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At least 1,513 records · Page 84Linked to original sources
PubMed2000

The initiation translation factor eIF-4A of Cryptosporidium parvum is encoded by two distinct mRNA forms and shows DNA sequence polymorphism distinguishing genotype 1 and 2 isolates.

The eukaryotic translation initiation factor eIF-4A is an ATP-dependent RNA helicase involved in ribosome attachment to the 5' end of mRNAs. Employing as a probe a Cryptosporidium parvum genomic amplicon encoding a partial polypeptide related to eIF-4A, we screened a C. parvum sporozoite cDNA library to clone the full length of the gene. Two complete cDNAs were characterized, Cp.F6 and Cp.F10, which consisted of 1,900 and 1,418 bp, respectively. The overlapping portions of the sequences shared 100% identity and encoded a polypeptide of 405 amino acids whose identity to known eIF-4A molecules ranged between 77 and 39%. The 2 cDNAs differed in the length of their respective 3' untranslated regions, of 577 bp in Cp.F6 and 72 bp in Cp.F10, in both of which a putative polyadenylation signal was identified. The structure of the cloned cDNAs, along with genomic Southern blot data indicating that eIF-4A is encoded by a single copy gene, strongly suggested that Cp.F6 and Cp.F10 reflect a differential 3' end processing of mRNA precursors, not observed so far in C. parvum. Northern blot analysis confirmed that the sporozoites express 2 eIF-4A mRNAs and showed that the lower molecular weight transcript is 10- to 20-fold more abundant. We also investigated the polymorphism of the eIF-4A gene and defined a novel polymerase chain reaction-restriction fragment length polymorphism marker discriminating between C. parvum isolates of genotypes 1 and 2.

Amino Acid Sequence↗
PubMed2004

Finding and estimating chemical property data for environmental assessment.

The ability to predict the behavior of a chemical substance in a biological or environmental system largely depends on knowledge of the physicochemical properties and reactivity of that substance. We focus here on properties, with the objective of providing practical guidance for finding measured values and using estimation methods when necessary. Because currently available computer software often makes it more convenient to estimate than to retrieve measured values, we try to discourage irrational exuberance for these tools by including comprehensive lists of Internet and hard-copy data resources. Guidance for assessors is presented in the form of a process to obtain data that includes establishment of chemical identity, identification of data sources, assessment of accuracy and reliability, substructure searching for analogs when experimental data are unavailable, and estimation from chemical structure. Regarding property estimation, we cover estimation from close structural analogs in addition to broadly applicable methods requiring only the chemical structure. For the latter, we list and briefly discuss the most widely used methods. Concluding thoughts are offered concerning appropriate directions for future work on estimation methods, again with an emphasis on practical applications.

Data Collection↗
PubMed2000

Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid.

We characterized an unusual tRNA-like sequence that had been found inserted in suppressive variants of the mitochondrial retroplasmid of Neurospora intermedia strain Varkud. We previously identified two forms of the tRNA-like sequence, one of 64 nt (TRL-64) and the other of 78 nt (TRL-78) containing a 14-nt internal insertion in the anticodon stem at a position expected for a nuclear tRNA intron. Here, we show that TRL-78 is encoded in Varkud mitochondrial (mt)DNA within a 7 kb sequence that is not present in Neurospora crassa wild-type 74 A mtDNA. This 7-kb insertion also contains a perfectly duplicated tRNA(Trp)gene, segments of several mitochondrial plasmids and numerous GC-rich palindromic sequences that are repeated elsewhere in the mtDNA. The mtDNA-encoded copy of TRL-78 is transcribed and apparently undergoes 5'- and 3'-end processing and 3' nucleotide addition by tRNA nucleotidyl transferase to yield a discrete tRNA-sized molecule. However, the 14 nt intron-like sequence in TRL-78, which is missing in the TRL-64 form, is not spliced detectably in vivo or in vitro. Our results show that TRL-78 is an unusual tRNA-like species that could be incorporated into suppressive retroplasmids by the same reverse transcription mechanism used to incorporate mt tRNAs. The tRNA-like sequence may have been derived from an intron-containing nuclear tRNA gene or it may serve some function, like mtRNA. Our results suggest that mt tRNAs or tRNA-like species may be integrated into mtDNA via reverse transcription, analogous to SINE elements in animal cells.

Base Sequence↗
PubMed1999

Reconstructing the duplication history of a tandem repeat.

One of the less well understood mutational transformations that act upon DNA is tandem duplication. In this process, a stretch of DNA is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present. An interesting feature of tandem repeats is that the duplicated copies are preserved together, making it possible to do "phylogenetic analysis" on a single sequence. This involves using the pattern of mutations among the copies to determine a minimal or a most likely history for the repeat. A history tries to describe the interwoven pattern of substitutions, indels, and duplication events in such a way as to minimize the number of identical mutations that arise independently. Because the copies are adjacent and ordered, the history problem can not be solved by standard phylogeny algorithms. In this paper, we introduce several versions of the tandem repeat history problem, develop algorithmic solutions and evaluate their performance. We also develop ways to visualize important features of a history with the goal of discovering properties of the duplication mechanism.

Algorithms↗
PubMed2002

TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing.

We have developed a novel, isothermal DNA amplification strategy that employs phi29 DNA polymerase and rolling circle amplification to generate high-quality templates for DNA sequencing reactions. The TempliPhi DNA amplification kits take advantage of the fact that cloned DNA is typically obtained in circular vectors, which are readily replicated in vitro using phi29 DNA polymerase by a rolling circle mechanism. This single subunit, proofreading DNA polymerase has excellent processivity and strand displacement properties for generation of multiple, tandem double-stranded copies of the circular DNA, generating as much as 10(7)-fold amplification. Large amounts of product (1-3 microg) can be obtained in as little as 4 hours. Input DNA can be as little as 0.01 ng of purified plasmid DNA, a single bacterial colony, or a 1 microL of a saturated overnight culture. Additionally, the presence of an associated proof reading function within the phi29 DNA polymerase ensures high-fidelity amplification. Once completed, the product DNA can be used directly in sequencing reactions. Additionally, the properties of phi29 DNA polymerase and its use in applications such as amplification ofhuman genomic DNA for genotyping studies is discussed.

Bacillus Phages↗
PubMed2003

The evolutionary demography of duplicate genes.

Although gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, the rates of origin, loss, and preservation of gene duplicates are not well understood. Applying steady-state demographic techniques to the age distributions of duplicate genes censused in seven completely sequenced genomes, we estimate the average rate of duplication of a eukaryotic gene to be on the order of 0.01/ gene/million years, which is of the same order of magnitude as the mutation rate per nucleotide site. However, the average half-life of duplicate genes is relatively small, on the order of 4.0 million years. Significant interspecific variation in these rates appears to be responsible for differences in species-specific genome sizes that arise as a consequence of a quasi-equilibrium birth-death process. Most duplicated genes experience a brief period of relaxed selection early in their history and a minority exhibit the signature of directional selection, but those that survive more than a few million years eventually experience strong purifying selection. Thus, although most theoretical work on the gene-duplication process has focused on issues related to adaptive evolution, the origin of a new function appears to be a very rare fate for a duplicate gene. A more significant role of the duplication process may be the generation of microchromosomal rearrangements through reciprocal silencing of alternative copies, which can lead to the passive origin of post-zygotic reproductive barriers in descendant lineages of incipient species.

Animals↗
PubMed2002

Histopathological assessment of the pattern of liver cirrhosis in a tropical population.

This study aims at establishing the pattern of liver cirrhosis. Histology slides and duplicate copies of reports were retrieved and re-examined while fresh sections were processed from original paraffin blocks when necessary. Cirrhosis was the second commonest cause of chronic liver disease after hepatocellular carcinoma. The commonest morphological type was macronodular cirrhosis. Micronodular cirrhosis is not as common in black Africans as among the Caucasians. This is not unexpected since alcoholic liver disease that is of aetiopathogenetic importance is also not as common as what is often found in Causasians. Biliary cirrhosis was reported in an 8 months old girl consequent upon congenital absence of gallbladder and biliary tree. There was male preponderance in the occurrence of cirrhosis with a male, female ratio of 2.5:1. The incidence gradually increased from early adult life but was highest in the middle age especially between the age group of 51-60 years and subsequently dropped sharply. Adequate diagnostic facilities should be provided to determine the incidence of hepatotropic viruses and their contribution to the incidence of chronic liver diseases. Case-controlled studies should be carried out to determine the role of local cultural practices on hepatocellular injury and the development of chronic liver disease.

Adolescent↗
PubMed2004

The pattern of malignant tumours of the liver in a tertiary health institution in Nigeria.

This study aims at establishing the histopathological pattern of liver cancers reported in the Department of Pathology, University of Ilorin Teaching Hospital between January 1979 and December 1996. Histopathological slides and duplicate copies of reports were retrieved and re-examined while fresh sections were processed from original paraffin blocks when necessary. Liver cancers constituted 56.6% of all liver biopsies. Hepatocellular carcinoma, which was commonest in the fifth decade, occurred in 64.1%, while metastatic tumours, which were commonest in the sixth decade, accounted for 24.7%. Primary sites could only be determined in 5 out of the 35 metastatic tumours. The age range of patients with Burkitt's lymphoma was 6-17 years with an average of 10.8 years and a male/female ratio of 3:2. Overall, there was preponderance of hepatocellular carcinoma in males while metastatic tumours were commoner in females. The pattern of Burkitt's lymphoma demonstrated in this study agrees with what generally obtains for endemic Burkitt's lymphoma in this environment.

Adenocarcinoma↗
PubMed2005

The Data-Gathering Broker--A User-Based Approach to Viable EPR Systems.

With the continued expansion of Electronic Patient Record systems ahead of comprehensive evidence, metrics, or future-proofing, European health informatics is embarking on a faith-driven adventure that also risks data swamping of end-users. An alternative approach is an information broker system, drawing from departmental data sources. A three-year study in health and social care has produced a first demonstrator which can search for specified information in heterogeneous distributed data stores, with source-specific permission can copy it, and then merge the search results in a real-time process.

Electronic Health Records↗
PubMed1990

Biological and molecular aspects on herpes simplex virus latency.

Latent reactivateable herpes simplex virus (HSV) infections of sensory neurons of peripheral ganglia are most plausibly the source of clinical herpetic recurrences. The establishment of latency is the result of a concert of both viral and cellular factors such as the neuroinvasiveness of the virus, the relative density of receptors binding virus to the nerve cell plasma membrane, the permissiveness of the infection, including the axonal transport of the viral nucleocapsids, and the restriction of virus replication. Several hypotheses have been presented suggesting various mechanisms for the restriction of the HSV infection of the neuron. Thus, for instance the the importance of thymidine kinase negative mutants, hypermethylation of viral DNA and the existence of latency-associated viral genes have been discussed. Activation of the latent infection to a virus-producing lytic infection by means of superinfection with a replication-incompetent mutant is probably a result of genetic complementation. Reactivation by means of superinfection with replication-competent virus seems dependent upon the multiplicity of the superinfecting virus and more than one copy of the virus genome is required for the initiation of the reactivating process. These observations would be consistent with the overcoming of a cellularly controlled restriction of the latent infection. The cellular control of latency which can be impaired mechanically and chemically seems particularly important for the maintenance of latent HSV infection. However, recent observations indicate that reactivation of latent HSV infection is also associated with the expression of a latency-related viral gene (LAT), whereas establishment of the latency apparently is influenced by other properties determined by the genome of the virus, as well as by the capacity of the cell to restrict the lytic infection.

Ganglia↗
PubMed2006

Mitochondrial DNA copy number is regulated by cellular proliferation: a role for Ras and p66(Shc).

The abundance of mitochondria is regulated by biogenesis and division. These processes are controlled by cellular factors, given that, for example, mitochondria have to replicate their DNA prior to cell division. However, the mechanisms that allow a synchronization of cell proliferation with mitochondrial genome replication are still obscure. We report here our investigations on the role of proliferation and the contribution of Ras and p66Shc in the regulation of mitochondrial DNA copy number. Ras proteins mediate a variety of receptor-transduced mitogenic signals and appear to play an essential role in the cellular response to growth factors. P66Shc is a genetic determinant of life span in mammals and has been implicated in the regulation of receptor signaling and various mitochondrial functions. First, we confirmed previous reports showing that mitochondrial DNA is replicated during a specific phase of the cell cycle (the pre-S phase) and provided novel evidences that this process is regulated by mitogenic growth factors. Second, we showed that mitochondrial DNA replication is activated following Ras-induced cellular hyper-proliferation. Finally, we showed that p66Shc expression induces mitochondrial DNA replication, both in vitro and in vivo. We suggest that mitochondria are target of intracellular signaling pathways leading to proliferation, involving Ras and p66Shc, which might function to integrate cellular bio-energetic requirements and the inheritance of mitochondrial DNA in a cell cycle-dependent manner.

Adaptor Proteins, Signal Transducing↗
PubMed2007

Derivation and characterization of cholesterol-independent non-GS NS0 cell lines for production of recombinant antibodies.

Presented is an antibody production platform based on the fed-batch culture of recombinant NS0-derived cell lines. NS0 host cells, obtained from the European Collection of Cell Cultures (ECACC, Salisbury, UK, Part No. 85110503), were first adapted to grow in a protein-free, cholesterol-free medium. The resulting host cell line was designated NS0-PFCF (protein-free, cholesterol-free). The five production cell lines presented here were generated using a common protocol consisting of transfection by electroporation and subcloning. The NS0-PFCF host cell line was transfected using a single expression vector containing the Escherichia coli xanthine-guanine phosphoribosyl transferase gene (gpt), and the antibody heavy and light chain genes driven by the CMV promoter. The five cell lines were chosen after one to three rounds of iterative subcloning, which resulted in a 19-64% increase in antibody productivity when four mother-daughter cell pairs were cultured in a fed-batch bioreactor process. The production cell lines were genetically characterized to determine antibody gene integrity, nucleotide sequences, copy number, and the number of insertion sites in the NS0 cell genome. Genetic characterization data indicate that each of the five production cell lines has a single stably integrated copy of the antibody expression vector, and that the antibody genes are correctly expressed. Stability of antibody production was evaluated for three of the five cell lines by comparing the early stage seed bank with the Working Cell Bank (WCB). Antibody productivity was shown to be stable in two of three cell lines evaluated, while one of the cell lines exhibited a 20% drop in productivity after passaging for approximately 4 weeks. These five NS0-derived production cell lines were successfully cultured to produce antibodies with acceptable product quality attributes in a standardized fed-batch bioreactor process, consistently achieving an average specific productivity of 20-60 pg/cell-day, and a volumetric productivity exceeding 120 mg/L-day (Burky et al., 2006). In contrast to the commonly available NS0 host cell line, which requires serum and cholesterol for growth, and the commonly used expression vector system, which uses a proprietary glutamine synthetase selection marker (GS-NS0), these NS0 cells are cholesterol-independent, grow well in a protein-free medium, use a non-proprietary selection marker, and do not require gene amplification for productivity improvement. These characteristics are advantageous for use of this NS0 cell line platform for manufacturing therapeutic antibodies.

Animals↗
PubMed2005

The effects of gray scale image processing on digital mammography interpretation performance.

RATIONALE AND OBJECTIVES: To determine the effects of three image-processing algorithms on diagnostic accuracy of digital mammography in comparison with conventional screen-film mammography. MATERIALS AND METHODS: A total of 201 cases consisting of nonprocessed soft copy versions of the digital mammograms acquired from GE, Fischer, and Trex digital mammography systems (1997-1999) and conventional screen-film mammograms of the same patients were interpreted by nine radiologists. The raw digital data were processed with each of three different image-processing algorithms creating three presentations-manufacturer's default (applied and laser printed to film by each of the manufacturers), MUSICA, and PLAHE-were presented in soft copy display. There were three radiologists per presentation. RESULTS: Area under the receiver operating characteristic curve for GE digital mass cases was worse than screen-film for all digital presentations. The area under the receiver operating characteristic for Trex digital mass cases was better, but only with images processed with the manufacturer's default algorithm. Sensitivity for GE digital mass cases was worse than screen film for all digital presentations. Specificity for Fischer digital calcifications cases was worse than screen film for images processed in default and PLAHE algorithms. Specificity for Trex digital calcifications cases was worse than screen film for images processed with MUSICA. CONCLUSION: Specific image-processing algorithms may be necessary for optimal presentation for interpretation based on machine and lesion type.

Algorithms↗
PubMed2026

Integrated signatures define mutational processes in prostate cancer.

Prostate cancer follows a long and heterogeneous disease course with incompletely understood aetiology1. Here we dissect the mutational processes shaping the genomes of 959 donors from the Pan Prostate Cancer Group and assess their clinical relevance. By integrating de novo extracted single-base substitution, insertion-deletion and copy-number signatures with six novel complex structural variant signatures, we identify eight integrated mutational footprints (IMFs) that collectively explain the mutational processes in 85% of primary prostate cancer genomes. IMFs were strongly influenced by regional biases in the genome, most prevalently androgen receptor-mediated mutagenesis and replication stress. Four IMFs, present in 37% of primary tumours, were significantly associated with shorter time to metastasis. These included reactive oxygen-species-driven mutagenesis and both canonical and non-canonical homologous recombination deficiency, the latter being enriched in patients of African ancestry. Extending to the metastatic setting, we found that IMFs predicted sensitivity to androgen receptor pathway inhibitors. Taken together, our study delineates the aetiologies and mutational processes that drive the genomic and clinical heterogeneity of prostate cancer, introduces IMFs as a unifying framework, and highlights their potential to improve both risk stratification and biomarker-guided treatment selection.

Journal Article↗
PubMed1976

A system for rapid analysis of long-term recordings of heart rate and other physiological parameters.

Using miniature cassette tape recorders, measurement of ECG and other physiological measures is possible in industrial or working situations. The development of a semi-automatic high speed processing system for analysis of the tape recorded data is described. This system decodes the signals on the tape, converts ECG to heart rate and presents a listing of the heart rate variation over the recording period, which may be up to 24 hours. A punched paper tape copy of the listing is used for input into a mainframe computer for subsequent analysis. The recorders and processing system have been used extensively for three years on a study of industrial work stress, and have proved reliable, accurate, and of sufficient sensitivity for in-depth analysis. They allow considerable data to be collected, permitting the thorough statistical analysis necessary for the interpretation of complex physiological responses.

Computers↗
PubMed1988

A single point mutation in the envelope gene is responsible for replication and XC fusion deficiency of the endogenous ecotropic C3H/He murine leukemia virus and for its repair in culture.

The molecular basis has been determined for differences in infectivity and XC phenotype of endogenous ecotropic murine leukemia virus of the low-leukemia mouse strain C3H/He, its relative in the high-leukemia mouse strain AKR, and highly infectious, XC-positive C3H virus variants selected in vitro. Endogenous ecotropic type C virus induced by iododeoxyuridine from the nontransformed C3H/10T1/2 cell line is XC negative and replication deficient. In contrast, viruses produced late after iododeoxyuridine induction in chemically transformed C3H/10T1/2 cells (MCA5) are XC positive and infectious. XC-negative viruses can be converted to XC-positive viruses by being grown in certain transformed cell lines. We have cloned the endogenous ecotropic provirus of C3H/He from MCA5 cells, which is XC negative and replication deficient, as well as two XC-positive C3H proviruses derived by in vitro conversion. Fragment exchange between the XC-negative molecular clone p110 and the XC-positive AKR virus clone p623 revealed that the defect in p110 lies 3' of the SalI site located in the pol region. Nucleotide sequencing established that the C3H p110 provirus was integrated within the R region of an endogenous VL30 long terminal repeat (LTR) in reverse orientation and that the virus differed from the infectious AKR p623 provirus by a point mutation, substituting Lys for Arg at the potential precursor cleavage site for gp70 and p15E. In vitro-converted XC-positive C3H proviral clones 3211 and 4211 are identical to XC-negative C3H p110, except that they have Arg at this site and the normal cleavage site is thus regenerated in these clones. The XC-negative C3H p110 was blocked in processing of Pr85env, whereas clones 3211 and 4211 had normal cleavage of the env precursor into gp70. Both the XC-negative C3H provirus and the in vitro-converted XC-positive C3H proviruses had a single copy of a 99-base-pair enhancer element in the LTR, whereas two copies of this sequence are present in the AKR proviral LTR. Substitution of Arg for Lys at the envelope precursor processing site of C3H p110 by site-directed mutagenesis is sufficient by itself to convert the virus to the XC-positive replication-competent phenotype. Thus, we have established that a single point mutation at the processing site of the envelope precursor protein Pr85 is responsible for the difference in the infectivity and XC phenotype of endogenous ecotropic murine leukemia virus from C3H/He and AKR mice and that the basis for in vitro conversion is a mutation at this site.

AKR murine leukemia virus↗
PubMed1986

Regulation of IncFII plasmid DNA replication. A quantitative model for control of plasmid NR1 replication in the bacterial cell division cycle.

A quantitative model for the regulation of replication of the low copy number IncFII plasmid NR1 in the Escherichia coli cell division cycle has been developed. The initiation of NR1 replication requires a cis-acting initiator protein whose synthesis is regulated by several mechanisms. The NR1 regulatory processes include co-operative protein-protein interactions in the formation of an active transcription repressor, the interaction of repressor with a rightward operator site in the control of transcription of the initiator gene, and the interaction of an inhibitor RNA transcript with the initiator mRNA in the control of translation of the initiation protein. A statistical thermodynamic model was used to predict probable configurations of the regulatory processes in a single growing cell. These probabilities were coupled by a kinetic model to the events of the cell cycle, such as initiation of mRNA transcription and protein translation, and the initiation of plasmid DNA replication. Parameter values were chosen so that the simulated values for plasmid copy number and the intracellular concentrations of repressor protein and mRNA agreed with experimentally determined estimates. A number of different copy number mutants that have altered one or another of the regulatory processes were simulated by the model. The contributions of each of the regulatory processes toward the overall stability of inheritance of plasmid NR1 in a population of cells in culture were examined. These simulations predict a very stable pattern of inheritance for plasmid NR1 despite its low copy number, in agreement with experimental observation.

Cell Cycle↗
PubMed2000

Retrotransposition of a bacterial group II intron.

Self-splicing group II introns may be the evolutionary progenitors of eukaryotic spliceosomal introns, but the route by which they invade new chromosomal sites is unknown. To address the mechanism by which group II introns are disseminated, we have studied the bacterial L1.LtrB intron from Lactococcus lactis. The protein product of this intron, LtrA, possesses maturase, reverse transcriptase and endonuclease enzymatic activities. Together with the intron, LtrA forms a ribonucleoprotein (RNP) complex which mediates a process known as retrohoming. In retrohoming, the intron reverse splices into a cognate intronless DNA site. Integration of a DNA copy of the intron is recombinase independent but requires all three activities of LtrA. Here we report the first experimental demonstration of a group II intron invading ectopic chromosomal sites, which occurs by a distinct retrotransposition mechanism. This retrotransposition process is endonuclease-independent and recombinase-dependent, and is likely to involve reverse splicing of the intron RNA into cellular RNA targets. These retrotranspositions suggest a mechanism by which splicesomal introns may have become widely dispersed.

Bacterial Proteins↗