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At least 1,063 records · Page 59Linked to original sources
PubMed1987

Characterization of the small RNA of the bacteriophage phi 29 DNA packaging machine.

The prohead connector of the bacteriophage luminal diameter 29 DNA packaging machine was reconstructed with the small RNA that regulates DNA packaging in vitro. The complete sequence of the 120 nucleotide RNA proved its origination from the promoter PE1(A1) of the left early region of phi 29 DNA, the end packaged first during assembly. The prohead RNA was clearly distinct from eubacterial 5S rRNA in sequence and composition.

Bacillus subtilis↗
PubMed2004

Packaging motor from double-stranded RNA bacteriophage phi12 acts as an obligatory passive conduit during transcription.

Double-stranded RNA viruses sequester their genomes within a protein shell, called the polymerase complex. Translocation of ssRNA into (packaging) and out (transcription) of the polymerase complex are essential steps in the life cycle of the dsRNA bacteriophages of the Cystoviridae family (phi6-phi14). Both processes require a viral molecular motor P4, an NTPase, which bears structural and functional similarities to hexameric helicases. In effect, switching between the packaging and the transcription mode requires the translocation direction of the P4 motor to reverse. However, the mechanism of the reversal remains elusive. Here we characterize the P4 protein from bacteriophage phi12 and exploit its purine nucleotide specificity to delineate P4 role in transcription. The results indicate that while P4 actively translocates RNA during packaging it acts as a passive conduit for RNA export. The directionality switching is accomplished via the regulation of P4 NTPase activity within the polymerase core.

Bacteriophage phi 6↗
PubMed2000

Interaction of the herpes simplex virus type 1 packaging protein UL15 with full-length and deleted forms of the UL28 protein.

The UL15 and UL28 proteins of herpes simplex virus type 1 are both required for the packaging of replicated viral DNA into the viral capsid. We have expressed UL28 and a functional epitope-tagged form of UL15 in mammalian and insect cells. Immunoprecipitation experiments confirmed that the two proteins can interact. In agreement with previous results, UL15, when expressed alone, entered the nucleus but UL28 remained cytoplasmic. When co-expressed the two proteins co-localized in the nucleus. Six UL28 deletion mutants were constructed and similarly analysed. The results obtained by immunoprecipitation and immunofluorescence were consistent and demonstrate that at least two separate regions of the UL28 polypeptide chain have the ability to interact with UL15. Surprisingly, three of the mutants prevented the UL15 protein from localizing to the cell nucleus, and these were not functional in a transient DNA packaging assay. Of the three UL28 mutant proteins that entered the nucleus with UL15, one containing an internal deletion of 13 amino acids was able to complement a UL28 null mutant in both DNA packaging and virus yield assays, demonstrating that this region of the protein is not essential for function. In addition to interacting with the UL28 protein we also demonstrated that UL15 molecules can interact with each other, and that sequences within the second exon contribute to this interaction.

Active Transport, Cell Nucleus↗
PubMed2001

Human immunodeficiency virus type 2 lentiviral vectors: packaging signal and splice donor in expression and encapsidation.

Retroviral vectors provide the means for gene transfer with long-term expression. The lentivirus subgroup of retroviruses, such as human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2), possesses a number of regulatory and accessory genes and other special elements. These features can be exploited to design vectors for transducing non-dividing as well as dividing cells with the potential for regulated transgene expression. Encapsidation of the transgene RNA in lentiviral vectors is determined by the leader sequence-based multipartite packaging signal. Embedded in the packaging signal is a major splice donor site that, this study shows, is not by itself essential for transgene expression or encapsidation. We designed HIV-2 vectors that contained all the sequence elements thought to be necessary and sufficient for vector RNA encapsidation. Unexpectedly, despite abundant expression, only a small fraction of the transgene RNA was encapsidated and the titre of the vector was low. Redesign of the vector with a mutant splice donor resulted in increased vector RNA encapsidation and yielded vectors with high titre. Inefficient encapsidation by the conventionally designed vector was not due to suboptimal Rev responsive element (RRE)-Rev function. Varying the length of RRE in the vector did not change vector RNA encapsidation, nor did the introduction of a synthetic intron into the mutant vector. The vector RNA with the intact splice donor may have been excessively spliced, decreasing the amount of packageable RNA. A titre of 10(5) transducing units (TU)/ml was readily obtained for vectors with the neo or GFP transgene, and the vector could be concentrated to a titre of 1-5x10(7) TU/ml.

Capsid↗
PubMed2003

Identification of cis-acting sequences required for selective packaging of bovine adenovirus type 3 DNA.

The assembly of adenovirus particles is a multistep process, in which viral genomic DNA is selected and subsequently inserted into preformed empty capsids. The selective encapsidation of the adenovirus genome is directed by cis-acting packaging motifs, termed A repeats due to their AT-rich character in DNA sequence. A repeats are usually located at the left end of the viral genome. In this report, the construction and analysis of bovine adenovirus type 3 (BAdV-3) mutants containing deletion mutations introduced into the AT-rich regions are described. The main cis-acting packaging domains of BAdV-3 were localized between nt 224 and 540 relative to the left end of the viral genome. They displayed a functional redundancy and followed a hierarchy of importance. In addition, the results demonstrated that not all of the AT-rich units functioned as cis-acting packaging motifs.

Base Sequence↗
PubMed1997

New techniques for applying anomalous-scattering and isomorphous-replacement data incorporated in ANOMIR - a general application package.

A computer package ANOMIR is described which can derive phases from anomalous scattering and/or isomorphous-replacement data in any combination. For anomalous scattering it incorporates five methods of applying one-wavelength data and three methods for multiple-wavelength data including SPIN, reported here for the first time. In addition there are three procedures for multiple-wavelength data - the first modifying data for different wavelengths to make them mutually consistent, the second estimating the contributions of the anomalous scatterers alone and the third which finds anomalous differences. For single isomorphous replacement or one-wavelength anomalous scattering the phase ambiguity can be resolved by the direct method [Fan, Han, Qian & Yao (1984). Acta Cryst. A40, 489- 495] but for multiple isomorphous replacement the main method is an adaptation of the probability-curve method [Blow & Crick (1959). Acta Cryst. 12, 794-802]. A new statistical method is described for estimating the standard error in measuring magnitudes which is independent of having subsets of centric reflections. A method is described whereby the weights associated with phase estimates are used to generate probability curves, through which it is possible to combine estimates from different methods and to produce a 'best phase' and figure-of-merit for every reflection. ANOMIR procedures are also available for handling combinations of one-wavelength anomalous scattering with single- or multiple-isomorphous replacement. A final process, which is always beneficial, is a single parallel application of the tangent formula. The ANOMIR package has been designed for easy use and is controlled throughout by KEYWORDS. Results for several structures are given and compared with those found from the MLPHARE program in the CCP4 package.

Journal Article↗
PubMed1998

SEDEM, a software package for EXAFS data extraction and modelling.

A software package for extended X-ray absorption fine structure (EXAFS) data extraction and modelling, running on DOS- or Windows-operated PCs, is described. This package is written with the aim of giving the user a tool to undertake all steps of data processing and modelling, rather than making use of the most recent programming facilities. However, it remains easy to use, and self-explanatory to those who have already worked with EXAFS. It is divided into two main executable pieces of software. The first one is used to extract the EXAFS k(n)chi(k) function from the data and isolate the shell contributions by Fourier filtering. A tool to sum the spectra before EXAFS extraction is provided. The second one is designed to model the EXAFS spectra or the shell contributions, using amplitude and phase data either from McKale's tables, computed from the FEFF program or extracted from experimental reference spectra. This modelling program allows either an optimization of the simulation by a least-mean-square gradient algorithm, with a statistical evaluation of the result of optimization, or, in the case of a single shell, a direct determination of the four main parameters (neighbour distance and number, energy shift and Debye-Waller factor) by decorrelation of the phase and amplitude. In the presence of anharmonicity, the cumulant expansion of the radial distribution of distances is obtained from the phase and amplitude decorrelation. This package is in use at the Collaborative Research Group on Interfaces (CRG-IF) bending-magnet #32 X-ray line (BM-32) at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France.

Journal Article↗
PubMed1990

A package design technique for size reduction of implantable bioelectronic systems.

This paper presents several substrate and package design techniques to minimize the overall size of bioelectronic systems, especially those that will be implanted for in vivo studies. The emphasis is on a new capacitor attachment and a new double-substrate design that have been successfully applied to the packaging of an implantable auditory prosthesis. The entire procedure for this case is described and compared with standard techniques to illustrate the advantages of this new approach in packaging.

Cochlear Implants↗
PubMed2005

A study of crosstalk effects on the packaged SAW by the FDTD method.

The purpose of this study is to estimate the complete crosstalk effects, including the package and the pads on the surface acoustic wave (SAW) substrate. The coupling influence from the SAW pattern is investigated by the full-wave approach. In order to combine the electromagnetic effects with the surface acoustic wave response, a new approach based on finite difference time domain (FDTD) with equivalent current source method is applied. The resistive voltage source model is carefully used to simulate the situations of measurement by the vector network analyzer more accurately. Two kinds of patterns of one-port SAW resonators with the same package structure and interdigital transducer (IDT) design are studied. From the simulated electromagnetic field distributions over the substrate, it can be seen that, as the pattern on the SAW substrate becomes closer, more input energy will be coupled directly to the parallel pads by crosstalk without filtering. This will lead to more coupling loss and, therefore, the insertion loss becomes universally lower by about 2 to 3 dB. Furthermore, it can be observed that the coupling interference from the SAW pattern is more serious than from the package in this case. Verification with the measurement results shows that our method is able to obtain good agreement and can be used to observe the influence from the SAW pattern that can seriously affect the performance of the SAW device.

Journal Article↗
PubMed1991

An evaluation of the Ulster Cancer Foundation's Nurses and Smoking Package and its impact on student nurses.

The Ulster Cancer Foundation's teaching package Nurses and Smoking was evaluated by testing nurses' knowledge and skills in the area of smoking-related health education. As smoking is still a major cause of mortality and morbidity, does the nurses' training equip them with an adequate knowledge of its consequences? Questionnaire data, together with material from in-depth interviews, were analysed and pre- and post-package results produced significant differences (P less than 0.001) between the experimental and control groups, suggesting that a teaching package significantly improves a nurse's knowledge and expertise with regard to smoking and its effect on both patients and their environment.

Attitude↗
PubMed2006

Use of packaged entrees as part of a weight-loss diet in overweight men: an 8-week randomized clinical trial.

AIM: This study assessed the efficacy of a weight-loss diet by using packaged portion-controlled entrees vs. a self-selected diet based on the United States Department of Agriculture Food Guide Pyramid (FGP). METHODS: Sixty healthy overweight men (body mass index (BMI) 26-42 kg/m2; aged 24-60 years) were randomized into two groups for an 8-week intervention. Group E consumed two portion-controlled entrees daily, plus recommended servings from the FGP. Group P consumed a self-selected diet consisting of a recommended number of servings from the FGP. Diets were designed to be isocaloric (1700 kcal) and identical in macronutrient composition (55% carbohydrate, 25% protein and 20% fat). Participants were instructed to make no changes in physical activity levels. Each group was blinded to the protocol of the other group, and received separate diet instructions, but no behavioural or diet counselling. Outcomes included weight, BMI, body composition by dual energy X-ray absorptiometry, waist and hip circumference, blood pressure (BP), fasting blood lipids, glucose, insulin and C-reactive protein. RESULTS: Fifty-one men completed the study. The portion-control group E (n = 25) experienced greater decreases in weight (-7.4 +/- 3.1 vs. -5.1 +/- 4.0 kg), BMI (-2.4 +/- 1.0 vs. -1.6 +/- 1.3 kg/m2), fat mass (-3.6 +/- 1.8 vs. -2.5 +/- 1.8 kg), waist circumference (-6.6 +/- 3.3 vs. -4.3 +/- 2.9 cm) and diastolic BP (-6.0 +/- 7.2 vs. + 0.2 +/- 10.1 mmHg) than group P (n = 26) (p < 0.05). Consumption of a packaged entree diet resulted in greater losses of weight and fat mass, and reduced BP. CONCLUSIONS: Use of packaged entrees as part of a weight-loss diet is an effective means of achieving portion control and enhancing losses of weight and fat mass in overweight men.

Adult↗
PubMed1999

Cumulative probability of clinical pregnancy and live birth after a multiple cycle IVF package: a more realistic assessment of overall and age-specific success rates?

OBJECTIVE: To provide an assessment of pregnancy and live birth probabilities for women presenting for in vitro fertilisation treatment for the first time, when committed in advance to have up to three cycles of treatment in one year. DESIGN: Up to three cycles of in vitro fertilisation within one year, committed in advance. SETTING: A tertiary referral centre for assisted reproduction. PARTICIPANTS: Two hundred and thirty-two women, undergoing a total of 536 cycles of in vitro fertilisation or intracytoplasmic sperm injection between August 1993 and December 1995. METHODS: Analysis of cumulative clinical pregnancy and live birth rates for women having IVF treatment for the first time and undertaking a three-cycle package, using the life-table approach. MAIN OUTCOME MEASURES: Cumulative clinical pregnancy and live birth rates. RESULTS: The cumulative probabilities of clinical pregnancy and live birth after two cycles of treatment were 38.2% and 33.2%, respectively, compared with 54.2% and 48.2%, respectively, after three cycles of treatment. Cumulative clinical pregnancy and live birth rates after three cycles of treatment for women up to the age of 40 years were 57.8% and 51.3%, respectively. Cumulative clinical pregnancy and live birth rates declined with increasing age (P = 0.02 and P= 0.01, respectively). CONCLUSION: The three-cycle package encourages couples to have multiple treatment cycles, thereby improving their ultimate chances of a live birth. The cumulative clinical pregnancy and live birth rates after such a package provide a more realistic assessment of overall and age-specific success rates after multiple treatment cycles.

Adult↗
PubMed1991

A packaged solution to the problems of testing arrhythmia control devices at implant.

A composite implantable arrhythmia control device (ACD) implements the functions of a bradycardia pacemaker, an antitachycardia pacemaker, a cardioverter, and a defibrillator in an integrated fashion. Given this broad spectrum of functionality, the implant testing for these devices can become a formidable endeavor requiring a large ensemble of expensive, complex support equipment, and a significant amount of time. However, if this procedure is not carried out correctly, the device might later fail to defibrillate. This article presents a unique packaging system for an ACD that allows the device to be used while it is still in its sterile package. The device may then be used during implant testing as the defibrillation test unit. This collapses the amount of support equipment that is required to just the ACD, its programmer, and an optional switch box. By providing additional support specifically for implant testing through the ACD programmer, implant testing may be reduced to a quick, easy-to-manage procedure. Since the device used during implant testing is the same device that will be implanted, this packaging system offers the further advantage that the physician can be confident that, once implanted, the ACD will function correctly.

Electric Countershock↗
PubMed2004

Development of packaging cell lines for generation of adeno-associated virus vectors by lentiviral gene transfer of trans-complementary components.

Adeno-associated virus (AAV) vector system has several useful advantages with regard to in vitro and in vivo gene transfer. However, their usages have been limited by cumbersome and labor-intensive vector production in the traditional method. To overcome limitations in AAV production, in this report, we explored the possibility of generating AAV packaging cell line, 293T R/C.VA.E2A.E4. cells, by using lentivirus-mediated transduction of Rep/Cap gene of AAV-2, VA RNA, E2A, and E4 genes of Ad5 into 293T cells. In packaging cell lines, it is important that supply of the AAV vector can be stably performed for long time. We showed that the 293T R/C.VA.E2A.E4. cells have stably maintained the transduced components after more than 10 passages and yielded high-titer AAV vectors, and the titer of AAV vectors did not decline even if culture of the packaging cells was continued for long time. The Rep/Cap and E4 gene products caused no remarkable cytotoxicity. The 293T R/C.VA.E2A.E4. cells might be able to tolerate the Rep/Cap and E4 gene products, or have less copy numbers of the Rep/Cap and E4 genes than the traditional method. Moreover, we showed that the AAV vectors derived from 293T R/C.VA.E2A.E4. cells infected the primary human CD34+ haematopoietic progenitor cells with high efficiency (50-70%). In the 293T R/C.VA.E2A.E4. cells, the AAV vectors can be generated by the transfection of one AAV vector plasmid, and large-scale AAV production can be easily achieved. It is important that cumbersome, variable, and costly transfection is avoided.

Base Sequence↗
PubMed1999

Dosimetric verification of two commercially available three-dimensional treatment planning systems using the TG 23 test package.

The Task Group 23 (TG-23) radiation treatment planning dosimetry verification package was used to evaluate the dosimetric accuracy of two commercially available treatment planning systems. The TG-23 test package contains experimentally measured beam data for two x-ray beams (4 and 18 MV) that can be used as input for 3D-RTP (three-dimensional radiation treatment planning) systems. Once the beam data is entered and modeled, a series of test cases are performed that isolate different aspects of the dose computational process. The computed values from the 3D-RTP system are compared against the measured dosimetry data, included in the package, for a set of comparison points within each test case. Both of the treatment planning systems that were studied provided excellent agreement between computed and measured doses. The cumulative 4 and 18 MV TG-23 test results for the convolution/superposition based planning system indicates that 96% of the dosimetric test points are within +/-2%, and 98% are within +/-3% of the tabulated TG-23 values. The dosimetric TG-23 test results for the pencil beam kernel based planning system are similar, with 96% of the test points falling within +/-2%, and 99% falling within +/-3% of the TG-23 measurements.

Algorithms↗
PubMed1987

In vivo uncoating and efficient expression of foreign mRNAs packaged in TMV-like particles.

The ribonucleocapsids of many plant viruses are extremely stable. The protein coat protects the RNA genome against degradation during the accumulation and spread of progeny virions. Chimeric single-stranded RNA molecules were transcribed in vitro from recombinant plasmids and later encapsidated, in vitro, into ribonucleoprotein particles (pseudoviruses) 60 nanometers long that resembled tobacco mosaic virus. Transcripts encoding an assayable enzyme, chloramphenicol acetyltransferase (CAT), were packaged into pseudovirus particles to assess the utility of this single-stranded RNA delivery system in a wide range of cell types. In all cases, packaged CAT messenger RNA was uncoated and transiently expressed. Significantly higher levels of CAT activity were detected with packaged than with naked CAT messenger RNA after inoculation of plant protoplasts in the presence of polyethylene glycol or abrasive inoculation of intact leaf surfaces. Structural events that lead to the uncoating and expression of CAT messenger RNA showed no cell specificity. This observation may support the view that the comparatively restricted host range of a true plant virus results from events that occur later during the infection cycle.

Acetyltransferases↗
PubMed1997

Use of rRNA gene restriction patterns to evaluate lactic acid bacterium contamination of vacuum-packaged sliced cooked whole-meat product in a meat processing plant.

Molecular typing was applied to an in-plant lactic acid bacterium (LAB) contamination analysis of a vacuum-packaged sliced cooked whole-meat product. A total of 982 LAB isolates from the raw mass, product, and the environment at different production stages were screened by restriction endonuclease (EcoRI and HindIII) analysis. rRNA gene restriction patterns were further determined for different strains obtained from each source. These patterns were used for recognizing the spoilage-causing LAB strains from the product on the sell-by day and tracing the sources and sites of spoilage LAB contamination during the manufacture. LAB typing resulted in 71 different ribotypes, of which 27 were associated with contamination routes. Raw material was distinguished as the source of the major spoilage strains. Contamination of the product surfaces after cooking was shown to be airborne. The removal of the product from the cooking forms was localized as a major site of airborne LAB contamination. Food handlers and some surfaces in contact with the product during the manufacture were also contaminated with the spoilage strains. Some LAB strains were also able to resist cooking in the core of the product bar. These strains may have an effect on the product shelf life by contaminating the slicing machine. The air in the slicing department and adjacent cold room contained very few LAB. Surface-mediated contamination was detected during the slicing and packaging stages. Food handlers also carried strains later found in the packaged product. Molecular typing provided useful information revealing the LAB contamination sources and sites of this product. The production line will be reorganized in accordance with these results to reduce spoilage LAB contamination.

Bacteria↗
PubMed1997

Two groups of bacteriophages infecting Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins.

A comparative study of 30 phages of Streptococcus thermophilus was performed based on DNA restriction profiles, DNA homology, structural proteins, packaging mechanisms, and host range data. All phages exhibited distinct DNA restriction profiles, with some phages displaying similarly sized restriction fragments. DNA homology was shown to be present among all 30 phages. The phages could be divided into two groups on the basis of their packaging mechanism as was derived from the appearance of submolar DNA fragments in restriction enzyme digests and the presence (cos-containing phages) or absence (pac-containing phages) of cohesive genomic extremities. Interestingly, the 19 identified cos-containing phages possessed two major structural proteins (32 and 26 kDa) in contrast to the remaining 11 pac-containing phages, which possessed three major structural proteins (41, 25, and 13 kDa). Southern hybridization demonstrated that all pac-containing phages tested contain homologs of the genes encoding the three major structural proteins of the pac-containing phage O1205, whereas all cos-containing phages tested exhibit homology to the gene specifying one of the structural components of the cos-containing phage phi 7201. Fifty-seven percent of the phages (both cos and pac containing) possessed the previously identified 2.2-kb EcoRI fragment of the temperate S. thermophilus phage Sfi18 (H. Brüssow, A. Probst, M. Frémont, and J. Sidoti, Virology 200:854-857, 1994). No obvious correlation was detected between grouping based on packaging mechanism and host range data obtained with 39 industrial S. thermophilus strains.

Genome, Viral↗