bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and Simple Cryopreservation of Anaerobic Ammonium-Oxidizing Bacteria
Authors: Heylen Kim , Ettwig Katharina , Hu Ziye , Jetten Mike , Kartal Boran 
Published: February 2012

ABSTRACT

A quick and simple protocol for long-term cryopreservation of anaerobic ammonium-oxidizing bacteria (anammox bacteria) was developed. After 29 weeks of preservation at −80°C, activity recovery for all tested cultures under at least one of the applied sets of preservation conditions was observed. Growth recovery was also demonstrated for a single-cell culture of “
Candidatus
Kuenenia stuttgartiensis.”
Identification of a
pheA
Gene Associated with Streptococcus mitis by Using Suppression Subtractive Hybridization
Authors: Park Hee Kuk , Dang Hien Thanh , Myung Soon Chul , Kim Wonyong 
Published: February 2012

ABSTRACT

We performed suppression subtractive hybridization to identify genomic differences between
Streptococcus mitis
and
Streptococcus pneumoniae
. Based on the
pheA
gene, a primer set specific to
S. mitis
detection was found in 18 out of 103
S. mitis
-specific clones. Our findings would be useful for discrimination of
S. mitis
from other closely related cocci in the oral environment.
Vibrio parahaemolyticus in Rhode Island Coastal Ponds and the Estuarine Environment of Narragansett Bay
Authors: Cox Annie M. , Gomez-Chiarri Marta 
Published: February 2012

ABSTRACT

Quantification of the abundance of
Vibrio parahaemolyticus
in water and oysters from Rhode Island showed the presence of environmental strains and low levels of potentially pathogenic strains when water temperatures were ≥18°C, with peak levels in late July to early August. A higher abundance of the
trh
gene than of the
tdh
gene was observed.
Seropathotypes, Phylogroups, Stx Subtypes, and Intimin Types of Wildlife-Carried, Shiga Toxin-Producing Escherichia coli Strains with the Same Characteristics as Human-Pathogenic Isolates
Authors: Mora Azucena , López Cecilia , Dhabi Ghizlane , López-Beceiro Ana M. , Fidalgo Luís E. , Díaz Eduardo A. , Martínez-Carrasco Carlos , Mamani Rosalía , Herrera Alexandra , Blanco Jesús E. , Blanco Miguel , Blanco Jorge 
Published: February 2012

ABSTRACTThe objectives of this study were to investigate the presence of Shiga toxin-producingEscherichia coli(STEC) strains in wildlife that have spread in Europe, living near human settlements; to analyze their epidemiological role in maintenance and transmission to domestic livestock; and to assess the potential health risk of wildlife-carried strains. STEC strains were recovered from 53% of roe deer, 8.4% of wild boars, and 1.9% of foxes sampled in the northwest of Spain (Galicia). Of the 40 serotypes identified, 21 were classified as seropathotypes associated with human disease, accounting for 81.5% of the wildlife-carried STEC strains, including the enterohemorrhagic serotypes O157:H7-D-eae-γ1, O26:[H11]-B1-eae-β1, O121:H19-B1-eae-ε1, and O145:[H28]-D-eae-γ1. None of the wildlife-carried strains belonged to the highly pathogenic serotype O104:H4-B1 from the recent Germany outbreak. Forty percent of wildlife-carried STEC strains shared serotypes, phylogroups, intimin types, and Stx profiles with isolates from human patients from the same geographic area. Furthermore, wildlife-carried strains belonging to serotypes O5:HNM-A, O26:[H11]-B1, O76:H19-B1, O145:[H28]-D, O146:H21-B1, and O157:H7-D showed pulsed-field gel electrophoresis (PFGE) profiles with >85% similarity to human-pathogenic STEC strains. We also found a high level of similarity among STEC strains of serotypes O5:HNM-A, O26:[H11]-B1, and O145:HNM-D of bovine (feces and beef) and wildlife origins. Interestingly, O146:H21-B1, the second most frequently detected serotype in this study, is commonly associated with human diarrhea and isolated from beef and vegetables sold in Galicia. Importantly, at least 3 STEC isolates from foxes (O5:HNM-A-eae-β1, O98:[H21]-B1-eae-ζ1, and O146:[H21]-B1) showed characteristics similar to those of human STEC strains. In conclusion, roe deer, wild boar, and fox in Galicia are confirmed to be carriers of STEC strains potentially pathogenic for humans and seem to play an important role in the maintenance of STEC.
Listeria monocytogenes Shows Temperature-Dependent and -Independent Responses to Salt Stress, Including Responses That Induce Cross-Protection against Other Stresses
Authors: Bergholz Teresa M. , Bowen Barbara , Wiedmann Martin , Boor Kathryn J. 
Published: February 2012

ABSTRACT

The food-borne pathogen
Listeria monocytogenes
experiences osmotic stress in many habitats, including foods and the gastrointestinal tract of the host. During transmission,
L. monocytogenes
is likely to experience osmotic stress at different temperatures and may adapt to osmotic stress in a temperature-dependent manner. To understand the impact of temperature on the responses this pathogen uses to adapt to osmotic stress, we assessed genome-wide changes in the
L. monocytogenes
H7858 transcriptome during short-term and long-term adaptation to salt stress at 7°C and 37°C. At both temperatures, the short-term response to salt stress included increased transcript levels of
sigB
and SigB-regulated genes, as well as
mrpABCDEFG
, encoding a sodium/proton antiporter. This antiporter was found to play a role in adaptation to salt stress at both temperatures; Δ
mrpABCDEFG
had a significantly longer lag phase than the parent strain in BHI plus 6% NaCl at 7°C and 37°C. The short-term adaptation to salt stress at 7°C included increased transcript levels of two genes encoding carboxypeptidases that modify peptidoglycan. These carboxypeptidases play a role in the short-term adaptation to salt stress only at 7°C, where the deletion mutants had significantly different lag phases than the parent strain. Changes in the transcriptome at both temperatures suggested that exposure to salt stress could provide cross-protection to other stresses, including peroxide stress. Short-term exposure to salt stress significantly increased H
2
O
2
resistance at both temperatures. These results provide information for the development of knowledge-based intervention methods against this pathogen, as well as provide insight into potential mechanisms of cross-protection.
Characterization of Esterase A, a Pseudomonas stutzeri A15 Autotransporter
Authors: Nicolay Toon , Devleeschouwer Ken , Vanderleyden Jos , Spaepen Stijn 
Published: February 2012

ABSTRACT

Autotransporters are a widespread family of proteins, generally known as virulence factors produced by Gram-negative bacteria. In this study, the esterase A (EstA) autotransporter of the rice root-colonizing beneficial bacterium
Pseudomonas stutzeri
A15 was characterized. A multiple sequence alignment identified EstA as belonging to clade II of the GDSL esterase family. Autologous overexpression allowed the investigation of several features of both autotransporter proteins and GDSL esterases. First, the correctly folded autotransporter was shown to be present in the membrane fraction. Unexpectedly, after separation of the membrane fraction, EstA was detected in the
N
-laurylsarcosine soluble fraction. However, evidence is presented for the surface exposure of EstA based on fluorescent labeling with EstA specific antibodies. Another remarkable feature is the occurrence of a C-terminal leucine residue instead of the canonical phenylalanine or tryptophan residue. Replacement of this residue with a phenylalanine residue reduced the stability of the β-barrel. Regarding the esterase passenger domain, we show the importance of the catalytic triad residues, with the serine and histidine residues being more critical than the aspartate residue. Furthermore, the growth of an
estA
-negative mutant was not impaired and cell mobility was not disabled compared to the wild type. No specific phenotype was detected for an
estA
-negative mutant. Overall,
P. stutzeri
A15 EstA is a new candidate for the surface display of proteins in environmentally relevant biotechnological applications.
Longitudinal Study of the Persistence of Antimicrobial-Resistant Campylobacter Strains in Distinct Swine Production Systems on Farms, at Slaughter, and in the Environment
Authors: Quintana-Hayashi Macarena P. , Thakur Siddhartha 
Published: February 2012

ABSTRACT

The objectives of this study were to compare and characterize the prevalence of antimicrobial-resistant (AR)
Campylobacter
in conventional and antimicrobial-free (ABF) production systems on farms, at slaughter, and in the environment. Fecal and environmental samples were collected from ABF farms (pigs, 1,239; environment, 797) and conventional farms (pigs, 1,650; environment, 1,325). At slaughter, we collected samples from carcasses, including postevisceration swabs, postchill swabs, and mesenteric lymph nodes from ABF systems (postevisceration swabs, 182; postchill swabs, 199; mesenteric lymph nodes, 184) and conventional systems (postevisceration swabs, 272; postchill swabs, 271; mesenteric lymph nodes, 255) at separate processing facilities. We also sampled the processing plant environment, including truck and lairage floor swab samples (ABF, 115; conventional, 90). Overall, a total of 2,908
Campylobacter
isolates, including
Campylobacter coli
(farm, 2,557, 99.8%; slaughter, 341, 98.3%) and
Campylobacter jejuni
(farm, 4, 0.2%; slaughter, 6, 1.7%), were isolated in the study. There was no significant difference in the prevalence of
Campylobacter
between ABF and conventionally raised pigs (farrowing,
P
= 0.20; nursery,
P
= 0.06; finishing,
P
= 0.24) and the environment (
P
= 0.37). At slaughter,
Campylobacter
was isolated from all of the stages, including postchill. The highest frequencies of resistance were exhibited against tetracycline (ABF, 48.2%; conventional, 88.3%). Ciprofloxacin-resistant
C. coli
isolates were observed in conventionally raised (17.1%) and ABF (1.2%) pigs (
P
= 0.11). Antimicrobial use data from conventional farms indicated significant associations between oxytetracycline use and tetracycline resistance in the nursery pigs (
P
= 0.01), between tiamulin exposure and azithromycin and erythromycin resistance in nursery (
P
< 0.01) and finishing (
P
< 0.01) pigs, and between enrofloxacin exposure and ciprofloxacin and nalidixic acid resistance in farrowing (
P
< 0.01) and nursery (
P
< 0.01) pigs. Identical antimicrobial resistance profiles were observed in the pigs and their environments on farms and at slaughter. In summary, our results highlight the persistence and dissemination of AR
Campylobacter
from farm to slaughter in ABF and conventionally raised pigs and their environments.
Piglets Are a Source of Pathogenic Yersinia enterocolitica on Fattening-Pig Farms
Authors: Virtanen Sonja , Salonen Laura , Laukkanen-Ninios Riikka , Fredriksson-Ahomaa Maria , Korkeala Hannu 
Published: February 2012

ABSTRACT

To study the origin and spread of
Yersinia enterocolitica
among pigs, fecal and blood samples were repeatedly taken on a fattening farm. A few piglets were found to be already infected on breeding farms. After the piglets were mixed, the infection spread through the whole unit. Eventually, all the pigs excreted the pathogen.
Rerouting Carbon Flux To Enhance Photosynthetic Productivity
Authors: Ducat Daniel C. , Avelar-Rivas J. Abraham , Way Jeffrey C. , Silver Pamela A. 
Published: February 2012

ABSTRACT

The bioindustrial production of fuels, chemicals, and therapeutics typically relies upon carbohydrate inputs derived from agricultural plants, resulting in the entanglement of food and chemical commodity markets. We demonstrate the efficient production of sucrose from a cyanobacterial species,
Synechococcus elongatus
, heterologously expressing a symporter of protons and sucrose (
cscB
).
cscB
-expressing cyanobacteria export sucrose irreversibly to concentrations of >10 mM without culture toxicity. Moreover, sucrose-exporting cyanobacteria exhibit increased biomass production rates relative to wild-type strains, accompanied by enhanced photosystem II activity, carbon fixation, and chlorophyll content. The genetic modification of sucrose biosynthesis pathways to minimize competing glucose- or sucrose-consuming reactions can further improve sucrose production, allowing the export of sucrose at rates of up to 36.1 mg liter
−1
h illumination
−1
. This rate of production exceeds that of previous reports of targeted, photobiological production from microbes. Engineered
S. elongatus
produces sucrose in sufficient quantities (up to ∼80% of total biomass) such that it may be a viable alternative to sugar synthesis from terrestrial plants, including sugarcane.
Evidence of an Evolutionarily Conserved LMBR1 Domain-Containing Protein That Associates with Endocytic Cups and Plays a Role in Cell Migration in Dictyostelium discoideum
Authors: Kelsey Jessica S. , Fastman Nathan M. , Blumberg Daphne D. 
Published: February 2012

ABSTRACT

The
ampA
gene plays a role in
Dictyostelium discoideum
cell migration. Loss of
ampA
function results in reduced ability of growing cells to migrate to folic acid and causes small plaques on bacterial lawns, while overexpression of AmpA results in a rapid-migration phenotype and correspondingly larger plaques than seen with wild-type cells. To help understand how the
ampA
gene functions, second-site suppressors were created by restriction enzyme-mediated integration (REMI) mutagenesis. These mutants were selected for their ability to reduce the large plaque size of the AmpA overexpresser strain. The
lmbd2B
gene was identified as a suppressor of an AmpA-overexpressing strain. The
lmbd2B
gene product belongs to the evolutionarily conserved LMBR1 protein family, some of whose known members are endocytic receptors associated with human diseases, such as anemia. In order to understand
lmbd2B
function, mRFP fusion proteins were created and
lmbd2B
knockout cell lines were established. Our findings indicate that the LMBD2B protein is found associated with endocytic cups. It colocalizes with proteins that play key roles in endocytic events and is localized to ruffles on the dorsal surfaces of growing cells. Vegetative
lmbd2B
-null cells display defects in cell migration. These cells have difficulty sensing the chemoattractant folic acid, as indicated by a decrease in their chemotactic index.
lmbd2B
-null cells also appear to have difficulty establishing a front/back orientation to facilitate migration. A role for
lmbd2B
in development is also suggested. Our research gives insight into the function of a previously uncharacterized branch of the LMBR1 family of proteins. We provide evidence of an LMBR1 family plasma membrane protein that associates with endocytic cups and plays a role in chemotaxis.
Delta-Aminolevulinate-Induced Host-Parasite Porphyric Disparity for Selective Photolysis of Transgenic Leishmania in the Phagolysosomes of Mononuclear Phagocytes: a Potential Novel Platform for Vaccine Delivery
Authors: Dutta Sujoy , Chang Celia , Kolli Bala Krishna , Sassa Shigeru , Yousef Malik , Showe Michael , Showe Louise , Chang Kwang-Poo 
Published: February 2012

ABSTRACTLeishmaniadouble transfectants (DTs) expressing the 2nd and 3rd enzymes in the heme biosynthetic pathway were previously reported to show neogenesis of uroporphyrin I (URO) when induced with delta-aminolevulinate (ALA), the product of the 1st enzyme in the pathway. The ensuing accumulation of URO in DT promastigotes rendered them light excitable to produce reactive oxygen species (ROS), resulting in their cytolysis. Evidence is presented showing that the DTs retained wild-type infectivity to their host cells and that the intraphagolysosomal/parasitophorous vacuolar (PV) DTs remained ALA inducible for uroporphyrinogenesis/photolysis. Exposure of DT-infected cells to ALA was noted by fluorescence microscopy to result in host-parasite differential porphyrinogenesis: porphyrin fluorescence emerged first in the host cells and then in the intra-PV amastigotes. DT-infected and control cells differed qualitatively and quantitatively in their porphyrin species, consistent with the expected multi- and monoporphyrinogenic specificities of the host cells and the DTs, respectively. After ALA removal, the neogenic porphyrins were rapidly lost from the host cells but persisted as URO in the intra-PV DTs. These DTs were thus extremely light sensitive and were lysed selectively by illumination under nonstringent conditions in the relatively ROS-resistant phagolysosomes. Photolysis of the intra-PV DTs returned the distribution of major histocompatibility complex (MHC) class II molecules and the global gene expression profiles of host cells to their preinfection patterns and, when transfected with ovalbumin, released this antigen for copresentation with MHC class I molecules. TheseLeishmaniamutants thus have considerable potential as a novel model of a universal vaccine carrier for photodynamic immunotherapy/immunoprophylaxis.
The TonB3 System in the Human Pathogen Vibrio vulnificus Is under the Control of the Global Regulators Lrp and Cyclic AMP Receptor Protein
Authors: Alice Alejandro F. , Crosa Jorge H. 
Published: February 2012

ABSTRACT

TonB systems transduce the proton motive force of the cytoplasmic membrane to energize substrate transport through a specific TonB-dependent transporter across the outer membrane.
Vibrio vulnificus
, an opportunistic marine pathogen that can cause a fatal septicemic disease in humans and eels, possesses three TonB systems. While the TonB1 and TonB2 systems are iron regulated, the TonB3 system is induced when the bacterium grows in human serum. In this work we have determined the essential roles of the leucine-responsive protein (Lrp) and cyclic AMP (cAMP) receptor protein (CRP) in the transcriptional activation of this system. Whereas Lrp shows at least four very distinctive DNA binding regions spread out from position −59 to −509, cAMP-CRP binds exclusively in a region centered at position −122.5 from the start point of the transcription. Our results suggest that both proteins bind simultaneously to the region closer to the RNA polymerase binding site. Importantly, we report that the TonB3 system is induced not only by serum but also during growth in minimal medium with glycerol as the sole carbon source and low concentrations of Casamino Acids. In addition to catabolite repression by glucose,
l
-leucine acts by inhibiting the binding of Lrp to the promoter region, hence preventing transcription of the TonB3 operon. Thus, this TonB system is under the direct control of two global regulators that can integrate different environmental signals (i.e., glucose starvation and the transition between “feast” and “famine”). These results shed light on new mechanisms of regulation for a TonB system that could be widespread in other organisms.
Evidence that a Single Monomer of Spx Can Productively Interact with RNA Polymerase in Bacillus subtilis
Authors: Lin Ann A. , Zuber Peter 
Published: February 2012

ABSTRACT

Spx activates transcription initiation in
Bacillus subtilis
by directly interacting with the C-terminal domain of the RNA polymerase (RNAP) holoenzyme α subunit, which generates a complex that recognizes the promoter regions of genes within the Spx regulon. Many Gram-positive species possess multiple paralogs of Spx, suggesting that two paralogous forms of Spx could simultaneously contact RNAP. The composition of Spx/RNAP was examined
in vitro
using an Spx variant (SpxΔCHA) bearing a 12-amino-acid deletion of the C terminus (SpxΔC) and a hemagglutinin (HA) epitope tag and Spxc-Myc, a full-length Spx with a C-terminal myelocytomatosis oncoprotein (c-Myc) epitope tag. All Spx/RNAP complexes bearing deletion or C-terminal-tagged variants were transcriptionally active
in vivo
and
in vitro
. Reaction mixtures containing SpxΔCHA and Spxc-Myc combined with RNAP were applied to either anti-HA or anti-c-Myc affinity columns. Eluted fractions contained RNAP with only one of the epitope-tagged Spx derivatives. The resin-bound RNAP complex bearing a single epitope-tagged Spx derivative was transcriptionally active.
In vivo
production of SpxΔC and SpxΔCHA followed by anti-HA affinity column chromatography of a cleared lysate resulted in retrieval of Spx/RNAP with only the SpxΔCHA derivative. Binding reactions that combined active Spxc-Myc, inactive Spx(R60E)ΔCHA, and RNAP, when applied to the anti-HA affinity column, yielded only inactive Spx(R60E)ΔCHA/RNAP complexes. The results strongly argue for a model in which a single Spx monomer engages RNAP to generate an active transcriptional complex.
Genome-Wide Definition of the SigF Regulon in Mycobacterium tuberculosis
Authors: Hartkoorn Ruben C. , Sala Claudia , Uplekar Swapna , Busso Philippe , Rougemont Jacques , Cole Stewart T. 
Published: February 2012

ABSTRACT

In
Mycobacterium tuberculosis
the alternative sigma factor SigF controls the expression of a particular subset of genes by altering RNA polymerase specificity. Here, we utilize two genome-wide approaches to identify SigF-binding sites: chromatin immunoprecipitation (ChIP-on-chip) and microarray analysis of SigF-mediated transcripts. Since SigF is not an abundant protein in the logarithmic phase of growth, a pristinamyin IA-inducible system was used to control its expression. We identified 67 high-affinity SigF-binding sites and 16 loci where a SigF promoter directs the expression of a transcript. These loci include
sigF
itself, genes involved in lipid and intermediary metabolism and virulence, and at least one transcriptional regulator (
Rv2884
), possibly acting downstream of SigF. In addition, SigF was also found to direct the transcription of the gene for small RNA F6. Many loci were also found where SigF may be involved in antisense transcription, and in two cases (
Rv1358
and
Rv1870c
) the SigF-dependent promoter was located within the predicted coding sequence. Quantitative PCR confirmed the microarray findings and 5′-rapid amplification of cDNA ends was used to map the SigF-specific transcriptional start points. A canonical SigF consensus promoter sequence GGTTT-N
(15-17)
-GGGTA was found prior to 11 genes. Together, these data help to define the SigF regulon and show that SigF not only governs expression of proteins such as the virulence factor, HbhA, but also impacts novel functions, such as noncoding RNAs and antisense transcripts.