bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting stents with local delivery of paclitaxel-loaded magnetic nanoparticles using uniform fields
Authors: Chorny Michael , Fishbein Ilia , Yellen Benjamin B. , Alferiev Ivan S. , Bakay Marina , Ganta Srinivas , Adamo Richard , Amiji Mansoor , Friedman Gary , Levy Robert J.
Published: April 2010

The use of stents for vascular disease has resulted in a paradigm shift with significant improvement in therapeutic outcomes. Polymer-coated drug-eluting stents (DES) have also significantly reduced the incidence of reobstruction post stenting, a disorder termed in-stent restenosis. However, the current DESs lack the capacity for adjustment of the drug dose and release kinetics to the disease status of the treated vessel. We hypothesized that these limitations can be addressed by a strategy combining magnetic targeting via a uniform field-induced magnetization effect and a biocompatible magnetic nanoparticle (MNP) formulation designed for efficient entrapment and delivery of paclitaxel (PTX). Magnetic treatment of cultured arterial smooth muscle cells with PTX-loaded MNPs caused significant cell growth inhibition, which was not observed under nonmagnetic conditions. In agreement with the results of mathematical modeling, significantly higher localization rates of locally delivered MNPs to stented arteries were achieved with uniform-field–controlled targeting compared to nonmagnetic controls in the rat carotid stenting model. The arterial tissue levels of stent-targeted MNPs remained 4- to 10-fold higher in magnetically treated animals vs. control over 5 days post delivery. The enhanced retention of MNPs at target sites due to the uniform field-induced magnetization effect resulted in a significant inhibition of in-stent restenosis with a relatively low dose of MNP-encapsulated PTX (7.5 μg PTX/stent). Thus, this study demonstrates the feasibility of site-specific drug delivery to implanted magnetizable stents by uniform field-controlled targeting of MNPs with efficacy for in-stent restenosis.
Identifying the dynamics of complex spatio-temporal systems by spatial recurrence properties
Authors: Mocenni Chiara , Facchini Angelo , Vicino Antonio
Published: April 2010

Complex spatio-temporal systems may exhibit irregular behaviors when driven far from equilibrium. Reaction-diffusion systems often lead to the formation of patterns and spatio-temporal chaos. When a limited number of observations is available, the reconstruction and identification of complex dynamical regimes become challenging problems. A method based on spatial recurrence properties is proposed to deal with this problem: generalized recurrence plots and generalized recurrence quantification analysis are exploited to show that detection of structural changes in spatially distributed systems can be performed by setting up appropriate diagrams accounting for different spatial recurrences. The method has been tested on two prototypical systems forming complex patterns: the complex Ginzburg–Landau equation and the Schnakenberg system. This work allowed us to identify changes in the stability of spiral wave solutions in the former system and to analyze the Turing bifurcations in the latter.
Sexual isolation of male moths explained by a single pheromone response QTL containing four receptor genes
Authors: Gould Fred , Estock Marie , Hillier N. Kirk , Powell Bekah , Groot Astrid T. , Ward Catherine M. , Emerson Jennifer L. , Schal Coby , Vickers Neil J.
Published: April 2010

Long distance sexual communication in moths has fascinated biologists because of the complex, precise female pheromone signals and the extreme sensitivity of males to specific pheromone molecules. Progress has been made in identifying some genes involved in female pheromone production and in male response. However, we have lacked information on the genetic changes involved in evolutionary diversification of these mate-finding mechanisms that is critical to understanding speciation in moths and other taxa. We used a combined quantitative trait locus (QTL) and candidate gene approach to determine the genetic architecture of sexual isolation in males of two congeneric moths,
Heliothis subflexa
and
Heliothis virescens
. We report behavioral and neurophysiological evidence that differential male responses to three female-produced chemicals (
Z
9-14:Ald,
Z
9-16:Ald,
Z
11-16:OAc) that maintain sexual isolation of these species are all controlled by a single QTL containing at least four odorant receptor genes. It is not surprising that pheromone receptor differences could control
H. subflexa
and
H. virescens
responses to
Z
9-16:Ald and
Z
9-14:Ald, respectively. However, central rather than peripheral level control over the positive and negative responses of
H. subflexa
and
H. virescens
to
Z
11-16:OAc had been expected. Tight linkage of these receptor genes indicates that mutations altering male response to complex blends could be maintained in linkage disequilibrium and could affect the speciation process. Other candidate genes such as those coding for pheromone binding proteins did not map to this QTL, but there was some genetic evidence of a QTL for response to
Z
11-16:OH associated with a sensory neuron membrane protein gene.
Esophageal cancer-related gene 4 is a secreted inducer of cell senescence expressed by aged CNS precursor cells
Authors: Kujuro Yuki , Suzuki Norihiro , Kondo Toru
Published: April 2010

Mammalian aging is thought to be partially caused by the diminished capacity of stem/precursor cells to undergo self-renewing divisions. Although many cell-cycle regulators are involved in this process, it is unknown to what extent cell senescence, first identified as irreversible growth arrest in vitro, contributes to the aging process. Here, using a serum-induced mouse oligodendrocyte precursor cell (mOPC) senescence model, we identified esophageal cancer-related gene 4 (
Ecrg4
) as a senescence inducer with implications for the senescence-like state of postmitotic cells in the aging brain. Although mOPCs could proliferate indefinitely when cultured using the appropriate medium (OPC medium), they became senescent in the presence of serum and maintained their senescent phenotype even when the serum was subsequently replaced by OPC medium. We show that
Ecrg4
was up-regulated in the senescent OPCs, its overexpression in OPCs induced senescence by accelerating the proteasome-dependent degradation of cyclins D1 and D3, and that its knockdown by a specific short hairpin RNA prevented these phenotypes. We also show that senescent OPCs secreted Ecrg4 and that recombinant Ecrg4 induced OPC senescence in culture. Moreover, increased Ecrg4 expression was observed in the OPCs and neural precursor cells in the aged mouse brain; this was accompanied by the expression of senescence-associated β-galactosidase activity, indicating the cells’ entrance into senescence. These results suggest that Ecrg4 is a factor linking neural-cell senescence and aging.
An actin-filament-binding interface on the Arp2/3 complex is critical for nucleation and branch stability
Authors: Goley Erin D. , Rammohan Aravind , Znameroski Elizabeth A. , Firat-Karalar Elif Nur , Sept David , Welch Matthew D.
Published: April 2010

The Arp2/3 complex polymerizes new actin filaments from the sides of existing filaments, forming Y-branched networks that are critical for actin-mediated force generation. Binding of the Arp2/3 complex to the sides of actin filaments is therefore central to its actin-nucleating and branching activities. Although a model of the Arp2/3 complex in filament branches has been proposed based on electron microscopy, this model has not been validated using independent approaches, and the functional importance of predicted actin-binding residues has not been extensively tested. Using a combination of molecular dynamics and protein-protein docking simulations, we derived an independent structural model of the interaction between two subunits of the Arp2/3 complex that are key to actin binding, ARPC2 and ARPC4, and the side of an actin filament. This model agreed remarkably well with the previous results from electron microscopy. Complementary mutagenesis experiments revealed numerous residues in ARPC2 and ARPC4 that were required for the biochemical activity of the entire complex. Functionally critical residues clustered together and defined a surface that was predicted by protein-protein docking to be buried in the interaction with actin. Moreover, key residues at this interface were crucial for actin nucleation and Y-branching, high-affinity F-actin binding, and Y-branch stability, demonstrating that the affinity of Arp2/3 complex for F actin independently modulates branch formation and stability. Our results highlight the utility of combining computational and experimental approaches to study protein-protein interactions and provide a basis for further elucidating the role of F-actin binding in Arp2/3 complex activation and function.
Responses of terrestrial ecosystems and carbon budgets to current and future environmental variability
Authors: Medvigy David , Wofsy Steven C. , Munger J. William , Moorcroft Paul R.
Published: April 2010

We assess the significance of high-frequency variability of environmental parameters (sunlight, precipitation, temperature) for the structure and function of terrestrial ecosystems under current and future climate. We examine the influence of hourly, daily, and monthly variance using the Ecosystem Demography model version 2 in conjunction with the long-term record of carbon fluxes measured at Harvard Forest. We find that fluctuations of sunlight and precipitation are strongly and nonlinearly coupled to ecosystem function, with effects that accumulate through annual and decadal timescales. Increasing variability in sunlight and precipitation leads to lower rates of carbon sequestration and favors broad-leaved deciduous trees over conifers. Temperature variability has only minor impacts by comparison. We also find that projected changes in sunlight and precipitation variability have important implications for carbon storage and ecosystem structure and composition. Based on Intergovernmental Panel on Climate Change model estimates for changes in high-frequency meteorological variability over the next 100 years, we expect that terrestrial ecosystems will be affected by changes in variability almost as much as by changes in mean climate. We conclude that terrestrial ecosystems are highly sensitive to high-frequency meteorological variability, and that accurate knowledge of the statistics of this variability is essential for realistic predictions of ecosystem structure and functioning.
Reversal of hippocampal neuronal maturation by serotonergic antidepressants
Authors: Kobayashi Katsunori , Ikeda Yumiko , Sakai Atsushi , Yamasaki Nobuyuki , Haneda Eisuke , Miyakawa Tsuyoshi , Suzuki Hidenori
Published: April 2010

Serotonergic antidepressant drugs have been commonly used to treat mood and anxiety disorders, and increasing evidence suggests potential use of these drugs beyond current antidepressant therapeutics. Facilitation of adult neurogenesis in the hippocampal dentate gyrus has been suggested to be a candidate mechanism of action of antidepressant drugs, but this mechanism may be only one of the broad effects of antidepressants. Here we show a distinct unique action of the serotonergic antidepressant fluoxetine in transforming the phenotype of mature dentate granule cells. Chronic treatments of adult mice with fluoxetine strongly reduced expression of the mature granule cell marker calbindin. The fluoxetine treatment induced active somatic membrane properties resembling immature granule cells and markedly reduced synaptic facilitation that characterizes the mature dentate-to-CA3 signal transmission. These changes cannot be explained simply by an increase in newly generated immature neurons, but best characterized as “dematuration” of mature granule cells. This granule cell dematuration developed along with increases in the efficacy of serotonin in 5-HT
4
receptor-dependent neuromodulation and was attenuated in mice lacking the 5-HT
4
receptor. Our results suggest that serotonergic antidepressants can reverse the established state of neuronal maturation in the adult hippocampus, and up-regulation of 5-HT
4
receptor-mediated signaling may play a critical role in this distinct action of antidepressants. Such reversal of neuronal maturation could affect proper functioning of the mature hippocampal circuit, but may also cause some beneficial effects by reinstating neuronal functions that are lost during development.
Selective and site-specific mobilization of dermal dendritic cells and Langerhans cells by Th1- and Th2-polarizing adjuvants
Authors: Sen Debasish , Forrest Luette , Kepler Thomas B. , Parker Ian , Cahalan Michael D.
Published: April 2010

Dendritic cells (DCs) initiate and polarize adaptive immune responses toward varying functional outcomes. By means of intravital two-photon microscopy, we report that dermal dendritic cells (DDCs) and Langerhans cells (LCs) are differentially mobilized during contact sensitization and by adjuvants such as unmethylated CpG oligonucleotide (CpG) and LPS that induce T helper type 1 (Th1) responses, or papain that induces T helper type 2 (Th2) responses. In ear pinna, contact sensitization, CpG, LPS, and papain all mobilized DDCs in three distinct phases: increased motility and dendritic probing, directed migration, and entry into lymphatic vessels. During the same treatments, the adjacent LCs in ear pinna remained immotile over a 48-hr period of observation. In contrast, footpads lacked DDCs and Th1-polarizing adjuvants selectively induced a delayed mobilization of LCs after 48 hr. Th1 polarization of CD4
+
T cells was independent of the immunization site, whereas ear immunization favored Th2 polarization, correlating with site-specific DC distribution and dynamics. Our results provide an initial description of peripheral DC dynamics in response to adjuvants and imply that LC mobilization enhances a Th1 response and is not sufficient to trigger a Th2 response, whereas mobilization of DDCs alone is sufficient to trigger T-cell proliferation and to polarize initial T-cell activation toward a Th2 response.
The high energy X-ray universe
Authors: Giacconi Riccardo
Published: April 2010

Since its beginning in the early 1960s, the field of X-ray astronomy has exploded, experiencing a ten-billion-fold increase in sensitivity, which brought it on par with the most advanced facilities at all wavelengths. I will briefly describe the revolutionary first discoveries prior to the launch of the Chandra and XMM-Newton X-ray observatories, present some of the current achievements, and offer some thoughts about the future of this field.
Differences in spawning date between populations of common frog reveal local adaptation
Authors: Phillimore Albert B. , Hadfield Jarrod D. , Jones Owen R. , Smithers Richard J.
Published: April 2010

Phenotypic differences between populations often correlate with climate variables, resulting from a combination of environment-induced plasticity and local adaptation. Species comprising populations that are genetically adapted to local climatic conditions should be more vulnerable to climate change than those comprising phenotypically plastic populations. Assessment of local adaptation generally requires logistically challenging experiments. Here, using a unique approach and a large dataset (>50,000 observations from across Britain), we compare the covariation in temperature and first spawning dates of the common frog (
Rana temporaria
) across space with that across time. We show that although all populations exhibit a plastic response to temperature, spawning earlier in warmer years, between-population differences in first spawning dates are dominated by local adaptation. Given climate change projections for Britain in 2050–2070, we project that for populations to remain as locally adapted as contemporary populations will require first spawning date to advance by ∼21–39 days but that plasticity alone will only enable an advance of ∼5–9 days. Populations may thus face a microevolutionary and gene flow challenge to advance first spawning date by a further ∼16–30 days over the next 50 years.
Studies of dark energy with x-ray observatories
Authors: Vikhlinin Alexey
Published: April 2010

I review the contribution of
Chandra
X-ray Observatory to studies of dark energy. There are two broad classes of observable effects of dark energy: evolution of the expansion rate of the Universe, and slow down in the rate of growth of cosmic structures.
Chandra
has detected and measured both of these effects through observations of galaxy clusters. A combination of the
Chandra
results with other cosmological datasets leads to 5% constraints on the dark energy equation-of-state parameter, and limits possible deviations of gravity on large scales from general relativity.
Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin
Authors: Lewis Zachary A. , Adhvaryu Keyur K. , Honda Shinji , Shiver Anthony L. , Selker Eric U.
Published: April 2010

Functionally distinct chromatin domains are delineated by distinct posttranslational modifications of histones, and in some organisms by differences in DNA methylation. Proper establishment and maintenance of chromatin domains is critical but not well understood. We previously demonstrated that heterochromatin in the filamentous fungus
Neurospora crassa
is marked by cytosine methylation directed by trimethylated Lysine 9 on histone H3 (H3K9me3). H3K9me3 is the product of the DIM-5 Lysine methyltransferase and is recognized by a protein complex containing heterochromatin protein-1 and the DIM-2 DNA methyltransferase. To identify additional components that control the establishment and function of DNA methylation and heterochromatin, we built a strain harboring two selectable reporter genes that are silenced by DNA methylation and employed this strain to select for mutants that are
defective in DNA methylation
(
dim
). We report a previously unidentified gene (
dim-7
) that is essential for H3K9me3 and DNA methylation. DIM-7 homologs are found only in fungi and are highly divergent. We found that DIM-7 interacts with DIM-5 in vivo and demonstrated that a conserved domain near the N terminus of DIM-7 is required for its stability. In addition, we found that DIM-7 is essential for recruitment of DIM-5 to form heterochromatin.
Solutes determine the temperature windows for microbial survival and growth
Authors: Chin Jason P. , Megaw Julianne , Magill Caroline L. , Nowotarski Krzysztof , Williams Jim P. , Bhaganna Prashanth , Linton Mark , Patterson Margaret F. , Underwood Graham J. C. , Mswaka Allen Y. , Hallsworth John E.
Published: April 2010

Microbial cells, and ultimately the Earth's biosphere, function within a narrow range of physicochemical conditions. For the majority of ecosystems, productivity is cold-limited, and it is microbes that represent the failure point. This study was carried out to determine if naturally occurring solutes can extend the temperature windows for activity of microorganisms. We found that substances known to disorder cellular macromolecules (chaotropes) did expand microbial growth windows, fungi preferentially accumulated chaotropic metabolites at low temperature, and chemical activities of solutes determined microbial survival at extremes of temperature as well as pressure. This information can enhance the precision of models used to predict if extraterrestrial and other hostile environments are able to support life; furthermore, chaotropes may be used to extend the growth windows for key microbes, such as saprotrophs, in cold ecosystems and manmade biomes.
Domain organization and function in GluK2 subtype kainate receptors
Authors: Das Utpal , Kumar Janesh , Mayer Mark L. , Plested Andrew J. R.
Published: April 2010

Glutamate receptor ion channels (iGluRs) are excitatory neurotransmitter receptors with a unique molecular architecture in which the extracellular domains assemble as a dimer of dimers. The structure of individual dimer assemblies has been established previously for both the isolated ligand-binding domain (LBD) and more recently for the larger amino terminal domain (ATD). How these dimers pack to form tetrameric assemblies in intact iGluRs has remained controversial. Using recently solved crystal structures for the GluK2 kainate receptor ATD as a guide, we performed cysteine mutant cross-linking experiments in full-length tetrameric GluK2 to establish how the ATD packs in a dimer of dimers assembly. A similar approach, using a full-length AMPA receptor GluA2 crystal structure as a guide, was used to design cysteine mutant cross-links for the GluK2 LBD dimer of dimers assembly. The formation of cross-linked tetramers in full-length GluK2 by combinations of ATD and LBD mutants which individually produce only cross-linked dimers suggests that subunits in the ATD and LBD layers swap dimer partners. Functional studies reveal that cross-linking either the ATD or the LBD inhibits activation of GluK2 and that, in the LBD, cross-links within and between dimers have different effects. These results establish that kainate and AMPA receptors have a conserved extracellular architecture and provide insight into the role of individual dimer assemblies in activation of ion channel gating.
Uncoupling of growth plate maturation and bone formation in mice lacking both Schnurri-2 and Schnurri-3
Authors: Jones Dallas C. , Schweitzer Michelle N. , Wein Marc , Sigrist Kirsten , Takagi Tsuyoshi , Ishii Shunsuke , Glimcher Laurie H.
Published: April 2010

Formation and remodeling of the skeleton relies on precise temporal and spatial regulation of genes expressed in cartilage and bone cells. Debilitating diseases of the skeletal system occur when mutations arise that disrupt these intricate genetic regulatory programs. Here, we report that mice bearing parallel null mutations in the adapter proteins Schnurri2 (Shn2) and Schnurri3 (Shn3) exhibit defects in patterning of the axial skeleton during embryogenesis. Postnatally, these compound mutant mice develop a unique osteochondrodysplasia. The deletion of Shn2 and Shn3 impairs growth plate maturation during endochondral ossification but simultaneously results in massively elevated trabecular bone formation. Hence, growth plate maturation and bone formation can be uncoupled under certain circumstances. These unexpected findings demonstrate that both unique and redundant functions reside in the Schnurri protein family that are required for proper skeletal patterning and remodeling.
Endocytic pathway is required for
Drosophila
Toll innate immune signaling
Authors: Huang Hon-Ren , Chen Zhijian J. , Kunes Sam , Chang Geen-Dong , Maniatis Tom
Published: April 2010

The Toll signaling pathway is required for the innate immune response against fungi and Gram-positive bacteria in
Drosophila
. Here we show that the endosomal proteins Myopic (Mop) and Hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) are required for the activation of the Toll signaling pathway. This requirement is observed in cultured cells and in flies, and epistasis experiments show that the Mop protein functions upstream of the MyD88 adaptor and the Pelle kinase. Mop and Hrs, which are critical components of the ESCRT-0 endocytosis complex, colocalize with the Toll receptor in endosomes. We conclude that endocytosis is required for the activation of the Toll signaling pathway.
Antigen affinity discrimination is an intrinsic function of the B cell receptor
Authors: Liu Wanli , Meckel Tobias , Tolar Pavel , Sohn Hae Won , Pierce Susan K.
Published: April 2010

Antibody affinity maturation, a hallmark of adaptive immune responses, results from the selection of B cells expressing somatically hypermutated B cell receptors (BCRs) with increased affinity for antigens. Despite the central role of affinity maturation in antibody responses, the molecular mechanisms by which the increased affinity of a B cell for antigen is translated into a selective advantage for that B cell in immune responses is incompletely understood. We use high resolution live-cell imaging to provide evidence that the earliest BCR-intrinsic events that follow within seconds of BCR–antigen binding are highly sensitive to the affinity of the BCR for antigen. High affinity BCRs readily form oligomers and the resulting microclusters grow rapidly, resulting in enhanced recruitment of Syk kinase and calcium fluxes. Thus, B cells are able to read the affinity of antigen by BCR-intrinsic mechanisms during the earliest phases of BCR clustering, leading to the initiation of B cell responses.
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data
Authors: Ivakhno Sergii , Tavaré Simon
Published: April 2010

Motivation: The current generation of single nucleotide polymorphism (SNP) arrays allows measurement of copy number aberrations (CNAs) in cancer at more than one million locations in the genome in hundreds of tumour samples. Most research has focused on single-sample CNA discovery, the so-called segmentation problem. The availability of high-density, large sample-size SNP array datasets makes the identification of recurrent copy number changes in cancer, an important issue that can be addressed using the cross-sample information.

Results: We present a novel approach for finding regions of recurrent copy number aberrations, called CNAnova, from Affymetrix SNP 6.0 array data. The method derives its statistical properties from a control dataset composed of normal samples and, in contrast to previous methods, does not require segmentation and permutation steps. For rigorous testing of the algorithm and comparison to existing methods, we developed a simulation scheme that uses the noise distribution present in Affymetrix arrays. Application of the method to 128 acute lymphoblastic leukaemia samples shows that CNAnova achieves lower error rate than a popular alternative approach. We also describe an extension of the CNAnova framework to identify recurrent CNA regions with intra-tumour heterogeneity, present in either primary or relapsed samples from the same patients.

Availability: The CNAnova package and synthetic datasets are available at http://www.compbio.group.cam.ac.uk/software.html

Contact:  sergii.ivakhno@cancer.org.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Roles of Buyang Huanwu Decoction in Anti‐Inflammation, Antioxidation and Regulation of Lipid Metabolism in Rats with Myocardial Ischemia
Authors: Liu Yu , Lin Rong , Shi Xiaolian , Fang Zhiyuan , Wang Weirong , Lin Qinqin , Zhang Jiye , Zhang Hui , Ji Qiaoli
Published: April 2010

Buyang Huanwu Decoction (BYHWD) is a well‐known Chinese medicine formula. Recent studies have reported that BYHWD can be used to treat ischemic heart disease. This study investigated the potential mechanism underlying the roles of BYHWD in alleviating the myocardial ischemia induced by isoproterenol (ISO) in rats. Different doses of BYHWD (25.68, 12.84 and 6.42 g kg−1) were lavaged to rats, respectively. Then the expression of the cluster of differentiation 40 (CD40) in the mononuclear cells was measured using flow cytometry, and the expressions of CD40 and its ligand (CD40L) in myocardial tissues were determined by western blotting. The serum biochemical values of superoxide dismutase (SOD) activity, the malondialdehyde (MDA) level and the free fatty acid (FFA) content were measured. The results showed that the SOD activities of BYHWD groups were significantly higher than that of the ISO group, while the MDA levels and FFA contents of all BYHWD groups were lower than that of the ISO group. BYHWD could decrease the expression of CD40 in the mononuclear cells and the CD40 and CD40L expressions in myocardial tissues. Our data suggest that the roles of BYHWD are not only related to its antioxidative action and regulation of lipid metabolisms, but also to the inhibition of inflammatory pathway by the decreased CD40 and CD40L expressions in rats with myocardial ischemia.
Proteomic Analysis of Biopsied Human Colonic Mucosa
Authors: Gourley Glenn R , Yang Libang , Higgins LeeAnn , Riviere Michael A , David Larry L
Published: April 2010

Background and Objectives:

Pediatric gastroenterologists have a unique opportunity to study the proteins in the gastrointestinal tract. To assess the power of proteomic studies we compared 2 methods for analysis of proteins in normal human colonic mucosa: 2‐dimensional gel electrophoresis (2DE) and 2‐dimensional liquid chromatography (2DLC) in conjunction with mass spectrometry. We used Ingenuity Pathway Analysis to examine these proteins regarding function, location, and relation to disease.

Results:

2DLC identified 550 proteins, whereas 2DE identified 107 proteins, 18 of which were not observed with 2DLC. The function associated with the largest number of proteins for both methods was cancer (236 proteins with 2DLC, 61 proteins with 2DE). The largest group of proteins was from the cytoplasm (49.3% from 2DE and 49.1% from 2DLC). Two hundred seventy of the total 568 proteins were related to 26 different categories of human disease and 200 of these 270 were described in large intestine, 227 were described in blood, and 149 were described in serum or plasma.

Conclusions:

These methods are complementary, although many more proteins were identified with 2DLC. This suggests that 2DLC should have greater utility in examining changes in the proteome of the colonic mucosa during disease than 2DE. However, some proteins found were unique to 2DE, and thus the methods chosen for a given analysis must be matched with the proteins to be studied. When pediatric gastroenterologists use proteomic methods, there is a new opportunity to increase our understanding of the gastrointestinal tract in health and disease.
Quality of Life in Children With Crohn Disease
Authors: Hill RJ , Lewindon PJ , Muir R , Grangé I , Connor FL , Ee LC , Withers GD , Cleghorn GJ , Davies PSW
Published: April 2010

Objectives:

Quality of life (QOL) is reportedly poor in children with Crohn disease (CD) but improves with increasing disease duration. This article aims to detail QOL in a cohort of Australian children with CD in relation to disease duration, disease activity, and treatment.

Materials and Methods:

QOL, assessed using the IMPACT‐III questionnaire, and disease activity measures, assessed using the Pediatric Crohn's Disease Activity Index (PCDAI), were available in 41 children with CD. For this cohort, a total of 186 measurements of both parameters were available.

Results:

QOL was found to be significantly lower, and disease activity significantly higher (F = 31.1, P = 0.00), in patients within 6 months of their diagnosis compared with those up to 2.5 years, up to 5 years, and beyond 5 years since diagnosis. Higher disease activity was associated with poorer QOL (r = −0.51, P = 0.00). Total QOL was highest in children on nil medications and lowest in children on enteral nutrition. The PCDAI (t = −6.0, P = 0.00) was a significant predictor of QOL, with the clinical history (t = −6.9, P = 0.00) and examination (t = −2.9, P = 0.01) sections of the PCDAI significantly predicting QOL. Disease duration, age, or sex was neither related to nor significant predictors of QOL, but height z score and type of treatment approached significance.

Conclusions:

Children with CD within 6 months of their diagnosis have impaired QOL compared with those diagnosed beyond 6 months. These patients, along with those with growth impairment, ongoing elevated disease activity with abdominal pain, diarrhoea and/or perirectal and extraintestinal complications, may benefit from regular assessments of QOL as part of their clinical treatment.
Characterization of the RNA content of chromatin
Authors: Mondal Tanmoy , Rasmussen Markus , Pandey Gaurav Kumar , Isaksson Anders , Kanduri Chandrasekhar
Published: April 2010

Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.
Learning discloses abnormal structural and functional plasticity at hippocampal synapses in the APP23 mouse model of Alzheimer's disease
Authors: Middei Silvia , Roberto Anna , Berretta Nicola , Panico Maria Beatrice , Lista Simone , Bernardi Giorgio , Mercuri Nicola B. , Ammassari-Teule Martine , Nisticò Robert
Published: April 2010

B6-Tg/Thy1APP23Sdz (APP23) mutant mice exhibit neurohistological hallmarks of Alzheimer's disease but show intact basal hippocampal neurotransmission and synaptic plasticity. Here, we examine whether spatial learning differently modifies the structural and electrophysiological properties of hippocampal synapses in APP23 and wild-type mice. While no genotypic difference was found in the pseudotrained mice, training elicited a stronger increase in spine density and a more rapid decay of long-term potentiation (LTP) in APP23 mutants. Thus, learning discloses mutation-related abnormalities regarding dendritic spine formation and LTP persistence, thereby suggesting that although unaltered in naïve synapses, plasticity becomes defective at the time it comes into play.
Structure of theMethanothermobacter thermautotrophicusexosome RNase PH ring
Authors: Ng C. Leong , Waterman David G. , Antson Alfred A. , Ortiz-Lombardía Miguel
Published: April 2010

The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase). While all six RNase PH monomers are catalytically active in the homohexameric RNase PH, only half of them are functional in the bacterial PNPase and in the archaeal exosome core and none are functional in the yeast and human exosome cores. Here, the crystal structure of the RNase PH ring from the exosome of the anaerobic methanogenic archaeonMethanothermobacter thermautotrophicusis described at 2.65 Å resolution. Free phosphate anions were found for the first time in the active sites of the RNase PH subunits of an exosome structure and provide structural snapshots of a critical intermediate in the phosphorolytic degradation of RNA by the exosome. Furthermore, the present structure highlights the plasticity of the surfaces delineating the polar regions of the RNase PH ring of the exosome, a feature that can facilitate both interaction with the many cofactors involved in exosome function and the processive activity of this enzyme.
Polymorphism of microcrystalline urate oxidase fromAspergillus flavus
Authors: Collings Ines , Watier Yves , Giffard Marion , Dagogo Sotonye , Kahn Richard , Bonneté Francoise , Wright Jonathan P. , Fitch Andrew N. , Margiolaki Irene
Published: April 2010

Different polymorphs of rasburicase, a recombinant urate oxidase enzyme (Uox) fromAspergillus flavus, were obtained as a series of polycrystalline precipitates. Different crystallization protocols were followed in which the salt type, pH and polyethylene glycol 8000 (PEG 8000) concentration were varied. The related crystalline phases were characterized by means of high-resolution synchrotron X-ray powder diffraction. In all cases, Uox complexed with the inhibitor 8-azaxanthine (AZA) was not altered from its robust orthorhombicI222 phase by variation of any of the factors listed above. However, in the absence of AZA during crystallization ligand-free Uox was significantly affected by the type of salt, resulting in different crystal forms for the four salts tested: sodium chloride, potassium chloride, ammonium chloride and ammonium sulfate. Remarkable alterations of some of these phases were observed upon gradual increase of the exposure time of the sample to the synchrotron beam in addition to variation of the PEG 8000 concentration. When Uox was crystallized in Tris buffer or pure water in the absence of salt, a distinct polymorph of orthorhombic symmetry (P21212) was obtained that was associated with significantly altered lattice dimensions in comparison to a previously reported isosymmetrical structure. The latter form of Uox exhibits enhanced stability to variation of pH and PEG 8000 concentration accompanied by minor modifications of the unit-cell dimensions in the ranges under study. Accurate lattice parameters were extracted for all crystalline phases. This study reveals the rich phase diagram of Uox, a protein of high pharmaceutical importance, which is associated with an enhanced degree of polymorphism. The outcome of our analysis verifies previously reported results as well as demonstrating polymorphs that have altered unit-cell dimensions with respect to known structural models.
Acoustic matrix microseeding: improving protein crystal growth with minimal chemical bias
Authors: Villaseñor Armando G. , Wong April , Shao Ada , Garg Ankur , Kuglstatter Andreas , Harris Seth F.
Published: April 2010

A crystal seeding technique is introduced that uses acoustic waves to deliver nanolitre volumes of seed suspension into protein drops. The reduction in delivery volume enables enhanced crystal growth in matrix-seeding experiments without concern for bias from chemical components in the seed-carrying buffer suspension. Using this technique, it was found that while buffer components alone without seed can marginally promote crystal growth in some cases, crystal seeding is far more effective in boosting the number of sparse-matrix conditions that yield protein crystals.
Analysis of multiple crystal forms ofBacillus subtilisBacB suggests a role for a metal ion as a nucleant for crystallization
Authors: Rajavel M. , Gopal B.
Published: April 2010

Bacillus subtilisBacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded β-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalizedB-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.
Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubledaaxis
Authors: Robbins Arthur H. , Domsic John F. , Agbandje-McKenna Mavis , McKenna Robert
Published: April 2010

The crystal structure of human carbonic anhydrase II with a doubledaaxis from that of the usually observed monoclinic unit cell has been determined and refined to 1.4 Å resolution. The diffraction data withh= 2n+ 1 were systematically weaker than those withh= 2n. Consequently, the scaling of the data, structure solution and refinement were challenging. The two molecules comprising the asymmetric unit are related by a noncrystallographic translation of ½ alonga, but one of the molecules has two alternate positions related by a rotation of approximately 2°. This rotation axis is located near the edge of the central β-sheet, causing a maximum distance disparity of 1.7 Å between equivalent atoms on the diametrically opposite side of the molecule. The crystal-packing contacts are similar to two sequential combined unit cells alongaof the previously determined monoclinic unit cell. Abnormally high finalRcrystandRfreevalues (20.2% and 23.7%, respectively) are not unusual for structures containing pseudo-translational symmetry and probably result from poor signal to noise in the weakh-odd data.
The human coronary collateral circulation
Authors: Seiler Christian
Published: April 2010

Eur J Clin Invest 2010; 40 (5): 465–476

Background  Coronary collaterals are an alternative source of blood supply to myocardium jeopardized by ischaemia. Well‐developed coronary collateral arteries in patients with coronary artery disease (CAD) mitigate myocardial infarcts and improve survival.

Methods and results  Collateral arteries preventing myocardial ischaemia during brief vascular occlusion are present in 1/3 of patients with CAD. Among individuals without relevant coronary stenoses, there are preformed collateral arteries preventing myocardial ischaemia in 20–25%. Collateral flow sufficient to prevent myocardial ischaemia during coronary occlusion amounts to ‡25% of the normal flow through the open vessel. Myocardial infarct size, the most important prognostic determinant after such an event, is the product of coronary artery occlusion time, area at risk for infarction and the inverse of collateral supply. Coronary collateral flow can be assessed only during vascular occlusion of the collateral‐receiving artery. The gold standard for coronary collateral assessment is the measurement of intracoronary occlusive pressure‐ or velocity‐derived collateral flow index expressing collateral as a fraction of flow during vessel patency. Approximately one of five patients with CAD cannot be revascularized by percutaneous coronary intervention or coronary artery bypass grafting. Therapeutic promotion of collateral growth is a valuable treatment strategy in those patients.

Conclusions  Promotion of collateral growth should aim at inducing the development of large conductive collateral arteries (i.e. arteriogenesis) and not so much the sprouting of capillary like vessels (i.e. angiogenesis). Large conductive collateral arteries appear to be effectively promoted via the activation of monocytes/macrophages by means of granulocyte‐colony stimulating factor or of augmenting coronary flow velocity.
Effect of experimental hyperglycaemia on renal haemodynamics in prediabetic patients with and without AT1 receptor blockade
Authors: Frank Helga , Pscherer Stefan , Fliser Danilo , Heemann Uwe
Published: April 2010

Eur J Clin Invest 2010; 40 (5): 414–421

Background and objectives  To prevent diabetic nephropathy, knowledge about early renal impairment caused by a disturbed glucose homoeostasis is essential. The purpose of our study was to investigate haemodynamic changes of the kidney in subjects with impaired glucose tolerance (prediabetics, IGT) during experimental hyperglycaemia and the effect of angiotensin receptor blockade.

Design  In our prospective case control study, we measured renal haemodynamics in 13 non‐albuminuric males with normal kidney function and IGT (diagnosed by an oral glucose tolerance test, OGTT) and in 13 matched controls with a normoglycemic response in the OGTT. Glomerular filtration rate (GFR) was assessed by determination of sinistrin clearance; renal plasma flow (RPF) by para‐aminohippuric acid clearance. All measurements were performed at rest and during hyperglycaemic stress testing (clamp technique; target blood glucose ∼170 mg dL−1). We examined renal effects of valsartan (4 weeks 160 mg day−1) at rest and during experimental hyperglycaemia. Metabolic (glycosylated haemoglobin, adiponectin) and inflammatory (high sensitive C‐reactive protein) parameters were compared with and without valsartan in both groups.

Results  During experimental hyperglycaemia, GFR and RPF decreased significantly more in prediabetics compared with controls. Under valsartan, the hyperglycaemia induced decrease of GFR and RPF was blunted in part by valsartan. Hs‐CRP and HbA1c were significantly higher in prediabetics when compared with controls and improved both under valsartan. Adiponectin was lower in prediabetics and increased significantly under valsartan.

Conclusions  Hyperglycaemia induces impairments of renal haemodynamics as well as inflammatory and metabolic parameters in subjects with impaired glucose tolerance, which improve under valsartan.
Community‐level effects of co‐occurring native and exotic ecosystem engineers
Authors: WARD JESSICA M. , RICCIARDI ANTHONY
Published: April 2010

1. Non‐indigenous ecosystem engineers can substantially affect native biodiversity by transforming the physical structure of habitats. In the Great Lakes–St. Lawrence River system, introduced dreissenid mussels (Dreissena polymorpha and D. bugensis) and the native benthic macroalga Cladophora act as ecosystem engineers by increasing substratum complexity and providing interstitial habitat for benthic macroinvertebrates.

2. We manipulated the topography and perimeter‐to‐area ratio of patches of dreissenid mussels in a series of colonisation experiments conducted at two sites in the St. Lawrence River. Experimental substrata were variably colonised by Cladophora, prompting us to examine (i) how the topography of Dreissena patches affects benthic macroinvertebrate diversity and (ii) the extent to which the effects of Dreissena are altered by the presence of another habitat‐modifying organism (Cladophora).

3. The results of our first experiment suggested that a patchy distribution of dreissenid mussels is an important driver of benthic diversity at small spatial scales. The results of our second and third experiments suggested that a native habitat engineer, Cladophora, modifies the impact of Dreissena on benthic macroinvertebrate communities.

4. While macroalgal blooms have been linked to the large‐scale impacts of Dreissena on light and nutrient availability, Dreissena shells inhibited Cladophora growth at our experimental scale. These findings demonstrate that the interactions between habitat‐modifying species can complicate efforts to predict the community‐level effects of an invasion.