bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphodiesterase‐4 blunts inotropism and arrhythmias but not sinoatrial tachycardia of (−)‐adrenaline mediated through mouse cardiac β1‐adrenoceptors
Authors: Galindo‐Tovar A , Kaumann A J 
Published: December 2007

Background and purpose:β1 and β2‐adrenoceptors coexist in murine heart but β2‐adrenoceptor‐mediated effects have not been detected in atrial and ventricular tissues, possibly due to marked phosphodiesterase (PDE) activity. We investigated the influence of the PDE3 inhibitor cilostamide and PDE4 inhibitor rolipram on the effects of (−)‐adrenaline in three regions of murine heart.Experimental approach:(−)‐Adrenaline‐evoked cardiostimulation was compared on sinoatrial beating rate, left atrial and right ventricular contractile force in isolated tissues from 129SvxC57B1/6 cross mice. Ventricular arrhythmic contractions were also assessed.Key results:Both rolipram (1 μM) and cilostamide (300 nM) caused transient sinoatrial tachycardia but neither enhanced the chronotropic potency of (−)‐adrenaline. Rolipram potentiated 19‐fold (left atrium) and 7‐fold (right ventricle) the inotropic effects of (−)‐adrenaline. (−)‐Adrenaline elicited concentration‐dependent ventricular arrhythmias that were potentiated by rolipram. All effects of (−)‐adrenaline were antagonized by the β1‐adrenoceptor‐selective antagonist CGP20712A (300 nM). Cilostamide (300 nM) did not increase the chronotropic and inotropic potencies of (−)‐adrenaline, but administered jointly with rolipram in the presence of CGP20712A, uncovered left atrial inotropic effects of (−)‐adrenaline that were prevented by the β2‐adrenoceptor‐selective antagonist ICI118551.Conclusions and implications:PDE4 blunts the β1‐adrenoceptor‐mediated effects of (−)‐adrenaline in left atrium and right ventricle but not in sinoatrial node. Both PDE3 and PDE4 reduce basal sinoatrial rate in a compartment distinct from the β1‐adrenoceptor compartment. PDE3 and PDE4, acting in concert, prevent left atrial β2‐adrenoceptor‐mediated inotropy. PDE4 partially protects the right ventricle against (−)‐adrenaline‐evoked arrhythmias. British Journal of Pharmacology (2008) 153, 710–720; doi:10.1038/sj.bjp.0707631; published online 17 December 2007
Celecoxib modulates adhesion of HT29 colon cancer cells to vascular endothelial cells by inhibiting ICAM‐1 and VCAM‐1 expression
Authors: Dianzani C , Brucato L , Gallicchio M , Rosa A C , Collino M , Fantozzi R 
Published: December 2007

Background and purpose:Cyclooxygenase‐2 (COX‐2) is highly expressed during inflammation and can promote the progression of colorectal cancer. Interactions between cancer cells and vascular endothelial cells are key events in this process. Recently, the selective COX‐2 inhibitor, celecoxib, was shown to inhibit expression of the adhesion molecules, ICAM‐1 and VCAM‐1, in the human colon cancer cell line HT29 and to inhibit adhesion of HT29 cells to FCS‐coated plastic wells. Here, we evaluated the effects of celecoxib on adhesion of HT29 cells to human umbilical vein endothelial cells (HUVEC), mediated by ICAM‐1 and VCAM‐1, to assess further the potential protective effects of celecoxib on cancer development.Experimental approach:Celecoxib was incubated for 4 h with HT29 cells and HUVEC and adhesion was quantified by a computerized micro‐imaging system. Expression analysis of ICAM‐1 and VCAM‐1 cell adhesion molecules was performed by western blot.Key results:Celecoxib (1 nM–10 μM) inhibited, with the same potency, adhesion of HT29 cells to resting HUVEC or to HUVEC stimulated by tumour necrosis factor‐α (TNF‐α), mimicking inflammatory conditions. Analysis of ICAM‐1 and VCAM‐1 expression showed that celecoxib inhibited expression of both molecules in TNF‐α‐stimulated HUVEC, but not in resting HUVEC; inhibition was concentration‐dependent and maximal (about 50%) at 10 μM celecoxib.Conclusions and implications:In conclusion, our data show that celecoxib inhibits HT29 cell adhesion to HUVEC and expression of ICAM‐1 and VCAM‐1, in stimulated endothelial cells. These effects may contribute to the chemopreventive activity of celecoxib in the development of colorectal cancer.British Journal of Pharmacology (2008) 153, 1153–1161; doi:10.1038/sj.bjp.0707636; published online 17 December 2007
Efficient peptide–MHC-I binding prediction for alleles with few known binders
Authors: Jacob Laurent , Vert Jean-Philippe 
Published: December 2007

Abstract
Motivation: In silico methods for the prediction of antigenic peptides binding to MHC class I molecules play an increasingly important role in the identification of T-cell epitopes. Statistical and machine learning methods in particular are widely used to score candidate binders based on their similarity with known binders and non-binders. The genes coding for the MHC molecules, however, are highly polymorphic, and statistical methods have difficulties building models for alleles with few known binders. In this context, recent work has demonstrated the utility of leveraging information across alleles to improve the performance of the prediction.
Results: We design a support vector machine algorithm that is able to learn peptide–MHC-I binding models for many alleles simultaneously, by sharing binding information across alleles. The sharing of information is controlled by a user-defined measure of similarity between alleles. We show that this similarity can be defined in terms of supertypes, or more directly by comparing key residues known to play a role in the peptide–MHC binding. We illustrate the potential of this approach on various benchmark experiments where it outperforms other state-of-the-art methods.
Availability: The method is implemented on a web server: http://cbio.ensmp.fr/kiss. All data and codes are freely and publicly available from the authors.
Contact: laurent.jacob@ensmp.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Natural Variation inRPS2-Mediated Resistance amongArabidopsisAccessions: Correlation between Gene Expression Profiles and Phenotypic Responses
Authors: Van Poecke Remco M.P. , Sato Masanao , Lenarz-Wyatt Lisa , Weisberg Sanford , Katagiri Fumiaki 
Published: December 2007

AbstractNatural variation in gene expression (expression traits or e-traits) is increasingly used for the discovery of genes controlling traits. An important question is whether a particular e-trait is correlated with a phenotypic trait. Here, we examined the correlations between phenotypic traits and e-traits among 10 Arabidopsis thaliana accessions. We studied defense against Pseudomonas syringae pv tomato DC3000 (Pst), with a focus on resistance gene–mediated resistance triggered by the type III effector protein AvrRpt2. As phenotypic traits, we measured growth of the bacteria and extent of the hypersensitive response (HR) as measured by electrolyte leakage. Genetic variation among accessions affected growth of Pst both with (Pst avrRpt2) and without (Pst) the AvrRpt2 effector. Variation in HR was not correlated with variation in bacterial growth. We also collected gene expression profiles 6 h after mock and Pst avrRpt2 inoculation using a custom microarray. Clusters of genes whose expression levels are correlated with bacterial growth or electrolyte leakage were identified. Thus, we demonstrated that variation in gene expression profiles of Arabidopsis accessions collected at one time point under one experimental condition has the power to explain variation in phenotypic responses to pathogen attack.
Quantifying Microbial Utilization of Petroleum Hydrocarbons in Salt Marsh Sediments by Using the
13
C Content of Bacterial rRNA
Authors: Pearson Ann , Kraunz Kimberly S. , Sessions Alex L. , Dekas Anne E. , Leavitt William D. , Edwards Katrina J. 
Published: December 2007

ABSTRACT

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the
13
C-enriched C
4
grass
Spartina alterniflora
and
13
C-depleted petroleum to monitor changes in the
13
C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the
13
C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of
Gamma
- and
Deltaproteobacteria
and
Firmicutes
in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the
13
C content of biomarker lipids.
N-Glycan Modification in
Aspergillus
Species
Authors: Kainz Elke , Gallmetzer Andreas , Hatzl Christian , Nett Juergen H. , Li Huijuan , Schinko Thorsten , Pachlinger Robert , Berger Harald , Reyes-Dominguez Yazmid , Bernreiter Andreas , Gerngross Tillmann , Wildt Stefan , Strauss Joseph 
Published: December 2007

ABSTRACT

The production by filamentous fungi of therapeutic glycoproteins intended for use in mammals is held back by the inherent difference in protein N-glycosylation and by the inability of the fungal cell to modify proteins with mammalian glycosylation structures. Here, we report protein N-glycan engineering in two
Aspergillus
species. We functionally expressed in the fungal hosts heterologous chimeric fusion proteins containing different localization peptides and catalytic domains. This strategy allowed the isolation of a strain with a functional α-1,2-mannosidase producing increased amounts of N-glycans of the Man
5
GlcNAc
2
type. This strain was further engineered by the introduction of a functional GlcNAc transferase I construct yielding GlcNAcMan
5
GlcNac
2
N-glycans. Additionally, we deleted
algC
genes coding for an enzyme involved in an early step of the fungal glycosylation pathway yielding Man
3
GlcNAc
2
N-glycans. This modification of fungal glycosylation is a step toward the ability to produce humanized complex N-glycans on therapeutic proteins in filamentous fungi.
Identification of a Putative Mexican Strain ofSerratia entomophilaPathogenic against Root-Damaging Larvae of Scarabaeidae (Coleoptera)
Authors: Nuñez-Valdez M. Eugenia , Calderón Marco A. , Aranda Eduardo , Hernández Luciano , Ramírez-Gama Rosa M. , Lina Laura , Rodríguez-Segura Zitlhally , Gutiérrez María del C. , Villalobos Francisco J. 
Published: December 2007

ABSTRACTThe larvae of scarab beetles, known as “white grubs” and belonging to the generaPhyllophagaandAnomala(Coleoptera: Scarabaeidae), are regarded as soil-dwelling pests in Mexico. During a survey conducted to find pathogenic bacteria with the potential to control scarab larvae, a nativeSerratiasp. (strain Mor4.1) was isolated from a dead third-instarPhyllophaga blanchardilarva collected from a cornfield in Tres Marías, Morelos, Mexico. Oral bioassays using healthyP. blanchardilarvae fed with the Mor4.1 isolate showed that this strain was able to cause an antifeeding effect and a significant loss of weight. Mortality was observed forP. blanchardi,P. trichodes, andP. obsoletain a multidose experiment. The Mor4.1 isolate also caused 100% mortality 24 h after intracoelomic inoculation of the larvae ofP. blanchardi,P. ravida,Anomala donovaniand the lepidopteran insectManduca sexta. Oral and injection bioassays were performed with concentrated culture broths of the Mor4.1 isolate to search for disease symptoms and mortality caused by extracellular proteins. The results have shown that Mor4.1 broths produce significant antifeeding effects and mortality. Mor4.1 broths treated with proteinase K lost the ability to cause disease symptoms and mortality, in both the oral and the injection bioassays, suggesting the involvement of toxic proteins in the disease. The Mor4.1 isolate was identified as a putativeSerratia entomophilaMor4.1 strain based on numerical taxonomy and phylogenetic analyses done with the 16S rRNA gene sequence. The potential ofS. entomophilaMor4.1 and its toxins to be used in an integrated pest management program is discussed.
Identification of a Ciliate (Oligohymenophorea: Scuticociliatia) Associated with Brown Band Disease on Corals of the Great Barrier Reef
Authors: Bourne David G. , Boyett Holly V. , Henderson Meegan E. , Muirhead Andrew , Willis Bette L. 
Published: December 2007

ABSTRACT
A ciliate associated with the coral disease brown band (BrB) was identified as a new species belonging to the class Oligohymenophorea, subclass Scuticociliatia. The ciliates were characterized by the presence of large numbers of intracellular dinoflagellates and displayed an elongated, tube-shaped body structure. They had uniform ciliature, except for three distinct cilia in the caudal region, and were typically 200 to 400 μm in length and 20 to 50 μm in width.
Heterologous Expression of the Pneumococcal Serotype 14 Polysaccharide inLactococcus lactisRequires LactococcalepsABCRegulatory Genes
Authors: Nierop Groot Masja N. , Godefrooij Jeroen , Kleerebezem Michiel 
Published: December 2007

ABSTRACTThe pneumococcal serotype 14 polysaccharide was produced inLactococcus lactisby coexpressing pneumococcal polysaccharide type 14-specific genes (cpsFGHIJKL14) with the lactococcal regulatory and priming glucosyltransferase-encoding genes specific for B40 polysaccharide (epsABCDB40). The polysaccharide produced byLactococcuswas secreted in the medium, simplifying downstream processing and polysaccharide isolation from culture broth.
Recovery of Spores from Thermophilic Dairy Bacilli and Effects of Their Surface Characteristics on Attachment to Different Surfaces
Authors: Seale R. B. , Flint S. H. , McQuillan A. J. , Bremer P. J. 
Published: December 2007

ABSTRACT

Spores from four
Geobacillus
spp. were isolated from a milk powder manufacturing line in New Zealand. Liquid sporulation media produced spore yields of ∼10
7
spores ml
−1
; spores were purified using a two-phase system created with polyethylene glycol 4000 and 3 M phosphate buffer. The zeta potentials of the spores from the four isolates ranged from −10 to −20 mV at neutral pH, with an isoelectric point between pH 3 and 4. Through contact angle measurements, spores were found to be hydrophilic and had relative hydrophobicity values of 10 to 40%, as measured by the microbial adhesion to hexadecane assay. The most hydrophilic spore isolate with the smallest negative charge attached in the highest numbers to Thermanox and stainless steel (1 × 10
4
spores cm
−2
), with fewer spores attaching to glass (3 × 10
3
spores cm
−2
). However, spores produced by the other three strains attached in similar numbers (
P
> 0.05) to all substrata (∼1 × 10
3
spores cm
−2
), indicating that there was no simple relationship between individual physicochemical interactions and spore adherence. Therefore, surface modifications which limit the attachment of one strain may not be effective for all stains, and control regimens need to be devised with reference to the characteristics of the particular strains of concern.
Miniprimer PCR, a New Lens for Viewing the Microbial World
Authors: Isenbarger Thomas A. , Finney Michael , Ríos-Velázquez Carlos , Handelsman Jo , Ruvkun Gary 
Published: December 2007

ABSTRACT

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and
Taq
polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.
Effect of Shadowing on Survival of Bacteria under Conditions Simulating the Martian Atmosphere and UV Radiation
Authors: Osman Shariff , Peeters Zan , La Duc Myron T. , Mancinelli Rocco , Ehrenfreund Pascale , Venkateswaran Kasthuri 
Published: December 2007

ABSTRACT

Spacecraft-associated spores and four non-spore-forming bacterial isolates were prepared in Atacama Desert soil suspensions and tested both in solution and in a desiccated state to elucidate the shadowing effect of soil particulates on bacterial survival under simulated Martian atmospheric and UV irradiation conditions. All non-spore-forming cells that were prepared in nutrient-depleted, 0.2-μm-filtered desert soil (DSE) microcosms and desiccated for 75 days on aluminum died, whereas cells prepared similarly in 60-μm-filtered desert soil (DS) microcosms survived such conditions. Among the bacterial cells tested,
Microbacterium schleiferi
and
Arthrobacter
sp. exhibited elevated resistance to 254-nm UV irradiation (low-pressure Hg lamp), and their survival indices were comparable to those of DS- and DSE-associated
Bacillus pumilus
spores. Desiccated DSE-associated spores survived exposure to full Martian UV irradiation (200 to 400 nm) for 5 min and were only slightly affected by Martian atmospheric conditions in the absence of UV irradiation. Although prolonged UV irradiation (5 min to 12 h) killed substantial portions of the spores in DSE microcosms (∼5- to 6-log reduction with Martian UV irradiation), dramatic survival of spores was apparent in DS-spore microcosms. The survival of soil-associated wild-type spores under Martian conditions could have repercussions for forward contamination of extraterrestrial environments, especially Mars.
Root Exudates Regulate Soil Fungal Community Composition and Diversity
Authors: Broeckling Corey D. , Broz Amanda K. , Bergelson Joy , Manter Daniel K. , Vivanco Jorge M. 
Published: December 2007

ABSTRACT

Plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. A few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. This study demonstrates that two model plant species (
Arabidopsis thaliana
and
Medicago truncatula
) are able to maintain resident soil fungal populations but unable to maintain nonresident soil fungal populations. This is mediated largely through root exudates: the effects of adding in vitro-generated root exudates to the soil fungal community were qualitatively and quantitatively similar to the results observed for plants grown in those same soils. This effect is observed for total fungal biomass, phylotype diversity, and overall community similarity to the starting community. Nonresident plants and root exudates influenced the fungal community by both positively and negatively impacting the relative abundance of individual phylotypes. A net increase in fungal biomass was observed when nonresident root exudates were added to resident plant treatments, suggesting that increases in specific carbon substrates and/or signaling compounds support an increased soil fungal population load. This study establishes root exudates as a mechanism through which a plant is able to regulate soil fungal community composition.
Anaerobic Conditions Promote Expression of Sfp Fimbriae and Adherence of Sorbitol-Fermenting Enterohemorrhagic
Escherichia coli
O157:NM to Human Intestinal Epithelial Cells
Authors: Müsken Anne , Bielaszewska Martina , Greune Lilo , Schweppe Christian H. , Müthing Johannes , Schmidt Herbert , Schmidt M. Alexander , Karch Helge , Zhang Wenlan 
Published: December 2007

ABSTRACT

The
sfp
gene cluster, unique to sorbitol-fermenting (SF) enterohemorrhagic
Escherichia coli
(EHEC) O157:NM strains, encodes fimbriae that mediate mannose-resistant hemagglutination in laboratory
E. coli
strains but are not expressed in wild-type SF EHEC O157:NM strains under standard laboratory conditions. We investigated whether Sfp fimbriae are expressed under conditions that mimic the intestinal environment and whether they contribute to the adherence of SF EHEC O157:NM strains to human intestinal epithelial cells. The transcription of
sfpA
(encoding the major fimbrial subunit) was upregulated in all strains investigated, and all expressed SfpA and possessed fimbriae that reacted with an anti-SfpA antibody when the strains were grown on solid media under anaerobic conditions. Sfp expression was absent under aerobic conditions and in liquid media. Sfp upregulation under anaerobic conditions was significantly higher on blood agar and a medium simulating the colonic environment than on a medium simulating the ileal environment (
P
< 0.05). The induction of Sfp fimbriae in SF
E. coli
O157:NM strains correlates with increased adherence to Caco-2 and HCT-8 cells. Our data indicate that the expression of Sfp fimbriae in SF
E. coli
O157:NM strains is induced under conditions resembling those of the natural site of infection and that Sfp fimbriae may contribute to the adherence of the organisms to human intestinal epithelium.
Effect of Hydroxyurea on Procyclic
Trypanosoma brucei
: an Unconventional Mechanism for Achieving Synchronous Growth
Authors: Chowdhury Arnab Roy , Zhao Zhixing , Englund Paul T. 
Published: December 2007

ABSTRACT

Procyclic
Trypanosoma brucei
cells were synchronized with 0.2 mM hydroxyurea. The cells did not arrest at the G
1
/S boundary but proceeded through one round of replication and arrested near the end of S phase. The mitochondrial genome (kinetoplast DNA network) replicated, forming two progeny networks, but the repair of minicircle gaps was inhibited.
Escherichia coli
Cytosolic Glycerophosphodiester Phosphodiesterase (UgpQ) Requires Mg
2+
, Co
2+
, or Mn
2+
for Its Enzyme Activity
Authors: Ohshima Noriyasu , Yamashita Saori , Takahashi Naoko , Kuroishi Chizu , Shiro Yoshitsugu , Takio Koji 
Published: December 2007

ABSTRACT

Escherichia coli
cytosolic glycerophosphodiester phosphodiesterase, UgpQ, functions in the absence of other proteins encoded by the
ugp
operon and requires Mg
2+
, Mn
2+
, or Co
2+
, in contrast to Ca
2+
-dependent periplasmic glycerophosphodiester phosphodiesterase, GlpQ. UgpQ has broad substrate specificity toward various glycerophosphodiesters, producing
sn
-glycerol-3-phosphate and the corresponding alcohols. UgpQ accumulates under conditions of phosphate starvation, suggesting that it allows the utilization of glycerophosphodiesters as a source of phosphate. These results clarify how
E. coli
utilizes glycerophosphodiesters using two homologous enzymes, UgpQ and GlpQ.