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At least 1,117 records · Page 62Linked to original sources
PubMed1990

Cloning and expression of packaging gene 3 of Salmonella phage P22.

Packaging genes 3 of Salmonella phage P22 wild type and two mutants with altered packaging properties (HT12/4 and NT1/1) have been cloned in an expression vector. By plasmid transduction, it has been shown that the amino terminus of gene 3 is not functional in DNA packaging when fused with the Escherichia coli lacZ gene. The reconstituted genes 3, however, express functional gp3. The transduction experiments also have shown that the pac signal, which is part of gene 3, is intact in all three phages. Expression of gene product gp3 has been demonstrated in the minicell system.

Base Sequence↗
PubMed1993

The development and evaluation of a sexual harassment contact person training package.

The effectiveness of a training package to teach listening and helping skills to three pairs of sexual harrassment contact person trainees was evaluated, using a multiple probe design. The training package comprised five components: behavioral specifications, rationales, situational examples, study guides, and role-play exercises, provided in a written instructional format based on guidelines developed by Fawcett and Fletcher. Evaluation involved pre- and posttraining measures of target behavior occurrence, relevant knowledge, and self-rated confidence level. Ratings of performance were also provided by potential consumers as a measure of social validity. Findings indicated that the package was effective in increasing listening and helping skills, knowledge, and confidence of trainees and that skills generalized to new simulated cases and were maintained over time.

Adult↗
PubMedDate not supplied

A comparison of learning activity packages and classroom instruction for diet management of patients with non-insulin-dependent diabetes mellitus.

Forty patients were randomly assigned to receive either the individualized learning activity packages or classroom instruction. Effectiveness was evaluated on the basis of fasting plasma glucose, glycosylated hemoglobin, percent of ideal body weight, and knowledge and behavior scores. No significant differences were found between the groups at entry or at the 2-month follow-up. At the 5-month follow-up, the group that received the learning activity packages scored significantly higher on knowledge assessment, significantly increased their behavior score, and decreased their percent of ideal body weight. Patients who received classroom instruction increased their behavior score and exhibited significantly decreased glycosylated hemoglobin levels. Behavior and blood glucose levels were significantly correlated. Although the learning activity packages proved effective in increasing knowledge, no significant improvement was observed in blood glucose levels.

Diabetes Mellitus, Type 2↗
PubMed2002

Highly efficient gene transfer into baboon marrow repopulating cells using GALV-pseudotype oncoretroviral vectors produced by human packaging cells.

Vector-containing medium harvested from murine packaging cell lines has been shown to contain factors that can negatively influence the transduction and maintenance of hematopoietic stem cells. Thus, we generated a human packaging cell line with a gibbon ape leukemia virus pseudotype (Phoenix-GALV), and we evaluated vectors produced by Phoenix-GALV for their ability to transduce hematopoietic progenitor/stem cells. In 3 baboons, we used a competitive repopulation assay to directly compare GALV-pseudotype retrovirus vectors produced by either Phoenix-GALV or by the NIH 3T3-derived packaging cell line, PG13. In 3 additional baboons we compared Phoenix-GALV-derived vectors to more recently developed lentiviral vectors. Gene transfer efficiency into hematopoietic repopulating cells was assessed by evaluating the number of genetically modified peripheral blood and marrow cells using flow cytometry and real-time polymerase chain reaction. Transduction efficiency of hematopoietic repopulating cells was significantly higher using the Phoenix-GALV-derived vector as compared with the PG13-derived vectors or lentiviral vectors, with stable transduction levels up to 25%. We followed 2 animals for more than one year. Flow cytometric analysis of hematopoietic subpopulations in these animals revealed transgene expression in CD13(+) granulocytes, CD20(+) B lymphocytes, CD3(+) T lymphocytes, CD61(+) platelets, as well as red blood cells, indicating multilineage engraftment of cells transduced by Phoenix-GALV-pseudotype vectors. In addition, transduction of human CD34(+) cells was significantly more efficient than transduction of baboon CD34(+) cells, suggesting that Phoenix-GALV-derived oncoretroviral vectors may be even more efficient in human stem cell gene therapy applications.

Animals↗
PubMed2006

AMDA: an R package for the automated microarray data analysis.

BACKGROUND: Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being performed. In spite of this fact, few and limited tools exist for quickly and easily analyzing the results. Microarray analysis can be challenging for researchers without the necessary training and it can be time-consuming for service providers with many users. RESULTS: To address these problems we have developed an automated microarray data analysis (AMDA) software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image analysis, quality controls, normalization, selection of differentially expressed genes, clustering, correspondence analysis and functional evaluation. Finally a LaTEX document is dynamically generated depending on the performed analysis steps. The generated report contains comments and analysis results as well as the references to several files for a deeper investigation. CONCLUSION: AMDA is freely available as an R package under the GPL license. The package as well as an example analysis report can be downloaded in the Services/Bioinformatics section of the Genopolis http://www.genopolis.it/.

Algorithms↗
PubMed2004

Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably?

During virus assembly, all retroviruses specifically encapsidate two copies of full-length viral genomic RNA in the form of a non-covalently linked RNA dimer. The absolute conservation of this unique genome structure within the Retroviridae family is strong evidence that a dimerized genome is of critical importance to the viral life cycle. An obvious hypothesis is that retroviruses have evolved to preferentially package two copies of genomic RNA, and that dimerization ensures the proper packaging specificity for such a genome. However, this implies that dimerization must be a prerequisite for genome encapsidation, a notion that has been debated for many years. In this article, we review retroviral RNA dimerization and packaging, highlighting the research that has attempted to dissect the intricate relationship between these two processes in the context of HIV-1, and discuss the therapeutic potential of these putative antiretroviral targets.

Anti-HIV Agents↗
PubMed2006

Inhibition of histone deacetylation in 293GPG packaging cell line improves the production of self-inactivating MLV-derived retroviral vectors.

BACKGROUND: Self-inactivating retroviral vectors (SIN) are often associated with very low titers. Promoter elements embedded within SIN designs may suppress transcription of packageable retroviral RNA which in turn results in titer reduction. We tested whether this dominant-negative effect involves histone acetylation state. We designed an MLV-derived SIN vector using the cytomegalovirus immediate early enhancer-promoter (CMVIE) as an embedded internal promoter (SINCMV) and transfected the pantropic 293GPG packaging cell line. RESULTS: The SINCMV retroviral producer had uniformly very low titers (approximately 10,000 infectious retroparticles per ml). Northern blot showed low levels of expression of retroviral mRNA in producer cells in particular that of packageable RNA transcript. Treatment of the producers with the histone deacetylase (HDAC) inhibitors sodium butyrate and trichostatin A reversed transcriptional suppression and resulted in an average 106.3 +/- 4.6 - fold (P = 0.002) and 15.5 +/- 1.3 - fold increase in titer (P = 0.008), respectively. A histone gel assay confirmed increased histone acetylation in treated producer cells. CONCLUSION: These results show that SIN retrovectors incorporating strong internal promoters such as CMVIE, are susceptible to transcriptional silencing and that treatment of the producer cells with HDAC inhibitors can overcome this blockade suggesting that histone deacetylation is implicated in the mechanism of transcriptional suppression.

Acetylation↗
PubMed2005

Development of efficient packaging method of oligodeoxynucleotides by a condensed nano particle in lipid envelope structure.

An efficient delivery system is required if antisense oligodeoxynucleotides (ODN) are to be utilized for gene therapy. We report herein on the development of a novel ODN delivery system, ODN-encapsulated nano particles (ODN-ENP) using an efficient and simple packaging method. The ODN-ENP consists of a condensed ODN particle and a lipid envelope, which can be equipped with various functional devices for the efficient delivery of ODN with a small diameter (150 nm). The encapsulation efficiency and ODN recovery of ODN-ENP were significantly higher than those of other packaging methods, such as a stabilized antisense-lipid particles method or a freeze-thaw method. Furthermore, the time required for the preparation of the ODN-ENP was shorter than the other methods. The method developed in this study is a simple and efficient packaging method for ODN with a condensed nano particle in lipid-envelope structure.

Base Sequence↗
PubMed2004

Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes.

Retroviruses specifically package two copies of their RNA genome in each viral particle, along with some small cellular RNAs, including tRNAs and 7S L RNA. We show here that Rous sarcoma virus (RSV) also packages U6 snRNA at approximately one copy per virion. In addition, trace amounts of U1 and U2 snRNAs were detected in purified virus by Northern blotting. U6 snRNA comigrated with the RSV 70S genomic RNA dimer on sucrose gradients. We observed reverse transcription of U6 snRNA in an endogenous reaction in which RSV particles were the source of both reverse transcriptase and RNA substrates. This finding led us to examine mammalian genomic sequences for the presence of snRNA pseudogenes. A survey of the human, mouse, and rat genomes revealed a high number of spliceosomal snRNA pseudogenes. U6 pseudogenes were the most abundant, with approximately 200 copies in each genome. In the human genome, 67% of U6 snRNA pseudogenes, and a significant number of the other snRNA pseudogenes, were associated with LINE, SINE, or retroviral LTR repeat sequences. We propose that the packaging of snRNAs in retroviral particles leads to their reverse transcription in an infected cell and the integration of snRNA/viral recombinants into the host genome.

Animals↗
PubMed2025

G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm.

G-quadruplexes (G4s) are nucleic acid secondary structures with important regulatory functions. Single-nucleotide variants (SNVs), one of the most common forms of genetic variation, can potentially impact the formation of G4 structures if they occur within G4 regions. However, there is currently a lack of software tools specifically designed to assess such effects. Here, we present an R/Bioconductor package named G4SNVHunter, which enables rapid detection of variants that may disrupt G4 structures. This tool, based on the core principles of the G4Hunter algorithm, can provide precise quantitative assessment of the propensity for G4 formation within genomic sequences. Specialized experimental methods can then be designed based on the results provided by G4SNVHunter to further verify the specific functions of the affected G4 structures, facilitating deeper insights into the biological impacts of genetic variants from the perspective of G4 structures. To showcase the functionality of the G4SNVHunter package, we analyzed the Neandertal and Denisovan archaic introgressed variants detected by the Sprime software, and identified approximately 5,800 variants located within G4 regions, among which around 230 may impair G4 structure formation propensity. The source code for the G4SNVHunter package has been publicly released under the MIT license at https://github.com/rongxinzh/G4SNVHunter and https://bioconductor.org/packages/devel/bioc/html/G4SNVHunter.html.

G-Quadruplexes↗
PubMed2004

Separate control of Rep and Cap expression using mutant and wild-type loxP sequences and improved packaging system for adeno-associated virus vector production.

Adeno-associated virus (AAV) vectors are a practical choice for gene transfer, and demand for them is increasing. To cope with the necessity in the near future, we have developed a number of approaches to establish packaging cell lines for the production of AAV vectors. In our previous study, a highly regulated expression of large Rep proteins was obtained by using the Cre-loxP switching system. Therefore, in the present study, to regulate Cap expression as well, we developed an inducible expression system for both Rep and Cap proteins by using an additional set of mutant loxP sequences. The mutants possess two base alterations in the spacer region of loxP and recombine specifically with the same counterpart in the presence of Cre. By using two separate plasmids, one with mutant and the other with wild-type loxP sequences, the expression of two different proteins can be induced simultaneously by Cre recombinase. When the LacZ-encoding plasmid vector was used as a packaging model, a significant packaging titer of 2.1 x 1010 genome copies per 10-cm dish was obtained. These results indicate the importance of controlling Cap expression, in addition to Rep, to achieve an optimum production rate for AAV vectors.

Cell Line↗
PubMed1997

RNA packaging of yeast retrotransposon Ty1 in the heterologous host, Escherichia coli.

Expression of components of the yeast retrotransposon Ty1 in E. coli was used to study early steps of retrotransposition. We find that polypeptides encompassing the capsid-forming component of Ty1 can assemble into particles in the heterologous host. Ty RNA can be detected in particle fractions. RNA packaging depends on features in the 5' part of Ty RNA, because deletion of 5' proximal sequences leads to decreased packaging efficiency. Protein domains required for the RNA packaging process reside between amino acids 146 and 394 of the capsid protein. The data presented also indicate that several early steps in the Ty1 life cycle can occur in a cellular environment which differs from yeast cytoplasm, supporting the notion that these steps are independent of host factors.

Escherichia coli↗
PubMed1977

Pyramid training of elementary school teachers to use a classroom management "skill package".

Three regular elementary teachers were trained in the use of a classroom management "skill package". Subsequently, each of these three teachers (tier 1 of training) trained three more teachers to use the same skill package (tier 2 of training). Direct behavioral measures of student disruptiveness were taken in the three tier-1 classrooms and four tier-2 classrooms, and permanent product measures of student productivity in arithmetic were taken in the three tier-1 classrooms. Results indicated that student disruptiveness decreased at least as much in the tier-2 classrooms as in the tier-1 classrooms. Data also indicated that serving as trainers benefited two of the tier-1 teachers who profited least from the original training by producing further reductions in disruptiveness in their respective classrooms. Productivity data suggested that use of the "skill package" increased classroom academic output, especially for those students below the median in productivity during baseline. The investigators' time investment in training a tier-2 teacher was one-fourth that of training a tier-1 teacher.

Journal Article↗
PubMed1977

A parent advice package for family shopping trips: development and evaluation.

THIS ARTICLE REPORTS ON THE PRIMARY STEPS IN THE DEVELOPMENT OF PARENT ADVICE FOR POPULAR DISSEMINATION: (a) developing advice for one specific problem situation, family shopping trips; (b) testing the advice program for benefit to children and convenience to adults; and (c) packaging the advice so it can be used successfully by interested parents. Systematic observation of 12 families using the written advice package on shopping trips revealed its effectiveness in reducing child disruptions and increasing positive interactions between parents and children. These findings, along with interview information from families, showed that the package is usable, effective, and popular with both parents and children, and thus is ready for dissemination to a wide audience of parents-a step that in itself should involve research and evaluation.

Journal Article↗
PubMed1990

Extended reductions in stereotypic behavior of students with autism through a self-management treatment package.

The literature suggests that self-management treatment packages have two potential strengths for the reduction or elimination of stereotypic behavior: (a) Self-management may be used for extended periods of time in the absence of a treatment provider, and (b) self-management techniques are easily adapated and used in a wide variety of natural settings. We assessed whether students with severe autistic disabilities could learn to use a self-management treatment package to reduce their stereotypic behavior within a multiple baseline across subjects design with withdrawals. The results showed that all of the students learned to use self-management procedures to reduce greatly levels of stereotypic behavior (typically to zero), and improvement occurred for extended periods of time in new settings without the presence of a treatment provider. The results are discussed in terms of the practical value of the treatment package and in terms of the implications for understanding autism.

Adolescent↗
PubMed1992

Effects of a videotape feedback package on the peer interactions of children with serious behavioral and emotional challenges.

Peer interactions are among the greatest challenges experienced by children who have severe emotional and behavioral problems. This study evaluated an intervention package designed to increase the ratio of these children's desirable to undesirable interactions. The package included three principal components: (a) observation of videotapes following regularly scheduled peer activity sessions; (b) self-evaluation of the children's peer interactions observed on the videotapes; and (c) delayed feedback and reinforcement for desirable peer interactions. Five students from two elementary schools participated. Multiple baseline designs and one reversal were used to evaluate the effects of the intervention package. The results showed that the intervention produced lower levels of undesirable peer interactions and higher ratios of desirable to undesirable interactions for all participants. The results are discussed in regard to their conceptual and applied implications and in terms of specific directions for future research.

Affective Symptoms↗
PubMed2006

Effectiveness of bans and laws in reducing traffic deaths: legalized Sunday packaged alcohol sales and alcohol-related traffic crashes and crash fatalities in New Mexico.

We determined the relative risk of alcohol-related motor vehicle accidents and fatalities after New Mexico lifted its ban on Sunday packaged alcohol sales. We extracted all alcohol-related crashes from New Mexico police reports for 3652 days between July 1, 1990, and June 30, 2000, and found a 29% increase in alcohol-related crashes and a 42% increase in alcohol-related crash fatalities on Sundays after the ban on Sunday packaged alcohol sales was lifted. There was an estimated excess of 543.1 alcohol-related crashes and 41.6 alcohol-related crash fatalities on Sundays after the ban was lifted. Repealing the ban on Sunday packaged alcohol sales introduced a public health and safety hazard in New Mexico.

Accidents, Traffic↗
PubMed1990

Information on tar and nicotine yields on cigarette packages.

We examined information on tar and nicotine yields on the packages of 160 cigarette brands, 58 percent of the 275 brands for which tar and nicotine yields were listed in a recent Federal Trade Commission report. The tar yield was indicated on 14 percent, the nicotine yield was indicated on 11 percent. As tar yield increased among brands, the yield was progressively less likely to be shown on the package and was not disclosed on the package of any cigarette yielding 11 mg or more of tar.

Humans↗