bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Identification of a
Paenibacillus polymyxa
Strain That Coproduces a Novel Lantibiotic and Polymyxin
Authors: He Zengguo , Kisla Duygu , Zhang Liwen , Yuan Chunhua , Green-Church Kari B. , Yousef Ahmed E. 
Published: December 2006

ABSTRACT

A new bacterial strain, displaying potent antimicrobial properties against gram-negative and gram-positive pathogenic bacteria, was isolated from food. Based on its phenotypical and biochemical properties as well as its 16S rRNA gene sequence, the bacterium was identified as
Paenibacillus polymyxa
and it was designated as strain OSY-DF. The antimicrobials produced by this strain were isolated from the fermentation broth and subsequently analyzed by liquid chromatography-mass spectrometry. Two antimicrobials were found: a known antibiotic, polymyxin E1, which is active against gram-negative bacteria, and an unknown 2,983-Da compound showing activity against gram-positive bacteria. The latter was purified to homogeneity, and its antimicrobial potency and proteinaceous nature were confirmed. The antimicrobial peptide, designated paenibacillin, is active against a broad range of food-borne pathogenic and spoilage bacteria, including
Bacillus
spp.,
Clostridium sporogenes
,
Lactobacillus
spp.,
Lactococcus lactis
,
Leuconostoc mesenteroides
,
Listeria
spp.,
Pediococcus cerevisiae
,
Staphylococcus aureus
, and
Streptococcus agalactiae
. Furthermore, it possesses the physico-chemical properties of an ideal antimicrobial agent in terms of water solubility, thermal resistance, and stability against acid/alkali (pH 2.0 to 9.0) treatment. Edman degradation, mass spectroscopy, and nuclear magnetic resonance were used to sequence native and chemically modified paenibacillin. While details of the tentative sequence need to be elucidated in future work, the peptide was unequivocally characterized as a novel lantibiotic, with a high degree of posttranslational modifications. The coproduction of polymyxin E1 and a lantibiotic is a finding that has not been reported earlier. The new strain and associated peptide are potentially useful in food and medical applications.
Rhizobium etli
USDA9032 Engineered To Produce a Phenazine Antibiotic Inhibits the Growth of Fungal Pathogens but Is Impaired in Symbiotic Performance
Authors: Krishnan Hari B. , Kang Beom Ryong , Hari Krishnan Ammulu , Kim Kil Yong , Kim Young Cheol 
Published: December 2006

ABSTRACT

Phenazine production was engineered in
Rhizobium etli
USDA9032 by the introduction of the
phz
locus of
Pseudomonas chlororaphis
O6. Phenazine-producing
R. etli
was able to inhibit the growth of
Botrytis cinerea
and
Fusarium oxysporum
in vitro. Black bean inoculated with phenazine-producing
R. etli
produced brownish Fix
−
nodules.
Synthetic Consolidants Attacked by Melanin-Producing Fungi: Case Study of the Biodeterioration of Milan (Italy) Cathedral Marble Treated with Acrylics
Authors: Cappitelli Francesca , Nosanchuk Joshua D. , Casadevall Arturo , Toniolo Lucia , Brusetti Lorenzo , Florio Sofia , Principi Pamela , Borin Sara , Sorlini Claudia 
Published: December 2006

ABSTRACT
Monuments and artistic stone surfaces are often consolidated and protected with synthetic polymers, in particular, acrylics. Although it is generally thought that acrylic polymers are resistant to biodeterioration, we report for the first time the systematic occurrence of dematiaceous meristematic fungi on many marble samples of the cathedral in Milan (Italy) previously treated with this material. Fourier transform infrared spectroscopy applied to the Milan cathedral stone samples revealed characteristic features of biodeteriorated synthetic resins that differentiated them from the aged but nonbiodeteriorated samples. Samples showing biological colonization were analyzed for the presence of fungi. Cultivation and morphological characterization and methods independent from cultivation, such as denaturing gradient gel electrophoresis coupled with partial 18S rRNA gene sequencing and immunofluorescence staining with melanin-binding antibodies, showed that melanin-producing species are heavily present on stone surfaces protected with acrylic resins. This observation raises the question of the effectiveness of acrylics in protecting stone artworks.
Analysis of a New Human Parechovirus Allows the Definition of Parechovirus Types and the Identification of RNA Structural Domains
Authors: Al-Sunaidi Mohammed , Williams Çiğdem H. , Hughes Pamela J. , Schnurr David P. , Stanway Glyn 
Published: December 2006

ABSTRACT

Human
parechoviruses (HPeV), members of the
Parechovirus
genus of
Picornaviridae
, are frequent pathogens but have been
comparatively poorly studied, and little is known of their diversity,
evolution, and molecular biology. To increase the amount of information
available, we have analyzed 7 HPeV strains isolated in California
between 1973 and 1992. We found that, on the basis of VP1 sequences,
these fall into two genetic groups, one of which has not been
previously observed, bringing the number of known groups to five. While
these correlate partly with the three known serotypes, two members of
the HPeV2 serotype belong to different genetic groups. In view of the
growing importance of molecular techniques in diagnosis, we suggest
that genotype is an important criterion for identifying viruses, and we
propose that the genetic groups we have defined should be termed human
parechovirus types 1 to 5. Complete nucleotide sequence analysis of two
of the Californian isolates, representing two types, confirmed the
identification of a new genetic group and suggested a role for
recombination in parechovirus evolution. It also allowed the
identification of a putative HPeV1
cis
-acting replication
element, which is located in the VP0 coding region, as well as the
refinement of previously predicted 5′ and 3′
untranslated region structures. Thus, the results have significantly
improved our understanding of these common
pathogens.
Human Metapneumovirus Fusion Protein Vaccines That Are Immunogenic and Protective in Cotton Rats
Authors: Cseke Gabriella , Wright David W. , Tollefson Sharon J. , Johnson Joyce E. , Crowe James E. , Williams John V. 
Published: December 2006

ABSTRACT
Human metapneumovirus (hMPV) is a recently described paramyxovirus that is a major cause of upper and lower respiratory infection in children and adults worldwide. A safe and effective vaccine could decrease the burden of disease associated with this novel pathogen. We previously reported the development of the cotton rat model of hMPV infection and pathogenesis (J. V. Williams et al., J. Virol. 79:10944-10951, 2005). We report here the immunogenicity of an hMPV fusion (F) protein in this model. We constructed DNA plasmids that exhibited high levels of expression of hMPV F in mammalian cells (DNA-F). These constructs were used to develop a novel strategy to produce highly pure, soluble hMPV F protein lacking the transmembrane domain (FΔTM). We then immunized cotton rats at 0 and 14 days with either control vector, DNA-F alone, DNA-F followed by FΔTM protein, or FΔTM alone. All groups were challenged intranasally at 28 days with live hMPV. All three groups that received some form of hMPV F immunization mounted neutralizing antibody responses and exhibited partial protection against virus shedding in the lungs compared to controls. The FΔTM-immunized animals showed the greatest degree of protection (>1,500-fold reduction in lung virus titer). All three immunized groups showed a modest reduction of nasal virus shedding. Neither evidence of a Th2-type response nor increased lung pathology were present in the immunized animals. We conclude that sequence-optimized hMPV F protein protects against hMPV infection when delivered as either a DNA or a protein vaccine in cotton rats.
Nuclear Import of the Preintegration Complex Is Blocked upon Infection by Human Immunodeficiency Virus Type 1 in Mouse Cells
Authors: Tsurutani Naomi , Yasuda Jiro , Yamamoto Naoki , Choi Byung-Il , Kadoki Motohiko , Iwakura Yoichiro 
Published: December 2006

ABSTRACTMouse cells do not support human immunodeficiency virus type 1 (HIV-1) replication because of host range barriers at steps including virus entry, transcription, RNA splicing, polyprotein processing, assembly, and release. The exact mechanisms for the suppression, however, are not completely understood. To elucidate further the barriers against HIV-1 replication in mouse cells, we analyzed the replication of the virus in lymphocytes from human CD4/CXCR4 transgenic mice. Although primary splenocytes and thymocytes allowed the entry and reverse transcription of HIV-1, the integration efficiency of the viral DNA was greatly reduced in these cells relative to human peripheral blood mononuclear cells, suggesting an additional block(s) before or at the point of host chromosome integration of the viral DNA. Preintegration processes were further analyzed using HIV-1 pseudotyped viruses. The reverse transcription step of HIV-1 pseudotyped with the envelope of murine leukemia virus or vesicular stomatitis virus glycoprotein was efficiently supported in both human and mouse cells, but nuclear import of the preintegration complex (PIC) of HIV-1 was blocked in mouse cells. We found that green fluorescent protein (GFP)-labeled HIV-1 integrase, which is known to be important in the nuclear localization of the PIC, could not be imported into the nucleus of mouse cells, in contrast to human cells. On the other hand, GFP-Vpr localized exclusively to the nuclei of both mouse and human cells. These observations suggest that, due to the dysfunction of integrase, the nuclear localization of PIC is suppressed in mouse cells.
Inhibition of Human Immunodeficiency Virus Envelope Glycoprotein- Mediated Single Cell Lysis by Low-Molecular-Weight Antagonists of Viral Entry
Authors: Madani Navid , Hubicki Amy M. , Perdigoto Ana Luisa , Springer Martin , Sodroski Joseph 
Published: December 2006

ABSTRACTThe coexpression of human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins and receptors leads to the lysis of single cells by a process that is dependent upon membrane fusion. This cell lysis was inhibited by low-molecular-weight compounds that interfere with receptor binding or with receptor-induced conformational transitions in the envelope glycoproteins. A peptide, T20, potently inhibited cell-cell fusion but had no effect on single cell lysis mediated by the HIV-1 envelope glycoproteins. Thus, critical events in the lysis of single cells by the HIV-1 envelope glycoproteins occur in intracellular compartments accessible only to small inhibitory compounds.
Prolonged Adherence of Human Immunodeficiency Virus-Derived Vector Particles to Hematopoietic Target Cells Leads to Secondary Transduction In Vitro and In Vivo
Authors: Pan Yung-Wei , Scarlett Jarrad M. , Luoh Tammy T. , Kurre Peter 
Published: December 2006

ABSTRACT
Human immunodeficiency virus type 1-derived lentivirus vectors bearing the vesicular stomatitis virus G (VSV-G) envelope glycoprotein demonstrate a wide host range and can stably transduce quiescent hematopoietic stem cells. In light of concerns about biosafety and potential germ line transmission, they have been used predominantly for ex vivo strategies, thought to ensure the removal of excess surface-bound particles and prevent in vivo dissemination. Studies presented here instead reveal prolonged particle adherence after ex vivo exposure, despite serial wash procedures, with subsequent transduction of secondary target cells in direct and transwell cocultures. We explored the critical parameters affecting particle retention and transfer and show that attachment to the cell surface selectively protects virus particles from serum complement-mediated inactivation. Moreover, studies with nonmyeloablated murine recipients show that transplantation of vector-exposed, washed hematopoietic cells results in systemic dissemination of functional VSV-G/lentivector particles. We demonstrate genetic marking by inadvertent transfer of vector particles and prolonged expression of transgene product in recipient tissues. Our findings have implications for biosafety, vector design, and cell biology research.
Coordinated Regulation and Widespread Cellular Expression of Interferon-Stimulated Genes (ISG) ISG-49, ISG-54, and ISG-56 in the Central Nervous System after Infection with Distinct Viruses
Authors: Wacher Christie , Müller Marcus , Hofer Markus J. , Getts Daniel R. , Zabaras Regina , Ousman Shalina S. , Terenzi Fulvia , Sen Ganes C. , King Nicholas J. C. , Campbell Iain L. 
Published: December 2006

ABSTRACTThe interferon (IFN)-stimulated genes (ISGs) ISG-49, ISG-54, and ISG-56 are highly responsive to viral infection, yet the regulation and function of these genes in vivo are unknown. We examined the simultaneous regulation of these ISGs in the brains of mice during infection with either lymphocytic choriomeningitis virus (LCMV) or West Nile virus (WNV). Expression of the ISG-49 and ISG-56 genes increased significantly during LCMV infection, being widespread and localized predominantly to common as well as distinct neuronal populations. Expression of the ISG-54 gene also increased but to lower levels and with a more restricted distribution. Although expression of the ISG-49, ISG-54, and ISG-56 genes was increased in the brains of LCMV-infected STAT1 and STAT2 knockout (KO) mice, this was blunted, delayed, and restricted to the choroid plexus, meninges, and endothelium. ISG-56 protein was regulated in parallel with the corresponding RNA transcript in the brain during LCMV infection in wild-type and STAT KO mice. Similar changes in ISG-49, ISG-54, and ISG-56 RNA levels and ISG-56 protein levels were observed in the brains of wild-type mice following infection with WNV. Thus, the ISG-49, ISG-54, and ISG-56 genes are coordinately upregulated in the brain during LCMV and WNV infection; this upregulation, in the case of LCMV, was totally (neurons) or partially (non-neurons) dependent on the IFN-signaling molecules STAT1 and STAT2. These findings suggest a dominant role for the ISG-49, ISG-54, and ISG-56 genes in the host response to different viruses in the central nervous system, where, particularly in neurons, these genes may have nonredundant functions.
Cell-Type-Specific Growth Restriction of Vesicular Stomatitis Virus polR Mutants Is Linked to Defective Viral Polymerase Function
Authors: Ostertag Derek , Hoblitzell-Ostertag Traci M. , Perrault Jacques 
Published: December 2006

ABSTRACTVesicular stomatitis virus polR mutants synthesize defective RNA replication products in vitro and display growth restriction in some cultured cells (J. L. Chuang, R. L. Jackson, and J. Perrault, Virology 229:57-67, 1997). We show here that a recombinant virus carrying the polR N protein mutation (R179H) yielded ∼100-fold- and ∼40-fold-lower amounts of infectious virus than the wild type in mouse L-929 and rat 3Y1 cells, respectively, but only ∼3-fold less in hamster BHK cells. Virus genome accumulation was inhibited 6- to 10-fold in restricting cells, but transcription was not affected. No defect in encapsidation of replication products was detected, but virus protein accumulation was reduced two- to threefold in both restricting and nonrestricting cells. polR virus particles released from the latter were 5- to 10-fold less infectious than the wild type but showed no difference in protein composition. Phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF-2α) was enhanced ∼3-fold in polR versus wild-type virus-infected L-929 cells, but neither inhibition of host gene transcription nor inhibition of double-stranded RNA (dsRNA)-activated protein kinase showed significant effects on restriction. Conditioned medium studies revealed no evidence for secretion of antiviral factors from restricting cells. We conclude that the block in polR growth is due to the combined effect of reduced genome replication and lower infectivity of released virus particles and may be due to overproduction of dsRNA. An accompanying paper (D. Ostertag, T. M. Hoblitzell-Ostertag, and J. Perrault, J. Virol. 81:503-513, 2007) provides compelling evidence for the role of dsRNA in this unique restriction phenomenon.
Overproduction of Double-Stranded RNA in Vesicular Stomatitis Virus-Infected Cells Activates a Constitutive Cell-Type-Specific Antiviral Response
Authors: Ostertag Derek , Hoblitzell-Ostertag Traci M. , Perrault Jacques 
Published: December 2006

ABSTRACT
In a companion paper (D. Ostertag, T. M. Hoblitzell-Ostertag, and J. Perrault, J. Virol. 81:492-502, 2007), we provided indirect evidence that cell-type-specific growth restriction of the vesicular stomatitis virus (VSV) polR mutants may be due to enhanced production of double-stranded RNA (dsRNA). We show here that polR growth in mouse L-929 cells was rescued by vaccinia virus coinfection and that sole expression of the vaccinia virus dsRNA-binding E3L protein, via coinfection with an engineered VSV minigenome, also restored polR growth. Expression of dsRNA-binding protein NS1A or NS1B from influenza virus, but not C protein from Sendai virus, which does not bind dsRNA, likewise effected polR rescue. The N-terminal dsRNA-binding domain of NS1A, only 73 amino acids in length, but not a full-size mutant NS1A lacking dsRNA-binding activity, restored polR growth. Both key aspects of polR growth restriction, namely inhibition of genome replication and release of low-infectivity virus particles, were countered by expression of the dsRNA-binding proteins. We tested the effects of overproducing dsRNA in wild-type VSV infections by coinfecting cells with a VSV recombinant expressing the sense strand of the enhanced green fluorescent protein gene (VSV-GFP) and one expressing the antisense strand (VSV-PFG). These coinfections mimicked all aspects of polR restriction, including host range, lack of effect on transcription, reduced virus particle infectivity, and insensitivity to inhibition of host gene transcription or dsRNA-activated protein kinase activity. We conclude that, for some cell types, overproduction of dsRNA during VSV infection triggers an immediate and constitutive host cell antiviral effector response independent of interferon induction or signaling.
Visualization of the Interaction between the Precursors of VPg, the Viral Protein Linked to the Genome ofTurnip Mosaic Virus, and the Translation Eukaryotic Initiation Factor iso 4E In Planta
Authors: Beauchemin Chantal , Boutet Nathalie , Laliberté Jean-François 
Published: December 2006

ABSTRACTThe RNA genome ofTurnip mosaic virusis covalently linked at its 5′ end to a viral protein known as VPg. This protein binds to the translation eukaryotic initiation factor iso 4E [eIF(iso)4E]. This interaction has been shown to be important for virus infection, although its exact biological function(s) has not been elucidated. In this study, we investigated the subcellular site of the VPg-eIF(iso)4E interaction using bimolecular fluorescence complementation (BiFC). As a first step, eIF(iso)4E, 6K-VPg-Pro, and VPg-Pro were expressed as full-length green fluorescent protein (GFP) fusions inNicotiana benthamiana, and their subcellular localizations were visualized by confocal microscopy. eIF(iso)4E was predominantly associated with the endoplasmic reticulum (ER), and VPg-Pro was observed in the nucleus and possibly the nucleolus, while 6K-VPg-Pro-GFP induced the formation of cytoplasmic vesicles budding from the ER. In BiFC experiments, reconstituted green fluorescence was observed throughout the nucleus, with a preferential accumulation in subnuclear structures when the GFP split fragments were fused to VPg-Pro and eIF(iso)4E. On the other hand, the interaction of 6K-VPg-Pro with eIF(iso)4E was observed in cytoplasmic vesicles embedded in the ER. These data suggest that the association of VPg with the translation factor might be needed for two different functions, depending of the VPg precursor involved in the interaction. VPg-Pro interaction with eIF(iso)4E may be involved in perturbing normal cellular functions, while 6K-VPg-Pro interaction with the translation factor may be needed for viral RNA translation and/or replication.
Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome:Chemical Modification and Comparative Sequence Analysis
Authors: Bailey Jennifer M. , Tapprich William E. 
Published: December 2006

ABSTRACT
Coxsackievirus B3 (CVB3) is a picornavirus which causes myocarditis and pancreatitis
and may play a role in type I diabetes. The viral genome is a single
7,400-nucleotide polyadenylated RNA encoding 11 proteins in a single
open reading frame. The 5′ end of the viral genome contains a
highly structured nontranslated region (5′NTR) which folds to
form an internal ribosome entry site (IRES) as well as structures
responsible for genome replication, both of which are critical for
virulence. A structural model of the CVB3 5′NTR, generated
primarily by comparative sequence analysis and energy minimization,
shows seven domains (I to VII). While this model provides a preliminary
basis for structural analysis, the model lacks comprehensive
experimental validation. Here we provide experimental evidence from
chemical modification analysis to determine the structure of the CVB3
5′NTR. Chemical probing results show that the theoretical model
for the CVB3 5′NTR is largely, but not completely, supported
experimentally. In combination with our chemical probing data, we have
used the RNASTRUCTURE algorithm and sequence comparison of 105
enterovirus sequences to provide evidence for novel secondary and
tertiary interactions. A comprehensive examination of secondary
structure is discussed, along with new evidence for tertiary
interactions. These include a loop E motif in domain III and a
long-range pairing interaction that links domain II to domain V. The
results of our work provide mechanistic insight into key functional
elements in the cloverleaf and IRES, thereby establishing a base of
structural information from which to interpret experiments with CVB3
and other
picornaviruses.
Borna Disease Virus Matrix Protein Is an Integral Component of the Viral Ribonucleoprotein Complex That Does Not Interfere with Polymerase Activity
Authors: Chase Geoffrey , Mayer Daniel , Hildebrand Antonia , Frank Ronald , Hayashi Yohei , Tomonaga Keizo , Schwemmle Martin 
Published: December 2006

ABSTRACT
We have recently shown that the matrix protein M of Borna disease virus (BDV) copurifies with the affinity-purified nucleoprotein (N) from BDV-infected cells, suggesting that M is an integral component of the viral ribonucleoprotein complex (RNP). However, further studies were hampered by the lack of appropriate tools. Here we generated an M-specific rabbit polyclonal antiserum to investigate the intracellular distribution of M as well as its colocalization with other viral proteins in BDV-infected cells. Immunofluorescence analysis revealed that M is located both in the cytoplasm and in nuclear punctate structures typical for BDV infection. Colocalization studies indicated an association of M with nucleocapsid proteins in these nuclear punctate structures. In situ hybridization analysis revealed that M also colocalizes with the viral genome, implying that M associates directly with viral RNPs. Biochemical studies demonstrated that M binds specifically to the phosphoprotein P but not to N. Binding of M to P involves the N terminus of P and is independent of the ability of P to oligomerize. Surprisingly, despite P-M complex formation, BDV polymerase activity was not inhibited but rather slightly elevated by M, as revealed in a minireplicon assay. Thus, unlike M proteins of other negative-strand RNA viruses, BDV-M seems to be an integral component of the RNPs without interfering with the viral polymerase activity. We propose that this unique feature of BDV-M is a prerequisite for the establishment of BDV persistence.