bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanomachining and clamping point optimization of silicon carbon nitride resonators using low voltage electron beam lithography and cold development
Authors: Mohammad M. A. , Guthy C. , Evoy S. , Dew S. K. , Stepanova M.
Published: December 2010

The authors report the nanomachining of sub-20-nm wide doubly clamped silicon carbon nitride resonators using low keV electron beam lithography with polymethyl methacrylate resist and cold development. Methodologies are developed for precisely controlling the resonator widths in the ultranarrow regime of 11–20 nm. Resonators with lengths of 1–20 μm and widths of 16–280 nm are characterized at room temperature in vacuum using piezoelectric actuation and optical interferometry. Clamping and surface losses are identified as the dominant energy loss mechanisms for a range of resonator widths. The resonator clamping points are optimized using an original electron beam lithography simulator. Various alternative clamping point designs are also modeled and fabricated in order to reduce the clamping losses.
Nondestructive detection of deviation in integrated circuits
Authors: Baghaei Leili , Dai Bing , Pianetta Piero , Pease R. Fabian W.
Published: December 2010

There exists a clear need for an inspection microscope that features suboptical resolution and high penetration but requires no ambient vacuum for the sample. The most prominent application of such microscope is the nondestructive examination of fabricated integrated circuits. Current semiconductor fabrication processes would require a resolution of approximately 10 nm to a penetration depth of 100 μm. These requirements are expected to increase over time due to process shrinks. The coherent x-ray diffraction microscope is a recent development where highly coherent x-ray sources are used without focusing optics. Instead, the diffraction pattern of the beam is recorded, and reconstruction of the sample image is achieved by recovering the phase information using computational algorithms.
Nanostructured silicon membranes for control of molecular transport
Authors: Srijanto Bernadeta R. , Retterer Scott T. , Fowlkes Jason D. , Doktycz Mitchel J.
Published: December 2010

A membrane that allows selective transport of molecular species requires precise engineering on the nanoscale. Membrane permeability can be tuned by controlling the physical structure and surface chemistry of the pores. Here, a combination of electron beam and optical lithography, along with cryogenic deep reactive ion etching, has been used to fabricate silicon membranes that are physically robust, have uniform pore sizes, and are directly integrated into a microfluidic network. Additional reductions in pore size were achieved using plasma enhanced chemical vapor deposition and atomic layer deposition of silicon dioxide to coat membrane surfaces. Cross sectioning of the membranes using focused ion beam milling was used to determine the physical shape of the membrane pores before and after coating. Functional characterization of the membranes was performed by using quantitative fluorescence microscopy to document the transport of molecular species across the membrane.
Paradoxical False Memory for Objects After Brain Damage
Authors: McTighe Stephanie M. , Cowell Rosemary A. , Winters Boyer D. , Bussey Timothy J. , Saksida Lisa M.
Published: December 2010

Novel or Familiar?

Amnesia is characterized by a number of memory deficits, including the apparent inability to distinguish between novel and familiar stimuli.

McTighe
et al.

(p.
1408
; see the Perspective by

Eichenbaum

) observed that the recognition memory of brain-damaged rats in a standard model of amnesia was impaired not because previously experienced objects seemed to be novel, but because objects not previously experienced seemed to be familiar. Furthermore, simply placing the animal in a visually deprived environment during the delay, reducing visual interference, completely rescued the impairment. This counterintuitive finding contradicts the predominant “multiple memory systems” model in which amnesia is usually considered and forces a reconsideration of fundamental assumptions underlying our understanding of amnesia.
Carbon Nanotubes with Temperature-Invariant Viscoelasticity from –196° to 1000°C
Authors: Xu Ming , Futaba Don N. , Yamada Takeo , Yumura Motoo , Hata Kenji
Published: December 2010

Shake It to Wake It

Viscoelastic materials combine the recoverable stretchiness found in elastic materials with the slow-flowing behavior of a thick fluid, like honey. When subjected to an oscillatory motion, the response will depend on the frequency. At low frequencies, the viscous behavior will dominate and lead to a dissipation of the applied energy as heat, while at fast frequencies the elastic behavior dominates.

Xu
et al.

(p.
1364
; see the Perspective by

Gogotsi

) developed a viscoelastic material with an exceptionally broad operating temperature range, based on a network of carbon nanotubes. The responsiveness of the material was probably caused by the “zipping” and “unzipping” of the nanotubes at points of contact.
Dynamical Response of the Tropical Pacific Ocean to Solar Forcing During the Early Holocene
Authors: Marchitto Thomas M. , Muscheler Raimund , Ortiz Joseph D. , Carriquiry Jose D. , van Geen Alexander
Published: December 2010

Sunny and Cool

Changes in solar output cause changes in the amount of radiation that Earth receives from the Sun, which in turn can cause climate variations. The effects of solar variations are not uniform over the globe—owing to the complexity of the climate system, larger solar fluxes may produce warming in one area but cooling in another.

Marchitto
et al.

(p.
1378
) present a record of Holocene sea surface temperature in the eastern equatorial Pacific Ocean that shows cooling as solar output increased and warming as the Sun dimmed. These temperature changes resulted from dynamical control of El Niño and La Niña episodes by solar radiative forcing of Earth's climate.
Rewiring of Genetic Networks in Response to DNA Damage
Authors: Bandyopadhyay Sourav , Mehta Monika , Kuo Dwight , Sung Min-Kyung , Chuang Ryan , Jaehnig Eric J. , Bodenmiller Bernd , Licon Katherine , Copeland Wilbert , Shales Michael , Fiedler Dorothea , Dutkowski Janusz , Guénolé Aude , van Attikum Haico , Shokat Kevan M. , Kolodner Richard D. , Huh Won-Ki , Aebersold Ruedi , Keogh Michael-Christopher , Krogan Nevan J. , Ideker Trey
Published: December 2010

DNA Damage Pathways Revealed

Despite the dynamic nature of cellular responses, the genetic networks that govern these responses have been mapped primarily as static snapshots.

Bandyopadhyay
et al.

(p.
1385
; see the Perspective by

Friedman and Schuldiner

) report a comparison of large genetic interactomes measured among all yeast kinases, phosphatases, and transcription factors, as the cell responded to DNA damage. The interactomes revealed were highly dynamic structures that changed dramatically with changing conditions. These dynamic interactions reveal genetic relationships that can be more effective than classical “static” interactions (for example, synthetic lethals and epistasis maps) in identifying pathways of interest.
How Neuromythologies Support Sex Role Stereotypes
Brain Storm
The Flaws in the Science of Sex Differences

by Rebecca M. Jordan-Young

Harvard University Press, Cambridge, MA, 2010. 408 pp. $35, £25.95, €31.50. ISBN 9780674057302.
Delusions of Gender
How Our Minds, Society, and Neurosexism Create Difference

by Cordelia Fine

Norton, New York, 2010. 368 pp. $25.95, C$32.50. ISBN 9780393068382.
Authors: Halpern Diane F.
Published: December 2010

Targeting conclusions that are closer to fiction than science, both Fine and Jordan-Young highlight exaggerations, unreplicated claims, and other silliness from research on neurological differences between the human sexes.
The Role of Particle Morphology in Interfacial Energy Transfer in CdSe/CdS Heterostructure Nanocrystals
Authors: Borys Nicholas J. , Walter Manfred J. , Huang Jing , Talapin Dmitri V. , Lupton John M.
Published: December 2010

An Upside of Asymmetry

Advances in synthetic techniques have enabled the preparation of nanometer-scale semiconductors in a wide range of precise shapes and sizes, including core-shell morphologies that layer several different materials in the same particle. Such two-in-one motifs are promising for light-harvesting applications because they allow optically induced charge separation across the internal interface.

Borys
et al.

(p.
1371
) studied a series of rod-shaped cadmium sulfide–cadmium selenide hybrid particles using single-particle–resolved optical spectroscopy and found that smooth versus bulbous geometries produced distinct emission spectra. Further analysis of more complex, tetrapodal particles (with four arms aligned tetrahedrally) suggested that nonuniform geometries facilitate interfacial charge transfer by reducing the likelihood of electronic band misalignment.
High-Temperature Rubber Made from Carbon Nanotubes
Authors: Gogotsi Yury
Published: December 2010

A mixture of carbon nanotubes creates a material that can recover its shape after deformation over a wide temperature range.
On Getting There from Here
Authors: McKnight Steven L.
Published: December 2010

Studies on a variety of interesting biological problems, ranging from circadian rhythm to cancer cell growth to longevity, have begun to give evidence that the physiological state of cells and tissues reflects both the cell’s regulatory systems and its state of intermediary metabolism. It is appreciated that the regulatory state of a cell or tissue, as driven by transcription factors and signaling pathways, can impose itself upon the dynamics of metabolic state. It follows that the reciprocal must also be the case, that metabolic state will feed back to impose itself on regulatory state. An appreciation and understanding of this reciprocity may be required to crack open problems in biological research that have heretofore been insoluble.
A New Approach to Fluorescence Microscopy
Authors: Bates Mark
Published: December 2010

Precise localization of switchable fluorescent molecules facilitates nanoscale biological imaging.
A Powerful and Perplexing New HIV Prevention Tool
Authors: Cohen Jon
Published: December 2010

Unlike the many HIV prevention trials that have failed or had positive but barely significant results, the Pre-Exposure Prophylaxis Initiative has showed unequivocally that the treated group had 44% fewer infections after an average of 1.2 years.
Brazilian Science: Riding a Gusher
Authors: Regalado Antonio
Published: December 2010

A fast-growing economy and oil discoveries are propelling Brazil's research to new heights. But scientific leaders must overcome a weak education system and a low-impact track record.
Talented But Underfunded: Brazil's Future Scientists
Authors: Regalado Antonio
Published: December 2010

Brazil must overcome deep social divisions in order to achieve its dream of becoming a major player in scientific research. Many say the task must begin with improving public schools, where poorly paid teachers offer rote lessons.
LIFE SCIENCE TECHNOLOGIES: Understanding Apoptosis
Authors: Smaglik Paul
Published: December 2010

Apoptosis is a simple concept with complex underpinnings--damaged cells are prompted to self-destruct through a series of molecular events, like dominos toppling over one by one. Unraveling the mechanisms underlying apoptosis is akin to determining the role each individual domino plays in a falling cascade--one strategically placed tile can trigger a cascade of several lines, and one misplaced tile can mean a dead end in the chain reaction. Techniques that pick apart this intricate process have been rapidly advancing, now offering more than the ability to look at a single event with high throughput, multiplexing capabilities, and in vivo imaging. Future technologies aim to help scientists visualize human cellular processes in vivo to aid researchers in tailoring and monitoring treatment for a variety of diseases, especially cancer.
Purified Hexameric Epstein-Barr Virus-Encoded BARF1 Protein for Measuring Anti-BARF1 Antibody Responses in Nasopharyngeal Carcinoma Patients
Authors: Hoebe E. K. , Hutajulu S. H. , van Beek J. , Stevens S. J. , Paramita D. K. , Greijer A. E. , Middeldorp J. M.
Published: December 2010

WHO type III nasopharyngeal carcinoma (NPC) is highly prevalent in Indonesia and 100% associated with Epstein-Barr virus (EBV). NPC tumor cells express viral proteins, including BARF1, which is secreted and is considered to have oncogenic and immune-modulating properties. Recently, we found conserved mutations in the BARF1 gene in NPC isolates. This study describes the expression and purification of NPC-derived BARF1 and analyzes humoral immune responses against prototype BARF1 (B95-8) and purified native hexameric BARF1 in sera of Indonesian NPC patients (
n
= 155) compared to healthy EBV-positive (
n
= 56) and EBV-negative (
n
= 16) individuals. BARF1 (B95-8) expressed in
Escherichia coli
and baculovirus, as well as BARF1-derived peptides, did not react with IgG or IgA antibodies in NPC. Purified native hexameric BARF1 protein isolated from culture medium was used in enzyme-linked immunosorbent assay (ELISA) and revealed relatively weak IgG and IgA responses in human sera, although it had strong antibody responses to other EBV proteins. Higher IgG reactivity was found in NPC patients (
P
= 0.015) than in regional Indonesian controls or EBV-negative individuals (
P
< 0.001). IgA responses to native BARF1 were marginal. NPC sera with the highest IgG responses to hexameric BARF1 in ELISA showed detectable reactivity with denatured BARF1 by immunoblotting. In conclusion, BARF1 has low immunogenicity for humoral responses and requires native conformation for antibody binding. The presence of antibodies against native BARF1 in the blood of NPC patients provides evidence that the protein is expressed and secreted as a hexameric protein in NPC patients.
Persistence, Replacement, and Rapid Clonal Expansion of Meningococcal Carriage Isolates in a 2008 University Student Cohort
Authors: Bidmos Fadil A. , Neal Keith R. , Oldfield Neil J. , Turner David P. J. , Ala'Aldeen Dlawer A. A. , Bayliss Christopher D.
Published: December 2010

A study of meningococcal carriage dynamics was performed with a cohort of 190 first-year students recruited from six residential halls at Nottingham University, United Kingdom. Pharyngeal swabs were obtained on four occasions between November 2008 and May 2009. Direct plating and culture on selective media were succeeded by identification and characterization of meningococci using PCR-based methodologies. Three serogroup Y clones and one serogroup 29E clone were highly prevalent in particular residential halls in November 2008, which is indicative of rapid clonal expansion since the start of the academic year. Persistent carriage of the same meningococcal strain for at least 5 to 6 months was observed in 45% of carriers, with infrequent evidence of antigenic variation in PorA. Sequential carriage of heterologous meningococcal strains occurred in 36% of carriers and involved strains with different capsules and antigenic variants of PorA and FetA in 83% of the cases. These clonal replacement strains also exhibited frequent differences in the presence and antigenic structures of two other surface proteins, NadA and HmbR. This study highlights the low level of antigenic variation associated with persistent carriage but, conversely, the importance of alterations in the repertoire of antigenic variants for sequential carriage of meningococcal strains. Rapid clonal expansion of potentially pathogenic strains in residential halls has implications for the implementation of public health interventions in university populations.
How To Detect NDM-1 Producers
Authors: Nordmann Patrice , Poirel Laurent , Carrër Amélie , Toleman Mark A. , Walsh Timothy R.
Published: December 2010

Enterobacterial isolates expressing the carbapenemase NDM-1 are emerging worldwide. Twenty-seven NDM-1-positive isolates of worldwide origin were included in this study to identify these strains as not only pathogens but also colonizers of normal flora for infection control screening. Although susceptibility to carbapenems varied, a combined test (IMP/IMP + EDTA), the Etest MBL, and automated susceptibility testing by Vitek2 (bioMérieux) identified those NDM-1 producers as verified by PCR using specific primers. Screening for carriers of NDM-1 producers may be based on media such as the ChromID ESBL culture medium routinely used to screen for extended-spectrum β-lactamase producers, which gives excellent detection levels with low limits of detection ranging from 8 × 10
0
to 5 × 10
2
CFU/ml. The CHROMagar KPC culture medium had higher limits of detection (1 × 10
1
to 5 × 10
5
CFU/ml) and may be proposed for the follow-up of outbreaks of infections with NDM-1 producers. Colonies growing on these screening media can be verified as NDM-1 producers with molecular methods as described herein.
Laboratory Detection of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae: Evaluation of Two Screening Agar Plates and Two Confirmation Techniques
Authors: Overdevest I. T. M. A. , Willemsen I. , Elberts S. , Verhulst C. , Kluytmans J. A. J. W.
Published: December 2010

The worldwide prevalence of extended-spectrum-beta-lactamase-producing ESBL-producing
Enterobacteriaceae
(ESBL-E) is increasing, making the need for optimized detection techniques more urgent. In this study we investigated the performance of two ESBL-E screening and two ESBL-E confirmation techniques. In accordance with the Dutch national guidelines (
www.wip.nl
), a collection of 642 highly resistant
Enterobacteriaceae
strains, as identified by Vitek2, was used to test the performances of two screening techniques (EbSA ESBL agar plate and ChromID ESBL agar plate) and of two confirmation techniques (MIC-strip ESBL and Vitek2 ESBL test panel). The individual test results were compared by using Etest, followed by a combination disk test if Etest results were inconclusive. Among group 1 isolates (
Escherichia coli
,
Klebsiella
spp.,
Proteus
spp.,
Salmonella
spp., and
Shigella
spp.) 291 (57.6%) were ESBL-E, versus 65 (47.4%) in group 2 (
Enterobacter
spp.,
Citrobacter
spp.,
Morganella morganii
,
Serratia
spp., and
Providencia
spp.). The sensitivities of all four tests for group 1 were comparable (EbSA, 96.6%; ChromID, 97.3%; MIC-strip, 99.6%; and Vitek2, 95.1%). The specificities of the EbSA and ChromID were the same (93.9%). However, the confirmation techniques produced many inconclusive test results, which reduces the applicability in routine laboratories. Only the two screening agar plates were validated for ESBL testing of group 2 microorganisms. They showed comparable sensitivities; however, the EbSA screening agar plate had a significantly higher specificity (78.6% versus 44.3%). In conclusion the screening agar plates performed better than the two confirmation techniques. The EbSA agar plate had the best overall performance.
Cell Type Specificity and Host Genetic Polymorphisms Influence Antibody-Dependent Enhancement of Dengue Virus Infection
Authors: Boonnak Kobporn , Dambach Kaitlyn M. , Donofrio Gina C. , Tassaneetrithep Boonrat , Marovich Mary A.
Published: December 2010

Antibody-dependent enhancement (ADE) is implicated in severe, usually secondary, dengue virus (DV) infections. Preexisting heterotypic antibodies, via their Fc-gamma receptor (FcγR) interactions, may increase disease severity through enhanced target cell infection. Greater numbers of infected target cells may contribute to higher viremia and excess cytokine levels often observed in severe disease. Monocytes, macrophages, and immature and mature dendritic cells (DC) are considered major cellular targets of DV. Apheresis of multiple donors allowed isolation of autologous primary myeloid target cell types for head-to-head comparison of infection rates, viral output, and cytokine production under direct infection (without antibody) or ADE conditions (with antibody). All studied cell types except immature DC supported ADE. All cells undergoing ADE secreted proinflammatory cytokines (interleukin-6 [IL-6] and tumor necrosis factor alpha [TNF-α]) at enhancement titers, but distinct cell-type-specific patterns were observed for other relevant proteins (alpha/beta interferon [IFN-α/β] and IL-10). Macrophages produced type I interferons (IFN-α/β) that were modulated by ADE. Mature DC mainly secreted IFN-β. Interestingly, only monocytes secreted IL-10, and only upon antibody-enhanced infection. While ADE infection rates were remarkably consistent in monocytes (10 to 15%) across donors, IL-10 protein levels varied according to previously described regulatory single nucleotide polymorphisms (SNPs) in the IL-10 promoter region. The homozygous GCC haplotype was associated with high-level IL-10 secretion, while the ACC and ATA haplotypes produced intermediate and low levels of IL-10, respectively. Our data suggest that ADE effects are cell type specific, are influenced by host genetics, and, depending on relative infection rates, may further contribute to the complexity of DV pathogenesis.
The Epstein-Barr Virus-Encoded BILF1 Protein Modulates Immune Recognition of Endogenously Processed Antigen by Targeting Major Histocompatibility Complex Class I Molecules Trafficking on both the Exocytic and Endocytic Pathways
Authors: Zuo Jianmin , Quinn Laura L. , Tamblyn Jennifer , Thomas Wendy A. , Feederle Regina , Delecluse Henri-Jacques , Hislop Andrew D. , Rowe Martin
Published: December 2010

Despite triggering strong immune responses, Epstein-Barr virus (EBV) has colonized more than 90% of the adult human population. Successful persistence of EBV depends on the establishment of a balance between host immune responses and viral immune evasion. Here we have extended our studies on the EBV-encoded BILF1 protein, which was recently identified as an immunoevasin that functions by enhancing degradation of major histocompatibility complex class I (MHC-I) antigens via lysosomes. We now demonstrate that disruption of the EKT signaling motif of BILF1 by a K122A mutation impairs the ability of BILF1 to enhance endocytosis of surface MHC-I molecules, while subsequent lysosomal degradation was impaired by deletion of the 21-residue C-terminal tail of BILF1. Furthermore, we identified another mechanism of BILF1 immunomodulation: it targets newly synthesized MHC-I/peptide complexesen routeto the cell surface. Importantly, although the diversion of MHC-I on the exocytic pathway caused a relatively modest reduction in cell surface MHC-I, presentation of endogenously processed target peptides to immune CD8+effector T cells was reduced by around 65%. The immune-modulating functions of BILF1 in the context of the whole virus were confirmed in cells lytically infected with a recombinant EBV in whichBILF1was deleted. This study therefore extends our initial observations on BILF1 to show that this immunoevasin can target MHC-I antigen presentation via both the exocytic and endocytic trafficking pathways. The results also emphasize the merits of including functional T cell recognition assays to gain a more complete picture of immunoevasin effects on the antigen presentation pathway.
NP Body Domain and PB2 Contribute to Increased Virulence of H5N1 Highly Pathogenic Avian Influenza Viruses in Chickens
Authors: Tada Tatsuya , Suzuki Koutaro , Sakurai Yu , Kubo Masanori , Okada Hironao , Itoh Toshihiro , Tsukamoto Kenji
Published: December 2010

The molecular basis of pathogenicity of H5N1 highly pathogenic avian influenza (HPAI) viruses in chickens remains largely unknown. H5N1 A/chicken/Yamaguchi/7/2004 virus (CkYM7) replicates rapidly in macrophages and vascular endothelial cells in chickens, causing sudden death without fever or gross lesions, while H5N1 A/duck/Yokohama/aq10/2003 virus (DkYK10) induces high fever, severe gross lesions, and a prolonged time to death, despite the 98% amino acid identity between the two viruses. To explore the molecular basis of this difference in pathogenicity, a series of eight single-gene reassortant viruses from these HPAI viruses were compared for pathogenicity in chickens. Two reassortants possessing the NP or PB2 gene from DkYK10 in the CkYM7 background reduced pathogenicity compared to other reassortants or CkYM7. Inversely, reassortants possessing the NP or PB2 gene of CkYM7 in the DkYK10 background (rgDkYK-PB2
Ck
, rgDkYK-NP
Ck
) replicated quickly and reached higher titers than DkYK10, accompanied by more rapid and frequent apoptosis of macrophages. The rgDkYK-NP
Ck
and rgDkYK-PB2
Ck
reassortants also replicated more rapidly in chicken embryo fibroblasts (CEFs) than did rgDkYK10, but replication of these viruses was similar to that of CkYM7 and DkYK10 in duck embryo fibroblasts. A comparison of pathogenicities of seven rgDkYK10 mutants with a single amino acid substitution in NP
Dk
demonstrated that valine at position 105 in the NP
Ck
was responsible for the increased pathogenicity in chickens. NP
Ck
, NP
105V
, and PB2
Ck
enhanced the polymerase activity of DkYK10 in CEFs. These results indicate that both NP and PB2 contribute to the high pathogenicity of the H5N1 HPAI viruses in chickens, and valine at position 105 of NP may be one of the determinants for adaptation of avian influenza viruses from ducks to chickens.
Structure-Function Analyses Point to a Polynucleotide-Accommodating Groove Essential for APOBEC3A Restriction Activities
Authors: Bulliard Yannick , Narvaiza Iñigo , Bertero Alessandro , Peddi Shyam , Röhrig Ute F. , Ortiz Millán , Zoete Vincent , Castro-Díaz Nataly , Turelli Priscilla , Telenti Amalio , Michielin Olivier , Weitzman Matthew D. , Trono Didier
Published: December 2010

Members of the human APOBEC3 family of editing enzymes can inhibit various mobile genetic elements. APOBEC3A (A3A) can block the retrotransposon LINE-1 and the parvovirus adeno-associated virus type 2 (AAV-2) but does not inhibit retroviruses. In contrast, APOBEC3G (A3G) can block retroviruses but has only limited effects on AAV-2 or LINE-1. What dictates this differential target specificity remains largely undefined. Here, we modeled the structure of A3A based on its homology with the C-terminal domain of A3G and further compared the sequence of human A3A to those of 11 nonhuman primate orthologues. We then used these data to perform a mutational analysis of A3A, examining its ability to restrict LINE-1, AAV-2, and foreign plasmid DNA and to edit a single-stranded DNA substrate. The results revealed an essential functional role for the predicted single-stranded DNA-docking groove located around the A3A catalytic site. Within this region, amino acid differences between A3A and A3G are predicted to affect the shape of the polynucleotide-binding groove. Correspondingly, transferring some of these A3A residues to A3G endows the latter protein with the ability to block LINE-1 and AAV-2. These results suggest that the target specificity of APOBEC3 family members is partly defined by structural features influencing their interaction with polynucleotide substrates.
Matrix Domain Modulates HIV-1 Gag's Nucleic Acid Chaperone Activity via Inositol Phosphate Binding
Authors: Jones Christopher P. , Datta Siddhartha A. K. , Rein Alan , Rouzina Ioulia , Musier-Forsyth Karin
Published: December 2010

Retroviruses replicate by reverse transcribing their single-stranded RNA genomes into double-stranded DNA using specific cellular tRNAs to prime cDNA synthesis. In HIV-1, human tRNA
3
Lys
serves as the primer and is packaged into virions during assembly. The viral Gag protein is believed to chaperone tRNA
3
Lys
placement onto the genomic RNA primer binding site; however, the timing and possible regulation of this event are currently unknown. Composed of the matrix (MA), capsid (CA), nucleocapsid (NC), and p6 domains, the multifunctional HIV-1 Gag polyprotein orchestrates the highly coordinated process of virion assembly, but the contribution of these domains to tRNA
3
Lys
annealing is unclear. Here, we show that NC is absolutely essential for annealing and that the MA domain inhibits Gag's tRNA annealing capability. During assembly, MA specifically interacts with inositol phosphate (IP)-containing lipids in the plasma membrane (PM). Surprisingly, we find that IPs stimulate Gag-facilitated tRNA annealing but do not stimulate annealing in Gag variants lacking the MA domain or containing point mutations involved in PM binding. Moreover, we find that IPs prevent MA from binding to nucleic acids but have little effect on NC or Gag. We propose that Gag binds to RNA either with both NC and MA domains or with NC alone and that MA-IP interactions alter Gag's binding mode. We propose that MA's interactions with the PM trigger the switch between these two binding modes and stimulate Gag's chaperone function, which may be important for the regulation of events such as tRNA primer annealing.
Foamy Retrovirus Integrase Contains a Pol Dimerization Domain Required for Protease Activation
Authors: Lee Eun-Gyung , Roy Jacqueline , Jackson Dana , Clark Patrick , Boyer Paul L. , Hughes Stephen H. , Linial Maxine L.
Published: December 2010

Unlike orthoretroviruses, foamy retroviruses (FV) synthesize Pol independently of Gag. The FV Pol precursor is cleaved only once between reverse transcriptase (RT) and integrase (IN) by the protease (PR), resulting in a PR-RT and an IN protein. Only the Pol precursor, not the cleaved subunits, is packaged into virions. Like orthoretroviral PRs, FV PR needs to dimerize to be active. Previously, we showed that a Pol mutant lacking IN has defects in PR activity and Pol packaging into virions. We now show that introduction of a leucine zipper (zip) dimerization motif in an IN truncation mutant can restore PR activity, leading to Pol processing in cells. However, these zip mutants neither cleave Gag nor incorporate Pol into virions. We propose that IN is required for Pol dimerization, which is necessary for the creation of a functional PR active site.
The 5′ and 3′ Downstream AUG Region Elements Are Required for Mosquito-Borne Flavivirus RNA Replication
Authors: Friebe Peter , Shi Pei-Yong , Harris Eva
Published: December 2010

Flaviviruses require complementarity between the 5′ and 3′ ends of the genome for RNA replication. For mosquito-borne flaviviruses, the cyclization sequences (CS) and upstream of AUG region (UAR) elements at the genomic termini are necessary for viral RNA replication, and a third motif, the downstream of AUG region (DAR), was recently designated for dengue virus. The 3′ DAR sequence is also part of a hairpin (HP-3′SL), and both complementarity between 5′ and 3′ DAR motifs and formation of the HP-3′SL in the absence of the 5′ end are conserved among mosquito-borne flaviviruses. Using West Nile virus as a model, we demonstrate that 5′-3′ DAR complementarity and HP-3′SL formation are essential for viral RNA replication.
Human Papillomavirus Type 16 (HPV-16) Genomes Integrated in Head and Neck Cancers and in HPV-16-Immortalized Human Keratinocyte Clones Express Chimeric Virus-Cell mRNAs Similar to Those Found in Cervical Cancers
Authors: Lace Michael J. , Anson James R. , Klussmann Jens P. , Wang Dong Hong , Smith Elaine M. , Haugen Thomas H. , Turek Lubomir P.
Published: December 2010

Many human papillomavirus (HPV)-positive high-grade lesions and cancers of the uterine cervix harbor integrated HPV genomes expressing the E6 and E7 oncogenes from chimeric virus-cell mRNAs, but less is known about HPV integration in head and neck cancer (HNC). Here we compared viral DNA status and E6-E7 mRNA sequences in HPV-16-positive HNC tumors to those in independent human keratinocyte cell clones derived from primary tonsillar or foreskin epithelia immortalized with HPV-16 genomes. Three of nine HNC tumors and epithelial clones containing unintegrated HPV-16 genomes expressed mRNAs spliced from HPV-16 SD880 to SA3358 and terminating at the viral early gene p(A) signal. In contrast, most integrated HPV genomes in six HNCs and a set of 31 keratinocyte clones expressed HPV-16 major early promoter (MEP)-initiated mRNAs spliced from viral SD880 directly to diverse cellular sequences, with a minority spliced to SA3358 followed by a cellular DNA junction. Sequence analysis of chimeric virus-cell mRNAs from HNC tumors and keratinocyte clones identified viral integration sites in a variety of chromosomes, with some located in or near growth control genes, including the c-
myc
protooncogene and the gene encoding FAP-1 phosphatase. Taken together, these findings support the hypothesis that HPV integration in cancers is a stochastic process resulting in clonal selection of aggressively expanding cells with altered gene expression of integrated HPV genomes and potential perturbations of cellular genes at or near viral integration sites. Furthermore, our results demonstrate that this selection also takes place and can be studied in primary human keratinocytes in culture.
Rescue from Cloned cDNAs and
In Vivo
Characterization of Recombinant Pathogenic Romero and Live-Attenuated Candid #1 Strains of Junin Virus, the Causative Agent of Argentine Hemorrhagic Fever Disease
Authors: Emonet Sebastien F. , Seregin Alexey V. , Yun Nadezhda E. , Poussard Allison L. , Walker Aida G. , de la Torre Juan C. , Paessler Slobodan
Published: December 2010

The New World arenavirus Junin virus (JUNV) is the causative agent of Argentine hemorrhagic fever (AHF), which is associated with high morbidity and significant mortality. Several pathogenic strains of JUNV have been documented, and a highly attenuated vaccine strain (Candid #1) was generated and used to vaccinate the human population at risk. The identification and functional characterization of viral genetic determinants associated with AHF and Candid #1 attenuation would contribute to the elucidation of the mechanisms contributing to AHF and the development of better vaccines and therapeutics. To this end, we used reverse genetics to rescue the pathogenic Romero and the attenuated Candid #1 strains of JUNV from cloned cDNAs. Both recombinant Candid #1 (rCandid #1) and Romero (rRomero) had the same growth properties and phenotypic features in cultured cells and
in vivo
as their corresponding parental viruses. Infection with rRomero caused 100% lethality in guinea pigs, whereas rCandid #1 infection was asymptomatic and provided protection against a lethal challenge with Romero. Notably, Romero and Candid #1
trans
-acting proteins, L and NP, required for virus RNA replication and gene expression were exchangeable in a minigenome rescue assay. These findings support the feasibility of studies aimed at determining the contribution of each viral gene to JUNV pathogenesis and attenuation. In addition, we rescued Candid #1 viruses with three segments that efficiently expressed foreign genes introduced into their genomes. This finding opens the way for the development of a safe multivalent arenavirus vaccine.
Export of Adenoviral Late mRNA from the Nucleus Requires the Nxf1/Tap Export Receptor
Authors: Yatherajam Gayatri , Huang Wenying , Flint S. J.
Published: December 2010

One important function of the human adenovirus E1B 55-kDa protein is induction of selective nuclear export of viral late mRNAs. This protein interacts with the viral E4 Orf6 and four cellular proteins to form an infected-cell-specific E3 ubiquitin ligase. The assembly of this enzyme is required for efficient viral late mRNA export, but neither the relevant substrates nor the cellular pathway that exports viral late mRNAs has been identified. We therefore examined the effects on viral late gene expression of inhibition of the synthesis or activity of the mRNA export receptor Nxf1, which was observed to colocalize with the E1B 55-kDa protein in infected cells. When production of Nxf1 was impaired by using RNA interference, the efficiency of viral late mRNA export was reduced to a corresponding degree. Furthermore, synthesis of a dominant-negative derivative of Nxf1 during the late phase of infection interfered with production of a late structural protein. These observations indicate that the Nxf1 pathway is responsible for export of viral late mRNAs. As the infected-cell-specific E3 ubiquitin ligase targets its known substrates for proteasomal degradation, we compared the concentrations of several components of this pathway (Nxf1, Thox1, and Thoc4) in infected cells that did or did not contain this enzyme. Although the concentration of a well-established substrate, Mre11, decreased significantly in cells infected by adenovirus type 5 (Ad5), but not in those infected by the E1B 55-kDa protein-null mutant Hr6, no E1B 55-kDa protein-dependent degradation of the Nxf1 pathway proteins was observed.
The Adenovirus E1b55K/E4orf6 Complex Induces Degradation of the Bloom Helicase during Infection
Authors: Orazio Nicole I. , Naeger Colleen M. , Karlseder Jan , Weitzman Matthew D.
Published: December 2010

The adenovirus (Ad) E1b55K and E4orf6 gene products assemble an E3 ubiquitin ligase complex that promotes degradation of cellular proteins. Among the known substrates are p53 and the Mre11-Rad50-Nbs1 (MRN) complex. Since members of the RecQ helicase family function together with MRN in genome maintenance, we investigated whether adenovirus affects RecQ proteins. We show that Bloom helicase (BLM) is degraded during adenovirus type 5 (Ad5) infection. BLM degradation is mediated by E1b55K/E4orf6 but is independent of MRN. We detected BLM localized at discrete foci around viral replication centers. These studies identify BLM as a new substrate for degradation by the adenovirus E1b55K/E4orf6 complex.
Crucial Role for Prion Protein Membrane Anchoring in the Neuroinvasion and Neural Spread of Prion Infection
Authors: Klingeborn Mikael , Race Brent , Meade-White Kimberly D. , Rosenke Rebecca , Striebel James F. , Chesebro Bruce
Published: December 2010

In nature prion diseases are usually transmitted by extracerebral prion infection, but clinical disease results only after invasion of the central nervous system (CNS). Prion protein (PrP), a host-encoded glycosylphosphatidylinositol (GPI)-anchored membrane glycoprotein, is necessary for prion infection and disease. Here, we investigated the role of the anchoring of PrP on prion neuroinvasion by studying various inoculation routes in mice expressing either anchored or anchorless PrP. In control mice with anchored PrP, intracerebral or sciatic nerve inoculation resulted in rapid CNS neuroinvasion and clinical disease (154 to 156 days), and after tongue, ocular, intravenous, or intraperitoneal inoculation, CNS neuroinvasion was only slightly slower (193 to 231 days). In contrast, in anchorless PrP mice, these routes resulted in slow and infrequent CNS neuroinvasion. Only intracerebral inoculation caused brain PrPres, a protease-resistant isoform of PrP, and disease in both types of mice. Thus, anchored PrP was an essential component for the rapid neural spread and CNS neuroinvasion of prion infection.
MAGNETIC PROPERTIES OF THE Dy1-xUxCo3 SYSTEM
Authors: LUPŞA ILEANA , PETRIŞOR T. , BALASZ-MUREŞAN I.
Published: December 2010

The magnetic properties of Dy 1-x U x Co 3 system were investigated in the 4.3–1150 K temperature range and magnetic field up to 120 kOe. The crystalline structure is rhombohedral of PuNi 3 type. For x≤0.8, the samples exhibit a ferrimagnetic behavior. The uranium substitution for dysprosium leads to the decreasing of the exchange field and the reducing of the magnetization and the transition temperatures. The Co mean moments (1.9μB/ Co for x=0) opposite to the dysprosium ones and the mean effective Co moments (3.75μB/ Co for x=0) are gradually decreasing as Dy is replaced by uranium.
PREPARATION OF LUMINESCENT PbWO4 MICROCRYSTALS WITH HIERARCHICAL STRUCTURES BY USING MICROWAVE IRRADIATION HEATING METHOD
Authors: WAN GENGPING , WANG GUIZHEN
Published: December 2010

Lead tungstate ( PbWO 4) microcrystals with hierarchical structures have been successfully synthesized via a facile microwave irradiation heating method. The cetyltrimethylammonium bromine (CTAB) and microwave-heated power were found to play an important role in the morphological control of resulting PbWO 4 mirocrystals. The products were characterized by the techniques of powder X-ray diffraction and field-emission scanning electron microscopy. A growth mechanism of PbWO 4 microstructures was proposed. The luminescence properties of the final products were investigated and the as-prepared PbWO 4 microcrystals displayed a very unique room-temperature photoluminescence compared to the reported results.
Culture, Mind, and the Brain: Current Evidence and Future Directions
Authors: Kitayama Shinobu , Uskul Ayse K.
Published: December 2010

Current research on culture focuses on independence and interdependence and documents numerous East-West psychological differences, with an increasing emphasis placed on cognitive mediating mechanisms. Lost in this literature is a time-honored idea of culture as a collective process composed of cross-generationally transmitted values and associated behavioral patterns (i.e., practices). A new model of neuro-culture interaction proposed here addresses this conceptual gap by hypothesizing that the brain serves as a crucial site that accumulates effects of cultural experience, insofar as neural connectivity is likely modified through sustained engagement in cultural practices. Thus, culture is “embrained,” and moreover, this process requires no cognitive mediation. The model is supported in a review of empirical evidence regarding (a) collective-level factors involved in both production and adoption of cultural values and practices and (b) neural changes that result from engagement in cultural practices. Future directions of research on culture, mind, and the brain are discussed.
The Neural Bases of Social Cognition and Story Comprehension
Authors: Mar Raymond A.
Published: December 2010

A great deal of research exists on the neural basis of theory-of-mind (ToM) or mentalizing. Qualitative reviews on this topic have identified a mentalizing network composed of the medial prefrontal cortex, posterior cingulate/precuneus, and bilateral temporal parietal junction. These conclusions, however, are not based on a quantitative and systematic approach. The current review presents a quantitative meta-analysis of neuroimaging studies pertaining to ToM, using the activation-likelihood estimation (ALE) approach. Separate ALE meta-analyses are presented for story-based and nonstory-based studies of ToM. The conjunction of these two meta-analyses reveals a core mentalizing network that includes areas not typically noted by previous reviews. A third ALE meta-analysis was conducted with respect to story comprehension in order to examine the relation between ToM and stories. Story processing overlapped with many regions of the core mentalizing network, and these shared regions bear some resemblance to a network implicated by a number of other processes.
Psychological Science on Pregnancy: Stress Processes, Biopsychosocial Models, and Emerging Research Issues
Authors: Dunkel Schetter Christine
Published: December 2010

Psychological science on pregnancy is advancing rapidly. A major focus concerns stress processes in pregnancy and effects on preterm birth and low birth weight. The current evidence points to pregnancy anxiety as a key risk factor in the etiology of preterm birth, and chronic stress and depression in the etiology of low birth weight. Key mediating processes to which these effects are attributed, that is neuroendocrine, inflammatory, and behavioral mechanisms, are examined briefly and research on coping with stress in pregnancy is examined. Evidence regarding social support and birth weight is also reviewed with attention to research gaps regarding mechanisms, partner relationships, and cultural influences. The neurodevelopmental consequences of prenatal stress are highlighted, and resilience resources among pregnant women are conceptualized. Finally, a multilevel theoretical approach for the study of pregnancy anxiety and preterm birth is presented to stimulate future research.
The Development of Problem Solving in Young Children: A Critical Cognitive Skill
Authors: Keen Rachel
Published: December 2010

Problem solving is a signature attribute of adult humans, but we need to understand how this develops in children. Tool use is proposed as an ideal way to study problem solving in children less than 3 years of age because overt manual action can reveal how the child plans to achieve a goal. Motor errors are as informative as successful actions. Research is reviewed on intentional actions, beginning with block play and progressing to picking up a spoon in different orientations, and finally retrieving objects with rakes and from inside tubes. Behavioral and kinematic measures of motor action are combined to show different facets of skill acquisition and mastery. We need to design environments that encourage and enhance problem solving from a young age. One goal of this review is to excite interest and spur new research on the beginnings of problem solving and its elaboration during development.
A Taxonomy of External and Internal Attention
Authors: Chun Marvin M. , Golomb Julie D. , Turk-Browne Nicholas B.
Published: December 2010

Attention is a core property of all perceptual and cognitive operations. Given limited capacity to process competing options, attentional mechanisms select, modulate, and sustain focus on information most relevant for behavior. A significant problem, however, is that attention is so ubiquitous that it is unwieldy to study. We propose a taxonomy based on the types of information that attention operates over—the targets of attention. At the broadest level, the taxonomy distinguishes between external attention and internal attention. External attention refers to the selection and modulation of sensory information. External attention selects locations in space, points in time, or modality-specific input. Such perceptual attention can also select features defined across any of these dimensions, or object representations that integrate over space, time, and modality. Internal attention refers to the selection, modulation, and maintenance of internally generated information, such as task rules, responses, long-term memory, or working memory. Working memory, in particular, lies closest to the intersection between external and internal attention. The taxonomy provides an organizing framework that recasts classic debates, raises new issues, and frames understanding of neural mechanisms.
Thirty Years and Counting: Finding Meaning in the N400 Component of the Event-Related Brain Potential (ERP)
Authors: Kutas Marta , Federmeier Kara D.
Published: December 2010

We review the discovery, characterization, and evolving use of the N400, an event-related brain potential response linked to meaning processing. We describe the elicitation of N400s by an impressive range of stimulus types—including written, spoken, and signed words or pseudowords; drawings, photos, and videos of faces, objects, and actions; sounds; and mathematical symbols—and outline the sensitivity of N400 amplitude (as its latency is remarkably constant) to linguistic and nonlinguistic manipulations. We emphasize the effectiveness of the N400 as a dependent variable for examining almost every aspect of language processing and highlight its expanding use to probe semantic memory and to determine how the neurocognitive system dynamically and flexibly uses bottom-up and top-down information to make sense of the world. We conclude with different theories of the N400's functional significance and offer an N400-inspired reconceptualization of how meaning processing might unfold.