bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Genome Expression Profiling Reveals That Inhibition of Host Innate Immune Response Pathways by Ebola Virus Can Be Reversed by a Single Amino Acid Change in the VP35 Protein
Authors: Hartman Amy L. , Ling Ling , Nichol Stuart T. , Hibberd Martin L. 
Published: March 2008

ABSTRACT
Ebola hemorrhagic fever is a rapidly progressing acute febrile illness characterized by high virus replication, severe immunosuppression, and case fatalities of ca. 80%. Inhibition of phosphorylation of interferon regulatory factor 3 (IRF-3) by the Ebola VP35 protein may block the host innate immune response and play an important role in the severity of disease. We used two precisely defined reverse genetics-generated Ebola viruses to investigate global host cell responses resulting from the inhibition of IRF-3 phosphorylation. The two viruses encoded either wild-type (WT) VP35 protein (recEbo-VP35/WT) or VP35 with an arginine (R)-to-alanine (A) amino acid substitution at position 312 (recEbo-VP35/R312A) within a previously defined IRF-3 inhibitory domain. When sucrose-gradient purified virus was used for infection, host cell whole-genome expression profiling revealed striking differences in human liver cell responses to these viruses differing by a single amino acid. The inhibition of host innate immune responses by WT Ebola virus was so potent that little difference in interferon and antiviral gene expression could be discerned between cells infected with purified WT, inactivated virus, or mock-infected cells. However, infection with recEbo-VP35/R312A virus resulted in a strong innate immune response including increased expression of MDA-5, RIG-I, RANTES, MCP-1, ISG-15, ISG-54, ISG-56, ISG-60, STAT1, IRF-9, OAS, and Mx1. The clear gene expression differences were obscured if unpurified virus stocks were used to initiate infection, presumably due to soluble factors present in virus-infected cell supernatant preparations. Ebola virus VP35 protein clearly plays a pivotal role in the potent inhibition of the host innate immune responses, and the present study indicates that VP35 has a wider effect on host cell responses than previously shown. The ability to eliminate this inhibitory effect with a single amino acid change in VP35 demonstrates the critical role this protein must play in the severe aspects this highly fatal disease.
Structural and Genetic Requirements for the Biogenesis of
Tobacco Rattle Virus
-Derived Small Interfering RNAs
Authors: Donaire Livia , Barajas Daniel , Martínez-García Belén , Martínez-Priego Llucia , Pagán Israel , Llave César 
Published: March 2008

ABSTRACT

In plants, small RNA-guided processes referred to as RNA silencing control gene expression and serve as an efficient antiviral mechanism. Plant viruses are inducers and targets of RNA silencing as infection involves the production of functional virus-derived small interfering RNAs (siRNAs). Here we investigate the structural and genetic components influencing the formation of
Tobacco rattle virus
(TRV)-derived siRNAs. TRV siRNAs are mostly 21 nucleotides in length and derive from positive and negative viral RNA strands, although TRV siRNAs of positive polarity are significantly more abundant. This asymmetry appears not to correlate with the presence of highly structured regions of single-stranded viral RNA. The Dicer-like enzyme DCL4, DCL3, or DCL2 targets, alone or in combination, viral templates to promote synthesis of siRNAs of both polarities from all regions of the viral genome. The heterogeneous distribution profile of TRV siRNAs reveals differential contributions throughout the TRV genome to siRNA formation. Indirect evidence suggests that DCL2 is responsible for production of a subset of siRNAs derived from the 3′ end region of TRV. TRV siRNA biogenesis and antiviral silencing are strongly dependent on the combined activity of the host-encoded RNA-dependent RNA polymerases RDR1, RDR2, and RDR6, thus providing evidence that perfectly complementary double-stranded RNA serves as a substrate for siRNA production. We conclude that the overall composition of viral siRNAs in TRV-infected plants reflects the combined action of several interconnected pathways involving different DCL and RDR activities.
An Alteration of Human Immunodeficiency Virus gp41 Leads to Reduced CCR5 Dependence and CD4 Independence
Authors: Taylor Brian M. , Foulke J. Scott , Flinko Robin , Heredia Alonso , DeVico Anthony , Reitz Marvin 
Published: March 2008

ABSTRACTHuman immunodeficiency virus (HIV) type 1 infection requires functional interactions of the viral surface (gp120) glycoprotein with cell surface CD4 and a chemokine coreceptor (usually CCR5 or CXCR4) and of the viral transmembrane (gp41) glycoprotein with the target cell membrane. Extensive genetic variability, generally in gp120 and the gp41 ectodomain, can result in altered coreceptor use, fusion kinetics, and neutralization sensitivity. Here we describe an R5 HIV variant that, in contrast to its parental virus, infects T-cell lines expressing low levels of cell surface CCR5. This correlated with an ability to infect cells in the absence of CD4, increased sensitivity to a neutralizing antibody recognizing the coreceptor binding site of gp120, and increased resistance to the fusion inhibitor T-20. Surprisingly, these properties were determined by alterations in gp41, including the cytoplasmic tail, a region not previously shown to influence coreceptor use. These data indicate that HIV infection of cells with limiting levels of cell surface CCR5 can be facilitated by gp41 sequences that are not exposed on the envelope ectodomain yet induce allosteric changes in gp120 that facilitate exposure of the CCR5 binding site.
Robust NK Cell-Mediated Human Immunodeficiency Virus (HIV)-Specific Antibody-Dependent Responses in HIV-Infected Subjects
Authors: Stratov Ivan , Chung Amy , Kent Stephen J. 
Published: March 2008

ABSTRACTAntibody-dependent cellular cytotoxicity (ADCC) is a potentially effective adaptive immune response to human immunodeficiency virus (HIV) infection. The study of ADCC responses has been hampered by the lack of simple methods to quantify these responses and map effective epitopes. We serendipitously observed that standard intracellular cytokine assays on fresh whole blood from a cohort of 26 HIV-infected subjects identified non-T lymphocytes expressing gamma interferon (IFN-γ) in response to overlapping linear peptides spanning HIV-1 proteins. The effector cells were CD3−CD4−CD8−CD14−CD2+CD56+/−NK lymphocytes and degranulated granzyme B and perforin in response to antigen stimulation. Serum transfer assays demonstrated that the specific response was mediated by immunoglobulin G. Fresh blood samples from half of the HIV-infected cohort demonstrated robust HIV peptide-specific IFN-γ expression by NK cells, predominately to Env, Pol, and Vpu HIV-1 proteins. Responses were readily mapped to define minimal epitopes utilizing this assay. Antibody-dependent, HIV-specific NK cell recognition, involving components of both innate and adaptive immune systems, represents a potentially effective immune response to induce by vaccination.
HLA Class I-Restricted T-Cell Responses May Contribute to the Control of Human Immunodeficiency Virus Infection, but Such Responses Are Not Always Necessary for Long-Term Virus Control
Authors: Emu Brinda , Sinclair Elizabeth , Hatano Hiroyu , Ferre April , Shacklett Barbara , Martin Jeffrey N. , McCune J. M. , Deeks Steven G. 
Published: March 2008

ABSTRACTA rare subset of human immunodeficiency virus (HIV)-infected individuals maintains undetectable HIV RNA levels without therapy (“elite controllers”). To clarify the role of T-cell responses in mediating virus control, we compared HLA class I polymorphisms and HIV-specific T-cell responses among a large cohort of elite controllers (HIV-RNA < 75 copies/ml), “viremic” controllers (low-level viremia without therapy), “noncontrollers” (high-level viremia), and“antiretroviral therapy suppressed” individuals (undetectable HIV-RNA levels on antiretroviral therapy). The proportion of CD4+and CD8+T cells that produce gamma interferon (IFN-γ) and interleukin-2 (IL-2) in response to Gag and Pol peptides was highest in the elite and viremic controllers (P< 0.0001). Forty percent of the elite controllers were HLA-B*57 compared to twenty-three percent of viremic controllers and nine percent of noncontrollers (P< 0.001). Other HLA class I alleles more common in elite controllers included HLA-B*13, HLA-B*58, and HLA-B*81 (P< 0.05 for each). Within elite and viremic controller groups, those with protective class I alleles had higher frequencies of Gag-specific CD8+T cells than those without these alleles (P= 0.01). Noncontrollers, with or without protective alleles, had low-level CD8+responses. Thus, certain HLA class I alleles are enriched in HIV controllers and are associated with strong Gag-specific CD8+IFN-γ+IL-2+T cells. However, the absence of evidence of T cell-mediated control in many controllers suggests the presence of alternative mechanisms for viral control in these individuals. Defining mechanisms for virus control in “non-T-cell controllers” might lead to insights into preventing HIV transmission or preventing virus replication.
Persistence of Transmitted Drug Resistance among Subjects with Primary Human Immunodeficiency Virus Infection
Authors: Little Susan J. , Frost Simon D. W. , Wong Joseph K. , Smith Davey M. , Pond Sergei L. Kosakovsky , Ignacio Caroline C. , Parkin Neil T. , Petropoulos Christos J. , Richman Douglas D. 
Published: March 2008

ABSTRACTFollowing interruption of antiretroviral therapy among individuals with acquired drug resistance, preexisting drug-sensitive virus emerges relatively rapidly. In contrast, wild-type virus is not archived in individuals infected with drug-resistant human immunodeficiency virus (HIV) and thus cannot emerge rapidly in the absence of selective drug pressure. Fourteen recently HIV-infected patients with transmitted drug-resistant virus were followed for a median of 2.1 years after the estimated date of infection (EDI) without receiving antiretroviral therapy. HIV drug resistance andpolreplication capacity (RC) in longitudinal plasma samples were assayed. Resistance mutations were characterized as pure populations or mixtures. The mean time to first detection of a mixture of wild-type and drug-resistant viruses was 96 weeks (1.8 years) (95% confidence interval, 48 to 192 weeks) after the EDI. The median time to loss of detectable drug resistance using population-based assays ranged from 4.1 years (conservative estimate) to longer than the lifetime of the individual (less conservative estimate). The transmission of drug-resistant virus was not associated with virus with reduced RC. Sexual transmission of HIV selects for highly fit drug-resistant variants that persist for years. The prolonged persistence of transmitted drug resistance strongly supports the routine use of HIV resistance genotyping for all newly diagnosed individuals.
Increased In Vivo Activation of Microglia and Astrocytes in the Brains of Mice Transgenic for an Infectious R5 Human Immunodeficiency Virus Type 1 Provirus and for CD4-Specific Expression of Human Cyclin T1 in Response to Stimulation by Lipopolysaccharides
Authors: Sun Jinglin , Zheng Jian Hua , Zhao Mengliang , Lee Sunhee , Goldstein Harris 
Published: March 2008

ABSTRACTInflammatory mediators and viral products produced by human immunodeficiency virus (HIV)-infected microglia and astrocytes perturb the function and viability of adjacent uninfected neuronal and glial cells and contribute to the pathogenesis of HIV-associated neurocognitive disorders (HAND). In vivo exposure to lipopolysaccharide (LPS) activates parenchymal microglia and astrocytes and induces cytokine and chemokine production in the brain. HIV-infected individuals display increased circulating LPS levels due to microbial translocation across a compromised mucosa barrier. We hypothesized that HIV-infected microglia and astrocytes display increased sensitivity to the proinflammatory effects of LPS, and this combines with the increased levels of systemic LPS in HIV-infected individuals to contribute to the development of HAND. To examine this possibility, we determined the in vivo responsiveness of HIV-infected microglia and astrocytes to LPS using our mouse model, JR-CSF/human cyclin T1 (JR-CSF/hu-cycT1) mice, which are transgenic for both an integrated full-length infectious HIV type 1 (HIV-1) provirus derived from the primary R5-tropic clinical isolate HIV-1JR-CSFregulated by the endogenous HIV-1 long terminal repeat and the hu-cycT1 gene under the control of a CD4 promoter. In the current report, we demonstrated that in vivo-administered LPS more potently activated JR-CSF/hu-cycT1 mouse microglia and astrocytes and induced a significantly higher degree of monocyte chemoattractant protein production by JR-CSF/hu-cycT1 astrocytes compared to that of the in vivo LPS response of control littermate mouse microglia and astrocytes. These results indicate that HIV infection increases the sensitivity of microglia and astrocytes to inflammatory stimulation and support the use of these mice as a model to investigate various aspects of the in vivo mechanism of HIV-induced neuronal dysfunction.
Coreceptor Tropism Can Be Influenced by Amino Acid Substitutions in the gp41 Transmembrane Subunit of Human Immunodeficiency Virus Type 1 Envelope Protein
Authors: Huang Wei , Toma Jonathan , Fransen Signe , Stawiski Eric , Reeves Jacqueline D. , Whitcomb Jeannette M. , Parkin Neil , Petropoulos Christos J. 
Published: March 2008

ABSTRACT

Many studies have demonstrated that the third variable region (V3) of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) is a major determinant of coreceptor tropism. Other regions in the surface gp120 subunit of Env can modulate coreceptor tropism in a manner that is not fully understood. In this study, we evaluated the effect of
env
determinants outside of V3 on coreceptor usage through the analysis of (i) patient-derived
env
clones that differ in coreceptor tropism, (ii) chimeric
env
sequences, and (iii) site-directed mutants. The introduction of distinct V3 sequences from CXCR4-using clones into an R5-tropic
env
backbone conferred the inefficient use of CXCR4 in some but not all cases. Conversely, in many cases, X4- and dual-tropic
env
backbones containing the V3 sequences of R5-tropic clones retained the ability to use CXCR4, suggesting that sequences outside of the V3 regions of these CXCR4-using clones were responsible for CXCR4 use. The determinants of CXCR4 use in a set of dual-tropic
env
sequences with V3 sequences identical to those of R5-tropic clones mapped to the gp41 transmembrane (TM) subunit. In one case, a single-amino-acid substitution in the fusion peptide of TM was able to confer CXCR4 use; however, TM substitutions associated with CXCR4 use varied among different
env
sequences. These results demonstrate that sequences in TM can modulate coreceptor specificity and that
env
sequences other than that of V3 may facilitate efficient CXCR4-mediated entry. We hypothesize that the latter plays an important role in the transition from CCR5 to CXCR4 coreceptor use.
Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus
Authors: Boni Maciej F. , Zhou Yang , Taubenberger Jeffery K. , Holmes Edward C. 
Published: March 2008

ABSTRACTTo determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (∼2%) in five different RNA segments that, after a multiple-comparison correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length (>100 nucleotides [nt]) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15 to 30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during amplification, laboratory artifacts provide an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus.
Nuclear Localization Sequences in Cytomegalovirus Capsid Assembly Proteins (UL80 Proteins) Are Required for Virus Production: Inactivating NLS1, NLS2, or Both Affects Replication to Strikingly Different Extents
Authors: Nguyen Nang L. , Loveland Amy N. , Gibson Wade 
Published: March 2008

ABSTRACT

Scaffolding proteins of spherical prokaryotic and eukaryotic viruses have critical roles in capsid assembly. The primary scaffolding components of cytomegalovirus, called the assembly protein precursor (pAP, pUL80.5) and the maturational protease precursor (pPR, pUL80a), contain two nuclear localization sequences (NLS1 and NLS2), at least one of which is required in coexpression experiments to translocate the major capsid protein (MCP, pUL85) into the nucleus. In the work reported here, we have mutated NLS1 and NLS2, individually or together, in human cytomegalovirus (HCMV, strain AD169) bacmid-derived viruses to test their effects on virus replication. Consistent with results from earlier transfection/coexpression experiments, both single-mutant bacmids gave rise to infectious virus but the double mutant did not. In comparisons with the wild-type virus, both mutants showed slower cell-to-cell spread; decreased yields of infectious virus (3-fold lower for NLS1
−
and 140-fold lower for NLS2
−
); reduced efficiency of pAP, pPR, and MCP nuclear translocation (sixfold lower for NLS1
−
and eightfold lower for NLS2
−
); increased amounts of a 120-kDa MCP fragment; and reduced numbers of intranuclear capsids. All effects were more severe for the NLS2
−
mutant than the NLS1
−
mutant, and a distinguishing feature of cells infected with the NLS2
−
mutant was the accumulation of large, UL80 protein-containing structures within the nucleus. We conclude that these NLS assist in the nuclear translocation of MCP during HCMV replication and that NLS2, which is unique to the betaherpesvirus UL80 homologs, may have additional involvements during replication.
Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napusL.) in China and Australia
Authors: Chen S. , Nelson M. N. , Ghamkhar K. , Fu T. , Cowling W. A. 
Published: March 2008

Oilseed rape ( Brassica napus ) in Australia and China have similar origins, with introductions from Europe, Canada, and Japan in the mid 20th century, and there has been some interchange of germplasm between China and Australia since that time. Allelic diversity of 72 B. napus genotypes representing contemporary germplasm in Australia and China, including samples from India, Europe, and Canada, was characterized by 55 polymorphic simple sequence repeat (SSR) markers spanning the entire B. napus genome. Hierarchical clustering and two-dimensional multidimensional scaling identified a Chinese group (China-1) that was separated from a “mixed” group of Australian, Chinese (China-2), European, and Canadian lines. A small group from India was distinctly separated from all other B. napus genotypes. Chinese genotypes, especially in the China-1 group, have inherited unique alleles from interspecific crossing, primarily with B. rapa, and the China-2 group has many alleles in common with Australian genotypes. The concept of “private alleles” is introduced to describe both the greater genetic diversity and the genetic distinctiveness of Chinese germplasm, compared with Australian germplasm, after 50 years of breeding from similar origins.
The development of a bin mapping population and the selective mapping of 103 markers in the diploidFragariareference map
Authors: Sargent D. J. , Cipriani G. , Vilanova S. , Gil-Ariza D. , Arús P. , Simpson D. W. , Tobutt K.R. , Monfort A. 
Published: March 2008

We have identified a set of plants (the bin set) to permit “selective” or “bin” mapping using the diploid strawberry mapping population FV × FN, derived from the F2cross F. vesca 815 × F. nubicola 601, which has been used to develop the Fragaria reference map. The bin set consists of 8 plants: the F. vesca 815 parent, the F1hybrid individual, and 6 seedlings of the F2population. This bin set divides the 578 cM of the diploid Fragaria genome into 46 bins, the largest mapping bin being 26 cM in length and the average bin size being 12.6 cM. To validate the FV × FN bin set, we used it to locate 103 loci into bins on the FV × FN map. These loci comprised 61 previously described SSRs, 38 new SSRs developed in this investigation from Fragaria × ananassa genomic DNA, EST and gene sequences, and 4 ripening-related genes developed for Prunus . The 103 markers were located to bins on all 7 linkage groups of the Fragaria map and a new mapping bin was identified with the novel markers, demonstrating that the map covers the majority of the diploid Fragaria genome and that the 6 bin-set seedlings selected were appropriate for bin mapping using this progeny.
Large genomes among caridean shrimp
Authors: Rees David J. , Belzile Claude , Glémet Hélène , Dufresne France 
Published: March 2008

Recent genome size estimates for Arctic amphipods have revealed the largest genomes known in the Crustacea. Here we provide additional data for 7 species of caridean shrimp collected from the Canadian Arctic and the Gulf of St. Lawrence. Genome sizes were estimated by flow cytometry and haploid C-values ranged from 8.53 ± 0.30 pg in Pandalus montagui (Pandalidae) to 40.89 ± 1.23 pg in Sclerocrangon ferox (Crangonidae). The value for S. ferox represents the largest decapod genome yet recorded and indicates a 38-fold variation in genome size within this order. These data suggest that large genomes may be relatively common in Arctic crustaceans, and underline the need for further comparative studies.
POSET REPRESENTATIONS OF DISTRIBUTIVE SEMILATTICES
Authors: WEHRUNG FRIEDRICH 
Published: March 2008

We prove that for every distributive 〈∨,0〉-semilattice S, there are a meet-semilattice P with zero and a map μ: P × P → S such that μ(x,z) ≤ μ(x,y) ∨ μ(y,z) and x ≤ y implies that μ(x,y) = 0, for all x, y, z ∈ P, together with the following conditions:. (P1) μ(v,u) = 0 implies that u = v, for all u ≤ v in P. (P2) For all u ≤ v in P and all a, b ∈ S, if μ(v,u) ≤ a ∨ b, then there are a positive integer n and a decomposition u = x0 ≤ x1 ≤ ⋯ ≤ xn = v such that either μ(xi + 1, xi) ≤ a or μ(xi+1, xi) ≤ b, for each i < n. (P3) The subset {μ(x,0) | x ∈ P} generates the semilattice S. Furthermore, every finite, bounded subset of P has a join, and P is bounded in case S is bounded. Furthermore, the construction is functorial on lattice-indexed diagrams of finite distributive 〈∨,0,1〉-semilattices.