bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of N-Linked Glycosylation for Sindbis Virus Infection and Replication in Vertebrate and Invertebrate Systems
Authors: Knight Ronald L. , Schultz Kimberly L. W. , Kent Rebekah J. , Venkatesan Meera , Griffin Diane E. 
Published: March 2009

ABSTRACT

Each Sindbis virus (SINV) surface glycoprotein has two sites for N-linked glycosylation (E1 positions 139 and 245 [E1-139 and E1-245] and E2 positions 196 and 318 [E2-196 and E2-318]). Studies of SINV strain TE12 mutants with each site eliminated identified the locations of carbohydrates by cryo-electron microscopy (S. V. Pletnev et al., Cell 105:127-136, 2001). In the current study, the effects of altered glycosylation on virion infectivity, growth in cells of vertebrates and invertebrates, heparin binding, virulence in mice, and replication in mosquitoes were assessed. Particle-to-PFU ratios for E1-139 and E2-196 mutant strains were similar to that for TE12, but this ratio for the E1-245 mutant was 100-fold lower than that for TE12. Elimination of either E2 glycosylation site increased virus binding to heparin and increased replication in BHK cells. Elimination of either E1 glycosylation site had no effect on heparin binding but resulted in an approximately 10-fold decrease in virus yield from BHK cells compared to the TE12 amount. No differences in pE2 processing were detected. E2-196 and E2-318 mutants were more virulent in mice after intracerebral inoculation, while E1-139 and E1-245 mutants were less virulent. The E1-245 mutant showed impaired replication in C7/10 mosquito cells and in
Culex quinquefasciatus
after intrathoracic inoculation. We conclude that the increased replication and virulence of E2-196 and E2-318 mutants are primarily due to increased efficiency of binding to heparan sulfate on mammalian cells. Lack of glycosylation at E1-139 or E1-245 impairs replication in vertebrate cells, while E1-245 also severely affects replication in invertebrate cells.
Cell-to-Cell Spread of the RNA Interference Response Suppresses Semliki Forest Virus (SFV) Infection of Mosquito Cell Cultures and Cannot Be Antagonized by SFV
Authors: Attarzadeh-Yazdi Ghassem , Fragkoudis Rennos , Chi Yi , Siu Ricky W. C. , Ülper Liane , Barry Gerald , Rodriguez-Andres Julio , Nash Anthony A. , Bouloy Michèle , Merits Andres , Fazakerley John K. , Kohl Alain 
Published: March 2009

ABSTRACT

In their vertebrate hosts, arboviruses such as Semliki Forest virus (SFV) (
Togaviridae
) generally counteract innate defenses and trigger cell death. In contrast, in mosquito cells, following an early phase of efficient virus production, a persistent infection with low levels of virus production is established. Whether arboviruses counteract RNA interference (RNAi), which provides an important antiviral defense system in mosquitoes, is an important question. Here we show that in
Aedes albopictus
-derived mosquito cells, SFV cannot prevent the establishment of an antiviral RNAi response or prevent the spread of protective antiviral double-stranded RNA/small interfering RNA (siRNA) from cell to cell, which can inhibit the replication of incoming virus. The expression of tombusvirus siRNA-binding protein p19 by SFV strongly enhanced virus spread between cultured cells rather than virus replication in initially infected cells. Our results indicate that the spread of the RNAi signal contributes to limiting virus dissemination.
Prion Protein Glycosylation Is Not Required for Strain-Specific Neurotropism
Authors: Piro Justin R. , Harris Brent T. , Nishina Koren , Soto Claudio , Morales Rodrigo , Rees Judy R. , Supattapone Surachai 
Published: March 2009

ABSTRACT

In this study, we tested the hypothesis that the glycosylation of the pathogenic isoform of the prion protein (PrP
Sc
) might encode the selective neurotropism of prion strains. We prepared unglycosylated cellular prion protein (PrP
C
) substrate molecules from normal mouse brain by treatment with PNGase F and used reconstituted serial protein cyclic misfolding amplification reactions to produce RML and 301C mouse prions containing unglycosylated PrP
Sc
molecules. Both RML- and 301C-derived prions containing unglycosylated PrP
Sc
molecules were infectious to wild-type mice, and neuropathological analysis showed that mice inoculated with these samples maintained strain-specific patterns of PrP
Sc
deposition and neuronal vacuolation. These results show that PrP
Sc
glycosylation is not necessary for strain-dependent prion neurotropism.
Identification of an Intercistronic Internal Ribosome Entry Site in a Marek's Disease Virus Immediate-Early Gene
Authors: Tahiri-Alaoui Abdessamad , Smith Lorraine P. , Baigent Suzan , Kgosana Lydia , Petherbridge Lawrence J. , Lambeth Luke S. , James William , Nair Venugopal 
Published: March 2009

ABSTRACT

In this study, we have identified an internal ribosome entry site (IRES) from the highly infectious herpesvirus Marek's disease virus (MDV). The IRES was mapped to the intercistronic region (ICR) of a bicistronic mRNA that we cloned from the MDV-transformed CD4
+
T-cell line MSB-1. The transcript is a member of a family of mRNAs expressed as immediate-early genes with two open reading frames (ORF). The first ORF encodes a 14-kDa polypeptide with two N-terminal splice variants, whereas the second ORF is contained entirely within a single exon and encodes a 12-kDa protein also known as RLORF9. We have shown that the ICR that separates the two ORFs functions as an IRES that controls the translation of RLORF9 when cap-dependent translation is inhibited. Deletion analysis revealed that there are two potential IRES elements within the ICR. Reverse genetic experiments with the oncogenic strain of MDV type 1 indicated that deletion of IRES-controlled RLORF9 does not significantly affect viral replication or MDV-induced mortality.
Cloud Variability over the Indian Monsoon Region as Observed from Satellites
Authors: Wonsick Margaret M. , Pinker Rachel T. , Govaerts Yves 
Published: March 2009

Abstract
This study focuses on documenting the seasonal progression of the Asian monsoon by analyzing clouds and convection in the pre-, peak-, and postmonsoon seasons. This effort was possible as a result of the movement of Meteosat-5 over the Indian continent during the Indian Ocean Experiment (INDOEX) starting in 1998. The Meteosat-5 observations provide a unique opportunity to study in detail the daytime diurnal variability of clouds and components of the radiation budget. Hourly Meteosat-5 observations are utilized to characterize the Indian monsoon daytime cloud variability on seasonal and diurnal time scales. Distinct patterns of variability can be identified during the various stages of the monsoon cycle. The daytime (0800–1500 LST) diurnal cycle of total cloud amounts is generally flat during the premonsoon season, U shaped during peak-monsoon season, and ascending toward an afternoon peak in the postmonsoon season. Low clouds dominate the Tibetan Plateau and northern Arabian Sea while high clouds are more frequent in the southern Bay of Bengal and Arabian Sea. An afternoon peak in high clouds is most prominent in central India and the Bay of Bengal. Afternoon convection peaks earlier over water than land. Preliminary comparison of cloud amounts from Meteosat-5, International Satellite Cloud Climatology Project (ISCCP) D1, and model output from the 40-yr ECMWF Re-Analysis (ERA-40) and the NCEP–NCAR reanalysis indicates a large disparity among cloud amounts from the various sources, primarily during the peak-monsoon period. The availability of the high spatial and temporal resolution of Meteosat-5 data is important for characterizing cloud variability in regions where clouds vary strongly in time and space and for the evaluation of numerical models known to have difficulties in predicting clouds correctly in this monsoon region. This study also has implications for findings on cloud variability from polar-orbiting satellites that might not correctly represent the daily average situation.
Comparative Evaluation of Two Ensembles for Long-Range Forecasting of Monsoon Rainfall
Authors: Goswami P. , Gouda K. C. 
Published: March 2009

Abstract
It is now well known that changes in initial conditions can give rise to substantial changes in the forecasts even at the long range. Ensemble averaging of forecasts from different initial conditions provides an efficient way of assessing and reducing uncertainties in the forecasts due to inherent uncertainties in the initial conditions. However, the procedure for generating the ensemble of forecasts has to be based on careful consideration. Although there now exist several well-tested frameworks for ensemble forecasting at the short range, the procedure for and impact of ensemble forecasting on long-range forecasting of monsoons remain relatively less explored. In particular, the procedure for the choice of the ensemble for long-range forecasting of monsoons needs special considerations. The Indian summer monsoon is characterized by a number of intraseasonal oscillations (ISOs) whose phases and amplitudes can significantly affect the monsoon forecast and that can be adequately sampled only using initial states spread over time scales comparable to the characteristic time scales of these ISOs. It is shown that use of initial states spread over a longer period (such as 1 April–1 May) results in a better ensemble average for long-range forecasting of Indian summer monsoon than that from an ensemble of closely packed states with a shorter lead. An optimized configuration for long-range forecasting of monsoons using a variable resolution general circulation model is adopted. The climatological monthly mean SST field is used to assess realizable skill, as use of observed SST provides only potential skill. Then five-member wide-lead (1 April–1 May) ensemble average forecasts are compared with five-member compact-lead (27 April–1 May) ensemble average forecasts for 24 (1980–2003) hindcasts; it is shown that the skill of the wide-lead ensemble average is superior to that of the compact-lead ensemble at different spatial and temporal scales in spite of the longer lead of the former.
How we treat cytomegalovirus in hematopoietic cell transplant recipients
Authors: Boeckh Michael , Ljungman Per 
Published: March 2009

AbstractCytomegalovirus (CMV) continues to cause major complications after hematopoietic cell transplantation (HCT). Over the past decade, most centers have adopted preemptive antiviral treatment or prophylaxis strategies to prevent CMV disease. Both strategies are effective but also have shortcomings with presently available drugs. Here, we review aspects of CMV treatment and prevention in HCT recipients, including currently used drugs and diagnostics, ways to optimize preemptive therapy strategies with quantitative polymerase chain reaction assays, the use of prophylaxis, management of CMV disease caused by wild-type or drug-resistant strains, and future strategies.
Digital PCR provides sensitive and absolute calibration for high throughput sequencing
Authors: White Richard A , Blainey Paul C , Fan H Christina , Quake Stephen R 
Published: March 2009

Abstract

Background
Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced. This requirement has two unfavorable consequences. First, large amounts of sample-typically micrograms-are needed for library preparation, thereby limiting the scope of samples which can be sequenced. For many applications, including metagenomics and the sequencing of ancient, forensic, and clinical samples, the quantity of input DNA can be critically limiting. Second, each library requires a titration sequencing run, thereby increasing the cost and lowering the throughput of sequencing.

Results
We demonstrate the use of digital PCR to accurately quantify 454 and Solexa sequencing libraries, enabling the preparation of sequencing libraries from nanogram quantities of input material while eliminating costly and time-consuming titration runs of the sequencer. We successfully sequenced low-nanogram scale bacterial and mammalian DNA samples on the 454 FLX and Solexa DNA sequencing platforms. This study is the first to definitively demonstrate the successful sequencing of picogram quantities of input DNA on the 454 platform, reducing the sample requirement more than 1000-fold without pre-amplification and the associated bias and reduction in library depth.

Conclusion
The digital PCR assay allows absolute quantification of sequencing libraries, eliminates uncertainties associated with the construction and application of standard curves to PCR-based quantification, and with a coefficient of variation close to 10%, is sufficiently precise to enable direct sequencing without titration runs.
The prevalence of BRCA1 mutations among young women with triple-negative breast cancer
Authors: Young SR , Pilarski Robert T , Donenberg Talia , Shapiro Charles , Hammond Lyn S , Miller Judith , Brooks Karen A , Cohen Stephanie , Tenenholz Beverly , DeSai Damini , Zandvakili Inuk , Royer Robert , Li Song , Narod Steven A 
Published: March 2009

Abstract

Background
Molecular screening for BRCA1 and BRCA2 mutations is now an established component of risk evaluation and management of familial breast cancer. Features of hereditary breast cancer include an early age-of-onset and over-representation of the 'triple-negative' phenotype (negative for estrogen-receptor, progesterone-receptor and HER2). The decision to offer genetic testing to a breast cancer patient is usually based on her family history, but in the absence of a family history of cancer, some women may qualify for testing based on the age-of-onset and/or the pathologic features of the breast cancer.

Methods
We studied 54 women who were diagnosed with high-grade, triple-negative invasive breast cancer at or before age 40. These women were selected for study because they had little or no family history of breast or ovarian cancer and they did not qualify for genetic testing using conventional family history criteria. BRCA1 screening was performed using a combination of fluorescent multiplexed-PCR analysis, BRCA1 exon-13 6 kb duplication screening, the protein truncation test (PTT) and fluorescent multiplexed denaturing gradient gel electrophoresis (DGGE). All coding exons of BRCA1 were screened. The two large exons of BRCA2 were also screened using PTT. All mutations were confirmed with direct sequencing.

Results
Five deleterious BRCA1 mutations and one deleterious BRCA2 mutation were identified in the 54 patients with early-onset, triple-negative breast cancer (11%).

Conclusion
Women with early-onset triple-negative breast cancer are candidates for genetic testing for BRCA1, even in the absence of a family history of breast or ovarian cancer.
Adenoviral vectors for highly selective gene expression in central serotonergic neurons reveal quantal characteristics of serotonin release in the rat brain
Authors: Benzekhroufa Kheira , Liu Beihui , Tang Feige , Teschemacher Anja G , Kasparov Sergey 
Published: March 2009

AbstractBackground5-hydroxytryptamine (5 HT, serotonin) is one of the key neuromodulators in mammalian brain, but many fundamental properties of serotonergic neurones and 5 HT release remain unknown. The objective of this study was to generate an adenoviral vector system for selective targeting of serotonergic neurones and apply it to study quantal characteristics of 5 HT release in the rat brain.ResultsWe have generated adenoviral vectors which incorporate a 3.6 kb fragment of the rat tryptophan hydroxylase-2 (TPH-2) gene which selectively (97% co-localisation with TPH-2) target raphe serotonergic neurones. In order to enhance the level of expression a two-step transcriptional amplification strategy was employed. This allowed direct visualization of serotonergic neurones by EGFP fluorescence. Using these vectors we have performed initial characterization of EGFP-expressing serotonergic neurones in rat organotypic brain slice cultures. Fluorescent serotonergic neurones were identified and studied using patch clamp and confocal Ca2+imaging and had features consistent with those previously reported using post-hoc identification approaches. Fine processes of serotonergic neurones could also be visualized in un-fixed tissue and morphometric analysis suggested two putative types of axonal varicosities. We used micro-amperometry to analyse the quantal characteristics of 5 HT release and found that central 5 HT exocytosis occurs predominantly in quanta of ~28000 molecules from varicosities and ~34000 molecules from cell bodies. In addition, in somata, we observed a minority of large release events discharging on average ~800000 molecules.ConclusionFor the first time quantal release of 5 HT from somato-dendritic compartments and axonal varicosities in mammalian brain has been demonstrated directly and characterised. Release from somato-dendritic and axonal compartments might have different physiological functions. Novel vectors generated in this study open a host of new experimental opportunities and will greatly facilitate further studies of the central serotonergic system.
Suppression of HIV-1 replication by microRNA effectors
Authors: Chable-Bessia Christine , Meziane Oussama , Latreille Daniel , Triboulet Robinson , Zamborlini Alessia , Wagschal Alexandre , Jacquet Jean-Marc , Reynes Jacques , Levy Yves , Saib Ali , Bennasser Yamina , Benkirane Monsef 
Published: March 2009

Abstract
The rate of HIV-1 gene expression is a key step that determines the kinetics of virus spread and AIDS progression. Viral entry and gene expression were described to be the key determinants for cell permissiveness to HIV. Recent reports highlighted the involvement of miRNA in regulating HIV-1 replication post-transcriptionally. In this study we explored the role of cellular factors required for miRNA-mediated mRNA translational inhibition in regulating HIV-1 gene expression. Here we show that HIV-1 mRNAs associate and co-localize with components of the RNA Induced Silencing Complex (RISC), and we characterize some of the proteins required for miRNA-mediated silencing (miRNA effectors). RCK/p54, GW182, LSm-1 and XRN1 negatively regulate HIV-1 gene expression by preventing viral mRNA association with polysomes. Interestingly, knockdown of RCK/p54 or DGCR8 resulted in virus reactivation in PBMCs isolated from HIV infected patients treated with suppressive HAART.
A randomized, double-blind, placebo-controlled pilot study of a probiotic in emotional symptoms of chronic fatigue syndrome
Authors: Rao A Venket , Bested Alison C , Beaulne Tracey M , Katzman Martin A , Iorio Christina , Berardi John M , Logan Alan C 
Published: March 2009

Abstract
Chronic fatigue syndrome (CFS) is complex illness of unknown etiology. Among the broad range of symptoms, many patients report disturbances in the emotional realm, the most frequent of which is anxiety. Research shows that patients with CFS and other so-called functional somatic disorders have alterations in the intestinal microbial flora. Emerging studies have suggested that pathogenic and non-pathogenic gut bacteria might influence mood-related symptoms and even behavior in animals and humans. In this pilot study, 39 CFS patients were randomized to receive either 24 billion colony forming units of Lactobacillus casei strain Shirota (LcS) or a placebo daily for two months. Patients provided stool samples and completed the Beck Depression and Beck Anxiety Inventories before and after the intervention. We found a significant rise in both Lactobacillus and Bifidobacteria in those taking the LcS, and there was also a significant decrease in anxiety symptoms among those taking the probiotic vs controls (p = 0.01). These results lend further support to the presence of a gut-brain interface, one that may be mediated by microbes that reside or pass through the intestinal tract.
Experimental investigation of sheet metal formability under various strain rates
Authors: Dariani B M , Liaghat G H , Gerdooei M 
Published: March 2009

Formability of sheet metals is often assessed by means of forming limit diagrams (FLD). In this paper, performing three different series of experiments, the effect of forming velocity on FLDs is investigated experimentally for Al 6061-T6 and AISI 1045 sheets. In addition to determining the conventional FLDs at quasi-static condition ( The results show that while a substantial improvement in high strain rate formability of the aluminium sheet can be obtained, this improvement is not considerable for the steel sheets. Also, under the effect of contact pressure between tool and sheet, the formability increases for both steel and aluminium sheets on impact.
Study of the delivery behaviour of a pump for common rail fuel injection equipment
Authors: Giuffrida A , Ficarella A , Laforgia D 
Published: March 2009

This work deals with the delivery flowrate of a radial piston pump for common rail fuel injection equipment. At first, attention is paid to the volumetric efficiency of the pump, presenting basic formulas and reviewing common theory. A new efficiency model is proposed and considerations regarding the pump running under large pressure differences between suction and delivery and variable driving speeds are formulated in order to realize difficulties in pump filling. Later, a numerical model simulating the working behaviour of the pump is used to investigate the effects of variable inlet pressures under high delivery pressure and different driving speeds. Comparisons between numerical results and experimental data referring to the delivery behaviour of the pump are reported, as well as in-cylinder pressure diagrams, necessary to realize filling deficiencies quickly. The flowrate delivered by the investigated pump depends on both the inlet and outlet pressures. Increasing the driving speed beyond certain values does not result in proportional flowrate at pump delivery.
Effects of friction modifiers on Pb-free plain bearing lubrication
Authors: Katafuchi T , Kasai M 
Published: March 2009

In order to improve fuel efficiency for automotive engines, decreasing oil viscosity and using friction modifiers (FMs) for engine oil have been widely used. On the other hand, the reduction of lead, which has been used for plain bearings in engines, is also advanced from the perspective of reducing environmental pollutants. Therefore, whether FMs contained in engine oil were effective even for lead-free plain bearings was investigated. In total, four kinds of bearing materials were tested. Two of them are Cu alloy on which Bi overlay was applied. Others are Al alloy on which Bi overlay was also applied. Two kinds of ashless FMs with and without sulphur were used as representatives of ashless ester-type FMs. As a result, the FMs with and without sulphur are effective, respectively, for Al alloy and Cu alloy plain bearings. They were also effective in preventing metal contact between the shaft and the plain bearing. This suggests that the interaction between the FM and the plain bearing material increased the oil film thickness between the shaft and the plain bearing.