bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic patterns of pleiotropy and the evolution of complexity
Authors: Wang Zhi , Liao Ben-Yang , Zhang Jianzhi
Published: September 2010

Pleiotropy refers to the phenomenon of a single mutation or gene affecting multiple distinct phenotypic traits and has broad implications in many areas of biology. Due to its central importance, pleiotropy has also been extensively modeled, albeit with virtually no empirical basis. Analyzing phenotypes of large numbers of yeast, nematode, and mouse mutants, we here describe the genomic patterns of pleiotropy. We show that the fraction of traits altered appreciably by the deletion of a gene is minute for most genes and the gene–trait relationship is highly modular. The standardized size of the phenotypic effect of a gene on a trait is approximately normally distributed with variable SDs for different genes, which gives rise to the surprising observation of a larger per-trait effect for genes affecting more traits. This scaling property counteracts the pleiotropy-associated reduction in adaptation rate (i.e., the “cost of complexity”) in a nonlinear fashion, resulting in the highest adaptation rate for organisms of intermediate complexity rather than low complexity. Intriguingly, the observed scaling exponent falls in a narrow range that maximizes the optimal complexity. Together, the genome-wide observations of overall low pleiotropy, high modularity, and larger per-trait effects from genes of higher pleiotropy necessitate major revisions of theoretical models of pleiotropy and suggest that pleiotropy has not only allowed but also promoted the evolution of complexity.
Elicitation of structure-specific antibodies by epitope scaffolds
Authors: Ofek Gilad , Guenaga F. Javier , Schief William R. , Skinner Jeff , Baker David , Wyatt Richard , Kwong Peter D.
Published: September 2010

Elicitation of antibodies against targets that are immunorecessive, cryptic, or transient in their native context has been a challenge for vaccine design. Here we demonstrate the elicitation of structure-specific antibodies against the HIV-1 gp41 epitope of the broadly neutralizing antibody 2F5. This conformationally flexible region of gp41 assumes mostly helical conformations but adopts a kinked, extended structure when bound by antibody 2F5. Computational techniques were employed to transplant the 2F5 epitope into select acceptor scaffolds. The resultant “2F5-epitope scaffolds” possessed nanomolar affinity for antibody 2F5 and a range of epitope flexibilities and antigenic specificities. Crystallographic characterization of the epitope scaffold with highest affinity and antigenic discrimination confirmed good to near perfect attainment of the target conformation for the gp41 molecular graft in free and 2F5-bound states, respectively. Animals immunized with 2F5-epitope scaffolds showed levels of graft-specific immune responses that correlated with graft flexibility (
p
 < 0.04), while antibody responses against the graft—as dissected residue-by-residue with alanine substitutions—resembled more closely those of 2F5 than sera elicited with flexible or cyclized peptides, a resemblance heightened by heterologous prime-boost. Lastly, crystal structures of a gp41 peptide in complex with monoclonal antibodies elicited by the 2F5-epitope scaffolds revealed that the elicited antibodies induce gp41 to assume its 2F5-recognized shape. Epitope scaffolds thus provide a means to elicit antibodies that recognize a predetermined target shape and sequence, even if that shape is transient in nature, and a means by which to dissect factors influencing such elicitation.
Structural basis for glucose-6-phosphate activation of glycogen synthase
Authors: Baskaran Sulochanadevi , Roach Peter J. , DePaoli-Roach Anna A. , Hurley Thomas D.
Published: September 2010

Regulation of the storage of glycogen, one of the major energy reserves, is of utmost metabolic importance. In eukaryotes, this regulation is accomplished through glucose-6-phosphate levels and protein phosphorylation. Glycogen synthase homologs in bacteria and archaea lack regulation, while the eukaryotic enzymes are inhibited by protein kinase mediated phosphorylation and activated by protein phosphatases and glucose-6-phosphate binding. We determined the crystal structures corresponding to the basal activity state and glucose-6-phosphate activated state of yeast glycogen synthase-2. The enzyme is assembled into an unusual tetramer by an insertion unique to the eukaryotic enzymes, and this subunit interface is rearranged by the binding of glucose-6-phosphate, which frees the active site cleft and facilitates catalysis. Using both mutagenesis and intein-mediated phospho-peptide ligation experiments, we demonstrate that the enzyme’s response to glucose-6-phosphate is controlled by Arg583 and Arg587, while four additional arginine residues present within the same regulatory helix regulate the response to phosphorylation.
Occurrence of maize detritus and a transgenic insecticidal protein (Cry1Ab) within the stream network of an agricultural landscape
Authors: Tank Jennifer L. , Rosi-Marshall Emma J. , Royer Todd V. , Whiles Matt R. , Griffiths Natalie A. , Frauendorf Therese C. , Treering David J.
Published: September 2010

Widespread planting of maize throughout the agricultural Midwest may result in detritus entering adjacent stream ecosystems, and 63% of the 2009 US maize crop was genetically modified to express insecticidal Cry proteins derived fromBacillus thuringiensis. Six months after harvest, we conducted a synoptic survey of 217 stream sites in Indiana to determine the extent of maize detritus and presence of Cry1Ab protein in the stream network. We found that 86% of stream sites contained maize leaves, cobs, husks, and/or stalks in the active stream channel. We also detected Cry1Ab protein in stream-channel maize at 13% of sites and in the water column at 23% of sites. We found that 82% of stream sites were adjacent to maize fields, and Geographical Information Systems analyses indicated that 100% of sites containing Cry1Ab-positive detritus in the active stream channel had maize planted within 500 m during the previous crop year. Maize detritus likely enters streams throughout the Corn Belt; using US Department of Agriculture land cover data, we estimate that 91% of the 256,446 km of streams/rivers in Iowa, Illinois, and Indiana are located within 500 m of a maize field. Maize detritus is common in low-gradient stream channels in northwestern Indiana, and Cry1Ab proteins persist in maize leaves and can be measured in the water column even 6 mo after harvest. Hence, maize detritus, and associated Cry1Ab proteins, are widely distributed and persistent in the headwater streams of a Corn Belt landscape.
Evidence for symmetry in the elementary process of bidirectional torque generation by the bacterial flagellar motor
Authors: Nakamura Shuichi , Kami-ike Nobunori , Yokota Jun-ichi P. , Minamino Tohru , Namba Keiichi
Published: September 2010

The bacterial flagellar motor can rotate in both counterclockwise (CCW) and clockwise (CW) directions. It has been shown that the sodium ion-driven chimeric flagellar motor rotates with 26 steps per revolution, which corresponds to the number of FliG subunits that form part of the rotor ring, but the size of the backward step is smaller than the forward one. Here we report that the proton-driven flagellar motor of
Salmonella
also rotates with 26 steps per revolution but symmetrical in both CCW and CW directions with occasional smaller backward steps in both directions. Occasional shift in the stepping positions is also observed, suggesting the frequent exchange of stators in one of the 11–12 possible anchoring positions around the rotor. These observations indicate that the elementary process of torque generation by the cyclic association/dissociation of the stator with every FliG subunit along the circumference of the rotor is symmetric in CCW and CW rotation even though the structure of FliG is highly asymmetric and suggests a 180° rotation of a FliG domain for the rotor-stator interaction to reverse the direction of rotation.
Organization and coordinated assembly of the type III secretion export apparatus
Authors: Wagner Samuel , Königsmaier Lisa , Lara-Tejero María , Lefebre Matthew , Marlovits Thomas C. , Galán Jorge E.
Published: September 2010

Type III protein secretion systems are unique bacterial nanomachines with the capacity to deliver bacterial effector proteins into eukaryotic cells. These systems are critical to the biology of many pathogenic or symbiotic bacteria for insects, plants, animals, and humans. Essential components of these systems are multiprotein envelope-associated organelles known as the needle complex and a group of membrane proteins that compose the so-called export apparatus. Here, we show that components of the export apparatus associate intimately with the needle complex, forming a structure that can be visualized by cryo-electron microscopy. We also show that formation of the needle complex base is initiated at the export apparatus and that, in the absence of export apparatus components, there is a significant reduction in the levels of needle complex base assembly. Our results show a substantial coordination in the assembly of the two central elements of type III secretion machines.
Revisiting the structures of several antibiotics bound to the bacterial ribosome
Authors: Bulkley David , Innis C. Axel , Blaha Gregor , Steitz Thomas A.
Published: September 2010

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from
Thermus thermophilus
suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of
Haloarcula marismortui
, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium
Deinococcus radiodurans
. Our structure of the antibiotic telithromycin bound to the
T. thermophilus
ribosome reveals a lactone ring with a conformation similar to that observed in the
H. marismortui
and
D. radiodurans
complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the
T. thermophilus
ribosome are consistent with biochemical studies performed on the
Escherichia coli
ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.
Inhibition of the visual cycle by A2E through direct interaction with RPE65 and implications in Stargardt disease
Authors: Moiseyev Gennadiy , Nikolaeva Olga , Chen Ying , Farjo Krysten , Takahashi Yusuke , Ma Jian-xing
Published: September 2010

Stargardt disease (STGD) is the major form of inherited juvenile macular degeneration. Pyridinium bis-retinoid A2E is a major component of lipofuscin which accumulates in retinal pigment epithelium (RPE) cells in STGD and contributes to the disease pathogenesis. However, the precise role of A2E in vision loss is unclear. Here we report that A2E efficiently inhibits RPE65 isomerohydrolase, a key enzyme in the visual cycle. Subretinal injection of A2E significantly inhibited retinoid isomerohydrolase activity in mice. Likewise, A2E also inhibited isomerohydrolase activity in cells coexpressing RPE65, lecithin retinol acyltransferase (LRAT), and cellular retinaldehyde-binding protein. In vitro isomerohydrolase activity assays confirmed that A2E inhibited enzymatic activity of recombinant RPE65 in a concentration-dependent manner, but did not inhibit LRAT activity. The inhibition type for isomerohydrolase was found to be reversible and competitive with
K

i

 = 13.6 μM. To determine the direct interaction of A2E with RPE65 protein, fluorescence binding assays were performed. As shown by fluorimetric titration, binding of purified RPE65 with A2E enhanced the bis-retinoid fluorescence. Consistently, the fluorescence of RPE65 decreased upon incubation with A2E. Both of these experiments suggest a direct, specific binding of A2E to RPE65. The binding constant for A2E and purified RPE65 was calculated to be 250 nM. These results demonstrate that A2E inhibits the regeneration of 11-
cis
retinal, the chromophore of visual pigments, which represents a unique mechanism by which A2E may impair vision in STGD.
Dietary inorganic nitrate reverses features of metabolic syndrome in endothelial nitric oxide synthase-deficient mice
Authors: Carlström Mattias , Larsen Filip J. , Nyström Thomas , Hezel Michael , Borniquel Sara , Weitzberg Eddie , Lundberg Jon O.
Published: September 2010

The metabolic syndrome is a clustering of risk factors of metabolic origin that increase the risk for cardiovascular disease and type 2 diabetes. A proposed central event in metabolic syndrome is a decrease in the amount of bioavailable nitric oxide (NO) from endothelial NO synthase (eNOS). Recently, an alternative pathway for NO formation in mammals was described where inorganic nitrate, a supposedly inert NO oxidation product and unwanted dietary constituent, is serially reduced to nitrite and then NO and other bioactive nitrogen oxides. Here we show that several features of metabolic syndrome that develop in eNOS-deficient mice can be reversed by dietary supplementation with sodium nitrate, in amounts similar to those derived from eNOS under normal conditions. In humans, this dose corresponds to a rich intake of vegetables, the dominant dietary nitrate source. Nitrate administration increased tissue and plasma levels of bioactive nitrogen oxides. Moreover, chronic nitrate treatment reduced visceral fat accumulation and circulating levels of triglycerides and reversed the prediabetic phenotype in these animals. In rats, chronic nitrate treatment reduced blood pressure and this effect was also present during NOS inhibition. Our results show that dietary nitrate fuels a nitrate–nitrite–NO pathway that can partly compensate for disturbances in endogenous NO generation from eNOS. These findings may have implications for novel nutrition-based preventive and therapeutic strategies against cardiovascular disease and type 2 diabetes.
Pharmacological chaperone for the structured domain of human prion protein
Authors: Nicoll Andrew J. , Trevitt Clare R. , Tattum M. Howard , Risse Emmanuel , Quarterman Emma , Ibarra Amaurys Avila , Wright Connor , Jackson Graham S. , Sessions Richard B. , Farrow Mark , Waltho Jonathan P. , Clarke Anthony R. , Collinge John
Published: September 2010

In prion diseases, the misfolded protein aggregates are derived from cellular prion protein (PrPC). Numerous ligands have been reported to bind to human PrPC(huPrP), but none to the structured region with the affinity required for a pharmacological chaperone. Using equilibrium dialysis, we screened molecules previously suggested to interact with PrP to discriminate between those which did not interact with PrP, behaved as nonspecific polyionic aggregates or formed a genuine interaction. Those that bind could potentially act as pharmacological chaperones. Here we report that a cationic tetrapyrrole [Fe(III)-TMPyP], which displays potent antiprion activity, binds to the structured region of huPrP. Using a battery of biophysical techniques, we demonstrate that Fe(III)-TMPyP forms a 1∶1 complex via the structured C terminus of huPrP with aKdof 4.5 ± 2 μM, which is in the range of its IC50for curing prion-infected cells of 1.6 ± 0.4 μM and the concentration required to inhibit protein-misfolding cyclic amplification. Therefore, this molecule tests the hypothesis that stabilization of huPrPC, as a principle, could be used in the treatment of human prion disease. The identification of a binding site with a defined 3D structure opens up the possibility of designing small molecules that stabilize huPrP and prevent its conversion into the disease-associated form.
Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex
Authors: Kobayashi Kan , Kikuno Izumi , Kuroha Kazushige , Saito Kazuki , Ito Koichi , Ishitani Ryuichiro , Inada Toshifumi , Nureki Osamu
Published: September 2010

No-go decay and nonstop decay are mRNA surveillance pathways that detect translational stalling and degrade the underlying mRNA, allowing the correct translation of the genetic code. In eukaryotes, the protein complex of Pelota (yeast Dom34) and Hbs1 translational GTPase recognizes the stalled ribosome containing the defective mRNA. Recently, we found that archaeal Pelota (aPelota) associates with archaeal elongation factor 1α (aEF1α) to act in the mRNA surveillance pathway, which accounts for the lack of an Hbs1 ortholog in archaea. Here we present the complex structure of aPelota and GTP-bound aEF1α determined at 2.3-Å resolution. The structure reveals how GTP-bound aEF1α recognizes aPelota and how aPelota in turn stabilizes the GTP form of aEF1α. Combined with the functional analysis in yeast, the present results provide structural insights into the molecular interaction between eukaryotic Pelota and Hbs1. Strikingly, the aPelota·aEF1α complex structurally resembles the tRNA·EF-Tu complex bound to the ribosome. Our findings suggest that the molecular mimicry of tRNA in the distorted “A/T state” conformation by Pelota enables the complex to efficiently detect and enter the empty A site of the stalled ribosome.
Genome-wide model for the normal eukaryotic DNA replication fork
Authors: Larrea Andres A. , Lujan Scott A. , McElhinny Stephanie A. Nick , Mieczkowski Piotr A. , Resnick Michael A. , Gordenin Dmitry A. , Kunkel Thomas A.
Published: September 2010

To investigate DNA replication enzymology across the nuclear genome of budding yeast, deep sequencing was used to establish the pattern of uncorrected replication errors generated by an asymmetric mutator variant of DNA polymerase δ (Pol δ). Sequencing of 16 genomes identified 1,206-bp substitutions generated over 33 generations by L612M Pol δ in a mismatch repair defective strain. Alignment of sequences flanking these substitutions identified “hotspot” motifs for Pol δ replication errors. The substitutions were distributed evenly across all 16 chromosomes. The vast majority were transitions that occurred with a strand bias that varied in a predictable manner relative to known functional origins of replication. This strand bias strongly supports the idea that Pol δ is primarily a lagging strand polymerase during replication across the entire nuclear genome.
Accumulation of driver and passenger mutations during tumor progression
Authors: Bozic Ivana , Antal Tibor , Ohtsuki Hisashi , Carter Hannah , Kim Dewey , Chen Sining , Karchin Rachel , Kinzler Kenneth W. , Vogelstein Bert , Nowak Martin A.
Published: September 2010

Major efforts to sequence cancer genomes are now occurring throughout the world. Though the emerging data from these studies are illuminating, their reconciliation with epidemiologic and clinical observations poses a major challenge. In the current study, we provide a mathematical model that begins to address this challenge. We model tumors as a discrete time branching process that starts with a single driver mutation and proceeds as each new driver mutation leads to a slightly increased rate of clonal expansion. Using the model, we observe tremendous variation in the rate of tumor development—providing an understanding of the heterogeneity in tumor sizes and development times that have been observed by epidemiologists and clinicians. Furthermore, the model provides a simple formula for the number of driver mutations as a function of the total number of mutations in the tumor. Finally, when applied to recent experimental data, the model allows us to calculate the actual selective advantage provided by typical somatic mutations in human tumors in situ. This selective advantage is surprisingly small—0.004 ± 0.0004—and has major implications for experimental cancer research.
Measurement and control of in-plane surface chemistry during the oxidation of H-terminated (111) Si
Authors: Gokce Bilal , Adles Eric J. , Aspnes David E. , Gundogdu Kenan
Published: September 2010

In-plane directional control of surface chemistry during interface formation can lead to new opportunities regarding device structures and applications. Control of this type requires techniques that can probe and hence provide feedback on the chemical reactivity of bonds not only in specific directions but also in real time. Here, we demonstrate both control and measurement of the oxidation of H-terminated (111) Si. Control is achieved by externally applying uniaxial strain, and measurement by second-harmonic generation (SHG) together with the anisotropic-bond model of nonlinear optics. In this system anisotropy results because bonds in the strain direction oxidize faster than those perpendicular to it, leading in addition to transient structural changes that can also be detected at the bond level by SHG.
A self-learning algorithm for biased molecular dynamics
Authors: Tribello Gareth A. , Ceriotti Michele , Parrinello Michele
Published: September 2010

A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences.
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes
Authors: Rychkova Anna , Vicatos Spyridon , Warshel Arieh
Published: September 2010

The understanding of the mechanism of insertion of transmembrane (TM) helixes through the translocon presents a major open challenge. Although the experimental information about the partition of the inserted helices between the membrane and the solution contains crucial information about this process, it is not clear how to extract this information. In particular, it is not clear how to rationalize the small apparent insertion energy, Δ
G
app
, of an ionized residue in the center of a TM helix. Here we explore the nature of the insertion energies, asking what should be the value of these parameters if their measurements represent equilibrium conditions. This is done using a coarse-grained model with advanced electrostatic treatment. Estimating the energetics of ionized arginine of a TM helix in the presence of neighboring helixes or the translocon provides a rationale for the observed Δ
G
app
of ionized residues. It is concluded that the apparent insertion free energy of TM with charged residues reflects probably more than just the free energy of moving the isolate single helix from water into the membrane. The present approach should be effective not only in exploring the mechanism of the operation of the translocon but also for studies of other membrane proteins.
Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in
Medicago truncatula
Authors: Zhou Rui , Jackson Lisa , Shadle Gail , Nakashima Jin , Temple Stephen , Chen Fang , Dixon Richard A.
Published: September 2010

Cinnamoyl CoA reductases (CCR) convert hydroxycinnamoyl CoA esters to their corresponding cinnamyl aldehydes in monolignol biosynthesis. We identified two
CCR
genes in the model legume
Medicago truncatula
. CCR1 exhibits preference for feruloyl CoA, but CCR2 prefers caffeoyl and 4-coumaroyl CoAs, exhibits sigmoidal kinetics with these substrates, and is substrate-inhibited by feruloyl and sinapoyl CoAs.
M. truncatula
lines harboring transposon insertions in
CCR1
exhibit drastically reduced growth and lignin content, whereas
CCR2
knockouts grow normally with moderate reduction in lignin levels.
CCR1
fully and
CCR2
partially complement the irregular xylem gene 4
CCR
mutation of
Arabidopsis
. The expression of caffeoyl CoA 3-
O
-methyltransferase (
CCoAOMT
) is up-regulated in
CCR2
knockout lines; conversely, knockout of
CCoAOMT
up-regulates
CCR2
. These observations suggest that CCR2 is involved in a route to monolignols in
Medicago
whereby coniferaldehyde is formed via caffeyl aldehyde which then is 3-
O
-methylated by caffeic acid
O
-methyltransferase.
Circadian CLOCK histone acetyl transferase localizes at ND10 nuclear bodies and enables herpes simplex virus gene expression
Authors: Kalamvoki Maria , Roizman Bernard
Published: September 2010

Expression of herpes simplex virus genes at the initiation of replication involves two steps that take place at ND10 nuclear bodies. These are suppression of cellular repressors that attempt to silence viral DNA and remodeling of the viral chromatin to make it accessible for transcription. In earlier studies we reported on the mechanism by which viral proteins ICP0 and U
S
3 protein kinase modify and disrupt the HDAC1/CoREST/REST/LSD1 repressor complex. The remodeling step requires in addition acetylation of histones bound to DNA. In an attempt to identify the enzyme, we took note of the observation that ICP0 physically and functionally interacts with Bmal1, a partner of the CLOCK histone acetyl transferase, and key members of the bHLH–PAS family of transcriptional factors. The Bmal11 and CLOCK heterodimer is best known as a regulator of the circadian oscillation in the mammalian CLOCK system. In this article we report the following: (
i
) in infected cells both Bmal1 and CLOCK localize at ND10 bodies; (
ii
) wild-type virus stabilizes the CLOCK protein; (
iii
) overexpression of CLOCK partially compensates for the absence of ICP0 and enables higher yields in cells infected with a ΔICP0 mutant and this activity is not expressed by CLOCK mutants lacking histone acetyl transferase activity; and (
iv
) depletion of CLOCK in cells infected with wild-type virus results in significant decrease in the expression of all viral proteins tested. We conclude that ICP0 interacts with Bmal1 and by extension with CLOCK histone acetyl transferase to remodel viral chromatin.
Brain plasticity related to the consolidation of motor sequence learning and motor adaptation
Authors: Debas Karen , Carrier Julie , Orban Pierre , Barakat Marc , Lungu Ovidiu , Vandewalle Gilles , Tahar Abdallah Hadj , Bellec Pierre , Karni Avi , Ungerleider Leslie G. , Benali Habib , Doyon Julien
Published: September 2010

This study aimed to investigate, through functional MRI (fMRI), the neuronal substrates associated with the consolidation process of two motor skills: motor sequence learning (MSL) and motor adaptation (MA). Four groups of young healthy individuals were assigned to either (
i
) a night/sleep condition, in which they were scanned while practicing a finger sequence learning task or an eight-target adaptation pointing task in the evening (test) and were scanned again 12 h later in the morning (retest) or (
ii
) a day/awake condition, in which they were scanned on the MSL or the MA tasks in the morning and were rescanned 12 h later in the evening. As expected and consistent with the behavioral results, the functional data revealed increased test–retest changes of activity in the striatum for the night/sleep group compared with the day/awake group in the MSL task. By contrast, the results of the MA task did not show any difference in test–retest activity between the night/sleep and day/awake groups. When the two MA task groups were combined, however, increased test–retest activity was found in lobule VI of the cerebellar cortex. Together, these findings highlight the presence of both functional and structural dissociations reflecting the off-line consolidation processes of MSL and MA. They suggest that MSL consolidation is sleep dependent and reflected by a differential increase of neural activity within the corticostriatal system, whereas MA consolidation necessitates either a period of daytime or sleep and is associated with increased neuronal activity within the corticocerebellar system.
The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair
Authors: Xu Ye , Sun Yingli , Jiang Xiaofeng , Ayrapetov Marina K. , Moskwa Patryk , Yang Shenghong , Weinstock David M. , Price Brendan D.
Published: September 2010

The complexity of chromatin architecture presents a significant barrier to the ability of the DNA repair machinery to access and repair DNA double-strand breaks (DSBs). Consequently, remodeling of the chromatin landscape adjacent to DSBs is vital for efficient DNA repair. Here, we demonstrate that DNA damage destabilizes nucleosomes within chromatin regions that correspond to the γ-H2AX domains surrounding DSBs. This nucleosome destabilization is an active process requiring the ATPase activity of the p400 SWI/SNF ATPase and histone acetylation by the Tip60 acetyltransferase. p400 is recruited to DSBs by a mechanism that is independent of ATM but requires mdc1. Further, the destabilization of nucleosomes by p400 is required for the RNF8-dependent ubiquitination of chromatin, and for the subsequent recruitment of brca1 and 53BP1 to DSBs. These results identify p400 as a novel DNA damage response protein and demonstrate that p400-mediated alterations in nucleosome and chromatin structure promote both chromatin ubiquitination and the accumulation of brca1 and 53BP1 at sites of DNA damage.
Coa3 and Cox14 are essential for negative feedback regulation of COX1 translation in mitochondria
Authors: Mick David U. , Vukotic Milena , Piechura Heike , Meyer Helmut E. , Warscheid Bettina , Deckers Markus , Rehling Peter
Published: September 2010

Regulation of eukaryotic cytochrome oxidase assembly occurs at the level of Cox1 translation, its central mitochondria-encoded subunit. Translation of COX1 messenger RNA is coupled to complex assembly in a negative feedback loop: the translational activator Mss51 is thought to be sequestered to assembly intermediates, rendering it incompetent to promote translation. In this study, we identify Coa3 (cytochrome oxidase assembly factor 3; Yjl062w-A), a novel regulator of mitochondrial COX1 translation and cytochrome oxidase assembly. We show that Coa3 and Cox14 form assembly intermediates with newly synthesized Cox1 and are required for Mss51 association with these complexes. Mss51 exists in equilibrium between a latent, translational resting, and a committed, translation-effective, state that are represented as distinct complexes. Coa3 and Cox14 promote formation of the latent state and thus down-regulate COX1 expression. Consequently, lack of Coa3 or Cox14 function traps Mss51 in the committed state and promotes Cox1 synthesis. Our data indicate that Coa1 binding to sequestered Mss51 in complex with Cox14, Coa3, and Cox1 is essential for full inactivation.
Quantifying Interhospital Patient Sharing as a Mechanism for Infectious Disease Spread
Authors: Huang Susan S. , Avery Taliser R. , Song Yeohan , Elkins Kristen R. , Nguyen Christopher C. , Nutter Sandra K. , Nafday Alaka A. , Condon Curtis J. , Chang Michael T. , Chrest David , Boos John , Bobashev Georgiy , Wheaton William , Frank Steven A. , Piatt Richard , Lipsitch Marc , Bush Robin M. , Eubank Stephen , Burke Donald S. , Lee Bruce Y.
Published: September 2010

Background.

Assessments of infectious disease spread in hospitals seldom account for interfacility patient sharing. This is particularly important for pathogens with prolonged incubation periods or carrier states.

Methods.

We quantified patient sharing among all 32 hospitals in Orange County (OC), California, using hospital discharge data. Same-day transfers between hospitals were considered “direct” transfers, and events in which patients were shared between hospitals after an intervening stay at home or elsewhere were considered “indirect” patient-sharing events. We assessed the frequency of readmissions to another OC hospital within various time points from discharge and examined interhospital sharing of patients with Clostridium difficile infection.

Results.

In 2005, OC hospitals had 319,918 admissions. Twenty-nine percent of patients were admitted at least twice, with a median interval between discharge and readmission of 53 days. Of the patients with 2 or more admissions, 75% were admitted to more than 1 hospital. Ninety-four percent of interhospital patient sharing occurred indirectly. When we used 10 shared patients as a measure of potential interhospital exposure, 6 (19%) of 32 hospitals “exposed” more than 50% of all OC hospitals within 6 months, and 17 (53%) exposed more than 50% within 12 months. Hospitals shared 1 or more patient with a median of 28 other hospitals. When we evaluated patients with C. difficile infection, 25% were readmitted within 12 weeks; 41% were readmitted to different hospitals, and less than 30% of these readmissions were direct transfers.

Conclusions.

In a large metropolitan county, interhospital patient sharing was a potential avenue for transmission of infectious agents. Indirect sharing with an intervening stay at home or elsewhere composed the bulk of potential exposures and occurred unbeknownst to hospitals.
Measuring symptoms in the irritable bowel syndrome: development of a framework for clinical trials
Authors: Spiegel B. M. R. , Bolus R. , Agarwal N. , Sayuk G. , Harris L. A. , Lucak S. , Esrailian E. , Chey W. D. , Lembo A. , Karsan H. , Tillisch K. , Talley J. , Chang L.
Published: September 2010

Aliment Pharmacol Ther 2010; 32: 1275–1291

Background  There is uncertainty about how to measure patient‐reported outcomes (PROs) in IBS. The Food and Drug Administration (FDA) emphasizes that PROs must be couched in a conceptual framework, yet existing IBS PROs were not based on such a framework.

Aim  To perform qualitative analyses to inform a new conceptual framework for IBS symptoms.

Methods  Following FDA guidance, we searched the literature for extant IBS questionnaires. We then performed interviews in IBS patients to learn about the illness experience in their own words. We cultivated vocabulary to inform a conceptual framework depicted with domains, sub‐domains, and item categories, per FDA guidance.

Results  We identified 13 questionnaires with items encompassing 18 symptoms. We recruited 123 IBS patients for cognitive interviews. Major themes included: pain and discomfort are different – asking about discomfort is nonspecific and should be avoided in future PROs; bowel urgency is multifaceted – PROs should measure bowel immediacy, controllability, and predictability; and PROs should divide bloating into how it feels vs. how it looks. Symptom experience may be determined by 35‐item categories within five domains: (i) pain; (ii) gas/bloat; (iii) diarrhoea; (iv) constipation; and (v) extraintestinal symptoms.

Conclusions  We applied FDA guidance to develop a framework that can serve as the foundation for developing a PRO for IBS clinical trials.
Sex‐related differences in hospital admissions attributed to adverse drug reactions in the Netherlands
Authors: Rodenburg Eline M. , Stricker Bruno H. Ch. , Visser Loes E.
Published: September 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

Women are more at risk for developing adverse drug reactions (ADRs) due to differences in pharmacokinetics, pharmacodynamics and drug use. ADRs regularly lead to hospital admissions.

WHAT THIS STUDY ADDS

There are differences between the sexes in hospital admissions attributed to ADRs. The risk of being hospitalized with an ADR varies between the sexes in the type of reaction and the causative drug.

AIMAdverse drug reactions (ADRs) are a major burden in health care, regularly leading to hospital admission, morbidity or death. Women tend to have a higher risk of adverse drug reactions with a 1.5 to 1.7‐fold greater risk than men. Our primary aim was to study differences in ADR‐related hospitalizations between the sexes.

METHODSWe conducted a nationwide study of all ADR‐related hospitalizations in the period between 2000 and 2005 in the Netherlands, which were selected from all 9 287 162 hospital admissions in this period. ADR–drug group combinations with at least 50 admissions in one of the sexes were selected. Relative risks and confidence intervals were calculated with respect to total admissions and total prescriptions with men as reference.

RESULTSIn total, 0.41% of the 4 236 368 admissions in men (95% CI 0.40, 0.42%) and 0.47% of the 5 050 794 admissions in women (95% CI 0.46, 0.48%) were attributed to an ADR by medical specialists (57% of all ADR‐related admissions were in women). Differences between the sexes in risk for ADR‐related hospitalization were found for antineoplastic and immunosuppressive drugs, antirheumatics, anticoagulants and salicylates, cardiovascular and neurological drugs, steroids and antibiotics. In certain drug categories, risks for hospitalization changed after taking into account total drug prescriptions.

CONCLUSIONIn all different drug classes, significant differences exist between the sexes in ADR‐related hospital admissions. Cardiovascular drugs account for the most pronounced differences between men and women. More research is needed to explain the clear sex differences in ADR‐related hospital admissions.
Von Willebrand factor and fibrinolytic parameters during the desmopressin test in patients with Cushing's disease
Authors: Giraldi Francesca Pecori , Ambrogio Alberto G. , Fatti Letizia M. , Rubini Valentina , Cozzi Giovanna , Scacchi Massimo , Federici Augusto B. , Cavagnini Francesco
Published: September 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Desmopressin is a known haemostatic agent and is also being used, albeit at lower doses, during the diagnostic work‐up of Cushing's syndrome, a condition characterized by excess cortisol concentrations and frequent thromboembolic events. No study has yet evaluated whether admininistration of desmopressin for diagnostic purposes induces significant, adverse changes in endothelial cell markers in these patients.

WHAT THIS STUDY ADDS

• Administration of desmopressin to patients with Cushing's disease induces changes in endothelial cell markers comparable with those observed in obese and normal weight subjects. It follows, that desmopressin testing does not induce disease‐specific untoward changes in coagulatory markers in patients with endogenous hypercortisolism and its use in this context appears safe.

AIMS Desmopressin, a vasopressin analogue, is used for various clinical purposes, including haemostasis and, in recent times, the diagnostic work‐up of patients with Cushing's syndrome, a condition associated with a known prothrombotic profile. We decided to evaluate whether and to what extent a diagnostic dose of desmopressin induces significant changes in endothelial parameters in patients with Cushing's disease (CD) and obese and normal weight controls.

METHODS Twelve patients with CD, 10 obese and five normal weight controls were studied. Von Willebrand antigen (VWF : Ag), tissue plasminogen activator (t‐PA) and plasminogen activator inhibitor type 1 (PAI‐1) were measured at baseline and up to 4 h after 10 µg desmopressin i.v.

RESULTS Desmopressin 10 µg transiently increased VWF : Ag and t‐PA and decreased PAI‐1 in all subjects. The magnitude of the VWF : Ag and t‐PA increases after desmopressin was comparable in the three groups (VWF : Ag peak‐to‐basal ratio 1.9 ± 0.17, 1.5 ± 0.11 and 1.8 ± 0.13 and t‐PA peak‐to‐basal ratio 1.6 ± 0.18, 1.6 ± 0.20 and 1.8 ± 0.24 for CD, obese and controls, respectively, all NS). The PAI‐1 decrease observed in patients with CD was comparable with obese (0.7 ± 0.07 and 0.6 ± 0.09, NS) and controls (0.7 ± 0.07 vs. 0.4 ± 0.09, P= 0.08).

CONCLUSIONS Administration of desmopressin to patients with CD for diagnostic purposes induces a transitory increase in VWF : Ag counterbalanced by a decrease in PAI‐1 and increase in t‐PA. The magnitude of these changes is largely comparable with that observed in obese and normal weight controls. Our data show that testing with desmopressin does not induce disease‐specific changes in endothelial markers in patients with CD.
Revisiting the particle‐size distribution of soils: comparison of different methods and sample pre‐treatments
Authors: Vdović N. , Obhođaš J. , Pikelj K.
Published: September 2010

The choice of analytical method and sample pretreatment has significant consequences for the shape of particle‐size distribution (PSD) frequency curves, and therefore for the evaluation of soil textural parameters. Here, the comparison of several granulometric methods based on different physical principles is presented: wet sieving (WS), based on gravity and the mechanical force of water, was combined with pipette (PP) sedimentation/settling velocity, Micromeritics SediGraph (MS) sedimentation/x‐ray attenuation and Coulter Counter (CC) electroresistance particle counting. The Malvern Mastersizer (MM), an instrument based on laser diffraction, was used without WS. Twelve typical temperate‐region soil types were chosen for this study on the basis of their mineral composition, organic matter content, conductivity and magnetic susceptibility. The modalities of PSD frequency curves obtained by different methods were compared. The results showed considerably larger clay‐fraction contents determined with the sedimentation techniques, PP and MS, than that obtained by CC or MM.

Statistical correlation and regression models were used to compare the fractions of clay, silt and sand obtained with different methods. Linear correlations were found in almost all cases, except those comparing clay fractions obtained by CC with those obtained by MM, PP and MS methods. These correlations were non‐linear. The observed difference was attributed to the presence of aggregates and/or magnetic properties of soil particles. However, more data are needed to verify this hypothesis. The implications of sample pre‐treatment with dispersant and hydrogen peroxide (H2O2) were evaluated by the MS and CC techniques and observed by the scanning electron microscope. H2O2 was found to be an efficient disaggregating agent. The use of dispersant resulted in the increased amount of the clay fraction measured by the MS method.
Investigating flow mechanisms in a forest soil by mixed‐effects modelling
Authors: Bogner C. , Gaul D. , Kolb A. , Schmiedinger I. , Huwe B.
Published: September 2010

Uniform and preferential flow produces typical infiltration patterns. We made three tracer experiments in a Norway spruce forest soil and qualitatively identified the dominant flow regime based on stained patterns. We analysed soil texture, fine root density and soil bulk density from preferential flow paths and the soil matrix by means of linear mixed‐effects models. These models can account for dependences in the data structure caused by hierarchical sampling and can deal with missing values. There were between 44% (topsoil) and 76% (subsoil) larger root densities in preferential flow paths than in the soil matrix. No significant differences in soil texture were detected. The bulk density was greater in the soil matrix by 0.12 g cm−3, which is probably because of a greater soil organic matter content of preferential flow paths. Using flow patterns and model results we identified the dominant flow mechanisms. At this study site, roots constituted the main preferential flow paths and induced macropore flow, especially in the topsoil. In the subsoil, root density decreased and inhomogeneous infiltration from preferential flow paths into the soil matrix caused unstable flow.
Are elevated δ15N values in herbivores in hot and arid environments caused by diet or animal physiology?
Authors: Hartman Gideon
Published: September 2010

1. Mammalian species from hot and arid environments often have elevated nitrogen isotope values compared to animals from similar trophic levels in more temperate climates. This pattern has most often been explained as the result of a physiological response by animals to heat and water stress. However, a positive correlation between rainfall and the δ15N values of plants and herbivorous mammalian species suggests that diet may be responsible.

2. This study uses the horn keratin of desert‐adapted bovids (Dorcas gazelle and Nubian ibex) to test whether the δ15N values of herbivore body tissues are determined by heat and water stress or by the isotopic composition of their diet. The δ15N values of horn keratin are compared against several climatic factors that affect heat and water stress to determine if a relationship exists. In addition, the range of δ15N values measured in desert vegetation is used to evaluate the contribution of the diet to the isotopic values of bovid body tissue.

3. The δ15N values of desert bovid horn keratin were correlated against individual climatic factors that induce water stress and were not found to be significant. When climatic factors were combined, a significant positive correlation was found between the δ15N values of Dorcas gazelles and temperature, humidity, and rainfall. This observation contradicts the physiological stress hypothesis that predicts a negative correlation between rainfall and humidity and δ15N values. Instead, this correlation is likely attributable to denitrification processes in the soil that directly affect the isotopic values of the plants. Values for δ15N of horn keratin fall within the range predicted by discrimination between diet and consumer (Δ = 4·1‰) which supports the diet hypothesis.

4. The results suggest that the isotopic composition of the diet is the dominant factor determining the δ15N values of herbivore body tissue.
CD56 (NCAM) expression in ameloblastomas and other odontogenic lesions
Authors: Cairns Lindsey , Naidu Aparna , Robinson Conrad Max , Sloan Philip , Wright John M , Hunter Keith D
Published: September 2010

Cairns L, Naidu A, Robinson C M, Sloan P, Wright J M & Hunter K D (2010) Histopathology 57, 544–548 CD56 (NCAM) expression in ameloblastomas and other odontogenic lesions

Aims:  Ameloblastomas recapitulate certain elements of tooth formation. CD56 is expressed by a variety of cells and is used in tumour diagnosis, but is also expressed in the enamel organ during tooth development. The aim of this study was to describe the expression of CD56 in odontogenic lesions with particular reference to the differential diagnosis of ameloblastoma and odontogenic keratocyst.

Methods:  Cases were selected from the pathology archives at Glasgow Royal Infirmary, Glasgow, Royal Victoria Infirmary, Newcastle and Department of Diagnostic Sciences, Texas A&M Health Science Center Baylor College of Dentistry, Dallas. The study population included 38 ameloblastomas, 19 odontogenic keratocysts and a number of other odontogenic lesions, including nine compound odontomes. All sections were examined for CD56 immunoreactivity and the extent of staining was recorded.

Results:  Thirty‐seven of 38 (97%) ameloblastomas expressed CD56 on the cell membrane of peripheral cells in tumour nests (16 extensively, 21 focally). Immunoreactivity was lost in areas of inflammation, acanthomatous differentiation, in areas of cystic change and upon fusion with overlying surface epithelium. One odontogenic keratocyst expressed CD56 (5%, P < 0.0001). CD56 was expressed very focally in two odontomes, exclusively in stratum intermedium‐like cells.

Conclusions:  CD56 expression in odontogenic epithelium is highly suggestive of ameloblastoma and can help in differentiating this from odontogenic keratocyst.