bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of Sn doping in In2O3 thin films on polymer substrates by pulsed-laser deposition at room temperature
Authors: Dekkers J. Matthijn , Rijnders Guus , Blank Dave H. A.
Published: April 2006

The influence of Sn doping in In2O3 thin films on conductance, transmission, and granular structure has been studied. By careful control of the pulsed-laser deposition parameters, films with high optical transmittance (>85%) and low resistivity (ρ=4.1×10−4Ωcm) are grown at room temperature on polyethylene terephthalate substrates. The films ablated from Sn-doped targets are more resistive compared to samples of pure In2O3. Due to increased scattering, the charge carrier mobility in Sn-doped films is lower compared to the undoped samples. A relation between the structural properties and the amount of Sn doping is observed. The electrical properties of films with different compositions are influenced by a different size and formation of grains during growth.
Self-collimation and superlensing in wavy-structured two-dimensional photonic crystals
Authors: Li Y. Y. , Gu P. F. , Zhang J. L. , Li M. Y. , Liu X.
Published: April 2006

Wavy-structured two-dimensional (2D) photonic crystal (PC) is possessed of isofrequency contours of rectangular form and is therefore capable of self-collimation. The self-guiding phenomenon is studied by calculating the intensity of the electromagnetic waves through slabs of the PC. Superlensing based on self-collimation of wavy-structured 2DPC is also investigated by analyzing the field pattern where point source is used. The full width at half maximum of image point is calculated to be 0.28λ. The position of the image is always located in the near-field domain of the slab. Image quality degrades gradually as the slab thickness or the source-slab distance increases.
Enhanced Curie temperatures in Fe and Co magnetic nanoparticle assembly on single-crystalline Al2O3∕NiAl(100) with normal metal capping layer
Authors: Lin Wen-Chin , Huang Po-Chun , Song Ker-Jar , Lin Minn-Tsong
Published: April 2006

The ferromagnetism of Fe nanoparticle assembly on Al2O3∕NiAl(100) is observed above 150K with the coverage larger than 5 ML (monolayer). Cu capping layer induces an enhancement of the Curie temperature (TC) in both Fe and Co magnetic nanoparticle assembly. The TC of Fe nanoparticle assembly with 2 and 6 ML Cu capping layer is enhanced by ∼20K and even higher, indicating the critical effects of metallic capping layer in such magnetic nanostructures as nanoparticle assembly. The capping layer effect would be crucial for the ex situ measurements and the nanostorage-related applications.
Persistence of spatial populations depends on returning home
Authors: Hastings Alan , Botsford Louis W.
Published: April 2006

There is a need for better description and heuristic understanding of the sustainability of populations connected over space by a dispersing stage, both for management purposes and to increase our basic knowledge of the dynamics of these populations. We show that persistence of such a population of connected subpopulations depends on whether the sum of the reproductive gains through all possible closed, between-patch reproductive paths through multiple generations, relative to the shortfall in self-persistence in each path, exceeds unity plus extra terms, which only appear if there are four or more patches. These extra terms have the heuristic explanation that they avoid double counting of reproductive paths that arise with four or more patches because there can be nonoverlapping subnetworks. Thus only those patterns of reproduction and connectivity which eventually lead to descendants returning to the patch from which they originate contribute to persistence. This result provides the basis for evaluating connectivity and habitat heterogeneity to understand reserve design, the effects of human fragmentation, the collapse of marine fisheries, and other conservation issues.
Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling
Authors: De Los Rios Paolo , Ben-Zvi Anat , Slutsky Olga , Azem Abdussalam , Goloubinoff Pierre
Published: April 2006

Hsp70s are highly conserved ATPase molecular chaperones mediating the correct folding of
de novo
synthesized proteins, the translocation of proteins across membranes, the disassembly of some native protein oligomers, and the active unfolding and disassembly of stress-induced protein aggregates. Here, we bring thermodynamic arguments and biochemical evidences for a unifying mechanism named entropic pulling, based on entropy loss due to excluded-volume effects, by which Hsp70 molecules can convert the energy of ATP hydrolysis into a force capable of accelerating the local unfolding of various protein substrates and, thus, perform disparate cellular functions. By means of entropic pulling, individual Hsp70 molecules can accelerate unfolding and pulling of translocating polypeptides into mitochondria in the absence of a molecular fulcrum, thus settling former contradictions between the power-stroke and the Brownian ratchet models for Hsp70-mediated protein translocation across membranes. Moreover, in a very different context devoid of membrane and components of the import pore, the same physical principles apply to the forceful unfolding, solubilization, and assisted native refolding of stable protein aggregates by individual Hsp70 molecules, thus providing a mechanism for Hsp70-mediated protein disaggregation.
Resting B cells as a transfer vehicle for Epstein–Barr virus infection of epithelial cells
Authors: Shannon-Lowe C. D. , Neuhierl B. , Baldwin G. , Rickinson A. B. , Delecluse H.-J.
Published: April 2006

Epstein–Barr virus (EBV), an orally transmitted herpesvirus, efficiently targets B lymphocytes through binding of the viral envelope glycoprotein gp350 to the complement receptor CD21. How the virus accesses epithelial cells is less well understood, because such cells are largely resistant to infection with cell-free virus
in vitro
. Here, we show that, after binding to primary B cells, most Epstein–Barr virions are not internalized but remain on the B cell surface and from there can transfer efficiently to CD21-negative epithelial cells, increasing epithelial infection by 10
3
- to 10
4
-fold compared with cell-free virus. Transfer infection is associated with the formation of B cell–epithelial conjugates with gp350/CD21 complexes focused at the intercellular synapse; transfer involves the gp85 and gp110 viral glycoproteins but is independent of gp42, the HLA class II ligand that is essential for B cell entry. Therefore, through efficient binding to the B cell surface, EBV has developed a means of simultaneously accessing both lymphoid and epithelial compartments; in particular, infection of pharyngeal epithelium by orally transmitted virus becomes independent of initial virus replication in the B cell system.
Homozygosity mapping with SNP arrays identifiesTRIM32, an E3 ubiquitin ligase, as a Bardet–Biedl syndrome gene (BBS11)
Authors: Chiang Annie P. , Beck John S. , Yen Hsan-Jan , Tayeh Marwan K. , Scheetz Todd E. , Swiderski Ruth E. , Nishimura Darryl Y. , Braun Terry A. , Kim Kwang-Youn A. , Huang Jian , Elbedour Khalil , Carmi Rivka , Slusarski Diane C. , Casavant Thomas L. , Stone Edwin M. , Sheffield Val C.
Published: April 2006

The identification of mutations in genes that cause human diseases has largely been accomplished through the use of positional cloning, which relies on linkage mapping. In studies of rare diseases, the resolution of linkage mapping is limited by the number of available meioses and informative marker density. One recent advance is the development of high-density SNP microarrays for genotyping. The SNP arrays overcome low marker informativity by using a large number of markers to achieve greater coverage at finer resolution. We used SNP microarray genotyping for homozygosity mapping in a small consanguineous Israeli Bedouin family with autosomal recessive Bardet–Biedl syndrome (BBS; obesity, pigmentary retinopathy, polydactyly, hypogonadism, renal and cardiac abnormalities, and cognitive impairment) in which previous linkage studies using short tandem repeat polymorphisms failed to identify a disease locus. SNP genotyping revealed a homozygous candidate region. Mutation analysis in the region of homozygosity identified a conserved homozygous missense mutation in theTRIM32gene, a gene coding for an E3 ubiquitin ligase. Functional analysis of this gene in zebrafish and expression correlation analyses among other BBS genes in an expression quantitative trait loci data set demonstrate thatTRIM32is a BBS gene. This study shows the value of high-density SNP genotyping for homozygosity mapping and the use of expression correlation data for evaluation of candidate genes and identifies the proteasome degradation pathway as a pathway involved in BBS.
Cysteinyl leukotriene 2 receptor and protease-activated receptor 1 activate strongly correlated early genes in human endothelial cells
Authors: Uzonyi Barbara , Lötzer Katharina , Jahn Steffen , Kramer Cornelia , Hildner Markus , Bretschneider Ellen , Radke Dörte , Beer Michael , Vollandt Rüdiger , Evans Jilly F. , Funk Colin D. , Habenicht Andreas J. R.
Published: April 2006

Cysteinyl leukotrienes (cysLT), i.e., LTC
4
, LTD
4
, and LTE
4
, are lipid mediators derived from the 5-lipoxygenase pathway, and the cysLT receptors cysLT
1
-R/cysLT
2
-R mediate inflammatory tissue reactions. Although endothelial cells (ECs) predominantly express cysLT
2
-Rs, their role in vascular biology remains to be fully understood. To delineate cysLT
2
-R actions, we stimulated human umbilical vein EC with LTD
4
and determined early induced genes. We also compared LTD
4
effects with those induced by thrombin that binds to protease-activated receptor (PAR)-1. Stringent filters yielded 37 cysLT
2
-R- and 34 PAR-1-up-regulated genes (>2.5-fold stimulation). Most LTD
4
-regulated genes were also induced by thrombin. Moreover, LTD
4
plus thrombin augmented gene expression when compared with each agonist alone. Strongly induced genes were studied in detail: Early growth response (EGR) and nuclear receptor subfamily 4 group A transcription factors; E-selectin; CXC ligand 2;
IL-8
; a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif 1 (
ADAMTS1
); Down syndrome critical region gene 1 (
DSCR1
); tissue factor (
TF
); and cyclooxygenase 2. Transcripts peaked at ≈60 min, were unaffected by a cysLT
1
-R antagonist, and were superinduced by cycloheximide. The EC phenotype was markedly altered: LTD
4
induced
de novo
synthesis of EGR1 protein and EGR1 localized in the nucleus; LTD
4
up-regulated IL-8 formation and secretion; and LTD
4
raised TF protein and TF-dependent EC procoagulant activity. These data show that cysLT
2
-R activation results in a proinflammatory EC phenotype. Because LTD
4
and thrombin are likely to be formed concomitantly
in vivo
, cysLT
2
-R and PAR-1 may cooperate to augment vascular injury.
Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform
Authors: Hausel Tamás
Published: April 2006

A Fourier transform technique is introduced for counting the number of solutions of holomorphic moment map equations over a finite field. This technique in turn gives information on Betti numbers of holomorphic symplectic quotients. As a consequence, simple unified proofs are obtained for formulas of Poincaré polynomials of toric hyperkähler varieties (recovering results of Bielawski–Dancer and Hausel–Sturmfels), Poincaré polynomials of Hilbert schemes of points and twisted Atiyah–Drinfeld–Hitchin–Manin (ADHM) spaces of instantons on ℂ2(recovering results of Nakajima–Yoshioka), and Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof of a conjecture of Kac on the number of absolutely indecomposable representations of a quiver is announced.
CD24 is expressed by myofiber synaptic nuclei and regulates synaptic transmission
Authors: Jevsek Marko , Jaworski Alexander , Polo-Parada Luis , Kim Natalie , Fan Jihua , Landmesser Lynn T. , Burden Steven J.
Published: April 2006

The genes encoding several synaptic proteins, including acetylcholine receptors, acetylcholinesterase, and the muscle-specific kinase, MuSK, are expressed selectively by a small number of myofiber nuclei positioned near the synaptic site. Genetic analysis of mutant mice suggests that additional genes, expressed selectively by synaptic nuclei, might encode muscle-derived retrograde signals that regulate the differentiation of motor axon terminals. To identify candidate retrograde signals, we used a microarray screen to identify genes that are preferentially expressed in the synaptic region of muscle, and we analyzed one such gene,CD24, further. We show thatCD24, which encodes a small, variably and highly glycosylated, glycosylphosphatidylinositol (GPI)-linked protein, is expressed preferentially by myofiber synaptic nuclei in embryonic and adult muscle, and thatCD24expression is restricted to the central region of muscle independent of innervation. Moreover, we show that CD24 has a role in presynaptic differentiation, because synaptic transmission is depressed and fails entirely, in a cyclical manner, after repetitive stimulation of motor axons inCD24mutant mice. These deficits in synaptic transmission, which are accompanied by aberrant stimulus-dependent uptake of AM1–43 from axons, indicate that CD24 is required for normal presynaptic maturation and function. BecauseCD24is also expressed in some neurons, additional experiments will be required to determine whether pre- or postsynaptic CD24 mediates these effects on presynaptic development and function.
Activation and repolarization of the normal human heart under complete physiological conditions
Authors: Ramanathan Charulatha , Jia Ping , Ghanem Raja , Ryu Kyungmoo , Rudy Yoram
Published: April 2006

Knowledge of normal human cardiac excitation stems from isolated heart or intraoperative mapping studies under nonphysiological conditions. Here, we use a noninvasive imaging modality (electrocardiographic imaging) to study normal activation and repolarization in intact unanesthetized healthy adults under complete physiological conditions. Epicardial potentials, electrograms, and isochrones were noninvasively reconstructed. The normal electrophysiological sequence during activation and repolarization was imaged in seven healthy subjects (four males and three females). Electrocardiographic imaging depicted salient features of normal ventricular activation, including timing and location of the earliest right ventricular (RV) epicardial breakthrough in the anterior paraseptal region, subsequent RV and left ventricular (LV) breakthroughs, apex-to-base activation of posterior LV, and late activation of LV base or RV outflow tract. The repolarization sequence was unaffected by the activation sequence, supporting the hypothesis that in normal hearts, local action potential duration (APD) determines local repolarization time. Mean activation recovery interval (ARI), reflecting local APD, was in the typical human APD range (235 ms). Mean LV apex-to-base ARI dispersion was 42 ms. Average LV ARI exceeded RV ARI by 32 ms. Atrial images showed activation spreading from the sinus node to the rest of the atria, ending at the left atrial appendage. This study provides previously undescribed characterization of human cardiac activation and repolarization under normal physiological conditions. A common sequence of activation was identified, with interindividual differences in specific patterns. The repolarization sequence was determined by local repolarization properties rather than by the activation sequence, and significant dispersion of repolarization was observed between RV and LV and from apex to base.
The tomato
FT
ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli
Authors: Lifschitz Eliezer , Eviatar Tamar , Rozman Alexander , Shalit Akiva , Goldshmidt Alexander , Amsellem Ziva , Alvarez John Paul , Eshed Yuval
Published: April 2006

The systemic model for floral induction, dubbed florigen, was conceived in photoperiod-sensitive plants but implies, in its ultimate form, a graft-transmissible signal that, although activated by different stimuli in different flowering systems, is common to all plants. We show that
SFT
(
SINGLE-FLOWER TRUSS
), the tomato ortholog of
FLOWERING LOCUS T
(
FT
), induces flowering in day-neutral tomato and tobacco plants and is encoded by
SFT
.
sft
tomato mutant plants are late-flowering, with altered architecture and flower morphology.
SFT
-dependent graft-transmissible signals complement all developmental defects in
sft
plants and substitute for long-day stimuli in
Arabidopsis
, short-day stimuli in Maryland Mammoth tobacco, and light-dose requirements in tomato
uniflora
mutant plants. The absence of donor SFT RNA from flowering receptor shoots and the localization of the protein in leaf nuclei implicate florigen-like messages in tomato as a downstream pathway triggered by cell-autonomous SFT RNA transcripts. Flowering in tomato is synonymous with termination of the shoot apical meristems, and systemic
SFT
messages attenuate the growth of apical meristems before and independent of floral production. Floral enhancement by systemic
SFT
signals is therefore one pleiotropic effect of
FT
orthologs.
Impaired neurogenesis and cardiovascular development in mice lacking the E3 ubiquitin ligases UBR1 and UBR2 of the N-end rule pathway
Authors: An Jee Young , Seo Jai Wha , Tasaki Takafumi , Lee Min Jae , Varshavsky Alexander , Kwon Yong Tae
Published: April 2006

The N-end rule relates the
in vivo
half-life of a protein to the identity of its N-terminal residue. A subset of degradation signals recognized by the N-end rule pathway comprises the signals, called N-degrons, whose determinants include destabilizing N-terminal residues. Our previous work identified a family of at least four mammalian E3 ubiquitin ligases, including UBR1 and UBR2, that share the UBR box and recognize N-degrons. These E3 enzymes mediate the multifunctional N-end rule pathway, but their individual roles are just beginning to emerge. Mutations of
UBR1
in humans are the cause of Johanson–Blizzard syndrome. UBR1 and UBR2 are 46% identical and appear to be indistinguishable in their recognition of N-degrons.

UBR1
−/−

mice are viable but have defects that include pancreatic insufficiency, similarly to

UBR1
−/−

human patients with Johanson–Blizzard syndrome.

UBR2
−/−

mice are inviable in some strain backgrounds and are defective in male meiosis. To examine functional relationships between UBR1 and UBR2, we constructed mouse strains lacking both of these E3s. We report here that

UBR1
−/−
UBR2
−/−

embryos die at midgestation, with defects in neurogenesis and cardiovascular development. These defects included reduced proliferation as well as precocious migration and differentiation of neural progenitor cells. The expression of regulators such as D-type cyclins and Notch1 was also altered in

UBR1
−/−
UBR2
−/−

embryos. We conclude that the functions of UBR1 and UBR2 are significantly divergent, in part because of differences in their expression patterns and possibly also because of differences in their recognition of protein substrates that contain degradation signals other than N-degrons.
Ascorbic acid supplementation does not attenuate post-exercise muscle soreness following muscle-damaging exercise but may delay the recovery process
Authors: Close Graeme L. , Ashton Tony , Cable Tim , Doran Dominic , Holloway Chris , McArdle Frank , MacLaren Don P. M.
Published: April 2006

Exercise involving lengthening muscle actions, such as downhill running, results in delayed onset muscle soreness (DOMS), which may be attributable to reactive oxygen species (ROS). Although exercise causes oxidative stress, any link between ROS and DOMS remains speculative. There is emerging evidence to suggest that ROS play an important physiological role, assisting in the recovery process and protecting the cell from future damage; however, this has not been fully established. Despite this uncertainty as to the precise role of ROS, attempts to prevent post-exercise ROS production through antioxidant intervention are still common. The study investigated the effects of ascorbic acid supplementation on ROS production and DOMS following downhill running. Subjects were assigned to two groups. The ascorbic acid group (group AA) received 1 g ascorbic acid 2 h pre-, and for 14 d post-downhill running, whilst the placebo group (Pl group) received a placebo. Blood samples were drawn pre-supplement, pre- and post-exercise, and then 1, 2, 3, 4, 7 and 14 d post-exercise for analysis of ascorbate, malonaldehyde and total glutathione. DOMS was assessed using a visual analogue scale and pressure algometry. Muscle function was assessed using isokinetic dynamometry. Plasma ascorbate was elevated throughout in group AA compared with the Pl group. Downhill running resulted in DOMS in both groups. Muscle function was impaired post-exercise in both groups, although a delayed recovery was noted in group AA. Malonaldehyde increased 4 d post-exercise in the Pl group only. Ascorbic acid supplementation attenuates ROS production following downhill running, without affecting DOMS. Furthermore, ascorbic acid supplementation may inhibit the recovery of muscle function.
Dietary acetic acid reduces serum cholesterol and triacylglycerols in rats fed a cholesterol-rich diet
Authors: Fushimi Takashi , Suruga Kazuhito , Oshima Yoshifumi , Fukiharu Momoko , Tsukamoto Yoshinori , Goda Toshinao
Published: April 2006

To investigate the efficacy of the intake of vinegar for prevention of hyperlipidaemia, we examined the effect of dietary acetic acid, the main component of vinegar, on serum lipid values in rats fed a diet containing 1% (w/w) cholesterol. Animals were allowed free access to a diet containing no cholesterol, a diet containing 1% cholesterol without acetic acid, or a diet containing 1% cholesterol with 0·3% (w/w) acetic acid for 19 d. Then, they were killed after food deprivation for 7 h. Cholesterol feeding increased serum total cholesterol and triacylglycerol levels. Compared with the cholesterol-fed group, the cholesterol and acetic acid-fed group had significantly lower values for serum total cholesterol and triacylglycerols, liver ATP citrate lyase (ATP-CL) activity, and liver 3-hydroxy-3-methylglutaryl-CoA content as well as liver mRNA levels of sterol regulatory element binding protein-1, ATP-CL and fatty acid synthase (P<,0·05). Further, the serum secretin level, liver acyl-CoA oxidase expression, and faecal bile acid content were significantly higher in the cholesterol and acetic acid-fed group than in the cholesterol-fed group (P<0·05). However, acetic acid feeding affected neither the mRNA level nor activity of cholesterol 7a-hydroxylase. In conclusion, dietary acetic acid reduced serum total cholesterol and triacylglycerol: first due to the inhibition of lipogenesis in liver; second due to the increment in faecal bile acid excretion in rats fed a diet containing cholesterol.
Influence of specific nutrients on progression of atherosclerosis, vascular function, haemostasis and inflammation in coronary heart disease patients: a systematic review
Authors: Hamer Mark , Steptoe Andrew
Published: April 2006

Epidemiological evidence suggests that the diet influences CHD risk, although the protective effects of dietary intervention for patients in diseased states has gained less attention. Secondary care prevention strategies for patients often involves drug therapy that is expensive and can result in undesirable side effects. Therefore, it is potentially beneficial to utilise other strategies, such as diet, in the management of CHD. A systematic review was conducted to examine the effects of specific nutrients on progression of atherosclerosis, vascular function, haemostasis and inflammation in CHD patients. Results show substantial evidence for the efficacy ofn–3 oils in reducing cardiovascular mortality and one mechanism may be related to the stabilisation of vulnerable atherosclerotic plaques, although the effects on progression of atherosclerosis, haemostatic activity and vascular inflammation remain equivocal. Promising data also exist for the efficacy of flavonoid-rich foods for improving endothelial function, although strong clinical endpoint evidence is lacking. The variation in the efficacy of certain nutrients in CHD patients may be explained by genetics, existing risk factors, psychosocial factors and methodological issues, although these are often not adequately taken into consideration. We conclude that there is a need to undertake more appropriately designed trials in specific clinical populations, controlling for additional lifestyle and risk factors, examining potential interactions with medications, and also establishing methods to increase compliance to dietary recommendations before specific nutrients can be widely prescribed for secondary prevention. Future research should also utilise techniques that provide a direct measure of atherosclerosis.
High tea consumption diminishes salivary 17β-estradiol concentration in Polish women
Authors: Kapiszewska Maria , Miskiewicz Malgorzata , Ellison Peter T. , Thune Inger , Jasienska Grazyna
Published: April 2006

We hypothesized that among reproductive-age women consuming large quantities of tea, the production of estradiol would be suppressed. It has been shown that catechins and theaflavines, the major constituents of tea, inhibit aromatase, an enzyme which catalyses the conversion of androgens to oestrogens. Our study included Polish women living in urban (n 61) and rural (n 48) areas. Women collected daily saliva samples for one complete menstrual cycle and filled out dietary questionnaires. Saliva samples were analysed by RIA for concentration of 17β-estradiol (E2). Women with high (above the median) average daily consumption of black tea had reduced levels of salivary E2 in comparison with women who drank less black tea (below the median). This effect was observed within the whole study group, as well as separately within urban (P=0·0006) and rural (P=0·013) groups. High intake of the sum of subclasses of tea catechins and epigallocatechin gallate, assessed using the United States Department of Agriculture database (http://www.nal.usda.gov), was also associated with lower concentrations of E2 within all women (P=0·01 and P=0·0001, respectively) and within the urban group (P=0·0001 and P0·004, respectively). Similar relationships were observed between the sum of subclasses of theaflavines and thearubigines and E2 levels for the whole group (P=0·002) and for urban women (P=0·02). Women with high consumption of tea had lower levels of E2 concentration throughout the entire menstrual cycle. These results may have implications for reducing hormone-related cancer risk by a relatively easy dietary intervention.
Effects of dietarycisandtransunsaturated and saturated fatty acids on the glucose metabolites and enzymes of rats
Authors: Bernal Claudio A. , Rovira Jordi , Colandré Maryé E. , Cussó Roser , Cadefau Joan A.
Published: April 2006

The aim of the present study was to examine whether the level of dietarycisfatty acid (c FA), or the isomers (trans or cis) and/or the saturation of the fatty acids at high dietary fat levels altered the intracellular glucose metabolites and certain regulatory enzyme activities in the skeletal muscle and liver of rats. The animals were fed for 30 d on either a recommended control diet (7% c FA, w/w) or a high-fat diet (20% fatty acids, w/w). The high-fat diet was enriched with either c FA,trans fattyacid (tFA), a moderate proportion of saturated fatty acid (MSFA), or a high proportion of saturated fatty acid (HSFA). The most striking findings were observed in the gastrocnemius muscle with a HSFA diet. There was a significant increase in glucose-6-phosphate (306 %), glucose-1-phosphate (245 %), fructose-6-phosphate (400 %), fructose-1,6-bisphosphate (86 %), glyceraldehyde- 3-phosphate (38 %), pyruvate (341 %), lactate (325 %), citrate (79 %) and the bisphosphorylated sugars as compared with the cFA diet. These changes were paralleled by an increase in muscle triacylglycerol content (49 %) and a decrease in glucose (39 %). In addition, the amount of cFA and the other types of fatty acid (i.e.tFA and MSFA) led to no great differences in glucose metabolism as compared with the respective control group. These data support the hypothesis that glucose changes induced by a HSFA diet are a multifaceted abnormality. Glucose and lactate transport and intracellular glucose metabolism could be the key biochemical defects involved in this detrimental effect on glucose metabolism.
Physiological pathway of differentiation of hematopoietic stem cell population into mural cells
Authors: Yamada Yoshihiro , Takakura Nobuyuki
Published: April 2006

Endothelial cells (ECs), which are a major component of blood vessels, have been reported to develop in adulthood from hematopoietic cell populations, especially those of the monocyte lineage. Here we show that mural cells (MCs), another component of blood vessels, develop physiologically during embryogenesis from a hematopoietic stem cell (HSC) population, based on the in vitro culture of HSCs and histological examination of acute myeloid leukemia 1 mutant embryos, which lack HSCs. As in the embryo, HSCs in adult bone marrow differentiate into CD45+CD11b+ cells before differentiating into MCs. Moreover, CD45+CD11b+ cells are composed of two populations, CD11bhigh and CD11blow cells, both of which can differentiate into MCs as well as ECs. Interestingly, in a murine ischemia model, MCs and ECs derived from the CD11blow population had a long-term potential to contribute to the formation of newly developed blood vessels in vivo compared with the CD11high population, which could not. Moreover, injection of the CD11bhigh population induced leaky blood vessels, but the CD11blow population did not. With respect to the permeability of vessels, we found that angiopoietin 1, which is a ligand for Tie2 receptor tyrosine kinase expressed on ECs and is suggested to induce cell adhesion between ECs and MCs, is produced by the CD11blow population and plays a critical role in the formation of nonleaky vessels. These observations suggested that the CD11low cell population serves as a good source of cells for in vivo blood vessel regeneration.
Postnatal acquisition of endotoxin tolerance in intestinal epithelial cells
Authors: Lotz Michael , Gütle Dominique , Walther Sabrina , Ménard Sandrine , Bogdan Christian , Hornef Mathias W.
Published: April 2006

The role of innate immune recognition by intestinal epithelial cells (IECs) in vivo is ill-defined. Here, we used highly enriched primary IECs to analyze Toll-like receptor (TLR) signaling and mechanisms that prevent inappropriate stimulation by the colonizing microflora. Although the lipopolysaccharide (LPS) receptor complex TLR4/MD-2 was present in fetal, neonatal, and adult IECs, LPS-induced nuclear factor κB (NF-κB) activation and chemokine (macrophage inflammatory protein 2 [MIP-2]) secretion was only detected in fetal IECs. Fetal intestinal macrophages, in contrast, were constitutively nonresponsive to LPS. Acquisition of LPS resistance was paralleled by a spontaneous activation of IECs shortly after birth as illustrated by phosphorylation of IκB-α and nuclear translocation of NF-κB p65 in situ as well as transcriptional activation of MIP-2. Importantly, the spontaneous IEC activation occurred in vaginally born mice but not in neonates delivered by Caesarean section or in TLR4-deficient mice, which together with local endotoxin measurements identified LPS as stimulatory agent. The postnatal loss of LPS responsiveness of IECs was associated with a posttranscriptional down-regulation of the interleukin 1 receptor–associated kinase 1, which was essential for epithelial TLR4 signaling in vitro. Thus, unlike intestinal macrophages, IECs acquire TLR tolerance immediately after birth by exposure to exogenous endotoxin to facilitate microbial colonization and the development of a stable intestinal host–microbe homeostasis.
Interleukin 25 regulates type 2 cytokine-dependent immunity and limits chronic inflammation in the gastrointestinal tract
Authors: Owyang Alexander M. , Zaph Colby , Wilson Emma H. , Guild Katherine J. , McClanahan Terrill , Miller Hugh R. P. , Cua Daniel J. , Goldschmidt Michael , Hunter Christopher A. , Kastelein Robert A. , Artis David
Published: April 2006

The cytokine interleukin (IL) 25 has been implicated in the initiation of type 2 immunity by driving the expression of type 2 cytokines such as IL-5 and IL-13, although its role in the regulation of immunity and infection-induced inflammation is unknown. Here, we identify a dual function for IL-25: first, in promoting type 2 cytokine-dependent immunity to gastrointestinal helminth infection and, second, in limiting proinflammatory cytokine production and chronic intestinal inflammation. Treatment of genetically susceptible mice with exogenous IL-25 promoted type 2 cytokine responses and immunity to Trichuris. IL-25 was constitutively expressed by CD4+ and CD8+ T cells in the gut of mouse strains that are resistant to Trichuris, and IL-25–deficient mice on a genetically resistant background failed to develop a type 2 immune response or eradicate infection. Furthermore, chronically infected IL-25−/− mice developed severe infection-induced intestinal inflammation associated with heightened expression of interferon-γ and IL-17, identifying a role for IL-25 in limiting pathologic inflammation at mucosal sites. Therefore, IL-25 is not only a critical mediator of type 2 immunity, but is also required for the regulation of inflammation in the gastrointestinal tract.
Identification of an interleukin (IL)-25–dependent cell population that provides IL-4, IL-5, and IL-13 at the onset of helminth expulsion
Authors: Fallon Padraic G. , Ballantyne Sarah J. , Mangan Niamh E. , Barlow Jillian L. , Dasvarma Ayan , Hewett Duncan R. , McIlgorm Ann , Jolin Helen E. , McKenzie Andrew N.J.
Published: April 2006

Type 2 immunity, which involves coordinated regulation of innate and adaptive immune responses, can protect against helminth parasite infection, but may lead to allergy and asthma after inappropriate activation. We demonstrate that il25−/− mice display inefficient Nippostrongylus brasiliensis expulsion and delayed cytokine production by T helper 2 cells. We further establish a key role for interleukin (IL)-25 in regulating a novel population of IL-4–, IL-5–, IL-13–producing non–B/non–T (NBNT), c-kit+, FcεR1− cells during helminth infection. A deficit in this population in il25−/− mice correlates with inefficient N. brasiliensis expulsion. In contrast, administration of recombinant IL-25 in vivo induces the appearance of NBNT, c-kit+, FcεR1− cells and leads to rapid worm expulsion that is T and B cell independent, but type 2 cytokine dependent. We demonstrate that these IL-25–regulated cells appear rapidly in the draining lymph nodes, implicating them as a source of type 2 cytokines during initiation of worm expulsion.
Tissue expression of PD-L1 mediates peripheral T cell tolerance
Authors: Keir Mary E. , Liang Spencer C. , Guleria Indira , Latchman Yvette E. , Qipo Andi , Albacker Lee A. , Koulmanda Maria , Freeman Gordon J. , Sayegh Mohamed H. , Sharpe Arlene H.
Published: April 2006

Programmed death 1 (PD-1), an inhibitory receptor expressed on activated lymphocytes, regulates tolerance and autoimmunity. PD-1 has two ligands: PD-1 ligand 1 (PD-L1), which is expressed broadly on hematopoietic and parenchymal cells, including pancreatic islet cells; and PD-L2, which is restricted to macrophages and dendritic cells. To investigate whether PD-L1 and PD-L2 have synergistic or unique roles in regulating T cell activation and tolerance, we generated mice lacking PD-L1 and PD-L2 (PD-L1/PD-L2−/− mice) and compared them to mice lacking either PD-L. PD-L1 and PD-L2 have overlapping functions in inhibiting interleukin-2 and interferon-γ production during T cell activation. However, PD-L1 has a unique and critical role in controlling self-reactive T cells in the pancreas. Our studies with bone marrow chimeras demonstrate that PD-L1/PD-L2 expression only on antigen-presenting cells is insufficient to prevent the early onset diabetes that develops in PD-L1/PD-L2−/− non-obese diabetic mice. PD-L1 expression in islets protects against immunopathology after transplantation of syngeneic islets into diabetic recipients. PD-L1 inhibits pathogenic self-reactive CD4+ T cell–mediated tissue destruction and effector cytokine production. These data provide evidence that PD-L1 expression on parenchymal cells rather than hematopoietic cells protects against autoimmune diabetes and point to a novel role for PD-1–PD-L1 interactions in mediating tissue tolerance.
Regulation of osteoclast function and bone mass by RAGE
Authors: Zhou Zheng , Immel David , Xi Cai-Xia , Bierhaus Angelika , Feng Xu , Mei Lin , Nawroth Peter , Stern David M. , Xiong Wen-Cheng
Published: April 2006

The receptor for advanced glycation end products (RAGE) is a member of the immunoglobulin superfamily that has multiple ligands and is implicated in the pathogenesis of various diseases, including diabetic complications, neurodegenerative disorders, and inflammatory responses. However, the role of RAGE in normal physiology is largely undefined. Here, we present evidence for a role of RAGE in osteoclast maturation and function, which has consequences for bone remodeling. Mice lacking RAGE had increased bone mass and bone mineral density and decreased bone resorptive activity in vivo. In vitro–differentiated RAGE-deficient osteoclasts exhibited disrupted actin ring and sealing zone structures, impaired maturation, and reduced bone resorptive activity. Impaired signaling downstream of αvβ3 integrin was observed in RAGE−/− bone marrow macrophages and precursors of OCs. These results demonstrate a role for RAGE in osteoclast actin cytoskeletal reorganization, adhesion, and function, and suggest that the osteosclerotic-like phenotype observed in RAGE knockout mice is due to a defect in osteoclast function.
Antioxidants protect from atherosclerosis by a heme oxygenase-1 pathway that is independent of free radical scavenging
Authors: Wu Ben J. , Kathir Krishna , Witting Paul K. , Beck Konstanze , Choy Katherine , Li Cheng , Croft Kevin D. , Mori Trevor A. , Tanous David , Adams Mark R. , Lau Antony K. , Stocker Roland
Published: April 2006

Oxidative stress is implicated in atherogenesis, yet most clinical trials with antioxidants, particularly vitamin E, have failed to protect against atherosclerotic diseases. A striking exception is probucol, which retards atherosclerosis in carotid arteries and restenosis of coronary arteries after angioplasty. Because probucol has in vitro cellular-protective effects independent of inhibiting lipid oxidation, we investigated the mode of action of probucol in vivo. We used three models of vascular disease: apolipoprotein E–deficient mice, a model of atherosclerosis; rabbit aortic balloon injury, a model of restenosis; and carotid injury in obese Zucker rats, a model of type 2 diabetes. Unexpectedly, we observed that the phenol moieties of probucol were insufficient, whereas its sulphur atoms were required for protection. Probucol and its sulphur-containing metabolite, but not a sulphur-free phenolic analogue, protected via cell-specific effects on inhibiting macrophage accumulation, stimulating reendothelialization, and inhibiting vascular smooth muscle cell proliferation. These processes were mediated via induction of heme oxygenase-1 (HO-1), an activity not shared by vitamin E. Our findings identify HO-1 as the molecular target of probucol. They indicate 2-electron rather than radical (1-electron) oxidants as important contributors to atherogenesis, and point to novel lead compounds for therapeutic intervention against atherosclerotic diseases.
Evidence for discrete stages of human natural killer cell differentiation in vivo
Authors: Freud Aharon G. , Yokohama Akihiko , Becknell Brian , Lee Melissa T. , Mao Hsiaoyin C. , Ferketich Amy K. , Caligiuri Michael A.
Published: April 2006

Human natural killer (NK) cells originate from CD34(+) hematopoietic progenitor cells, but the discrete stages of NK cell differentiation in vivo have not been elucidated. We identify and functionally characterize, from human lymph nodes and tonsils, four NK cell developmental intermediates spanning the continuum of differentiation from a CD34(+) NK cell progenitor to a functionally mature NK cell. Analyses of each intermediate stage for CD34, CD117, and CD94 cell surface expression, lineage differentiation potentials, capacity for cytokine production and natural cytotoxicity, and ETS-1, GATA-3, and T-BET expression provide evidence for a new model of human NK cell differentiation in secondary lymphoid tissues.
Lipoprotein oxidation in cardiovascular disease: chief culprit or innocent bystander?
Authors: Heinecke Jay W.
Published: April 2006

Oxidation of low-density lipoprotein (LDL) is thought to contribute to atherosclerosis and cardiovascular disease. Consistent with this idea, the antioxidant drug probucol reduces the risk of restenosis, a form of cardiovascular disease, in humans. However, a new study now suggests that the protective effect of probucol depends not on its ability to inhibit lipid oxidation, but on its ability to induce the stress-induced antiinflammatory enzyme heme oxygenase (HO)-1. This might explain why other antioxidants, such as vitamin E, fail to prevent cardiovascular disease in humans.
New battlefields for costimulation
Authors: Martin-Orozco Natalia , Dong Chen
Published: April 2006

Costimulation regulates the activation of naive T cells as they first encounter antigens in the secondary lymphoid organs. But recently characterized costimulatory molecules of the B7 family appear to have roles beyond initial T cell activation. New evidence shows that negative costimulators expressed by tumors and normal tissues afford local protection from T cell–mediated attack.
The Polyamine Binding Site in Inward Rectifier K+ Channels
Authors: Kurata Harley T. , Marton Laurence J. , Nichols Colin G.
Published: April 2006

Strongly inwardly rectifying potassium channels exhibit potent and steeply voltage-dependent block by intracellular polyamines. To locate the polyamine binding site, we have examined the effects of polyamine blockade on the rate of MTSEA modification of cysteine residues strategically substituted in the pore of a strongly rectifying Kir channel (Kir6.2[N160D]). Spermine only protected cysteines substituted at a deep location in the pore, between the “rectification controller” residue (N160D in Kir6.2, D172 in Kir2.1) and the selectivity filter, against MTSEA modification. In contrast, blockade with a longer synthetic polyamine (CGC-11179) also protected cysteines substituted at sites closer to the cytoplasmic entrance of the channel. Modification of a cysteine at the entrance to the inner cavity (169C) was unaffected by either spermine or CGC-11179, and spermine was clearly “locked” into the inner cavity (i.e., exhibited a dramatically slower exit rate) following modification of this residue. These data provide physical constraints on the spermine binding site, demonstrating that spermine stably binds at a deep site beyond the “rectification controller” residue, near the extracellular entrance to the channel.
AuberGene—a sensitive genome alignment tool
Authors: Szklarczyk Radek , Heringa Jaap
Published: April 2006

Motivation: The accumulation of genome sequences will only accelerate in the coming years. We aim to use this abundance of data to improve the quality of genomic alignments and devise a method which is capable of detecting regions evolving under weak or no evolutionary constraints.

Results: We describe a genome alignment program AuberGene, which explores the idea of transitivity of local alignments. Assessment of the program was done based on a 2 Mbp genomic region containing the CFTR gene of 13 species. In this region, we can identify 53% of human sequence sharing common ancestry with mouse, as compared with 44% found using the usual pairwise alignment. Between human and tetraodon 93 orthologous exons are found, as compared with 77 detected by the pairwise human-tetraodon comparison.

AuberGene allows the user to (1) identify distant, previously undetected, conserved orthogonal regions such as ORFs or regulatory regions; (2) identify neutrally evolving regions in related species which are often overlooked by other alignment programs; (3) recognize false orthologous genomic regions. The increased sensitivity of the method is not obtained at the cost of reduced specificity. Our results suggest that, over the CFTR region, human shares 10% more sequence with mouse than previously thought (∼50%, instead of 40% found with the pairwise alignment).

Availability: The source code and tracks for UCSC Genome Browser generated with the program are available from .

Contact:  heringa@cs.vu.nl
Analysis assistant for single-molecule force spectroscopy data on membrane proteins—MPTV
Authors: Mueller Frank , Muller Daniel J. , Labudde Dirk
Published: April 2006

Summary: Force-distance (F-D) curves of single membrane proteins reveal information on inter- and intramolecular interactions occurring within a protein and between proteins. However, the analysis of single-molecule force spectroscopy data is a time consuming and complex process requiring objective criteria. In most cases the user requires additional information to interpret F-D curves. Therefore we developed a software assistant representing the force or molecular interaction pattern and the topology or the 3D structure of the membrane protein. This representation establishes a basis for detailed interpretation of the protein structure and its underlying molecular interactions. Various integrated bioinformatic features further assist in the interpretation of measured and assigned molecular interactions that determine membrane protein folding, structure, stability and function. Web queries and programs about the topology are directly linked. Motifs, helix types, representation of Venn diagrams and the complete functionality of the program Jmol belong to it.

Availability: The program MPTV is freely available from the website at

Contact:  dirk.labudde@biotec.tu.dresden.de
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
Authors: Herrgård Markus J. , Lee Baek-Seok , Portnoy Vasiliy , Palsson Bernhard Ø.
Published: April 2006

We describe the use of model-driven analysis of multiple data types relevant to transcriptional regulation of metabolism to discover novel regulatory mechanisms in Saccharomyces cerevisiae. We have reconstructed the nutrient-controlled transcriptional regulatory network controlling metabolism in S. cerevisiae consisting of 55 transcription factors regulating 750 metabolic genes, based on information in the primary literature. This reconstructed regulatory network coupled with an existing genome-scale metabolic network model allows in silico prediction of growth phenotypes of regulatory gene deletions as well as gene expression profiles. We compared model predictions of gene expression changes in response to genetic and environmental perturbations to experimental data to identify potential novel targets for transcription factors. We then identified regulatory cascades connecting transcription factors to the potential targets through a systematic model expansion strategy using published genome-wide chromatin immunoprecipitation and binding-site-motif data sets. Finally, we show the ability of an integrated metabolic and regulatory network model to predict growth phenotypes of transcription factor knockout strains. These studies illustrate the potential of model-driven data integration to systematically discover novel components and interactions in regulatory and metabolic networks in eukaryotic cells.