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At least 739 records · Page 41Linked to original sources
PubMed1986

Differential processing of RNA transcribed from the single-copy Drosophila myosin heavy chain gene produces four mRNAs that encode two polypeptides.

We report the sequence of genomic DNA at the 3' end of the single-copy Drosophila myosin heavy chain (MHC) gene and the structure and sequence at the 3' end of four MHC mRNAs. Two mRNAs, 7.2-kilobases (kb) and 8.0 kb in length, are expressed in all stages of development in which detectable levels of muscle-specific mRNAs accumulate. These mRNAs differ by alternate choice of two poly(A) sites within the same exon. Sequence information predicts that these two mRNAs can encode one MHC polypeptide. Two additional MHC mRNAs, 8.0 kb and 8.6 kb in length, are expressed only in late pupal and adult stages of development. These two stage-specific MHC mRNAs use the same poly(A) sites as the MHC mRNAs described above but have a different splicing pattern and thus include an additional exon. Sequence information predicts that these two stage-specific MHC mRNAs encode a second MHC polypeptide with a different COOH terminus.

Animals↗
PubMed1989

Proteolytic activity of the plum pox potyvirus NIa-protein on excess of natural and artificial substrates in Escherichia coli.

The plum pox potyvirus (PPV) NIa protease expressed from a medium copy number plasmid was able to process an excess of substrate expressed from a high copy number plasmid, in a binary Escherichia coli expression system. The delta B7 NIa protease mutant only partially processed the NIb-CP junction but its efficiency was independent of the amount of substrate. The delta B7 mutant essentially did not recognize an artificial cleavage site which was quite efficiently recognized by the wild-type protease. No competitive inhibition of the proteolytic activity by the presence of excess of different protease mutants was observed.

Amino Acid Sequence↗
PubMed1997

The intranuclear organization of normal, hemizygous and excision-deficient rRNA genes during developmental amplification in Tetrahymena thermophila.

In the ciliated protozoan, Tetrahymena thermophila, the diploid germinal micronucleus contains two allelic copies of the gene for ribosomal RNA (rDNA). During genesis of new somatic macronuclei the germline rDNA gene is excised by developmentally programmed chromosome breakage and preferentially amplified to approximately 9, 000 copies. We have studied this process by fluorescence in situ hybridization. We find that initially rDNA amplification is restricted to two separate and highly confined regions of the nucleus. Analysis of nuclei that are hemizygous for the rDNA locus reveals that each focus of hybridization is derived from a single allele of the rDNA. As rDNA amplification progresses these two foci of hybridization disperse and spread throughout the macronucleus, eventually forming approximately 100-500 new nucleoli. These events are correlated with morphologically distinct developmental stages. We investigated the amplification of the C3 allele of the rDNA that confers a replication advantage over the B allele during vegetative propagation, and find no evidence for preferential amplification of the C3 early in rDNA maturation. We also show that the rmm 11 rDNA mutant allele, which is defective for developmentally programmed rDNA excision, can be amplified during the two-foci stage in mutant homozygotes and heterozygotes, but fails to amplify further and disperse into multiple nucleoli. These data indicate that amplification of the rmm 11 allele is not delayed during the initial rounds of amplification, and suggest that efficient excision is not required for this amplification to occur. We propose that rDNA amplification is a two-step process. First, the two rDNA alleles are independently amplified, while allelic copies remain closely associated. Later, copies of the rDNA disperse and are further amplified, presumably because rDNA excision has occurred, generating fully mature rDNA minichromosomes that are able to replicate to high copy number.

Alleles↗
PubMed2001

Enhanced visualization processing: effect on workflow.

RATIONALE AND OBJECTIVES: Soft-copy viewing of digital radiographs allows for image processing to improve visualization of anatomy and lesions, but it can take more time than film-based viewing. Enhanced visualization processing (EVP) was developed to increase the latitude of an image without reducing the vital contrast, potentially reducing the need for the radiologist to manipulate images. This study examined the influence of processing radiographic images with EVP on workflow in a picture archiving and communications system (PACS). MATERIALS AND METHODS: Portable computed radiographic chest images were obtained and processed either with EVP or without. A security camera with a videocassette recorder was positioned above the PACS workstation. Four radiologists reviewed the images during their normal work schedule. The current diagnostic image was used to determine if the case contained EVP or non-EVP images. The videotapes of the sessions were reviewed to determine diagnostic viewing times and how zoom and/or window and level manipulation was used. RESULTS: Viewing time was significantly longer for the non-EVP than the EVP cases. The difference occurred with all readers. Window and level manipulation was used on 35% of the EVP and 41% of the non-EVP images. Zoom was used on 64% of the EVP and 69% of the non-EVP images. Average time spent using zoom and window and level manipulation was significantly shorter with the EVP than with the non-EVP images. CONCLUSION: EVP of chest images displayed on PACS monitors significantly improved workflow as measured by viewing time. EVP decreased use of window and level manipulation and zooming and the amount of time each one was used.

Humans↗
PubMed1991

Composition and chromosomal localization of the small multigene family encoding mouse U3B nucleolar RNA.

U3 small nucleolar RNA, which is believed to play a role in eukaryotic rRNA processing, is encoded by a small family of genes (5-10 copies/haploid genome) in mammals. In mouse, functional genes encoding the major U3B RNA form have been isolated, with all copies identified so far having evolved in a tightly concerted fashion. However, knowledge of the precise number and relative localization of all gene-family members has been hampered by the presence of multiple copies of U3B-processed pseudogenes in the mouse genome. In this study, we took advantage of a probe that is specific for functional U3B genes to address this question, using both Southern hybridization of genomic DNA and in situ hybridization of metaphase chromosomes. We show that the mouse haploid genome contains four functional U3B genes, all of which are clustered in a single chromosomal locus. They map to the C-D bands of mouse chromosome 11, within one of the most extended segments of gene-linkage conservation known between the mouse and human genomes, corresponding to a major portion of human chromosome 17. By contrast, the multiple (nonfunctional) U3 retrogenes are dispersed over several mouse chromosomes.

Animals↗
PubMed1998

Tam3 in Antirrhinum majus is exceptional transposon in resistant to alteration by abortive gap repair: identification of nested transposons.

Most transposon families consist of heterogeneous copies with varying sizes. In contrast, the Tam3 copies in Antirrhinum majus are known to have exceptionally conserved structures of uniform size. Gap repair has been reported to be involved in the structural alteration of copies from several transposon families. In this study, we have asked whether or not gap repair has affected Tam3 copies. Five Tam3 copies carrying aberrant sequences were selected from 40 independent Tam3 clones and their sequences were analyzed. Two of the five copies contain insertions in the Tam3 sequence. These two insertions, designated Tam356 and Tam661, are typical transposon-like sequences, which have terminal inverted repeats and cause target site duplication. These nested transposons were obviously associated with transpositional events, and did not originate from the gap-repair process. The remaining three copies had lost large parts of the Tam3 sequence. We could not find any relationship between the deletions of Tam3 sequence in the three copies and gap repair. PCR analysis of a Tam3 excision site in the nivea(recurrence:Tam3) mutant also showed that most of the repair events after the Tam3 excision involved end-joining. In addition to the results obtained here, among the other clones isolated, we could not find any of the internally deleted copies that comprise a major part of other transposon families. All of these data suggest that some feature of the Tam3 structure suppresses the structural alterations that are otherwise generated during the gap repair process.

Alleles↗
PubMed2024

TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.

Transcription is a key cell process that consists of synthesizing several copies of RNA from a gene DNA sequence. This process is highly regulated and closely linked to the ability of transcription factors to bind specifically to DNA. TFinder is an easy-to-use Python web portal allowing the identification of Individual Motifs (IM) such as Transcription Factor Binding Sites (TFBS). Using the NCBI API, TFinder extracts either promoter or gene terminal regulatory regions, through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. TFinder searches for Individual Motifs in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows de novo generations of a Position Weight Matrix (PWM) and the use of already established PWM. Finally, the data are provided in a tabular and a graph format showing the relevance and the P-value of the Individual Motifs found as well as their location relative to the Transcription Start Site (TSS) or the terminal region of the gene. The results are then sent by email to users facilitating the subsequent data analysis and sharing. TFinder is written in Python and freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder. It can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app. Resources are available on Streamlit "Resources" tab. TFINDER strength is that it relies on an all-in-one intuitive tool allowing users inexperienced with bioinformatics tools to retrieve gene regulatory regions sequences in multiple species and to search for individual motifs in a huge number of genes.

Transcription Factors↗
PubMed2006

Accurate and reliable high-throughput detection of copy number variation in the human genome.

This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self-self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method.

Algorithms↗
PubMed2005

Breakdown of spatial parallel coding in children's drawing.

When drawing real scenes or copying simple geometric figures young children are highly sensitive to parallel cues and use them effectively. However, this sensitivity can break down in surprisingly simple tasks such as copying a single line where robust directional errors occur despite the presence of parallel cues. Before we can conclude that this directional bias is a limiting case it needs to be shown that any given parallel cues are indeed being processed. We achieved this by using a texture-defined contour where parallel cues are integral to the stimulus and thus cannot be ignored. Here we report that even when prolific parallel cues must have been processed, young children make robust directional errors when copying single lines. This finding demonstrates a major constraint on young children's spatial parallel coding.

Age Factors↗
PubMed1996

Observer performance in the localization of tubes and catheters on digital chest images: the role of expertise and image enhancement.

RATIONALE AND OBJECTIVES: To determine whether observer performance in the localization of tubes and catheters on computed radiography (CR) chest images can be improved by using an automatic image-processing algorithm. METHODS: Comparisons were made of CR hard-copy, CR soft-copy, and CR enhanced soft-copy images obtained with an image-processing algorithm. The enhanced images used gray-level optimization and nonlinear unsharp masking to emphasize the edges of the devices. Chest radiologists (n = 4), general radiologists (n = 4), and interns (n = 6) read 45 images that contained endotracheal tubes, pulmonary artery catheters, and central venous catheters. RESULTS: Chest radiologists had the smallest mean interobserver localization variability (4 mm), followed by general radiologists (6 mm) and interns (8 mm). Localization variability was greatest for hard-copy images and least for enhanced soft-copy images. CONCLUSION: Use of an automatic imaging-processing algorithm reduced localization variability and enabled the medical interns to perform at approximately the same level as the chest radiologists.

Algorithms↗
PubMed2005

ARFGAP1 plays a central role in coupling COPI cargo sorting with vesicle formation.

Examining how key components of coat protein I (COPI) transport participate in cargo sorting, we find that, instead of ADP ribosylation factor 1 (ARF1), its GTPase-activating protein (GAP) plays a direct role in promoting the binding of cargo proteins by coatomer (the core COPI complex). Activated ARF1 binds selectively to SNARE cargo proteins, with this binding likely to represent at least a mechanism by which activated ARF1 is stabilized on Golgi membrane to propagate its effector functions. We also find that the GAP catalytic activity plays a critical role in the formation of COPI vesicles from Golgi membrane, in contrast to the prevailing view that this activity antagonizes vesicle formation. Together, these findings indicate that GAP plays a central role in coupling cargo sorting and vesicle formation, with implications for simplifying models to describe how these two processes are coupled during COPI transport.

ADP-Ribosylation Factor 1↗
PubMed1999

Assembly of the cleavage and polyadenylation apparatus requires about 10 seconds in vivo and is faster for strong than for weak poly(A) sites.

We have devised a cis-antisense rescue assay of cleavage and polyadenylation to determine how long it takes the simian virus 40 (SV40) early poly(A) signal to commit itself to processing in vivo. An inverted copy of the poly(A) signal placed immediately downstream of the authentic one inhibited processing by means of sense-antisense duplex formation in the RNA. The antisense inhibition was gradually relieved when the inverted signal was moved increasing distances downstream, presumably because cleavage and polyadenylation occur before the polymerase reaches the antisense sequence. Antisense inhibition was unaffected when the inverted signal was moved upstream. Based on the known rate of transcription, we estimate that the cleavage-polyadenylation process takes between 10 and 20 s for the SV40 early poly(A) site to complete in vivo. Relief from inhibition occurred earlier for shorter antisense sequences than for longer ones. This indicates that a brief period of assembly is sufficient for the poly(A) signal to shield itself from a short (50- to 70-nucleotide) antisense sequence but that more assembly time is required for the signal to become immune to the longer ones (approximately 200 nucleotides). The simplest explanation for this target size effect is that the assembly process progressively sequesters more and more of the RNA surrounding the poly(A) signal up to a maximum of about 200 nucleotides, which we infer to be the domain of the mature apparatus. We compared strong and weak poly(A) sites. The SV40 late poly(A) site, one of the strongest, assembles several times faster than the weaker SV40 early or synthetic poly(A) site.

3' Untranslated Regions↗
PubMed1999

Evaluation of the clonal relationship between primary and metastatic renal cell carcinoma by comparative genomic hybridization.

The outcome of patients with renal cell carcinoma is limited by the development of metastasis after nephrectomy. To evaluate the genetic basis underlying metastatic progression of human renal cell carcinoma in vivo, we performed a comparative genomic hybridization analysis in 32 clear-cell renal-cell carcinoma metastases. The most common losses involved chromosomes 3p (25%), 4q (28%), 6q (28%), 8p (31%), and 9p (47%). The most common gains were detected at 17q (31%) and Xq (28%). There was one high-level gene amplification at chromosome 11q22-23. The mean number of aberrations in lymph node (4.8 +/- 2.8) and lung metastases (6.2 +/- 4.0) was lower than in other hematogenous metastases (11.5 +/- 8.7, P < 0.05), suggesting that hematogenous dissemination is linked to an acquisition of complex genomic alterations. As genetic differences between primary tumors and metastases give information on genetic changes that have contributed to the metastatic process, relative DNA sequence copy number changes in 19 matched tumor pairs were compared. Genomic changes, which frequently occurred in metastases but not in the corresponding primary tumor were losses of 8p and 9p and gains of 17q and Xq. An abnormal function of genes in these regions may contribute to the metastatic process. According to a statistical analysis of shared genetic changes in matched tumor pairs, a high probability of a common clonal progenitor was found in 11 of 19 patients (58%). Six metastases (32%) were genetically almost completely different from the primary, suggesting that detection of genomic alterations in primary tumors gives only a restricted view of the biological properties of metastatic renal cell carcinoma.

Carcinoma, Renal Cell↗
PubMed1998

A comprehensive physical image quality evaluation of a selenium based digital x-ray imaging system for thorax radiography.

A selenium based digital x-ray system dedicated to chest radiography has been installed by the UK Department of Health's Medical Devices Agency at Leeds General Infirmary, UK, to undergo a comprehensive evaluation, including the physical image quality. The underlying characteristics which define the overall image quality of a system are the following: sensitometric response, modulation transfer function, and noise power spectrum. These have been measured objectively on preprocessed digital data acquired under relevant radiographic conditions. The image data is further processed prior to hard copy display. The displayed image quality may only be measured subjectively; threshold contrast detail detectability is such a measure which can be related to the objective measures of image quality. The objective imaging characteristics suggest that Thoravision has a significant advantage over conventional radiography imaging systems. However, subjective measures have demonstrated that the image processing can have a significant effect on the perceived image quality. Thoravision has the potential to deliver a significantly improved image quality to clinicians with no increase in radiation exposure to the patient, or image quality may be maintained with a reduction in radiation exposure. Digital image processing is central to the efficiency with which it achieves this.

Biophysical Phenomena↗
PubMed1991

Cytoduction in Chlamydomonas reinhardtii.

After conjugation between Chlamydomonas gametes of opposite mating type, a transient dikaryon is formed. The two nuclei fuse within 4-6 hr after mating. The young diploid zygote differentiates into dormant zygospore competent to complete meiosis, or more rarely (2-10% of cases) it undergoes mitosis to produce a stable diploid progeny. We here bring genetical, biochemical, and cytological evidence that among the mitotic zygotes, a large proportion of them undergo cytokinesis without fusion of the nuclei-a process that has been termed "cytoduction." By using appropriate genetic markers, haploid cytoductants that possess the nuclear genotype of one parent and the chloroplast marker of the other parent can easily be isolated. Genetical analysis and hybridization experiments moreover show that many haploid cytoductants transmit the chloroplast DNA molecules of both parents and that, as in diploids, these DNA copies occasionally recombine. This process of cytoduction extends the life cycle of Chlamydomonas and provides new tools for its genetic analysis.

Cell Nucleus↗
PubMed1994

High-level secretion of correctly processed beta-lactamase from Saccharomyces cerevisiae using a high-copy-number secretion vector.

We have sought to obtain a convenient system for the high-level production of secreted proteins in yeast. With the aid of a secretion reporter cassette we examined the secretion of beta-lactamase (Bla) as a model protein and found the highest expression in Saccharomyces cerevisiae using a high-copy-number plasmid. We further developed the high-copy-number plasmid introducing a secretion cassette that has a convenient cloning site coinciding with the sequence encoding the KEX2 cleavage site. Large quantities of correctly-processed product can therefore be obtained. We show that 0.3 g/l of correctly processed beta-lactamase can be obtained in fed-batch cultures without the need for selective media or significant loss of the plasmid.

Amino Acid Sequence↗
PubMed1990

Are transposons a cause of ageing?

A hypothesis for ageing is proposed based on the properties of transposons. During the process of transposition, one copy of the DNA sequence generally remains at the same position while the other copy moves to another location in the genome. In this manner the DNA sequence of the transposon is effectively duplicated. With time the number of transposons increases exponentially and since in their new location they can inactivate an essential gene, they will eventually kill a cell line or organism. Thus transposons could be a cause of ageing. This hypothesis is attractive because it can explain many of the properties of senescent cells. Other processes capable of DNA self-duplication (e.g., reverse transcription) could also contribute to the increase in transposable DNA sequences.

Aging↗
PubMed2003

Equivalence between two-qubit entanglement and secure key distribution.

We study the problem of secret key distillation from bipartite states in the scenario where Alice and Bob can perform measurements only at the single-copy level and classically process the obtained outcomes. Even with these limitations, secret bits can be asymptotically distilled by the honest parties from any two-qubit entangled state, under any individual attack. Our results point out a complete equivalence between two-qubit entanglement and secure key distribution: a key can be established through a one-qubit channel if and only if it allows one to distribute entanglement. These results can be generalized to a higher dimension for all those states that are one-copy distillable.

Journal Article↗