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Biomedical subjects

S Spengler

Publications and source records attributed to S Spengler.

12 recordsLinked to original sources
PubMed2001

Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.

Algorithms↗
PubMed2001

Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.

Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The current study investigates the hypothesis that splicing of tissue-specific alternative exons is regulated in part by control sequences in adjacent introns and that such elements may be recognized via computational analysis of exons sharing a highly specific expression pattern. We have identified 25 brain-specific alternative cassette exons, compiled a dataset of genomic sequences encompassing these exons and their adjacent introns and used word contrast algorithms to analyze key features of these nucleotide sequences. By comparison to a control group of constitutive exons, brain-specific exons were often found to possess the following: divergent 5' splice sites; highly pyrimidine-rich upstream introns; a paucity of GGG motifs in the downstream intron; a highly statistically significant over-representation of the hexanucleotide UGCAUG in the proximal downstream intron. UGCAUG was also found at a high frequency downstream of a smaller group of muscle-specific exons. Intriguingly, UGCAUG has been identified previously in a few intron splicing enhancers. Our results indicate that this element plays a much wider role than previously appreciated in the regulated tissue-specific splicing of many alternative exons.

Algorithms↗
PubMed1999

Analysis of ribosomal RNA sequences by combinatorial clustering.

We present an analysis of multi-aligned eukaryotic and procaryotic small subunit rRNA sequences using a novel segmentation and clustering procedure capable of extracting subsets of sequences that share common sequence features. This procedure consists of: i) segmentation of aligned sequences using a dynamic programming procedure, and subsequent identification of likely conserved segments; ii) for each putative conserved segment, extraction of a locall homogeneous cluster using a novel polynomial procedure; and iii) intersection of clusters associated with each conserved segment. Aside from their utilit in processing large gap-filled multi-alignments, these algorithms can be applied to a broad spectrum of rRNA analysis functions such as subalignment, phylogenetic subtree extraction and construction, and organism tree-placement, and can serve as a framework to organize sequence data in an efficient and easily searchable manner. The sequence classification we obtained using the method presented here shows a remarkable consistency with the independently constructed eukaryotic phylogenetic tree.

Algorithms↗
PubMed1993

Atomic force microscopy of biochemically tagged DNA.

Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphylococcal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein.

Bacterial Proteins↗
PubMed1990

Purification of glycogen phosphorylase from bovine brain and immunocytochemical examination of rat glial primary cultures using monoclonal antibodies raised against this enzyme.

The physiological function in brain of glycogen and the enzyme catalyzing the rate-limiting step in glycogenolysis, glycogen phosphorylase (EC 2.4.1.1), is unknown. As a first step toward elucidating such a function, we have purified bovine brain glycogen phosphorylase isozyme BB 1,700-fold to a specific activity of 24 units/mg protein. When analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and subsequent silver staining, a single major protein band corresponding to an apparent molecular mass of 97 kDa was observed. Mouse monoclonal antibodies raised against the enzyme were purified and shown to be monospecific as indicated by immunoblotting. Immunocytochemical examination of astroglia-rich primary cultures of rat brain cells revealed a colocalization of glycogen phosphorylase with the astroglial marker glial fibrillary acidic protein in many cells. The staining for the enzyme appeared at two levels of intensity. There were other cells in the culture showing no specific staining under the experimental conditions employed. Neurons in neuron-rich primary cultures did not show positive staining. The data suggest that glycogen phosphorylase may be predominantly an astroglial enzyme and that astroglia cells play an important role in the energy metabolism of the brain.

Animals↗
PubMed1981

Effect of tautomeric shift on mutation: N4-methoxycytidine forms hydrogen bonds with adenosine in polymers.

N4-Methoxycytidine (mo4C), previously found to act only as uridine (U) in transcription [Singer, B., & Spengler, S. (1981) Biochemistry 20, 1127], was tested for its ability to base pair as U in copolymers of (U,mo4C) annealed with poly(A) or transcribed with ATP and DNA-dependent RNA polymerase. Mixing curves have now indicated that the derivative is retained in a poly(U,39% mo4C).poly(A) helix, unlike unmodified C in poly(U,35% C). The presence of 13-39% mo4C in U polymers lowered the melting temperature, Tm, observed in annealed complexes both with poly(A) and after transcription with ATP. However, complexes isolated after transcription had a large hyperchromicity and melted cooperatively, which indicated that they are hydrogen bonded. The decreased Tm for poly(U,mo4C).poly(A) compared to that for poly(U).poly(A) can be attributed to stacking changes and adjacent base-pair disruption by mo4C. The greater cooperative melting of transcribed poly(U,39% mo4C) as compared to the annealed complex may indicate that the methoxy substituent is normally a mixture of rotamers and that the syn rotamer is required for transcription. The interference of the methoxy substituent was also shown by the loss of helix formation by poly(C,mo4C) in acid solution. mo4C decreased the Tm much more than A, which stacks well in acid. U, which neither stacks nor participates in an acid structure, caused more distortion than either of the other bases. It is inferred that mo4C has the base-pairing ability of U but that the planarity of the substituent is lost.

Adenosine↗
PubMed1981

Transcriptional errors and ambiguity resulting from the presence of 1,N6-ethenoadenosine or 3,N4-ethenocytidine in polyribonucleotides.

1,N6-Ethenoadenosine (epsilon A) and 3,N4-Ethenocytidine (epsilon C) in copolymers with unmodified nucleosides were transcribed using DNA-dependent RNA polymerase in the presence of Mn2+. Nearest neighbor analysis of the products showed that epsilon A directed incorporation of A much greater than U greater than C while epsilon C directed the incorporation of U greater than or equal to A much greater than C Neither directed G into the complementary polymer. Such misincorporations resulting from epsilon A and epsilon C, compounds that are formed in vivo by the carcinogen vinyl chloride, may have a biological role as promutagens.

Adenosine↗
PubMed1981

Tissue-dependent enzyme-mediated repair or removal of O-ethyl pyrimidines and ethyl purines in carcinogen-treated rats.

Treatment of perinatal rats with N-ethyl-N-nitrosourea (EtNU) leads predominantly to brain tumors. The DNA in tissues of 10-day-old BD IX rats is alkylated by this ultimate carcinogen at the same sites as is DNA in mammalian cell cultures or DNA in solution. Similar proportions of the derivatives quantitated (O6-EtG, 7-EtG, 3-EtA, O2-EtT, O4EtT, O2EtC, and ethyl phosphotriesters) are found in each tissue examined 1 h after treatment with EtNU. Most of the ethylated bases are poorly removed (or, in the case of O4-EtT, not at all) from DNA in the brain, the target tissue of oncogenicity. A pool of five other tissues, excluding liver, exhibits a similar pattern of ethyl base persistence over a 75 h period. In contrast, liver apparently contains enzymes capable of removing all of the ethylated bases. In all tissues used, ethyl phosphotriesters are very stable. The observed kinetics imply that removal of ethylated bases would be complete within 10 days in liver, while over 50% of the chemically ethylated stable bases would persist in other tissues, including brain, for many weeks. We propose that any or all persistent promutagenic derivatives (O6-EtG, O2EtT, O4-EtT, O2-EtC) can be important in the initiation of carcinogenesis by somatic mutation, given that the damage DNA is expressed. The differing rates of removal of the ethyl purines and pyrimidines in brain, liver and pooled tissues imply that mammals possess multiple independent repair systems.

Alkylation↗