalenone, followed by a spontaneous decarboxylation. The growth of
G. roseum
was not inhibited by zearalenone, and the lactonase may protect
G. roseum
from the toxic effects of this mycotoxin. We inactivated
zes2
, the gene encoding zearalenone lactonase in
G. roseum
, by inserting a hygromycin resistance cassette into the coding sequence of the gene by means of
Agrobacterium tumefaciens
-mediated genetic transformation. The
zes2
disruption mutants could not hydrolyze the lactone bond of zearalenone and were more sensitive to zearalenone. These data are consistent with a hypothesis that resorcylic acid lactones exemplified by zearalenone act to reduce growth competition by preventing competing fungi from colonizing substrates occupied by zearalenone producers and suggest that they may play a role in fungal defense against mycoparasites.
Functional Analysis of
Burkholderia cepacia
Genes
bceD
and
bceF
, Encoding a Phosphotyrosine Phosphatase and a Tyrosine Autokinase, Respectively: Role in Exopolysaccharide Biosynthesis and Biofilm Formation
Authors: Ferreira Ana S. , Leitão Jorge H. , Sousa Sílvia A. , Cosme Ana M. , Sá-Correia Isabel , Moreira Leonilde M. 
Published: November 2006

ABSTRACT

The biosynthesis of the exopolysaccharide (EPS) cepacian by
Burkholderia cepacia
complex strains requires the 16.2-kb
bce
cluster of genes. Two of the clustered genes,
bceD
and
bceF
, code for two proteins homologous to phosphotyrosine phosphatases and tyrosine kinases, respectively. We show experimental evidence indicating that BceF is phosphorylated on tyrosine and that the conserved lysine residue present at position 563 in the Walker A ATP-binding motif is required for this autophosphorylation. It was also proved that BceD is capable of dephosphorylating the phosphorylated BceF. Using the artificial substrate
p
-nitrophenyl phosphate (PNPP), BceD exhibited a
V
max
of 8.8 μmol of PNPP min
−1
mg
−1
and a

K
m

of 3.7 mM PNPP at 30°C. The disruption of
bceF
resulted in the abolishment of cepacian accumulation in the culture medium, but 75% of the parental strain's EPS production yield was still registered for the
bceD
mutant. The exopolysaccharide produced by the
bceD
mutant led to less viscous solutions and exhibited the same degree of acetylation as the wild-type cepacian, suggesting a lower molecular mass for this mutant biopolymer. The size of the biofilm produced in vitro by
bceD
and
bceF
mutant strains is smaller than the size of the biofilm formed by the parental strain, and this phenotype was confirmed by complementation assays, indicating that BceD and BceF play a role in the establishment of biofilms of maximal size.
Molecular Analysis of Arsenate-Reducing Bacteria within Cambodian Sediments following Amendment with Acetate
Authors: Lear G. , Song B. , Gault A. G. , Polya D. A. , Lloyd J. R. 
Published: November 2006

ABSTRACT

The health of millions is threatened by the use of groundwater contaminated with sediment-derived arsenic for drinking water and irrigation purposes in Southeast Asia. The microbial reduction of sorbed As(V) to the potentially more mobile As(III) has been implicated in release of arsenic into groundwater, but to date there have been few studies of the microorganisms that can mediate this transformation in aquifers. With the use of stable isotope probing of nucleic acids, we present evidence that the introduction of a proxy for organic matter (
13
C-labeled acetate) stimulated As(V) reduction in sediments collected from a Cambodian aquifer that hosts arsenic-rich groundwater. This was accompanied by an increase in the proportion of prokaryotes closely related to the dissimilatory As(V)-reducing bacteria
Sulfurospirillum
strain NP-4 and
Desulfotomaculum auripigmentum
. As(V) respiratory reductase genes (
arrA
) closely associated with those found in
Sulfurospirillum barnesii
and
Geobacter uraniumreducens
were also detected in active bacterial communities utilizing
13
C-labeled acetate in microcosms. This study suggests a direct link between inputs of organic matter and the increased prevalence and activity of organisms which transform As(V) to the potentially more mobile and thus hazardous As(III) via dissimilatory As(V) reduction.
Influence of Dangling Ends and Surface-Proximal Tails of Targets on Probe-Target Duplex Formation in 16S rRNA Gene-Based Diagnostic Arrays
Authors: Stedtfeld Robert D. , Wick Lukas M. , Baushke Samuel W. , Tourlousse Dieter M. , Herzog Amanda B. , Xia Yongmei , Rouillard Jean Marie , Klappenbach Joel A. , Cole James R. , Gulari Erdogan , Tiedje James M. , Hashsham Syed A. 
Published: November 2006

ABSTRACT
Dangling
ends and surface-proximal tails of gene targets influence probe-target
duplex formation and affect the signal intensity of probes on
diagnostic microarrays. This phenomenon was evaluated using an
oligonucleotide microarray containing 18-mer probes corresponding to
the 16S rRNA genes of 10 waterborne pathogens and a number of synthetic
and PCR-amplified gene targets. Signal intensities for Klenow/random
primer-labeled 16S rRNA gene targets were dissimilar from those for
45-mer synthetic targets for nearly 73% of the probes tested.
Klenow/random primer-labeled targets resulted in an interaction with a
complex mixture of 16S rRNA genes (used as the background) 3.7 times
higher than the interaction of 45-mer targets with the same mixture. A
7-base-long dangling end sequence with perfect homology to another
single-stranded background DNA sequence was sufficient to produce a
cross-hybridization signal that was as strong as the signal obtained by
the probe-target duplex itself. Gibbs free energy between the target
and a well-defined background was found to be a better indicator of
hybridization signal intensity than the sequence or length of the
dangling end alone. The dangling end (Gibbs free energy of −7.6
kcal/mol) was found to be significantly more prone to target-background
interaction than the surface-proximal tail (Gibbs free energy of−
64.5 kcal/mol). This study underlines the need for careful
target preparation and evaluation of signal intensities for diagnostic
arrays using 16S rRNA and other gene targets due to the potential for
target interaction with a complex
background.
Phylogenetic Analysis of the pPT23A Plasmid Family of
Pseudomonas syringae
Authors: Ma Zhonghua , Smith James J. , Zhao Youfu , Jackson Robert W. , Arnold Dawn L. , Murillo Jesús , Sundin George W. 
Published: November 2006

ABSTRACT

The pPT23A plasmid family of
Pseudomonas syringae
contains members that contribute to the ecological and pathogenic fitness of their
P. syringae
hosts. In an effort to understand the evolution of these plasmids and their hosts, we undertook a comparative analysis of the phylogeny of plasmid genes and that of conserved chromosomal genes from
P. syringae
. In total, comparative sequence and phylogenetic analyses were done utilizing 47 pPT23A family plasmids (PFPs) from 16 pathovars belonging to six genomospecies. Our results showed that the plasmid replication gene (
repA
), the only gene currently known to be distributed among all the PFPs, had a phylogeny that was distinct from that of the
P. syringae
hosts of these plasmids and from those of other individual genes on PFPs. The phylogenies of two housekeeping chromosomal genes, those for DNA gyrase B subunit (
gyrB
) and primary sigma factor (
rpoD
), however, were strongly associated with genomospecies of
P. syringae
. Based on the results from this study, we conclude that the pPT23A plasmid family represents a dynamic genome that is mobile among
P. syringae
pathovars.
Sulfur-Oxidizing Bacteria in Soap Lake (Washington State), a Meromictic, Haloalkaline Lake with an Unprecedented High Sulfide Content
Authors: Sorokin Dimitry Y. , Foti Mirjam , Pinkart Holly C. , Muyzer Gerard 
Published: November 2006

ABSTRACTCulture-dependent and -independent techniques were used to study the diversity of chemolithoautotrophic sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake containing an unprecedentedly high sulfide concentration in the anoxic monimolimnion. Both approaches revealed the dominance of bacteria belonging to the genusThioalkalimicrobium, which are common inhabitants of soda lakes. A dense population ofThioalkalimicrobium(up to 107cells/ml) was found at the chemocline, which is characterized by a steep oxygen-sulfide gradient. TwelveThioalkalimicrobiumstrains exhibiting three different phenotypes were isolated in pure culture from various locations in Soap Lake. The isolates fell into two groups according to 16S rRNA gene sequence analysis. One of the groups was closely related toT. cyclicum, which was isolated from Mono Lake (California), a transiently meromictic, haloalkaline lake. The second group, consisting of four isolates, was phylogenetically and phenotypically distinct from knownThioalkalimicrobiumspecies and unique to Soap Lake. It represented a new species, for which we suggest the nameThioalkalimicrobium microaerophilumsp. nov.
Use of Quantum Dot Luminescent Probes To Achieve Single-Cell Resolution of Human Oral Bacteria in Biofilms
Authors: Chalmers Natalia I. , Palmer Robert J. , Du-Thumm Laurence , Sullivan Richard , Shi Wenyuan , Kolenbrander Paul E. 
Published: November 2006

ABSTRACT
Oral biofilms are multispecies communities, and in their nascent stages of development, numerous bacterial species engage in interspecies interactions. Better insight into the spatial relationship between different species and how species diversity increases over time can guide our understanding of the role of interspecies interactions in the development of the biofilms. Quantum dots (QD) are semiconductor nanocrystals and have emerged as a promising tool for labeling and detection of bacteria. We sought to apply QD-based primary immunofluorescence for labeling of bacterial cells with in vitro and in vivo biofilms and to compare this approach with the fluorophore-based primary immunofluorescence approach we have used previously. To investigate QD-based primary immunofluorescence as the means to detect distinct targets with single-cell resolution, we conjugated polyclonal and monoclonal antibodies to the QD surface. We also conducted simultaneous QD conjugate-based and fluorophore conjugate-based immunofluorescence and showed that these conjugates were complementary tools in immunofluorescence applications. Planktonic and biofilm cells were labeled effectively by considering two factors: the final nanomolar concentration of QD conjugate and the amount of antibody conjugated to the QD, which we define as the degree of labeling. These advances in the application of QD-based immunofluorescence for the study of biofilms in vitro and in vivo will help to define bacterial community architecture and to facilitate investigations of interactions between bacterial species in these communities.
Ste12 Transcription Factor Homologue CpST12 Is Down-Regulated by HypovirusInfection and Required for Virulence and Female Fertility of the Chestnut Blight Fungus
Cryphonectria parasitica
Authors: Deng Fuyou , Allen Todd D. , Nuss Donald L. 
Published: November 2006

ABSTRACT

A
putative homologue of the
Saccharomyces cerevisiae
Ste12
transcription factor was identified in a series of expressed sequence
tag-based microarray analyses as being down-regulated in strains of the
chestnut blight fungus,
Cryphonectria parasitica
, infected by
virulence-attenuating hypoviruses. Cloning of the corresponding gene,
cpst12
, confirmed a high level of similarity to Ste12
homologues of other filamentous fungi. Disruption of
cpst12
resulted in no alterations in in vitro growth characteristics or colony
morphology and an increase in the production of asexual spores,
indicating that CpST12 is dispensable for vegetative growth and
conidiation on artificial medium. However, the disruption mutants
showed a very substantial reduction in virulence on chestnut tissue and
a complete loss of female fertility, two symptoms normally conferred by
hypovirus infection. Both virulence and female fertility were restored
by complementation with the wild-type
cpst12
gene. Analysis of
transcriptional changes caused by
cpst12
gene disruption with
a custom
C. parastica
cDNA microaray chip identified 152
responsive genes. A significant number of these putative
CpST12-regulated genes were also responsive to hypovirus infection.
Thus,
cpst12
encodes a cellular transcription factor, CpST12,
that is down-regulated by hypovirus infection and required for female
fertility, virulence and regulated expression of a subset of hypovirus
responsive host
genes.
Radial Mass Density, Charge, and Epitope Distribution in theCryptococcus neoformansCapsule
Authors: Maxson Michelle E. , Dadachova Ekaterina , Casadevall Arturo , Zaragoza Oscar 
Published: November 2006

ABSTRACTExposure ofCryptococcus neoformanscells to gamma radiation results in a gradual release of capsular polysaccharide, in a dose-dependent manner. This method allows the systematic exploration of different capsular regions. Using this methodology, capsule density was determined to change according to the radial distribution of glucuronoxylomannan and total polysaccharide, becoming denser at the inner regions of the capsule. Scanning electron microscopy of cells following gamma radiation treatment confirmed this finding. The zeta potential of the capsule also increased as the capsule size decreased. However, neither charge nor density differences were correlated with any change in sugar composition (xylose, mannose, and glucuronic acid) in the different capsular regions, since the proportions of these sugars remained constant throughout the capsule. Analysis of the capsular antigenic properties by monoclonal antibody binding and Scatchard analysis revealed fluctuations in the binding affinity within the capsule but not in the number of antibody binding sites, suggesting that the spatial organization of high- and low-affinity epitopes within the capsule changed according to radial position. Finally, evidence is presented that the structure of the capsule changes with capsule age, since the capsule of older cells became more resistant to gamma radiation-induced ablation. In summary, the capsule ofC. neoformansis heterogeneous in its spatial distribution and changes with age. Furthermore, our results suggest several mechanisms by which the capsule may protect the fungal cell against exogenous environmental factors.
Vesicular Polysaccharide Export in
Cryptococcus neoformans
Is a Eukaryotic Solution to the Problem of Fungal Trans-Cell Wall Transport
Authors: Rodrigues Marcio L. , Nimrichter Leonardo , Oliveira Débora L. , Frases Susana , Miranda Kildare , Zaragoza Oscar , Alvarez Mauricio , Nakouzi Antonio , Feldmesser Marta , Casadevall Arturo 
Published: November 2006

ABSTRACT

The mechanisms by which macromolecules are transported through the cell wall of fungi are not known. A central question in the biology of
Cryptococcus neoformans
, the causative agent of cryptococcosis, is the mechanism by which capsular polysaccharide synthesized inside the cell is exported to the extracellular environment for capsule assembly and release. We demonstrate that
C. neoformans
produces extracellular vesicles during in vitro growth and animal infection. Vesicular compartments, which are transferred to the extracellular space by cell wall passage, contain glucuronoxylomannan (GXM), a component of the cryptococcal capsule, and key lipids, such as glucosylceramide and sterols. A correlation between GXM-containing vesicles and capsule expression was observed. The results imply a novel mechanism for the release of the major virulence factor of
C. neoformans
whereby polysaccharide packaged in lipid vesicles crosses the cell wall and the capsule network to reach the extracellular environment.
Pseudomonas aeruginosa
LecB Is Involved in Pilus Biogenesis and Protease IV Activity but Not in Adhesion to Respiratory Mucins
Authors: Sonawane Avinash , Jyot Jeevan , Ramphal Reuben 
Published: November 2006

ABSTRACT

Pseudomonas aeruginosa
expresses two lectins which are implicated in adhesion and biofilm formation. In this study, we demonstrate that
P. aeruginosa
LecB is involved in pilus biogenesis and proteolytic activity. Moreover, neither lectin was involved in adhesion to human tracheobronchial mucin. We infer that some of the ascribed functions are secondary effects on other systems rather than effects of the lectins themselves.
Pathway Confirmation and Flux Analysis of Central Metabolic Pathways in
Desulfovibrio vulgaris
Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry
Authors: Tang Yinjie , Pingitore Francesco , Mukhopadhyay Aindrila , Phan Richard , Hazen Terry C. , Keasling Jay D. 
Published: November 2006

ABSTRACT

Flux distribution in central metabolic pathways of
Desulfovibrio vulgaris
Hildenborough was examined using
13
C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (GC-MS) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) indicate the lack of an oxidatively functional tricarboxylic acid (TCA) cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80% of the lactate was converted to acetate and that the reactions involved are the primary route of energy production [NAD(P)H and ATP production]. Independently of the TCA cycle, direct cleavage of acetyl coenzyme A to CO and 5,10-methyl tetrahydrofuran also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or the reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (
S
)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in
D. vulgaris
and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.
Role of a Putative Polysaccharide Locus in
Bordetella
Biofilm Development
Authors: Parise Gina , Mishra Meenu , Itoh Yoshikane , Romeo Tony , Deora Rajendar 
Published: November 2006

ABSTRACT

Bordetellae are gram-negative bacteria that colonize the respiratory tracts of animals and humans. We and others have recently shown that these bacteria are capable of living as sessile communities known as biofilms on a number of abiotic surfaces. During the biofilm mode of existence, bacteria produce one or more extracellular polymeric substances that function, in part, to hold the cells together and to a surface. There is little information on either the constituents of the biofilm matrix or the genetic basis of biofilm development by
Bordetella
spp. By utilizing immunoblot assays and by enzymatic hydrolysis using dispersin B (DspB), a glycosyl hydrolase that specifically cleaves the polysaccharide poly-β-1,6-
N
-acetyl-
d
-glucosamine (poly-β-1,6-GlcNAc), we provide evidence for the production of poly-β-1,6-GlcNAc by various
Bordetella
species (
Bordetella bronchiseptica
,
B. pertussis
, and
B. parapertussis
) and its role in their biofilm development. We have investigated the role of a
Bordetella
locus, here designated
bpsABCD
, in biofilm formation. The
bps
(
Bordetella
polysaccharide) locus is homologous to several bacterial loci that are required for the production of poly-β-1,6-GlcNAc and have been implicated in bacterial biofilm formation. By utilizing multiple microscopic techniques to analyze biofilm formation under both static and hydrodynamic conditions, we demonstrate that the
bps
locus, although not essential at the initial stages of biofilm formation, contributes to the stability and the maintenance of the complex architecture of
Bordetella
biofilms.