bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergistic interaction of the histone deacetylase inhibitor SAHA with the proteasome inhibitor bortezomib in mantle cell lymphoma
Authors: Heider Ulrike , Metzler Ivana von , Kaiser Martin , Rosche Marleen , Sterz Jan , Rötzer Susanne , Rademacher Jessica , Jakob Christian , Fleissner Claudia , Kuckelkorn Ulrike , Kloetzel Peter‐Michael , Sezer Orhan 
Published: July 2010

AbstractObjectives:  Mantle cell lymphoma (MCL) is an incurable B cell lymphoma, and novel treatment strategies are urgently needed. We evaluated the effects of combined treatment with the proteasome inhibitor bortezomib and the histone deacetylase inhibitor (HDACi) suberoylanilide hydroxamic acid (SAHA) on MCL. Bortezomib acts by targeting the proteasome, and – among other mechanisms – results in a reduced nuclear factor‐kappa B (NF‐κB) activity. HDACi promote histone acetylation, and also interfere with NF‐κB signaling.Methods:  Human MCL cell lines (JeKo‐1, Granta‐519 and Hbl‐2) were exposed to bortezomib and/or SAHA. Cell viability and apoptosis were quantified by the MTT and annexin‐V assay, respectively. Reactive oxygen species (ROS) were analyzed using the fluorophore H2DCFDA. In addition, activated caspases, proteasome‐ and NF‐κB activity were quantified.Results:  Combined incubation with bortezomib and SAHA resulted in synergistic cytotoxic effects, as indicated by combination index values <1 using the median effect method of Chou and Talalay. The combination of both inhibitors led to a strong increase in apoptosis as compared to single agents and was accompanied by enhanced ROS generation, while each agent alone only modestly induced ROS. The free radical scavenger N‐acetyl‐l‐cysteine blocked the ROS generation and reduced the apoptosis significantly. In addition, coexposure of bortezomib and SAHA led to increased caspase‐3, ‐8 and ‐9 activity, marked reduction of proteasome activity and decrease of NF‐κB activity.Conclusions:  This is the first report giving evidence that SAHA and bortezomib synergistically induce apoptosis in MCL cells. These data build the framework for clinical trials using combined proteasome and histone deacetylase inhibition in the treatment of MCL.
A 1‐Year Controlled Clinical Trial of Immediate Implants Placed in Fresh Extraction Sockets: Stability Measurements and Crestal Bone Level Changes
Authors: Huber Sandra , Rentsch‐Kollàr Andrea , Grogg Fabiana , Katsoulis Joannis , Mericske Regina 
Published: July 2010

ABSTRACTPurpose: The aim of this study was to measure stability and crestal bone level changes of implants placed in fresh extraction sockets in elderly patients.Methods: Thirty‐five patients who were in need of tooth extractions were recruited for this study. They received a total of 65 implants in both jaws to support fixed or removable prostheses. The teeth were carefully extracted, the implants set directly in the root socket, and resonance frequency analysis (RFA) measurements were simultaneously performed (Time 1 = T1). After a healing time of 6 to 10 weeks the measurements were repeated (Time 2 = T2). Orthograd periapical radiographs were taken when the new prostheses were fabricated and after 1 year of loaded period. The distance between the first visible bone implant contact (BIC) and the implant‐shoulder was measured and crestal bone loss was calculated (ΔBIC). Mean RFA and BIC were compared for various subgroups (p < .05). By means of a fixed effects model, the impact of the parameters gender, jaw, and prosthetic indication on RFA measurements was analyzed (p < .016).Results: The mean implant stability quotient (ISQ) values were 64.4 ± 6.7 at T1 and 64.0 ± at 8.6 T2, with a trend to higher values for male patients. The mixed model showed that only the jaw had a statistically significant impact on ISQ values, with higher values for the mandible. Mean crestal bone loss was small with 0.49 ± 0.81 mm, ranging form 0.1 to 2.4 mm. Twenty percent of the implant sites lost more than 1‐mm crestal bone. No differences were found in subgroups.Conclusions: Good primary and secondary stability of the implants was reached in both jaws. Crestal bone loss was small but may not be fully predictable for a single site. This treatment modality can be applied successfully in elderly patients and can be suggested for various prosthetic indications in both jaws.
Ex Vivo and In Vivo Biomechanical Test of Implant Attachment to Various Materials: Introduction of a New User‐Friendly Removal Torque Equipment
Authors: Johansson Carina B. , Jimbo Ryo , Stefenson Per 
Published: July 2010

ABSTRACTObjective: The removal torque (RTQ) analysis is commonly used for biomechanical evaluation of osseointegration. The overall aim of this study was to verify results obtained with a newly developed equipment for biomechanical testing of osseointegration.Methods: Verification of the new equipment for biomechanical tests involved three experiments: Part I, comparison of RTQ between implants placed in four different types of dental synthetic plasters. Part II, comparison of RTQ between custom made, experimentally used implants to self‐tapping, commercially available implants molded in the same type of dental plaster. Part III, comparison of RTQ between commercially pure titanium implants to Ti6Al4V implants placed in rabbit bone, 6 weeks after insertion. Briefly, for all experiments, the peak RTQ values and the removal process were recorded every 0.01 seconds up to 10 seconds. After the measurements, peak RTQ values were converted to shear strength.Results: The developed equipment sensitively responded to the changes of properties related to the molding plasters, implant topographies, and materials. The monitored graphs corresponded well to the expected properties of the different implants and tested materials.Conclusion: The new RTQ equipment proved to be accurate and could add new knowledge in understanding the biomechanical aspects of osseointegration.
Comparing Nonsynergistic Gamma Models with Interaction Models To Predict Growth of EmeticBacillus cereuswhen Using Combinations of pH and Individual Undissociated Acids as Growth-Limiting Factors
Authors: Biesta-Peters Elisabeth G. , Reij Martine W. , Gorris Leon G. M. , Zwietering Marcel H. 
Published: July 2010

ABSTRACTA combination of multiple hurdles to limit microbial growth is frequently applied in foods to achieve an overall level of protection. Quantification of hurdle technology aims at identifying synergistic or multiplicative effects and is still being developed. The gamma hypothesis states that inhibitory environmental factors aiming at limiting microbial growth rates combine in a multiplicative manner rather than synergistically. Its validity was tested here with respect to the use of pH and various concentrations of undissociated acids, i.e., acetic, lactic, propionic, and formic acids, to control growth ofBacillus cereusin brain heart infusion broth. The key growth parameter considered was the maximum specific growth rate, μmax, as observed by determination of optical density. A variety of models from the literature describing the effects of various pH values and undissociated acid concentrations on μmaxwere fitted to experimental data sets and compared based on a predefined set of selection criteria, and the best models were selected. The cardinal model developed by Rosso (for pH dependency) and the model developed by Luong (for undissociated acid) were found to provide the best fit and were combined in a gamma model with good predictive performance. The introduction of synergy factors into the models was not able to improve the quality of the prediction. On the contrary, inclusion of synergy factors led to an overestimation of the growth boundary, with the inherent possibility of leading to underestimation of the risk under the conditions tested in this research.
Antimicrobial Activity of Simulated Solar Disinfection against Bacterial, Fungal, and Protozoan Pathogens and Its Enhancement by Riboflavin
Authors: Heaselgrave Wayne , Kilvington Simon 
Published: July 2010

ABSTRACT

Riboflavin significantly enhanced the efficacy of simulated solar disinfection (SODIS) at 150 watts per square meter (W m
−2
) against a variety of microorganisms, including
Escherichia coli
,
Fusarium solani
,
Candida albicans
, and
Acanthamoeba polyphaga
trophozoites (>3 to 4 log
10
after 2 to 6 h;
P
< 0.001). With
A. polyphaga
cysts, the kill (3.5 log
10
after 6 h) was obtained only in the presence of riboflavin and 250 W m
−2
irradiance.
Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy
Authors: Jones D. S. , Tobler D. J. , Schaperdoth I. , Mainiero M. , Macalady J. L. 
Published: July 2010

ABSTRACT

We performed a microbial community analysis of biofilms inhabiting thermal (35 to 50°C) waters more than 60 m below the ground surface near Acquasanta Terme, Italy. The groundwater hosting the biofilms has 400 to 830 μM sulfide, <10 μM O
2
, pH of 6.3 to 6.7, and specific conductivity of 8,500 to 10,500 μS/cm. Based on the results of 16S rRNA gene cloning and fluorescent
in situ
hybridization (FISH), the biofilms have low species richness, and lithoautotrophic (or possibly mixotrophic)
Gamma
- and
Epsilonproteobacteria
are the principle biofilm architects.
Deltaproteobacteria
sequences retrieved from the biofilms have <90% 16S rRNA similarity to their closest relatives in public databases and may represent novel sulfate-reducing bacteria. The Acquasanta biofilms share few species in common with Frasassi cave biofilms (13°C, 80 km distant) but have a similar community structure, with representatives in the same major clades. The ecological success of
Sulfurovumales
-group
Epsilonproteobacteria
in the Acquasanta biofilms is consistent with previous observations of their dominance in sulfidic cave waters with turbulent water flow and high dissolved sulfide/oxygen ratios.
Diffusion Measurements inside Biofilms by Image-Based Fluorescence Recovery after Photobleaching (FRAP) Analysis with a Commercial Confocal Laser Scanning Microscope
Authors: Waharte François , Steenkeste Karine , Briandet Romain , Fontaine-Aupart Marie-Pierre 
Published: July 2010

ABSTRACT

Research about the reactional and structural dynamics of biofilms at the molecular level has made great strides, owing to efficient fluorescence imaging methods in terms of spatial resolution and fast acquisition time but also to noninvasive conditions of observation consistent with
in situ
biofilm studies. In addition to conventional fluorescence intensity imaging, the fluorescence recovery after photobleaching (FRAP) module can now be routinely implemented on commercial confocal laser scanning microscopes (CLSMs). This method allows measuring of local diffusion coefficients in biofilms and could become an alternative to fluorescence correlation spectroscopy (FCS). We present here an image-based FRAP protocol to improve the accuracy of FRAP measurements inside “live” biofilms and the corresponding analysis. An original kymogram representation allows control of the absence of perturbing bacterial movement during image acquisition. FRAP data analysis takes into account molecular diffusion during the bleach phase and uses the image information to extract molecular diffusion coefficients. The fluorescence spatial intensity profile analysis used here for the first time with biofilms is supported both by our own mathematical model and by a previously published one. This approach was validated to FRAP experiments on fluorescent-dextran diffusion inside
Lactoccocus lactis
and
Stenotrophomonas maltophilia
biofilms, and the results were compared to previously published FCS measurements.
Rapidly Growing Nontuberculous Mycobacteria Cultured from Home Tap and Shower Water
Authors: van Ingen Jakko , Blaak Hetty , de Beer Jessica , de Roda Husman Ana Maria , van Soolingen Dick 
Published: July 2010

ABSTRACT

Tap and shower water at two locations in the Netherlands was examined for the presence of rapidly growing nontuberculous mycobacteria. Cultures yielded
Mycobacterium peregrinum
,
M. salmoniphilum
,
M. llatzerense
,
M. septicum
, and three potentially novel species, a distribution different from that in clinical samples.
Cloning and Expression of a Novel NADP(H)-Dependent Daidzein Reductase, an Enzyme Involved in the Metabolism of Daidzein, from Equol-Producing
Lactococcus
Strain 20-92
Authors: Shimada Yoshikazu , Yasuda Setsuko , Takahashi Masayuki , Hayashi Takashi , Miyazawa Norihiro , Sato Ikutaro , Abiru Yasuhiro , Uchiyama Shigeto , Hishigaki Haretsugu 
Published: July 2010

ABSTRACT

Equol is a metabolite produced from daidzein by enteric microflora, and it has attracted a great deal of attention because of its protective or ameliorative ability against several sex hormone-dependent diseases (e.g., menopausal disorder and lower bone density), which is more potent than that of other isoflavonoids. We purified a novel NADP(H)-dependent daidzein reductase (L-DZNR) from
Lactococcus
strain 20-92 (
Lactococcus
20-92; S. Uchiyama, T. Ueno, and T. Suzuki, international patent WO2005/000042) that is involved in the metabolism of soy isoflavones and equol production and converts daidzein to dihydrodaidzein. Partial amino acid sequences were determined from purified L-DZNR, and the gene encoding L-DZNR was cloned. The nucleotide sequence of this gene consists of an open reading frame of 1,935 nucleotides, and the deduced amino acid sequence consists of 644 amino acids. L-DZNR contains two cofactor binding motifs and an 4Fe-4S cluster. It was further suggested that L-DZNR was an NAD(H)/NADP(H):flavin oxidoreductase belonging to the
o
ld
y
ellow
e
nzyme (OYE) family. Recombinant histidine-tagged L-DZNR was expressed in
Escherichia coli
. The recombinant protein converted daidzein to (
S
)-dihydrodaidzein with enantioselectivity. This is the first report of the isolation of an enzyme related to daidzein metabolism and equol production in enteric bacteria.
Genomic Island TnSmu2 of
Streptococcus mutans
Harbors a Nonribosomal Peptide Synthetase-Polyketide Synthase Gene Cluster Responsible for the Biosynthesis of Pigments Involved in Oxygen and H
2
O
2
Tolerance
Authors: Wu Chenggang , Cichewicz Robert , Li Yihong , Liu Jinman , Roe Bruce , Ferretti Joseph , Merritt Justin , Qi Fengxia 
Published: July 2010

ABSTRACT

The oral biofilm community consists of >800 microbial species, among which
Streptococcus mutans
is considered a primary pathogen for dental caries. The genomic island TnSmu2 of
S. mutans
comprises >2% of the genome. In this study, we demonstrate that TnSmu2 harbors a gene cluster encoding nonribosomal peptide synthetases (NRPS), polyketide synthases (PKS), and accessory proteins and regulators involved in nonribosomal peptide (NRP) and polyketide (PK) biosynthesis. Interestingly, the sequences of these genes and their genomic organizations and locations are highly divergent among different
S. mutans
strains, yet each TnSmu2 region encodes NRPS/PKS and accessory proteins. Mutagenesis of the structural genes and putative regulatory genes in strains UA159, UA140, and MT4653 resulted in colonies that were devoid of their yellow pigmentation (for strains UA140 and MT4653). In addition, these mutant strains also displayed retarded growth under aerobic conditions and in the presence of H
2
O
2
. High-performance liquid chromatography profiling of cell surface extracts identified unique peaks that were missing in the mutant strains, and partial characterization of the purified product from UA159 demonstrated that it is indeed a hybrid NRP/PK, as predicted. A genomic survey of 94 clinical
S. mutans
isolates suggests that the TnSmu2 gene cluster may be more prevalent than previously recognized.
Response of Porcine Intestinal
In Vitro
Organ Culture Tissues following Exposure to
Lactobacillus plantarum
JC1 and
Salmonella enterica
Serovar Typhimurium SL1344
Authors: Collins J. W. , Coldham N. G. , Salguero F. J. , Cooley W. A. , Newell W. R. , Rastall R. A. , Gibson G. R. , Woodward M. J. , La Ragione R. M. 
Published: July 2010

ABSTRACT

The development of novel intervention strategies for the control of zoonoses caused by bacteria such as
Salmonella
spp. in livestock requires appropriate experimental models to assess their suitability. Here, a novel porcine intestinal
in vitro
organ culture (IVOC) model utilizing cell crown (CC) technology (CCIVOC) (Scaffdex) was developed. The CCIVOC model was employed to investigate the characteristics of association of
S. enterica
serovar Typhimurium strain SL1344 with porcine intestinal tissue following exposure to a
Lactobacillus plantarum
strain. The association of bacteria to host cells was examined by light microscopy and electron microscopy (EM) after appropriate treatments and staining, while changes in the proteome of porcine jejunal tissues were investigated using quantitative label-free proteomics. Exposure of porcine intestinal mucosal tissues to
L. plantarum
JC1 did not reduce the numbers of
S.
Typhimurium bacteria associating to the tissues but was associated with significant (
P
< 0.005) reductions in the percentages of areas of intestinal IVOC tissues giving positive staining results for acidic mucins. Conversely, the quantity of neutrally charged mucins present within the goblet cells of the IVOC tissues increased significantly (
P
< 0.05). In addition, tubulin-α was expressed at high levels following inoculation of jejunal IVOC tissues with
L. plantarum
. Although
L. plantarum
JC1 did not reduce the association of
S.
Typhimurium strain SL1344 to the jejunal IVOC tissues, detection of increased acidic mucin secretion, host cytoskeletal rearrangements, and proteins involved in the porcine immune response demonstrated that this strain of
L. plantarum
may contribute to protecting the pig from infections by
S.
Typhimurium or other pathogens.
Candida albicans Cyclin Clb4 Carries S-Phase Cyclin Activity
Authors: Ofir Ayala , Kornitzer Daniel 
Published: July 2010

ABSTRACT

Cyclin-dependent kinases (CDKs) are key regulators of eukaryotic cell cycle progression. The cyclin subunit activates the CDK and also imparts to the complex, at least in some cases, substrate specificity.
Saccharomyces cerevisiae
, an organism in which the roles of individual cyclins are best studied, contains nine cyclins (three G
1
cyclins and six B-type cyclins) capable of activating the main cell cycle CDK, Cdc28. Analysis of the genome of the pathogenic yeast
Candida albicans
revealed only two sequences corresponding to B-type cyclins,
C. albicans
Clb2 (CaClb2) and CaClb4. Notably, no homolog of the
S. cerevisiae
S-phase-specific cyclins, Clb5/Clb6, could be detected. Here, we performed an
in vitro
analysis of the activity of CaClb2 and CaClb4 and of three G
1
cyclins, as well as an analysis of the phenotype of
S. cerevisiae
cells expressing CaClb2 or CaClb4 instead of Clb5. Remarkably, replacement of
CLB5
by Ca
CLB4
caused rapid diploidization of
S. cerevisiae.
In addition, both
in vivo
and
in vitro
analyses indicate that, in spite of the higher sequence similarity of CaClb2 to Clb5/Clb6, CaClb4 is the functional homolog of Clb5/Clb6. The activity of a CaClb2/CaClb4 cyclin hybrid suggests that the cyclin box domain of CaClb4 carries the functional specificity of the protein. These results have implications for our understanding of the evolution of specificity of the cell cycle cyclins.
Multiple Promoters Contribute to Swarming and the Coordination of Transcription with Flagellar Assembly in
Salmonella
Authors: Wozniak Christopher E. , Chevance Fabienne F. V. , Hughes Kelly T. 
Published: July 2010

ABSTRACT

In
Salmonella
, there are three classes of promoters in the flagellar transcriptional hierarchy. This organization allows genes needed earlier in the construction of flagella to be transcribed before genes needed later. Four operons (
fliAZY
,
flgMN
,
fliDST
, and
flgKL
) are expressed from both class 2 and class 3 promoters. To investigate the purpose for expressing genes from multiple flagellar promoters, mutants were constructed for each operon that were defective in either class 2 transcription or class 3 transcription. The mutants were checked for defects in swimming through liquids, swarming over surfaces, and transcriptional regulation. The expression of the hook-associated proteins (FlgK, FlgL, and FliD) from class 3 promoters was found to be important for swarming motility. Both
flgMN
promoters were involved in coordinating class 3 transcription with the stage of assembly of the hook-basal body. Finally, the
fliAZY
class 3 promoter lowered class 3 transcription in stationary phase. These results indicate that the multiple flagellar promoters respond to specific environmental conditions and help coordinate transcription with flagellar assembly.
Characterization of the Structure and Biological Functions of a Capsular Polysaccharide Produced by
Staphylococcus saprophyticus
Authors: Park Sunny , Kelley Kathryn A. , Vinogradov Evgeny , Solinga Robert , Weidenmaier Christopher , Misawa Yoshiki , Lee Jean C. 
Published: July 2010

ABSTRACT

Staphylococcus saprophyticus
is a common cause of uncomplicated urinary tract infections in women.
S. saprophyticus
strain ATCC 15305 carries two staphylococcal cassette chromosome genetic elements, SCC
15305RM
and SCC
15305cap
. The SCC
15305cap
element carries 13 open reading frames (ORFs) involved in capsular polysaccharide (CP) biosynthesis, and its G+C content (26.7%) is lower than the average G+C content (33.2%) for the whole genome.
S. saprophyticus
strain ATCC 15305
capD
,
capL
, and
capK
(

capD
Ssp

,

capL
Ssp

, and

capK
Ssp

) are homologous to genes encoding UDP-FucNAc biosynthesis, and
gtaB
and

capI
Ssp

show homology to genes involved in UDP-glucuronic acid synthesis.
S. saprophyticus
ATCC 15305 CP, visualized by immunoelectron microscopy, was extracted and purified using anionic-exchange and size exclusion chromatography. Analysis of the purified CP by
1
H and
13
C nuclear magnetic resonance (NMR) spectroscopy and gas-liquid chromatography revealed two types of branched tetrasaccharide repeating units composed of the following:

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \[\begin{array}{c}\mathbf{-4)-{\beta}-Glc}-\mathbf{(1-3)-Sug}-\mathbf{(1-4)-{\beta}-GlcA}-(\mathbf{1-}\\\mathbf{{\vert}}\\\mathbf{{\beta}-GlcNAc}-\mathbf{(1-2)}\end{array}\] \end{document}

Sug represents two stereoisomers of 2-acetamido-2,6-dideoxy-hexos-4-ulose residues, one of which has an
arabino
configuration. The encapsulated ATCC 15305 strain was resistant to complement-mediated opsonophagocytic killing by human neutrophils, whereas the acapsular mutant C1 was susceptible. None of 14 clinical isolates reacted with antibodies to the ATCC 15305 CP. However, 11 of the 14
S. saprophyticus
isolates were phenotypically encapsulated based on their resistance to complement-mediated opsonophagocytic killing and their failure to hemagglutinate when cultivated aerobically. Ten of the 14 clinical strains carried homologues of the conserved staphylococcal
capD
gene or the
S. saprophyticus gtaB
gene, or both. Our results suggest that some strains of
S. saprophyticus
are encapsulated and that more than one capsular serotype exists.