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Biomedical subjects

J Hamm

Publications and source records attributed to J Hamm.

At least 55 records · Page 3Linked to original sources
PubMed1989

Identification of the RNA binding segment of human U1 A protein and definition of its binding site on U1 snRNA.

The interaction between the U1 snRNP-specific U1 A protein and U1 snRNA has been analysed. The binding site for the protein on the RNA is shown to be in hairpin II, which extends from positions 48 to 91 in the RNA. Within this hairpin the evolutionarily conserved loop sequence is crucial for interaction with U1 A protein. U1 A protein can also bind the loop sequence when it is part of an artificial RNA which cannot form a stable hairpin structure. The region of the protein required to bind to U1 snRNA consists of a conserved 80 amino acid motif, previously identified in many ribonucleoprotein (RNP) proteins, together with (maximally) 11 N-terminal and 10 C-terminal flanking amino acids. Point mutations introduced into two of the most highly conserved regions of this motif abolish RNA binding. U1 snRNA mutants from which the U1 A binding site has been deleted are shown to be capable of assembly into RNP particles which are immunoprecipitable by patient antisera which recognize U1 A protein. The role of RNA-protein and protein-protein interactions in U snRNP assembly are discussed.

Animals↗
PubMed1989

An abundant U6 snRNP found in germ cells and embryos of Xenopus laevis.

The particle state of U snRNPs was analyzed in oocytes, eggs, embryos and testes from Xenopus laevis. In each case both the relative abundance and the composition of some U snRNPs were found to differ from that of somatic cells. U2 and U6 snRNPs were the most prominent U snRNPs in germ cells and early embryos. In particular, the concentration of U6 snRNA was 10-20 times higher than that of U4 snRNA. Most of the U6 snRNA was not associated with U4 snRNA and migrated on sucrose gradients as a U6 snRNP. The structure of this novel U snRNP was analyzed. A single protein of 50 kd was copurified with U6 snRNPs by a combination of gradient fractionation, immunodepletion with anti-Sm antibodies and immunoprecipitation with anti-6-methyl adenosine antibodies. Although the U6 snRNP did not contain Sm proteins it migrated into the nucleus when U6 snRNA was injected into the cytoplasm of oocytes. Two U6 snRNA elements have been identified. The first is essential for nuclear migration in oocytes, but not for the formation of U4/6 snRNPs in vitro and might be the binding site of a U6-specific protein. The second element was required for interaction with U4 snRNPs but not for nuclear targeting.

Animals↗
PubMed1989

Functional analysis of mutant Xenopus U2 snRNAs.

Methods for studying pre-mRNA splicing in Xenopus oocytes have been improved to allow simultaneous analysis of the splicing reaction and the formation of splicing complexes in vivo. The number, order of appearance, and dependence on intact U1 and U2 snRNPs of complexes formed in vivo on a pre-mRNA substrate are similar but not identical to those observed in vitro. The migration on native gels of the complexes formed in vivo and in vitro is, however, dissimilar. RNAase H-mediated inhibition of splicing caused by oligonucleotide microinjection can be overcome by coinjection of a gene encoding the U snRNA that is targeted for cleavage. Transcripts from the injected gene complement the defect in splicing by assembling into functionally active U snRNPs. Using this assay, mutant U2 snRNAs have been tested for their ability to function in splicing and in splicing complex formation. The results indicate that much of the U2 snRNA, including regions essential for detectable binding of the U2-specific proteins A' and B", is dispensable for splicing.

Animals↗
PubMed1989

Probing the structure and function of U2 snRNP with antisense oligonucleotides made of 2'-OMe RNA.

We have used oligonucleotides made of 2'-OMe RNA to analyze the role of separate domains of U2 snRNA in the splicing process. We show that antisense 2'-OMe RNA oligonucleotides bind efficiently and specifically to U2 snRNP and demonstrate that masking of two separate regions of U2 snRNA can inhibit splicing by affecting different steps in the spliceosome assembly pathway. Masking the 5' terminus of U2 snRNA does not prevent U2 snRNP binding to pre-mRNA but blocks subsequent assembly of a functional spliceosome. By contrast, masking of U2 sequences complementary to the pre-mRNA branch site completely inhibits binding of pre-mRNA. Hybrid formation at the branch site complementary region also triggers a specific change which affects the 5' terminus of U2 snRNA.

Cell Nucleus↗
PubMed1988

Loop I of U1 small nuclear RNA is the only essential RNA sequence for binding of specific U1 small nuclear ribonucleoprotein particle proteins.

The binding of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins C, A, and 70K to U1 small nuclear RNA (snRNA) was analyzed. Assembly of U1 snRNAs from bean and soybean and a set of mutant Xenopus U1 snRNAs into U1 snRNPs in Xenopus egg extracts was studied. The ability to bind proteins was analyzed by immunoprecipitation with monospecific antibodies and by a protein-sequestering assay. The only sequence essential for binding of the U1-specific proteins was the conserved loop sequence in the 5' hairpin of U1. Further analysis suggested that protein C binds directly to the loop and that the assembly of proteins A and 70K into the RNP requires mainly protein-protein interactions. Protein C apparently recognizes a specific RNA sequence rather than a secondary structural element in the RNA.

Animals↗
PubMed1987

The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing.

Systematic oligonucleotide-directed mutagenesis within the internal control region of the Xenopus laevis somatic 5S RNA gene identifies three distinct sequence elements that regulate transcription activity: box A, containing the common, conserved class III promoter domain, and two 5S-gene-specific segments, termed intermediate element and box C. Analysis of the individual steps in the formation of the stable initiation complex reveals that the two 5S-gene-specific elements are the main determinants for the stable binding of TFIIIA. In contrast, TFIIIC binding appears to be dependent on interactions with TFIIIA and on direct DNA interactions in box A as well as probably in box C. Alterations of the spacing between the two major promoter domains of from -3 to +10 nucleotides are tolerated, although they reduce transcription activity and were found to prevent the formation of a stable initiation complex.

Animals↗
PubMed1987

In vitro assembly of U1 snRNPs.

An efficient system for the in vitro assembly of U1 snRNPs is described. RNA-protein interactions in a series of U1 snRNA mutants assembled both in vivo and in vitro were studied in order to verify the accuracy of the system. Two discrete protein binding sites are defined by immunoprecipitation with antibodies against different protein components of the U1 snRNP and a newly developed protein sequestering assay. The U1 snRNP-specific proteins 70K and A require only the 5'-most stem-loop structure of U1 snRNA for binding, the common U snRNP proteins require the conserved Sm binding site (AUnG). Interactions between these two groups of proteins are detected. These results are combined to derive a model of the U1 snRNP structure. The potential use of the in vitro system in the functional analysis of U1 snRNP proteins is discussed.

Animals↗
PubMed1987

Toxicity of methylenedioxymethamphetamine (MDMA) in the dog and the rat.

Methylenedioxymethamphetamine (MDMA) was administered to dogs and rats orally once a day for a 28-day period to evaluate the morphological and neuropathological effects. Major clinical signs associated with the administration of MDMA in the dog included circling, depression, dilated pupils, hyperactivity, rapid breathing, and salivation. Major clinical signs in the rat included hyperactivity, excitability, piloerection, exophthalmos, and salivation. Gross observations at necropsy in the dog possibly related to administration of the test article included reduced testicular size (one high and one medium dose) and prostatic enlargement in two high-dose animals. No gross lesions were seen in the rats at necropsy. The medium- and the high-dose groups in both sexes in both the rats and the dogs gained significantly less weight than the control and low-dose groups. Food consumption decreased the first week for the high- and medium-dose groups, but a significant reversal toward more normal consumption was noted in the following weeks in both the rats and the dogs. Hematologic, clinical chemistry, and urinalysis values did not appear to be affected by the administration of the test article in the dog. In the rat clinical pathology variables showing a trend to decrease with dose included urinary pH, blood urea nitrogen, glucose, creatinine (females), lactate dehydrogenase (LDH) (females), and chloride. Clinical pathology variables showing a trend to increase with dose included total white blood cell count and phosphorus. Microscopically, testicular atrophy was present in one medium-dose and two high-dose male dogs. Prostatic hyperplasia was present in two high-dose male dogs. No test article-related lesions were seen in the brains of either species.

3,4-Methylenedioxyamphetamine↗
PubMed1985

Functional domains of the Xenopus laevis 5S gene promoter.

To study the fine structure of the Xenopus laevis somatic 5S gene internal control region, we have created 15 different transversions using mutagenic oligonucleotide primers. The effects of these mutations on 5S DNA transcription in vitro as well as on stable complex formation with transcription factor TF III A and TF III C in crude nuclear extracts were analyzed. Mutations in the common class III 5' promoter element (nucleotides 50-61 in the 5S gene) interfere with transcription activity and stable complex formation whenever they contradict the tDNA box A consensus sequence. The second promoter element is defined by a major sequence block (nucleotides 80-89, box C) and two additional internal residues (70 and 71) at a distance of roughly one helical turn from both the major 3' and 5' control sequences; these two 3' elements contain the primary TF III A binding domain. The remaining nucleotides (62-69 and 71-79) when mutated do not interfere with transcription activity or factor binding and thus they constitute two spacer elements within a symmetrically structured 5S gene promoter. An increase in the relative spacing of box A and box C by insertion of 3 bp between nucleotides 66 and 67 leads to a drastic reduction in transcription activity and the ability to form a stable complex with TF III A and/or TF III C. Thus, accurate spacing is essential for the proper orientation of TF III A on 5S DNA and/or TF III C binding.

Animals↗
PubMed1983

The house sparrow (Passer domesticus) as a sentinel for St. Louis encephalitis virus.

Birds are the primary hosts for St. Louis encephalitis (SLE) virus in most of North America. Because the increased prevalence of antibody in House Sparrows (Passer domesticus) has been related to human cases, this species has been frequently used as a sentinel of SLE virus activity in urban areas. This study investigated the susceptibility of House Sparrows to two strains of SLE virus, measured antibody profiles, and evaluated the use of House Sparrows in an urban surveillance system. House Sparrows were susceptible to both strains of SLE virus inoculated, although not equally, and produced viremias sufficient to infect vector mosquitoes. Both hemagglutination-inhibiting (HI) and neutralizing (N) antibody developed rapidly and to high titers within 2 weeks after inoculation. Detectable humoral antibody began to disappear by 3 months, but persisted for 2 years in 27% for HI and 36% for N antibody of the surviving birds. However, all of the surviving birds were resistant to reinfection with SLE virus at 2 years after inoculation. The titer of HI antibody appeared to be useful in determining recent exposure to SLE virus. The experimental data on HI antibody development and persistence was related to field serologic data from House Sparrows. The monthly prevalences of SLE antibody for independent samples of sera from House Sparrows collected in Memphis, Tennessee, in 1980 were similar. SLE amplification in the House Sparrow population was delayed until September. The Memphis arbovirus surveillance system detected the amplification quickly, and responded with increased adult mosquito control in the focal areas. Urban surveillance of SLE utilizing House Sparrows as sentinels is discussed.

Animals↗
PubMed1981

[Clinical and endoscopic diagnosis of bronchogenic cancer].

Incidence of bronchogenic cancer has increased steadily over the past three decades. In spite of many advances in diagnostic and therapeutic procedures, unselected groups have a 5-year survival rate of about 5% compared to 2% previously. The most valuable methods are related to the flexible fiberoptic bronchoscope and the mediastinoscope along with a variety of biopsy techniques for the preoperative assessment (staging, grading, typing). Our present diagnostic techniques do not permit the early detection of lung cancer. This may become possible with the discovery of new tumor markers, tumor-specific fluorescence and radioisotopes combined with fiberoptic bronchoscopy.

Biopsy↗