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PubMed2002

The extended version of the computer package CST for conversions, standardization and transformations of the spin Hamiltonian and the crystal-field Hamiltonian.

The computer package CST (Conversions, Standardization and Transformations) is useful for general manipulations of the zero-field splitting (ZFS) and crystal field (CF) parameters for various systems, especially for transition ions at orthorhombic and lower symmetry sites in crystals. The ZFS parameters are extensively used in the EMR and related spectroscopic and magnetic studies (e.g. magnetic susceptibility, magnetic anisotropy, Mössbauer spectroscopy), whereas the CF parameters in optical absorption spectroscopy, inelastic neutron scattering, and infrared spectroscopy. An extended version of the CST package developed recently is presented in this paper. The standardization, including the standardization errors, for the five possible non-standard ranges of the 'rhombicity' parameter for monoclinic and triclinic symmetry in the local axis system has been worked out. The handling of the border points in the standardization module has been improved. The rotational invariants used before only for the transformations of the CF parameters have been incorporated into the standardization module for the CF and ZFS parameters expressed in any of the major tensor operator notations. The input option in the Euler angles has been added into the transformation module, and the newest physical constants in the unit conversions module have been adopted. Specific applications of the CST package for the CF and ZFS parameters will be presented elsewhere.

Journal Article↗
PubMed2000

Packaging of small molecules into VP1-virus-like particles of the human polyomavirus JC virus.

Recombinantly expressed VP1-virus-like particles (VP1-VLP) of human polyomavirus JC virus (JCV) were described recently as a new DNA transporter system. It was shown that DNA molecules could be packaged into VP1-VLP during a controlled chemical reassociation/dissociation process. In the present study VP1-VLP were studied as carriers for pharmaceutical substances. Propidium iodide (PI) was packaged into VP1-VLP as a reporter molecule. The PI-containing VP1-VLP could be detected directly by flow cytometry. The fluorescence intensity of the VP1-VLP depended strongly on the initial PI concentration. This packaging method is easy to handle and applicable to viruses and VP1-VLP which can be dissociated and reassociated chemically.

Capsid↗
PubMed1998

Optimization of packaging of adeno-associated virus gene therapy vectors using plasmid transfections.

Adeno-associated Virus (AAV) is attracting wide attention as a potential human gene therapy vector. The advantages of this vector system are that it is naturally defective, it readily integrates into the target cell's genome and is considered to be nonpathogenic. AAV infects a wide variety of cell and tissue types. The major disadvantages of the vector are its small size and the labor-intensive procedures required to prepare large amounts of the vector for clinical studies. In this manuscript we have systematically tested a number of variables in the packaging procedure to determine the optimal conditions for successful vector preparation. Using an AAV vector that expresses the green fluorescent protein and the most commonly used packaging plasmid, pAAV/Ad, we determined the optimal conditions for; lysis of the transfected cultures, ratio of packaging to vector plasmids, day of harvest after transfection, storage conditions, multiplicity of infection of helper adenovirus, and the time of adenovirus infection. These results have important relevance for investigators that are using AAV vectors for heterologous gene transfer studies.

Cytopathogenic Effect, Viral↗
PubMed2000

Nuclear-labeling index analysis (NLIA), a software package used to perform accurate automation of cell nuclear-labeling index analysis on immunohistochemically stained rat liver samples.

The nuclear labeling index (labeled nuclei/100 nuclei) and the apoptotic index (apoptotic cells/100 cells) are important parameters of cell growth and death. Automatic counting of labeled nuclei is desirable since manual counting is tedious, time-consuming, and with a greater potential for inaccuracies. A nuclear-labeling index analysis (NLIA) software package was developed in this laboratory to perform the counting process automatically and accurately. This software package consists of an application program NLIA and a set of macros for obtaining nuclear data that is used in Scion Image. It is designed to work cooperatively with Scion Image, Adobe Photoshop, and Microsoft Office. NLIA has two basic functions: building nuclear data files and analyzing nuclear data. A color image captured from an immunohistochemically stained or autoradiographic sample is loaded into NLIA. Nuclear data can be entered into the program manually, automatically, or in combination. In the manual data entering mode, NLIA acts as an object-counting tool, while in the automatic mode it acts as a data picker: picking up the data generated by Scion Image into memory. A method to enter nuclear data (both labeled nuclei and unlabeled nuclei) in the automatic mode is described. The color image is processed in Adobe Photoshop, where the interested color ranges are selected and separated. These are then analyzed in Scion Image with the help of the macros for obtaining nuclear data. Since the advanced particle analysis function is used, the counting process is automatic and rapid. Data from thousands of nuclei can be obtained within seconds. To ensure the accuracy of the analysis, a nuclear data checking and edit feature is employed in NLIA: results of computer-generated counting can be compared with the original color image by overlaying the plot of counting results onto the original color image. In this way any computer counting mistakes can be easily discovered and corrected by the operator. Corrected nuclear data (including nuclear size, location, shape) are then stored in data files. These data files can be used in NLIA to obtain cell density and nuclear labeling indices. Because criteria for obtaining nuclear data (truncation diameter, shape factor) can be set by the operator in NLIA, nuclear size distribution and shape variation can be analyzed. This method provides a fast and accurate way to determine cell nuclear-labeling indices. Currently, Scion Image is a freeware on the internet, and NLIA software package is available from our lab home page. Methods presented here expand the Scion Image ability to analyze color images by using color separation techniques in a commercial graphic application. The instrumentation required can be relatively inexpensive, and the methods described may be useful in studies of cell kinetics, lesion growth, and tumor therapy.

Animals↗
PubMedDate not supplied

Circularization of retroviral genomic RNA and the control of RNA translation, packaging and reverse transcription.

Translation, packaging and reverse transcription of the genomic RNA of retroviruses appear to be regulated by short and long range RNA-RNA interactions which take place within the 5'-600 nt and between the 5' and 3' untranslated sequences. The 5' (R and U5) and 3' (Dr and U3) domains of the genomic RNA together with the nucleic acid binding protein (NBP) would control the balance between the open state of the viral genomic RNA, correlated with an efficient RNA translation and the closed state, with the circular viral RNA efficiently packaged into virions. Retroviral NBP might well drive the packaging of the viral RNA as well as improve reverse transcription of the circular virion RNA.

Amino Acid Sequence↗
PubMed2001

A randomised trial of an intervention package designed to promote external cephalic version at term.

OBJECTIVE: To evaluate the effectiveness of an intervention package to promote external cephalic version (ECV). STUDY DESIGN: (1) Design and Setting--A randomised-controlled trial of 20 consultant-based maternity units in the West Midlands NHS Region. (2) Intervention Units--One consultant obstetrician from each unit was encouraged to promote changes in clinical practice within their unit. A multifaceted package including a workshop, written material, guidelines and videos was delivered to these consultants. (3) Control Units--No intervention. (4) Main Outcome Measure--The percentage of women with breech presentation at term who were offered ECV in the antenatal clinic, before and after the intervention. RESULTS: Pre-intervention, there was no difference between the intervention and control units in the proportion of women offered ECV (20 and 19%, respectively). Post-intervention, the proportions were 15% in the control group and 36% in the intervention group (P=0.016). CONCLUSION: This type of intervention package can alter clinical practice and increase the proportion of women with breech presentation at term being offered ECV after the intervention.

Breech Presentation↗
PubMed2000

QED v 1.0: a software package for quantitative electron diffraction data treatment.

A new software package for quantitative electron diffraction data treatment of unknown structures is described. No "a priori" information is required by the package which is able to perform in successive steps the 2-D indexing of digitised diffraction patterns, the extraction of the intensity of the collected reflections and the 3-D indexing of all recorded patterns, giving as results the lattice parameters of the investigated structure and a series of data files (one for each diffraction pattern) containing the measured intensities and the relative e.s.d.s of the 3-D indexed reflections. The software package is mainly conceived for the treatment of diffraction patterns taken with a Gatan CCD Slow-Scan Camera, but it can also deal with generic digitised plates. The program is designed to extract intensity data suitable for structure solution techniques in electron crystallography. The integration routine is optimised for a correct background evaluation, a necessary condition to deal with weak spots of irregular shape and an intensity just above the background.

Algorithms↗
PubMed1999

A helper virus-free packaging system for recombinant adeno-associated virus vectors.

Adeno-associated virus (AAV) is a human parvovirus that is currently receiving widespread attention for its potential use as a gene therapy vector. Construction of the recombinant AAV vector (rAAV) involves replacing most of the viral genome with a transgene of interest and then packaging this recombinant genome into an infectious virion. Most current protocols for generating rAAV entail the co-transfection of a vector plasmid and a packaging plasmid that expresses the viral replication and structural genes onto adenovirus (Ad) infected cells growing in culture. Limitations of this procedure include (1) contamination of rAAV with the Ad helper virus, (2) low yields of rAAV and (3) production of replication-competent AAV. In this report we describe new helper plasmids (pSH3 and pSH5) that eliminate the Ad co-infection requirement. The helper plasmids express the AAV rep and cap genes and the Ad E2A, VAI and E4 genes. When the helper plasmids are co-transfected onto human 293 cells with a vector plasmid in the absence of Ad infection, the rAAV vector yield is up to 80-fold greater than those obtained with the pAAV/Ad packaging plasmid. Moreover, replication competent AAV in the rAAV preparations is less than 0.00125%. The major advantages of this system are (1) the absence of infectious adenovirus and (2) the use of only two plasmids, which enhances transfection efficiencies and hence vector production. We believe that this two-plasmid transfection system will allow for more widespread use of the AAV vector system because of its simplicity and high yields. This system will be especially useful for preclinical analyses of multiple rAAV vectors.

Cell Line↗
PubMed1998

Learning voice analysis using an interactive multi-media package: development and preliminary evaluation.

An important outcome of education for speech-language pathology practice is the ability to analyze voices perceptually, a complex task that is often difficult for novices. This article describes an interactive multi-media package, "A Sound Judgement," that is designed to help students develop skills in perceptual voice analysis and to link their perceptions to laryngeal physiology. The package presents a range of clients with vocal impairments at increasing levels of complexity. Each case has a videoed interview, endoscopic views and animations of the larynx, and case history information. Students make perceptual ratings of clients' voices on a format designed specifically for this package and feedback is provided using ratings made by expert speech-language pathologists. High levels of consensus for the perceptual judgments were achieved among the expert raters. Preliminary evaluations by students have demonstrated that "A Sound Judgement" is likely to be a valuable educational tool.

Computer-Assisted Instruction↗
PubMed1995

DNA packaging intermediates of bacteriophage φX174

BACKGROUND: Like many viruses, bacteriophage phi X174 packages its DNA genome into a procapsid that is assembled from structural intermediates and scaffolding proteins. The procapsid contains the structural proteins F, G and H, as well as the scaffolding proteins B and D. Provirions are formed by packaging of DNA together with the small internal J proteins, while losing at least some of the B scaffolding proteins. Eventually, loss of the D scaffolding proteins and the remaining B proteins leads to the formation of mature virions. RESULTS: phi X174 108S 'procapsids' have been purified in milligram quantities by removing 114S (mature virion) and 70S (abortive capsid) particles from crude lysates by differential precipitation with polyethylene glycol. 132S 'provirions' were purified on sucrose gradients in the presence of EDTA. Cryo-electron microscopy (cryo-EM) was used to obtain reconstructions of procapsids and provirions. Although these are very similar to each other, their structures differ greatly from that of the virion. The F and G proteins, whose atomic structures in virions were previously determined from X-ray crystallography, were fitted into the cryo-EM reconstructions. This showed that the pentamer of G proteins on each five-fold vertex changes its conformation only slightly during DNA packaging and maturation, whereas major tertiary and quaternary structural changes occur in the F protein. The procapsids and provirions were found to contain 120 copies of the D protein arranged as tetramers on the two-fold axes. DNA might enter procapsids through one of the 30 A diameter holes on the icosahedral three-fold axes. CONCLUSIONS: Combining cryo-EM image reconstruction and X-ray crystallography has revealed the major conformational changes that can occur in viral assembly. The function of the scaffolding proteins may be, in part, to support weak interactions between the structural proteins in the procapsids and to cover surfaces that are subsequently required for subunit-subunit interaction in the virion. The structures presented here are, therefore, analogous to chaperone proteins complexed with folding intermediates of a substrate.

Bacteriophage phi X 174↗
PubMed2003

The Xplor-NIH NMR molecular structure determination package.

We announce the availability of the Xplor-NIH software package for NMR biomolecular structure determination. This package consists of the pre-existing XPLOR program, along with many NMR-specific extensions developed at the NIH. In addition to many features which have been developed over the last 20 years, the Xplor-NIH package contains an interface with a new programmatic framework written in C++. This interface currently supports the general purpose scripting languages Python and TCL, enabling rapid development of new tools, such as new potential energy terms and new optimization methods. Support for these scripting languages also facilitates interaction with existing external programs for structure analysis, structure manipulation, visualization, and spectral analysis.

Molecular Structure↗
PubMed2001

The packaging signal of influenza viral RNA molecules.

The packaging signal present in influenza viral RNA molecules is shown not to constitute a separate structural element, but to reside within the 5'-bulged promoter structure, as caused by the central unpaired residue A10 in its 5' branch. Upon insertion of two uridine residues in the 3' branch opposite A10, the minus-strand viral RNA (vRNA) promoter is converted into a 3'-bulged structure, whereas the plus-strand cRNA promoter instead adopts the 5'-bulged conformation. In this promoter variant it is exclusively the cRNA that is found packaged in the progeny virions. Upon insertion of only a single uridine nucleotide opposite 5'A10, the two debulged structures of the vRNA and cRNA promoters are rendered identical, and both vRNA and cRNA molecules are packaged indiscriminately, in a 1:1 ratio, but at lower rates. We propose that the binding interactions of viral polymerase with either of the two differently bulged vRNA and cRNA promoter structures result in two different conformations of the enzyme protein. Only the 5' bulged RNA-associated polymerase conformation appears to be recognized for nuclear export, which depends on nuclear matrix protein M1 and nonstructural protein NS2. And the respective wild-type vRNP- or insertion mutant cRNP complex is observed to enter the cytoplasm and hence is included in the viral encapsidation process, which takes place at the plasma membrane.

Animals↗
PubMed1991

Secondary conformational polymorphism of nucleic acids as a possible functional link between cellular parameters and DNA packaging processes.

Circular dichroism and electron microscopy studies of various in vitro DNA packaging systems indicate that all the factors which induce and modulate the secondary conformation of DNA molecules are capable of eliciting nucleic acids condensation processes into tight, highly ordered tertiary structures as well as altering the extent of order and compactness within the resulting species. Specifically, such factors include the ionic strength, the presence of particular dehydrating agents and polyamines, as well as the pH values. It is proposed that slight alterations of these parameters induce the formation of short non-B-DNA segments that propagate as a perturbation along the B-DNA double helix. The structural fluctuations of the dsDNA molecules that result from the conformational discontinuities formed at the junction sites between the B motif and the conformationally altered segments alter the elastic response of the nucleic acids and facilitate cooperative condensation processes. Moreover, the type and frequency of the structurally modified clusters interspersed within the B conformation and determined by the environmental parameters are shown to provide a means for continuous regulation of the extent and mode of DNA packaging. The ionic strength and hydrophobic environment in the close vicinity of the DNA molecules are controlled and modulated in vivo by DNA-binding proteins such as histones and protamines; similarly, pH values and polyamine concentrations are constantly regulated in living systems. It is suggested, therefore, that the secondary structural polymorphism which characterizes the DNA molecules might display a regulatory role by acting as a functional link between cellular parameters and the extent, mode, and timing of nucleic acid packaging processes.

Cadaverine↗
PubMed2000

Chromatin packaging as an indicator of human sperm dysfunction.

PURPOSE: Understanding the causes of fertilization failure is an important research field in assisted reproductive programs. The present study aimed to evaluated the possible relationship between chromatin packaging quality (CMA3 staining) and (i) normal morphology and (ii) its ability to predict the functional integrity of spermatozoa in both in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) treatment programs. METHODS: Semen of 140 men from IVF and ICSI couples were analyzed for sperm concentration, motility, morphology, and chromatin packaging (CMA3). For CMA3 classification, two cutoff values were used, namely, 44.5% +/- 13 and 1 SD above the mean, i.e., 57.5% (rounded off to 60%). IVF and ICSI data were stratified using three basic cutoff values for CMA3 staining, namely, < 44%, > 44-60%, and > 60%. RESULTS: Based on CMA3 results patients were divided into four groups, namely, group A, < 44% CMA3 (n = 15, IVF); group B, > or = 44% and < 60% CMA3 (n = 39, IVF); group C, > or = 60% CMA3 (n = 45 IVF); and group D, > or = 60% CMA3 (n = 41 ICSI). During receiver operator characteristic analyses the estimated cutoff value for CMA3 staining, to distinguish between < 4% and > or = 4% morphology groups, was 60%. The area under the curve was 0.89, sensitivity of 75%, and specificity of 100%. When IVF rates of > 60% and < 60% were used, the optimal CMA3 value for prediction of fertilization success again was recorded at 60%. The area under the curve was 0.76, sensitivity of 81.5%, and specificity of 63.6%. CONCLUSIONS: Chromatin packaging assessments should be included as a complementary assay to the sequential diagnostic approach of the male-factor patients.

Chromatin↗
PubMed2000

Structure of the bacteriophage phi29 DNA packaging motor.

Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we describe the motor that packages the double-stranded DNA of the Bacillus subtilis bacteriophage phi29 into a precursor capsid. We determined the structure of the head-tail connector--the central component of the phi29 DNA packaging motor--to 3.2 A resolution by means of X-ray crystallography. We then fitted the connector into the electron densities of the prohead and of the partially packaged prohead as determined using cryo-electron microscopy and image reconstruction analysis. Our results suggest that the prohead plus dodecameric connector, prohead RNA, viral ATPase and DNA comprise a rotary motor with the head-prohead RNA-ATPase complex acting as a stator, the DNA acting as a spindle, and the connector as a ball-race. The helical nature of the DNA converts the rotary action of the connector into translation of the DNA.

Adenosine Triphosphatases↗
PubMed2004

Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus.

All retroviruses specifically package two copies of their genomes during virus assembly, a requirement for strand-transfer-mediated recombination during reverse transcription. Genomic RNA exists in virions as dimers, and the overlap of RNA elements that promote dimerization and encapsidation suggests that these processes may be coupled. Both processes are mediated by the nucleocapsid domain (NC) of the retroviral Gag polyprotein. Here we show that dimerization-induced register shifts in base pairing within the Psi-RNA packaging signal of Moloney murine leukaemia virus (MoMuLV) expose conserved UCUG elements that bind NC with high affinity (dissociation constant = 75 +/- 12 nM). These elements are base-paired and do not bind NC in the monomeric RNA. The structure of the NC complex with a 101-nucleotide 'core encapsidation' segment of the MoMuLV Psi site reveals a network of interactions that promote sequence- and structure-specific binding by NC's single CCHC zinc knuckle. Our findings support a structural RNA switch mechanism for genome encapsidation, in which protein binding sites are sequestered by base pairing in the monomeric RNA and become exposed upon dimerization to promote packaging of a diploid genome.

Base Pairing↗
PubMed1997

A rapid screening procedure for the identification of high-titer retrovirus packaging clones.

We have developed a viral RNA (vRNA) dot blot assay for rapid identification of high-titer retrovirus vector production by packaging cell clones. The procedure employs Trizol LS reagent to purify vRNA from packaging cell supernatants, a sensitive dot blot assay, and Phosphorlmager technology to quantify packaged viral genomes in 2 days. Experiments performed on viral supernatants of known biological titer demonstrated that the vRNA dot blot assay was extremely sensitive and that dot intensity correlated directly with viral titer. It is often necessary to analyze approximately 100 virus producing cell clones, making this method useful as a rapid screen to identify the highest virus producing clones. The vRNA dot blot assay consistently identified a subset of candidate high-titer producer cell clones. In three independent screens the supernatant with the highest biological titer was produced by one of the previously defined candidate high-titer producer clones. Our procedure greatly facilitates virus titration by: (1) rapidly eliminating the vast majority of low-titer producer cell clones; (2) accurately identifying the subset of candidate high-titer producer clones for further biological titration and assessment of the proviral genomic structure; and (3) reducing laborious tissue culture manipulations to a minimum. Furthermore, the reliance of this method on molecular detection makes it ideally suited for the isolation of high-titer clones lacking a drug selection marker.

Gene Transfer Techniques↗
PubMed1999

Production of recombinant adeno-associated virus vectors using a packaging cell line and a hybrid recombinant adenovirus.

Recombinant adeno-associated virus (rAAV) vectors are under consideration for a wide variety of gene therapy applications. One of the limitations of the rAAV vector system has been the difficulty in producing the vector in sufficient quantity for adequate preclinical and clinical evaluation. A common method for vector production involves large-scale transient transfection of multiple plasmids into cultured cells. Because this approach might not be feasible for clinical scale manufacturing, we have sought approaches for rAAV vector production that avoid transient transfection procedures. In previously reported work, we generated an AAV packaging cell line that produces infectious rAAV when the vector genome is transfected into the cell line as plasmid DNA. We have now extended this approach by constructing a hybrid recombinant adenovirus (rAd) that contains a complete rAAV vector genome in the E1 region. This hybrid virus is used to deliver the rAAV genome to the packaging cell line (in the place of plasmid transfection). rAAV is produced when the packaging cell line is infected with the hybrid adenovirus and wild-type adenovirus. This method avoids the need for plasmid transfection and is adaptable to large-scale manufacturing processes.

Adenoviridae↗