A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans.

Eukaryotes have evolved elaborate mechanisms to ensure that chromosomes segregate with high fidelity during mitosis and meiosis, and yet specific aneuploidies can be adaptive during environmental stress. Here, we identify a chromatin-based system required for inducible aneuploidy in a human pathogen. Candida albicans utilizes chromosome missegregation to acquire tolerance to antifungal drugs and for nonmeiotic ploidy reduction after mating. We discovered that the ancestor of C. albicans and 2 related pathogens evolved a variant of histone 2A (H2A) that lacks the conserved phosphorylation site for kinetochore-associated Bub1 kinase, a key regulator of chromosome segregation. Using engineered strains, we show that the relative gene dosage of this variant versus canonical H2A controls the fidelity of chromosome segregation and the rate of acquisition of tolerance to antifungal drugs via aneuploidy. Furthermore, whole-genome chromatin precipitation analysis reveals that Centromere Protein A/ Centromeric Histone H3-like Protein (CENP-A/Cse4), a centromeric histone H3 variant that forms the platform of the eukaryotic kinetochore, is depleted from tetraploid-mating products relative to diploid parents and is virtually eliminated from cells exposed to aneuploidy-promoting cues. We conclude that genetically programmed and environmentally induced changes in chromatin can confer the capacity for enhanced evolvability via chromosome missegregation

Conformational Flexibility in the Enterovirus RNA Replication Platform

A presumed RNA cloverleaf (5′CL), located at the 5′-most end of the noncoding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem–loop B (SLB) and stem–loop D (SLD), the two largest stem–loops within the 5′CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5′CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering. In the absence of magnesium, the structure adopts an open, somewhat extended conformation. In the presence of magnesium, the structure compacts, bringing SLB and SLD into close contact, a geometry that creates an extensive accessible major groove surface, and permits interaction between the proteins that target each stem–loop

Results of pancreas transplantation after steroid withdrawal under tacrolimus immunosuppression

Purpose. The results of steroid withdrawal in pancreas transplant recipients under tacrolimus immunosuppression were analyzed. Methods. From July 4, 1994 until April 30, 1998, 147 pancreas transplantations were performed in 141 patients, including 126 simultaneous pancreas-kidney transplantations, 13 pancreas after kidney transplantation, and 8 pancreas transplantations alone. Baseline immunosuppression consisted of tacrolimus and steroids without antilymphocyte induction. Twenty-three patients were excluded from analysis because of early graft loss in 17 cases, retransplantation in 5 cases, and simultaneous pancreas-kidney transplantation after heart transplantation in 1 patient. Results. With a mean follow-up of 2.8±1.1 years (range 1.0 to 4.8 years), complete steroid withdrawal was achieved in 58 (47%) patients with a mean time to steroid withdrawal of 15.2±8 months (range 4 to 40 months after transplantation). Of the entire cohort of 141 patients, overall 1-, 2-, and 4-year patient survival rates were 98%, 95.5%, and 86%, respectively. Overall 1-, 2-, and 4- year graft survival rates were 83%, 80%, and 71% (pancreas) and 95%, 91%, and 84% (kidney), respectively. Of the 124 patients analyzed for steroid withdrawal, 1-, 2-, and 4-year patient survival rates were 98%, 97%, and 92%, respectively. Overall 1-, 2-, and 4-year graft survival rates were 98%, 91.5%, 83% (pancreas) and 97%, 95%, and 91% (kidney). Patient, pancreas, and kidney survival rates at 1 year were 100%, 100%, and 98% (off steroids) versus 97%, 91%, and 96% (on steroids, all NS) and at 4 years were 100%, 94%, and 95% (off steroids) versus 78%, 68%, and 85% (on steroids, P=0.01, 0.002, and NS, respectively). The cumulative risk of rejection at the time of follow-up was 76% for patients on steroids versus 74% for patients off steroids (P=NS). Seven patients originally tapered off steroids were treated for subsequent rejection episodes, which were all steroid sensitive, and two of these seven patients are currently off steroids. Thirteen patients received antilymphocyte therapy for steroid-resistant rejection, five of whom are now off steroids. Tacrolimus trough levels were 9.3±2.4 ng/ml (off steroids) and 9.7±4.3 (on steroids, P=NS). Mean fasting glucose levels were 98±34 mg/dl (off steroids) and 110±41 mg/dl (on steroids, P=NS). Mean glycosylated hemoglobin levels were 5.2±0.9% (off steroids) and 6.2±2.1% (on steroids, P=0.02), and mean serum creatinine levels were 1.4±0.8 mg/dl (off steroids) and 1.7±1.0 mg/dl (on steroids, P=0.02). Conclusion. These data show for the first time that steroid withdrawal can be safely accomplished in pancreas transplant recipients maintained on tacrolimus-based immunosuppression. Steroid withdrawal is associated with excellent patient and graft survival with no increase in the cumulative risk of rejection

Can One Trust Quantum Simulators?

Various fundamental phenomena of strongly-correlated quantum systems such as high-$T_c$ superconductivity, the fractional quantum-Hall effect, and quark confinement are still awaiting a universally accepted explanation. The main obstacle is the computational complexity of solving even the most simplified theoretical models that are designed to capture the relevant quantum correlations of the many-body system of interest. In his seminal 1982 paper [Int. J. Theor. Phys. 21, 467], Richard Feynman suggested that such models might be solved by "simulation" with a new type of computer whose constituent parts are effectively governed by a desired quantum many-body dynamics. Measurements on this engineered machine, now known as a "quantum simulator," would reveal some unknown or difficult to compute properties of a model of interest. We argue that a useful quantum simulator must satisfy four conditions: relevance, controllability, reliability, and efficiency. We review the current state of the art of digital and analog quantum simulators. Whereas so far the majority of the focus, both theoretically and experimentally, has been on controllability of relevant models, we emphasize here the need for a careful analysis of reliability and efficiency in the presence of imperfections. We discuss how disorder and noise can impact these conditions, and illustrate our concerns with novel numerical simulations of a paradigmatic example: a disordered quantum spin chain governed by the Ising model in a transverse magnetic field. We find that disorder can decrease the reliability of an analog quantum simulator of this model, although large errors in local observables are introduced only for strong levels of disorder. We conclude that the answer to the question "Can we trust quantum simulators?" is... to some extent.Comment: 20 pages. Minor changes with respect to version 2 (some additional explanations, added references...

Dynamics of allosteric regulation of the phospholipase C-γ isozymes upon recruitment to membranes

Numerous receptor tyrosine kinases and immune receptors activate phospholipase C-γ (PLC-γ) isozymes at membranes to control diverse cellular processes including phagocytosis, migration, proliferation, and differentiation. The molecular details of this process are not well understood. Using hydrogen-deuterium exchange mass spectrometry, we show that PLC-γ1 is relatively inert to lipid vesicles that contain its substrate, phosphatidylinositol 4,5-bisphosphate (PIP2), unless first bound to the kinase domain of the fibroblast growth factor receptor (FGFR1). Exchange occurs throughout PLC-γ1 and is exaggerated in PLC-γ1 containing an oncogenic substitution (D1165H) that allosterically activates the lipase. These data support a model whereby initial complex formation shifts the conformational equilibrium of PLC-γ1 to favor activation. This receptor-induced priming of PLC-γ1 also explains the capacity of a kinase-inactive fragment of FGFR1 to modestly enhance the lipase activity of PLC-γ1 operating on lipid vesicles but not a soluble analog of PIP2 and highlights potential cooperativity between receptor engagement and membrane proximity. Priming is expected to be greatly enhanced for receptors embedded in membranes and nearly universal for the myriad of receptors and co-receptors that bind the PLC-γ isozymes

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Os retratos de Maria Isabel e Maria Francisca de Bragança, de Nicolas-Antoine Taunay

Nicolas-Antoine Taunay, French landscape painter, produced also several portraits during his stay at the Rio de Janeiro Court. In this city, in 1816, he paints the queen Carlota Joaquina and all her daughters. In this group, two portraits have a very special way: the paintings still today catalogued as Maria Francisca and Maria Teresa, but probably being Maria Isabel and Maria Francisca de Assis - princesses that, in this year, left Brazil to marry the Spanish King Fernando VII, and his brother Carlos Maria Isidro de Bourbon. In this article, beyond to describe these portraits (and analyse the identities of the portrayed princesses), I analyse their functions in the Court society and the mains artists of this gender in Europe. I will discuss, as well, the hypothesis about the Taunay choices. In this sense, I will analyse the possible circulation of the typologies of portrait between Italy, Portugal, Spain and France, understanding these productions by Taunay and the functions occupied by these portraits in the political relations between Brazil and Europe.Nicolas-Antoine Taunay, pintor de paisagens francês, também realizou alguns retratos durante sua estadia na corte do Rio de Janeiro. Nessa cidade, em 1816, ele pinta a rainha Carlota Joaquina e todas as suas filhas. Nesse conjunto, dois retratos sobressaem-se de modo especial: os hoje ainda inventariados como de Maria Francisca e de Maria Teresa, mas que provavelmente são o de Maria Isabel e o de Maria Francisca de Assis - princesas que, nesse ano, deixavam o Brasil para casar-se, respectivamente, com Fernando VII, o rei espanhol, e com seu irmão Carlos Isidro de Bourbon. Neste artigo, além de descrevermos os retratos (e analisarmos a questão da identidade das princesas retratadas), abordamos suas funções na sociedade das cortes e os principais artistas do gênero na Europa. Discutimos, também, as hipóteses que permeiam as escolhas de Taunay para sua execução. Nesse sentido, tratamos da possível circulação de tipologias entre Itália, Portugal, Espanha e França, buscando entender a forma como Taunay os realizou e as funções que doravante tais retratos ocupariam nas relações entre o Brasil e a Europa.Universidade Federal de São Paulo (UNIFESP)UNIFESPSciEL

The chlL ( frxC ) gene: Phylogenetic distribution in vascular plants and DNA sequence from Polystichum acrostichoides ( Pteridophyta ) and Synechococcus sp. 7002 ( Cyanobacteria )

We examined chlL ( frxC ) gene evolution using several approaches. Sequences from the chloroplast genome of the fern Polystichum acrostichoides and from the cyanobacterium Synechococcus sp. 7002 were determined and found to be highly conserved. A complete physical map of the fern chloroplast genome and partial maps of other vascular plant taxa show that chlL is located primarily in the small single copy region as in Marchantia polymorpha. A survey of a wide variety of non-angiospermous vascular plant DNAs shows that chlL is widely distributed but has been lost in the pteridophyte Psilotum and (presumably independently) within the Gnetalean gymnosperms.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41636/1/606_2004_Article_BF00994092.pd

Human Disease-Drug Network Based on Genomic Expression Profiles

BACKGROUND: Drug repositioning offers the possibility of faster development times and reduced risks in drug discovery. With the rapid development of high-throughput technologies and ever-increasing accumulation of whole genome-level datasets, an increasing number of diseases and drugs can be comprehensively characterized by the changes they induce in gene expression, protein, metabolites and phenotypes. METHODOLOGY/PRINCIPAL FINDINGS: We performed a systematic, large-scale analysis of genomic expression profiles of human diseases and drugs to create a disease-drug network. A network of 170,027 significant interactions was extracted from the approximately 24.5 million comparisons between approximately 7,000 publicly available transcriptomic profiles. The network includes 645 disease-disease, 5,008 disease-drug, and 164,374 drug-drug relationships. At least 60% of the disease-disease pairs were in the same disease area as determined by the Medical Subject Headings (MeSH) disease classification tree. The remaining can drive a molecular level nosology by discovering relationships between seemingly unrelated diseases, such as a connection between bipolar disorder and hereditary spastic paraplegia, and a connection between actinic keratosis and cancer. Among the 5,008 disease-drug links, connections with negative scores suggest new indications for existing drugs, such as the use of some antimalaria drugs for Crohn's disease, and a variety of existing drugs for Huntington's disease; while the positive scoring connections can aid in drug side effect identification, such as tamoxifen's undesired carcinogenic property. From the approximately 37K drug-drug relationships, we discover relationships that aid in target and pathway deconvolution, such as 1) KCNMA1 as a potential molecular target of lobeline, and 2) both apoptotic DNA fragmentation and G2/M DNA damage checkpoint regulation as potential pathway targets of daunorubicin. CONCLUSIONS/SIGNIFICANCE: We have automatically generated thousands of disease and drug expression profiles using GEO datasets, and constructed a large scale disease-drug network for effective and efficient drug repositioning as well as drug target/pathway identification