bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ebolavirus Glycoprotein GP Masks both Its Own Epitopes and the Presence of Cellular Surface Proteins
Authors: Reynard Olivier , Borowiak Malgorzata , Volchkova Valentina A. , Delpeut Sebastien , Mateo Mathieu , Volchkov Viktor E. 
Published: July 2009

ABSTRACT
Ebolavirus (EBOV) is the etiological agent of a severe hemorrhagic fever with a high mortality rate. The spike glycoprotein (GP) is believed to be one of the major determinants of virus pathogenicity. In this study, we demonstrated the molecular mechanism responsible for the downregulation of surface markers caused by EBOV GP expression. We showed that expression of mature GP on the plasma membrane results in the masking of cellular surface proteins, including major histocompatibility complex class I. Overexpression of GP also results in the masking of certain antigenic epitopes on GP itself, causing an illusory effect of disappearance from the plasma membrane.
The Closest Relatives of Icosahedral Viruses of Thermophilic Bacteria Are among Viruses and Plasmids of the Halophilic Archaea
Authors: Jalasvuori Matti , Jaatinen Silja T. , Laurinavičius Simonas , Ahola-Iivarinen Elina , Kalkkinen Nisse , Bamford Dennis H. , Bamford Jaana K. H. 
Published: July 2009

ABSTRACTWe have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus P23-77 ofThermus thermophilus. P23-77 has an ∼17-kb circular double-stranded DNA genome, which was annotated to contain 37 putative genes. Virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. Analysis of the bacteriophage genome revealed it to be evolutionarily related to anotherThermusphage (IN93), archaealHalobacteriumplasmid (pHH205), a genetic element integrated intoHaloarculagenome (designated here as IHP for integratedHaloarculaprovirus), and theHaloarculavirus SH1. These genetic elements share two major capsid proteins and a putative packaging ATPase. The ATPase is similar with the ATPases found in the PRD1-type viruses, thus providing an evolutionary link to these viruses and furthering our knowledge on the origin of viruses.
Two Small RNAs Encoded within the First 1.5 Kilobases of the Herpes Simplex Virus Type 1 Latency-Associated Transcript Can Inhibit Productive Infection and Cooperate To Inhibit Apoptosis
Authors: Shen Wenwen , Sa e Silva Mariana , Jaber Tareq , Vitvitskaia Olga , Li Sumin , Henderson Gail , Jones Clinton 
Published: July 2009

ABSTRACT
The herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) is abundantly expressed in latently infected trigeminal ganglionic sensory neurons. Expression of the first 1.5 kb of LAT coding sequences is sufficient for the wild-type reactivation phenotype in small animal models of infection. The ability of the first 1.5 kb of LAT coding sequences to inhibit apoptosis is important for the latency-reactivation cycle. Several studies have also concluded that LAT inhibits productive infection. To date, a functional LAT protein has not been identified, suggesting that LAT is a regulatory RNA. Two small RNAs (sRNAs) were previously identified within the first 1.5 kb of LAT coding sequences. In this study, we demonstrated that both LAT sRNAs were expressed in the trigeminal ganglia of mice latently infected with an HSV-1 strain that expresses LAT but not when mice were infected with a LAT null mutant. LAT sRNA1 and sRNA2 cooperated to inhibit cold shock-induced apoptosis in mouse neuroblastoma cells. LAT sRNA1, but not LAT sRNA2, inhibited apoptosis less efficiently than both sRNAs. When rabbit skin cells were cotransfected with plasmids that express LAT sRNA1 and HSV-1 genomic DNA, the amount of infectious virus released was reduced approximately 3 logs. Although LAT sRNA2 was less effective at inhibiting virus production, it inhibited expression of infected cell protein 4 (ICP4). Neither LAT sRNA had an obvious effect on ICP0 expression. These studies suggested that expression of two LAT sRNAs plays a role in the latency-reactivation cycle by inhibiting apoptosis and productive infection.
Increased eIF2α Phosphorylation Attenuates Replication of Herpes Simplex Virus 2 vhs Mutants in Mouse Embryonic Fibroblasts and Correlates with Reduced Accumulation of the PKR Antagonist ICP34.5
Authors: Wylie Kristine M. , Schrimpf Jane E. , Morrison Lynda A. 
Published: July 2009

ABSTRACT
Herpes simplex virus 2 (HSV-2) strains containing mutations in the virion host shutoff (vhs) protein are attenuated for replication compared with wild-type virus in mouse embryonic fibroblasts (MEFs). However, HSV-2 vhs mutants replicate to near wild-type levels in the absence of the RNA-activated protein kinase (PKR). PKR is one of several kinases that phosphorylates the eukaryotic initiation factor 2α (eIF2α) to inhibit translation initiation, and we previously found that more of the phosphorylated form of eIF2α accumulates in MEFs infected with HSV-2 vhs mutants than with wild-type virus. Here, we show that this increase in phosphorylated eIF2α is primarily PKR dependent. Using MEFs expressing nonphosphorylatable eIF2α, we demonstrate that phosphorylated eIF2α is the primary cause of attenuated replication of HSV-2 vhs mutants and that attenuation correlates with decreased accumulation of viral proteins. Normally, HSV antagonizes eIF2α phosphorylation through the action of ICP34.5, which redirects protein phosphatase 1α (PP1α) to dephosphorylate eIF2α during infection. We show that ICP34.5 does not accumulate efficiently in MEFs infected with HSV-2 vhs mutant viruses, suggesting that the accumulation of phosphorylated eIF2α and the attenuated phenotype of HSV-2 vhs mutants in MEFs result from a deficiency in ICP34.5.
Impact of Cytotoxic-T-Lymphocyte Memory Induction without Virus-Specific CD4
+
T-Cell Help on Control of a Simian Immunodeficiency Virus Challenge in Rhesus Macaques
Authors: Tsukamoto Tetsuo , Takeda Akiko , Yamamoto Takuya , Yamamoto Hiroyuki , Kawada Miki , Matano Tetsuro 
Published: July 2009

ABSTRACT

Despite many efforts to develop AIDS vaccines eliciting virus-specific T-cell responses, whether induction of these memory T cells by vaccination before human immunodeficiency virus (HIV) exposure can actually contribute to effective T-cell responses postinfection remains unclear. In particular, induction of HIV-specific memory CD4
+
T cells may increase the target cell pool for HIV infection because the virus preferentially infects HIV-specific CD4
+
T cells. However, virus-specific CD4
+
helper T-cell responses are thought to be important for functional CD8
+
cytotoxic-T-lymphocyte (CTL) induction in HIV infection, and it has remained unknown whether HIV-specific memory CD8
+
T cells induced by vaccination without HIV-specific CD4
+
T-cell help can exert effective responses after virus exposure. Here we show the impact of CD8
+
T-cell memory induction without virus-specific CD4
+
T-cell help on the control of a simian immunodeficiency virus (SIV) challenge in rhesus macaques. We developed a prophylactic vaccine by using a Sendai virus (SeV) vector expressing a single SIV Gag
241-249
CTL epitope fused with enhanced green fluorescent protein (EGFP). Vaccination resulted in induction of SeV-EGFP-specific CD4
+
T-cell and Gag
241-249
-specific CD8
+
T-cell responses. After a SIV challenge, the vaccinees showed dominant Gag
241-249
-specific CD8
+
T-cell responses with higher effector memory frequencies in the acute phase and exhibited significantly reduced viral loads. These results demonstrate that virus-specific memory CD8
+
T cells induced by vaccination without virus-specific CD4
+
T-cell help could indeed facilitate SIV control after virus exposure, indicating the benefit of prophylactic vaccination eliciting virus-specific CTL memory with non-virus-specific CD4
+
T-cell responses for HIV control.
Insight into Poliovirus Genome Replication and Encapsidation Obtained from Studies of 3B-3C Cleavage Site Mutants
Authors: Oh Hyung Suk , Pathak Harsh B. , Goodfellow Ian G. , Arnold Jamie J. , Cameron Craig E. 
Published: July 2009

ABSTRACT

A poliovirus (PV) mutant (termed GG), which is incapable of producing 3AB, VPg, and 3CD proteins due to a defective cleavage site between the 3B and 3C proteins, replicated, producing 3BC-linked RNA rather than the VPg-linked RNA produced by the wild type (WT). GG PV RNA is quasi-infectious. The yield of infectious GG PV relative to replicated RNA is reduced by almost 5 logs relative to that of WT PV. Proteolytic activity required for polyprotein processing is normal for the GG mutant. 3BC-linked RNA can be encapsidated as efficiently as VPg-linked RNA. However, a step after genome replication but preceding virus assembly that is dependent on 3CD and/or 3AB proteins limits production of infectious GG PV. This step may involve release of replicated genomes from replication complexes. A pseudorevertant (termed EG) partially restored cleavage at the 3B-3C cleavage site. The reduced rate of formation of 3AB and 3CD caused corresponding reductions in the observed rate of genome replication and infectious virus production by EG PV without impacting the final yield of replicated RNA or infectious virus relative to that of WT PV. Using EG PV, we showed that genome replication and encapsidation were distinct steps in the multiplication cycle. Ectopic expression of 3CD protein reversed the genome replication phenotype without alleviating the infectious-virus production phenotype. This is the first report of a
trans
-complementable function for 3CD for any picornavirus. This observation supports an interaction between 3CD protein and viral and/or host factors that is critical for genome replication, perhaps formation of replication complexes.
Effects of symbiotic bacteria and tree chemistry on the growth and reproduction of bark beetle fungal symbionts
Authors: Adams A.S. , Currie C.R. , Cardoza Y. , Klepzig K.D. , Raffa K.F. 
Published: July 2009

Bark beetles are associated with diverse assemblages of microorganisms, many of which affect their interactions with host plants and natural enemies. We tested how bacterial associates of three bark beetles with various types of host relationships affect growth and reproduction of their symbiotic fungi. Fungi were exposed to volatiles from bacteria in an arena that imposed physical separation but shared airspace. We also exposed fungi to vapors of the host compound, α-pinene, and to combinations of bacterial volatiles and α-pinene. Bacterial volatiles commonly stimulated growth of Leptographium procerum (W.B. Kendr.) M.J. Wingf. and Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & Wingf., which are symbiotic fungi of Dendroctonus valens LeConte and Dendroctonus ponderosae Hopkins, respectively. They less commonly stimulated growth of Ophiostoma ips (Rumbold) Nannf., which is associated with Ips grandicollis Eichhoff. Some bacteria inhibited L. procerum, Ophiostoma montium (Rumbold) von Arx (another associate of D. ponderosae), and O. ips. Bacteria greatly stimulated spore production of symbionts of D. valens and D. ponderosae. α-Pinene strongly affected some of these relationships, causing amplification, reduction, or reversal of the interactions among the bacteria and fungi. Our results show that some bacteria associated with bark beetles directly affect fungal symbionts and interact with tree chemistry to affect fungal growth and sporulation. The strongest effects were induced by bacteria associated with beetles adapted to attacking living trees with vigorous defenses, and on fungal reproductive structures.
Tree growth at stand and individual scales in two dual-species mixture experiments in southern Washington State, USA
Authors: Erickson Heather E. , Harrington Constance A. , Marshall David D. 
Published: July 2009

Planting with mixtures of tree species rather than single species is often considered during reforestation because of the potential increased productivity and other benefits. We examined tree growth at the stand and individual tree scales in two experiments contrasting monocultures with a 1:1 mixture of tree species: (1) Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) with a conifer of similar shade tolerance (western white pine ( Pinus monticola Dougl. ex D. Don)) and (2) Douglas-fir with a more shade-tolerant conifer (western hemlock ( Tsuga heterophylla (Raf.) Sarg.)). There was no effect of mixture on growth or yield in the Douglas-fir – western white pine combination. In the Douglas-fir – western hemlock combination, yields in the mixture equaled those in Douglas-fir stands because of the enhanced performance of Douglas-fir in the mixture. For Douglas-fir, the height/diameter (h/d) ratio was significantly less in mixture, suggesting reduced competition for light when grown with western hemlock. In contrast, the h/d ratio for western hemlock was significantly greater in mixture, suggesting increased competition for light when grown with Douglas-fir. Neighborhood analyses showed that tree growth was directly related to initial size and inversely related to relative neighbor size and that the h/d ratio was positively related to relative neighbor size. In general, the size of a neighboring tree influenced growth more than species identity. Relationships between h/d ratios and growth rates suggest that growth differences between Douglas-fir and western hemlock in mixture will eventually increase.
Fire regimes of the piñon–juniper woodlands of Big Bend National Park and the Davis Mountains, west Texas, USA
Authors: Poulos H.M. , Gatewood R.G. , Camp A.E. 
Published: July 2009

While piñon woodlands cover much of arid North America, surprisingly little is known about the role of fire in maintaining piñon forest structure and species composition. The lack of region-specific fire regime data for piñon–juniper woodlands presents a roadblock to managers striving to implement process-based management. This study characterized piñon–juniper fire regimes and forest stand dynamics in Big Bend National Park (BIBE) and the Davis Mountains Preserve of the Nature Conservancy (DMTNC) in west Texas. Mean fire return intervals were 36.5 and 11.2 years for BIBE and DMTNC, respectively. Point fire return intervals were 150 years at BIBE and 75 years at DMTNC. Tree regeneration in west Texas piñon–juniper woodlands occurred historically during favorable climatic conditions following fire years. The presence of multiple fire scars on our fire-scar samples and the multicohort stands of piñon suggested that low intensity fires were common. This study represents one of the few fire-scar-based fire regime studies for piñon–juniper woodlands. Our results differ from other studies in less topographically dissected landscapes that have identified stand-replacing fire as the dominant fire regime for piñon–juniper woodlands. This suggests that mixed-severity fire regimes are typical across southwestern piñon forests, and that topography is an important influence on fire frequency and intensity.
Ontogenetic strategy shift in sapling architecture of Fagus crenata in the dense understorey vegetation of canopy gaps created by selective cutting
Authors: Yagi Takanobu 
Published: July 2009

Ontogenetic architectural variation is a key aspect of the light foraging of saplings under canopy gaps, where the interactions with the surrounding understorey plants are intense and change as saplings grow. Therefore, relationships between the allometry of 58 Fagus saplings (15–184 cm tall) and both the surrounding vegetation and light environment were investigated in the dense understorey of canopy gaps. The light available to the saplings exhibited a positive exponential relationship to their height, and at a given sapling height, it was inversely related to the height of the surrounding understorey. The slenderness of the saplings' stems increased as their height increased, and their crown architecture shifted from horizontally spread monolayer to vertically extended multilayer forms, indicating an ontogenetic strategy shift from shade tolerance to shade avoidance. These changes in sapling architecture were independent of the height of the surrounding understorey and, therefore, light availability, although the length of their current-year shoots (reflecting the rate of architectural development) was inversely related to the surrounding understorey height. Thus, ontogenetic architectural variation in Fagus saplings probably has the character of a developmentally programmed growth trajectory preadjusted to the most likely environments; the surrounding environments mainly affect the rate at which saplings move along this trajectory.
Chapter 10 Baryon Spectrum
Authors: Bian Jian-Ming , Bytev Vladimir , Chen Ying , Jin Hong-Ying , Jin Shan , Qin Hu , Shen Xiao-Yan , Wu Ning , Xu Guo-Fa , Zhang Zhen-Xia , Zhao Qiang , Zhemchugov Alexey , Zheng Han-Qing , Zhu Shi-Lin , Zou Bing-Song 
Published: July 2009

The following sections are included: Baryons as qqq States Outstanding Problems in Baryon Spectroscopy Baryon Spectroscopy at BESI and BESII Prospects for Baryon Spectroscopy at BESIII
Chapter 18 Hadronic Decays
Authors: Chen Yu-Qi , He Zhi-Guo , Mo Xiaohu , Wang Ping , Yuan Changzheng , Barnes T. , Rong G. , Zhang D.H. , Ma H.L. , Ping Ronggang 
Published: July 2009

The following sections are included: Light Hadron Decay P-Wave hc Decay ρ - π Puzzle Open-Flavor Decays ψ(3770) Non-[Formula: see text] Decays Baryonic Decays ψ(3770) and ψ(4415) Decays to [Formula: see text]
Chapter 19 Rare and Forbidden Charmonium Decays
Authors: Li Haibo , Ma Jianping , Zhang Xinmin 
Published: July 2009

The following sections are included: Weak Decays of Charmonium Search for the Invisible Decays of Quarkonium Search for C or P Violating Processes in J/ψ Decays Lepton Flavor Violating Processes in Decays of J/ψ
Time Trends in the Incidence of Testicular Cancer in Childhood and Young Adulthood
Authors: Lacerda Hadriano M. , Akre Olof , Merletti Franco , Richiardi Lorenzo 
Published: July 2009

AbstractBackground: There has been a steep increase in the incidence of adult testicular cancer in many populations, but in spite of numerous studies, the etiology of testicular cancer remains elusive. The time trends of childhood testicular tumors are less clear and have been studied in a few populations. To further evaluate whether or not adult and childhood cancers share trend determinants and whether future adult testicular cancer incidences can be predicted through childhood testicular cancer incidences, their rates were compared.Method: Data on testicular cancer incidence in childhood and in young adulthood were extracted from the IARC Cancer Incidence in the Five Continents Database limited to two 10-year time periods (1967-1976 and from 1987-1996) to allow for truncation-free analyses within the same birth cohort.Results: Childhood testicular cancer incidence varied 3- to 4-fold, whereas adult testicular cancer incidence varied 10- to 11-fold between the studied populations. No positive correlation between childhood and adulthood incidence of testicular cancer was found.Conclusion: These data indicate that the incidence of testicular cancer in adulthood is influenced by factors, either prenatal or postnatal exposures different than those determining the trends among children. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2042–5)
Isolation of Stool-Derived Mucus Provides a High Yield of Colonocytes Suitable for Early Detection of Colorectal Carcinoma
Authors: White Victoria , Scarpini Cinzia , Barbosa-Morais Nuno L. , Ikelle Emili , Carter Stephanie , Laskey Ronald A. , Miller Richard , Coleman Nicholas 
Published: July 2009

Abstract
Background: Promising stool-based screening tests for colorectal carcinoma (CRC) rely on detection of exfoliated colonocytes or their contents. However, methods of colonocyte retrieval have not been studied systematically and current approaches are restricted by low yields. We examined colonocyte numbers in stool wash fractions and assessed the suitability of retrieved cells for immunocytochemistry for minichromosome maintenance protein 2 (MCM2), a marker of the proliferative deregulation that characterizes malignancy.
Methods: Colonocyte numbers were accurately quantified in 129 wash fractions derived from 18 stools, comparing the mucus retained by a 125-μm filter (F fraction) with the fine and coarse content in the filtrate (S and P fractions, respectively). MCM2 immunocytochemistry was done on sections of fibrin clot containing filter-derived mucus, obtained from stools of eight independent subjects.
Results: Total colonocyte yield in the F fraction (mean, 433.8 per 100 μL) was higher than in the S (140.3) and P (204.6) fractions (P = 0.004 and 0.03, respectively) due to increased numbers of morphologically abnormal cells, which predominantly represented malignant cells in samples from CRC patients. Several thousand abnormal cells could be obtained from stool-derived mucus in all CRC patients, an order of magnitude greater than numbers in subjects without CRC. Median MCM2 labeling index in abnormal cells was 50% (range, 30-60%) in CRC patients and 0% in subjects without CRC. Cells in clot sections were well preserved and not obscured by fecal debris.
Conclusions: Isolation of stool-derived mucus is technically straightforward and can improve the performance of protein-based and/or nucleic acid–based approaches to CRC screening. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2006–13)
Fine-Mapping and Family-Based Association Analyses of Prostate Cancer Risk Variants at Xp11
Authors: Lu Lingyi , Sun Jielin , Isaacs Sarah D. , Wiley Kathleen E. , Smith Shelly , Pruett Kristen , Zhu Yi , Zhang Zheng , Wiklund Fredrik , Grönberg Henrik , Walsh Patrick C. , Chang Bao-Li , Zheng S. Lilly , Isaacs William B. , Xu Jianfeng 
Published: July 2009

Abstract
Two single nucleotide polymorphisms (SNP; rs5945572 and rs5945619) at Xp11 were recently implicated in two genome-wide association studies of prostate cancer. Using a family-based association test for these two SNPs in 168 families with prostate cancer, we showed in this study that the risk alleles of the two reported SNPs were overtransmitted to the affected offspring (P= 0.009 for rs5945372 and P = 0.03 for rs5945619), which suggested that the observed association in case-control studies were not driven by potential population stratification. We also did a fine-mapping study in the ∼800 kb region at Xp11 between two independent case-control studies, including 1,527 cases and 482 controls from Johns Hopkins Hospital and 1,172 cases and 1,157 controls from the Prostate, Lung, Colon and Ovarian Cancer screening trial. The strongest association was found with SNPs in the haplotype block in which the two initial reported SNPs were located, although many SNPs in the ∼140 kb region were highly significant in the combined allelic tests (P = 10−5 to 10−6). The second strongest association was observed with SNPs in the ∼286 kb region at another haplotype block (P = 10−4 to 10−5), ∼94 kb centromeric to the first region. The significance of SNPs in the second region decreased considerably after adjusting for SNPs at the first region, although P values remained at &lt;0.05. Additional studies are warranted to test independent prostate cancer associations at these two regions. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2132–6)