bluuebunny/crossref_metadata_2025 huggingface dataset:
Grain-⟨111⟩-oriented anisotropy in the bonded giant magnetostrictive material
Authors: Meng Hao , Zhang Tianli , Jiang Chengbao , Xu Huibin
Published: March 2010

A strong ⟨111⟩ preferred orientation is induced along the axis of the TbDyFe/epoxy bonded giant magnetostrictive rods by curing the epoxy under a moderate magnetic field. TbDyFe particles with a size distribution of 200–300 μm align in an epoxy matrix, showing an approximate chain structure. A high magnetostrictive performance resulting from the grain-⟨111⟩-oriented anisotropy is achieved with the longitudinal magnetostriction λ∥ up to 1360×10−6 under the prestress of 17 MPa.
Morphology and bonding states of chemical vapor deposition diamond films nucleation surface
Authors: Shpilman Z. , Gouzman I. , Grossman E. , Akhvlediani R. , Hoffman A.
Published: March 2010

The morphology and chemical bonding of the nucleation surface of polycrystalline diamond films were studied following the removal of the silicon substrate by acid etching and mild plasma cleaning. Atomic force microscopy characterization of this surface revealed a mosaic structure of cracks arranged in hexagonal patterns. These cracks are correlated with etched twin grain boundaries that surrounded hexagonal diamond crystals at the initial growth stages of the diamond films. High resolution electron energy loss spectroscopy studies indicate that mild annealing of the diamond film caused desorption of various oxides exposing a damaged diamond surface.
Plasma effects on subcellular structures
Authors: Gweon Bomi , Kim Daeyeon , Kim Dan Bee , Jung Heesoo , Choe Wonho , Shin Jennifer H.
Published: March 2010

Atmospheric pressure helium plasma treated human hepatocytes exhibit distinctive zones of necrotic and live cells separated by a void. We propose that plasma induced necrosis is attributed to plasma species such as oxygen radicals, charged particles, metastables and/or severe disruption of charged cytoskeletal proteins. Interestingly, uncharged cytoskeletal intermediate filaments are only minimally disturbed by plasma, elucidating the possibility of plasma induced electrostatic effects selectively destroying charged proteins. These bona fide plasma effects, which inflict alterations in specific subcellular structures leading to necrosis and cellular detachment, were not observed by application of helium flow or electric field alone.
Improvement of quantum efficiency by employing active-layer-friendly lattice-matched InAlN electron blocking layer in green light-emitting diodes
Authors: Kim Hee Jin , Choi Suk , Kim Seong-Soo , Ryou Jae-Hyun , Yoder P. Douglas , Dupuis Russell D. , Fischer Alec M. , Sun Kewei , Ponce Fernando A.
Published: March 2010

Improvement of the internal quantum efficiency in green-light emitting diodes has been achieved using lattice-matched InAlN electron-blocking layers. Higher electroluminescence intensities have been obtained due to better electron confinement in the device active region. The device efficiency has also been found to significantly depend on the InAlN growth temperature. Optimized InAlN growth at ∼840 °C results in a lower growth rate and longer growth times than at ∼780 °C. The observed reduction in emission efficiency for InAlN layers grown at higher temperatures is possibly attributed to thermal damage in the green active region.
Characteristics of a pentacene thin film transistor with periodic groove patterned poly(methylmethacrylate) dielectrics
Authors: Sun Qijun , Kim Ju-Hyung , Park Jung-Hwan , Seo Soonmin
Published: March 2010

Soft contact lamination enabled to assess the effects of angle variation of the periodic groove patterns on the same pentacene thin film transistors with a 140 nm periodic groove patterned dielectric layer. An angle was formed when the source-drain current and the groove direction of the dielectric layer were crossed. As the angle decreased from 90° to 0°, the current-output and carrier mobility increased and the threshold voltage of the device was shifted. Since pentacene molecules were oriented by the periodic groove patterns formed on the dielectric layer, the current-output and carrier mobility increased as the angle decreased.
Uniform-field transverse electroreflectance using a mode-locked laser and a radio-frequency bias
Authors: Wahlstrand J. K. , Zhang H. , Cundiff S. T.
Published: March 2010

We describe a technique for transverse electroreflectance that uses broadband optical pulses from a mode-locked laser and a rapidly oscillating bias with a frequency near half the laser repetition rate. Since the electrodes are electrically isolated from the sample, highly nonuniform trap-enhanced fields do not occur. Because the time-averaged electric field is zero, space charges do not build up. Experimental results are presented for semi-insulating GaAs. The technique is also useful in ultrafast experiments that require a uniform transverse electric field.
Readout for phase qubits without Josephson junctions
Authors: Steffen Matthias , Kumar Shwetank , DiVincenzo David , Keefe George , Ketchen Mark , Rothwell Mary Beth , Rozen Jim
Published: March 2010

We present a readout scheme for phase qubits which eliminates the read-out superconducting quantum interference device so that the entire qubit and measurement circuitry only require a single Josephson junction. Our scheme capacitively couples the phase qubit directly to a transmission line and detects its state after the measurement pulse by determining a frequency shift observable in the forward scattering parameter of the readout microwaves. This readout is extendable to multiple phase qubits coupled to a common readout line and can in principle be used for other flux biased qubits having two quasistable readout configurations.
Impacts of grazing management options on pasture and animal productivity in a Heteropogon contortus (black speargrass) pasture in central Queensland. 2. Population dynamics of Heteropogon contortus and Stylosanthes scabra cv. Seca
Authors: Orr D. M. , Yee M. C. , Rutherford M. T. , Paton C. J.
Published: March 2010

The dynamics of Heteropogon contortus and Stylosanthes scabra cv. Seca populations were studied in a subset of treatments in an extensive grazing study conducted in central Queensland between 1988 and 2001. These treatments were 4 stocking rates in native pasture and 2 of these stocking rates in legume oversown and supplement/spring burning treatments. For the 1999–2000 summer, population data for H. contortus in 5 of these native pasture and supplement/burning treatments were compared with those for an additional burnt treatment. Seasonal rainfall throughout this study was below the long-term mean and mean annual pasture utilisation ranged from 24 to 61%. Increasing stocking rate from 5 to 2 ha/steer in native pasture reduced H. contortus plant density. Increasing stocking rate reduced seedling recruitment as a result of its effect on soil seedbanks. Seedling recruitment was the major determinant of change in plant density, although some individual H. contortus plants did survive throughout the study. Burning in spring 1999, particularly at light stocking rate, promoted seedling recruitment above that in both unburnt native and legume oversown pasture and resulted in increased H. contortus plant density. In the legume oversown treatments, S. scabra cv. Seca density increased rapidly from 15 plants/m2 in 1988 to 140 plants/m2 in 2001 following a lag phase between 1988 and 1993. This increased S. scabra density was associated with an eventual decline in H. contortus plant density through reduced seedling recruitment. It was concluded that H. contortus population density is sustainable at stocking rates of 4 and 5 ha/steer (30% pasture utilisation) and that spring burning at light stocking rate can promote H. contortus populations. Increasing densities of S. scabra need to be managed to prevent its dominance.
Consumption-based accounting of CO
2
emissions
Authors: Davis Steven J. , Caldeira Ken
Published: March 2010

CO
2
emissions from the burning of fossil fuels are the primary cause of global warming. Much attention has been focused on the CO
2
directly emitted by each country, but relatively little attention has been paid to the amount of emissions associated with the consumption of goods and services in each country. Consumption-based accounting of CO
2
emissions differs from traditional, production-based inventories because of imports and exports of goods and services that, either directly or indirectly, involve CO
2
emissions. Here, using the latest available data, we present a global consumption-based CO
2
emissions inventory and calculations of associated consumption-based energy and carbon intensities. We find that, in 2004, 23% of global CO
2
emissions, or 6.2 gigatonnes CO
2
, were traded internationally, primarily as exports from China and other emerging markets to consumers in developed countries. In some wealthy countries, including Switzerland, Sweden, Austria, the United Kingdom, and France, >30% of consumption-based emissions were imported, with net imports to many Europeans of >4 tons CO
2
per person in 2004. Net import of emissions to the United States in the same year was somewhat less: 10.8% of total consumption-based emissions and 2.4 tons CO
2
per person. In contrast, 22.5% of the emissions produced in China in 2004 were exported, on net, to consumers elsewhere. Consumption-based accounting of CO
2
emissions demonstrates the potential for international carbon leakage. Sharing responsibility for emissions among producers and consumers could facilitate international agreement on global climate policy that is now hindered by concerns over the regional and historical inequity of emissions.
Perceptual priming leads to reduction of gamma frequency oscillations
Authors: Moldakarimov Samat , Bazhenov Maxim , Sejnowski Terrence J.
Published: March 2010

Oscillations of neural activity are ubiquitous in the brain and are critical for normal cognitive function. In the visual system, repetitive presentation of a stimulus results in the reduction of power elicited in the gamma frequency band. However, this reduction does not result in degradation of perception; on the contrary, perception is improved by prior experience with the stimulus. To explain how reduction of gamma frequency oscillations, observed in priming experiments, can lead to improvement in behavior, we assume that visual processing takes place in two distinct stages: representation sharpening in the early visual areas and competitive interaction among representations in the higher visual areas and the prefrontal cortex. Here, we present a network model of spiking neurons that demonstrates how stimulus repetition leads to a decrease in power of the local field potential oscillations in the gamma frequency range in the early layer and also improves network response by reducing the latency to reach a decision in the higher area.
Glacier and landslide feedbacks to topographic relief in the Himalayan syntaxes
Authors: Korup Oliver , Montgomery David R. , Hewitt Kenneth
Published: March 2010

Despite longstanding research on the age and formation of the Tibetan Plateau, the controls on the erosional decay of its margins remain controversial. Pronounced aridity and highly localized rock uplift have traditionally been viewed as limits to the dissection of the plateau by bedrock rivers. Recently, however, glacier dynamics and landsliding have been argued to retard headward fluvial erosion into the plateau interior by forming dams and protective alluvial fill. Here, we report a conspicuous clustering of hundreds of natural dams along the Indus and the Tsangpo Rivers where these cross the Himalayan syntaxes. The Indus is riddled by hundreds of dams composed of debris from catastrophic rock avalanches, forming the largest concentration of giant landslide dams known worldwide, whereas the Tsangpo seems devoid of comparable landslide dams. In contrast, glacial dams such as river-blocking moraines in the headwaters of both rivers are limited to where isolated mountain ranges intersect the regional snowline. We find that to first-order, high local topographic relief along both rivers corresponds to conspicuously different knickzones and differences in the type and potential longevity of these dams. In both syntaxes, glacier and landslide dams act as a negative feedback in response to fluvial dissection of the plateau margins. Natural damming protects bedrock from river incision and delays headward knickpoint migration, thereby helping stabilize the southwestern and southeastern margins of the Tibetan Plateau in concert with the effects of upstream aridity and localized rock uplift.
Dual coding in alternative reading frames correlates with intrinsic protein disorder
Authors: Kovacs Erika , Tompa Peter , Liliom Karoly , Kalmar Lajos
Published: March 2010

Numerous human genes display dual coding within alternatively spliced regions, which give rise to distinct protein products that include segments translated in more than one reading frame. To resolve the ensuing protein structural puzzle, we identified 67 human genes with alternative splice variants comprising a dual-coding region at least 75 nucleotides in length and analyzed the structural status of the protein segments they encode. The inspection of their amino acid composition and predictions by the IUPred and PONDR® VSL2 algorithms suggest a high propensity for structural disorder in dual-coding regions. In the case of +1 frameshifts, the average level of disorder in the two frames is similarly high (47.2% in the ancestral frame, 58.2% in the derived frame, with the average level of disorder in human proteins being approximately 30%), whereas in the case of -1 frameshifts, there is a significant tendency to become more disordered upon shifting the frame (16.7% in the ancestral frame, 56.3% in the derived frame). The regions encoded by the derived frame are mostly disordered (disorder percentage > 50%) in 39 out of 62 cases, which strongly suggests that structural disorder enables these protein products to exist and function without the need of a highly evolved 3D fold. The potential advantages are also demonstrated by the appearance of novel functions and the high incidence of transcripts escaping nonsense-mediated decay. By discussing several examples, we demonstrate that dual coding may be an effective mechanism for the evolutionary appearance of novel intrinsically disordered regions with new functions.
New perspectives on anthropoid origins
Authors: Williams Blythe A. , Kay Richard F. , Kirk E. Christopher
Published: March 2010

Adaptive shifts associated with human origins are brought to light as we examine the human fossil record and study our own genome and that of our closest ape relatives. However, the more ancient roots of many human characteristics are revealed through the study of a broader array of living anthropoids and the increasingly dense fossil record of the earliest anthropoid radiations. Genomic data and fossils of early primates in Asia and Africa clarify relationships among the major clades of primates. Progress in comparative anatomy, genomics, and molecular biology point to key changes in sensory ecology and brain organization that ultimately set the stage for the emergence of the human lineage.
p38 MAPK/MK2-mediated induction of miR-34c following DNA damage prevents Myc-dependent DNA replication
Authors: Cannell Ian G. , Kong Yi W. , Johnston Samantha J. , Chen Melissa L. , Collins Hilary M. , Dobbyn Helen C. , Elia Androulla , Kress Theresia R. , Dickens Martin , Clemens Michael J. , Heery David M. , Gaestel Matthias , Eilers Martin , Willis Anne E. , Bushell Martin
Published: March 2010

The DNA damage response activates several pathways that stall the cell cycle and allow DNA repair. These consist of the well-characterized ATR (Ataxia telangiectasia and Rad-3 related)/CHK1 and ATM (Ataxia telangiectasia mutated)/CHK2 pathways in addition to a newly identified ATM/ATR/p38MAPK/MK2 checkpoint. Crucial to maintaining the integrity of the genome is the S-phase checkpoint that functions to prevent DNA replication until damaged DNA is repaired. Inappropriate expression of the proto-oncogene c-Myc is known to cause DNA damage. One mechanism by which c-Myc induces DNA damage is through binding directly to components of the prereplicative complex thereby promoting DNA synthesis, resulting in replication-associated DNA damage and checkpoint activation due to inappropriate origin firing. Here we show that following etoposide-induced DNA damage translation of c-Myc is repressed by miR-34c via a highly conserved target-site within the 3
′
UTR. While miR-34c is induced by p53 following DNA damage, we show that in cells lacking p53 this is achieved by an alternative pathway which involves p38 MAPK signalling to MK2. The data presented here suggest that a major physiological target of miR-34c is c-Myc. Inhibition of miR-34c activity prevents S-phase arrest in response to DNA damage leading to increased DNA synthesis, DNA damage, and checkpoint activation in addition to that induced by etoposide alone, which are all reversed by subsequent c-Myc depletion. These data demonstrate that miR-34c is a critical regulator of the c-Myc expression following DNA damage acting downstream of p38 MAPK/MK2 and suggest that miR-34c serves to remove c-Myc to prevent inappropriate replication which may otherwise lead to genomic instability.
Membrane nanotubes facilitate long-distance interactions between natural killer cells and target cells
Authors: Chauveau Anne , Aucher Anne , Eissmann Philipp , Vivier Eric , Davis Daniel M.
Published: March 2010

Membrane nanotubes are membranous tethers that physically link cell bodies over long distances. Here, we present evidence that nanotubes allow human natural killer (NK) cells to interact functionally with target cells over long distances. Nanotubes were formed when NK cells contacted target cells and moved apart. The frequency of nanotube formation was dependent on the number of receptor/ligand interactions and increased on NK cell activation. Most importantly, NK cell nanotubes contained a submicron scale junction where proteins accumulated, including DAP10, the signaling adaptor that associates with the activating receptor NKG2D, and MHC class I chain-related protein A (MICA), a cognate ligand for NKG2D, as occurs at close intercellular synapses between NK cells and target cells. Quantitative live-cell fluorescence imaging suggested that MICA accumulated at small nanotube synapses in sufficient numbers to trigger cell activation. In addition, tyrosine-phosphorylated proteins and Vav-1 accumulated at such junctions. Functionally, nanotubes could aid the lysis of distant target cells either directly or by moving target cells along the nanotube path into close contact for lysis via a conventional immune synapse. Target cells moving along the nanotube path were commonly polarized such that their uropods faced the direction of movement. This is the opposite polarization than for normal cell migration, implying that nanotubes can specifically drive target cell movement. Finally, target cells that remained connected to an NK cell by a nanotube were frequently lysed, whereas removing the nanotube using a micromanipulator reduced lysis of these target cells.
RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in
Arabidopsis
Authors: Ren Zhonghai , Zheng Zhimin , Chinnusamy Viswanathan , Zhu Jianhua , Cui Xinping , Iida Kei , Zhu Jian-Kang
Published: March 2010

Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different
Arabidopsis
accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg
erecta
(L
er
; salt and ABA sensitive) × Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL,
Response to ABA and Salt 1 (RAS1
), revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of
RAS1
by transfer-DNA insertion in Col or RNA interference in L
er
leads to decreased salt and ABA sensitivity, whereas overexpression of the L
er
allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha.
Multiple modes of interconverting dynamic pattern formation by bacterial cell division proteins
Authors: Ivanov Vassili , Mizuuchi Kiyoshi
Published: March 2010

Min proteins of the
Escherichia coli
cell division system oscillate between the cell poles in vivo. In vitro on a solid-surface supported lipid bilayer, these proteins exhibit a number of interconverting modes of collective ATP-driven dynamic pattern formation including not only the previously described propagating waves, but also near uniformity in space surface concentration oscillation, propagating filament like structures with a leading head and decaying tail and moving and dividing amoeba-like structures with sharp edges. We demonstrate that the last behavior most closely resembles in vivo system behavior. The simple reaction-diffusion models previously proposed for the Min system fail to explain the results of the in vitro self-organization experiments. We propose the hypotheses that initiation of MinD binding to the surface is controlled by counteraction of initiation and dissociation complexes; the binding of MinD/E is stimulated by MinE and involves polymerization-depolymerization dynamics; polymerization of MinE over MinD oligomers triggers dynamic instability leading to detachment from the membrane. The physical properties of the lipid bilayer are likely to be one of the critical determinants of certain aspects of the dynamic patterns observed.
Structural basis underlying the dual gate properties of KcsA
Authors: Imai Shunsuke , Osawa Masanori , Takeuchi Koh , Shimada Ichio
Published: March 2010

KcsA is a prokaryotic pH-dependent potassium (K) channel. Its activation, by a decrease in the intracellular pH, is coupled with its subsequent inactivation, but the underlying mechanisms remain elusive. Here, we have investigated the conformational changes and equilibrium of KcsA by using solution NMR spectroscopy. Controlling the temperature and pH of KcsA samples produced three distinct methyl-TROSY and NOESY spectra, corresponding to the resting, activated, and inactivated states. The pH-dependence of the signals from the extracellular side was affected by the mutation of H25 on the intracellular side, indicating the coupled conformational changes of the extracellular and intracellular gates. K
+
titration and NOE experiments revealed that the inactivated state was obtained by the replacement of K
+
with H
2
O, which may interfere with the K
+
-permeation. This structural basis of the activation-coupled inactivation is closely related to the C-type inactivation of other K channels.
Orm1 and Orm2 are conserved endoplasmic reticulum membrane proteins regulating lipid homeostasis and protein quality control
Authors: Han Sumin , Lone Museer A. , Schneiter Roger , Chang Amy
Published: March 2010

Yeast members of the ORMDL family of endoplasmic reticulum (ER) membrane proteins play a central role in lipid homeostasis and protein quality control. In the absence of yeast Orm1 and Orm2, accumulation of long chain base, a sphingolipid precursor, suggests dysregulation of sphingolipid synthesis. Physical interaction between Orm1 and Orm2 and serine palmitoyltransferase, responsible for the first committed step in sphingolipid synthesis, further supports a role for the Orm proteins in regulating sphingolipid synthesis. Phospholipid homeostasis is also affected in
orm1
Δ
orm2
Δ cells: the cells are inositol auxotrophs with impaired transcriptional regulation of genes encoding phospholipid biosynthesis enzymes. Strikingly, impaired growth of
orm1
Δ
orm2
Δ cells is associated with constitutive unfolded protein response, sensitivity to stress, and slow ER-to-Golgi transport. Inhibition of sphingolipid synthesis suppresses
orm1
Δ
orm2
Δ phenotypes, including ER stress, suggesting that disrupted sphingolipid homeostasis accounts for pleiotropic phenotypes. Thus, the yeast Orm proteins control membrane biogenesis by coordinating lipid homeostasis with protein quality control.
Gene duplication and the evolution of ribosomal protein gene regulation in yeast
Authors: Wapinski Ilan , Pfiffner Jenna , French Courtney , Socha Amanda , Thompson Dawn Anne , Regev Aviv
Published: March 2010

Coexpression of genes within a functional module can be conserved at great evolutionary distances, whereas the associated regulatory mechanisms can substantially diverge. For example, ribosomal protein (RP) genes are tightly coexpressed in
Saccharomyces cerevisiae
, but the
cis
and
trans
factors associated with them are surprisingly diverged across
Ascomycota
fungi. Little is known, however, about the functional impact of such changes on actual expression levels or about the selective pressures that affect them. Here, we address this question in the context of the evolution of the regulation of RP gene expression by using a comparative genomics approach together with cross-species functional assays. We show that an activator (Ifh1) and a repressor (Crf1) that control RP gene regulation in normal and stress conditions in
S. cerevisiae
are derived from the duplication and subsequent specialization of a single ancestral protein. We provide evidence that this regulatory innovation coincides with the duplication of RP genes in a whole-genome duplication (WGD) event and may have been important for tighter control of higher levels of RP transcripts. We find that subsequent loss of the derived repressor led to the loss of a stress-dependent repression of RPs in the fungal pathogen
Candida glabrata
. Our comparative computational and experimental approach shows how gene duplication can constrain and drive regulatory evolution and provides a general strategy for reconstructing the evolutionary trajectory of gene regulation across species.
Cooperative behavior cascades in human social networks
Authors: Fowler James H. , Christakis Nicholas A.
Published: March 2010

Theoretical models suggest that social networks influence the evolution of cooperation, but to date there have been few experimental studies. Observational data suggest that a wide variety of behaviors may spread in human social networks, but subjects in such studies can choose to befriend people with similar behaviors, posing difficulty for causal inference. Here, we exploit a seminal set of laboratory experiments that originally showed that voluntary costly punishment can help sustain cooperation. In these experiments, subjects were randomly assigned to a sequence of different groups to play a series of single-shot public goods games with strangers; this feature allowed us to draw networks of interactions to explore how cooperative and uncooperative behaviors spread from person to person to person. We show that, in both an ordinary public goods game and in a public goods game with punishment, focal individuals are influenced by fellow group members’ contribution behavior in future interactions with other individuals who were not a party to the initial interaction. Furthermore, this influence persists for multiple periods and spreads up to three degrees of separation (from person to person to person to person). The results suggest that each additional contribution a subject makes to the public good in the first period is tripled over the course of the experiment by other subjects who are directly or indirectly influenced to contribute more as a consequence. These results show experimentally that cooperative behavior cascades in human social networks.
Four generations of transition-state analogues for human purine nucleoside phosphorylase
Authors: Ho Meng-Chiao , Shi Wuxian , Rinaldo-Matthis Agnes , Tyler Peter C. , Evans Gary B. , Clinch Keith , Almo Steven C. , Schramm Vern L.
Published: March 2010

Inhibition of human purine nucleoside phosphorylase (PNP) stops growth of activated T-cells and the formation of 6-oxypurine bases, making it a target for leukemia, autoimmune disorders, and gout. Four generations of ribocation transition-state mimics bound to PNP are structurally characterized. Immucillin-H (

, first-generation) contains an iminoribitol cation with four asymmetric carbons. DADMe-Immucillin-H (

, second-generation), uses a methylene-bridged dihydroxypyrrolidine cation with two asymmetric centers. DATMe-Immucillin-H (

, third-generation) contains an open-chain amino alcohol cation with two asymmetric carbons. SerMe-ImmH (

, fourth-generation) uses achiral dihydroxyaminoalcohol seramide as the ribocation mimic. Crystal structures of PNPs establish features of tight binding to be; 1) ion-pair formation between bound phosphate (or its mimic) and inhibitor cation, 2) leaving-group interactions to N1, O6, and N7 of 9-deazahypoxanthine, 3) interaction between phosphate and inhibitor hydroxyl groups, and 4) His257 interacting with the 5′-hydroxyl group. The first generation analogue is an imperfect fit to the catalytic site with a long ion pair distance between the iminoribitol and bound phosphate and weaker interactions to the leaving group. Increasing the ribocation to leaving-group distance in the second- to fourth-generation analogues provides powerful binding interactions and a facile synthetic route to powerful inhibitors. Despite chemical diversity in the four generations of transition-state analogues, the catalytic site geometry is almost the same for all analogues. Multiple solutions in transition-state analogue design are available to convert the energy of catalytic rate enhancement to binding energy in human PNP.
The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro
Authors: Arbuckle Jesse H. , Medveczky Maria M. , Luka Janos , Hadley Stephen H. , Luegmayr Andrea , Ablashi Dharam , Lund Troy C. , Tolar Jakub , De Meirleir Kenny , Montoya Jose G. , Komaroff Anthony L. , Ambros Peter F. , Medveczky Peter G.
Published: March 2010

Previous research has suggested that human herpesvirus-6 (HHV-6) may integrate into host cell chromosomes and be vertically transmitted in the germ line, but the evidence—primarily fluorescence in situ hybridization (FISH)—is indirect. We sought, first, to definitively test these two hypotheses. Peripheral blood mononuclear cells (PBMCs) were isolated from families in which several members, including at least one parent and child, had unusually high copy numbers of HHV-6 DNA per milliliter of blood. FISH confirmed that HHV-6 DNA colocalized with telomeric regions of one allele on chromosomes 17p13.3, 18q23, and 22q13.3, and that the integration site was identical among members of the same family. Integration of the HHV-6 genome into TTAGGG telomere repeats was confirmed by additional methods and sequencing of the integration site. Partial sequencing of the viral genome identified the same integrated HHV-6A strain within members of families, confirming vertical transmission of the viral genome. We next asked whether HHV-6A infection of naïve cell lines could lead to integration. Following infection of naïve Jjhan and HEK-293 cell lines by HHV-6, the virus integrated into telomeres. Reactivation of integrated HHV-6A virus from individuals’ PBMCs as well as cell lines was successfully accomplished by compounds known to induce latent herpesvirus replication. Finally, no circular episomal forms were detected even by PCR. Taken together, the data suggest that HHV-6 is unique among human herpesviruses: it specifically and efficiently integrates into telomeres of chromosomes during latency rather than forming episomes, and the integrated viral genome is capable of producing virions.
Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle
Authors: Murat Dorothée , Quinlan Anna , Vali Hojatollah , Komeili Arash
Published: March 2010

Although membrane-bounded compartments are commonly considered a unique eukaryotic characteristic, many species of bacteria have organelles. Compartmentalization is well studied in eukaryotes; however, the molecular factors and processes leading to organelle formation in bacteria are poorly understood. We use the magnetosome compartments of magnetotactic bacteria as a model system to investigate organelle biogenesis in a prokaryotic system. The magnetosome is an invagination of the cell membrane that contains a specific set of proteins able to direct the synthesis of a nanometer-sized magnetite crystal. A well-conserved region called the magnetosome island (MAI) is known to be essential for magnetosome formation and contains most of the genes previously implicated in magnetosome formation. Here, we present a comprehensive functional analysis of the MAI genes in a magnetotactic bacterium,
Magnetospirillum magneticum
AMB-1. By characterizing MAI deletion mutants, we show that parts of its conserved core are not essential for magnetosome biogenesis and that nonconserved genes are important for crystal formation. Most importantly, we show that the
mamAB
gene cluster encodes for factors important for magnetosome membrane biogenesis, for targeting of proteins to this compartment and for several steps during magnetite production. Altogether, this genetic analysis defines the function of more than a dozen factors participating in magnetosome formation and shows that magnetosomes are assembled in a step-wise manner in which membrane biogenesis, magnetosome protein localization, and biomineralization are placed under discrete genetic control.
Constraints within major histocompatibility complex class I restricted peptides: Presentation and consequences for T-cell recognition
Authors: Theodossis Alex , Guillonneau Carole , Welland Andrew , Ely Lauren K. , Clements Craig S. , Williamson Nicholas A. , Webb Andrew I. , Wilce Jacqueline A. , Mulder Roger J. , Dunstone Michelle A. , Doherty Peter C. , McCluskey James , Purcell Anthony W. , Turner Stephen J. , Rossjohn Jamie
Published: March 2010

Residues within processed protein fragments bound to major histocompatibility complex class I (MHC-I) glycoproteins have been considered to function as a series of “independent pegs” that either anchor the peptide (p) to the MHC-I and/or interact with the spectrum of αβ-T-cell receptors (TCRs) specific for the pMHC-I epitope in question. Mining of the extensive pMHC-I structural database established that many self- and viral peptides show extensive and direct interresidue interactions, an unexpected finding that has led us to the idea of “constrained” peptides. Mutational analysis of two constrained peptides (the HLA B44 restricted self-peptide (B44DPα–EEFGRAFSF) and an H2-D
b
restricted influenza peptide (D
b
PA, SSLENFRAYV) demonstrated that the conformation of the prominently exposed arginine in both peptides was governed by interactions with MHC-I-orientated flanking residues from the peptide itself. Using reverse genetics in a murine influenza model, we revealed that mutation of an MHC-I-orientated residue (SSLEN
F
RAYV → SSLEN
A
RAYV) within the constrained PA peptide resulted in a diminished cytotoxic T lymphocyte (CTL) response and the recruitment of a limited pMHC-I specific TCR repertoire. Interactions between individual peptide positions can thus impose fine control on the conformation of pMHC-I epitopes, whereas the perturbation of such constraints can lead to a previously unappreciated mechanism of viral escape.
Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB ofEscherichia coli
Authors: Takatsuka Yumiko , Chen Cheng , Nikaido Hiroshi
Published: March 2010

The AcrB trimeric multidrug efflux transporter ofEscherichia colipumps out a very wide spectrum of compounds. Although minocycline and doxorubicin have been cocrystallized within the large binding pocket in the periplasmic domain of the binding protomer, nothing is known about the binding of many other ligands to this protein. We used computer docking to evaluate the interaction of about 30 compounds with the binding protomer and found that many of them are predicted to bind to a narrow groove at one end of the pocket whereas some others prefer to bind to a wide cave at the other end. Competition assays using nitrocefin efflux and covalent labeling of Phe615Cys mutant AcrB with fluorescein-5-maleimide showed that presumed groove-binders competed against each other, but cave-binders did not compete against groove-binders, although the number of compounds tested was limited. These results give us at least a hypothesis to be tested by more biochemical and genetic experiments in the future.
Transgenic expression of CBBP, a CXC domain protein, establishes paramutation in maize
Authors: Brzeska Katarzyna , Brzeski Jan , Smith Jacquelyn , Chandler Vicki L.
Published: March 2010

Paramutation is the ability of specific DNA sequences to communicate in trans to establish meiotically heritable expression states. Paramutation at the maize
b1
locus is mediated by seven unique noncoding transcribed tandem repeats of 853 bp that are required to establish and maintain the meiotically heritable expression and distinct chromatin states associated with
b1
paramutation. In this study, we report the identification of a CXC-domain protein CBBP (CXC domain
b1
-repeat binding protein) that binds to a defined region within the
b1
tandem repeat sequence in vivo and in vitro. When CBBP is expressed from a transgene in maize, it can induce a silent state at the
b1
locus that is heritable in progeny no longer containing the transgene, and the silent epiallele is capable of silencing an active epiallele, characteristic of paramutation. Accumulation of the CBBP protein correlates with
b1
silencing in transgenic and nontransgenic plants. The ability of CBBP to form multimers and to bind to the
b1
tandem repeats suggests a model for counting the number of
b1
repeats. In contrast to previously identified proteins involved in paramutation, CBBP does not share similarity to the known components of the
Arabidopsis
RNAi heterochromatin silencing pathway. Thus, this study defines another class of protein that is involved in heritable gene silencing.
Maximum entropy models for antibody diversity
Authors: Mora Thierry , Walczak Aleksandra M. , Bialek William , Callan Curtis G.
Published: March 2010

Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM sequences in zebrafish. These models are based solely on pairwise correlations between residue positions but correctly capture the higher order statistical properties of the repertoire. By exploiting the interpretation of these models as statistical physics problems, we make several predictions for the collective properties of the sequence ensemble: The distribution of sequences obeys Zipf’s law, the repertoire decomposes into several clusters, and there is a massive restriction of diversity because of the correlations. These predictions are completely inconsistent with models in which amino acid substitutions are made independently at each site and are in good agreement with the data. Our results suggest that antibody diversity is not limited by the sequences encoded in the genome and may reflect rapid adaptation to antigenic challenges. This approach should be applicable to the study of the global properties of other protein families.
Mycobacterium tuberculosis infection induces il12rb1 splicing to generate a novel IL-12Rβ1 isoform that enhances DC migration
Authors: Robinson Richard T. , Khader Shabaana A. , Martino Cynthia A. , Fountain Jeffrey J. , Teixeira-Coelho Maria , Pearl John E. , Smiley Stephen T. , Winslow Gary M. , Woodland David L. , Walter Michael J. , Conejo-Garcia Jose R. , Gubler Ueli , Cooper Andrea M.
Published: March 2010

RNA splicing is an increasingly recognized regulator of immunity. Here, we demonstrate that after Mycobacterium tuberculosis infection (mRNA) il12rb1 is spliced by dendritic cells (DCs) to form an alternative (mRNA) il12rb1Δtm that encodes the protein IL-12Rβ1ΔTM. Compared with IL-12Rβ1, IL-12Rβ1ΔTM contains an altered C-terminal sequence and lacks a transmembrane domain. Expression of IL-12Rβ1ΔTM occurs in CD11c+ cells in the lungs during M. tuberculosis infection. Selective reconstitution of il12rb1−/− DCs with (mRNA) il12rb1 and/or (mRNA) il12rb1Δtm demonstrates that IL-12Rβ1ΔTM augments IL-12Rβ1-dependent DC migration and activation of M. tuberculosis-specific T cells. It cannot mediate these activities independently of IL12Rβ1. We hypothesize that M. tuberculosis-exposed DCs express IL-12Rβ1ΔTM to enhance IL-12Rβ1-dependent migration and promote M. tuberculosis–specific T cell activation. IL-12Rβ1ΔTM thus represents a novel positive-regulator of IL12Rβ1-dependent DC function and of the immune response to M. tuberculosis.
IL-15 trans-presentation by pulmonary dendritic cells promotes effector CD8 T cell survival during influenza virus infection
Authors: McGill Jodi , Van Rooijen Nico , Legge Kevin L.
Published: March 2010

We have recently demonstrated that peripheral CD8 T cells require two separate activation hits to accumulate to high numbers in the lungs after influenza virus infection: a primary interaction with mature, antigen-bearing dendritic cells (DCs) in the lymph node, and a second, previously unrecognized interaction with MHC I–viral antigen–bearing pulmonary DCs in the lungs. We demonstrate that in the absence of lung-resident DC subsets, virus-specific CD8 T cells undergo significantly increased levels of apoptosis in the lungs; however, reconstitution with pulmonary plasmacytoid DCs and CD8α+ DCs promotes increased T cell survival and accumulation in the lungs. Further, our results show that the absence of DCs after influenza virus infection results in significantly reduced levels of IL-15 in the lungs and that pulmonary DC–mediated rescue of virus-specific CD8 T cell responses in the lungs requires trans-presentation of IL-15 via DC-expressed IL-15Rα. This study demonstrates a key, novel requirement for DC trans-presented IL-15 in promoting effector CD8 T cell survival in the respiratory tract after virus infection, and suggests that this trans-presentation could be an important target for the development of unique antiviral therapies and more effective vaccine strategies.
Cubic polynomial maps with periodic critical orbit, Part II: Escape regions
Authors: Bonifant Araceli , Kiwi Jan , Milnor John
Published: March 2010

The parameter space

S

p

\mathcal {S}_p

for monic centered cubic polynomial maps with a marked critical point of period

p
p

is a smooth affine algebraic curve whose genus increases rapidly with

p
p

. Each

S

p

\mathcal {S}_p

consists of a compact connectedness locus together with finitely many escape regions, each of which is biholomorphic to a punctured disk and is characterized by an essentially unique Puiseux series. This note will describe the topology of

S

p

\mathcal {S}_p

, and of its smooth compactification, in terms of these escape regions. In particular, it computes the Euler characteristic. It concludes with a discussion of the real sub-locus of

S

p

\mathcal {S}_p

.
Effect of diabetes and hypertension on left ventricular diastolic function in a high‐risk population without evidence of heart disease
Authors: Russo Cesare , Jin Zhezhen , Homma Shunichi , Rundek Tatjana , Elkind Mitchell S.V. , Sacco Ralph L. , Di Tullio Marco R.
Published: March 2010

Aims

To assess the independent and combined effects of diabetes and hypertension on left ventricular (LV) diastolic function in a community‐based cohort at high cardiovascular risk.

Methods and results

Two‐dimensional echocardiography was performed in 708 subjects from the Cardiac Abnormalities and Brain Lesions (CABL) study. Peak diastolic early (E) and late (A) transmitral flow, and tissue Doppler‐derived early mitral annulus velocity (E′) were recorded, and E/A and E/E′ ratios were calculated. The population was divided into four groups: those without hypertension or diabetes (HT−/DM−), those with only hypertension (HT), only diabetes (DM), and with hypertension plus diabetes (HT + DM). In multivariate analysis, hypertension and diabetes were independent predictors of worse diastolic function. The coexistence of hypertension and diabetes was associated with greater impairment of diastolic function (higher E/E′ ratio than HT−/DM−, HT, or DM, all P < 0.05), independent of covariates. The negative, synergistic effect of hypertension and diabetes on LV diastolic function was present both in lean participants and in overweight/obese ones. An E/E′ ratio >15, suggestive of increased LV filling pressure, was found in 2.2% of HT−/DM−, 8.9% of HT, 5.9% of DM, and 14.7% of HT + DM (P < 0.01).

Conclusion

Hypertension and diabetes are independently associated with impaired LV diastolic function, independent of the effect of overweight/obesity and other covariates. Their coexistence results in a negative synergistic effect on LV diastolic mechanics and is associated with higher LV filling pressures than either condition alone.
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates
Authors: Matsumoto Jun , Dewar Ken , Wasserscheid Jessica , Wiley Graham B. , Macmil Simone L. , Roe Bruce A. , Zeller Robert W. , Satou Yutaka , Hastings Kenneth E.M.
Published: March 2010

Pre-mRNA 5′ spliced-leader (SL) trans-splicing occurs in some metazoan groups but not in others. Genome-wide characterization of the trans-spliced mRNA subpopulation has not yet been reported for any metazoan. We carried out a high-throughput analysis of the SL trans-spliced mRNA population of the ascidian tunicate Ciona intestinalis by 454 Life Sciences (Roche) pyrosequencing of SL-PCR-amplified random-primed reverse transcripts of tailbud embryo RNA. We obtained ∼250,000 high-quality reads corresponding to 8790 genes, ∼58% of the Ciona total gene number. The great depth of this data revealed new aspects of trans-splicing, including the existence of a significant class of “infrequently trans-spliced” genes, accounting for ∼28% of represented genes, that generate largely non-trans-spliced mRNAs, but also produce trans-spliced mRNAs, in part through alternative promoter use. Thus, the conventional qualitative dichotomy of trans-spliced versus non-trans-spliced genes should be supplanted by a more accurate quantitative view recognizing frequently and infrequently trans-spliced gene categories. Our data include reads representing ∼80% of Ciona frequently trans-spliced genes. Our analysis also revealed significant use of closely spaced alternative trans-splice acceptor sites which further underscores the mechanistic similarity of cis- and trans-splicing and indicates that the prevalence of ±3-nt alternative splicing events at tandem acceptor sites, NAGNAG, is driven by spliceosomal mechanisms, and not nonsense-mediated decay, or selection at the protein level. The breadth of gene representation data enabled us to find new correlations between trans-splicing status and gene function, namely the overrepresentation in the frequently trans-spliced gene class of genes associated with plasma/endomembrane system, Ca2+ homeostasis, and actin cytoskeleton.