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At least 163 records · Page 9Linked to original sources

PubMed2004

The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster.

We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p[RS3] and p[RS5], to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate >12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence.

Animals↗

PubMed1998

A stochastic model for the rapid emergence of specific vertebrate immunity incorporating horizontal transfer of systems enabling duplication and combinational diversification.

Recent molecular data indicate that the antigen-specific combinatorial immune response is restricted to jawed vertebrates where it is found in representatives of all class from cartilagenous fishes to mammals. Here, we analyse the relatively rapid emergence of the combinatorial system terms of three stochastic process, with the system reaching essentially full capacity in immunoglobulin recognition elements and diversification and recombination of gene segments in an evolutionary span of time of less than 20 million years. The mechanisms for inducibility were coopted from ancient and widely spread processes in phylogeny for regulation of cell division. The proposed process of formation entailed the evolution of unknown ancestral genes into those specifying bona fide immunoglobulin domains, and the generation of multiple copies of these via a series of events facilitated by horizontal transfer of site-specific recombinases and recombination signal sequences most probably from microbial and fungal sources. The second process is one of rapid "decay" (evolution) which occurred in about 10 million year under stringent selective conditions to generate proper conserved canonical sequences. The third process is that of the long term evolution of these characteristic immunoglobulin domains over the 450 million years since their emergence. As a first approximation the rates of these three processes were computed using first order differential equations. The rate of formation has a magnitude of 10-7 substitutions per site per year, and that of rapid modifications is 10-8 substitutions per site per year. The long term rate of immunoglobulin evolution is comparable to that of other moderately conserved proteins, (1-3) x 10-9 substitutions per site per year). This model is testable by searching for "footprints" of microbial and fungal DNA processing enzymes and recombination mechanisms. The hypothesis raises the general concept that horizontal transfer of genes facilitating rearrangement and duplication can catalyse major steps of macroevolution.

Animals↗

PubMed1993

Three-step PCR mutagenesis for 'linker scanning'.

'Linker scanning' has been used as an efficient method for systematically surveying a segment of DNA for functional elements by mutagenesis. A three-step PCR method was developed to simplify this process. In this method, a set of 'mutation primers' was made with 6 to 8 base substitutions in the center of the primers. In the first PCR reaction, these 'mutation primers' are paired with an 3' primer from the opposite end of the analyzed sequences to form a 'ladder' of fragments containing the base pair substitutions. These are used as templates in the second PCR with the 3' primer as the only primer to generate single stranded sequences, which are used as primers in the third PCR paired with an 5' primer to complete the mutagenesis. We have tested the method in a mutation screen of the steroid sulfatase promoter. Its application to general site specific mutagenesis is discussed.

Arylsulfatases↗

PubMed1986

Rescue of a tk-plasmid from transgenic mice reveals its episomal transmission.

This communication demonstrates the usefulness of the plasmid rescue procedure for recovery of plasmids from transgenic mice. We have microinjected the plasmid pSK1 harbouring the Herpes simplex virus thymidine kinase gene into fertilized mouse oocytes and succeeded in recovering plasmids from newborns by transformation of E. coli either with HindIII cut cellular DNA or with uncut DNA. The majority of the rescued plasmids were indistinguishable from pSK1 by restriction analysis. The rescued plasmids proved to be functionally active in a transient expression assay in mouse Ltk- cells. The pSK1 DNA sequences were inherited by up to 90% of the second generation progeny mice, which is not in agreement with a Mendelian transmission of heterozygous markers integrated into a single site of the chromosome. These data support the assumption that germ line transmission of non-integrated episomal plasmids can occur.

Animals↗

PubMed2006

Can amnesic patients learn without awareness? New evidence comparing deterministic and probabilistic sequence learning.

Can associative learning take place without awareness? We explore this issue in a sequence learning paradigm with amnesic and control participants, who were simply asked to react to one of four possible stimuli on each trial. Unknown to them, successive stimuli occurred in a sequence. We manipulated the extent to which stimuli followed the sequence in a deterministic manner (noiseless condition) or only probabilistically so (noisy condition). Through this paradigm, we aimed at addressing two central issues: first, we asked whether sequence learning takes place in either condition with amnesic patients. Second, we asked whether this learning takes place without awareness. To answer this second question, participants were asked to perform a subsequent sequence generation task under inclusion and exclusion conditions, as well as a recognition task. Reaction times results show that amnesic patients learned the sequence only in the deterministic condition. However, they failed to be able to reproduce the sequence in the generation task. In contrast, we found learning for both sequence structures in control participants, but only control participants exposed to a deterministic sequence were successful in performing the generation task, thus suggesting that the acquired knowledge can be used consciously in this condition. Neither amnesic nor control participants showed correct old/new judgments in the recognition task. The results strengthen the claim that implicit learning is at least partly spared in amnesia, and the role of contextual information available for learning is discussed.

Adult↗

PubMed1998

Genomic DNA transfer with a high-capacity adenovirus vector results in improved in vivo gene expression and decreased toxicity.

Many applications for human gene therapy would be facilitated by high levels and long duration of physiologic gene expression. Adenoviral vectors are frequently used for gene transfer because of their high cellular transduction efficiency in vitro and in vivo. Expression of viral proteins and the low capacity for foreign DNA limits the clinical application of first- and second-generation adenoviral vectors. Adenoviral vectors with all viral coding sequences deleted offer the prospect of decreased host immune responses to viral proteins, decreased cellular toxicity of viral proteins and increased capacity to accommodate large regulatory DNA regions. Currently most vectors used in vivo for preclinical and clinical studies express cDNAs under the control of heterologous eukaryotic or viral promoters. Using an adenoviral vector with all viral coding sequences deleted and containing the complete human alpha1-antitrypsin (PI) locus, we observed tissue-specific transcriptional regulation in cell culture and in vivo; intravenous injection in mice resulted in high levels of very stable expression for more than ten months and decreased acute and chronic toxicity. These results indicate significant advantages of regulated gene expression using genomic DNA for gene transfer and of adenoviral gene transfer vectors devoid of all viral coding sequences.

Adenoviridae↗

PubMed1997

Cancer-associated mutations at the INK4a locus cancel cell cycle arrest by p16INK4a but not by the alternative reading frame protein p19ARF.

The INK4a gene, one of the most frequently disrupted tumor suppressor loci in human cancer, encodes two unrelated proteins, p16INK4a and p19ARF, each of which is capable of inducing cell cycle arrest. Splicing of alternative first exons (1 alpha vs. 1 beta) to a common second exon within INK4a generates mRNAs in which exon 2 sequences are translated in two different reading frames. One of the products, the cyclin D-dependent kinase inhibitor p16INK4a, is functionally inactivated by mutations or deletions in a wide variety of cancers. However, because many such mutations reside in exon 2, they also affect the alternative reading frame (ARF) protein. To determine whether such mutations disrupt p19ARF function, we introduced naturally occurring missense mutations into mouse INK4a exon 2 sequences and tested mutant p16INK4a and p19ARF proteins for their ability to inhibit cell cycle progression. Six p19ARF point mutants remained fully active in mediating cell cycle arrest in NIH 3T3 fibroblasts, whereas two of the corresponding mutations within p16INK4a resulted in complete loss of activity. Analysis of p19ARF deletion mutants indicated that the unique aminoterminal domain encoded by exon 1 beta was both necessary and sufficient for inducing G1 arrest. Therefore, cancer-associated mutations within exon 2 of the INK4a gene specifically target p16INK4a, and not p19ARF, for inactivation.

3T3 Cells↗

PubMed2002

Stochastic pairwise alignments.

MOTIVATION: The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and regions of almost perfect sequence identity may occur in the same pair of molecules. The reliability of an alignment therefore strongly depends on the level of local sequence similarity. Especially in regions of high variability, many alignments of almost equal quality exist, and the optimal alignment is highly arbitrary. RESULTS: We discuss two approaches which deal with the inherent ambiguity of the alignment problem based on the computation of the partition function over all canonical pairwise alignments. The ensemble of possible alignments can be described by the probabilities P(ij) of a match between position i in the first and position j in the second sequence. Alternatively, we introduce a probabilistic backtracking procedure that generates ensembles of suboptimal alignments with correct statistical weights. A comparison between structure based alignments and large samples of stochastic alignments shows that the ensemble contains correct alignments with significant probabilities even though the optimal alignment deviates significantly from the structural alignment. Ensembles of suboptimal alignments obtained by stochastic backtracking can be used as input to any bioinformatics method based on pairwise alignment in order to gain reliability information not available from a single optimal alignment. AVAILABILITY: The software described in this contribution is available for downloading at http://www.tbi.univie.ac.at/~ulim/probA/

Algorithms↗

PubMed1998

Recruitment and loading of the E1 initiator protein: an ATP-dependent process catalysed by a transcription factor.

Initiation of DNA replication critically depends on ori recognition as well as on catalytic activities of the initiator complex. For replication of papillomaviruses the catalytic activities for initiation are provided by the E1 protein. Here, we show that the transcription factor E2 acts to assemble E1 into a complex active for ori distortion in two steps. First, cooperative DNA binding of E1 and E2 generates a sequence-specific ori recognition complex. In the second ATP-dependent step, E2 is displaced and additional E1 molecules are incorporated. The net result is a final complex with low sequence specificity deposited onto a specific sequence in the DNA. This may be a general strategy to accomplish specific positioning of protein complexes with low sequence specificity.

Adenosine Triphosphate↗

PubMed2003

Reevaluating human gene annotation: a second-generation analysis of chromosome 22.

We report a second-generation gene annotation of human chromosome 22. Using expressed sequence databases, comparative sequence analysis, and experimental verification, we have extended genes, fused previously fragmented structures, and identified new genes. The total length in exons of annotation was increased by 74% over our previously published annotation and includes 546 protein-coding genes and 234 pseudogenes. Thirty-two potential protein-coding annotations are partial copies of other genes, and may represent duplications on an evolutionary path to change or loss of function. We also identified 31 non-protein-coding transcripts, including 16 possible antisense RNAs. By extrapolation, we estimate the human genome contains 29,000-36,000 protein-coding genes, 21,300 pseudogenes, and 1500 antisense RNAs. We suggest that our revised annotation criteria provide a paradigm for future annotation of the human genome.

Animals↗

PubMed1989

Retroviral src gene expression in continuous marrow culture increases the self-renewal capacity of multilineage hematopoietic stem cells.

To define the action of the retroviral src gene on hematopoietic stem cells, C57BL/6 x DBA/2 (B6D2F1) mouse long-term marrow cultures were infected at initiation with Moloney murine leukemia virus (MuLV) pseudotypes of src-recombinant retroviruses with the src gene inserted in the env region of an amphotropic MuLV (src-Ampho), or in the gag region of Moloney MuLV (src-Mo). Other cultures were infected with Friend spleen focus-forming virus polycythemia-inducing strain (SFFVp), Moloney MuLV, or amphotropic MuLV, or were uninfected controls. Harvested nonadherent cells were tested weekly for multilineage, granulocyte-erythroid-megakaryocyte macrophage (CFU-GEMM) colony formation in vitro in recombinant murine IL-3 and erythropoietin, and individual colonies were removed, split 1:2, with half of each replated for in vitro self-renewal and the other half examined morphologically for number of hematopoietic cellular lineages, or tested for release of MuLV and src virus. Cultures infected with src-Ampho, src-Mo, or SFFVp demonstrated a significant increase in cumulative nonadherent cell and CFU-GEMM production. There was prolonged self-renewal over seven serial transfers of individual CFU-GEMM from src virus-infected cultures over seven serial transfers, and five of 61 individual colonies from the second or third generations contained detectable v-src gene sequences, but none released detectable src virus. Self-renewal of CFU-GEMM was similar to that with permanent IL-3-dependent cell line B6SUtA. In contrast, MuLV-infected or control uninfected cultures produced fewer cells, and self-renewal of CFU-GEMM did not exceed three generations. IL-3-dependent clonal hematopoietic progenitor cell lines, derived from each culture group, formed no detectable tumors in vivo; however, each released the original helper and/or transforming virus. Adherent cell lines, derived from src-Ampho-infected cultures released src virus and formed fibro-sarcomas in vivo. The data support the conclusion that src-recombinant virus expression in long-term marrow cultures increases the self-renewal capacity of multilineage hematopoietic stem cells.

Animals↗

PubMed1998

Reduced amide pseudopeptide analogues of a malaria peptide possess secondary structural elements responsible for induction of functional antibodies which react with native proteins expressed in Plasmodium falciparum erythrocyte stages.

A psi[CH2NH] isoster bond was introduced by replacing one peptide bond at a time within the 1513 malaria peptide KEKMV motif to obtain a set of five pseudopeptides. The motif belongs to a Plasmodium falciparum malarial peptide coded 1513, derived from the MSP-1 protein. This high-binding motif included in the 1513 peptide is involved in the attachment of the malarial parasite to human erythrocytes. The novel malaria 1513 psi[CH2NH] surrogates were analyzed using RP-HPLC and MALDI-TOF mass spectrometry techniques. Nuclear magnetic resonance experiments allowed definition of the five pseudopeptide analogues' secondary structural features. Such structures are present in only a very few molecules in the 1513 parent peptide. A molecular model demonstrating the solution of the three-dimensional structure of the 1 513 peptide Pse-437 analogue was constructed on the basis of 1H-NMR spectral parameters. Monoclonal antibodies were generated to the five 1513 malaria peptide pseudopeptide analogues. These antibodies not only recognize the native MSP-1 (195 kDa) and its 83 kDa and 42 kDa proteolytic processing proteins but also different SPf(66)n malaria vaccine batches containing the native sequence. In addition, the mAbs were able to modify the kinetics of Plasmodium falciparum parasites' intraerythrocytic development and their ability to invade new RBCs. The presented evidence suggests that peptide bond-modified peptides could reproduce a transient state in 1513's native sequence and represent useful candidates in the development of a second generation of effective malarial vaccines.

Amides↗

PubMed1990

Nucleotide sequence analysis of human beta-globin gene by the quantification method: mutations in 3'-splice junction sequence and beta-thalassemia.

The nucleotide sequence at the intron-exon junction in the human beta-globin gene was analyzed by the quantification method (categorical discriminant analysis) proposed previously. Using the sample score of a 16-nucleotide sequence at a 3'-splice junction, we studied to what extent such a sequence contains the 3'-splice signal. To examine the applicability of our method, we further studied several mutants of beta-thalassemia, where nucleotide changes exist at 3'-splice junction sequences of the first and second introns. Other mutants involve point mutations which generate new 3'-splice signals within the first intron. Experimental results on the abnormal splicing in those mutants could be explained in terms of the sample scores of 16-nucleotide sequences and their locations relative to the branch point.

Base Sequence↗

PubMed1998

Libraries of green fluorescent protein fusions generated by transposition in vitro.

Two artificial transposons have been constructed that carry a gene encoding Green Fluorescent Protein and can be used for generating libraries of GFP fusions in a gene of interest. One such element, AT2GFP, can be used to generate GFP insertions in frame with the amino acid sequence of the protein of interest, with a stop codon at the end of the GFP coding sequence; AT2GFP also contains a selectable marker that confers trimethoprim resistance in bacteria. The second element, GS, can be used to generate tribrid GFP fusions because there is no stop codon in the GFP transposon, and the resulting fusion proteins contain the entire amino acid sequence encoded by the gene. The GS element consists of a gfp open reading frame and a supF amber suppressor tRNA gene; the supF portion of the GS transposon can be utilized as a selectable marker in bacteria. Its sequence contains a fortuitous open reading frame, and thus it can be translated continuously with the gfp amino acid sequence. As a target for GFP insertions, we used a plasmid carrying the native Ty1 retrotransposon of the yeast Sacharomyces cerevisiae. The resulting multiple GFP fusions to Ty1 capsid protein Gag and Ty1 integrase were useful in determining the cellular localization of these proteins. Libraries of GFP fusions generated by transposition in vitro represent a novel and potentially powerful method to study the cell distribution and cellular localization signals of proteins.

Animals↗

PubMed1996

Quantitative magnetic resonance methods for in vivo investigation of the human liver and spleen. Technical aspects and preliminary clinical results.

This project was initiated with the introduction of magnetic resonance (MR) in Denmark in order to evaluate the possibilities of this technique as a diagnostic aid in non-focal liver and splenic diseases. The signal intensities in the MR image are sensitive to the longitudinal relaxation (T1), the transverse relaxation (T2), flow and chemical shift. All these parameters may be quantified by developing specific pulse sequences sensitive to the parameter in question. Previous studies had indicated that relaxation time measurements might be of value in the diagnosis of liver cirrhosis and haemochromatosis. Measuring relaxation times in these 2 groups of patients posed different challenges. In patients with liver cirrhosis a method had to be developed for simultaneous T1 and T2 relaxation time measurements, which was robust to the respiratory motion of the liver. A combination of multi-echo pulse sequences with different repetition times was chosen, because motion effects were partly refocused. Multi-acquisition was used to improve the signal-to-noise ratio in the heavily saturated experiments with short repetition times, to further reduce the sensitivity to motion. To test the quality of this pulse sequence, phantom experiments were performed, and sensitivity to motion was tested by measuring with and without respiratory synchronization. Respiratory synchronization gave a marked improvement in focal liver diseases, whereas no difference was found in non-focal diseases. Standard imaging sequences with a minimum echo time of 30 ms could not be used to measure the short T2 relaxation times found in patients with increased liver iron. A volume-selective multi-echo spectroscopic pulse was developed with a minimum echo time of 4 ms. Biexponential signal decay could be shown in patients with increased liver iron by using this sequence. Patients with liver cirrhosis, as a group, had increased T1 relaxation times compared to normal volunteers, but an overlap in T1 values was found. No correlation between the degree of fibrosis and the T1 relaxation time was found. Liver iron concentration could be quantified either by using the fast component of the T2 signal decay or by using the decreased signal in spin-echo and gradient echo images. Patients with leukemias and myeloproliferative disorders had prolonged T1 relaxation times in the spleen, but a considerable overlap was found between this group and a group of patients with benign hyperplasia and patients with splenomegaly secondary to portal hypertension. Volume-selective proton spectroscopy was developed and used to quantify the liver fat concentration. The accuracy of the method was about 3 g/100 g. With the implementation of a second generation scanner system it became possible to develop a pulse sequence, using the phase information in the MR signal, to measure portal vein flow during breath-holding. This method made it possible to estimate the portal vein flow during fasting, and the flow increase after eating. Quantitative MR methods may contribute to the diagnosis of non-focal liver diseases by estimation of liver fat and liver iron and by assessment of portal vein blood flow. Increased T1 relaxation time is a sign of a disease process in the liver rather than specific for any liver disease.

Humans↗

PubMed1996

Focal adhesion kinase-related fakB is regulated by the integrin LFA-1 and interacts with the SH3 domain of phospholipase C gamma 1.

Signal transduction through integrin molecules expressed on platelets and nonlymphoid cells involves activation of the intracellular focal adhesion kinase ppI25FAK (FAK) to phosphorylate substrate proteins on tyrosine residues. Similar mechanisms are also functional in T-lymphocytes through the beta 1-integrin VLA-4. A putative FAK-related phosphoprotein (fakB) was identified that is responsive to intracellular signals induced through ligation of antigen receptors on both T- and B-lymphocytes, and whose induced tyrosine phosphorylation is augmented by TCR costimulation through the adhesion/costimulatory receptors CD2 and CD4. In this report, fakB is shown to respond to extracellular signals through the beta 2-integrin LFA-1 in the absence of primary signals through the TCR. Protein-protein complex formation was observed involving an association between fakB, phospholipase C gamma 1 (PLC gamma 1), and the tyrosine phosphoprotein pp35-36. Evidence is provided here that fakB interacts with PLC gamma 1 through its SH3 domain. The association between fakB and PLC gamma 1 does not appear to require T-cell activation, whereas the induced tyrosine phosphorylation of the protein complex components occurs following engagement of LFA-1. These data indicate that the beta2-integrin LFA-1 expressed on T-lymphocytes stimulates a novel, FAK-related molecule that may function in the interplay between adhesion receptors and intracellular signaling enzymes responsible for downstream second messenger generation.

Amino Acid Sequence↗

PubMed1987

Proteolytic processing of the Ada protein that repairs DNA O6-methylguanine residues in E. coli.

In extracts of E. coli treated with an adapting regime of MNNG, the induced 39kd Ada protein having O6-MeG-DNA methyltransferase activity is processed to a 19kd active domain corresponding to the C-terminal half of the intact protein. This proteolytic processing has been followed on Western immunoblots using antisera raised against the 19kd fragment. Initial processing at 25 degrees C or 37 degrees C mainly generates a fragment of mol. wt. 24kd which then undergoes a slower second cleavage to generate the 19kd active domain. Preceding this second cleavage site is a sequence of amino acids Thr- -Gly-Met-Thr- -Lys that also occurs at another site in the N-terminal half of the 39kd methyltransferase. It is proposed that this sequence is a recognition site for proteolytic activity. On the basis of cleavage of the Ada protein at either one or both of these sites, fragments may be generated of mol. wt. 24kd and 19kd containing the active site for O6-methylguanine and O4-methylthymine repair, and 15kd and 20kd, containing the active site for methylphosphotriester repair. These observations explain previous reports by others on the existence in cell extracts of multiple methyltransferase activities of different sizes recognizing O-methyl lesions in DNA. The cellular protease involved is resistant to a wide range of protease inhibitors.

Bacterial Proteins↗

PubMed1990

Cloning and expression of the luxY gene from Vibrio fischeri strain Y-1 in Escherichia coli and complete amino acid sequence of the yellow fluorescent protein.

Vibrio fischeri strain Y-1 (ATCC 33715) emits light with a lambda max of 545 nm rather than the 485-nm emission typical of other strains of V. fischeri. The yellow emission is due to the interaction of the enzyme luciferase with a yellow fluorescent protein (YFP). On the basis of the N-terminal amino acid sequence of YFP, a mixed-sequence oligonucleotide probe was synthesized and used to isolate a 1.6-kbp HindIII fragment containing the first 208 bases of the gene that codes for YFP (luxY). Another synthetic oligonucleotide complementary to bases 167-184 of the YFP coding sequence was used to isolate a second (ca. 1.9 kbp) DNA fragment generated by digestion with both EcoRI and ClaI that contained the remainder of the luxY gene. The intact luxY gene, which encoded a 22,211-dalton polypeptide composed of 194 amino acid residues, was reconstructed from the two primary clones and is contained within a 765-bp SspI-XhoII fragment. Both strands of the entire luxY coding sequence were determined from the reconstructed gene, while the region surrounding the junction used in the reconstruction was also determined from the original partial clones. As with other genes that have been studied from V. fischeri, the luxY gene was unusually AT-rich. The sequence of luxY did not bear any apparent similarity to any of the sequences contained in the current GenBank database. Escherichia coli containing a plasmid with the luxY gene expresses a protein that reacts with antibody raised to authentic YFP.

Amino Acid Sequence↗