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PubMed2006

Microplitis demolitor bracovirus genome segments vary in abundance and are individually packaged in virions.

Polydnaviruses (PDVs) are distinguished by their unique association with parasitoid wasps and their segmented, double-stranded (ds) DNA genomes that are non-equimolar in abundance. Relatively little is actually known, however, about genome packaging or segment abundance of these viruses. Here, we conducted electron microscopy (EM) and real-time polymerase chain reaction (PCR) studies to characterize packaging and segment abundance of Microplitis demolitor bracovirus (MdBV). Like other PDVs, MdBV replicates in the ovaries of females where virions accumulate to form a suspension called calyx fluid. Wasps then inject a quantity of calyx fluid when ovipositing into hosts. The MdBV genome consists of 15 segments that range from 3.6 (segment A) to 34.3 kb (segment O). EM analysis indicated that MdBV virions contain a single nucleocapsid that encapsidates one circular DNA of variable size. We developed a semi-quantitative real-time PCR assay using SYBR Green I. This assay indicated that five (J, O, H, N and B) segments of the MdBV genome accounted for more than 60% of the viral DNAs in calyx fluid. Estimates of relative segment abundance using our real-time PCR assay were also very similar to DNA size distributions determined from micrographs. Analysis of parasitized Pseudoplusia includens larvae indicated that copy number of MdBV segments C, B and J varied between hosts but their relative abundance within a host was virtually identical to their abundance in calyx fluid. Among-tissue assays indicated that each viral segment was most abundant in hemocytes and least abundant in salivary glands. However, the relative abundance of each segment to one another was similar in all tissues. We also found no clear relationship between MdBV segment and transcript abundance in hemocytes and fat body.

Animals↗

PubMed2004

Comparison of serum sensitivities of pseudotype retroviruses produced from newly established packaging cell lines of human and feline origins.

To apply retrovirus vectors for in vivo gene therapy in cats, it is necessary to develop vector systems that are not inactivated by cat serum. In this study, the retrovirus packaging cell lines 2SC-1 and AHCeB7 were newly established from human embryonic kidney (HEK) 293 and feline fibroblastic AH927 cells, respectively. Then the sensitivities of pseudotype viruses released from these cell lines to fresh sera from humans and cats were compared. Pseudotype viruses from the 2SC-1 cells were inactivated efficiently by cat serum but not by human serum. Pseudotype viruses from the AHCeB7 cells were also inactivated efficiently by human serum, however they were rather resistant to cat serum. When the xenoantigenicity of the cell lines was examined by flow cytometry, AH927 cells reacted with human serum, however, HEK293 cells did not react with cat serum. These results suggested that pseudotype viruses from 2SC-1 cells were inactivated by the fresh cat serum in an antibody-independent manner. Chelating experiments revealed that certain temperature-sensitive factor(s) other than complements might be involved in the inactivation. The usage of feline cells as packaging cells is suitable for in vivo gene therapy in cats.

Animals↗

PubMed2004

Nonstructural proteins involved in genome packaging and replication of rotaviruses and other members of the Reoviridae.

Rotaviruses, members of family Reoviridae, are a major cause of acute gastroenteritis of infants and young children. The rotavirus genome consists of 11 segments of double-stranded (ds)RNA and the virion is an icosahedron composed of multiple layers of protein. The virion core is formed by a layer of VP2 and contains multiple copies of the RNA-dependent RNA polymerase VP1 and the mRNA-capping enzyme VP3. Double-layered particles (DLPs), representing cores surrounded by a layer of VP6, direct the synthesis of viral mRNAs. Rotavirus core- and DLP-like replication intermediates (RIs) catalyze the synthesis of dsRNA from viral template mRNAs coincidentally with the packaging of the mRNAs into the pre-capsid structures of RIs. In addition to structural proteins, the nonstructural proteins NSP2 and NSP5 are components of RIs with replicase activity. NSP2 self assembles into octameric structures that have affinity for ssRNA and NTPase and helix-destabilizing activites. Its interaction with nucleotides induces a conformational shift in the octamer to a more condensed form. Phosphate residues generated by the NTPase activity are believed to be transferred from NSP2 to NSP5, leading to the hyperphosphorylation of the latter protein. It is suspected that the transfer of the phosphate group to NSP5 allows NSP2 to return to its noncondensed state and, thus, to accept another NTP molecule. The NSP5-mediated cycling of NSP2 from condensed to noncondensed combined with its RNA binding and helix-destabilizing activities are consistent with NSP2 functioning as a molecular motor to facilitate the packaging of template mRNAs into the pre-capsid structures of RIs. Similarities with the bluetongue virus protein NS2 and the reovirus proteins sigmaNS and micro2 suggest that they may be functional homologs of rotavirus NSP2 and NSP5.

Amino Acid Sequence↗

PubMed2004

Replication and packaging properties of short Paramyxovirus defective RNAs.

In the course of a Sendai virus infection, short genome versions (called defective) are frequently produced. These compete with the full length genome for replication (hence called interfering) and decrease the severity of the infection. The portion of the defective genome required for this effect can be limited, much shorter than the size of the defective genome. We postulated then that defective genome size follows from conditions required for their production more than for exerting the protective effect. Therefore, we set up experiments to determine which of the steps involved in their production may require this larger size. We constructed a series of Sendai virus mini-genomes, increasing their size from the smallest possible and we followed their ability to replicate, to amplify through multiples cycles of infection and to be packaged into virus particles, all steps required for their efficient production. We found that the mini-genomes replicated and amplified efficiently regardless of their size. The uptake into virus particles, however, depended on a threshold length. The data suggest no limitation in the ability of the viral RNA polymerase to generate and amplify very short size defective genomes. They however, point to limitations in the ability of short genomes to be packaged into virus particles.

Animals↗

PubMed2005

Generation of serum-stabilized retroviruses: reduction of alpha1,3gal-epitope synthesis in a murine NIH3T3-derived packaging cell line by expression of chimeric glycosyltransferases.

Retroviral vectors released from mouse-derived packaging cell lines are inactivated in human sera by naturally occurring antibodies due to the recognition of Galalpha1,3Galbeta1,4GlcNAc (alphagal-epitope) decorated surface proteins. In this study, an extensive analysis of the glycosylation potential of NIH3T3-derived PA317 packaging cells using combined MALDI/TOF-MS and HPAE-PAD reveals that 34% of the N-glycan moiety represents alphagal-epitope containing structures. Stable expression of glycosyltransferases and transport signal chimeras has been demonstrated to represent an efficient tool to alter cell- and species-specific glycosylation (Grabenhorst and Conradt, 1999. J. Biol. Chem. 274, 36107-36116). In order to reduce alphagal-epitope synthesis selected chimeric glycosyltransferases were constructed by fusing Golgi-signal sequences for compartment-specific localization with the catalytic domain of alpha2,3-sialyltransferase (ST3). Stable expression of these constructs in these cells resulted in a significant reduced alphagal-epitope synthesis, and moreover, a release of retroviral vectors showing an up to 3.5-fold increase in serum stability. Thus, our results suggest that the stably transfected cells stably transfected with chimeric glycosyltransferases compete efficiently with endogenous alpha1,3-galactosyltransferase. This approach allows favored glycodesign and we anticipate the applicability of such improved retroviral vectors produced by glycosylation engineered host cells for in vivo gene therapy and, furthermore, suggest the therapeutic benefit of this technology for xenotransplantation.

Animals↗

PubMed1984

RECFIT: a microcomputer-based nonlinear regression curve-fitting package for the quantitative resolution of beta-adrenoceptor subtypes and estimation of nonspecific binding.

A dedicated nonlinear regression based curve-fitting packages has been developed for quantitative analysis of beta-adrenoceptor subtypes. A feature of this package is the provision to obtain initial parameter estimates using a conversational graphical technique where the user is prompted for parameter estimates, and the resulting curve is displayed over the data. Data are then fitted to a one- or two-binding site model with user-selected weighting and constraints on the parameters. A novel feature is the provision to estimate the nonspecific binding component in the assays as a parameter in the model. The printout for each model consists of the parameters and their standard deviations, estimates of the goodness of fit, an analysis of residuals, and a graph of the data points overlayed with the fitted curve. The nonlinear regression algorithm is based on that of Gauss-Newton. When unweighted, the values determined by RECFIT are essentially the same as those found using the BMDPAR programs on an ICL 2976 mainframe computer. The implementation is reasonably efficient; a typical run for a two-site fit, using nine data points and estimating nonspecific binding, took a total time of about 8 min, excluding data entry and derivation of initial estimates, 4 min for the fitting, 30 sec for graph generation, and 2-3 min for printing of the graph and data.

Binding Sites↗

PubMed2001

Java-based graphical user interface for MRUI, a software package for quantitation of in vivo/medical magnetic resonance spectroscopy signals.

This article describes a Java-based graphical user interface for the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo/medical MR spectroscopy data. We have found that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI system. We also have established that MR quantitation algorithms, programmed in the past in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI).

Algorithms↗

PubMed2000

Packaging of up to 240 subunits of a 17 kDa nuclease into the interior of recombinant hepatitis B virus capsids.

The icosahedral nucleocapsid of hepatitis B virus (HBV) consists of multiple subunits of a single 183 amino acids (aa) core protein encasing the viral genome. However, recombinant core protein alone also forms capsid-like particles. We have recently shown that a 238 aa protein centrally inserted into the core protein can be displayed on the particle surface. Here we demonstrate that replacement of the C-terminal basic domain by the 17 kDa Staphylococcus aureus nuclease also yields particles but that in these the foreign domains are located in the interior. The packaged nuclease is enzymatically active, and the chimeric protein forms mosaic particles with the wild-type core protein. Hence the HBV capsid is useful as a molecular platform which, dependent on the fusion site, allows foreign protein domains to either be packaged into or be exposed on the exterior of the particle. These results are of relevance for the use of the HBV capsid as a vaccine carrier, and as a target for antiviral therapy.

Amino Acid Sequence↗

PubMed1997

The packaging capacity of adeno-associated virus (AAV) and the potential for wild-type-plus AAV gene therapy vectors.

Because of its ability to integrate chromosomally and its non-pathogenic nature, adeno-associated virus (AAV) has significant potential as a human gene therapy vector. Here we investigate the maximum amount of DNA which can be inserted into the AAV genome and still allow efficient packaging into an infectious virus particle. Altered wild-type AAV genomes were constructed with inserts, which increased in size by 100 bp, ligated at map unit 96. These large wild-type-plus genomes were able to replicate and produce infectious virus, at levels slightly reduced but comparable to normal sized wild type, until the insert size reached 1 kb. These data indicate that the maximum effective packaging capacity of AAV is approximately 900 bp larger than wild type, or 119%. Furthermore, it is demonstrated that these large AAV genomes are able to latently infect cells by chromosomal integration as does wild-type AAV. These data suggest that therapy vectors carrying a foreign gene of 900 bp or less can be generated from AAV, by ligation into non-essential locations, and result in a recombinant AAV virus with a fully wild-type phenotype. Such wild-type-plus AAV vectors will have both advantages and disadvantages over defective recombinant AAV virus - the most important advantages being the ease in which high titers of infectious virus can be generated and the ability to specifically integrate within chromosome 19. Once the concern subsides over the presence of wild-type AAV in clinical applications, wild-type AAV vectors may find specific application niches for use in human gene therapy.

Cells, Cultured↗

PubMed1980

Gas chromatographic determination of vinylidene chloride monomer in packaging films and in foods.

Headspace electron-capture-gas chromatographic methods are described for the quantification of vinylidene chloride monomer in poly(vinylidene chloride) containing films and in film-packaged foodstuffs. Quantification of vinylidene chloride was possible at levels down to 0.001 mg/m2 in the films and 0.005 ppm in the foodstuffs. The results of a small survey of the amounts of this compound in packaging films and foodstuffs purchased from retail outlets are reported.

Chromatography, Gas↗

PubMed2002

Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal.

The packaging signal (Psi) of the human immunodeficiency virus type 1 (HIV-1) enables encapsidation of the full-length genomic RNA against a background of a vast excess of cellular mRNAs. The core HIV-1 Psi is approximately 109 nucleotides and contains sequences critical for viral genomic dimerisation and splicing, in addition to the packaging signal. It consists of a series of stem-loops (termed SL-1 to SL-4), which can be arranged in a cloverleaf secondary structure. Using a combination of NMR spectroscopy, UV melting experiments, molecular modeling and phylogenetic analyses, we have explored the structure of two conserved internal loops proximal to the palindromic sequence of SL-1. Internal loop A, composed of six purines, forms a flexible structure that is strikingly similar to the Rev responsive element motif when bound to Rev protein. This result suggests that it may function as a protein-binding site. The absolutely conserved four-purine internal loop B is instead conformationally and thermodynamically unstable, and exhibits multiple conformations in solution. By introducing a double AGG to GGA mutation within this loop, its conformation is stabilised to form a new intra-molecular G:A:G base-triplet. The structure of the GGA mutant explains the relative instability of the wild-type loop. In a manner analogous to SL-3, we propose that conformational flexibility at this site may facilitate melting of the structure during Gag protein capture or genomic RNA dimerisation.

Base Pairing↗

PubMed2003

Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness.

We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent characterization of the loading process of the genome inside the phi29 bacteriophage capsid. Our emphasis is on the modelling of double-stranded DNA as a flexible thick polymer (tube) instead of a beads-and-springs chain. By using finite-size scaling to extrapolate our results to genome lengths appropriate for phi29, we find that the thickness-induced force may account for up to half the one measured experimentally at high packing densities. An analogous agreement is found for the total work that has to be spent in the packaging process. Remarkably, such agreement can be obtained in the absence of any tunable parameters and is a mere consequence of the DNA thickness. Furthermore, we provide a quantitative estimate of how the persistence length of a polymer depends on its thickness. The expression accounts for the significant difference in the persistence lengths of single and double-stranded DNA (again with the sole input of their respective sections and natural nucleotide/base-pair spacing).

Bacteriophages↗

PubMed1990

Bacteriophage T7 DNA packaging. III. A "hairpin" end formed on T7 concatemers may be an intermediate in the processing reaction.

An unusual left end (M-end) has been identified on bacteriophage T7 DNA isolated from T7-infected cells. This end has a "hairpin" structure and is formed at a short inverted repeat sequence centered around nucleotide 39,587 of T7, 190 base-pairs to the left of the site where a mature left end is formed on the T7 concatemer. We do not detect the companion right end that would be formed if the M-end is produced by a double-stranded cut on the T7 concatemer. This suggests that the hairpin left end may be generated from a single-stranded cut in the DNA that is used to prime rightward DNA synthesis. The formation of M-end does not require the products of T7 genes 10, 18 or 19, proteins that are essential for the formation of mature T7 ends. During infection with a T7 gene 3 (endonuclease) mutant, phage DNA synthesis is reduced and the concatemers are not processed into unit length DNA molecules, but both M-end and the mature right end are formed on the concatemer DNA. These two ends are also found associated with the large, rapidly sedimenting concatemers formed during a normal T7 infection while the mature left end is present only on unit length T7 DNA molecules. We propose that DNA replication primed from the hairpin end produced by a nick in the inverted repeat sequence provides a mechanism to duplicate the terminal repeat before DNA packaging. Packaging is initiated with the formation of a mature right end on the branched concatemer and, as the phage head is filled, the T7 gene 3 endonuclease may be required to trim the replication forks from the DNA. Concatemer processing is completed by the removal of the 190 base-pair hairpin end to produce the mature left end.

Base Sequence↗

PubMed1996

Vesamicol, an inhibitor of acetylcholine vesicle packaging, increases synaptophysin phosphorylation in rat cortical synaptosomes.

Vesamicol (AH5183) is an inhibitor (IC50, 50 nM) of acetylcholine (ACh) vesicle packaging. Vesamicol increases the phosphorylation pattern of synaptophysin (p38), identified as a vesicle-specific phosphoprotein involved in vesicle-mediated neurotransmitter release. Percoll fractionation of the rat cortex yielded a cholinergic-enriched synaptosomal Fraction 4. Fraction 4 contained the highest enrichment of cholineacetyl-transferase activity (86 +/- 4.6 mumole AcCh/g protein/hr.) in the Percoll gradient. Fraction 4 demonstrated oxygen consumption (108 +/- 23.4 nmole/mg protein), levels of adenosine triphosphate, ATP, (10.29 +/- 0.45 nmole/mg protein) and adenosine diphosphate, ADP, (10.54 +/- 2.72 nmole/mg protein), energy potential (ATP/[ADP] [Pi], (0.49) phosphate uptake (65-80 nmoles phosphate/mg tissue), 32Pi labelling (130 +/- 12 x 10(5) DPM/mg tissue; 74 +/- 9.8 x 10(2) nmoles phosphate/mg tissue). Synaptophysin was identified by Western blotting and confirmed by qualitative immunoprecipitation. Synaptophysin phosphorylation was confirmed by autoradiograph. Synaptophysin phosphorylation increased (225%) in the presence of vesamicol (ED50, 1 nM) in Fraction 4. Vesamicol (50 nM) and vanadate (54 microM) were compared for their effects on synaptophysin. This study suggests that during the inhibition of acetylcholine packaging by vesamicol that synaptophysin is phosphorylated. Therefore, the phosphorylation and dephosphorylation of synaptophysin may be involved in the transport of acetylcholine in or out of the synaptic vesicle.

Acetylcholine↗

PubMed2003

Vibrational Markovian modelling of footprints after the interaction of antibiotics with the packaging region of HIV type 1.

The design of novel anti-HIV compounds has now become a crucial area for scientists working in numerous interrelated fields of science such as molecular biology, medicinal chemistry, mathematical biology, molecular modelling and bioinformatics. In this context, the development of simple but physically meaningful mathematical models to represent the interaction between anti-HIV drugs and their biological targets is of major interest. One such area currently under investigation involves the targets in the HIV-RNA-packaging region. In the work described here, we applied Markov chain theory in an attempt to describe the interaction between the antibiotic paromomycin and the packaging region of the RNA in Type-1 HIV. In this model, a nucleic acid squeezed graph is used. The vertices of the graph represent the nucleotides while the edges are the phosphodiester bonds. A stochastic (Markovian) matrix was subsequently defined on this graph, an operation that codifies the probabilities of interaction between specific nucleotides of HIV-RNA and the antibiotic. The strength of these local interactions can be calculated through an inelastic vibrational model. The successive power of this matrix codifies the probabilities with which the vibrations after drug-RNA interactions vanish along the polynucleotide main chain. The sums of self-return probabilities in the k-vicinity of each nucleotide represent physically meaningful descriptors. A linear discriminant function was developed and gave rise to excellent discrimination in 80.8% of interacting and footprinted nucleotides. The Jackknife method was employed to assess the stability and predictability of the model. On the other hand, a linear regression model predicted the local binding affinity constants between a specific nucleotide and the antibiotic (R(2)=0.91, Q(2)=0.86). These kinds of models could play an important role either in the discovery of new anti-HIV compounds or the study of their mode of action.

Anti-HIV Agents↗

PubMed1988

Multiple neuropeptides derived from a common precursor are differentially packaged and transported.

The ELH prohormone is proteolytically processed into at least nine peptides which govern egg-laying behavior in Aplysia. Quantitative immunocytochemistry demonstrates that peptides derived from the prohormone are packaged into distinct vesicle classes. Further experiments suggest the segregation occurs via a rapid initial proteolytic cleavage of the prohormone followed by sorting at the trans Golgi. Egg-laying hormone (ELH) immunoreactivity is localized to the cell body and processes, while bag cell peptide (BCP) immunoreactivity is greater in the cell body. Steady state levels of the amino-terminal set of peptides including the BCPs are 3- to 8-fold lower than the carboxy-terminal cleavage products, such as ELH. Thus, intracellular packaging and routing of the peptides cleaved from a single prohormone regulate their localization and levels in these neurons.

Animals↗

PubMed2000

The use of buck and ram extenders and two packaging systems to cryopreserve aoudad (Ammotragus lervia) spermatozoa.

Because the aoudad has been hunted to near extinction, cryopreservation of their semen would be useful for DNA conservation and for the possible re-establishment of captive bred animals to their former ranges. This study was conducted to investigate the effectiveness of cryopreserving aoudad spermatozoa. Semen samples from four post-pubertal animals were collected using electro-ejaculation. Microscopic analysis was performed to assess the percentages of progressively and non-progressively motile spermatozoa as well as intact acrosomes in samples prior to freezing and post-thaw. Extended samples (0.2 mL) were frozen using 2 different extenders and packaging systems and stored in LN2 Post-thaw data were arcsine-transformed and analyzed using ANOVA, 2 x 2 factorial. Samples that were processed using the ram/straw method had a significantly higher percentage (P < 0.05) of spermatozoa with intact acrosomes than did any other system. In addition, samples that were processed with the buck/pellet system had significantly greater percentages (P < 0.05) of progressive and non-progressively motile spermatozoa than the samples processed using either extender and packaged in straws. This study illustrates that some aoudad spermatozoa may be cryopreserved using the extender/processing systems developed for the domestic buck and ram.

Animals↗

PubMed2001

Industrial application of an antilisterial strain of Lactobacillus sakei as a protective culture and its effect on the sensory acceptability of cooked, sliced, vacuum-packaged meats.

The application of a protective lactic acid bacterium (LAB) during the commercial production of cooked meat products is described. The LAB, a strain of Lactobacillus sakei, was previously isolated from cooked ham and inhibited growth of Listeria monocytogenes and Escherichia coli O157:H7 in this product. L. sakei was applied to the cooked products at a concentration of 10(5)-10(6) cfu/g immediately before slicing and vacuum-packaging using a hand-operated spraying bottle. The LAB strain inhibited growth of 10(3) cfu/g of a cocktail of three rifampicin resistant mutant L. monocytogenes strains both at 8 degrees C and 4 degrees C. Consumer acceptance tests of cooked ham and of servelat sausage, a Norwegian non-fermented cooked meat sausage, showed that control and inoculated products were equally acceptable. The products were still acceptable after storage for 28 days at 4 degrees C and, after opening the packages, for a further 5 days at 4 degrees C. The findings presented here confirm that the L. sakei strain is suitable for use as a protective culture and may technically easily be implemented in the commercial production of cooked meat products.

Animals↗