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PubMed1996

Characterization of a binding site for the herpes simplex virus type 1 UL9 origin-binding protein within the UL9 gene.

Gene UL9 of herpes simplex virus type 1 (HSV-1) encodes a sequence-specific origin-binding protein (OBP) that plays a direct and essential role in viral DNA synthesis. A search of the complete HSV-1 genomic sequence for possible OBP binding sites lying outside the known origins of replication revealed the presence of a very close match to the OBP recognition sequence within the UL9 coding region. The ability of OBP to bind to this site (referred to as the 'UL9 box') was confirmed by DNase I footprinting and gel retardation assays, and filter binding experiments demonstrated that the affinity of OBP for the UL9 box was of the same order as for its high affinity sites within the three replication origins. To investigate whether binding of OBP to the UL9 box played a role during viral replication we constructed a mutant virus in which the sequence was altered in such a way as to preserve the encoded amino acid sequence whilst abolishing the ability of OBP to bind. Growth of the virus was indistinguishable from wild-type and no alterations were observed in the accumulation of transcripts from the UL9 region of the genome. In addition, a DNA fragment containing the UL9 box sequence did not exhibit origin activity in a transient assay for viral DNA synthesis. We therefore conclude that binding of OBP to the UL9 box is not essential for virus growth and that expression of the UL9 gene is unlikely to be autoregulated through this site.

Base Sequence↗
PubMed1998

High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLalpha.

Genetic studies have suggested that chromatin structure is involved in repression of the silent mating type loci in Saccharomyces cerevisiae. Chromatin mapping at nucleotide resolution of the transcriptionally silent HMLalpha and the active MATalpha shows that unique organized chromatin structure characterizes the silent state of HMLalpha. Precisely positioned nucleosomes abutting the silencers extend over the alpha1 and alpha2 coding regions. The HO endonuclease recognition site, nuclease hypersensitive at MATalpha, is protected at HMLalpha. Although two precisely positioned nucleosomes incorporate transcription start sites at HMLalpha, the promoter region of the alpha1 and alpha2 genes is nucleosome free and more nuclease sensitive in the repressed than in the transcribed locus. Mutations in genes essential for HML silencing disrupt the nucleosome array near HML-I but not in the vicinity of HML-E, which is closer to the telomere of chromosome III. At the promoter and the HO site, the structure of HMLalpha in Sir protein and histone H4 N-terminal deletion mutants is identical to that of the transcriptionally active MATalpha. The discontinuous chromatin structure of HMLalpha contrasts with the continuous array of nucleosomes found at repressed a-cell-specific genes and the recombination enhancer. Punctuation at HMLalpha may be necessary for higher-order structure or karyoskeleton interactions. The unique chromatin architecture of HMLalpha may relate to the combined requirements of transcriptional repression and recombinational competence.

Base Sequence↗
PubMedDate not supplied

[Spectral characteristics of muscle aspartyl- and valyl-tRNA- synthetases and their complexes with substrates in normal conditions and after prolonged starvation].

Spectral characteristics of aminoacyl-tRNA-synthetases (ARSases) isolated from muscles of normal rabbits and of those fasted for a long time were studied by the methods of fluorescence and differential spectroscopy. Fluorescence spectra and differential absorption spectra of the compared proteins evidenced for more hydrophobic surrounding of tryptophanyls and their less accessibility for Cs+ ions in proteins of fasted animals. Interaction of aspartyl- and valyl-tRNA-synthetases from muscles of normal and long-fasted rabbits with substrates is accompanied by the essential quenching of tryptophan fluorescence of ARSases. Equilibrium constants of substrate binding calculated from the fluorescence quenching curves are higher for specific amino acids than for non-specific ones. The effect of a long-wave shift of fluorescence spectra under marginal excitation of tryptophan residues was used to determine structural differences of enzymes in norm and under fasting and to find their structural peculiarities during formation of aminoacyl adenylate. Aminoacyl-tRNA-synthetases (ARSases) are key enzymes of the protein biosynthesis. High specificity of their interaction with substrates is the basis for the accuracy of genetic information implementation, namely translation of the genetic code. Molecular mechanisms of substrates "recognition" by ARSases are the objects of great attention of researchers.

Amino Acyl-tRNA Synthetases↗
PubMed1997

Immune response associated with nonmelanoma skin cancer.

It is now clear that UV radiation causes nonmelanoma skin cancer in at least two ways: by causing permanent changes in the genetic code and by preventing immunologic recognition of mutant cells. These are interacting rather than separate mechanisms. Damage to DNA results in disregulation of cellular proliferation and initiates immune suppression by stimulating the production of suppressive cytokines. These cytokines contribute to the loss of immunosurveillance. Ultraviolet radiation has both local and systemic immunosuppressive effects. Locally, it depletes and alters antigen-presenting LC at the site of UV irradiation. Systemic suppression results when Ts cells are induced, by altered LC, by inflammatory macrophages that enter the skin following UV irradiation, or by the action of cytokines. Damage to DNA appears to be one of the triggering events in inducing systemic immunosuppression via the release of immunosuppressive cytokines and mediators. Immunologic approaches to treating skin cancers so far have concentrated on nonspecifically stimulating immune cells that infiltrate these tumors, but induction of specific immune responses against these tumors with antitumor vaccines has received little attention as yet. Preventive measures include sun avoidance and the use of sunscreens to prevent DNA damage by UV light. Future strategies may employ means to reverse UV-induced immunosuppression by using anti-inflammatory agents, biologicals that accelerate DNA repair or prevent the generation of immunosuppressive cytokines, and specific immunotherapy with tumor antigens. New approaches for studying the immunology of human skin cancers are needed to accelerate progress in this field.

Animals↗
PubMed1996

The sensory match effect in recognition memory: perceptual fluency or episodic trace?

The sensory match effect in recognition memory refers to the finding that recognition is better when the sensory form in which an item is tested is the same as that in which it was studied. This paper examines the basis for the sensory match effect by manipulating whether a studied fragmented picture is tested with the same or a complementary set of fragments in a recognition memory test (Experiment 1) and in a fragment-identification test (Experiment 2). Assuming that fragment identification is a direct measure of perceptual fluency, we expected identical patterns of results across the two tests if perceptual fluency accounted for the sensory match effect in recognition memory. Instead, recognition memory showed a robust overall sensory match effect (the same fragmented image was recognized better than the complementary image), whereas fragment identification showed no overall sensory match effect (the same fragmented image was identified no better than the complementary fragmented image). Experiments 3 and 4 combined the two responses and showed that the basis for the sensory match effect in recognition memory was a subject's ability to recognize the matching fragments in the absence of conceptual information (when the test stimulus could not be identified), supporting the idea that the episodic trace of the sensory code is responsible for the sensory match effect in recognition memory. Experiment 5 demonstrated that subjects are able to use this sensory code as the sole basis for recognition memory.

Form Perception↗
PubMed1990

The yeast Yarrowia lipolytica has two, functional, signal recognition particle 7S RNA genes.

Cells containing a deletion of either the SCR1 or SCR2 genes, which code for the 7SL RNA component of the signal recognition particle (SRP) homologue, were found to be viable. Two independent approaches demonstrated that cells containing deletions of both genes were inviable. Therefore, Yarrowia lipolytica contains two (and only two) functional 7SL RNA genes.

Blotting, Southern↗
PubMed1988

'Recognition units' at the top of a neuronal hierarchy? Prepacemaker neurons in Eigenmannia code the sign of frequency differences unambiguously.

The electric fish, Eigenmannia, is able to discriminate the sign of the frequency difference, Df, between a neighbor's electric organ discharges (EODs) and its own. The fish lowers its EOD frequency for positive Dfs and raises its frequency for negative Dfs to minimize jamming of its electrolocation ability by a neighbor's EODs of similar frequency. This jamming avoidance response (JAR) is controlled by a group of 'sign-selective' neurons in the prepacemaker nucleus (PPN) that is located at the boundary of the midbrain and the diencephalon (Fig. 1). Extracellular recordings from a total of 35 neurons revealed a great similarity between behavioral and neuronal response properties: 1. All neurons fired vigorously for negative Dfs and were almost silent for positive Dfs, regardless of the orientation of the jamming stimulus, and thus discriminated the sign of Df unambiguously (Fig. 2). 2. In accordance with behavioral observations, individual neurons failed to discriminate the sign of Df when the jamming stimulus had the same field geometry as the signal mimicking the animal's own EOD (Fig. 3). 3. Df magnitudes which evoke strongest JARs, usually 4 to 8 Hz, also induced most vigorous responses in sign-selective neurons (Fig. 5). 4. Behavioral and neuronal thresholds for the detection of small jamming signals were similar. Threshold for sign selectivity was reached when the amplitude ratio of the jamming signal to the EOD mimic, measured near the head surface, was 0.001. This value corresponds to a maximal temporal disparity (a necessary cue for performing a correct JAR) of 1 to 2 microseconds for signals received by the two sides of the body in a transverse jamming field (Fig. 7). 5. The effects of two jamming fields, offered orthogonally to each other, may interact nonlinearly at the behavioral as well as at the neuronal level. A positive Df presented in one field may suppress behavioral and neuronal responses to modulations of the sign of Df in the other field (Fig. 8c).

Animals↗
PubMed1984

Nucleotide sequence of the gene encoding pilin of Bacteroides nodosus, the causal organism of ovine footrot.

The nucleotide sequence encoding pilin, the monomer protein subunit of the pilus from Bacteroides nodosus, has been determined. The sequence predicts a short, positively charged, amino-terminal segment which is absent from the amino acid sequence of mature pilin. The coding sequence is preceded upstream by a sequence of five nucleotides complementary to the 3' end of 16S rRNA of Escherichia coli--a potentially good ribosome binding site--and even further upstream by an AT-rich region preceding several potential recognition sites for RNA polymerase. The coding sequence is followed by a region of hyphenated dyad symmetry having the potential to act as a rho-independent terminator of transcription.

Amino Acid Sequence↗
PubMed1992

Assessment of protein coding measures.

A number of methods for recognizing protein coding genes in DNA sequence have been published over the last 13 years, and new, more comprehensive algorithms, drawing on the repertoire of existing techniques, continue to be developed. To optimize continued development, it is valuable to systematically review and evaluate published techniques. At the core of most gene recognition algorithms is one or more coding measures--functions which produce, given any sample window of sequence, a number or vector intended to measure the degree to which a sample sequence resembles a window of 'typical' exonic DNA. In this paper we review and synthesize the underlying coding measures from published algorithms. A standardized benchmark is described, and each of the measures is evaluated according to this benchmark. Our main conclusion is that a very simple and obvious measure--counting oligomers--is more effective than any of the more sophisticated measures. Different measures contain different information. However there is a great deal of redundancy in the current suite of measures. We show that in future development of gene recognition algorithms, attention can probably be limited to six of the twenty or so measures proposed to date.

Algorithms↗
PubMed1978

Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox.

The 40,000-fold variation in eukaryote haploid DNA content is unrelated to organismic complexity or to the numbers of protein-coding genes. In eukaryote microorganisms, as well as in animals and plants, DNA content is strongly correlated with cell volume and nuclear volume, and with cell cycle length and minimum generation time. These correlations are simply explained by postulating that DNA has 2 major functions unrelated to its protein-coding capacity: (1) the control of cell volume by the number of replicon origins, and (2) the determination of nuclear volume by the overall bulk of the DNA: cell growth rates are determined by the cell volume and by the area of the nuclear envelope available for nucleocytoplasmic transport of RNA, which in turn depends on the nuclear volume and therefore on the DNA content. During evolution nuclear volume, and therefore DNA content, has to be adjusted to the cell volume to allow reasonable growth rates. The great diversity of cell volumes and growth rates, and therefore of DNA contents, among eukaryotes results from a varying balance in different species between r-selection, which favours small cells and rapid growth rates and therefore low DNA C-values, and K-selection which favours large cells and slow growth rates and therefore high DNA C-values. In multicellular organisms cell size needs to vary in different tissues: size differences between somatic cells result from polyteny, endopolyploidy, or the synthesis of nucleoskeletal RNA. Conflict between the need for large ova and small somatic cells explains why lampbrush chromosomes, nurse cells, chromatin diminution and chromosome elimination evolved. Similar evolutionary considerations clarify the nature of polygenes, the significance of the distribution of haploidy, diploidy and dikaryosis in life cycles and of double fertilization in angiosperms, and of heteroploidy despite DNA constancy in cultured cells, and other puzzles in eukaryote chromosome biology. Eukaryote DNA can be divided into genic DNA (G-DNA), which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA) which exists only because of its nucleoskeletal role in determining the nuclear volume (which it shares with G-DNA, and performs not only directly, but also indirectly by coding for nucleoskeletal RNA). Mechanistic and evolutionary implications of this are discussed.

Animals↗
PubMed1998

Automatic prediction of trauma registry procedure codes from emergency room dictations.

Current natural language processing techniques for recognition of concepts in the electronic medical record have been insufficient to allow their broad use for coding information automatically. We have undertaken a preliminary investigation into the use of machine learning methods to recognize procedure codes from emergency room dictations for a trauma registry. Our preliminary results indicate moderate success, and we believe future enhancements with additional learning techniques and selected natural language processing approaches will be fruitful.

Artificial Intelligence↗
PubMed1986

Structure of rat calmodulin processed genes with implications for a mRNA-mediated process of insertion.

Two distinct processed calmodulin genes of rat (lambda SC8 and lambda SC9) were identified, cloned and their DNA sequences determined. The existence of direct repeats of 19 base-pairs for lambda SC8 or 9 base-pairs for lambda SC9 at both ends of the coding plus non-coding regions suggested a possible involvement of a mRNA-mediated process of insertion. Total genomic Southern hybridization suggested the existence of at least three different calmodulin-related genes in the rat genome. The other gene was the bona fide calmodulin gene (lambda SC4) which was split into at least five exons. lambda SC9 contained insertions of one nucleotide and two 17 base-pair direct repeats in the coding region. These insertions cause frameshift mutations probably preventing it from encoding a functional calmodulin. It also carried an insertion of a rat middle repetitive sequence, identifier sequence (IDS: Sutcliffe et al., 1982) in the 3'-non-coding region. Otherwise, it consisted of an almost identical DNA sequence to that of the bona fide calmodulin gene (lambda SC4), including the 3'-non-coding region down to the poly(A) recognition signal, A-A-T-A-A-A. On the other hand, lambda SC8 did not possess frameshift mutations in the coding region, and hence was capable of encoding a functional protein. In fact, a probe specific to the lambda SC8 sequence identified a band in Northern blotting whose size was 300 nucleotides smaller than that of authentic calmodulin mRNA. Comparison of the nucleotide sequences showed that only the coding regions of these two processed genes were homologous, indicating that the divergence of these two processed genes from the common ancestor calmodulin was an ancient event.

Amino Acid Sequence↗
PubMed1998

Animal lectins as cell adhesion molecules.

Protein-carbohydrate interaction is exploited in cell adhesion mechanisms besides the recognition of peptide motifs. The sugar code thus significantly contributes to the intriguing specificity of cellular selection of binding partners. Focusing on two classes of lectins (selectins and galectins), it is evident that their functionality for mediation of adhesive contacts is becoming increasingly appreciated, as is the integration of this type of interaction with other recognition modes to yield the noted specificity. The initial contact formation between leukocytes and activated endothelium makes use of selectins to guide lymphocyte trafficking. In addition to the three selectins which bind a distinct array of ligands, galectin-1 and galectin-3 and possibly other members of this family are involved in cell-cell or cell-matrix interactions. This review summarizes structural and functional aspects of these two classes of endogenous lectins relevant for cell adhesion.

Animals↗
PubMed1997

Recognition of follicle stimulating hormone (alpha-subunit) by a recombinant receptor protein domain coded by an alternately spliced mRNA and expressed in Escherichia coli.

To assess the functional significance of putative proteins encoded by alternately spliced mRNA of the sheep testicular FSH receptor, a short form cDNA comprising of the first four exons (117 residues mature protein) was engineered for expression in Escherichia coli. The expressed protein of molecular mass 15 kDa was purified to homogeneity and verified by reaction with an antibody against a synthetic peptide sequence unique to the amino (N)-terminal region FSH receptor. The purified FSH receptor domain protein bound 125I-labeled hFSH in a ligand blot on polyvinylidine difluoride membranes. Further analyses by slot blot revealed high affinity of the immobilized protein with significant reaction at 10 pmol. As the immobilized receptor protein also reacted with structurally related hormones (125I-labeled LH/125I-labeled human chorionic gonadotropin), we confirmed that interaction most probably occurred via the common alpha-subunit of these glycoprotein hormones. Our results reveal that this N-terminal portion of the FSH receptor contain(s) major site(s) for hormone recognition that could be mediated via the alpha-subunit. A rabbit antibody to the receptor inhibited FSH action in receptor bearing cells, revealing the utility of such recombinant FSH receptor protein(s) for modulation of hormone action.

Alternative Splicing↗
PubMedDate not supplied

Cloning and sequencing of the yeast Saccharomyces cerevisiae SEC1 gene localized on chromosome IV.

The SEC1 gene of yeast Saccharomyces cerevisiae was cloned by complementing the temperature-sensitive mutation of sec1-1 at 37 degrees C, and its nucleotide sequence was determined. SEC1 is a single copy gene and encodes a protein of 724 amino acids and 83,490 daltons with a predicted pI value of 6.11. Hydrophobicity plotting showed no clearly hydrophobic regions suggesting a soluble nature for the protein. Amino acid sequence comparisons revealed no obvious homologies with the proteins in the SWISSPROT databank. Two consensus sequence for the cdc2 encoded protein kinase recognition site were revealed within Sec1p. The codon usage suggests a low expression level for SEC1. The 5' non-translated region contains two TATA-like sequences at -52 and -215 nucleotides from the translation start site. Two potential regulatory sequences for DNA binding proteins were found in the non-coding 5' region: a HAP2/HAP3 consensus recognition sequence at nucleotide-154 and a BAF1 consensus recognition sequence at nucleotide-136. The SEC1 specific probe detected a 2400 nucleotides long transcript, which was in reasonable agreement with the 2172 nucleotides long open reading frame.

Amino Acid Sequence↗
PubMedDate not supplied

Avoidance of DNA methylation. A virus-encoded methylase inhibitor and evidence for counterselection of methylase recognition sites in viral genomes.

The ocr+ gene of bacterial virus T7 codes for the first protein recognized to inhibit a specific group of DNA methylases. The recognition sequences of several other DNA methylases, not susceptible to Ocr inhibition, are significantly suppressed in the virus genome. The bacterial virus T3 encodes an Ado-Met hydrolase, destroying the methyl donor and causing T3 DNA to be totally unmethylated. These observations could stimulate analogous investigations into the regulation of DNA methylation patterns of eukaryotic viruses and cells. For instance, an underrepresentation of methylation sites (5'-CG) is also true for animal DNA viruses. Moreover, we were able to disclose some novel properties of DNA restriction-modification enzymes concerning the protection of DNA recognition sequences in which only one strand can be methylated (e.g., type III enzyme EcoP15) and the primary resistance of (unmethylated) DNA recognition sites towards type II restriction endonuclease EcoRII.

Base Sequence↗
PubMed1983

6-Phosphogluconate dehydrogenase activity variants in Musca domestica L.: A further allele at the Pgd locus as proved by densitometric assay.

A new electrophoretic variant of 6-phosphogluconate dehydrogenase (6PGD) has been detected in flies of a laboratory Musca domestica strain. This variant is to be added to the two already described, PGD-A and PGD-B, identified by a fast-weak and a slow-thick electrophoretic band, respectively. The new variant, PGD-C, has the same mobility as PGD-A but provides a more intensely stained band; therefore it can be described as a fast-thick phenotype. The staining intensity of PGD-C is slightly lower than that of PGD-B. Genetic and densitometric tests have shown that the different levels of enzymatic activity of the two fast variants A and C are inherited as alternative genetic units, and they have been interpreted as one aspect of the phenotypic expression of two Pgd alleles, namely, PgdA and PgdC. These alleles determine both the rates of electrophoretic mobility (fast in both cases) and the levels of activity (low for A, strong for C; shown by weak or thick stained electrophoretic bands). Similarly, the two distinctive features of PGD-B, namely, slow mobility and high activity level, are always jointly inherited and appear as two pleiotropic aspects of the phenotype coded for by the PgdB allele. The PgdB/PgdC heterozygous flies provide a slightly asymmetrical three-banded zymogram, while the PgdA/PgdC combination leads to a single-banded pattern, showing the same mobility as the parents and an intermediate staining intensity. The quantitative analysis of enzyme activity of 6PGD zymograms, performed through densitometric methods, has led to the recognition of three different activity levels coded for by Pgd alleles, one of which, namely, PgdC, would not have been detected using electrophoretic methods alone.

Alleles↗