bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correction of breathing‐induced errors in magnetic resonance thermometry of hyperthermia using multiecho field fitting techniques
Authors: Wyatt Cory R. , Soher Brian J. , MacFall James R. 
Published: December 2010

Purpose:Breathing motion can create large errors when performing magnetic resonance (MR) thermometry of the breast. Breath holds can be used to minimize these errors, but not eliminate them. Between breath holds, the referenceless method can be used to further reduce errors by relying on regions of nonheated fatty tissue surrounding the heated region. When the surrounding tissue is heated (i.e., for a hyperthermia treatment), errors can result due to phase changes of the small amounts of water in the tissue. Therefore, an extension of the referenceless method is proposed which fits for the field in fatty tissue independent of temperature change and extrapolates it to the water‐rich regions.Methods:Nonheating experiments were performed with male volunteers performing breath holds on top of a phantom mimicking a breast with a tumor. Heating experiments were also conducted with the same phantom while mechanically simulated breath holds were performed. A nonheating experiment was also performed with a healthy female breast. For each experiment, a nonlinear fitting algorithm was used to fit for temperature change and field inside of the fatty tissue. The field changes were then extrapolated into water‐rich (tumor) portions of the image using a least‐squares fit to a fifth‐order equation, to correct for field changes due to breath hold changes. Similar results were calculated using the image phase, to mimic the use of the referenceless method.Results:Phantom results showed large reduction of mean error and standard deviation. In the non‐heating experiments, the traditional referenceless method and our extended method both corrected by similar amounts. However, in the heating experiments, the average deviation of the temperature calculated with the extended method from a fiber optic probe temperature was approximately 50% less than the deviation with the referenceless method. The in vivo breast results demonstrated reduced standard deviation and mean.Conclusions:In this paper, we have developed an extension of the referenceless method to correct for breathing errors using multiecho fitting methods to fit for the field in the fatty tissue and using measured field changes as references to extrapolate field corrections into a water‐only (tumor) region. This technique has been validated in a number of situations, and in all cases, the correction method has been shown to greatly reduce temperature error in water‐rich regions. The method has also been shown to be an improvement over similar methods that use image phase changes instead of field changes, particularly when temperature changes are induced.
Different Genetic Elements Carrying the
tet
(W) Gene in Two Human Clinical Isolates of
Streptococcus suis
Authors: Palmieri Claudio , Princivalli Maria Stella , Brenciani Andrea , Varaldo Pietro E. , Facinelli Bruna 
Published: November 2010

ABSTRACT

The genetic support for
tet
(W), an emerging tetracycline resistance determinant, was studied in two strains of
Streptococcus suis
, SsCA and SsUD, both isolated in Italy from patients with meningitis. Two completely different
tet
(W)-carrying genetic elements, sharing only a
tet
(W)-containing segment barely larger than the gene, were found in the two strains. The one from strain SsCA was nontransferable, and aside from an
erm
(B)-containing insertion, it closely resembled a genomic island recently described in an
S. suis
Chinese human isolate in sequence, organization, and chromosomal location. The
tet
(W)-carrying genetic element from strain SsUD was transferable (at a low frequency) and, though apparently noninducible following mitomycin C treatment, displayed a typical phage organization and was named ΦSsUD.1. Its full sequence was determined (60,711 bp), the highest BLASTN score being
Streptococcus pyogenes
Φm46.1. ΦSsUD.1 exhibited a unique combination of antibiotic and heavy metal resistance genes. Besides
tet
(W), it contained a MAS (macrolide-aminoglycoside-streptothricin) fragment with an
erm
(B) gene having a deleted leader peptide and a
cadC
/
cadA
cadmium efflux cassette. The MAS fragment closely resembled the one recently described in pneumococcal transposons Tn
6003
and Tn
1545
. These resistance genes found in the ΦSsUD.1 phage scaffold differed from, but were in the same position as, cargo genes carried by other streptococcal phages. The chromosome integration site of ΦSsUD.1 was at the 3′ end of a conserved tRNA uracil methyltransferase (
rum
) gene. This site, known to be an insertional hot spot for mobile elements in
S. pyogenes
, might play a similar role in
S. suis
.
Detection of Airborne Lactococcal Bacteriophages in Cheese Manufacturing Plants
Authors: Verreault Daniel , Gendron Louis , Rousseau Geneviève M. , Veillette Marc , Massé Daniel , Lindsley William G. , Moineau Sylvain , Duchaine Caroline 
Published: November 2010

ABSTRACT

The dairy industry adds starter bacterial cultures to heat-treated milk to control the fermentation process during the manufacture of many cheeses. These highly concentrated bacterial populations are susceptible to virulent phages that are ubiquitous in cheese factories. In this study, the dissemination of these phages by the airborne route and their presence on working surfaces were investigated in a cheese factory. Several surfaces were swabbed, and five air samplers (polytetrafluoroethylene filter, polycarbonate filter, BioSampler, Coriolis cyclone sampler, and NIOSH two-stage cyclone bioaerosol personal sampler) were tested. Samples were then analyzed for the presence of two
Lactococcus lactis
phage groups (936 and c2), and quantification was done by quantitative PCR (qPCR). Both lactococcal phage groups were found on most swabbed surfaces, while airborne phages were detected at concentrations of at least 10
3
genomes/m
3
of air. The NIOSH sampler had the highest rate of air samples with detectable levels of lactococcal phages. This study demonstrates that virulent phages can circulate through the air and that they are ubiquitous in cheese manufacturing facilities.
Substantiation in
Enterococcus faecalis
of Dose-Dependent Resistance and Cross-Resistance to Pore-Forming Antimicrobial Peptides by Use of a Polydiacetylene-Based Colorimetric Assay
Authors: Mehla Jitender , Sood S. K. 
Published: November 2010

ABSTRACT

A better understanding of the antimicrobial peptide (AMP) resistance mechanisms of bacteria will facilitate the design of effective and potent AMPs. Therefore, to understand resistance mechanisms and for
in vitro
assessment, variants of
Enterococcus faecalis
that are resistant to different doses of the fungal AMP alamethicin (Alm
r
) were selected and characterized. The resistance developed was dose dependent, as both doses of alamethicin and degrees of resistance were colinear. The formation of bacterial cell aggregates observed in resistant cells may be the prime mechanism of resistance because overall, a smaller cell surface in aggregated cells is exposed to AMPs. Increased rigidity of the membranes of Alm
r
variants, because of their altered fatty acids, was correlated with limited membrane penetration by alamethicin. Thus, resistance developed against alamethicin was an adaptation of the bacterial cells through changes in their morphological features and physiological activity and the composition of membrane phospholipids. The Alm
r
variants showed cross-resistance to pediocin, which indicated that resistance developed against both AMPs may share a mechanism, i.e., an alteration in the cell membrane. High percentages of colorimetric response by both AMPs against polydiacetylene/lipid biomimetic membranes of Alm
r
variants confirmed that altered phospholipid and fatty acid compositions were responsible for acquisition of resistance. So far, this is the only report of quantification of resistance and cross-resistance using an
in vitro
colorimetric approach. Our results imply that a single AMP or AMP analog may be effective against bacterial strains having a common mechanism of resistance. Therefore, an understanding of resistance would contribute to the development of a single efficient, potent AMP against resistant strains that share a mechanism of resistance.
Interaction of Transcriptional Repressor ArgR with Transcriptional Regulator FarR at the
argB
Promoter Region in
Corynebacterium glutamicum
Authors: Lee Soo Youn , Park Jae-Min , Lee Jin Hyung , Chang Suk-Tai , Park Jin-Soo , Kim Yang-Hoon , Min Jiho 
Published: November 2010

ABSTRACT

In
Corynebacterium glutamicum
, the ArgR protein, a transcriptional repressor, affects the expression level of the
argB
gene through binding to its promoter region. The
argB
promoter region (positions −77 to −25) has been found by
in vitro
electrophoretic mobility shift assay (EMSA) results and
in silico
analysis to be important for the DNA binding of ArgR. Proline supplementation prevented the DNA binding of ArgR to the
argB
promoter region and triggered an increase of the
argB
mRNA level. Additional mutational analyses of the
argB
promoter region found nucleotides critical for ArgR binding (G located at position −58, C at position −55, and A at position −41 of the
argB
promoter) in that region. Another transcriptional repressor, FarR, was also demonstrated to bind to the
argB
promoter region. This binding was delimited to positions −57 to −77 on the
argB
promoter. FarR has only one putative binding domain located at positions −57 to −77, but this region exactly overlapped with the binding region located from positions −55 to −77 for the binding of ArgR within the
argB
promoter; thus, if ArgR bound with the
argB
promoter first, the binding of FarR was not observed in this region. However, if FarR bound to the binding domain located at positions −57 to −77 first, ArgR could bind other binding sites located at positions −49 to −25 within the
argB
promoter. Finally, this study suggests that ArgR can affect FarR binding to the
argB
promoter region, as protein binding is dominated by the protein most able to do so.
New Approach To Produce Water Free of Bacteria, Viruses, and Halogens in a Recyclable System
Authors: Ahmed Abd El-Shafey I. , Cavalli Gabriel , Bushell Michael E. , Wardell John N. , Pedley Steve , Charles Katarina , Hay John N. 
Published: November 2010

ABSTRACTThe antimicrobial activity of a new cross-linkedN-halamine polymer against bacteria and viruses was evaluated. The polymer achieved a 9-log10reduction of bacteria (bothEscherichia coliandStaphylococcus aureus) in 1.5 h and a 5-log10reduction of bacteriophage PRD1 in 3 h. At the same time, the ability of the nonhalogenated polymer to trap halide ions was examined. The polymer was incorporated into a multifiltration system to study the ability to produce water free of bacteria, viruses, and halide ions. The antimicrobial activity, useful lifetime, halide ion level, and recycling possibilities of the system were quantified on a laboratory scale. A design for a large-scale multifiltration system based on this polymer is proposed.
The Candida albicans Sur7 Protein Is Needed for Proper Synthesis of the Fibrillar Component of the Cell Wall That Confers Strength
Authors: Wang Hong X. , Douglas Lois M. , Aimanianda Vishukumar , Latgé Jean-Paul , Konopka James B. 
Published: November 2010

ABSTRACT

The
Candida albicans
plasma membrane plays important roles in interfacing with the environment, morphogenesis, and cell wall synthesis. The role of the Sur7 protein in cell wall structure and function was analyzed, since previous studies showed that this plasma membrane protein is needed to prevent abnormal intracellular growth of the cell wall. Sur7 localizes to stable patches in the plasma membrane, known as MCC (membrane compartment occupied by Can1), that are associated with eisosome proteins. The
sur7
Δ mutant cells displayed increased sensitivity to factors that exacerbate cell wall defects, such as detergent (SDS) and the chitin-binding agents calcofluor white and Congo red. The
sur7
Δ cells were also slightly more sensitive to inhibitors that block the synthesis of cell wall chitin (nikkomycin Z) and β-1,3-glucan (caspofungin). In contrast, Fmp45, a paralog of Sur7 that also localizes to punctate plasma membrane patches, did not have a detectable role in cell wall synthesis. Chemical analysis of cell wall composition demonstrated that
sur7
Δ cells contain decreased levels of β-glucan, a glucose polymer that confers rigidity on the cell wall. Consistent with this,
sur7
Δ cells were more sensitive to lysis, which could be partially rescued by increasing the osmolarity of the medium. Interestingly, Sur7 is present in static patches, whereas β-1,3-glucan synthase is mobile in the plasma membrane and is often associated with actin patches. Thus, Sur7 may influence β-glucan synthesis indirectly, perhaps by altering the functions of the cell signaling components that localize to the MCC and eisosome domains.
Rapid Tagging and Integration of Genes in Giardia intestinalis
Authors: Gourguechon Stéphane , Cande W. Zacheus 
Published: November 2010

ABSTRACT

We developed a series of plasmids that allow C-terminal tagging of any gene in its endogenous locus in
Giardia intestinalis
, with different epitope tags (triple hemagglutinin [3HA] and triple Myc [3Myc]) and selection markers (puromycin, neomycin, and a newly developed marker, blasticidin). Using these vectors, cyclin B and aurora kinase were tagged, expressed, and localized.
TheTreponema denticolaChymotrypsin-Like Protease Dentilisin Induces Matrix Metalloproteinase-2-Dependent Fibronectin Fragmentation in Periodontal Ligament Cells
Authors: Miao Di , Fenno J. Christopher , Timm John C. , Joo Nam Eok , Kapila Yvonne L. 
Published: November 2010

ABSTRACTPeriodontal disease is a bacterially mediated chronic inflammatory disease that results in destruction of the periodontal ligament (PDL) and alveolar bone that surround and support the dentition. While their precise roles are not well understood, periodontal pathogens, includingTreponema denticola, are believed to initiate the destructive inflammatory responses and dysregulation of tissue homeostasis that characterize the disease. These responses are believed to result from both proinflammatory effects of acylated bacterial membrane components (lipopolysaccharides and lipoproteins) and degradative effects of secreted bacterial proteases. Host-derived matrix metalloproteinases (MMPs) are key enzymes both in tissue homeostasis and tissue destruction. MMP expression is modulated in part by specific proteolytic fragments of fibronectin (FN), which are associated with periodontal disease. FN is a predominant extracellular matrix component in the periodontium. We examined the ability ofTreponema denticolaand its acylated outer membrane PrtP protease complex to induce both activation of MMP-2 and generation of FN fragments in human PDL cell culture supernatants.T. denticolaparent and isogenic mutant strains, as well as MMP-2 small interfering RNA and specific inhibitors of MMP-2 and PrtP activity, were used to examine protein expression, gelatinolytic activity, and FN fragmentation in culture supernatants.T. denticolaand its purified protease induced both MMP-2 activation and FN fragmentation. Here, we demonstrate that PrtP proteolytic activity induces the activation of MMP-2 and that active MMP-2 is required for FN fragmentation. These results suggest a specific mechanism by which theT. denticolaprotease may disrupt homeostatic processes required for the maintenance of periodontal health.
Autocrine Effects of Interleukin-6 Mediate Acute-Phase Proinflammatory and Tissue-Reparative Transcriptional Responses of Canine Bladder Mucosa
Authors: Wood Michael W. , Breitschwerdt Edward B. , Gookin Jody L. 
Published: November 2010

ABSTRACTDuring early urinary tract infection (UTI) the interplay between invading bacteria and the urothelium elicits a mucosal response aimed at clearing infection. Unfortunately, the resultant inflammation and associated local tissue injury are responsible for patient symptoms. Interleukin-6 (IL-6), a cytokine released during acute UTI, has both pro- and anti-inflammatory effects on other body systems. Within the urothelium, the IL-6 native-tissue origin, the target cell type(s), and ultimate effect of the cytokine on target cells are largely unknown. In the present study we modeled the UTI IL-6 responseex vivousing canine bladder mucosa mounted in Ussing chambers to determine the inflammatory and reparative role of IL-6. We demonstrated that uropathogenicEscherichia coliinfection stimulates the synthesis of IL-6 by all urothelial cell layers, with the urothelial cells alone representing the only site of unequivocal IL-6 receptor expression. Autocrine effects of IL-6 were supported by the activation of urothelial STAT3 signaling and SOCS3 expression. Using exogenous IL-6, a microarray approach, and quantitative reverse transcriptase PCR (q-RT-PCR), 5 target genes (tumor necrosis factor alpha, interleukin-1β, matrix metallopeptidase 2, heparan sulfated-glucosaminyl 3-O-sulfotransferase 3A1, and hyaluronan synthase 2) that have direct or indirect roles in promoting a proinflammatory state were identified. Two of these genes, heparan sulfated-glucosaminyl 3-O-sulfotransferase 3A1 and hyaluronan synthase 2, are also potentially important mediators of wound repair via the production of glycosaminoglycan components. These findings suggest that IL-6 secretion during acute UTI may serve a dual biological role by initiating the inflammatory response while also repairing urothelial defenses.
Sustaining N
2
-Dependent Growth in the Presence of CO
Authors: Kerby Robert L. , Roberts Gary P. 
Published: November 2010

ABSTRACT

Low levels of carbon monoxide inhibit the N
2
-dependent growth of
Rhodospirillum rubrum
unless the ∼100-residue CowN protein is expressed. Expression requires the CO-responsive regulator RcoM and is maximal in cells grown in the presence of CO and a poor nitrogen source, consistent with the role of CowN in N
2
fixation.
Rotavirus Disrupts Calcium Homeostasis by NSP4 Viroporin Activity
Authors: Hyser Joseph M. , Collinson-Pautz Matthew R. , Utama Budi , Estes Mary K. 
Published: December 2010

ABSTRACT

Many viruses alter intracellular calcium homeostasis. The rotavirus nonstructural protein 4 (NSP4), an endoplasmic reticulum (ER) transmembrane glycoprotein, increases intracellular levels of cytoplasmic Ca
2+
([Ca
2+
]cyto) through a phospholipase C-independent pathway, which is required for virus replication and morphogenesis. However, the NSP4 domain and mechanism that increases [Ca
2+
]cyto are unknown. We identified an NSP4 domain (amino acids [aa] 47 to 90) that inserts into membranes and has structural characteristics of viroporins, a class of small hydrophobic viral proteins that disrupt membrane integrity and ion homeostasis to facilitate virus entry, assembly, or release. Mutational analysis showed that NSP4 viroporin activity was mediated by an amphipathic α-helical domain downstream of a conserved lysine cluster. The lysine cluster directed integral membrane insertion of the viroporin domain and was critical for viroporin activity. In epithelial cells, expression of wild-type NSP4 increased the levels of free cytoplasmic Ca
2+
by 3.7-fold, but NSP4 viroporin mutants maintained low levels of [Ca
2+
]cyto, were retained in the ER, and failed to form cytoplasmic vesicular structures, called puncta, which surround viral replication and assembly sites in rotavirus-infected cells. When [Ca
2+
]cyto was increased pharmacologically with thapsigargin, viroporin mutants formed puncta, showing that elevation of calcium levels and puncta formation are distinct functions of NSP4 and indicating that NSP4 directly or indirectly responds to elevated cytoplasmic calcium levels. NSP4 viroporin activity establishes the mechanism for NSP4-mediated elevation of [Ca
2+
]cyto, a critical event that regulates rotavirus replication and virion assembly.

IMPORTANCE
Rotavirus is the leading cause of viral gastroenteritis in children and young animals. Rotavirus infection and expression of nonstructural protein 4 (NSP4) alone dramatically increase cytosolic calcium, which is essential for replication and assembly of infectious virions. This work identifies the intracellular mechanism by which NSP4 disrupts calcium homeostasis by showing that NSP4 is a viroporin, a class of virus-encoded transmembrane pores. Mutational analyses identified residues critical for viroporin activity. Viroporin mutants did not elevate the levels of cytoplasmic calcium in mammalian cells and were maintained in the endoplasmic reticulum rather than forming punctate vesicular structures that are critical for virus replication and morphogenesis. Pharmacological elevation of cytoplasmic calcium levels rescued puncta formation in viroporin mutants, demonstrating that elevation of calcium levels and puncta formation are distinct NSP4 functions. While viroporins typically function in virus entry or release, elevation of calcium levels by NSP4 viroporin activity may serve as a regulatory function to facilitate virus replication and assembly.
FtsZ in Bacterial Cytokinesis: Cytoskeleton and Force Generator All in One
Authors: Erickson Harold P. , Anderson David E. , Osawa Masaki 
Published: November 2010

SUMMARYFtsZ, a bacterial homolog of tubulin, is well established as forming the cytoskeletal framework for the cytokinetic ring. Recent work has shown that purified FtsZ, in the absence of any other division proteins, can assemble Z rings when incorporated inside tubular liposomes. Moreover, these artificial Z rings can generate a constriction force, demonstrating that FtsZ is its own force generator. Here we review light microscope observations of how Z rings assemble in bacteria. Assembly begins with long-pitch helices that condense into the Z ring. Once formed, the Z ring can transition to short-pitch helices that are suggestive of its structure. FtsZ assemblesin vitrointo short protofilaments that are ∼30 subunits long. We present models for how these protofilaments might be further assembled into the Z ring. We discuss recent experiments on assembly dynamics of FtsZin vitro, with particular attention to how two regulatory proteins, SulA and MinC, inhibit assembly. Recent efforts to develop antibacterial drugs that target FtsZ are reviewed. Finally, we discuss evidence of how FtsZ generates a constriction force: by protofilament bending into a curved conformation.