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At least 973 records · Page 54Linked to original sources
PubMed2005

Mechanism of force generation of a viral DNA packaging motor.

A large family of multimeric ATPases are involved in such diverse tasks as cell division, chromosome segregation, DNA recombination, strand separation, conjugation, and viral genome packaging. One such system is the Bacillus subtilis phage phi 29 DNA packaging motor, which generates large forces to compact its genome into a small protein capsid. Here we use optical tweezers to study, at the single-molecule level, the mechanism of force generation in this motor. We determine the kinetic parameters of the packaging motor and their dependence on external load to show that DNA translocation does not occur during ATP binding but is likely triggered by phosphate release. We also show that the motor subunits act in a coordinated, successive fashion with high processivity. Finally, we propose a minimal mechanochemical cycle of this DNA-translocating ATPase that rationalizes all of our findings.

Adenosine Diphosphate↗
PubMed2007

Determination of isopropyl-9H-thioxanthen-9-one in packaged beverages by solid-phase extraction clean-up and liquid chromatography with tandem mass spectrometry detection.

A simple method was developed and validated for the trace determination of 2-isopropylthioxanthone (ITX) in packaged drinks. Samples were extracted from the food matrix using acetonitrile:water (60:40, v/v), and further subjected to clean-up and preconcentration using solid-phase extraction prior to analysis by liquid chromatography-tandem mass spectrometry using multiple reaction monitoring (MRM) mode. The use of 2-isopropyl-[(2)H7]thioxanthen-9-one was incorporated into the method as an internal standard. Excellent 3-day interday precision data (RSD 0.72%, n=10), and intraday precision data (RSD 0.52%, n=10) were obtained on a 0.10 microg/L standard solution. Spiked samples (n=8) were used to gauge the accuracy of the method at the concentration levels of 2.5, 100, and 500 microg/kg in food; recoveries ranged from 97.0 to 103.0%. These excellent validation data suggest the exciting possibility of using this method for the determination of low levels of ITX migrating from printed food packaging materials into beverages with a method quantitation limit of 0.50 microg/kg. For the first time, analysis on a range of milk, juice, tea and yoghurt drinks, as well as their respective food packaging materials were performed for comparative studies on their ITX content.

Beverages↗
PubMed2005

Packages of vitreous collagen (type II) in the human retina: an indication of postnatal collagen turnover?

The purpose of this study was to evaluate the vitreoretinal border in the (pre-)equatorial area in nonpathologic human donor eyes, because the majority of retinal defects induced by posterior vitreous detachment (PVD) are located there. Nine eyes (24-80 years) were fixed and embedded in Technovit 8100. After evaluation by light microscope, areas of interest were selected for immunotransmission electron microscope. Anti-type II collagen antibody was used to stain vitreous fibrils and lamellae; anti-type IV collagen antibody was used to identify the internal limiting lamina (ILL); anti-vimentin and anti-CD-68 antibodies stained retinal Muller cells and macrophages, respectively. Observations included fusing of lamellae with the ILL, an intravitreal course of the ILL, and clear focal interruptions in the ILL. In addition, an obvious finding was the presence of intraretinal packages of type II collagen. Interestingly these collagen packages were closely related to Muller cells and, in several eyes, also to macrophages, cell debris and interruptions in the ILL. In our opinion, the collagen packages can reflect the net result of a process of interactive remodelling, in which both breakdown and synthesis of vitreous and ILL collagens take place. Connections between vitreous and intraretinal collagen networks can make the (pre-)equatorial area more vulnerable to tearing and retinal detachment in the case of liquefaction and PVD.

Adult↗
PubMed2006

Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.

Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to expansion of the polymerase complex, minus and plus strand RNA synthesis, and assembly of the nucleocapsid. The phi6 in vitro assembly and packaging system is a valuable model for dsRNA virus replication. The structure of the nucleocapsid at 7.5 A resolution presented here reveals the secondary structure of the two major capsid proteins. Asymmetric P1 dimers organize as an inner T = 1 shell, and P8 trimers organize as an outer T = 13 laevo shell. The organization of the P1 molecules in the unexpanded and expanded polymerase complex suggests that the expansion is accomplished by rigid body movements of the P1 monomers. This leads to exposure of new potential RNA binding surfaces to control the sequential packaging of the genome segments.

Bacteriophage phi 6↗
PubMed2004

The DNA cleavage and packaging protein encoded by the UL33 gene of herpes simplex virus 1 associates with capsids.

The U(L)33 gene of herpes simplex virus 1 (HSV-1) encodes a protein (pU(L)33) that is essential for the cleavage and packaging of concatameric herpesvirus DNA into preformed capsids. Previous data have suggested that the U(L)33 protein interacts with the cleavage and packaging proteins encoded by U(L)15 and U(L)28 that are known to associate with capsids. Examination of purified A capsids that lack DNA and are derived from aborted packaging events, B capsids that lack DNA, and C capsids that contain DNA revealed an association of the U(L)33 protein with all three capsid types. More U(L)33 protein was detected in A capsids than was present in B capsids. Capsid association was susceptible to guanidine-HCl treatment and independent of the presence of U(L)15 or U(L)28. Capsid association of pU(L)33 was also independent of U(L)6, which is believed to encode the portal into which DNA is inserted. These data suggest that pU(L)33 may act as part of the capsid-associated molecular machinery that translocates cleaved genomic DNA into the capsid interior.

Animals↗
PubMed2006

Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage.

Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulation of the hexamer within the procapsid. Here we use hydrogen-deuterium exchange and mass spectrometry to delineate the interactions of the P4 hexamer with the bacteriophage phi12 procapsid. P4 associates with the procapsid via its C-terminal face. The interactions also stabilize subunit interfaces within the hexamer. The conformation of the virus-bound hexamer is more stable than the hexamer in solution, which is prone to spontaneous ring openings. We propose that the stabilization within the viral capsid increases the packaging processivity and confers selectivity during RNA loading.

Adenosine Triphosphatases↗
PubMed2006

Localizing the reovirus packaging signals using an engineered m1 and s2 ssRNA.

Using in vitro engineered and transcribed reovirus m1 and s2 ssRNAs, we demonstrate that the nucleotides used to identify these ssRNAs are localized to the 5' and not the 3' termini. To demonstrate this, we used our previously reported S2-CAT reovirus and we report the creation of an engineered M1-CAT reovirus. The M1 gene of this virus retains 124 nucleotides from the wild type M1 gene preceding the CAT gene and 172 nucleotides from the wild type gene following the CAT gene. The engineered M1-CAT ssRNA is 1048 nucleotides in length, much shorter than the wild type M1 at 2304 nucleotides. We have used a set of chimeric s2.m1 ssRNAs to localize the packaging signals within these RNAs. By packaging signals we mean that the presence of these signals in engineered ssRNAs results in these ssRNAs being replicated to dsRNA and packaged into progeny virus. An engineered ssRNA with a 5' sequence identical with the wild type s2 ssRNA, supported by a 3' sequence from either the m1 or s2 ssRNA, is incorporated into a virus as an S2 dsRNA. Likewise, an ssRNA with an m1 5' end is incorporated as an M1 dsRNA.

Animals↗
PubMed2000

Status of nutrition labeling, health claims, and nutrient content claims for processed foods: 1997 Food Label and Package Survey.

The Food and Drug Administration (FDA) conducts studies of food labels as part of its ongoing monitoring of the nutritional status of the US population. In 1994 FDA nutrition labeling rules were implemented and in 1997 the Food Label and Package Survey characterized various aspects of the labeling of processed, packaged foods, including nutrition labeling, health claims, and nutrient content claims. For the survey, FDA selected a multistage, representative sample of food products from the SCAN-TRACK food sales database (AC Nielsen Co, Schaumburg, Ill). FDA identified 58 product groups and selected those product classes from the database that accounted for 80% of sales in each group. From each product class, FDA selected the 3 top-selling product brands and randomly selected follower brands. Based on label information from a final sample of 1,267 food products, FDA determined the percentage of products sold that bear Nutrition Facts labels, health claims, and nutrient content claims. The purpose of this article was to present FDA findings regarding the status of food labels 3 years after implementation of the nutrition labeling rules. Nutrition-labeled products accounted for an estimated 96.5% of the annual sales of processed, packaged foods. An additional 3.4% of products sold were exempt from labeling regulations. Nutrient content claims and health claims appeared on an estimated 39% and 4%, respectively, of the products sold. Dietitians and other health care professionals can use this survey information to identify food types with specific label information and to assist the US consumer in making more varied and healthful food choices in the marketplace.

Food Labeling↗
PubMed2003

Packaging of single DNA molecules by the yeast mitochondrial protein Abf2p.

Mitochondrial and nuclear DNA are packaged by proteins in a very different manner. Although protein-DNA complexes called "nucleoids" have been identified as the genetic units of mitochondrial inheritance in yeast and man, little is known about their physical structure. The yeast mitochondrial protein Abf2p was shown to be sufficient to compact linear dsDNA, without the benefit of supercoiling, using optical and atomic force microscopy single molecule techniques. The packaging of DNA by Abf2p was observed to be very weak as evidenced by a fast Abf2p off-rate (k(off) = 0.014 +/- 0.001 s(-1)) and the extremely small forces (<0.6 pN) stabilizing the condensed protein-DNA complex. Atomic force microscopy images of individual complexes showed the 190-nm structures are loosely packaged relative to nuclear chromatin. This organization may leave mtDNA accessible for transcription and replication, while making it more vulnerable to damage.

Binding Sites↗
PubMedDate not supplied

Repair of benzo[a]pyrene diol epoxide damaged bacteriophage T7 DNA determined by survival of phage made by in vitro packaging.

DNA from bacteriophage T7 was treated with benzo[a]pyrene diol epoxide (BPDE) and the number of covalently bound adducts per T7 genome was determined. BPDE treated T7 DNA was then incubated in an in vitro DNA packaging system so as to form infective T7 phage. The observed reduced survival of these phage measured with Escherichia coli uvrA- indicator bacteria showed that the BPDE treated DNA was in fact utilized by the in vitro packaging system and that the resulting phage contained DNA damage caused by in vitro exposure to BPDE. T7 DNA damage by BPDE was also incubated in an in vitro DNA repair system that used partially purified uvrABC proteins from E. coli. Alkaline sucrose gradient analysis demonstrated that nicks were introduced into the damaged DNA and that these incisions were repaired to yield nearly intact DNA molecules of about the size of a T7 genome. Encapsulation of the repaired DNA with the packaging system yielded phage that showed higher survival than the unrepaired control when plated on uvrA- indicator bacteria.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1998

The extended packaging sequence of MoMLV contains a constitutive mRNA nuclear export function.

The present report shows that incorporation of defined sequences from the Moloney murine leukaemia virus (MoMLV) into Rex dependent expression vectors based on the human T-cell leukaemia virus (HTLV-1) allows Rex independent gene expression. Deletion mutagenesis of the MoMLV derived sequences allowed this function to be localised to a 312 nt length sequence overlapping the MoMLV gag p15/p12 open reading frame. This 'extended packaging sequence' has been reported to markedly increase the titre of in vitro packaged retroviral vectors. Using fluorescent in situ hybridisation combined with confocal microscopy we show that the 312 nt element can replace Rex mediated nuclear export and expression of transcripts containing HTLV-1 cis acting repressive elements. Our observations are consistent with the extended packaging sequence of MoMLV exerting a constitutive mRNA nuclear export function.

Base Sequence↗
PubMed2003

Multiple headspace solid-phase microextraction for the quantitative determination of volatile organic compounds in multilayer packagings.

The theory of multiple headspace solid-phase microextraction (HS-SPME) and a method based on multiple HS-SPME for the quantitative determination of volatile organic compounds (VOCs) in packaging materials is presented. The method allows the direct analysis of solid samples without using organic solvents to extract analytes. Multiple headspace solid-phase microextraction is a stepwise method proposed to eliminate the influence of the sample matrix on the quantitative analysis of solid samples by HS-SPME. Different amounts of packaging and different volumes of standard solution were studied in order to remove a substantial quantity of analytes from the headspace at each extraction and obtain the theoretical exponential decay of the peak area of the four successive extractions and, thus, the total area was calculated from these four extractions. In addition, two fibres were compared: carboxen-polydimethylsiloxane (CAR-PDMS) and divinylbenzene-carboxen-polydimethylsiloxane (DVB-CAR-PDMS), as they showed differences in the linearity of the exponential decay with the number of extractions depending on the compound. The CAR-PDMS fibre was better for the VOCs with a low molecular mass, whereas the DVB-CAR-PDMS fibre was better for the VOCs with a high molecular mass. Finally, the method was characterised in terms of linearity, detection limit and reproducibility and applied to analyse four multilayer packaging samples with different VOCs contents.

Organic Chemicals↗
PubMed1990

RNA dependence of the bacteriophage phi 29 DNA packaging ATPase.

The activity of the DNA packaging adenosine triphosphatase (ATPase) of the Bacillus subtilis bacteriophage phi 29 is dependent upon prohead RNA. The 174 nucleotide viral-encoded RNA is positioned on the head-tail connector at the portal vertex of the phi 29 precursor shell (prohead). Here, the RNA interacts with the ATP-binding gene 16 product (gp16) to constitute the DNA-packaging ATPase and initiate DNA packaging in vitro. Both the prohead connector (gene 10 product, gp10) and gp16 may utilize an RNA recognition motif characteristic of a number of RNA-associated proteins, and the binding of gp16 by proheads shields the prohead RNA from RNase A. The ATPase activity of gp16 is stimulated fourfold by RNA and tenfold by proheads with RNA. RNA is needed continuously for the gp16/RNA ATPase activity and is essential for the gp16/prohead ATPase activity. The prohead, with its connector, RNA and associated gp16 in an assembly-regulated configuration, hydrolyzes ATP and drives phi 29 DNA translocation.

Adenosine Triphosphatases↗
PubMed1990

Role of gene 6 exonuclease in the replication and packaging of bacteriophage T7 DNA.

When bacteriophage T7 gene 6 exonuclease is genetically removed from T7-infected cells, degradation of intracellular T7 DNA is observed. By use of rate zonal centrifugation, followed by either pulsed-field agarose gel electrophoresis or restriction endonuclease analysis, in the present study, the following observations were made. (1) Most degradation of intracellular DNA requires the presence of T7 gene 3 endonuclease and is independent of DNA packaging; rapidly sedimenting, branched DNA accumulates when both the gene 3 and gene 6 products are absent. (2) A comparatively small amount of degradation requires packaging and occurs at both the joint between genomes in a concatemer and near the left end of intracellular DNA; DNA packaging is only partially blocked and end-to-end joining of genomes is not blocked in the absence of gene 6 exonuclease. (3) Fragments produced in the absence of gene 6 exonuclease are linear and do not further degrade; precursors of the fragments are non-linear. (4) Some, but not most, of the cleavages that produce these fragments occur selectively near two known origins of DNA replication. On the basis of these observations, the conclusion is drawn that most degradation that occurs in the absence of T7 gene 6 exonuclease is caused by cleavage at branches. The following hypothesis is presented: most, possibly all, of the extra branching induced by removal of gene 6 exonuclease is caused by strand displacement DNA synthesis at the site of RNA primers of DNA synthesis; the RNA primers, produced by multiple initiations of DNA replication, are removed by the RNase H activity of gene 6 exonuclease during a wild-type T7 infection. Observation of joining of genomes in the absence of gene 6 exonuclease and additional observations indicate that single-stranded terminal repeats required for concatamerization are produced by DNA replication. The observed selective shortening of the left end indicates that gene 6 exonuclease is required for formation of most, possibly all, mature left ends.

Centrifugation, Density Gradient↗
PubMed1984

Steps in the stabilization of newly packaged DNA during phage P22 morphogenesis.

The protein products of three adjacent P22 genes, 4, 10 and 26, are required for the stabilization of DNA newly packaged into P22 phage capsids. We have isolated unstable DNA containing capsids from cells infected with mutants defective in these genes. All three classes could be converted into mature phage in vitro, confirming that they represent intermediates in particle maturation. The first of the three proteins to add to the newly filled capsids is gp4, followed by gp10 and gp26. The active form of gp4 sediments at 3 S, while the active forms of both gp10 and gp26 sediment at 5 S. These soluble subunits appear to polymerize onto the newly filled capsids to form the neck of the mature phage, the channel for DNA injection. Since gp4 is the first protein to act after DNA packaging, the unstable DNA containing capsids from 4- -infected cells must represent the direct product of the packaging of DNA into procapsids. The major fraction of these capsids lost activity with a half-life of 1.1 minutes at 23 degrees C, though they were much more stable at 0 degree C. Electron microscopic observations indicated that the loss of activity was due to the DNA exiting from the incomplete capsids. The marginal stability of the condensed DNA molecules within capsids is consistent with models of ATP-driven condensation and spontaneous DNA ejection. The basis of the stability of these highly condensed molecules remains to be determined.

Capsid↗
PubMed1989

The development of an AIDS Awareness Package for schools.

The Eastern Health and Social Services Board (EHSSB) in Belfast, developed an AIDS Strategy in autumn 1986. One part of that Strategy highlighted the need for health education and health promotion, with school children as a priority group. The development of an AIDS Awareness Package for Schools by a multidisciplinary team from Health and Education sectors is described. The importance of a joint approach to the project is highlighted, and the various steps taken to gain support and acceptance for the package are outlined. The necessity for training in the use of the AIDS Awareness Package and the future use and development of the material is discussed.

Acquired Immunodeficiency Syndrome↗
PubMed2003

Packaging of human endogenous retrovirus sequences is undetectable in porcine endogenous retrovirus particles produced from human cells.

The chronic shortage of human donor organs and tissues for allotransplantation could be relieved if clinical xenotransplantation were to become a viable clinical therapy. Balanced against the benefits of xenotransplantation are the possible consequences of zoonotic infections, and in particular, infection by porcine endogenous retrovirus (PERV). An often-proclaimed risk of PERV infection is the possible recombination of PERV with human endogenous retroviruses (HERV). To address this issue, we examined the potential for HERV sequences to be cross-packaged into PERV particles produced from infected human 293 cells. Although HERV-K, W, E, R, and ERV-9 RNA transcripts are expressed in 293 cells, we did not detect cross-packaging of any of these HERV groups. Quantitative analysis indicated that less than approximately 1 in 10(4)-10(7) PERV particles might contain HERV sequences. In comparison, we found that murine leukemia virus (MLV)-based vector transcripts were cross-packaged at a rate of approximately one copy in 10(4) PERV particles. Our results indicate that the potential for recombination of PERV and HERV sequences is low and that novel viruses generated by this mechanism are unlikely to represent a significant risk for xenotransplantation.

Animals↗
PubMed2001

Effects of holding time during cooling and of type of package on plasma membrane integrity, motility and in vitro oocyte penetration ability of frozen-thawed boar spermatozoa.

The effect of a prolonged holding time (HT) during cooling on plasma membrane integrity (PMI), motility and in vitro oocyte penetration ability of boar spermatozoa frozen-thawed in different types of package was investigated. Boar semen was frozen in a split-sample design using 3 different HTs (3, 10 and 20 h) during cooling and three different types of freezing package: Maxi-straws, Medium-straws and FlatPacks. Assessment of PMI (SYBR-14 and propidium iodide, fluorescence microscopy) and sperm motility (visually and with CASA) was done during cooling (at 32 degrees C, 15 degrees C, 5 degrees C) and post-thaw (PT). The in vitro oocyte penetration ability of the spermatozoa was tested only PT, using a homologous in vitro penetration assay (hIVP). During cooling the HTs used had no significant (p<0.05) effect on either PMI or percentage of motile spermatozoa Post-thaw PMI was significantly higher (p<0.05) for 10 h and 20 h HT compared with 3 h, and the percentage of motile spermatozoa decreased significantly with 20 h HT as opposed to 3 h and 10 h. Regarding the freezing packages, the FlatPacks and Maxi-straws yielded significantly more PMI than did the Medium-straws (p<0.05). Post-thaw motility was significantly higher for FlatPacks than for straws, in terms of both percentage motile spermatozoa, and sperm velocity and lateral head displacement (LHD). The hIVP did not show any significant differences among the HTs, although FlatPacks yielded a significantly higher penetration rate and more spermatozoa per penetrated oocyte (p<0.05) than did the straws. Changes in motility patterns, toward a more circular motility during cooling and PT, could be noticed where individual spermatozoa showed a capacitation-like motility pattern. The changes were more obvious with 10-h and 20-h HTs than with 3-h HT.

Animals↗