bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reverse Genetics Recovery of Lujo Virus and Role of Virus RNA Secondary Structures in Efficient Virus Growth
Authors: Bergeron Éric , Chakrabarti Ayan K. , Bird Brian H. , Dodd Kim A. , McMullan Laura K. , Spiropoulou Christina F. , Nichol Stuart T. , Albariño César G. 
Published: July 2012

ABSTRACT
Arenaviruses are rodent-borne viruses with a bisegmented RNA genome. A genetically unique arenavirus, Lujo virus, was recently discovered as the causal agent of a nosocomial outbreak of acute febrile illness with hemorrhagic manifestations in Zambia and South Africa. The outbreak had a case fatality rate of 80%. A reverse genetics system to rescue infectious Lujo virus from cDNA was established to investigate the biological properties of this virus. Sequencing the genomic termini showed unique nucleotides at the 3′ terminus of the S segment promoter element. While developing this system, we discovered that reconstructing infectious Lujo virus using the previously reported L segment intergenic region (IGR), comprising the arenaviral transcription termination signal, yielded an attenuated Lujo virus. Resequencing revealed that the correct L segment IGR was 36 nucleotides longer, and incorporating it into the reconstructed Lujo virus restored the growth rate to that of the authentic clinical virus isolate. These additional nucleotides were predicted to more than double the free energy of the IGR main stem-loop structure. In addition, incorporating the newly determined L-IGR into a replicon reporter system enhanced the expression of a luciferase reporter L segment. Overall, these results imply that an extremely stable secondary structure within the L-IGR is critical for Lujo virus propagation and viral protein production. The technology for producing recombinant Lujo virus now provides a method to precisely investigate the molecular determinants of virulence of this newly identified pathogen.
Entry of Influenza A Virus with a α2,6-Linked Sialic Acid Binding Preference Requires Host Fibronectin
Authors: Leung Horasis S. Y. , Li Olive T. W. , Chan Renee W. Y. , Chan Michael C. W. , Nicholls John M. , Poon Leo L. M. 
Published: July 2012

ABSTRACT
The receptor binding specificity of influenza A virus is one of the major determinants of viral tropism and host specificity. In general, avian viral hemagglutinin prefers to bind to α2,3-linked sialic acid, whereas the human viral hemagglutinin prefers to bind to α2,6-linked sialic acid. Here, we demonstrate that host fibronectin protein plays an important role in the life cycle of some influenza A viruses. Treating cells with anti-fibronectin antibodies or fibronectin-specific small interfering RNA can inhibit the virus replication of human H1N1 influenza A viruses. Strikingly, these inhibitory effects cannot be observed in cells infected with H5N1 viruses. By using reverse genetics techniques, we observed that the receptor binding specificity, but not the origin of the hemagglutinin subtype, is responsible for this differential inhibitory effect. Changing the binding preference of hemagglutinin from α2,6-linked sialic acid to α2,3-linked sialic acid can make the virus resistant to the anti-fibronectin antibody treatment and vice versa. Our further characterizations indicate that anti-fibronectin antibody acts on the early phase of viral replication cycle, but it has no effect on the initial binding of influenza A virus to cell surface. Our subsequent investigations further show that anti-fibronectin antibody can block the postattachment entry of influenza virus. Overall, these results indicate that the sialic acid binding preference of influenza viral hemagglutinin can modulate the preferences of viral entry pathways, suggesting that there are subtle differences between the virus entries of human and avian influenza viruses.
Nonstructural Nipah Virus C Protein Regulates both the Early Host Proinflammatory Response and Viral Virulence
Authors: Mathieu Cyrille , Guillaume Vanessa , Volchkova Valentina A. , Pohl Christine , Jacquot Frederique , Looi Ren Yih , Wong Kum Thong , Legras-Lachuer Catherine , Volchkov Viktor E. , Lachuer Joel , Horvat Branka 
Published: July 2012

ABSTRACT
Nipah virus (NiV) is a highly pathogenic, negative-strand RNA paramyxovirus that has recently emerged from flying foxes to cause serious human disease. We have analyzed the role of the nonstructural NiV C protein in viral immunopathogenesis using recombinant virus lacking the expression of NiV C (NiVΔC). While wild-type NiV was highly pathogenic in the hamster animal model, NiVΔC was strongly attenuated. Replication of NiVΔC was followed by the production of NiV-specific antibodies and associated with higher recruitment of inflammatory cells and less intensive histopathological lesions in different organs than in wild-type-NiV-infected animals. To analyze the molecular basis of NiVΔC attenuation, we studied early changes in gene expression in infected primary human endothelial cells, a major cellular target of NiV infection. The transcriptomic approach revealed the striking difference between wild-type and mutant NiV in the expression of genes involved in immunity, with the particularly interesting differential patterns of proinflammatory cytokines. Compared to wild-type virus, NiVΔC induced increased expression of interleukin 1 beta (IL-1β), IL-8, CXCL2, CXCL3, CXCL6, CCL20, and beta interferon. Furthermore, the expression of NiV C in stably transfected cells decreased the production of the same panel of cytokines, revealing a role of the C protein in the regulation of cytokine balance. Together, these results suggest that NiV C regulates expression of proinflammatory cytokines, therefore providing a signal responsible for the coordination of leukocyte recruitment and the chemokine-induced immune response and controlling the lethal outcome of the infection.
Increased Genetic and Phenotypic Stability of a Promising Live-Attenuated Respiratory Syncytial Virus Vaccine Candidate by Reverse Genetics
Authors: Luongo Cindy , Winter Christine C. , Collins Peter L. , Buchholz Ursula J. 
Published: July 2012

ABSTRACT

Human respiratory syncytial virus (RSV) is the most important viral cause of serious pediatric respiratory illness worldwide. Currently, the most promising live-attenuated vaccine candidate is a temperature-sensitive (
ts
) cDNA-derived virus named rA2
cp248/404/1030
ΔSH, in reference to its set of attenuating mutations. In a previous clinical study, more than one-third of postvaccination nasal wash isolates exhibited partial loss of the
ts
phenotype. Most of this instability appeared to be due to reversion at a missense point mutation called
1030
. This
1030
mutation is a single-nucleotide tyrosine-to-asparagine substitution at position 1321 (Y1321N) of the polymerase L protein that contributes to the
ts
and attenuation phenotypes of the vaccine candidate. The goals of the present study were to identify a reversion-resistant codon at position 1321 conferring a comparable level of attenuation and to use this to develop a genetically stable version of the vaccine virus. We modified wild-type (wt) RSV to insert each of the 20 possible amino acids at position 1321; 19 viruses were recoverable. We also investigated small deletions at or near this position, but these viruses were not recoverable. Phenotypic analysis identified alternative attenuating amino acids for position 1321. Several of these amino acids were predicted, based on the genetic code, to be refractory to deattenuation. Classical genetics, using temperature stress tests
in vitro
combined with nucleotide sequencing, confirmed this stability but identified a second site with a compensatory mutation at position 1313. It was possible to stabilize the 1313 site as well, providing a stable
1030
mutation. Further stress tests identified additional incidental mutations, but these did not reverse the
ts
/attenuation phenotype. An improved version of the vaccine candidate virus was constructed and validated
in vitro
by temperature stress tests and
in vivo
by evaluation of attenuation in seronegative chimpanzees. In addition to developing an improved version of this promising live-attenuated RSV vaccine candidate, this study demonstrated the propensity of an RNA virus to escape from attenuation but also showed that, through systematic analysis, genetics can be used to cut off the routes of escape.
Chikungunya Virus nsP3 Blocks Stress Granule Assembly by Recruitment of G3BP into Cytoplasmic Foci
Authors: Fros Jelke J. , Domeradzka Natalia E. , Baggen Jim , Geertsema Corinne , Flipse Jacky , Vlak Just M. , Pijlman Gorben P. 
Published: July 2012

ABSTRACT
Chikungunya virus nonstructural protein nsP3 has an essential but unknown role in alphavirus replication and interacts with Ras-GAP SH3 domain-binding protein (G3BP). Here we describe the first known function of nsP3, to inhibit stress granule assembly by recruiting G3BP into cytoplasmic foci. A conserved SH3 domain-binding motif in nsP3 is essential for both nsP3-G3BP interactions and viral RNA replication. This study reveals a novel role for nsP3 as a regulator of the cellular stress response.
CHARACTER EXPANSION FOR HOMFLY POLYNOMIALS III: ALL 3-STRAND BRAIDS IN THE FIRST SYMMETRIC REPRESENTATION
Authors: ITOYAMA H. , MIRONOV A. , MOROZOV A. , MOROZOV AND. 
Published: July 2012

We continue the program of systematic study of extended HOMFLY polynomials, suggested in [A. Mironov, A. Morozov and And. Morozov, arXiv:1112.5754] and [A. Mironov, A. Morozov and And. Morozov, J. High Energy Phys. 03, 034 (2012), arXiv:1112.2654]. Extended polynomials depend on infinitely many time-variables, are close relatives of integrable τ-functions, and depend on the choice of the braid representation of the knot. They possess natural character decompositions, with coefficients which can be defined by exhaustively general formula for any particular number m of strands in the braid and any particular representation R of the Lie algebra GL(∞). Being restricted to "the topological locus" in the space of time-variables, the extended HOMFLY polynomials reproduce the ordinary knot invariants. We derive such a general formula, for m = 3, when the braid is parametrized by a sequence of integers (a1, b1, a2, b2, …) and for the first nonfundamental representation R = [2]. Instead of calculating the mixing matrices directly, as suggested [A. Mironov, A. Morozov and And. Morozov, J. High Energy Phys. 03, 034 (2012), arXiv:1112.2654], we deduce them from comparison with the known answers for torus and composite knots. A simple reflection symmetry converts the answer for the symmetric representation [2] into that for the antisymmetric one [1, 1]. The result applies, in particular, to the figure eight knot 41, and was further extended to superpolynomials in arbitrary symmetric and antisymmetric representations in H. Itoyama, A. Mironov, A. Morozov and And. Morozov, arXiv:1203.5978.
LUTTINGER LIQUID, SINGULAR INTERACTION AND QUANTUM CRITICALITY IN CUPRATE MATERIALS
Authors: DI CASTRO C. , CAPRARA S. 
Published: July 2012

With particular reference to the role of the renormalization group (RG) approach and Ward identities (WI's), we start by recalling some old features of the one-dimensional Luttinger liquid as the prototype of non-Fermi-liquid behavior. Its dimensional crossover to the Landau normal Fermi liquid implies that a non-Fermi liquid, as, e.g., the normal phase of the cuprate high temperature superconductors, can be maintained in d>1 only in the presence of a sufficiently singular effective interaction among the charge carriers. This is the case when, nearby an instability, the interaction is mediated by critical fluctuations. We are then led to introduce the specific case of superconductivity in cuprates as an example of avoided quantum criticality. We will disentangle the fluctuations which act as mediators of singular electron–electron interaction, enlightening the possible order competing with superconductivity and a mechanism for the non-Fermi-liquid behavior of the metallic phase. This paper is not meant to be a comprehensive review. Many important contributions will not be considered. We will also avoid using extensive technicalities and making full calculations for which we refer to the original papers and to the many good available reviews. We will here only follow one line of reasoning which guided our research activity in this field.
Impaired IFN-α Production by Plasmacytoid Dendritic Cells Favors Regulatory T-cell Expansion That May Contribute to Breast Cancer Progression
Authors: Sisirak Vanja , Faget Julien , Gobert Michael , Goutagny Nadège , Vey Nelly , Treilleux Isabelle , Renaudineau Sarah , Poyet Gaelle , Labidi-Galy Sana Intidhar , Goddard-Leon Sophie , Durand Isabelle , Le Mercier Isabelle , Bajard Agathe , Bachelot Thomas , Puisieux Alain , Puisieux Isabelle , Blay Jean-Yves , Ménétrier-Caux Christine , Caux Christophe , Bendriss-Vermare Nathalie 
Published: July 2012

AbstractInfiltration and dysfunction of immune cells have been documented in many types of cancers. We previously reported that plasmacytoid dendritic cells (pDC) within primary breast tumors correlate with an unfavorable prognosis for patients. The role of pDC in cancer remains unclear but they have been shown to mediate immune tolerance in other pathophysiologic contexts. We postulated that pDC may interfere with antitumor immune response and favor tolerance in breast cancer. The present study was designed to decipher the mechanistic basis for the deleterious impact of pDC on the clinical outcome. Using fresh human breast tumor biopsies (N = 60 patients), we observed through multiparametric flow cytometry increased tumor-associated (TA) pDC (TApDC) rates in aggressive breast tumors, i.e., those with high mitotic index and the so-called triple-negative breast tumors (TNBT). Furthermore, TApDC expressed a partially activated phenotype and produced very low amounts of IFN-α following toll-like receptor activation in vitro compared with patients' blood pDC. Within breast tumors, TApDC colocalized and strongly correlated with TA regulatory T cells (TATreg), especially in TNBT. Of most importance, the selective suppression of IFN-α production endowed TApDC with the unique capacity to sustain FoxP3+ Treg expansion, a capacity that was reverted by the addition of exogenous IFN-α. These findings indicate that IFN-α–deficient TApDC accumulating in aggressive tumors are involved in the expansion of TATreg in vivo, contributing to tumor immune tolerance and poor clinical outcome. Thus, targeting pDC to restore their IFN-α production may represent an attractive therapeutic strategy to overcome immune tolerance in breast cancer. Cancer Res; 72(20); 5188–97. ©2012 AACR.
Platelets and P-Selectin Control Tumor Cell Metastasis in an Organ-Specific Manner and Independently of NK Cells
Authors: Coupland Lucy A. , Chong Beng H. , Parish Christopher R. 
Published: July 2012

Abstract
The prometastatic role of platelets has long been recognized with proposed mechanisms of action including shielding tumor cells from natural killer (NK) cell destruction and aiding endothelial attachment and extravasation of tumor cells with platelet P-selectin being implicated in these processes. However, many aspects of the prometastatic function of platelets remain unclear. In this study, we used mouse models of metastatic breast cancer and melanoma to investigate the platelet effect, focusing on organ specificity, the relationship with NK cells and the relative importance of platelet-derived versus endothelial-derived P-selectin. We found that platelets promote lung metastasis in the absence of NK cells in both acute and spontaneous metastasis models. In addition, the prometastatic action of platelets was found to be organ specific, clearly enhancing lung metastasis but not affecting B16F1 liver metastasis, in fact, liver metastasis was enhanced in the absence of platelets. Furthermore, the profound antimetastatic activity of NK cells was equally effective in the presence or absence of platelets and chronologically distinct from the prometastatic role of platelets. Finally, it was shown that endothelial-derived P-selectin is just as important as platelet-derived P-selectin in promoting lung metastasis and also plays an important role in liver metastasis. Taken together, our findings help clarify the roles of platelets, NK cells and P-selectin in metastasis, and they identify P-selectin as an attractive therapeutic target for preventing metastasis in multiple organs. Cancer Res; 72(18); 4662–71. ©2012 AACR.
Systemic Combination Virotherapy for Melanoma with Tumor Antigen-Expressing Vesicular Stomatitis Virus and Adoptive T-cell Transfer
Authors: Rommelfanger Diana M. , Wongthida Phonphimon , Diaz Rosa M. , Kaluza Karen M. , Thompson Jill M. , Kottke Timothy J. , Vile Richard G. 
Published: July 2012

Abstract
Oncolytic virotherapy offers the potential to treat tumors both as a single agent and in combination with traditional modalities such as chemotherapy and radiotherapy. Here we describe an effective, fully systemic treatment regimen, which combines virotherapy, acting essentially as an adjuvant immunotherapy, with adoptive cell transfer (ACT). The combination of ACT with systemic administration of a vesicular stomatitis virus (VSV) engineered to express the endogenous melanocyte antigen glycoprotein 100 (gp100) resulted in regression of established melanomas and generation of antitumor immunity. Tumor response was associated with in vivo T-cell persistence and activation as well as treatment-related vitiligo. However, in a proportion of treated mice, initial tumor regressions were followed by recurrences. Therapy was further enhanced by targeting an additional tumor antigen with the VSV-antigen + ACT combination strategy, leading to sustained response in 100% of mice. Together, our findings suggest that systemic virotherapy combined with antigen-expressing VSV could be used to support and enhance clinical immunotherapy protocols with adoptive T-cell transfer, which are already used in the clinic. Cancer Res; 72(18); 4753–64. ©2012 AACR.
MicroRNA-21 Modulates the Levels of Reactive Oxygen Species by Targeting SOD3 and TNFα
Authors: Zhang Xiangming , Ng Wooi-Loon , Wang Ping , Tian LinLin , Werner Erica , Wang Huichen , Doetsch Paul , Wang Ya 
Published: July 2012

Abstract
MicroRNA-21 (miR-21) is an oncomir overexpressed in most human tumors in that it promotes malignant growth and progression by acting on multiple targets. Here, we broaden the impact of miR-21 in cancer by showing that it regulates the formation of reactive oxygen species (ROS) that promote tumorigenesis. Key targets of miR-21 in mediating this function were SOD3 and TNFα. We found that miR-21 inhibited the metabolism of superoxide to hydrogen peroxide, produced either by endogenous basal activities or exposure to ionizing radiation (IR), by directing attenuating SOD3 or by an indirect mechanism that limited TNFa production, thereby reducing SOD2 levels. Importantly, both effects contributed to an elevation of IR-induced cell transformation. Our findings, therefore, establish that miR-21 promotes tumorigenesis to a large extent through its regulation of cellular ROS levels. Cancer Res; 72(18); 4707–13. ©2012 AACR.
Biological variation in tPA-induced plasma clot lysis time
Authors: Talens Simone , Malfliet Joyce J. M. C. , Rudež Goran , Spronk Henri M. H. , Janssen Nicole A. H. , Meijer Piet , Kluft Cornelis , de Maat Moniek P. M. , Rijken Dingeman C. 
Published: July 2012

SummaryHypofibrinolysis is a risk factor for venous and arterial thrombosis, and can be assessed by using a turbidimetric tPA-induced clot lysis time (CLT) assay. Biological variation in clot lysis time may affect the interpretation and usefulness of CLT as a risk factor for thrombosis. Sufficient information about assay variation and biological variation in CLT is not yet available. Thus, this study aimed to determine the analytical, within-subject and between-subject variation in CLT. We collected blood samples from 40 healthy individuals throughout a period of one year (average 11.8 visits) and determined the CLT of each plasma sample in duplicate. The mean (± SD) CLT was 83.8 (± 11.1) minutes. The coefficients of variation for total variation, analytical variation, within-subject variation and between-subject variation were 13.4%, 2.6%, 8.2% and 10.2%, respectively. One measurement can estimate the CLT that does not deviate more than 20% from its true value. The contribution of analytical variation to the within-subject variation was 5.0%, the index of individuality was 0.84 and the reference change value was 23.8%. The CLT was longer in the morning compared to the afternoon and was slightly longer in older individuals (> 40 years) compared to younger (≤40 years) individuals. There was no seasonal variation in CLT and no association with air pollution. CLT correlated weakly with fibrinogen, C-reactive protein, prothrombin time and thrombin generation. This study provides insight into the biological variation of CLT, which can be used in future studies testing CLT as a potential risk factor for thrombosis.
Alteration of the platelet transcriptome in chronic kidney disease
Authors: Plé Hélène , Maltais Manon , Corduan Aurélie , Rousseau Guy , Madore François , Provost Patrick 
Published: July 2012

SummaryBleeding and thrombotic disorders are major complications affecting patients with chronic kidney disease (CKD). Exposure of circulating platelets to uraemic toxins and contact with artificial surfaces during dialysis induce platelet abnormalities and alter the platelet proteome. We hypothesised that these changes may be subsequent to changes in the composition and/or regulation of the platelet transcriptome. In this study, we investigated the circulating platelets of 10 CKD patients (i.e. five chronic haemodialysis patients and five stage 4 CKD uraemic patients) and five age- and sex-matched healthy subjects. We observed an alteration of the platelet messenger RNA (mRNA) and microRNA transcriptome in CKD patients. Impaired in uraemic platelets, the levels of some mRNAs and of most microRNAs appeared to be corrected by dialysis, which is consistent with a beneficial effect of dialysis and a mRNA regulatory role of platelet microRNAs. Reduced in platelets of uraemic patients, phosphatidylcholine transfer protein (PCTP) and WD repeat-containing protein 1 (WDR1) were found to be regulated by microRNAs, the latter of which involving hsa-miR-19b, a microRNA increased in platelets of uraemic patients and involved in platelet reactivity. These results suggest that an alteration of microRNA-based mRNA regulatory mechanisms may underlie the platelet response to uremia and entail the development of platelet-related complications in CKD.