bluuebunny/crossref_metadata_2025 huggingface dataset:
An assessment of the mobility degradation induced by remote charge scattering
Authors: Ji Z. , Zhang J. F. , Zhang W. , Groeseneken G. , Pantisano L. , De Gendt S. , Heyns M. M.
Published: December 2009

Carrier mobility reduces when the gate SiON becomes thinner than 2 nm or high-k layer is used. Agreement has not yet been reached on the level of reduction and on the underlying mechanism. Remote charge scattering has been proposed to be responsible for the mobility reduction and this work assesses its importance. By increasing charge density at 0.56–1 nm from the substrate interface to the order of 1020 cm−3, it is found that both electron and hole mobility changes little.
Complete basis set limit second-order Møller–Plesset calculations for the fcc lattices of neon, argon, krypton, and xenon
Authors: Hermann Andreas , Schwerdtfeger Peter
Published: December 2009

Complete basis set (CBS) limit calculations using second-order Møller–Plesset (MP2) theory for electron correlation within a many-body expansion of the interaction potential up to third order are carried out for the fcc lattices of Ne, Ar, Kr, and Xe. Lattice constants and cohesive energies from recent localized MP2 solid-state calculations by Halo et al. [Chem. Phys. Lett. 467, 294 (2009)] are in reasonable agreement with our CBS limit results. A detailed analysis reveals that MP2 severely underestimates long-range three-body effects, thus the Axilrod–Teller term is incorrectly described causing bond contractions for all rare gas solids considered. Further, any deviations in the MP2 lattice constant, cohesive energy, and bulk modulus can be traced back to inaccuracies in the binding energy and equilibrium distance of the rare gas dimer. Without inclusion of phonon dispersion, MP2 prefers the hcp over the fcc crystal structure for all rare gas solids considered.
Contact and channel resistances of organic field-effect transistors based on benzodithiophene-dimer films deposited on pentacene crystallinity control layers
Authors: Kurokawa A. , Matsumoto Y. , Shibamoto K. , Kajimoto Kaori , Osuga H. , Yamakado Hideo , Uno K. , Tanaka Ichiro
Published: December 2009

We have investigated contact and channel resistances of organic field-effect transistors (FETs) based on benzodithiophene (BDT)-dimer films deposited on thin pentacene layers used as crystallinity control layers (CCLs). The contact resistance of source/drain electrodes made of conductive organic films instead of Au films has been reduced for pentacene-CCL/BDT-dimer FETs; the carrier mobility has been improved to 1.2 cm2 V−1 s−1 at maximum. Because the channel resistance of the pentacene-CCL/BDT-dimer FETs is found to be lower than that of reference pentacene FETs, the carrier transport in the BDT-dimer layers is more important than that in the pentacene CCLs for the high mobility.
Europium dimer: van der Waals molecule with extremely weak antiferromagnetic spin coupling
Authors: Buchachenko Alexei A. , Chałasiński Grzegorz , Szczęśniak Małgorzata M.
Published: December 2009

High-level ab initio calculations reveal that the Eu2 dimer is a van der Waals molecule with extremely weak antiferromagnetic spin coupling. The Heisenberg spin-exchange model, validated by the multireference configuration interaction method, is used to construct the full set of model interaction potentials for the states with the total spin S ranging from 0 to 7 at the coupled cluster level of theory. This model establishes the singlet ∑+g1 state as the ground one of the dimer with the binding energy of 710 cm−1, the vibrational frequency of 23 cm−1 and the effective spin-coupling constant J estimated approximately −0.3 cm−1.
Atmospheric CO2concentrations during ancient greenhouse climates were similar to those predicted for A.D. 2100
Authors: Breecker D. O. , Sharp Z. D. , McFadden L. D.
Published: December 2009

Quantifying atmospheric CO2concentrations ([CO2]atm) during Earth’s ancient greenhouse episodes is essential for accurately predicting the response of future climate to elevated CO2levels. Empirical estimates of [CO2]atmduring Paleozoic and Mesozoic greenhouse climates are based primarily on the carbon isotope composition of calcium carbonate in fossil soils. We report that greenhouse [CO2]atmhave been significantly overestimated because previously assumed soil CO2concentrations during carbonate formation are too high. More accurate [CO2]atm, resulting from better constraints on soil CO2, indicate that large (1,000s of ppmV) fluctuations in [CO2]atmdid not characterize ancient climates and that past greenhouse climates were accompanied by concentrations similar to those projected for A.D. 2100.
Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures
Authors: Meents Alke , Gutmann Sascha , Wagner Armin , Schulze-Briese Clemens
Published: December 2009

Radiation damage is the major impediment for obtaining structural information from biological samples by using ionizing radiation such as x-rays or electrons. The knowledge of underlying processes especially at cryogenic temperatures is still fragmentary, and a consistent mechanism has not been found yet. By using a combination of single-crystal x-ray diffraction, small-angle scattering, and qualitative and quantitative radiolysis experiments, we show that hydrogen gas, formed inside the sample during irradiation, rather than intramolecular bond cleavage between non-hydrogen atoms, is mainly responsible for the loss of high-resolution information and contrast in diffraction experiments and microscopy. The experiments that are presented in this paper cover a temperature range between 5 and 160 K and reveal that the commonly used temperature in x-ray crystallography of 100 K is not optimal in terms of minimizing radiation damage and thereby increasing the structural information obtainable in a single experiment. At 50 K, specific radiation damage to disulfide bridges is reduced by a factor of 4 compared to 100 K, and samples can tolerate a factor of 2.6 and 3.9 higher dose, as judged by the increase of
R
free
values of elastase and cubic insulin crystals, respectively.
G protein–coupled receptor kinase 2 (GRK2) modulation and cell cycle progression
Authors: Penela Petronila , Rivas Verónica , Salcedo Alicia , Mayor Federico
Published: December 2009

Cell cycle progression requires changes in the activity or levels of a variety of key signaling proteins. G protein–coupled receptor kinase 2 (GRK2) plays a central role in G protein–coupled receptor regulation. Recent research is uncovering its involvement in additional cellular functions, but the potential role of GRK2 in the cell cycle has not been addressed. We report that GRK2 protein levels are transiently down-regulated during the G2/M transition by a mechanism involving CDK2-mediated phosphorylation of GRK2 at Serine670, which triggers binding to the prolyl-isomerase Pin1 and subsequent degradation. Prevention of GRK2 phosphorylation at S670 impedes normal GRK2 down-regulation and markedly delays cell cycle progression. Interestingly, we find that endogenous GRK2 down-regulation is prevented on activation of the G2/M checkpoint by doxorubicin and that stabilized GRK2 levels in such conditions inversely correlate with the p53 response and the induction of apoptosis, suggesting that GRK2 participates in the regulatory network controlling cell cycle arrest and survival in such conditions.
Dental development and life history in living African and Asian apes
Authors: Kelley Jay , Schwartz Gary T.
Published: December 2009

Life-history inference is an important aim of paleoprimatology, but life histories cannot be discerned directly from the fossil record. Among extant primates, the timing of many life-history attributes is correlated with the age at emergence of the first permanent molar (M1), which can therefore serve as a means to directly compare the life histories of fossil and extant species. To date, M1 emergence ages exist for only a small fraction of extant primate species and consist primarily of data from captive individuals, which may show accelerated dental eruption compared with free-living individuals. Data on M1 emergence ages in wild great apes exist for only a single chimpanzee individual, with data for gorillas and orangutans being anecdotal. This paucity of information limits our ability to make life-history inferences using the M1 emergence ages of extinct ape and hominin species. Here we report reliable ages at M1 emergence for the orangutan,Pongo pygmaeus(4.6 y), and the gorilla,Gorilla gorilla(3.8 y), obtained from the dental histology of wild-shot individuals in museum collections. These ages and the one reported age at M1 emergence in a free-living chimpanzee of approximately 4.0 y are highly concordant with the comparative life histories of these great apes. They are also consistent with the average age at M1 emergence in relation to the timing of life-history events in modern humans, thus confirming the utility of M1 emergence ages for life-history inference and providing a basis for making reliable life-history inferences for extinct apes and hominins.
Model of human low-density lipoprotein and bound receptor based on CryoEM
Authors: Ren Gang , Rudenko Gabby , Ludtke Steven J. , Deisenhofer Johann , Chiu Wah , Pownall Henry J.
Published: December 2009

Human plasma low-density lipoproteins (LDL), a risk factor for cardiovascular disease, transfer cholesterol from plasma to liver cells via the LDL receptor (LDLr). Here, we report the structures of LDL and its complex with the LDL receptor extracellular domain (LDL·LDLr) at extracellular pH determined by cryoEM. Difference imaging between LDL·LDLr and LDL localizes the site of LDLr bound to its ligand. The structural features revealed from the cryoEM map lead to a juxtaposed stacking model of cholesteryl esters (CEs). High density in the outer shell identifies protein-rich regions that can be accounted for by a single apolipoprotein (apo B-100, 500 kDa) leading to a model for the distribution of its α-helix and
β
-sheet rich domains across the surface. The structural relationship between the apo B-100 and CEs appears to dictate the structural stability and function of normal LDL.
Reducing the desire for cocaine with subthalamic nucleus deep brain stimulation
Authors: Rouaud Tiphaine , Lardeux Sylvie , Panayotis Nicolas , Paleressompoulle Dany , Cador Martine , Baunez Christelle
Published: December 2009

Deep brain stimulation (DBS) is a reversible technique that is currently used for the treatment of Parkinson disease and may be suitable for the treatment of psychiatric disorders. Whether DBS inactivates the target structure is still a matter of debate. Here, from findings obtained in rats, we propose DBS of the subthalamic nucleus (STN) as a possible treatment for cocaine addiction to be further tested in human studies. We show that STN DBS reversibly reduces the motivation to work for an i.v. injection of cocaine, and it increases motivation to work for sucrose pellets. These opposite effects may result from STN DBS effect on the positive affective properties of these rewards. Indeed, we further show that STN DBS reduces the preference for a place previously associated with the rewarding properties of cocaine, and it increases the preference for a place associated with food. Because these findings are consistent with those observed after STN lesions [Baunez C, Dias C, Cador M, Amalric M (2005)
Nat Neurosci
8:484–489], they suggest that STN DBS mimics an inactivation of the STN on motivational processes. Furthermore, given that one of the major challenges for cocaine addiction is to find a treatment that reduces the craving for the drug without diminishing the motivation for naturally rewarding activities, our findings validate STN as a good target and DBS as the appropriate technique for a promising therapeutic strategy in the treatment of cocaine addiction.
Widespread occurrence of nitrate storage and denitrification among Foraminifera andGromiida
Authors: Piña-Ochoa Elisa , Høgslund Signe , Geslin Emmanuelle , Cedhagen Tomas , Revsbech Niels Peter , Nielsen Lars Peter , Schweizer Magali , Jorissen Frans , Rysgaard Søren , Risgaard-Petersen Nils
Published: December 2009

Benthic foraminifers inhabit a wide range of aquatic environments including open marine, brackish, and freshwater environments. Here we show that several different and diverse foraminiferal groups (miliolids, rotaliids, textulariids) andGromia, another taxon also belonging to Rhizaria, accumulate and respire nitrates through denitrification. The widespread occurrence among distantly related organisms suggests an ancient origin of the trait. The diverse metabolic capacity of these organisms, which enables them to respire with oxygen and nitrate and to sustain respiratory activity even when electron acceptors are absent from the environment, may be one of the reasons for their successful colonization of diverse marine sediment environments. The contribution of eukaryotes to the removal of fixed nitrogen by respiration may equal the importance of bacterial denitrification in ocean sediments.
The Polycomb group protein EED couples TNF receptor 1 to neutral sphingomyelinase
Authors: Philipp Stephan , Puchert Malte , Adam-Klages Sabine , Tchikov Vladimir , Winoto-Morbach Supandi , Mathieu Sabine , Deerberg Andrea , Kolker Ljudmila , Marchesini Norma , Kabelitz Dieter , Hannun Yusuf A. , Schütze Stefan , Adam Dieter
Published: December 2009

The phospholipase neutral sphingomyelinase (N-SMase) has been recognized as a major mediator of processes such as inflammation, development and growth, differentiation and death of cells, as well as in diseases such as Alzheimer’s, atherosclerosis, heart failure, ischemia/reperfusion damage, or combined pituitary hormone deficiency. Although activation of N-SMase by the proinflammatory cytokine TNF was described almost two decades ago, the underlying signaling pathway is unresolved. Here, we identify the Polycomb group protein EED (embryonic ectodermal development) as an interaction partner of nSMase2. In yeast, the N terminus of EED binds to the catalytic domain of nSMase2 as well as to RACK1, a protein that modulates the activation of nSMase2 by TNF in concert with the TNF receptor 1 (TNF-R1)-associated protein FAN. In mammalian cells, TNF causes endogenous EED to translocate from the nucleus and to colocalize and physically interact with both endogenous nSMase2 and RACK1. As a consequence, EED and nSMase2 are recruited to the TNF-R1•FAN•RACK1-complex in a timeframe concurrent with activation of nSMase2. After knockdown of EED by RNA interference, the TNF-dependent activation of nSMase2 is completely abrogated, identifying EED as a protein that both physically and functionally couples TNF-R1 to nSMase2, and which therefore represents the “missing link” that completes one of the last unresolved signaling pathways of TNF-R1.
Optimizing infectious disease interventions during an emerging epidemic
Authors: Wallinga Jacco , van Boven Michiel , Lipsitch Marc
Published: December 2009

The emergence and global impact of the novel influenza A(H1N1)v highlights the continuous threat to public health posed by a steady stream of new and unexpected infectious disease outbreaks in animals and humans. Once an emerging epidemic is detected, public health authorities will attempt to mitigate the epidemic by, among other measures, reducing further spread as much as possible. Scarce and/or costly control measures such as vaccines, anti-infective drugs, and social distancing must be allocated while epidemiological characteristics of the disease remain uncertain. Here we present first principles for allocating scarce resources with limited data. We show that under a broad class of assumptions, the simple rule of targeting intervention measures at the group with the highest risk of infection per individual will achieve the largest reduction in the transmission potential of a novel infection. For vaccination of susceptible persons, the appropriate risk measure is force of infection; for social distancing, the appropriate risk measure is incidence of infection. Unlike existing methods that rely on detailed knowledge of group-specific transmission rates, the method described here can be implemented using only data that are readily available during an epidemic, and allows ready adaptation as the epidemic progresses. The need to observe risk of infection helps to focus the ongoing planning and design of new infectious disease surveillance programs; from the presented first principles for allocating scarce resources, we can adjust the prioritization of groups for intervention when new observations on an emerging epidemic become available.
Alzheimer’s-related endosome dysfunction in Down syndrome is Aβ-independent but requires APP and is reversed by BACE-1 inhibition
Authors: Jiang Ying , Mullaney Kerry A. , Peterhoff Corrinne M. , Che Shaoli , Schmidt Stephen D. , Boyer-Boiteau Anne , Ginsberg Stephen D. , Cataldo Anne M. , Mathews Paul M. , Nixon Ralph A.
Published: December 2009

An additional copy of the β-amyloid precursor protein (APP) gene causes early-onset Alzheimer’s disease (AD) in trisomy 21 (DS). Endosome dysfunction develops very early in DS and AD and has been implicated in the mechanism of neurodegeneration. Here, we show that morphological and functional endocytic abnormalities in fibroblasts from individuals with DS are reversed by lowering the expression of APP or β-APP-cleaving enzyme 1 (BACE-1) using short hairpin RNA constructs. By contrast, endosomal pathology can be induced in normal disomic (2N) fibroblasts by overexpressing APP or the C-terminal APP fragment generated by BACE-1 (βCTF), all of which elevate the levels of βCTFs. Expression of a mutant form of APP that cannot undergo β-cleavage had no effect on endosomes. Pharmacological inhibition of APP γ-secretase, which markedly reduced Aβ production but raised βCTF levels, also induced AD-like endosome dysfunction in 2N fibroblasts and worsened this pathology in DS fibroblasts. These findings strongly implicate APP and the βCTF of APP, and exclude Aβ and the αCTF, as the cause of endocytic pathway dysfunction in DS and AD, underscoring the potential multifaceted value of BACE-1 inhibition in AD therapeutics.
NeuroD1 induces terminal neuronal differentiation in olfactory neurogenesis
Authors: Boutin Camille , Hardt Olaf , de Chevigny Antoine , Coré Nathalie , Goebbels Sandra , Seidenfaden Ralph , Bosio Andreas , Cremer Harold
Published: December 2009

After their generation and specification in periventricular regions, neuronal precursors maintain an immature and migratory state until their arrival in the respective target structures. Only here are terminal differentiation and synaptic integration induced. Although the molecular control of neuronal specification has started to be elucidated, little is known about the factors that control the latest maturation steps. We aimed at identifying factors that induce terminal differentiation during postnatal and adult neurogenesis, thereby focusing on the generation of periglomerular interneurons in the olfactory bulb. We isolated neuronal precursors and mature neurons from the periglomerular neuron lineage and analyzed their gene expression by microarray. We found that expression of the bHLH transcription factor NeuroD1 strikingly coincides with terminal differentiation. Using brain electroporation, we show that overexpression of NeuroD1 in the periventricular region in vivo leads to the rapid appearance of cells with morphological and molecular characteristics of mature neurons in the subventricular zone and rostral migratory stream. Conversely, shRNA-induced knockdown of NeuroD1 inhibits terminal neuronal differentiation. Thus, expression of a single transcription factor is sufficient to induce neuronal differentiation of neural progenitors in regions that normally do not show addition of new neurons. These results suggest a considerable potential of NeuroD1 for use in cell-therapeutic approaches in the nervous system.
Axl is an essential epithelial-to-mesenchymal transition-induced regulator of breast cancer metastasis and patient survival
Authors: Gjerdrum Christine , Tiron Crina , Høiby Torill , Stefansson Ingunn , Haugen Hallvard , Sandal Tone , Collett Karin , Li Shan , McCormack Emmet , Gjertsen Bjørn Tore , Micklem David R. , Akslen Lars A. , Glackin Carlotta , Lorens James B.
Published: December 2009

Metastasis underlies the majority of cancer-related deaths. Thus, furthering our understanding of the molecular mechanisms that enable tumor cell dissemination is a vital health issue. Epithelial-to-mesenchymal transitions (EMTs) endow carcinoma cells with enhanced migratory and survival attributes that facilitate malignant progression. Characterization of EMT effectors is likely to yield new insights into metastasis and novel avenues for treatment. We show that the presence of the receptor tyrosine kinase Axl in primary breast cancers independently predicts strongly reduced overall patient survival, and that matched patient metastatic lesions show enhanced Axl expression. We demonstrate that Axl is strongly induced by EMT in immortalized mammary epithelial cells that establishes an autocrine signaling loop with its ligand, Gas6. Epiallelic RNA interference analysis in metastatic breast cancer cells delineated a distinct threshold of Axl expression for mesenchymal-like in vitro cell invasiveness and formation of tumors in foreign and tissue-engineered microenvironments in vivo. Importantly, in two different optical imaging-based experimental breast cancer models, Axl knockdown completely prevented the spread of highly metastatic breast carcinoma cells from the mammary gland to lymph nodes and several major organs and increased overall survival. These findings suggest that Axl represents a downstream effector of the tumor cell EMT that is required for breast cancer metastasis. Thus, the detection and targeted treatment of Axl-expressing tumors represents an important new therapeutic strategy for breast cancer.
Coordinate-dependent diffusion in protein folding
Authors: Best Robert B. , Hummer Gerhard
Published: December 2009

Diffusion on a low-dimensional free-energy surface is a remarkably successful model for the folding dynamics of small single-domain proteins. Complicating the interpretation of both simulations and experiments is the expectation that the effective diffusion coefficient
D
will in general depend on the position along the folding coordinate, and this dependence may vary for different coordinates. Here we explore the position dependence of
D
, its connection to protein internal friction, and the consequences for the interpretation of single-molecule experiments. We find a large decrease in
D
from unfolded to folded, for reaction coordinates that directly measure fluctuations in Cartesian configuration space, including those probed in single-molecule experiments. In contrast,
D
is almost independent of
Q
, the fraction of native amino acid contacts: Near the folded state, small fluctuations in position cause large fluctuations in
Q
, and vice versa for the unfolded state. In general, position-dependent free energies and diffusion coefficients for any two good reaction coordinates that separate reactant, product, and transition states, are related by a simple transformation, as we demonstrate. With this transformation, we obtain reaction coordinates with position-invariant
D
. The corresponding free-energy surfaces allow us to justify the assumptions used in estimating the speed limit for protein folding from experimental measurements of the reconfiguration time in the unfolded state, and also reveal intermediates hidden in the original free-energy projection. Lastly, we comment on the design of future single-molecule experiments that probe the position dependence of
D
directly.
Cytoplasmic protein quality control degradation mediated by parallel actions of the E3 ubiquitin ligases Ubr1 and San1
Authors: Heck Jarrod W. , Cheung Samantha K. , Hampton Randolph Y.
Published: December 2009

Eukaryotic cells maintain proteostasis by quality control (QC) degradation. These pathways can specifically target a wide variety of distinct misfolded proteins, and so are important for management of cellular stress. Although a number of conserved QC pathways have been described in yeast, the E3 ligases responsible for cytoplasmic QC are unknown. We now show that Ubr1 and San1 mediate chaperone-dependent ubiquitination of numerous misfolded cytoplasmic proteins. This action of Ubr1 is distinct from its role in the “N-end rule.” In this capacity, Ubr1 functions to protect cells from proteotoxic stresses. Our phenotypic and biochemical studies of Ubr1 and San1 indicate that two strategies are employed for cytoplasmic QC: chaperone-assisted ubiquitination by Ubr1 and chaperone-dependent delivery to nuclear San1. The broad conservation of Ubr ligases and the relevant chaperones indicates that these mechanisms will be important in understanding both basic and biomedical aspects of cellular proteostasis.
Human thalamus contributes to perceptual stability across eye movements
Authors: Ostendorf Florian , Liebermann Daniela , Ploner Christoph J.
Published: December 2009

We continuously move our eyes when we inspect a visual scene. Although this leads to a rapid succession of discontinuous and fragmented retinal snapshots, we perceive the world as stable and coherent. Neural mechanisms underlying visual stability may depend on internal monitoring of planned or ongoing eye movements. In the macaque brain, a pathway for the transmission of such signals has been identified that is relayed by central thalamic nuclei. Here, we studied a possible role of this pathway for perceptual stability in a patient with a selective lesion affecting homologous regions of the human thalamus. Compared with controls, the patient exhibited a unilateral deficit in monitoring his eye movements. This deficit was manifest by a systematic inaccuracy both in successive eye movements and in judging the locations of visual stimuli. In addition, perceptual consequences of oculomotor targeting errors were erroneously attributed to external stimulus changes. These findings show that the human brain draws on transthalamic monitoring signals to bridge the perceptual discontinuities generated by our eye movements.
Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility
Authors: Pancera Marie , Majeed Shahzad , Ban Yih-En Andrew , Chen Lei , Huang Chih-chin , Kong Leopold , Kwon Young Do , Stuckey Jonathan , Zhou Tongqing , Robinson James E. , Schief William R. , Sodroski Joseph , Wyatt Richard , Kwong Peter D.
Published: December 2009

The viral spike of HIV-1 is composed of three gp120 envelope glycoproteins attached noncovalently to three gp41 transmembrane molecules. Viral entry is initiated by binding to the CD4 receptor on the cell surface, which induces large conformational changes in gp120. These changes not only provide a model for receptor-triggered entry, but affect spike sensitivity to drug- and antibody-mediated neutralization. Although some of the details of the CD4-induced conformational change have been visualized by crystal structures and cryoelectron tomograms, the critical gp41-interactive region of gp120 was missing from previous atomic-level characterizations. Here we determine the crystal structure of an HIV-1 gp120 core with intact gp41-interactive region in its CD4-bound state, compare this structure to unliganded and antibody-bound forms to identify structurally invariant and plastic components, and use ligand-oriented cryoelectron tomograms to define component mobility in the viral spike context. Newly defined gp120 elements proximal to the gp41 interface complete a 7-stranded β-sandwich, which appeared invariant in conformation. Loop excursions emanating from the sandwich form three topologically separate—and structurally plastic—layers, topped off by the highly glycosylated gp120 outer domain. Crystal structures, cryoelectron tomograms, and interlayer chemistry were consistent with a mechanism in which the layers act as a shape-changing spacer, facilitating movement between outer domain and gp41-associated β-sandwich and providing for conformational diversity used in immune evasion. A “layered” gp120 architecture thus allows movement among alternative glycoprotein conformations required for virus entry and immune evasion, whereas a β-sandwich clamp maintains gp120–gp41 interaction and regulates gp41 transitions.
Molecular and functional basis of phenotypic convergence in white lizards at White Sands
Authors: Rosenblum Erica Bree , Römpler Holger , Schöneberg Torsten , Hoekstra Hopi E.
Published: December 2009

There are many striking examples of phenotypic convergence in nature, in some cases associated with changes in the same genes. But even mutations in the same gene may have different biochemical properties and thus different evolutionary consequences. Here we dissect the molecular mechanism of convergent evolution in three lizard species with blanched coloration on the gypsum dunes of White Sands, New Mexico. These White Sands forms have rapidly evolved cryptic coloration in the last few thousand years, presumably to avoid predation. We use cell-based assays to demonstrate that independent mutations in the same gene underlie the convergent blanched phenotypes in two of the three species. Although the same gene contributes to light phenotypes in these White Sands populations, the specific molecular mechanisms leading to reduced melanin production are different. In one case, mutations affect receptor signaling and in the other, the ability of the receptor to integrate into the melanocyte membrane. These functional differences have important ramifications at the organismal level. Derived alleles in the two species show opposite dominance patterns, which in turn affect their visibility to selection and the spatial distribution of alleles across habitats. Our results demonstrate that even when the same gene is responsible for phenotypic convergence, differences in molecular mechanism can have dramatic consequences on trait expression and ultimately the adaptive trajectory.
Listening to tailor-made notched music reduces tinnitus loudness and tinnitus-related auditory cortex activity
Authors: Okamoto Hidehiko , Stracke Henning , Stoll Wolfgang , Pantev Christo
Published: December 2009

Maladaptive auditory cortex reorganization may contribute to the generation and maintenance of tinnitus. Because cortical organization can be modified by behavioral training, we attempted to reduce tinnitus loudness by exposing chronic tinnitus patients to self-chosen, enjoyable music, which was modified (“notched”) to contain no energy in the frequency range surrounding the individual tinnitus frequency. After 12 months of regular listening, the target patient group (
n
= 8) showed significantly reduced subjective tinnitus loudness and concomitantly exhibited reduced evoked activity in auditory cortex areas corresponding to the tinnitus frequency compared to patients who had received an analogous placebo notched music treatment (
n
= 8). These findings indicate that tinnitus loudness can be significantly diminished by an enjoyable, low-cost, custom-tailored notched music treatment, potentially via reversing maladaptive auditory cortex reorganization.
RBBP9: A tumor-associated serine hydrolase activity required for pancreatic neoplasia
Authors: Shields David J. , Niessen Sherry , Murphy Eric A. , Mielgo Ainhoa , Desgrosellier Jay S. , Lau Steven K. M. , Barnes Leo A. , Lesperance Jacqueline , Bouvet Michael , Tarin David , Cravatt Benjamin F. , Cheresh David A.
Published: December 2009

Pancreatic cancer is one of the most lethal malignancies. To discover functionally relevant modulators of pancreatic neoplasia, we performed activity-based proteomic profiling on primary human ductal adenocarcinomas. Here, we identify retinoblastoma-binding protein 9 (RBBP9) as a tumor-associated serine hydrolase that displays elevated activity in pancreatic carcinomas. Whereas RBBP9 is expressed in normal and malignant tissues at similar levels, its elevated activity in tumor cells promotes anchorage-independent growth in vitro as well as pancreatic carcinogenesis in vivo. At the molecular level, RBBP9 activity overcomes TGF-β-mediated antiproliferative signaling by reducing Smad2/3 phosphorylation, a previously unknown role for a serine hydrolase in cancer biology. Conversely, loss of endogenous RBBP9 or expression of mutationally inactive RBBP9 leads to elevated Smad2/3 phosphorylation, implicating this serine hydrolase as an essential suppressor of TGF-β signaling. Finally, RBBP9-mediated suppression of TGF-β signaling is required for E-cadherin expression as loss of the serine hydrolase activity leads to a reduction in E-cadherin levels and a concomitant decrease in the integrity of tumor cell–cell junctions. These data not only define a previously uncharacterized serine hydrolase activity associated with epithelial neoplasia, but also demonstrate the potential benefit of functional proteomics in the identification of new therapeutic targets.
Optimization of DNA polymerase mutation rates during bacterial evolution
Authors: Loh Ern , Salk Jesse J. , Loeb Lawrence A.
Published: December 2009

Mutation rate is an important determinant of evolvability. The optimal mutation rate for different organisms during evolution has been modeled in silico and tested in vivo, predominantly through pairwise comparisons. To characterize the fitness landscape across a broad range of mutation rates, we generated a panel of 66 DNA polymerase I mutants in
Escherichia coli
with comparable growth properties, yet with differing DNA replication fidelities, spanning 10
3
-fold higher and lower than that of wild type. These strains were competed for 350 generations in six replicate cultures in two different environments. A narrow range of mutation rates, 10- to 47-fold greater than that of wild type, predominated after serial passage. Mutants exhibiting higher mutation rates were not detected, nor were wild-type or antimutator strains. Winning clones exhibited shorter doubling times, greater maximum culture densities, and a growth advantages in pairwise competition relative to their precompetition ancestors, indicating the acquisition of adaptive phenotypes. To investigate the basis for mutator selection, we undertook a large series of pairwise competitions between mutator and wild-type strains under conditions where, in most cases, one strain completely overtook the culture within 18 days. Mutators were the most frequent winners but wild-type strains were also observed winning, suggesting that the competitive advantage of mutators is due to a greater probability of developing selectably advantageous mutations rather than from an initial growth advantage conferred by the polymerase variant itself. Our results indicate that under conditions where organism fitness is not yet maximized for a particular environment, competitive adaptation may be facilitated by enhanced mutagenesis.
HOXB9, a gene overexpressed in breast cancer, promotes tumorigenicity and lung metastasis
Authors: Hayashida Tetsu , Takahashi Fumiyuki , Chiba Naokazu , Brachtel Elena , Takahashi Motomi , Godin-Heymann Nadia , Gross Kenneth W. , Vivanco Maria d. M. , Wijendran Vasuki , Shioda Toshihiro , Sgroi Dennis , Donahoe Patricia K. , Maheswaran Shyamala
Published: December 2009

The mechanisms underlying tumoral secretion of signaling molecules into the microenvironment, which modulates tumor cell fate, angiogenesis, invasion, and metastasis, are not well understood. Aberrant expression of transcription factors, which has been implicated in the tumorigenesis of several types of cancers, may provide a mechanism that induces the expression of growth and angiogenic factors in tumors, leading to their local increase in the tumor microenvironment, favoring tumor progression. In this report, we demonstrate that the transcription factor HOXB9 is overexpressed in breast carcinoma, where elevated expression correlates with high tumor grade. HOXB9 induces the expression of several angiogenic factors (VEGF, bFGF, IL-8, and ANGPTL-2), as well as ErbB (amphiregulin, epiregulin, and neuregulins) and TGF-ß, which activate their respective pathways, leading to increased cell motility and acquisition of mesenchymal phenotypes. In vivo, HOXB9 promotes the formation of large, well-vascularized tumors that metastasize to the lung. Thus, deregulated expression of HOXB9 contributes to breast cancer progression and lung metastasis by inducing several growth factors that alter tumor-specific cell fates and the tumor stromal microenvironment.
Probing the reaction mechanism of IspH protein by x-ray structure analysis
Authors: Gräwert Tobias , Span Ingrid , Eisenreich Wolfgang , Rohdich Felix , Eppinger Jörg , Bacher Adelbert , Groll Michael
Published: December 2009

Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovered deoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl-2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PP
i
reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of
Lewis
-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the β-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP).
A bicomponent
Plasmodium falciparum
investigational vaccine composed of protein-peptide conjugates
Authors: Kubler-Kielb Joanna , Majadly Fathy , Biesova Zuzana , Mocca Christopher P. , Guo Chunyan , Nussenzweig Ruth , Nussenzweig Victor , Mishra Satish , Wu Yimin , Miller Louis H. , Keith Jerry M. , Liu Teh-Yung , Robbins John B. , Schneerson Rachel
Published: December 2009

There is yet no licensed vaccine against malaria, a serious human disease affecting mostly children, with an annual death rate of about one million.
Plasmodia
, the malaria-causing parasites, have two obligatory hosts: mammals or birds, in which they multiply asexually, and mosquitoes with sexual multiplication. The most common and serious type of malaria is caused by
Plasmodium falciparum
. The circumsporozoite protein (CSP), a major surface antigen of sporozoites, is a protective antigen. A unique feature of
P. falciparum
CSP is its large central domain composed of over 30 tetrapeptide repeats of Asn-Ala-Asn-Pro (NANP). Several NANP peptide-protein conjugates were tested clinically but elicited a low level of CSP antibodies for a short duration. To provide a CSP-based candidate vaccine, we investigated recombinant CSP and NANP conjugates of various peptide lengths, with different N-terminal amino acids, bound at different ratios to various carrier proteins. Injected into mice, CSP alone and CSP or NANP conjugates induced antibodies with booster responses and were positive by the sporozoite imunofluorescent assay. The use of the mosquito stage
P. falciparum
ookinete surface protein, Pfs25, cross-linked onto itself as a carrier for NANP, induced in mice high levels of uniquely long-lasting antibodies to both vaccine components with secondary biological activities, that will provide immunity to liver infection by sporozoites and block transmission by mosquitoes.
Functional diversity among a family of human skeletal muscle myosin motors
Authors: Resnicow Daniel I. , Deacon John C. , Warrick Hans M. , Spudich James A. , Leinwand Leslie A.
Published: December 2009

Human skeletal muscle fibers express five highly conserved type-II myosin heavy chain (MyHC) genes in distinct spatial and temporal patterns. In addition, the human genome contains an intact sixth gene, MyHC-IIb, which is thought under most circumstances not to be expressed. The physiological and biochemical properties of individual muscle fibers correlate with the predominantly expressed MyHC isoform, but a functional analysis of homogenous skeletal muscle myosin isoforms has not been possible. This is due to the difficulties of separating the multiple isoforms usually coexpressed in muscle fibers, as well as the lack of an expression system that produces active recombinant type II skeletal muscle myosin. In this study we describe a mammalian muscle cell expression system and the functional analysis of all six recombinant human type II skeletal muscle myosin isoforms. The diverse biochemical activities and actin-filament velocities of these myosins indicate that they likely have distinct functions in muscle. Our data also show that ATPase activity and motility are generally correlated for human skeletal muscle myosins. The exception, MyHC-IIb, encodes a protein that is high in ATPase activity but slow in motility; this is the first functional analysis of the protein from this gene. In addition, the developmental isoforms, hypothesized to have low ATPase activity, were indistinguishable from adult-fast MyHC-IIa and the specialized MyHC-Extraocular isoform, that was predicted to be the fastest of all six isoforms but was functionally similar to the slower isoforms.
Maerlants Fische
Authors: Berteloot Amand
Published: December 2009

Der Vergleich zwischen dem Fischebuch aus Jacob van Maerlants Der naturen bloeme und dem entsprechenden Kapitel aus Thomas von Cantimprés Liber de natura rerum erlaubt es, die bisherigen Ansichten über die von Maerlant benutzte Redaktion des Textes und möglicherweise sogar über das benutzte Manuskript zu präzisieren. Maerlant hat seine Quelle augenscheinlich relativ planlos um etwa ein Drittel gekürzt und hegte bei seiner Textauswahl offenbar eine besondere Vorliebe für den Nutzwert, den Geschmack und die Zubereitung verschiedener Fischarten. A comparison between Jacob van Maerlant’s fish book from Der naturen bloeme and the corresponding chapter from Thomas von Cantimpré’s Liber de natura rerum offers a specification of previous aspects concerning Maerlant’s compilation of the text and possibly even of the manuscript he used. It seems that Maerlant haphazardly abridged his source by approximately one third, evidently marking in his choices a special penchant for the usefulness, preparation and taste of different fish species.
Le loup a l’âme bonne, ou quand le lupus revêt la peau du lepus
Authors: Puttero Giorgia
Published: December 2009

La fable de Phèdre Lupus et Vulpes iudice Simio (I, 10) est assez connue: le loup accuse de vol le renard, lequel, de son côté, nie tout crime. Le juge singe, qui connaît bien la mauvaise réputation des deux contendants, ne s’enquiert pas trop de savoir ce qui s’est effectivement passé et condamne les adversaires au partage du butin. François Le Moine, avocat normand du XVIIe siècle dont il nous reste un fablier manuscrit, reprend cet apologue, mais avec un changement de taille: le singe reconnaît au loup une âme bonne et il le considère incapable de mystifier la vérité. La surprise devant ces affirmations a déclenché une recherche qui nous a mené sur les traces d’un lupus qui, à un moment donné, dans la tradition des Isopets, est devenu un lepus; ce voyage à rebours permet de mieux comprendre cette sentence du juge et de formuler une hypothèse sur la diffusion des Isopets, bien plus vaste qu’on ne le croit habituellement.
Essential role of Mannose-binding lectin-associated serine protease-1 in activation of the complement factor D
Authors: Takahashi Minoru , Ishida Yumi , Iwaki Daisuke , Kanno Kazuko , Suzuki Toshiyuki , Endo Yuichi , Homma Yoshimi , Fujita Teizo
Published: December 2009

The complement system is an essential component of innate immunity, participating in the pathogenesis of inflammatory diseases and in host defense. In the lectin complement pathway, mannose-binding lectin (MBL) and ficolins act as recognition molecules, and MBL-associated serine protease (MASP) is a key enzyme; MASP-2 is responsible for the lectin pathway activation. The function of other serine proteases (MASP-1 and MASP-3) is still obscure. In this study, we generated a MASP-1– and MASP-3–deficient mouse model (Masp1/3−/−) and found that no activation of the alternative pathway was observed in Masp1/3−/− serum. Mass spectrometric analysis revealed that circulating complement factor D (Df) in Masp1/3−/− mice is a zymogen (pro-Df) with the activation peptide QPRGR at its N terminus. These results suggested that Masp1/3−/− mice failed to convert pro-Df to its active form, whereas it was generally accepted that the activation peptide of pro-Df is removed during its secretion and factor D constitutively exists in an active form in the circulation. Furthermore, recombinant MASP-1 converted pro-Df to the active form in vitro, although the activation mechanism of pro-Df by MASP-1 is still unclear. Thus, it is clear that MASP-1 is an essential protease of both the lectin and alternative complement pathways.
Negative regulation of autoimmune demyelination by the inhibitory receptor CLM-1
Authors: Xi Hongkang , Katschke Kenneth J. , Helmy Karim Y. , Wark Paige A. , Kljavin Noelyn , Clark Hilary , Eastham-Anderson Jeffrey , Shek Theresa , Roose-Girma Merone , Ghilardi Nico , van Lookeren Campagne Menno
Published: December 2009

Multiple sclerosis and its preclinical model, experimental autoimmune encephalomyelitis, are marked by perivascular inflammation and demyelination. Myeloid cells, derived from circulating progenitors, are a prominent component of the inflammatory infiltrate and are believed to directly contribute to demyelination and axonal damage. How the cytotoxic activity of these myeloid cells is regulated is poorly understood. We identify CMRF-35–like molecule-1 (CLM-1) as a negative regulator of autoimmune demyelination. CLM-1 is expressed on inflammatory myeloid cells present in demyelinating areas of the spinal cord after immunization of mice with MOG35-55 (myelin oligodendrocyte glycoprotein) peptide. Absence of CLM-1 resulted in significantly increased nitric oxide and proinflammatory cytokine production, along with increased demyelination and worsened clinical scores, whereas T cell responses in the periphery or in the spinal cord remained unaffected. This study thus identifies CLM-1 as a negative regulator of myeloid effector cells in autoimmune demyelination.