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Human-mouse differences in the embryonic expression patterns of developmental control genes and disease genes

HUMAN MOLECULAR GENETICS 2000年第2期9卷 165-173页

作者： Fougerousse, F Bullen, P Herasse, M Lindsay, S Richard, I Wilson, D Suel, L Durand, M Robson, S Abitbol, M Beckmann, JS Strachan, T Newcastle Univ Human Genet Unit Sch Biochem & Genet Newcastle Upon Tyne NE1 7RU Tyne & Wear England CNRS URA 1922 Genethon F-91002 Evry France Fac Cochin Port Royal Lab Histoembroyol & Cytogenet F-75014 Paris France Fac Necker Certo F-75015 Paris France

Our understanding of early human development has been impeded by the general difficulty in obtaining suitable samples for study, As a result, and because of the extraordinarily high degree of evolutionary conservation of many developmentally important genes and developmental pathways, great reliance has been placed on extrapolation from animal models of development, principally the mouse, However, the strong evolutionary conservation of coding sequence for developmentally important genes does not necessarily mean that their expression patterns are as highly conserved, The very recent availability of human embryonic samples for gene expression studies has now permitted for the first time an assessment of the degree to which we can confidently extrapolate from studies of rodent gene expression patterns. We have found significant human-mouse differences in embryonic expression patterns for a variety of genes, We present detailed data for two illustrative examples. Wnt7a, a very highly conserved gene known to be important in early development, shows significant differences in spatial and temporal expression patterns in the developing brain (midbrain, telencephalon) of man and mice. CAPN3, the locus for LGMD2A limb girdle muscular dystrophy, and its mouse orthologue differ extensively in expression in embryonic heart, lens and smooth muscle, Our study also shows how molecular analyses, while providing explanations for the observed differences, can be important in providing insights into mammalian evolution.

关键词： Gene Expression Regulation Developmental Genes Structural Hereditary Diseases 基因表达调控发育期基因结构遗传性疾病 Hereditary Diseases Genes human development coding sequence limb girdle muscular dystrophy Gene Expression Regulation

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RNase E-based degradosome modulates polyadenylation of mRNAs after Rho-independent transcription terminators in Escherichia coli

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MOLECULAR MICROBIOLOGY 2016年第4期101卷 645-655页

作者： Mildenhall, Kristen B. Wiese, Nicholas Chung, Daewhan Maples, Valerie F. Mohanty, Bijoy K. Kushner, Sidney R. Univ Georgia Dept Microbiol Athens GA 30602 USA Univ Georgia Dept Genet Athens GA 30602 USA Univ Wisconsin Dept Bacteriol Madison WI 53706 USA Natl Renewable Energy Ctr Golden CO 80401 USA Ctr Dis Control Atlanta GA 30333 USA

Here we demonstrate that the RNase E-based degradosome is required for poly(A) polymerase I (PAP I)-dependent polyadenylation after Rho-independent transcription terminators for both mono- and polycistronic transcripts. Disruption of degradosome assembly in mutants lacking the polynucleotide phosphorylase (PNPase) binding domain led to a significant increase in the level of PNPase synthesized polynucleotide tails in the rpsJ and rpsM polycistronic transcripts and the lpp monocistronic transcript. The polynucleotide tails were mostly located within the coding sequences in the degradosome mutants compared to the wild type control where the majority of the PAP I synthesized poly(A) tails were after the Rho-independent transcription terminators. For the Rho terminated metNIQ operon, the tails for all three mRNAs were predominately polynucleotide and were located within the coding sequences in both wild type and degradosome mutant strains. Furthermore, by employing a pnp-R100D point mutant that encodes a catalytically inactive PNPase protein that still forms intact degradosomes, we show that a catalytically active PNPase is required for normal mRNA polyadenylation by PAP I. Our data suggest that polyadenylation requires a functional degradosome to maintain an equilibrium between free PNPase and the PAP I polyadenylation complex.

关键词： ribonuclease E Terminator Device Component Tails PNPT1 gene Wild type Genetic Transcription degradosome Tail Polyadenylation Pathway coding sequence Annexin A5 Polyadenylation Polynucleotides Mutants

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Two independent type III secretion mechanisms for YopE in Yersinia enterocolitica

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MOLECULAR MICROBIOLOGY 1997年第4期24卷 757-765页

作者： Cheng, LW Anderson, DM Schneewind, O UNIV CALIF LOS ANGELES SCH MEDDEPT MICROBIOL & IMMUNOLLOS ANGELESCA 90095 UNIV CALIF LOS ANGELES SCH MEDINST MOL BIOLLOS ANGELESCA 90095

Pathogenic Yersinia species escape the infected host's defense mechanisms by targeting cytotoxic Yop proteins into the cytoplasm of macrophages via a type III secretion pathway. Two separate secretion signals contained in YopE were identified, each of which were sufficient but not necessary for the secretion of reporter molecules. One signal is located within the coding sequence of the first 15 amino acids and is sufficient for the secretion of fusion proteins but not required for YopE secretion. The second signal is located downstream at residues 15-100 of YopE and is only recognized by the type III machinery when it is bound to SycE. We propose the existence of two independent mechanisms that allow for the secretion of Yap proteins.

关键词： Gram-negative bacteria Chaperone-like protein Transposon tn5 Target-cell Gene Determinants Expression Resistance Mutations Selection Yersinia sp. SGCG gene fusion proteins Genes Determinants Sufficient Target cells coding sequence Bodily Secretions Yersinia enterocolitica Mutation Gram-Negative Bacteria

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NUCLEOTIDE SEQUENCING ANALYSIS OF A LEU GENE OF CANDIDA-MALTOSA WHICH COMPLEMENTS LEUB MUTATION OF ESCHERICHIA-COLI AND LEU2 MUTATION OF SACCHAROMYCES-CEREVISIAE

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CURRENT GENETICS 1987年第6-7期11卷 451-457页

作者： TAKAGI, M KOBAYASHI, N SUGIMOTO, M FUJII, T WATARI, J YANO, K 1. Department of Agricultural Chemistry University of Tokyo 113 Bunkyo-ku Tokyo Japan

The expression of a LEU gene from Candida Maltosa (designated as C-LEU2) isolated previously (Kawamura et al. 1983) was shown to be regulated, when transferred into Saccharomyces cerevisiae, by leucine and threonine in the medium, as in the case of LEU2 gene of S. cerevisiae. The coding region together with the regulatory region was subcloned and the nucleotide sequence was determined. When the sequence of the coding region was compared with that of LEU2, the homology was 72% for base pairs and 76% for deduced amino acids. Comparison of the regulatory region of C-LEU2 with those of LEU1 and LEU2 suggested a few short consensus sequences which are involved in regulation of gene expression by leucine and threonine in the medium.

关键词： Candida maltosa C-LEU2 coding sequence Regulatory sequence

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sequence OF A PSEUDOGENE IN THE LEGUMIN GENE FAMILY OF PEA (PISUM-SATIVUM-L)

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NUCLEIC ACIDS RESEARCH 1985年第12期13卷 4527-4538页

作者： BOWN, D LEVASSEUR, M CROY, RRD BOULTER, D GATEHOUSE, JA Department of Botany Durham UniversitySouth Road Durham DH1 3LE UK

A second legumin gene, denotedψLeg D, has been located on the pea genomic cloneλLeg 1, approx.1.3 Kbases 3′of Leg A, in the same orientation. The complete sequence ofψLeg D shows that it is a pseudogene, having two stop codons near the 5′end of its predicted coding sequence, as well as deletions and frame shift errors when compared to Leg A. No transcripts from this gene could be detected in developing pea seeds. Leg A andψLeg D are homologous over their coding sequences, and partially homologous in the intron sequences and the immediate 5′flanking sequences. Other flanking sequences of the two genes show no significant homology, apart from the presence of polyadenylation signals 3′to both coding sequences. The introns in the two genes occur in corresponding positions in the sequences, but a deletion inψLeg D affects the 3′boundary of IVS-2. Hybridisation ofψLeg D to pea genomic DNA suggests that it does not represent a hitherto undetected subfamily

关键词： Flank PISUM Pseudogenes Introns Peas Genes sequences Homologous Leg deuterium ABSORBED DOSE coding sequence coding Polyadenylation legumin

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Strategy for Robust Detection of Insertions, Deletions, and Point Mutations in CEBPA, a GC-Rich Content Gene, Using 454 Next-Generation Deep-Sequencing Technology

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JOURNAL OF MOLECULAR DIAGNOSTICS 2011年第2期13卷 129-136页

作者： Grossmann, Vera Schnittger, Susanne Schindela, Sonja Klein, Hans-Ulrich Eder, Christiane Dugas, Martin Kern, Wolfgang Haferlach, Torsten Haferlach, Claudia Kohlmann, Alexander MLL Munich Leukemia Lab D-81377 Munich Germany Univ Munster Dept Med Informat & Biomath Munster Germany

CEBPA mutations are of prognostic relevance in acute myeloid leukemia (AML) and are currently detected using a combination of denaturing high-performance liquid chromatography (DHPLC), gene scan/fragment length analysis, and direct Sanger sequencing. Next-generation deep pyrosequencing, principally, allows for the highly sensitive detection of molecular mutations. However, standard 454 chemistry laboratory procedures lack efficient amplification of guanine-cytosine (GC)-rich amplicons during the emulsion PCR (emPCR) steps allowing direct massively parallel clonal amplification of PCR products. To solve this problem, we investigated six distinct emPCR conditions. The coding sequence of CEBPA was subdivided into four overlapping amplicons: GC content for amplicon 1, 74%;amplicon 2, 76%;amplicon 3, 77%;and amplicon 4, 69%. A new emPCR condition, improving the standard titanium assay, presents a robust solution to sequence amplicons with a GC content of up to 77%. Moreover, this assay was subsequently tested on a larger independent cohort of 23 AML patients. For each patient, a median of 737 reads was generated (coverage range, 397-fold to 1194-fold) and therefore allowed a robust detection of insertions, deletions, and point mutations. In conclusion, next-generation amplicon sequencing enables the highly sensitive detection of molecular mutations and is a feasible assay for routine assessment of GC-rich content amplicons. (J Mol Dian 2011, 13:129-134. DOI: 10.1016/***.2010.09.001)

关键词： Amplicon Acute Myelocytic Leukemias G+C Composition deletions coding sequence Point Mutation Robust solution

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A eubacterial gene conferring spectinomycin resistance on Chlamydomonas reinhardtii: Integration into the nuclear genome and gene expression

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GENETICS 1997年第1期145卷 97-110页

作者： Cerutti, H Johnson, AM Gillham, NW Boynton, JE DUKE UNIV DEPT BOTDEV CELL & MOL BIOL GRPDURHAMNC 27708 DUKE UNIV DEPT ZOOLDEV CELL & MOL BIOL GRPDURHAMNC 27708

We have constructed a dominant selectable marker for nuclear transformation of C. reinhardtii, composed of the coding sequence of the eubacterial aadA gene (conferring spectinomycin resistance) fused to the 5' and 3' untranslated regions of tile endogenous RbcS2 gene. Spectinomycin-resistant transformants isolated by direct selection (1) contain the chimeric gene(s) stably integrated into the nuclear genome, (2) show cosegregation of the resistance phenotype with the introduced DNA, and (3) synthesize the expected mRNA and protein. Small linearized plasmids appeared to be inserted into the nuclear genome preferentially through their ends, with relatively few large deletions and/or rearrangements. Multiple copy transformants often integrated concatemers of transforming DNA. Our detailed analysis of the complex integration patterns of plasmid DNA in C. reinhardtii nuclear transformants should be useful for improving the technique of insertional mutagenesis. We also found that the spectinomycin-resistance phenotype was unstable in about half of the transformants. When maintained under nonselective conditions, neither the aadA mRNA nor the AadA protein were detected in these subclones. Moreover, since the integrated transforming DNA was not altered or lost, expression of the RbcS2::aadA::RbcS2 gene(s) appears to be repressed. Measurements of transcriptional activity, mRNA accumulation, and mRNA stability suggest that expression of this chimeric gene(s) may also be affected by rapid RNA degradation, presumably due to defects in mRNA processing and/or nuclear export. Thus, both gene silencing and transcript instability, rather than biased codon usage, may explain the difficulties Encountered in the expression of foreign genes in the nuclear genome of Chlamydomonas.

关键词： .transformants inserted linearized transforming plasmids coding sequence chimeric gene eubacterial concatemers spectinomycin

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Polytime coding as a means of pulse compression

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IEEE TRANSACTIONS ON AEROSPACE AND ELECTRONIC SYSTEMS 1999年第2期35卷 716-721页

作者： Fielding, JE Radian Int Austin TX 78720 USA

A set of code sequences is proposed for radar applications in which all phase steps are equal and the time duration of each phase state is varied in order to properly approximate either a stepped-RE waveform or a linear FM waveform, Since these proposed waveforms have varying time durations at each phase state, they are referred to as "Polytime" codes. Polytime code sequences have the advantage that arbitrary time-bandwidth waveforms can be generated with a few phase states. Of particular interest are cases where phase is quantized into two states (i.e., 0 degrees and 180 degrees).

关键词： modulation coding phase coding pulse compression radar signal processing sequential codes Doppler tolerance Polytime coding arbitrary time-bandwidth waveforms code sequences linear FM waveform phase quantization radar applications stepp Radar signal processing phase coding waveforms sequential codes Pulse compression STATE(PHASE) Radar applications coding sequence modulation coding

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FINE-STRUCTURE MAP OF THE HUMAN RIBOSOMAL-PROTEIN GENE RPS14

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MOLECULAR AND CELLULAR BIOLOGY 1992年第4期12卷 1680-1686页

作者： DIAZ, JJ ROUFA, DJ KANSAS STATE UNIV AGR & APPL SCI CTR BASIC CANC RESDIV BIOLMANHATTANKS 66506

We have used polymerase chain reaction-mediated chemical mutagenesis (J.-J. Diaz, D. D. Rhoads, and D. J. Roufa, BioTechniques 11:204-211, 1991) to analyze the genetic fine structure of a human ribosomal protein gene, RPS14. Eighty-three DNA clones containing 158 random single-base substitution mutations were isolated. Mutant RPS14 alleles were tested for biological activity by transfection into cultured Chinese hamster cells. The resulting data permitted us to construct a map of the S14-coding sequence that is comparable to available fine-structure genetic maps of many prokaryotic and lower eukaryotic gene loci. As predicted from the multiplicity of protein-protein and protein-RNA interactions required for ribosomal protein transport and assembly into functional ribosomal subunits, the distribution of null mutations indicated that S14 is composed of multiple, functionally distinct polypeptide domains. Two of the protein's internal domains, designated domains B and D, were essential for S14 biological activity. In contrast, mutations which altered or deleted S14's amino-terminal 20 amino acid residues (domain A) had no observable effect on the protein's assembly and function in mammalian ribosomes. Interestingly, S14 structural domains deduced by in vitro mutagenesis correlate well with the RPS14 gene's exon boundaries.

关键词： .transfection single-base Biological activity coding sequence DNAs ribosomal subunits Chinese hamster protein gene DNA clones human ribosomal Fine-Structure

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Editorial

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THEORY IN BIOSCIENCES 2009年第3期128卷 151-152页

作者： Breidbach, Olaf Univ Jena Inst Geschichte Med Nat Wissensch & Tech D-07743 Jena Germany

Theory in Biosciences has been designed as a discussion platform that will allow dealing with relevant problems in the formation of a theoretical framing for biosciences. Herein, the phenomenon of inheritance and especially the gene concept is of central relevance. The gene seems to represent the attributum crucis of life forms. Chemical systems may form out self organisational features, crystals will assimilate molecules to grow on according to a preconfigurated schedule, but only in organisms we find a specific substance that may act as a coding sequence to organise a bulk of chemical reactions within such an organism and to transfer that information to organise it via various entities in a continuous process throughout the different generations of species. So far, one could feel good about the gene, as it will allow us to separate organic and inorganic realms in a quite easy way.

关键词： Biosciences central organisms Continuous production Organism Central chemical reactions Biological Science Disciplines Crux coding sequence

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