Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Copying Processes”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources
PubMed2004

The application of LTR retrotransposons as molecular markers in plants.

Retrotransposons are major, dispersed components of most eukaryotic genomes. They replicate by a cycle of transcription, reverse transcription, and integration of new copies, without excising from the genome in the process. Because they represent a major share of the genome, cause easily detectable genetic changes having known ancestral and derived states, and contain conserved regions for which polymerase chain reaction (PCR) primers may be designed, retrotransposon insertions can be exploited as powerful molecular marker systems. Here, we describe the background and strategies, as well as give detailed laboratory protocols, for four key retrotransposon-based methods: SSAP, IRAP, REMAP, and RBIP. The SSAP, IRAP, and REMAP methods are multiplex and generate anonymous marker bands; RBIP scores individual loci, much as microsatellite-based marker systems do. The methods are variously suited to marker detection on agarose and polyacrylamide slab gels, slab and capillary sequencing devices, and arrays on solid supports. The different strengths and weaknesses of these approaches and their performance relative to conventional marker methods are discussed, together with their applicability to marker-assisted breeding, phylogenetic analyses, biodiversity determinations, and evolutionary studies.

Biomarkers↗
PubMed2002

DNA array analysis in a Microsoft Windows environment.

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.

Databases, Nucleic Acid↗
PubMed1989

[Digital luminescence radiography. A new method of study in thoracic diagnosis at the intensive care unit].

The digital luminescence-radiography (DLR) technique relies on a complete digitalization of the X-ray image. Luminescence crystals on the imaging plate serve as an energy reservoir following their exposure to ionized radiation from any conventional X-ray source. A Helium-Neon laser stimulates the electrons in their high energy bands and therefore will be dropped back emitting luminescence. This luminescence is digitized by the DLR-System thus delivering a complete digital image to the image processor for subsequent processing and evaluation. The processed digital image is then recorded on a conventional film or a monitor screen. More than 3000 chest examinations using DLR have been performed on intensive care unit (ICU) patients at the University Hospital Eppendorf following the first eleven months since the clinical introduction of this new technique. The positive aspects of DLR such as high-contrast resolution and optimal reproducibility were clinically evaluated under ICU conditions. It was shown that DLR greatly improves the quality of the chest X-rays of all ICU patients and offers the following advantages: reproducibility, lateral chest projection, no insufficient exposure, reduction of exposure dose, electronical post-processing and storage, quality preserving digital storage and copying.

Humans↗
PubMed1995

A rare cryptic translation product is presented by Kb major histocompatibility complex class I molecule to alloreactive T cells.

The identity of allogeneic peptide/major histocompatibility complex (MHC) complexes that elicit vigorous T cell responses has remained an interesting problem for both practical and theoretical reasons. Although a few abundant MHC class I-bound peptides have been purified and sequenced, identifying the unique T cell-stimulating peptides from among the thousands of existing peptides is still a very difficult undertaking. In this report, we identified the antigenic peptide that is recognized by an alloreactive bm1 anti-B6 T cell clone using a novel genetic strategy that is based upon measurement of T cell receptor occupancy in single T cells. Using lacZ-inducible T cells as a probe, we screened a splenic cDNA library in transiently transfected antigen-presenting cells (APCs) and isolated a cDNA clone that allowed expression of the appropriate peptide/Kb MHC complex in APC. The antigenic octapeptide (SVVEFSSL) exactly matched the consensus Kb MHC motif, but was surprisingly encoded by a non-ATG defined translation reading frame. Furthermore, the abundance of the naturally processed analog in untransfected cells was estimated to be <10 copies per cell. These results illustrate a novel strategy for identifying T cell-stimulating antigens in general and directly show that alloreactive T cells can respond to rather rare peptide/MHC complexes. These results also suggest that the total pool of processed peptides expressed on the APC surface may include those generated by cryptic translation of normally expressed transcripts.

Amino Acid Sequence↗
PubMed2006

Craniofacial reconstruction using a combined statistical model of face shape and soft tissue depths: methodology and validation.

Forensic facial reconstruction aims at estimating the facial outlook associated with an unidentified skull specimen. Estimation is generally based on tabulated average values of soft tissue thicknesses measured at a sparse set of landmarks on the skull. Traditional 'plastic' methods apply modeling clay or plasticine on a cast of the skull, approximating the estimated tissue depths at the landmarks and interpolating in between. Current computerized techniques mimic this landmark interpolation procedure using a single static facial surface template. However, the resulting reconstruction is biased by the specific choice of the template and no face-specific regularization is used during the interpolation process. We reduce the template bias by using a flexible statistical model of a dense set of facial surface points, combined with an associated sparse set of skull-based landmarks. This statistical model is constructed from a facial database of (N = 118) individuals and limits the reconstructions to statistically plausible outlooks. The actual reconstruction is obtained by fitting the skull-based landmarks of the template model to the corresponding landmarks indicated on a digital copy of the skull to be reconstructed. The fitting process changes the face-specific statistical model parameters in a regularized way and interpolates the remaining landmark fit error using a minimal bending thin-plate spline (TPS)-based deformation. Furthermore, estimated properties of the skull specimen (BMI, age and gender, e.g.) can be incorporated as conditions on the reconstruction by removing property-related shape variation from the statistical model description before the fitting process. The proposed statistical method is validated, both in terms of accuracy and identification success rate, based on leave-one-out cross-validation tests applied on the facial database. Accuracy results are obtained by statistically analyzing the local 3D facial surface differences of the reconstructions and their corresponding ground truth. Identification success rate is obtained by comparing, based on correlation, Euclidean distance matrix (EDM) signatures of the reconstructed and the original 3D facial surfaces in the database. A subjective identification success rate is quantified based on face-pool tests. Finally a qualitative comparison is made between facial reconstructions of a real-case skull, based on two typical static face models and our statistical model, showing the shortcomings of current face models and the improved performance of the statistical model.

Adolescent↗
PubMed1999

The specificity of proteasomes: impact on MHC class I processing and presentation of antigens.

We have studied polypeptide processing by purified proteasomes, with regard to proteolytic specificity and cytotoxic T-lymphocyte (CTL) epitope generation. Owing to defined preferences with respect to cleavage sites and fragment length, proteasomes degrade polypeptide substrates into cohorts of overlapping oligopeptides. Many of the proteolytic fragments exhibit structural features in common with major histocompatibility complex (MHC) class I ligands including fragment size and frequencies of amino acids at fragment boundaries. Proteasomes frequently generate definitive MHC class I ligands and/or slightly longer peptides, while substantially larger peptides are rare. Individual CTL epitopes are produced in widely varying amounts, often consistent with immunohierarchies among CTL epitopes. We further found that polypeptide processing is remarkably conserved among proteasomes of eukaryotic origin and that invertebrate proteasomes can efficiently produce known high-copy MHC class I ligands, suggesting evolutionary adaptation of the transporter associated with antigen processing and MHC class I to ancient constraints imposed by proteasomal protein degradation.

ATP-Binding Cassette Transporters↗
PubMed2004

Glass pattern studies of local and global processing of contrast variations.

Using Glass patterns [Nature 223 (1969) 578; Nature 246 (1973) 360; Perception 5 (1976) 67], we have studied the role of contrast differences in local and global processes of form perception. The virtue of these patterns (composed of a set of randomly distributed elements combined with a geometrically transformed copy) for studying object formation is that they allow ready isolation of local processes, the combination of dots to form a perceptual pair, from global processes, the combination of dipoles into the percept of an overall rotational or translational pattern. We find that a contrast difference within dot-pairs reduces the ability to resolve local features; large differences totally abolish the perception of the pattern. Contrast differences between dot-pairs lessen, but do not abolish, the global integration among local features. In both cases the effect is proportional to the ratio of the two contrast levels employed. Effects which differ for rotations and translations, are consistent with the greater areal integration required to resolve rotational patterns.

Algorithms↗
PubMed1989

Evolution of the immunoglobulin heavy chain variable region (Igh-V) locus in the genus Mus.

The evolution of the mouse immunoglobulin heavy chain variable region (Igh-V) locus was investigated by the comprehensive analysis of variable region (Vh) gene family content and restriction fragment polymorphism in the genus Mus. The examination of natural Mus domesticus populations suggests an important role for recombination in the generation of the considerable restriction fragment polymorphism found at the Igh-V locus. Although the sizes of individual Vh gene families vary widely both within and between different Mus species, evolutionary trends of Vh gene family copy number are revealed by the analysis of homologues of mouse Vh gene families in Rattus and Peromyscus. Processes of duplication, deletion, and sequence divergence all contribute to the evolution of Vh gene copy number. Certain Vh gene families have expanded or contracted differently in the various muroid lineages examined. Collectively, these findings suggest that the evolution of individual Vh family size is not driven by strong selective pressure but is relatively neutral, and that gene flow, rather than selection, serves to maintain the high level of restriction fragment polymorphism seen in M. domesticus.

Animals↗
PubMed2002

ARFGAP1 promotes the formation of COPI vesicles, suggesting function as a component of the coat.

The role of GTPase-activating protein (GAP) that deactivates ADP-ribosylation factor 1 (ARF1) during the formation of coat protein I (COPI) vesicles has been unclear. GAP is originally thought to antagonize vesicle formation by triggering uncoating, but later studies suggest that GAP promotes cargo sorting, a process that occurs during vesicle formation. Recent models have attempted to reconcile these seemingly contradictory roles by suggesting that cargo proteins suppress GAP activity during vesicle formation, but whether GAP truly antagonizes coat recruitment in this process has not been assessed directly. We have reconstituted the formation of COPI vesicles by incubating Golgi membrane with purified soluble components, and find that ARFGAP1 in the presence of GTP promotes vesicle formation and cargo sorting. Moreover, the presence of GTPgammaS not only blocks vesicle uncoating but also vesicle formation by preventing the proper recruitment of GAP to nascent vesicles. Elucidating how GAP functions in vesicle formation, we find that the level of GAP on the reconstituted vesicles is at least as abundant as COPI and that GAP binds directly to the dilysine motif of cargo proteins. Collectively, these findings suggest that ARFGAP1 promotes vesicle formation by functioning as a component of the COPI coat.

ADP-Ribosylation Factors↗
PubMed2003

Are electronic medical records trustworthy? Observations on copying, pasting and duplication.

As routine use of on-line progress notes in US Department of Veterans Affairs facilities grew rapidly in the past decade, health information managers and clinicians began to notice that authors sometimes copied text from old notes into new notes. Other sources of duplication were document templates that inserted boilerplate text or patient data into notes. Word-processing and templates aided the transition to electronic notes, but enabled author copying and sometimes led to lengthy, hard-to-read records stuffed with data already available on-line. Investigators at a VA center recognized for pioneering a fully electronic record system analyzed author copying and template-generated duplication with adapted plagiarism-detection software. Nine percent of progress notes studied contained copied or duplicated text. Most copying and duplication was benign, but some introduced misleading errors into the record and some seemed possibly unethical or potentially unsafe. High-risk author copying occurred once for every 720 notes, but one in ten electronic charts contained an instance of high-risk copying. Careless copying threatens the integrity of on-line records. Clear policies, practitioner consciousness-raising and development of effective monitoring procedures are recommended to protect the value of electronic patient records.

Hospitals, Veterans↗
PubMed2005

Nuclear envelope breakdown is coordinated by both Nup358/RanBP2 and Nup153, two nucleoporins with zinc finger modules.

When higher eukaryotic cells transition into mitosis, the nuclear envelope, nuclear pore complexes, and nuclear lamina are coordinately disassembled. The COPI coatomer complex, which plays a major role in membrane remodeling at the Golgi, has been implicated in the process of nuclear envelope breakdown and requires interactions at the nuclear pore complex for recruitment to this new site of action at mitosis. Nup153, a resident of the nuclear pore basket, was found to be involved in COPI recruitment, but the molecular nature of the interface between COPI and the nuclear pore has not been fully elucidated. To better understand what occurs at the nuclear pore at this juncture, we have probed the role of the nucleoporin Nup358/RanBP2. Nup358 contains a repetitive zinc finger domain with overall organization similar to a region within Nup153 that is critical to COPI association, yet inspection of these two zinc finger domains reveals features that also clearly distinguish them. Here, we found that the Nup358 zinc finger domain, but not a zinc finger domain from an unrelated protein, binds to COPI and dominantly inhibits progression of nuclear envelope breakdown in an assay that robustly recapitulates this process in vitro. Moreover, the Nup358 zinc finger domain interferes with COPI recruitment to the nuclear rim. Consistent with a role for this pore protein in coordinating nuclear envelope breakdown, Nup358-specific antibodies impair nuclear disassembly. Significantly, targeting either Nup153 or Nup358 for inhibition perturbs nuclear envelope breakdown, supporting a model in which these nucleoporins play nonredundant roles, perhaps contributing to COPI recruitment platforms on both the nuclear and cytoplasmic faces of the pore. We found that an individual zinc finger is the minimal interface for COPI association, although tandem zinc fingers are optimal. These results provide new information about the critical components of nuclear membrane remodeling and lay the foundation for a better understanding of how this process is regulated.

Amino Acid Sequence↗
PubMed2006

Proteolytic processing of the receptor-type protein tyrosine phosphatase PTPBR7.

The single-copy mouse gene Ptprr gives rise to different protein tyrosine phosphatase (PTP) isoforms in neuronal cells through the use of distinct promoters, alternative splicing, and multiple translation initiation sites. Here, we examined the array of post-translational modifications imposed on the PTPRR protein isoforms PTPBR7, PTP-SL, PTPPBSgamma42 and PTPPBSgamma37, which have distinct N-terminal segments and localize to different parts of the cell. All isoforms were found to be short-lived, constitutively phosphorylated proteins. In addition, the transmembrane isoform, PTPBR7, was subject to N-terminal proteolytic processing, in between amino acid position 136 and 137, resulting in an additional, 65-kDa transmembrane PTPRR isoform. Unlike for some other receptor-type PTPs, the proteolytically produced N-terminal ectodomain does not remain associated with this PTPRR-65. Shedding of PTPBR7-derived polypeptides at the cell surface further adds to the molecular complexity of PTPRR biology.

Animals↗
PubMed1994

Analysis of the inductive effect of the genomic equivalent of HALF1 sequence in the reversion of rat dedifferentiated hepatoma cells.

HALF1 (human activator of liver function 1) is a closed DNA duplex implicated in reversion of rat dedifferentiated C2 hepatoma cells to a well-differentiated state. A copy of HALF1 is found in high-molecular-weight DNA in the human genome. The genomic equivalent of HALF1 and its flanking sequences [gH(5'-3') fragment] have previously been cloned and sequenced. To analyze the ability of the gH(5'-3') fragment to induce reversion process of C2 cells, two series of transfections were performed: (1) cotransfection of gH(5'-3') and plasmid pSVneo1 and (2) transfection of gH(5'-3') inserted into pSVneo1. The frequency of reversion was enhanced in transfected cells from the first experiment whereas no revertants were obtained from transfected cells in the second one. DNA analysis of the revertant clones revealed that reversion is associated with the transient presence of nonintegrated gH(5'-3') molecules. C2 cells were also transfected with gH(5'-3') cloned in pSV2dhfr. In the products of this transfection, the genesis of revertants correlated with amplification process of the gH(5'-3') sequence. We conclude that the presence of integrated copies of gH(5'-3'), even in high copy number, is not sufficient to induce the reversion process. We propose that extrachromosomal forms of gH(5'-3'), either given to cells or formed during amplification cycles, are involved in the reversion process of C2 cells.

Animals↗
PubMed2002

A survey of unequal crossover systems and their mathematical properties.

We present a model of gene duplication by means of unequal crossover (UCO) where the probability of any given pairing between homologous sequences scales as a penalty factor pz < or = 1, with z the number of mismatches due to asymmetric sequence alignment. From this general representation, we derive several limiting case models of UCO, some of which have been treated elsewhere in the literature. One limiting case is random unequal crossover (RUCO), obtained by setting p = 1 (corresponding to equiprobable pairings at each site). Another limiting case scenario (the 'Krueger-Vogel' model) proposes an optimal 'endpoint' alignment which strongly penalizes both overhang and deviations from endpoint matching positions. For both of these scenarios, we make use of the symmetry properties of the transition operator (together with the more general UCO properties of copy number conservation and equal parent-offspring mean copy number) to derive the stationary distribution of gene copy number generated by UCO. For RUCO, the stationary distribution of genotypes is shown to be a negative binomial, or alternatively, a convolution of geometric distributions on 'haplotype' frequencies. A different type of model derived from the general representation only allows recombination without overhang (internal UCO or IntUCO). This process has the special property of converging to a single copy length or a distribution on a pair of copy lengths in the absence of any other evolutionary forces. For UCO systems in general, we also show that selection can readily act on gene copy number in all of the UCO systems we investigate due to the perfect heritability (h 2 = 1) imposed by conservation of copy number. Finally, some preliminary work is presented which suggests that the more general models based on misalignment probabilities seem to also converge to stationary distributions, which are most likely functions of parameter value p.

Animals↗
PubMed2001

A neural model of smooth pursuit control and motion perception by cortical area MST.

Smooth pursuit eye movements (SPEMs) are eye rotations that are used to maintain fixation on a moving target. Such rotations complicate the interpretation of the retinal image, because they nullify the retinal motion of the target, while generating retinal motion of stationary objects in the background. This poses a problem for the oculomotor system, which must track the stabilized target image while suppressing the optokinetic reflex, which would move the eye in the direction of the retinal background motion (opposite to the direction in which the target is moving). Similarly, the perceptual system must estimate the actual direction and speed of moving objects in spite of the confounding effects of the eye rotation. This paper proposes a neural model to account for the ability of primates to accomplish these tasks. The model simulates the neurophysiological properties of cell types found in the superior temporal sulcus of the macaque monkey, specifically the medial superior temporal (MST) region. These cells process signals related to target motion, background motion, and receive an efference copy of eye velocity during pursuit movements. The model focuses on the interactions between cells in the ventral and dorsal subdivisions of MST, which are hypothesized to process target velocity and background motion, respectively. The model explains how these signals can be combined to explain behavioral data about pursuit maintenance and perceptual data from human studies, including the Aubert--Fleischl phenomenon and the Filehne Illusion, thereby clarifying the functional significance of neurophysiological data about these MST cell properties. It is suggested that the connectivity used in the model may represent a general strategy used by the brain in analyzing the visual world.

Animals↗
PubMed1989

Ribosome-binding sites and RNA-processing sites in the transcript of the Escherichia coli unc operon.

The polycistronic mRNA encoding the nine genes of the unc operon of Escherichia coli was studied. We demonstrated the ribosome-binding capabilities of six of the nine unc genes, uncB, uncE, uncF, uncH, uncA, and uncD, by using the technique of primer extension inhibition or "toeprinting." No toeprint was detected for the other genes, uncI, uncG, and uncC. The lack of a toeprint for uncG suggests that this gene is expressed by some form of translational coupling, such that either uncG is read by ribosomes which have translated the preceding gene, uncA, or translation of uncA is required for ribosome binding at the uncG site. RNA sequencing and primer extension in the regions of uncI and uncC, the first and last genes in the operon, respectively, gave less intense signals than those obtained for the other unc genes. This suggested that there are fewer copies of those regions of the transcript and that processing of the unc transcript occurred. Using primer extension and RNA sequencing, we identified sites in the unc transcript at which processing appears to take place, including a site which may remove much of the uncI portion of the transcript. Northern (RNA) blot analysis of unc RNA is consistent with the presence of an RNA-processing site in the uncI region of the transcript and another in the uncH region. These processing events may account for some of the differential levels of expression of the unc genes.

Base Sequence↗
PubMed2006

Intracellular trafficking of KA2 kainate receptors mediated by interactions with coatomer protein complex I (COPI) and 14-3-3 chaperone systems.

Assembly and trafficking of neurotransmitter receptors are processes contingent upon interactions between intracellular chaperone systems and discrete determinants in the receptor proteins. Kainate receptor subunits, which form ionotropic glutamate receptors with diverse roles in the central nervous system, contain a variety of trafficking determinants that promote either membrane expression or intracellular sequestration. In this report, we identify the coatomer protein complex I (COPI) vesicle coat as a critical mechanism for retention of the kainate receptor subunit KA2 in the endoplasmic reticulum. COPI subunits immunoprecipitated with KA2 subunits from both cerebellum and COS-7 cells, and beta-COP protein interacted directly with immobilized KA2 peptides containing the arginine-rich retention/retrieval determinant. Association between COPI proteins and KA2 subunits was significantly reduced upon alanine substitution of this signal in the cytoplasmic tail of KA2. Temperature-sensitive degradation of COPI complex proteins was correlated with an increase in plasma membrane localization of the homologous KA2 receptor. Assembly of heteromeric GluR6a/KA2 receptors markedly reduced association of KA2 and COPI. Finally, the reduction in COPI binding was correlated with an increased association with 14-3-3 proteins, which mediate forward trafficking of other integral signaling proteins. These interactions therefore represent a critical early checkpoint for biosynthesis of functional KARs.

14-3-3 Proteins↗
PubMed1986

Hyperalimentation worksheet.

Parenteral hyperalimentation is an important means of nutritional support for critically ill patients. Calculating the amount of additives necessary for the appropriate compounding of hyperalimentations is a tedious process with many opportunities for error. A new computer program written in Pascal has been created to reduce pharmacy processing time. Menus and single-keystroke entry are implemented wherever practicable. A hard-copy printout and an individualized label are generated on command. Program testing has resulted in an 88% reduction of processing time.

Computers↗