bluuebunny/crossref_metadata_2025 huggingface dataset:
Biguanide metformin acts on tau phosphorylation via mTOR/protein phosphatase 2A (PP2A) signaling
Authors: Kickstein Eva , Krauss Sybille , Thornhill Paul , Rutschow Désirée , Zeller Raphael , Sharkey John , Williamson Ritchie , Fuchs Melanie , Köhler Andrea , Glossmann Hartmut , Schneider Rainer , Sutherland Calum , Schweiger Susann
Published: November 2010

Hyperphosphorylated tau plays an important role in the formation of neurofibrillary tangles in brains of patients with Alzheimer's disease (AD) and related tauopathies and is a crucial factor in the pathogenesis of these disorders. Though diverse kinases have been implicated in tau phosphorylation, protein phosphatase 2A (PP2A) seems to be the major tau phosphatase. Using murine primary neurons from wild-type and human tau transgenic mice, we show that the antidiabetic drug metformin induces PP2A activity and reduces tau phosphorylation at PP2A-dependent epitopes in vitro and in vivo. This tau dephosphorylating potency can be blocked entirely by the PP2A inhibitors okadaic acid and fostriecin, confirming that PP2A is an important mediator of the observed effects. Surprisingly, metformin effects on PP2A activity and tau phosphorylation seem to be independent of AMPK activation, because in our experiments (
i
) metformin induces PP2A activity before and at lower levels than AMPK activity and (
ii
) the AMPK activator AICAR does not influence the phosphorylation of tau at the sites analyzed. Affinity chromatography and immunoprecipitation experiments together with PP2A activity assays indicate that metformin interferes with the association of the catalytic subunit of PP2A (PP2Ac) to the so-called MID1-α4 protein complex, which regulates the degradation of PP2Ac and thereby influences PP2A activity. In summary, our data suggest a potential beneficial role of biguanides such as metformin in the prophylaxis and/or therapy of AD.
Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia
Authors: Paulsson Kajsa , Forestier Erik , Lilljebjörn Henrik , Heldrup Jesper , Behrendtz Mikael , Young Bryan D. , Johansson Bertil
Published: November 2010

High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. It is characterized by gain of chromosomes, typically +X, +4, +6, +10, +14, +17, +18, and +21,+21; little is known about additional genetic aberrations. Approximately 20% of the patients relapse; therefore it is clinically important to identify risk-stratifying markers. We used SNP array analysis to investigate a consecutive series of 74 cases of high hyperdiploid ALL. We show that the characteristic chromosomal gains are even more frequent than previously believed, indicating that karyotyping mistakes are common, and that almost 80% of the cases display additional abnormalities detectable by SNP array analysis. Subclonality analysis strongly implied that the numerical aberrations were primary and arose before structural events, suggesting that step-wise evolution of the leukemic clone is common. An association between duplication of 1q and +5 was seen (
P
= 0.003). Other frequent abnormalities included whole-chromosome uniparental isodisomies (wUPIDs) 9 and 11, gain of 17q not associated with isochromosome formation, extra gain of part of 21q, deletions of ETS variant 6 (
ETV6
), cyclin-dependent kinase inhibitor 2A (
CKDN2A
) and paired box 5 (
PAX5
), and PAN3 poly(A) specific ribonuclease subunit homolog (
PAN3
) microdeletions. Comparison of whole-chromosome and partial UPID9 suggested different pathogenetic outcomes, with the former not involving
CDKN2A
. Finally, two cases had partial deletions of AT rich interactive domain 5B (ARID5B), indicating that acquired as well as constitutional variants in this locus may be associated with pediatric ALL. Here we provide a comprehensive characterization of the genetic landscape of high hyperdiploid childhood ALL, including the heterogeneous pattern of secondary genetic events.
Rotational and constitutional dynamics of caged supramolecules
Authors: Kühne Dirk , Klappenberger Florian , Krenner Wolfgang , Klyatskaya Svetlana , Ruben Mario , Barth Johannes V.
Published: November 2010

The confinement of molecular species in nanoscale environments leads to intriguing dynamic phenomena. Notably, the organization and rotational motions of individual molecules were controlled by carefully designed, fully supramolecular host architectures. Here we use an open 2D coordination network on a smooth metal surface to steer the self-assembly of discrete trimeric guest units, identified as noncovalently bound dynamers. Each caged chiral supramolecule performs concerted, chirality-preserving rotary motions within the template honeycomb pore, which are visualized and quantitatively analyzed using temperature-controlled scanning tunneling microscopy. Furthermore, with higher thermal energies, a constitutional system dynamics appears, which is revealed by monitoring repetitive switching events of the confined supramolecules’ chirality signature, reflecting decay and reassembly of the caged units.
Receptor interacting protein kinases mediate retinal detachment-induced photoreceptor necrosis and compensate for inhibition of apoptosis
Authors: Trichonas George , Murakami Yusuke , Thanos Aristomenis , Morizane Yuki , Kayama Maki , Debouck Christine M. , Hisatomi Toshio , Miller Joan W. , Vavvas Demetrios G.
Published: November 2010

Apoptosis has been shown to be a significant form of cell loss in many diseases. Detachment of photoreceptors from the retinal pigment epithelium, as seen in various retinal disorders, causes photoreceptor loss and subsequent vision decline. Although caspase-dependent apoptotic pathways are activated after retinal detachment, caspase inhibition by the pan-caspase inhibitor Z-VAD fails to prevent photoreceptor death; thus, we investigated other pathways leading to cell loss. Here, we show that receptor interacting protein (RIP) kinase-mediated necrosis is a significant mode of photoreceptor cell loss in an experimental model of retinal detachment and when caspases are inhibited, RIP-mediated necrosis becomes the predominant form of death. RIP3 expression, a key activator of RIP1 kinase, increased more than 10-fold after retinal detachment. Morphological assessment of detached retinas treated with Z-VAD showed decreased apoptosis but significantly increased necrotic photoreceptor death. RIP1 kinase inhibitor necrostatin-1 or
Rip3
deficiency substantially prevented those necrotic changes and reduced oxidative stress and mitochondrial release of apoptosis-inducing factor. Thus, RIP kinase-mediated programmed necrosis is a redundant mechanism of photoreceptor death in addition to apoptosis, and simultaneous inhibition of RIP kinases and caspases is essential for effective neuroprotection and may be a novel therapeutic strategy for treatment of retinal disorders.
DNA damage regulates the mobility of Brca2 within the nucleoplasm of living cells
Authors: Jeyasekharan Anand D. , Ayoub Nabieh , Mahen Robert , Ries Jonas , Esposito Alessandro , Rajendra Eeson , Hattori Hiroyoshi , Kulkarni Rajan P. , Venkitaraman Ashok R.
Published: November 2010

How the biochemical reactions that lead to the repair of DNA damage are controlled by the diffusion and availability of protein reactants within the nucleoplasm is poorly understood. Here, we use gene targeting to replace Brca2 (a cancer suppressor protein essential for DNA repair) with a functional enhanced green fluorescent protein (EGFP)-tagged form, followed by fluorescence correlation spectroscopy to measure Brca2-EGFP diffusion in the nucleoplasm of living cells exposed to DNA breakage. Before damage, nucleoplasmic Brca2 molecules exhibit complex states of mobility, with long dwell times within a sub-fL observation volume, indicative of restricted motion. DNA damage significantly enhances the mobility of Brca2 molecules in the S/G2 phases of the cell cycle, via signaling through damage-activated protein kinases. Brca2 mobilization is accompanied by increased binding within the nucleoplasm to its cargo, the Rad51 recombinase, measured by fluorescence cross-correlation spectroscopy. Together, these results suggest that DNA breakage triggers the redistribution of soluble nucleoplasmic Brca2 molecules from a state of restricted diffusion, into a mobile fraction available for Rad51 binding. Our findings identify signal-regulated changes in nucleoplasmic protein diffusion as a means to control biochemical reactions in the cell nucleus.
Trial-to-trial variability of the prefrontal neurons reveals the nature of their engagement in a motion discrimination task
Authors: Hussar Cory , Pasternak Tatiana
Published: November 2010

During motion discrimination tasks, many prefrontal cortex (PFC) neurons are strongly modulated by the behavioral context, suggesting their involvement in sensory discriminations. Recent studies suggest that trial-to-trial variability of spiking activity characteristic of cortical neurons could be a source of information about the state of neurons and their participation in behavioral tasks. We tested this hypothesis by examining the variability of putative pyramidal PFC neurons, a likely source of top-down influences. The variability of these neurons was calculated as a ratio of spike count variance to its mean (fano factor, FF), while monkeys compared the directions of two moving stimuli, sample and test, separated by a delay. We found that the FF tracked consecutive components of the task, dropping rapidly with the onset of stimuli being discriminated and declining more slowly before each salient event of the trial: The sample, the test, and the response. These time-dependent signals were less consistent in direction selective neurons and were largely absent during passive fixation. Furthermore, neurons with test responses that reflected the remembered sample decreased their FF well before the test, revealing the predictive nature of response variability, an effect present only during the active task. The FF was also sensitive to behavioral performance, exhibiting different temporal dynamics on error trials. These changes did not depend on firing rates and were often the only metric correlated with task demands. Our results demonstrate that trial-to-trial variability provides a sensitive measure of the engagement of putative pyramidal PFC neurons in circuits subserving discrimination tasks.
Deletion of hensin/DMBT1 blocks conversion of β- to α-intercalated cells and induces distal renal tubular acidosis
Authors: Gao XiaoBo , Eladari Dominique , Leviel Francoise , Tew Ben Yi , Miró-Julià Cristina , Cheema Faisal H. , Miller Lance , Nelson Raoul , Păunescu Teodor G. , McKee Mary , Brown Dennis , Al-Awqati Qais
Published: November 2010

Acid–base transport in the renal collecting tubule is mediated by two canonical cell types: the β-intercalated cell secretes HCO
3
by an apical Cl:HCO
3
named pendrin and a basolateral vacuolar (V)-ATPase. Acid secretion is mediated by the α-intercalated cell, which has an apical V-ATPase and a basolateral Cl:HCO
3
exchanger (kAE1). We previously suggested that the β-cell converts to the α-cell in response to acid feeding, a process that depended on the secretion and deposition of an extracellular matrix protein termed hensin (DMBT1). Here, we show that deletion of hensin from intercalated cells results in the absence of typical α-intercalated cells and the consequent development of complete distal renal tubular acidosis (dRTA). Essentially all of the intercalated cells in the cortex of the mutant mice are canonical β-type cells, with apical pendrin and basolateral or diffuse/bipolar V-ATPase. In the medulla, however, a previously undescribed cell type has been uncovered, which resembles the cortical β-intercalated cell in ultrastructure, but does not express pendrin. Polymerization and deposition of hensin (in response to acidosis) requires the activation of β1 integrin, and deletion of this gene from the intercalated cell caused a phenotype that was identical to the deletion of hensin itself, supporting its critical role in hensin function. Because previous studies suggested that the conversion of β- to α-intercalated cells is a manifestation of terminal differentiation, the present results demonstrate that this differentiation proceeds from HCO
3
secreting to acid secreting phenotypes, a process that requires deposition of hensin in the ECM.
Directed epitope delivery across the
Escherichia coli
outer membrane through the porin OmpF
Authors: Housden Nicholas G. , Wojdyla Justyna A. , Korczynska Justyna , Grishkovskaya Irina , Kirkpatrick Nadine , Brzozowski A. Marek , Kleanthous Colin
Published: November 2010

The porins OmpF and OmpC are trimeric β-barrel proteins with narrow channels running through each monomer that exclude molecules > 600 Da while mediating the passive diffusion of small nutrients and metabolites across the Gram-negative outer membrane (OM). Here, we elucidate the mechanism by which an entire soluble protein domain (> 6 kDa) is delivered through the lumen of such porins. Following high-affinity binding to the vitamin B
12
receptor in
Escherichia coli
, the bacteriocin ColE9 recruits OmpF or OmpC using an 83-residue intrinsically unstructured translocation domain (IUTD) to deliver a 16-residue TolB-binding epitope (TBE) in the center of the IUTD to the periplasm where it triggers toxin entry. We demonstrate that the IUTD houses two OmpF-binding sites, OBS1 (residues 2–18) and OBS2 (residues 54–63), which flank the TBE and bind with
K

d

s of 2 and 24 μM, respectively, at pH 6.5 and 25 ºC. We show the two OBSs share the same binding site on OmpF and that the colicin must house at least one of them for antibiotic activity. Finally, we report the structure of the OmpF-OBS1 complex that shows the colicin bound within the porin lumen spanning the membrane bilayer. Our study explains how colicins exploit porins to deliver epitope signals to the bacterial periplasm and, more broadly, how the inherent flexibility and narrow cross-sectional area of an IUP domain can endow it with the ability to traverse a biological membrane via the constricted lumen of a β-barrel membrane protein.
Metal spectra as indicators of development
Authors: Graedel T. E. , Cao J.
Published: November 2010

We have assembled extensive information on the cycles of seven industrial metals in 49 countries, territories, or groups of countries, drawn from a database of some 200,000 material flows, and have devised analytical approaches to treat the suite of metals as composing an approach to a national “materials metabolism.” We demonstrate that in some of the more developed countries, per capita metal use is more than 10 times the global average. Additionally, countries that use more than the per capita world average of any metal do so for all metals, and vice versa, and countries that are above global average rates of use are very likely to be above global average rates at all stages of metal life cycles from fabrication onward. We show that all countries are strongly dependent on international trade to supply the spectrum of nonrenewable resources that modern technology requires, regardless of their level of development. We also find that the rate of use of the spectrum of metals stock is highly correlated to per capita gross domestic product, as well as to the Human Development Index and the Global Competitiveness Innovation Index. The implication is that as wealth and technology increase in developing countries, strong demand will be created not for a few key resources, but across the entire spectrum of the industrial metals. Long-term metal demand can be estimated given gross domestic product projections; the results suggest overall metal flow into use in 2050 of 5–10 times today’s level should supplies permit.
Hoxb4 transduction down-regulates Geminin protein, providing hematopoietic stem and progenitor cells with proliferation potential
Authors: Ohno Yoshinori , Yasunaga Shin'ichiro , Ohtsubo Motoaki , Mori Sayaka , Tsumura Miyuki , Okada Satoshi , Ohta Tomohiko , Ohtani Kiyoshi , Kobayashi Masao , Takihara Yoshihiro
Published: November 2010

Retrovirus-mediated transduction of Hoxb4 enhances hematopoietic stem cell (HSC) activity and enforced expression of Hoxb4 induces in vitro development of HSCs from differentiating mouse embryonic stem cells, but the underlying molecular mechanism remains unclear. We previously showed that the HSC activity was abrogated by accumulated Geminin, an inhibitor for the DNA replication licensing factor Cdt1 in mice deficient in
Rae28
(also known as
Phc1
), which encodes a member of Polycomb-group complex 1. In this study we found that Hoxb4 transduction reduced accumulated Geminin in
Rae28
-deficient mice, despite increasing the mRNA, and restored the impaired HSC activity. Supertransduction of Geminin suppressed the HSC activity induced by Hoxb4 transduction, whereas knockdown of Geminin promoted the clonogenic and replating activities, indicating the importance of Geminin regulation in the molecular mechanism underlying Hoxb4 transduction-mediated enhancement of the HSC activity. This facilitated our investigation of how transduced Hoxb4 reduced Geminin. We showed in vitro and in vivo that Hoxb4 and the Roc1 (also known as Rbx1)-Ddb1-Cul4a ubiquitin ligase core component formed a complex designated as RDCOXB4, which acted as an E3 ubiquitin ligase for Geminin and down-regulated Geminin through the ubiquitin-proteasome system. Down-regulated Geminin and the resultant E2F activation may provide cells with proliferation potential by increasing a DNA prereplicative complex loaded onto chromatin. Here we suggest that transduced Hoxb4 down-regulates Geminin protein probably by constituting the E3 ubiquitin ligase for Geminin to provide hematopoietic stem and progenitor cells with proliferation potential.
Using return on investment to maximize conservation effectiveness in Argentine grasslands
Authors: Murdoch William , Ranganathan Jai , Polasky Stephen , Regetz James
Published: November 2010

The rapid global loss of natural habitats and biodiversity, and limited resources, place a premium on maximizing the expected benefits of conservation actions. The scarcity of information on the fine-grained distribution of species of conservation concern, on risks of loss, and on costs of conservation actions, especially in developing countries, makes efficient conservation difficult. The distribution of ecosystem types (unique ecological communities) is typically better known than species and arguably better represents the entirety of biodiversity than do well-known taxa, so we use conserving the diversity of ecosystem types as our conservation goal. We define conservation benefit to include risk of conversion, spatial effects that reward clumping of habitat, and diminishing returns to investment in any one ecosystem type. Using Argentine grasslands as an example, we compare three strategies: protecting the cheapest land (“minimize cost”), maximizing conservation benefit regardless of cost (“maximize benefit”), and maximizing conservation benefit per dollar (“return on investment”). We first show that the widely endorsed goal of saving some percentage (typically 10%) of a country or habitat type, although it may inspire conservation, is a poor operational goal. It either leads to the accumulation of areas with low conservation benefit or requires infeasibly large sums of money, and it distracts from the real problem: maximizing conservation benefit given limited resources. Second, given realistic budgets, return on investment is superior to the other conservation strategies. Surprisingly, however, over a wide range of budgets, minimizing cost provides more conservation benefit than does the maximize-benefit strategy.
Simultaneous magnetic resonance imaging of ventilation distribution and gas uptake in the human lung using hyperpolarized xenon-129
Authors: Mugler John P. , Altes Talissa A. , Ruset Iulian C. , Dregely Isabel M. , Mata Jaime F. , Miller G. Wilson , Ketel Stephen , Ketel Jeffrey , Hersman F. William , Ruppert Kai
Published: November 2010

Despite a myriad of technical advances in medical imaging, as well as the growing need to address the global impact of pulmonary diseases, such as asthma and chronic obstructive pulmonary disease, on health and quality of life, it remains challenging to obtain in vivo regional depiction and quantification of the most basic physiological functions of the lung—gas delivery to the airspaces and gas uptake by the lung parenchyma and blood—in a manner suitable for routine application in humans. We report a method based on MRI of hyperpolarized xenon-129 that permits simultaneous observation of the 3D distributions of ventilation (gas delivery) and gas uptake, as well as quantification of regional gas uptake based on the associated ventilation. Subjects with lung disease showed variations in gas uptake that differed from those in ventilation in many regions, suggesting that gas uptake as measured by this technique reflects such features as underlying pathological alterations of lung tissue or of local blood flow. Furthermore, the ratio of the signal associated with gas uptake to that associated with ventilation was substantially altered in subjects with lung disease compared with healthy subjects. This MRI-based method provides a way to quantify relationships among gas delivery, exchange, and transport, and appears to have significant potential to provide more insight into lung disease.
Protein structure determination by exhaustive search of Protein Data Bank derived databases
Authors: Stokes-Rees Ian , Sliz Piotr
Published: November 2010

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from
Trichoplusia ni
. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.
Organization of the polarization splay modulated smectic liquid crystal phase by topographic confinement
Authors: Ki Yoon Dong , Deb Rajdeep , Chen Dong , Körblova Eva , Shao Renfan , Ishikawa Ken , Rao Nandiraju V. S. , Walba David M. , Smalyukh Ivan I. , Clark Noel A.
Published: November 2010

Recently, the topographic patterning of surfaces by lithography and nanoimprinting has emerged as a new and powerful tool for producing single structural domains of liquid crystals and other soft materials. Here the use of surface topography is extended to the organization of liquid crystals of bent-core molecules, soft materials that, on the one hand, exhibit a rich, exciting, and intensely studied array of novel phases, but that, on the other hand, have proved very difficult to align. Among the most notorious in this regard are the polarization splay modulated (B7) phases, in which the symmetry-required preference for ferroelectric polarization to be locally bouquet-like or “splayed” is expressed. Filling space with splay of a single sign requires defects and in the B7 splay is accommodated in the form of periodic splay stripes spaced by defects and coupled to smectic layer undulations. Upon cooling from the isotropic phase this structure grows via a first order transition in the form of an exotic array of twisted filaments and focal conic defects that are influenced very little by classic alignment methods. By contrast, growth under conditions of confinement in rectangular topographic channels is found to produce completely new growth morphology, generating highly ordered periodic layering patterns. The resulting macroscopic order will be of great use in further exploration of the physical properties of bent-core phases and offers a route for application of difficult-to-align soft materials as are encountered in organic electronic and optical applications.
Strategies for stabilizing superoxide dismutase (SOD1), the protein destabilized in the most common form of familial amyotrophic lateral sclerosis
Authors: Auclair Jared R. , Boggio Kristin J. , Petsko Gregory A. , Ringe Dagmar , Agar Jeffrey N.
Published: November 2010

Amyotrophic lateral sclerosis (ALS) is a disorder characterized by the death of both upper and lower motor neurons and by 3- to 5-yr median survival postdiagnosis. The only US Food and Drug Administration-approved drug for the treatment of ALS, Riluzole, has at best, moderate effect on patient survival and quality of life; therefore innovative approaches are needed to combat neurodegenerative disease. Some familial forms of ALS (fALS) have been linked to mutations in the Cu/Zn superoxide dismutase (SOD1). The dominant inheritance of mutant SOD1 and lack of symptoms in knockout mice suggest a “gain of toxic function” as opposed to a loss of function. A prevailing hypothesis for the mechanism of the toxicity of fALS-SOD1 variants, or the gain of toxic function, involves dimer destabilization and dissociation as an early step in SOD1 aggregation. Therefore, stabilizing the SOD1 dimer, thus preventing aggregation, is a potential therapeutic strategy. Here, we report a strategy in which we chemically cross-link the SOD1 dimer using two adjacent cysteine residues on each respective monomer (Cys111). Stabilization, measured as an increase in melting temperature, of ∼20 °C and ∼45 °C was observed for two mutants, G93A and G85R, respectively. This stabilization is the largest for SOD1, and to the best of our knowledge, for any disease-related protein. In addition, chemical cross-linking conferred activity upon G85R, an otherwise inactive mutant. These results demonstrate that targeting these cysteine residues is an important new strategy for development of ALS therapies.
Malignant cells facilitate lung metastasis by bringing their own soil
Authors: Duda Dan G. , Duyverman Annique M. M. J. , Kohno Mitsutomo , Snuderl Matija , Steller Ernst J. A. , Fukumura Dai , Jain Rakesh K.
Published: November 2010

Metastatic cancer cells (seeds) preferentially grow in the secondary sites with a permissive microenvironment (soil). We show that the metastatic cells can bring their own soil—stromal components including activated fibroblasts—from the primary site to the lungs. By analyzing the efferent blood from tumors, we found that viability of circulating metastatic cancer cells is higher if they are incorporated in heterotypic tumor–stroma cell fragments. Moreover, we show that these cotraveling stromal cells provide an early growth advantage to the accompanying metastatic cancer cells in the lungs. Consistent with this hypothesis, we demonstrate that partial depletion of the carcinoma-associated fibroblasts, which spontaneously spread to the lung tissue along with metastatic cancer cells, significantly decreases the number of metastases and extends survival after primary tumor resection. Finally, we show that the brain metastases from lung carcinoma and other carcinomas in patients contain carcinoma-associated fibroblasts, in contrast to primary brain tumors or normal brain tissue. Demonstration of the direct involvement of primary tumor stroma in metastasis has important conceptual and clinical implications for the colonization step in tumor progression.
Dicer controls CD8+T-cell activation, migration, and survival
Authors: Zhang Nu , Bevan Michael J.
Published: November 2010

The RNaseIII enzyme Dicer is required for mature microRNA production. Although extensive investigation has been carried out to determine the role of Dicer/miRNAs in the immune system, their function in mature CD8+T cells has not been examined. We deleted Dicer in mature polyclonal and TCR transgenic CD8+T cells using either tat-cre or the distal lck promoter, which drives cre expression after the stage of positive selection. Following antigenic challenge by a pathogen infection in vivo, Dicer-deleted CD8+T cells failed to accumulate at the usual peak of the response. Surprisingly however, we found that deletion of Dicer in mature CD8+T cells allowed them to respond more rapidly than control cells to TCR stimuli in vitro. In response to anti-CD3 plus anti-CD28 stimulation, Dicer-deleted T cells up-regulated CD69 faster and entered the first mitosis earlier than control T cells. In addition, activated Dicer−/−cells failed to rapidly down-regulate CD69 when removed from the TCR stimulus. As a probable consequence of this sustained CD69 expression, Dicer−/−T cells showed defective migration out of the central lymphoid organs in vivo. We identify miR-130/301, which are dramatically up-regulated following T-cell activation, as able to down-regulate CD69 expression via binding to a conserved site in the 3′UTR of CD69 mRNA. Thus, cellular functions dependent on Dicer expression are not required for the early steps in CD8+T-cell activation, but are essential for their survival and accumulation.
Phosphorylated Rad18 directs DNA Polymerase η to sites of stalled replication
Authors: Day Tovah A. , Palle Komariah , Barkley Laura R. , Kakusho Naoko , Zou Ying , Tateishi Satoshi , Verreault Alain , Masai Hisao , Vaziri Cyrus
Published: November 2010

The E3 ubiquitin ligase Rad18 guides DNA Polymerase eta (Polη) to sites of replication fork stalling and mono-ubiquitinates proliferating cell nuclear antigen (PCNA) to facilitate binding of Y family trans-lesion synthesis (TLS) DNA polymerases during TLS. However, it is unclear exactly how Rad18 is regulated in response to DNA damage and how Rad18 activity is coordinated with progression through different phases of the cell cycle. Here we identify Rad18 as a novel substrate of the essential protein kinase Cdc7 (also termed Dbf4/Drf1-dependent Cdc7 kinase [DDK]). A serine cluster in the Polη-binding motif of Rad18 is phosphorylated by DDK. Efficient association of Rad18 with Polη is dependent on DDK and is necessary for redistribution of Polη to sites of replication fork stalling. This is the first demonstration of Rad18 regulation by direct phosphorylation and provides a novel mechanism for integration of S phase progression with postreplication DNA repair to maintain genome stability.
Drosophila Boi limits Hedgehog levels to suppress follicle stem cell proliferation
Authors: Hartman Tiffiney R. , Zinshteyn Daniel , Schofield Heather K. , Nicolas Emmanuelle , Okada Ami , O'Reilly Alana M.
Published: November 2010

Stem cells depend on signals from cells within their microenvironment, or niche, as well as factors secreted by distant cells to regulate their maintenance and function. Here we show that Boi, a Hedgehog (Hh)-binding protein, is a novel suppressor of proliferation of follicle stem cells (FSCs) in the Drosophila ovary. Hh is expressed in apical cells, distant from the FSC niche, and diffuses to reach FSCs, where it promotes FSC proliferation. We show that Boi is expressed in apical cells and exerts its suppressive effect on FSC proliferation by binding to and sequestering Hh on the apical cell surface, thereby inhibiting Hh diffusion. Our studies demonstrate that cells distant from the local niche can regulate stem cell function through ligand sequestration, a mechanism that likely is conserved in other epithelial tissues.
IL-27 supports germinal center function by enhancing IL-21 production and the function of T follicular helper cells
Authors: Batten Marcel , Ramamoorthi Nandhini , Kljavin Noelyn M. , Ma Cindy S. , Cox Jennifer H. , Dengler Hart S. , Danilenko Dimitry M. , Caplazi Patrick , Wong Melanie , Fulcher David A. , Cook Matthew C. , King Cecile , Tangye Stuart G. , de Sauvage Frederic J. , Ghilardi Nico
Published: November 2010

Maturation and selection of high-affinity B cell clones in the germinal center (GC) relies on support from T follicular helper (TFH) cells. TFH cells are characterized by their localization to the B cell follicle and their high expression of the costimulatory molecules ICOS and PD1 and the cytokine IL-21, which promotes immunoglobulin (Ig) class switching and production by B cells. We show that the heterodimeric cytokine IL-27 is critical for the function of TFH cells and for normal and pathogenic GC responses. IL-27 signaling to T cells results in the production of IL-21, a known autocrine factor for the maintenance of TFH cells, in a STAT3-dependent manner. IL-27 also enhances the survival of activated CD4+ T cells and the expression of TFH cell phenotypic markers. In vivo, expression of the IL-27Rα chain is required to support IL-21 production and TFH cell survival in a T cell–intrinsic manner. The production of high-affinity antibodies is reduced, and pristane-elicited autoantibodies and glomerulonephritis are significantly diminished, in Il27ra−/− mice. Together, our data show a nonredundant role for IL-27 in the development of T cell–dependent antibody responses.
VEGF receptor signaling links inflammation and tumorigenesis in colitis-associated cancer
Authors: Waldner Maximilian J. , Wirtz Stefan , Jefremow André , Warntjen Moritz , Neufert Clemens , Atreya Raja , Becker Christoph , Weigmann Benno , Vieth Michael , Rose-John Stefan , Neurath Markus F.
Published: November 2010

Whereas the inhibition of vascular endothelial growth factor (VEGF) has shown promising results in sporadic colon cancer, the role of VEGF signaling in colitis-associated cancer (CAC) has not been addressed. We found that, unlike sporadic colorectal cancer and control patients, patients with CAC show activated VEGFR2 on intestinal epithelial cells (IECs). We then explored the function of VEGFR2 in a murine model of colitis-associated colon cancer characterized by increased VEGFR2 expression. Epithelial cells in tumor tissue expressed VEGFR2 and responded to VEGF stimulation with augmented VEGFR2-mediated proliferation. Blockade of VEGF function via soluble decoy receptors suppressed tumor development, inhibited tumor angiogenesis, and blocked tumor cell proliferation. Functional studies revealed that chronic inflammation leads to an up-regulation of VEGFR2 on IECs. Studies in conditional STAT3 mutant mice showed that VEGFR signaling requires STAT3 to promote epithelial cell proliferation and tumor growth in vivo. Thus, VEGFR-signaling acts as a direct growth factor for tumor cells in CAC, providing a molecular link between inflammation and the development of colon cancer.
DUST EMISSION AND STAR FORMATION IN STEPHAN'S QUINTET
Authors: Natale G. , Tuffs R. J. , Xu C. K. , Popescu C. C. , Fischera J. , Lisenfeld U. , Lu N. , Appleton P. , Dopita M. , Duc P.-A. , Gao Y. , Reach W. , Sulentic J. , Yun M.
Published: November 2010

We analyze a comprehensive set of MIR/FIR observations of Stephan's Quintet (SQ), taken with the Spitzer Space Telescope. Our study reveals the presence of a luminous (L
IR ≈ 4.6 × 1043 erg s-1) and extended component of infrared dust emission, not connected with the main bodies of the galaxies, but roughly coincident with the X-ray halo of the group. We fitted the inferred dust emission spectral energy distribution of this extended source and the other main infrared emission components of SQ, including the intergalactic shock, to elucidate the mechanisms powering the dust and polycyclic aromatic hydrocarbon emission, taking into account collisional heating by the plasma and heating through UV and optical photons. Combining the inferred direct and dust-processed UV emission to estimate the star formation rate (SFR) for each source we obtain a total SFR for SQ of 7.5 M
☉ yr-1, similar to that expected for non-interacting galaxies with stellar mass comparable to the SQ galaxies. Although star formation in SQ is mainly occurring at, or external to the periphery of the galaxies, the relation of SFR per unit physical area to gas column density for the brightest sources is similar to that seen for star formation regions in galactic disks. We also show that available sources of dust in the group halo can provide enough dust to produce up to L
IR ≈ 1042 erg s-1 powered by collisional heating. Though a minority of the total infrared emission (which we infer to trace distributed star-formation), this is several times higher than the X-ray luminosity of the halo, so could indicate an important cooling mechanism for the hot intergalactic medium (IGM) and account for the overall correspondence between FIR and X-ray emission. We investigate two potential modes of star formation in SQ consistent with the data, fueled either by gas from a virialized hot IGM continuously accreting onto the group, whose cooling is enhanced by grains injected from an in situ population of intermediate mass stars, or by interstellar gas stripped from the galaxies. The former mode offers a natural explanation for the observed baryon deficiency in the IGM of SQ as well as for the steep L
X–T
X relation of groups such as SQ with lower velocity dispersions.
Myocardial expression of FOXO3a–Atrogin‐1 pathway in human heart failure
Authors: Galasso Gennaro , De Rosa Roberta , Piscione Federico , Iaccarino Guido , Vosa Carlo , Sorriento Daniela , Piccolo Raffaele , Rapacciuolo Antonio , Walsh Kenneth , Chiariello Massimo
Published: November 2010

Aims

Several studies have shown that muscle mass loss is an important pathogenic issue in heart failure (HF). Atrogin‐1 is a F‐box protein selectively expressed in cardiac and skeletal muscle tissue, which plays a pivotal role in muscle wasting regulation. The aim of this study was to investigate the expression of Atrogin‐1 and the molecular pathway involved in Atrogin‐1 regulation in human HF.

Methods and results

Cardiac tissue from patients with HF (HF group: n = 10) or with normal left ventricular function (control group: n = 9) was studied by western blot and real time‐PCR analysis. Linear regression analysis between patients left ventricular ejection fraction (LVEF) and Atrogin1 or its regulator Forkhead box O 3a (Foxo3a) myocardial expression was performed to test correlations between protein expression and LVEF. Western blot analysis revealed that the myocardial expression of Atrogin‐1 in the HF group was 2.5‐fold increased compared with controls (P = 0.007). Accordingly, Atrogin‐1 mRNA was 1.5 higher than in controls (P = 0.003). The expression of Foxo3a and its up‐stream regulator AKT were also measured. Western blot analysis demonstrated in the HF group a 2.56‐fold reduction of AKT phosphorylation and a 3.32‐fold increase of Foxo3a as compared with controls (P = 0.002 and P = 0.001, respectively). Finally, linear regression showed a significant relationship between Foxo3a or Atrogin‐1 expression and LVEF (R = 0.976, P < 0.0001 and R = 0.895, P = 0.003, respectively).

Conclusion

Our results suggest that in human HF, the activity of AKT decreases, with activation of Foxo3a and induction of Atrogin‐1, thereby leading to a molecular state that favours heart muscle loss and left ventricular dysfunction.
Genome-Wide Computational Function Prediction of Arabidopsis Proteins by Integration of Multiple Data Sources
Authors: Kourmpetis Yiannis A.I. , van Dijk Aalt D.J. , van Ham Roeland C.H.J. , ter Braak Cajo J.F.
Published: November 2010

Although Arabidopsis (Arabidopsis thaliana) is the best studied plant species, the biological role of one-third of its proteins is still unknown. We developed a probabilistic protein function prediction method that integrates information from sequences, protein-protein interactions, and gene expression. The method was applied to proteins from Arabidopsis. Evaluation of prediction performance showed that our method has improved performance compared with single source-based prediction approaches and two existing integration approaches. An innovative feature of our method is that it enables transfer of functional information between proteins that are not directly associated with each other. We provide novel function predictions for 5,807 proteins. Recent experimental studies confirmed several of the predictions. We highlight these in detail for proteins predicted to be involved in flowering and floral organ development.
Ultra-Gradient Test Cavity for Testing SRF Wafer Samples
Authors: Pogue Nathaniel J. , McIntyre Peter M. , Sattarov Akhdiyor I. , Reece Charles
Published: November 2010

A 1.3 GHz test cavity has been designed to test wafer samples of superconducting materials. This mushroom shaped cavity, operating in TE01mode, creates a unique distribution of surface fields. The surface magnetic field on the sample wafer is 3.75 times greater than elsewhere on the Niobium cavity surface. This field design is made possible through dielectrically loading the cavity by locating a hemisphere of ultra-pure sapphire just above the sample wafer. The sapphire pulls the fields away from the walls so the maximum field the Nb surface sees is 25% of the surface field on the sample. In this manner, it should be possible to drive the sample wafer well beyond the BCS limit for Niobium while still maintaining a respectable Q. The sapphire's purity must be tested for its loss tangent and dielectric constant to finalize the design of the mushroom test cavity. A sapphire loaded CEBAF cavity has been constructed and tested. The results on the dielectric constant and loss tangent will be presented.
Effects of Auron‐Misheil‐Therapy in human in vitro skin models
Authors: SCHEELE Jürgen , MAPPES Marion , DORN Annette , NIAZI Faiz
Published: November 2010

Auron‐Misheil‐Therapy (AMT) is currently under development as an anticancer treatment. The aim of the present study was the identification of possible effects and properties of AMT with regard to human skin. The study consisted of three experimental phases. Phase 1 assessed the effects of AMT on the viability of 2‐D evaluated and accredited cell cultures of three cell types of human skin, namely: keratinocytes, melanocytes and fibroblasts. Three separate assays were used in this phase. Phase 2 was designed to clarify the effects of AMT on cell viability to investigate the mode of action of AMT. Two possible modes of action were investigated: proliferation inhibition and apoptosis. There was one assay to assess proliferation, and two independent assays to assess apoptosis. The third phase assessed the effects of AMT on two different types of 3‐D skin models, an ex vivo model and a de novo reconstituted model. In the phase 1 tests, reduction of cell viability by AMT was demonstrated in all three cell types. In phase 2, the cell proliferation assay showed decreased proliferation rates in the presence of AMT in three out of four cell populations. In phase 3, histochemical investigations with 3‐D models indicated that AMT induces desquamation, most likely as the result of apoptosis of epidermal cells. The experiments generally showed that AMT does not harm human skin at concentrations up to 3%.
Shrinkage and quality characteristics of whole fruit of Chinese jujube (Zizyphus jujuba Miller) in microwave drying
Authors: Fang Shuzheng , Wang Zhengfu , Hu Xiaosong , Li Hui , Long Wanrong , Wang Ran
Published: November 2010

Drying characteristics of whole fruit Chinese jujube was studied as distinct from fruit slices. Shrinkage, density, vitamin C, colour and rehydration of Chinese jujube were measured in microwave drying at power level of 1.2, 1.67 and 2.5 W/g (dry base, db). Unlike fruit slices or lumps where, no matter at the beginning or at the end of drying, shrinkage volume typically equals the volume of removed water, ratio of the shrinkage volume to the volume of removed water of Chinese jujube could range from 2 to 2.6 at the beginning of drying, and at the end of drying, it could be 1.15 for higher microwave level (2.5 W/g, db), whereas, for lower power level (1.2 W/g, db), it was about 1. Unlike shrinkage curves in hot air drying that could be described with a three‐segment linear model, shrinkage curves in microwave drying could be well described with a cubic polynomial (R2 > 0.99). When compared with the low power level (1.2 W/g, db), higher microwave power level(2.5 W/g, db) increased by 87.9% of the retention of vitamin C, 14.6% of the density and 8.7% of the extent of browning, decreased by 12.9% of the soluble solids content.
The effect of pea (Pisum sativumL.)‐originated asparaginase on acrylamide formation in certain bread types
Authors: Tuncel Necati B. , Yılmaz Neşe , Şener Erol
Published: November 2010

The aim of this study was to investigate the effect of pea (Pisum sativumL.)‐originated asparaginase on acrylamide formation in white wheat, wheat bran and whole‐grain wheat breads. Two‐day germinated pea flour was used at 0%, 1%, 3% and 5% levels for each bread type. Acrylamide analysis was performed with liquid chromatography–mass spectrometry. Besides, colour and sensory properties of the breads were evaluated to search out the effects of pea flour substitution on the consumer acceptance. Reduction of acrylamide in white wheat bread was not found significant and addition of pea flour decreased the acceptance. However, it was found that acrylamide level can be reduced by 57% and 68% with addition of 5% pea flour in wheat bran and whole‐grain breads, respectively, without any negative impact on colour and sensory properties.
Application of inverse methods in the osmotic dehydration of acerola
Authors: Silva Mirtes A. C. , Corrêa Jefferson L. G. , Da Silva Zaqueu E.
Published: November 2010

This work presents a study of the mass transfer of osmotically dehydrated West Indian cherry, also known as acerola. The experiments were performed by immersing the fruits in a sucrose solution at 65ºBrix for 12 h at ambient temperature (27 °C), using three different fruit:solution ratios (1:4; 1:10 and 1:15 (w:w)). The kinetics of water loss, solids gain and weight reduction was determined. Effective mass diffusivity was calculated by the inverse method, using the Levenberg‐Marquardt minimisation algorithm. The mathematical model used to describe the physical phenomenon of osmotic dehydration was based on Fick’s Second Law, considering the fruits as geometrically perfect spheres. The influence of the fruit:solution ratio was not significant in the range of this study. Diffusivity ranged from 1.558 × 10−10 to 1.760 × 10−10 m2 s−1.
A novel dielectric drying method of sea cucumber
Authors: Duan Xu , Zhang Min , Mujumdar Arun S. , Huang Lue L. , Wang Hui
Published: November 2010

The sea cucumber autolyses readily so it must be dehydrated for preservation. Traditional drying methods of sea cucumber need very long time and have adverse effect on quality. Hence, a novel microwave freeze drying technique was developed to dry sea cucumber. Because microwave heating is a function of dielectric properties of the material in microwave field, dielectric properties of sea cucumber were determined. As expected, the dielectric loss factor of sea cucumbers was very low in frozen state, and several pretreatments (nanoscale calcium carbonate impregnation and vacuum impregnation, salt impregnation, etc.) were analysed to improve the dielectric properties of sea cucumber. Vacuum impregnation with nanoscale calcium carbonate combined with microwave freeze drying was found to be an efficient drying method for sea cucumber by anova (P < 0.01). Compared with microwave freeze drying method without any treatments, this drying method could reduce the drying time by up to two hours.