bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Different Filling, Cooling, and Storage Conditions on the Growth ofAlicyclobacillus acidoterrestrisCRA7152 in Orange Juice
Authors: Spinelli Ana Cláudia N. F. , Sant'Ana Anderson S. , Rodrigues-Junior Salatir , Massaguer Pilar R. 
Published: October 2009

ABSTRACTThe prevention of spoilage byAlicyclobacillus acidoterrestrisis a current challenge for fruit juice and beverage industries worldwide due to the bacterium's acidothermophilic growth capability, heat resistance, and spoilage potential. This study examined the effect of storage temperature onA. acidoterrestrisgrowth in hot-filled orange juice. The evolution of theA. acidoterrestrispopulation was monitored under six different storage conditions after pasteurization (at 92°C for 10 s), maintenance at 85°C for 150 s, and cooling with water spray to 35°C in about 30 min and using two inoculum levels: <101and 101spores/ml. Final cooling and storage conditions were as follows: treatment 1, 30°C for the bottle cold point and storage at 35°C; treatment 2, 30°C for 48 h and storage at 35°C; treatment 3, 25°C for the bottle cold point and storage at 35°C; treatment 4, 25°C for 48 h and storage at 35°C; treatment 5, storage at 20°C (control); and treatment 6, filling and storage at 25°C. It was found that only in treatment 5 did the population remain inhibited during the 6 months of orange juice shelf life. By examining treatments 1 to 4, it was observed thatA. acidoterrestrispredicted growth parameters were significantly influenced (P< 0.05) either by inoculum level or cooling and storage conditions. The time required to reach a 104CFU/ml population ofA. acidoterrestriswas considered to be an adequate parameter to indicate orange juice spoilage byA. acidoterrestris. Therefore, hot-filled orange juice should be stored at or below 20°C to avoid spoilage by this microorganism. This procedure can be considered a safe and inexpensive alternative to other treatments proposed earlier.
Diversity of
nirK
Denitrifying Genes and Transcripts in an Agricultural Soil
Authors: Wertz Sophie , Dandie Catherine E. , Goyer Claudia , Trevors Jack T. , Patten Cheryl L. 
Published: October 2009

ABSTRACT

Environmental conditions can change dramatically over a crop season and among locations in an agricultural field and can increase denitrification and emissions of the potent greenhouse gas nitrous oxide. In a previous study, changes in the overall size of the denitrifier community in a potato crop field were relatively small and did not correlate with variations in environmental conditions or denitrification rates. However, denitrifying bacteria are taxonomically diverse, and different members of the community may respond differently to environmental changes. The objective of this research was to understand which portion of the
nirK
denitrifying community is active and contributes to denitrification under conditions in a potato crop field. Denaturing gradient gel electrophoresis (DGGE) of
nirK
genes in soil-extracted DNA showed changes in the composition of the
nirK
denitrifier community over the growing season and among spatial locations in the field. By contrast, the composition of the active
nirK
denitrifier community, as determined by DGGE analysis of
nirK
transcripts derived from soil-extracted mRNA, changed very little over time, although differences in the relative abundance of some specific transcripts were observed between locations. Our results indicate that the soil denitrifier populations bearing
nirK
genes are not all contributing to denitrification and that the denitrifying populations that are active are among the most abundant and ubiquitous
nirK
-bearing denitrifiers. Changes in the community composition of the total and active
nirK
denitrifiers were not strongly correlated with changes in environmental factors and denitrification activity.
Dynamics of Clinical and Environmental
Vibrio parahaemolyticus
Strains during Seafood-Related Summer Diarrhea Outbreaks in Southern Chile
Authors: García Katherine , Torres Rafael , Uribe Paulina , Hernández Cristina , Rioseco M. Luisa , Romero Jaime , Espejo Romilio T. 
Published: October 2009

ABSTRACT

Seafood consumption-related diarrhea became prevalent in Chile when the pandemic strain of
Vibrio parahaemolyticus
serotype O3:K6 reached a region in the south of Chile (Region de los Lagos) where approximately 80% of the country's seafood is produced. In spite of the large outbreaks of clinical infection, the load of
V. parahaemolyticus
in shellfish of this region is relatively low. The pandemic strain constitutes a small but relatively stable group of a diverse
V. parahaemolyticus
population, composed of at least 28 genetic groups. Outbreaks in Region de los Lagos began in 2004 and reached a peak in 2005 with 3,725 clinical cases, all associated with the pandemic strain. After 2005, reported cases steadily decreased to a total of 477 cases in 2007. At that time, 40% of the clinical cases were associated with a pandemic strain of a different serotype (O3:K59), and 27% were related to
V. parahaemolyticus
isolates unrelated to the pandemic strain. In the results published here, we report that in the summer of 2008, when reported cases unexpectedly increased from 477 to 1,143, 98% of the clinical cases were associated with the pandemic strain serotype O3:K6, a change from 2007. Nevertheless, in 2009, when clinical cases decreased to 441, only 64% were related to the pandemic strain; the remaining cases were related to a nonpandemic
tdh-
and
trh
-negative strain first identified in shellfish in 2006. Overall, our observations indicate that the pandemic strain has become a relatively stable subpopulation and that when the number of diarrhea cases related to the pandemic strain is low, previously undetected
V. parahaemolyticus
pathogenic strains become evident.
Phenotypic and Gene Expression Changes among Clonal Type I Strains of
Toxoplasma gondii
Authors: Khan Asis , Behnke Michael S. , Dunay Ildiko R. , White Michael W. , Sibley L. David 
Published: October 2009

ABSTRACT

Toxoplasma gondii
has an unusual population structure consisting of three clonal lineages that predominate in North America and Europe. This simple pattern has encouraged the use of only a few laboratory isolates that are representative of each lineage. Principle among these is the type I RH strain, originally isolated from a child with encephalitis some 70 years ago. Comparison of different passages of the RH strain that have been propagated differently over the intervening time period revealed that the commonly used clonal line called RH-ERP was not representative of natural isolates of the type I lineage. Notably, RH-ERP formed much larger plaques than other type 1 strains, including a separate, earlier derived isolate of the RH strain. The RH-ERP variant also showed enhanced extracellular survival, faster growth, and decreased differentiation compared to the prototype type I strain GT1. Comparison of gene expression differences in the RH-ERP line revealed that several ABC transporters were upregulated, which may provide a growth advantage in vitro. These findings illustrate that dramatic phenotypic changes can arise in laboratory strains, emphasizing the need for comparison with recent clinical isolates.
Molecular Regulation of Arabinan and
l
-Arabinose Metabolism in
Hypocrea jecorina
(
Trichoderma reesei
)
Authors: Akel Eda , Metz Benjamin , Seiboth Bernhard , Kubicek Christian P. 
Published: October 2009

ABSTRACT

Hypocrea jecorina
(anamorph:
Trichoderma reesei
) can grow on plant arabinans by the aid of secreted arabinan-degrading enzymes. This growth on arabinan and its degradation product
l
-arabinose requires the operation of the aldose reductase XYL1 and the
l
-arabinitol dehydrogenase LAD1. Growth on arabinan and
l
-arabinose is also severely affected in a strain deficient in the general cellulase and hemicellulase regulator XYR1, but this impairment can be overcome by constitutive expression of the
xyl1
encoding the aldose reductase. An inspection of the genome of
H. jecorina
reveals four genes capable of degrading arabinan, i.e., the α-
l
-arabinofuranosidase encoding genes
abf1
,
abf2
, and
abf3
and also
bxl1
, which encodes a β-xylosidase with a separate α-
l
-arabinofuranosidase domain and activity but no endo-arabinanase. Transcriptional analysis reveals that in the parent strain QM9414 the expression of all of these genes is induced by
l
-arabinose and to a lesser extent by
l
-arabinitol and absent on
d
-glucose. Induction by
l
-arabinitol, however, is strongly enhanced in a Δ
lad1
strain lacking
l
-arabinitol dehydrogenase activity and severely impaired in an aldose reductase (Δ
xyl1
) strain, suggesting a cross talk between
l
-arabinitol and the aldose reductase XYL1 in an α-
l
-arabinofuranosidase gene expression. Strains bearing a knockout in the cellulase regulator
xyr1
do not show any induction of
abf2
and
bxl1
, and this phenotype cannot be reverted by constitutive expression of
xyl1
. The loss of function of
xyr1
has also a slight effect on the expression of
abf1
and
abf3
. We conclude that the expression of the four α-
l
-arabinofuranosidases of
H. jecorina
for growth on arabinan requires an early pathway intermediate (
l
-arabinitol or
l
-arabinose), the first enzyme of the pathway XYL1, and in the case of
abf2
and
bxl1
also the function of the cellulase regulator XYR1.
Structure and Distribution of Organelles and Cellular Location of Calcium Transporters in
Neurospora crassa
Authors: Bowman Barry J. , Draskovic Marija , Freitag Michael , Bowman Emma Jean 
Published: October 2009

ABSTRACT

We wanted to examine the cellular locations of four
Neurospora crassa
proteins that transport calcium. However, the structure and distribution of organelles in live hyphae of
N. crassa
have not been comprehensively described. Therefore, we made recombinant genes that generate translational fusions of putative organellar marker proteins with green or red fluorescent protein. We observed putative endoplasmic reticulum proteins, encoded by
grp-78
and
dpm
, in the nuclear envelope and associated membranes. Proteins of the vacuolar membrane, encoded by
vam-3
and
vma-1
, were in an interconnected network of small tubules and vesicles near the hyphal tip, while in more distal regions they were in large and small spherical vacuoles. Mitochondria, visualized with tagged ARG-4, were abundant in all regions of the hyphae. Similarly, we tagged the four
N. crassa
proteins that transport calcium with green or red fluorescent protein to examine their cellular locations. NCA-1 protein, a homolog of the SERCA-type Ca
2+
-ATPase of animal cells, colocalized with the endoplasmic reticulum markers. The NCA-2 and NCA-3 proteins are homologs of Ca
2+
-ATPases in the vacuolar membrane in yeast or in the plasma membrane in animal cells. They colocalized with markers in the vacuolar membrane, and they also occurred in the plasma membrane in regions of the hyphae more than 1 mm from the tip. The
cax
gene encodes a Ca
2+
/H
+
exchange protein found in vacuoles. As expected, the CAX protein localized to the vacuolar compartment. We observed, approximately 50 to 100 μm from the tip, a few spherical organelles that had high amounts of tagged CAX protein and tagged subunits of the vacuolar ATPase (VMA-1 and VMA-5). We suggest that this organelle, not described previously in
N. crassa
, may have a role in sequestering calcium.
Flexible Gates: Dynamic Topologies and Functions for FG Nucleoporins in Nucleocytoplasmic Transport
Authors: Terry Laura J. , Wente Susan R. 
Published: October 2009

ABSTRACT
The nuclear envelope is a physical barrier between the nucleus and cytoplasm and, as such, separates the mechanisms of transcription from translation. This compartmentalization of eukaryotic cells allows spatial regulation of gene expression; however, it also necessitates a mechanism for transport between the nucleus and cytoplasm. Macromolecular trafficking of protein and RNA occurs exclusively through nuclear pore complexes (NPCs), specialized channels spanning the nuclear envelope. A novel family of NPC proteins, the FG-nucleoporins (FG-Nups), coordinates and potentially regulates NPC translocation. The extensive repeats of phenylalanine-glycine (FG) in each FG-Nup directly bind to shuttling transport receptors moving through the NPC. In addition, FG-Nups are essential components of the nuclear permeability barrier. In this review, we discuss the structural features, cellular functions, and evolutionary conservation of the FG-Nups.
Toll-Like Receptors 2 and 4 Contribute to Sepsis-Induced Depletion of Spleen Dendritic Cells
Authors: Pène Frédéric , Courtine Emilie , Ouaaz Fatah , Zuber Benjamin , Sauneuf Bertrand , Sirgo Gonzalo , Rousseau Christophe , Toubiana Julie , Balloy Viviane , Chignard Michel , Mira Jean-Paul , Chiche Jean-Daniel 
Published: October 2009

ABSTRACT

Depletion of dendritic cells (DC) in secondary lymphoid organs is a hallmark of sepsis-induced immune dysfunction. In this setting, we investigated if Toll-like receptor (TLR)-dependent signaling might modulate the maturation process and the survival of DC. Using a model of sublethal polymicrobial sepsis induced by cecal ligation and puncture, we investigated the quantitative and functional features of spleen DC in wild-type, TLR2
−/−
, TLR4
−/−
, and TLR2
−/−
TLR4
−/−
mice. By 24 h, a decrease in the relative percentage of CD11c
high
spleen DC occurred in wild-type mice but was prevented in TLR2
−/−
, TLR4
−/−
, and TLR2
−/−
TLR4
−/−
mice. In wild-type mice, sepsis dramatically affected both CD11c
+
CD8α
+
and CD11c
+
CD8α
−
subsets. In all three types of knockout mice studied, the CD11c
+
CD8α
+
subset followed a depletion pattern similar to that for wild-type mice. In contrast, the loss of CD11c
+
CD8α
−
cells was attenuated in TLR2
−/−
and TLR4
−/−
mice and completely prevented in TLR2
−/−
TLR4
−/−
mice. Accordingly, apoptosis of spleen DC was increased in septic wild-type mice and inhibited in knockout mice. In addition we characterized the functional features of spleen DC obtained from septic mice. As shown by increased expression of major histocompatibility complex class II and CD86, polymicrobial sepsis induced maturation of DC, with subsequent increased capacity to prime T lymphocytes, similarly in wild-type and knockout mice. In response to CpG DNA stimulation, production of interleukin-12 was equally impaired in DC obtained from wild-type and knockout septic mice. In conclusion, although dispensable for the DC maturation process, TLR2 and TLR4 are involved in the mechanisms leading to depletion of spleen DC following polymicrobial sepsis.
The Glycosylphosphatidylinositol-Anchored Protease Sap9 Modulates the Interaction ofCandida albicanswith Human Neutrophils
Authors: Hornbach Anke , Heyken Antje , Schild Lydia , Hube Bernhard , Löffler Jürgen , Kurzai Oliver 
Published: October 2009

ABSTRACTHuman polymorphonuclear neutrophils (PMNs) play a major role in the immune defense against invasiveCandida albicansinfection. This fungal pathogen produces a set of aspartic proteases that directly contributes to virulence properties such as adhesion, tissue invasion, and immune evasion. We show here that, in contrast to other secreted proteases, the cell surface-associated isoform Sap9 has a major impact on the recognition ofC. albicansby PMNs.SAP9is required for the induction of PMN chemotaxis towardC. albicansfilaments, an essential prerequisite of effective PMN activation. Furthermore, deletion ofSAP9leads to a mitigated release of reactive oxygen intermediates (ROI) in human PMNs and decreasesC. albicans-induced apoptosis triggered by ROI formation. In confrontation assays, killing of aSAP9deletion mutant is reduced in comparison to wild-typeC. albicans. These data clearly implicate Sap9 protease activity in the initiation of protective innate immunity and suggest novel molecular mechanisms inC. albicans-host interaction leading to neutrophil activation.
Regulated Delayed Expression of
rfaH
in an Attenuated
Salmonella
enterica
Serovar Typhimurium Vaccine Enhances Immunogenicity of Outer Membrane Proteins and a Heterologous Antigen
Authors: Kong Qingke , Liu Qing , Roland Kenneth L. , Curtiss Roy 
Published: October 2009

ABSTRACT

RfaH is a transcriptional antiterminator that reduces the polarity of long operons encoding secreted and surface-associated cell components of
Salmonella enterica
serovar Typhimurium, including O antigen and lipopolysaccharide core sugars. A Δ
rfaH
mutant strain is attenuated in mice (50% lethal dose [LD
50
], >10
8
CFU). To examine the potential for using
rfaH
in conjunction with other attenuating mutations, we designed a series of strains in which we replaced the native
rfaH
promoter with the tightly regulated arabinose-dependent
araC
P
BAD
promoter so that
rfaH
expression was dependent on exogenously supplied arabinose provided during in vitro growth. Following colonization of host lymphoid tissues, where arabinose was not available, the P
BAD
promoter was no longer active and
rfaH
was not expressed. In the absence of RfaH, O antigen and core sugars were not synthesized. We constructed three mutant strains that expressed different levels of RfaH by altering the ribosome-binding sequence and start codon. One mutation, ΔP
rfaH178
, was introduced into the attenuated vaccine strain χ9241 (Δ
pabA
Δ
pabB
Δ
asdA
) expressing the pneumococcal surface protein PspA from an Asd
+
balanced-lethal plasmid. Mice immunized with this strain and boosted 4 weeks later induced higher levels of serum immunoglobulin G specific for PspA and for outer membrane proteins from other enteric bacteria than either an isogenic Δ
rfaH
derivative or the isogenic RfaH
+
parent. Eight weeks after primary oral immunization, mice were challenged with 200 LD
50
of virulent
S
treptococcus
pneumoniae
WU2. Immunization with ΔP
rfaH178
mutant strains led to increased levels of protection compared to that of the parent χ9241 and of a Δ
rfaH
derivative of χ9241.
A Family of Transcriptional Antitermination Factors Necessary for Synthesis of the Capsular Polysaccharides of
Bacteroides fragilis
Authors: Chatzidaki-Livanis Maria , Coyne Michael J. , Comstock Laurie E. 
Published: October 2009

ABSTRACT

A single strain of
Bacteroides fragilis
synthesizes eight distinct capsular polysaccharides, designated PSA to PSH. These polysaccharides are synthesized by-products encoded by eight separate polysaccharide biosynthesis loci. The genetic architecture of each of these eight loci is similar, including the fact that the first gene of each locus is a paralog of the first gene of each of the other PS loci. These proteins are designated the UpxY family, where x is replaced by a to h, depending upon the polysaccharide locus from which it is produced. Mutational analysis of three separate
upxY
genes demonstrated that they are necessary and specific for transcription of their respective polysaccharide biosynthesis operon and that they function in
trans
. Transcriptional reporter constructs, reverse transcriptase PCR, and deletion analysis demonstrated that the UpxYs do not affect initiation of transcription, but rather prevent premature transcriptional termination within the 5′ untranslated region between the promoter and the
upxY
gene. The UpxYs have conserved motifs that are present in NusG and NusG-like proteins. Mutation of two conserved residues within the conserved KOW motif abrogated UpaY activity, further confirming that these proteins belong to the NusG-like (NusG
SP
) family. Alignment of highly similar UpxYs led to the identification of a small region of these proteins predicted to confer specificity for their respective loci. Construction of an
upaY-upeY
hybrid that produced a protein in which a 17-amino-acid segment of UpaY was changed to that of UpeY altered UpaY's specificity, as it was now able to function in transcriptional antitermination of the PSE biosynthesis operon.
Cag3 Is a Novel Essential Component of theHelicobacter pyloriCag Type IV Secretion System Outer Membrane Subcomplex
Authors: Pinto-Santini Delia M. , Salama Nina R. 
Published: October 2009

ABSTRACTHelicobacter pyloristrains harboring thecagpathogenicity island (PAI) have been associated with more severe gastric disease in infected humans. ThecagPAI encodes a type IV secretion (T4S) system required for CagA translocation into host cells as well as induction of proinflammatory cytokines, such as interleukin-8 (IL-8).cagPAI genes sharing sequence similarity with T4S components from other bacteria are essential for Cag T4S function. OthercagPAI-encoded genes are also essential for Cag T4S, but lack of sequence-based or structural similarity with genes in existing databases has precluded a functional assignment for the encoded proteins. We have studied the role of one such protein, Cag3 (HP0522), in Cag T4S and determined Cag3 subcellular localization and protein interactions. Cag3 is membrane associated and copurifies with predicted inner and outer membrane Cag T4S components that are essential for Cag T4S as well as putative accessory factors. Coimmunoprecipitation and cross-linking experiments revealed specific interactions with HpVirB7 and CagM, suggesting Cag3 is a new component of the Cag T4S outer membrane subcomplex. Finally, lack of Cag3 lowers HpVirB7 steady-state levels, further indicating Cag3 makes a subcomplex with this protein.
Activated by Different Signals, the PhoP/PhoQ Two-Component System Differentially Regulates Metal Uptake
Authors: Choi Eunna , Groisman Eduardo A. , Shin Dongwoo 
Published: October 2009

ABSTRACT

The PhoP/PhoQ two-component system controls several physiological and virulence functions in
Salmonella enterica
. This system is activated by low Mg
2+
, acidic pH, and antimicrobial peptides, but the biological consequences resulting from sensing multiple signals are presently unclear. Here, we report that the PhoP/PhoQ system regulates different
Salmonella
genes depending on whether the inducing signal is acidic pH or low Mg
2+
. When
Salmonella
experiences acidic pH, the PhoP/PhoQ system promotes Fe
2+
uptake in a process that requires the response regulator RstA, activating transcription of the Fe
2+
transporter gene
feoB
. In contrast, the PhoP-induced RstA protein did not promote
feoB
expression at neutral pH with low Mg
2+
. The PhoP/PhoQ system promotes the expression of the Mg
2+
transporter
mgtA
gene only when activated in bacteria starved for Mg
2+
. This is because
mgtA
transcription promoted at high Mg
2+
concentrations by the acidic-pH-activated PhoP protein failed to reach the
mgtA
coding region due to the
mgtA
leader region functioning as a Mg
2+
sensor. Our results show that a single two-component regulatory system can regulate distinct sets of genes in response to different input signals.