bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schematic homotopy types and non-abelian Hodge theory
Authors: Katzarkov L. , Pantev T. , Toën B. 
Published: May 2008

AbstractWe use Hodge theoretic methods to study homotopy types of complex projective manifolds with arbitrary fundamental groups. The main tool we use is the schematization functor$X \mapsto (X\otimes \mathbb {C})^{\mathrm {sch}}$, introduced by the third author as a substitute for the rationalization functor in homotopy theory in the case of non-simply connected spaces. Our main result is the construction of a Hodge decomposition on $(X\otimes \mathbb {C})^{\mathrm {sch}}$. This Hodge decomposition is encoded in an action of the discrete group $\mathbb {C}^{\times \delta }$ on the object $(X\otimes \mathbb {C})^{\mathrm {sch}}$ and is shown to recover the usual Hodge decomposition on cohomology, the Hodge filtration on the pro-algebraic fundamental group, and, in the simply connected case, the Hodge decomposition on the complexified homotopy groups. We show that our Hodge decomposition satisfies a purity property with respect to a weight filtration, generalizing the fact that the higher homotopy groups of a simply connected projective manifold have natural mixed Hodge structures. As applications we construct new examples of homotopy types which are not realizable as complex projective manifolds and we prove a formality theorem for the schematization of a complex projective manifold.
Highly Sensitive and Specific PCR Assay for Reliable Detection of
Cyclospora cayetanensis
Oocysts
Authors: Lalonde Laura F. , Gajadhar Alvin A. 
Published: May 2008

ABSTRACT

Multiple outbreaks of food-borne gastroenteritis caused by the coccidian parasite
Cyclospora cayetanensis
have been reported annually in North America since 1995. Detection of
C. cayetanensis
contamination typically relies on laborious and subjective microscopic examination of produce washes. Molecular detection methods based on nested PCR, restriction fragment length polymorphism, or multiplex PCR have been developed for
C. cayetanensis
; however, they have not been adequately validated for use on food products. Further challenges include reliably extracting DNA from coccidian oocysts since their tough outer wall is resistant to lysis and overcoming PCR inhibitors in sample matrices. We describe preliminary validation of a reliable DNA extraction method for
C. cayetanensis
oocysts and a sensitive and specific novel PCR assay. The sensitivity and repeatability of the developed methods were evaluated by multiple DNA extractions and PCR amplifications using 1,000-, 100-, 10-, or 1-ooycst aliquots of
C. cayetanensis
oocysts in water or basil wash sediment. Successful PCR amplification was achieved on 15 and 5 replicates extracted from aliquots containing 1,000 oocysts in water and basil wash, respectively. All 45 replicates of the 100-oocyst aliquots in water and 5 in basil wash were amplified successfully, as were 43/45 and 41/45 of the 10- and 1-oocyst aliquots in water and 9/15 and 2/15 in basil wash, respectively. The developed primers showed no cross-reactivity when tested against bacteria, nematodes, and protozoans, including
Eimeria
,
Giardia
, and
Cryptosporidium
. Our results indicate that these methods are specific, can reliably detect a single oocyst, and overcome many of the limitations of microscopic diagnosis.
Genomic and Functional Characterization of the Modular Broad-Host-Range RA3 Plasmid, the Archetype of the IncU Group
Authors: Kulinska Anna , Czeredys Magdalena , Hayes Finbarr , Jagura-Burdzy Grazyna 
Published: May 2008

ABSTRACT

IncU plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. The IncU archetype is conjugative plasmid RA3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class I integron different from that of other IncU replicons. Functional analysis demonstrated that RA3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and gammaproteobacteria. RA3 contains 50 open reading frames clustered in distinct functional modules. The replication module encompasses the
repA
and
repB
genes embedded in long repetitive sequences. RepA, which is homologous to antitoxin proteins from alpha- and gammaproteobacteria, contains a Cro/cI-type DNA-binding domain present in the XRE family of transcriptional regulators. The
repA
promoter is repressed by RepA and RepB. The minireplicon encompasses
repB
and the downstream repetitive sequence r1/r2. RepB shows up to 80% similarity to putative replication initiation proteins from environmental plasmids of beta- and gammaproteobacteria, as well as similarity to replication proteins from alphaproteobacteria and
Firmicutes
. Stable maintenance functions of RA3 are most like those of IncP-1 broad-host-range plasmids and comprise the active partitioning apparatus formed by IncC (ParA) and KorB (ParB), the antirestriction protein KlcA, and accessory stability components KfrA and KfrC. The RA3 origin of transfer was localized experimentally between the maintenance and conjugative-transfer operons. The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids.
Spontaneous Deletion of a 209-Kilobase-Pair Fragment from the
Escherichia coli
Genome Occurs with Acquisition of Resistance to an Assortment of Infectious Phages
Authors: Tanji Yasunori , Hattori Kenji , Suzuki Kohichi , Miyanaga Kazuhiko 
Published: May 2008

ABSTRACT

To breed resistance to an assortment of infectious phages, continuous cultures of
Escherichia coli
JM109 grown in a chemostat were exposed to phage mixtures prepared from sewage influent. Four sequential chemostat-grown cultures were each infected with a different phage mixture. At the end of a chemostat run, one phage-resistant colony was isolated and used to inoculate the subsequent culture. This process was repeated, and increased phage resistance of the input bacterial strain resulted from the successive challenges with different phage cocktails. Multiple mutations apparently accumulated progressively. A mutant isolated at the end of the four runs, designated D198, showed resistance to 38 of 40 phages that infect the parent strain, JM109. D198 produced less outer membrane protein C (OmpC) than JM109. However, restoration of the OmpC protein by plasmid-mediated complementation did not completely restore the susceptibility of D198 to the 38 phages. Therefore, alterations beyond the level of OmpC protein production contribute to the phage resistance of D198. PCR-based genetic analysis revealed that D198 has a genome that is 209 kbp (about 200 genes) smaller than JM109. The deletion includes the chromosomal section from
ompC
to
wbbL
that encodes the rhamnosyl transferase involved in lipopolysaccharide biosynthesis. Strains D198 and JM109 were comparable in their growth characteristics and their abilities to express a recombinant protein.
Analysis of Vaginal Lactobacilli from Healthy and Infected Brazilian Women
Authors: Martinez Rafael C. R. , Franceschini Sílvio A. , Patta Maristela C. , Quintana Silvana M. , Nunes Álvaro C. , Moreira João L. S. , Anukam Kingsley C. , Reid Gregor , De Martinis Elaine C. P. 
Published: May 2008

ABSTRACT

Culture-dependent PCR-amplified rRNA gene restriction analysis and culture-independent (PCR-denaturing gradient gel electrophoresis) methodologies were used to examine vaginal lactobacilli from Brazilian women who were healthy or had been diagnosed with vulvovaginal candidiasis (VVC) or bacterial vaginosis. Only
Lactobacillus crispatus
was detected accordingly by both methods, and H
2
O
2
-producing lactobacilli were not associated with protection against VVC.
Agrobacterium
-Mediated Disruption of a Nonribosomal Peptide Synthetase Gene in the Invertebrate Pathogen
Metarhizium anisopliae
Reveals a Peptide Spore Factor
Authors: Moon Yong-Sun , Donzelli Bruno G. G. , Krasnoff Stuart B. , McLane Heather , Griggs Mike H. , Cooke Peter , Vandenberg John D. , Gibson Donna M. , Churchill Alice C. L. 
Published: May 2008

ABSTRACT

Numerous secondary metabolites have been isolated from the insect pathogenic fungus
Metarhizium anisopliae
, but the roles of these compounds as virulence factors in disease development are poorly understood. We targeted for disruption by
Agrobacterium tumefaciens
-mediated transformation a putative nonribosomal peptide synthetase (NPS) gene, Ma
NPS1
. Four of six gene disruption mutants identified were examined further. Chemical analyses showed the presence of serinocyclins, cyclic heptapeptides, in the extracts of conidia of control strains, whereas the compounds were undetectable in ΔMa
nps1
mutants treated identically or in other developmental stages, suggesting that Ma
NPS1
encodes a serinocyclin synthetase. Production of the cyclic depsipeptide destruxins,
M. anisopliae
metabolites also predicted to be synthesized by an NPS, was similar in ΔMa
nps1
mutant and control strains, indicating that Ma
NPS1
does not contribute to destruxin biosynthesis. Surprisingly, a Ma
NPS1
fragment detected DNA polymorphisms that correlated with relative destruxin levels produced in vitro, and Ma
NPS1
was expressed concurrently with in vitro destruxin production. ΔMa
nps1
mutants exhibited in vitro development and responses to external stresses comparable to control strains. No detectable differences in pathogenicity of the ΔMa
nps1
mutants were observed in bioassays against beet armyworm and Colorado potato beetle in comparison to control strains. This is the first report of targeted disruption of a secondary metabolite gene in
M. anisopliae
, which revealed a novel cyclic peptide spore factor.
Potential Prebiotic Properties of Almond (Amygdalus communisL.) Seeds
Authors: Mandalari G. , Nueno-Palop C. , Bisignano G. , Wickham M. S. J. , Narbad A. 
Published: May 2008

ABSTRACTAlmonds are known to have a number of nutritional benefits, including cholesterol-lowering effects and protection against diabetes. They are also a good source of minerals and vitamin E, associated with promoting health and reducing the risk for chronic disease. For this study we investigated the potential prebiotic effect of almond seeds in vitro by using mixed fecal bacterial cultures. Two almond products, finely ground almonds (FG) and defatted finely ground almonds (DG), were subjected to a combined model of the gastrointestinal tract which included in vitro gastric and duodenal digestion, and the resulting fractions were subsequently used as substrates for the colonic model to assess their influence on the composition and metabolic activity of gut bacteria populations. FG significantly increased the populations of bifidobacteria andEubacterium rectale, resulting in a higher prebiotic index (4.43) than was found for the commercial prebiotic fructooligosaccharides (4.08) at 24 h of incubation. No significant differences in the proportions of gut bacteria groups were detected in response to DG. The increase in the numbers ofEubacterium rectaleduring fermentation of FG correlated with increased butyrate production. In conclusion, we have shown that the addition of FG altered the composition of gut bacteria by stimulating the growth of bifidobacteria andEubacterium rectale.
Retail Survey of Brazilian Milk and Minas Frescal Cheese and a Contaminated Dairy Plant To Establish Prevalence, Relatedness, and Sources of
Listeria monocytogenes
Isolates
Authors: Brito J. Renaldi F. , Santos Emilia M. P. , Arcuri Edna F. , Lange Carla C. , Brito Maria A. V. P. , Souza Guilherme N. , Cerqueira Mônica M. P. O. , Beltran J. Marcela Soto , Call Jeffrey E. , Liu Yanhong , Porto-Fett Anna C. S. , Luchansky John B. 
Published: May 2008

ABSTRACT

A study was designed to recover
Listeria monocytogenes
from pasteurized milk and Minas frescal cheese (MFC) sampled at retail establishments (REs) and to identify the contamination source(s) of these products in the corresponding dairy processing plant. Fifty milk samples (9 brands) and 55 MFC samples (10 brands) were tested from REs located in Juiz de Fora, Minas Gerais, Brazil. All milk samples and 45 samples from 9 of 10 MFC brands tested negative for
L. monocytogenes
; however, “brand F” of MFC obtained from REs 119 and 159 tested positive. Thus, the farm/plant that produced brand F MFC was sampled; all samples from the milking parlor tested negative for
L. monocytogenes
, whereas several sites within the processing plant and the MFC samples tested positive. All 344 isolates recovered from retail MFC, plant F MFC, and plant F environmental samples were serotype 1/2a and displayed the same AscI or ApaI fingerprints. Since these results established that the storage coolers served as the contamination source of the MFC, plant F was closed so that corrective renovations could be made. Following renovation, samples from sites that previously tested positive for the pathogen were collected from the processing environment and from MFC on multiple visits; all tested negative for
L. monocytogenes
. In addition, on subsequent visits to REs 159 and 119, all MFC samples tested negative for the pathogen. Studies are ongoing to quantify the prevalence, levels, and types of
L. monocytogenes
in MFC and associated processing plants to lessen the likelihood of listeriosis in Brazil.
Role of the White Collar 1 Photoreceptor in Carotenogenesis, UV Resistance, Hydrophobicity, and Virulence of
Fusarium oxysporum
Authors: Ruiz-Roldán M. Carmen , Garre Victoriano , Guarro Josep , Mariné Marçal , Roncero M. Isabel G. 
Published: May 2008

ABSTRACT

Knockout mutants of
Fusarium oxysporum
lacking the putative photoreceptor Wc1 were impaired in aerial hyphae, surface hydrophobicity, light-induced carotenogenesis, photoreactivation after UV treatment, and upregulation of photolyase gene transcription. Infection experiments with tomato plants and immunodepressed mice revealed that Wc1 is dispensable for pathogenicity on plants but required for full virulence on mammals.
Candida albicans
Ferric Reductases Are Differentially Regulated in Response to Distinct Forms of Iron Limitation by the Rim101 and CBF Transcription Factors
Authors: Baek Yong-Un , Li Mingchun , Davis Dana A. 
Published: May 2008

ABSTRACT

Iron is an essential nutrient that is severely limited in the mammalian host.
Candida albicans
encodes a family of 15 putative ferric reductases, which are required for iron acquisition and utilization. Despite the central role of ferric reductases in iron acquisition and mobilization, relatively little is known about the regulatory networks that govern ferric reductase gene expression in
C. albicans
. Here we have demonstrated the differential regulation of two ferric reductases,
FRE2
and
FRP1
, in response to distinct iron-limited environments.
FRE2
and
FRP1
are both induced in alkaline-pH environments directly by the Rim101 transcription factor. However,
FRP1
but not
FRE2
is also induced by iron chelation. We have identified a CCAAT motif as the critical regulatory sequence for chelator-mediated induction and have found that the CCAAT binding factor (CBF) is essential for
FRP1
expression in iron-limited environments. We found that a
hap5
Δ/
hap5
Δ mutant, which disrupts the core DNA binding activity of CBF, is unable to grow under iron-limited conditions.
C. albicans
encodes three CBF-dependent transcription factors, and we identified the Hap43 protein as the CBF-dependent transcription factor required for iron-limited responses. These studies provide key insights into the regulation of ferric reductase gene expression in the fungal pathogen
C. albicans
.
Pet191 Is a Cytochrome
c
Oxidase Assembly Factor in
Saccharomyces cerevisiae
Authors: Khalimonchuk Oleh , Rigby Kevin , Bestwick Megan , Pierrel Fabien , Cobine Paul A. , Winge Dennis R. 
Published: May 2008

ABSTRACT

The twin-Cx
9
C motif protein Pet191 is essential for cytochrome
c
oxidase maturation. The motif Cys residues are functionally important and appear to be present in disulfide linkages within a large oligomeric complex associated with the mitochondrial inner membrane. The import of Pet191 differs from that of other twin-Cx
9
C motif class of proteins in being independent of the Mia40 pathway.
A Class 1 Integron Present in a Human Commensal Has a Hybrid Transposition Module Compared to Tn
402
: Evidence of Interaction with Mobile DNA from Natural Environments
Authors: Labbate M. , Chowdhury P. Roy , Stokes H. W. 
Published: May 2008

ABSTRACT

In a survey of class 1 integrons from human stools, an unusual class 1 integron from a strain of
Enterobacter cloacae
was isolated and characterized in detail. Sequence analysis of a fosmid containing the class 1 integron revealed a complex set of transposons which included two Tn
402
-like transposons. One of these transposons, Tn
6007
, included a class 1 integron with two non-antibiotic-resistance-type gene cassettes and a complete transposition module. This
tni
module is a hybrid with a boundary within the
res
site compared to Tn
402
, implying that a site-specific recombination event generated either Tn
6007
or Tn
402
. The second Tn
402
-like transposon, Tn
6008
, possesses neither a
mer
operon nor an integron, and most of its
tni
module has been deleted. Tn
6007
, Tn
6008
, and the 2,478 bases between them, collectively designated Tn
6006
, have transposed into a Tn
5036
/Tn
3926
-like transposon as a single unit. Tn
6006
, Tn
6007
, and Tn
6008
could all transpose as discrete entities. Database analysis also revealed that a version of Tn
6008
was present in the genome of
Xanthomonas campestris
pv. vesicatoria. Overall, the
E. cloacae
isolate further demonstrated that functional class 1 integrons/transposons are probably common in bacterial communities and have the potential to add substantially to the problem of multidrug-resistant nosocomial infections.
Type II Secretory Pathway for Surface Secretion of DraD Invasin from the Uropathogenic
Escherichia coli
Dr
+
Strain
Authors: Zalewska-Piątek Beata , Bury Katarzyna , Piątek Rafał , Bruździak Piotr , Kur Józef 
Published: May 2008

ABSTRACT

The virulence of the uropathogenic
Escherichia coli
Dr
+
IH11128 strain is associated with the presence of Dr fimbrial structures and a DraD invasin which can act as a fimbrial capping domain at the bacterial cell surface. However, a recent study suggests that the DraD protein is surface exposed in two forms: fimbria associated and fimbria nonassociated (prone to interaction with the N-terminal extension of the DraE protein located on the fimbrial tip). The actual mechanism of DraD surface secretion is presently unknown. We identified a previously unrecognized type II secretory pathway (secreton) in the uropathogenic
E. coli
Dr
+
strain which is well conserved among gram-negative bacteria and used mainly for secretion of virulence determinants. An active secreton is composed of 12 to 15 different proteins, among which GspD functions as an outer-membrane channel to permit extrusion of proteins in a folded state. Therefore, we inactivated the pathway by inserting the group II intron into a
gspD
gene of the type II secretion machinery by site-specific recombination. DraD secretion by the
E. coli
Dr
+
and
gspD
mutant strains was determined by immunofluorescence microscopy (with antibodies raised against DraD) and an assay of cell binding between bacteria and HeLa cells. The specificity of DraD-mediated bacterial binding for the integrin receptor was confirmed by examination of the adhesion of DraD-coated beads to HeLa cells in the presence and absence of α
5
β
1
monoclonal antibodies. The investigations that we performed showed that type II secretion in
E. coli
Dr
+
strains leads to DraD translocation at the bacterial cell surfaces.
Cell Cycle Characteristics of
Crenarchaeota
: Unity among Diversity
Authors: Lundgren Magnus , Malandrin Laurence , Eriksson Stefan , Huber Harald , Bernander Rolf 
Published: May 2008

ABSTRACT

The hyperthermophilic archaea
Acidianus hospitalis
,
Aeropyrum pernix
,
Pyrobaculum aerophilum
,
Pyrobaculum calidifontis
, and
Sulfolobus tokodaii
representing three different orders in the phylum
Crenarchaeota
were analyzed by flow cytometry and combined phase-contrast and epifluorescence microscopy. The overall organization of the cell cycle was found to be similar in all species, with a short prereplicative period and a dominant postreplicative period that accounted for 64 to 77% of the generation time. Thus, in all
Crenarchaeota
analyzed to date, cell division and initiation of chromosome replication occur in close succession, and a long time interval separates termination of replication from cell division. In
Pyrobaculum
, chromosome segregation overlapped with or closely followed DNA replication, and further genome separation appeared to occur concomitant with cellular growth. Cell division in
P. aerophilum
took place without visible constriction.
The Production In Vivo of Microcin E492 with Antibacterial Activity Depends on Salmochelin and EntF
Authors: Mercado Gabriela , Tello Mario , Marín Macarena , Monasterio Octavio , Lagos Rosalba 
Published: May 2008

ABSTRACTMicrocin E492 is a channel-forming bacteriocin that is found in two forms, namely, a posttranslationally modified form obtained by the covalent linkage of salmochelin-like molecules to serine 84 and an unmodified form. The production of modified microcin E492 requires the synthesis of enterochelin, which is subsequently glycosylated by MceC and converted into salmochelin.mceCmutants produced inactive microcin E492, and this phenotype was reversed either by complementation withiroBfromSalmonella entericaor by the addition of exogenous salmochelin. Cyclic salmochelin uptake byEscherichia colioccurred mainly through the outer membrane catecholate siderophore receptor Fiu. The production of inactive microcin E492 by mutants inentBandentCwas reverted by the addition of the end product of the respective mutated pathway (2,3-dihydroxybenzoic acid and enterochelin/salmochelin, respectively), while mutants inentFdid not produce active microcin E492 in the presence of enterochelin or salmochelin. The EntF adenylation domain was the only domain required for this microcin E492 maturation step. Inactivation of the enzymatic activity of this domain by site-directed mutagenesis did not prevent the synthesis of active microcin E492 in the presence of salmochelin, indicating that the adenylation activity is not essential for the function of EntF at this stage of microcin E492 maturation.
Xenorhabdus nematophila lrhAIs Necessary for Motility, Lipase Activity, Toxin Expression, and Virulence inManduca sextaInsects
Authors: Richards Gregory R. , Herbert Erin E. , Park Youngjin , Goodrich-Blair Heidi 
Published: May 2008

ABSTRACTThe gram-negative insect pathogenXenorhabdus nematophilapossesses potential virulence factors including an assortment of toxins, degradative enzymes, and regulators of these compounds. Here, we describe thelysR-likehomologA(lrhA) gene, a gene required byX. nematophilafor full virulence inManduca sextainsects. In several other gram-negative bacteria, LrhA homologs are transcriptional regulators involved in the expression (typically repression) of virulence factors. Based on phenotypic and genetic evidence, we report thatX. nematophilaLrhA has a positive effect on transcription and expression of certain potential virulence factors, including a toxin subunit-encoding gene,xptD1. Furthermore, anlrhAmutant lacks in vitro lipase activity and has reduced swimming motility compared to its wild-type parent. Quantitative PCR revealed that transcript levels of flagellar genes, a lipase gene, andxptD1were significantly lower in thelrhAmutant than in the wild type. In addition,lrhAitself is positively regulated by the global regulator Lrp. This work establishes a role for LrhA as a vital component of a regulatory hierarchy necessary forX. nematophilapathogenesis and expression of surface-localized and secreted factors. Future research is aimed at identifying and characterizing virulence factors within the LrhA regulon.