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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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Strategems in vitro for gene therapies directed to dominant mutations

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HUMAN MOLECULAR GENETICS 1997年第9期6卷 1415-1426页

作者： MillingtonWard, S ONeill, B Tuohy, G AlJandal, N Kiang, AS Kenna, PF Palfi, A Hayden, P Mansergh, F Kennan, A Humphries, P Farrar, GJ UNIV DUBLIN TRINITY COLL DEPT GENETWELLCOME OCULAR GENET UNITDUBLIN 2IRELAND ATTILA JOZSEF UNIV DEPT ZOOL & CELL BIOLH-6722 SZEGEDHUNGARY

A major difficulty associated with the design of gene therapies for autosomal dominant diseases is the immense intragenic heterogeneity often encountered in such conditions, In order to overcome such difficulties we have designed, and evaluated in vitro, three strategies which avoid a requirement to target individual mutations for genetic suppression, In the first, normal and mutant alleles are suppressed by targeting sequences in transcribed but untranslated regions of transcript (UTRs), enabling introduction of a replacement gene with the correct coding sequencing but altered UTRs to prevent suppression, A second approach involves suppression in coding sequence and concurrent introduction of a replacement gene by exploiting the degeneracy of the genetic code, A third strategy utilises intragenic polymorphism to suppress the disease allele specifically, the advantage being that a proportion of patients with different disease mutations have the same polymorphism, These approaches provide a wider choice of target sequence than those directed to single disease mutations and are appropriate for many mutations within a given gene, General methods for suppression may be directed towards the primary defect or a secondary effect associated with the disease process, such as apoptosis, Three general methods targeting the primary defect which circumvent problems of allelic genetic heterogeneity are explored in vitro using hammerhead ribozymes designed to target transcripts from the rhodopsin, peripherin and collagen 1A1 and 1A2 genes, extensive genetic heterogeneity being a feature of associated disease pathologies.

关键词： .intragenic designed specifically Replacement mutant alleles coding sequence degeneracy gene therapies dominant diseases

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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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Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes

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WILEY INTERDISCIPLINARY REVIEWS-RNA 2013年第1期4卷 93-105页

作者： Koonin, Eugene V. Csuros, Miklos Rogozin, Igor B. NIH Natl Ctr Biotechnol Informat NLM Bethesda MD 20892 USA Univ Montreal Dept Comp Sci & Operat Res Montreal PQ Canada

In eukaryotes, protein-coding sequences are interrupted by non-coding sequences known as introns. During mRNA maturation, introns are excised by the spliceosome and the coding regions, exons, are spliced to form the mature coding region. The intron densities widely differ between eukaryotic lineages, from 6 to 7 introns per kb of coding sequence in vertebrates, some invertebrates and green plants, to only a few introns across the entire genome in many unicellular eukaryotes. Evolutionary reconstructions using maximum likelihood methods suggest intron-rich ancestors for each major group of eukaryotes. For the last common ancestor of animals, the highest intron density of all extant and extinct eukaryotes was inferred, at 120130% of the human intron density. Furthermore, an intron density within 5374% of the human values was inferred for the last eukaryotic common ancestor. Accordingly, evolution of eukaryotic genes in all lines of descent involved primarily intron loss, with substantial gain only at the bases of several branches including plants and animals. These conclusions have substantial biological implications indicating that the common ancestor of all modern eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. Alternative splicing most likely initially appeared as an inevitable result of splicing errors and only later was employed to generate structural and functional diversification of proteins. WIREs RNA 2013, 4:93105. doi: 10.1002/wrna.1143 For further resources related to this article, please visit the WIREs website. This article is a U.S. Government work, and as such, is in the public domain in the United States of America.

关键词： ancestor Spliceosomes Genes Eukaryota coding sequence last common ancestor Green Plants Introns maximum likelihood

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A NEW BIOASSAY FOR AUXINS AND CYTOKININS

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PLANT PHYSIOLOGY 1992年第3期99卷 1090-1098页

作者： BOERJAN, W GENETELLO, C VANMONTAGU, M INZE, D STATE UNIV GHENT GENET LAB B-9000 GENT BELGIUM STATE UNIV GHENT INRA B-9000 GENT BELGIUM

The authors have developed a sensitive bioassay that can be used to detect auxins as well as cytokinins. The bioassay is based on the expression in transformed tobacco (Nicotiana tabacum) mesophyll protoplasts of a chimeric gene, consisting of the upstream sequences of the Agrobacterium tumefaciens gene 5, coupled to the coding sequence of the beta-glucuronidase. The expression of this gene is induced by the presence of both auxin and cytokinin in the culture medium. Using this assay, indole-3-acetic acid was detected at 5 x 10(-8) molar, whereas trans-zeatin could be detected at 5 x 10(-11) molar. The assay can be performed in microtiter plates, allowing numerous samples to be analyzed simultaneously. Only 2.5 x 10(5) protoplasts are required for one individual assay in 250 microliters of culture medium and for qualitative results, the reaction is readily visualized by ultraviolet light.

关键词： .culture medium Auxins indole mesophyll tabacum coding sequence chimeric gene trans-zeatin microtiter New Bioassay

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Mutation of a nuclear respiratory factor 2 binding site in the 5′ untranslated region of the ADSL gene in three patients with adenylosuccinate lyase deficiency

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AMERICAN JOURNAL OF HUMAN GENETICS 2002年第1期71卷 14-21页

作者： Marie, S Race, V Nassogne, MC Vincent, MF Van den Berghe, G Christian Duve Inst Cellular Pathol Physiol Chem Lab B-1200 Brussels Belgium Catholic Univ Louvain B-1200 Brussels Belgium

Adenylosuccinate lyase (ADSL;also called "adenylosuccinase") catalyzes two steps in the synthesis of purine nucleotides: (1) the conversion of succinylaminoimidazolecarboxamide ribotide into aminoimidazolecarboxamide ribotide and (2) the conversion of adenylosuccinate into adenosine monophosphate. ADSL deficiency, a recessively inherited disorder, causes variable-but most often severe-mental retardation, frequently accompanied by epilepsy and/or autism. It is characterized by the accumulation, in body fluids, of succinylaminoimidazolecarboxamide riboside and succinyladenosine, the dephosphorylated derivatives of the two substrates of the enzyme. Analysis of the ADSL gene of three unrelated patients with ADSL deficiency, in whom one of the ADSL alleles displayed a normal coding sequence, revealed a -49T-->C mutation in the 5 untranslated region of this allele. Measurements of the amount of mRNA transcribed from the latter allele showed that it was reduced to similar to33% of that transcribed from the alleles mutated in their coding sequence. Further investigations showed that the -49T-->C mutation provokes a reduction to 25% of wild-type control of promoter function, as evaluated by luciferase activity and mRNA level in transfection experiments. The mutation also affects the binding of nuclear respiratory factor 2 (NRF-2), a known activator of transcription, as assessed by gel-shift studies. Our findings indicate that a mutation of a regulatory region of the ADSL gene might be an unusually frequent cause of ADSL deficiency, and they suggest a role for NRF-2 in the gene regulation of the purine biosynthetic pathway.

关键词： .transcribed nucleotides binding site coding sequence luciferase ribotide van den Berghe Nuclear Respiratory Adenylosuccinate lyase ADSL adenylosuccinase succinylaminoimidazolecarboxamide TrC mutation

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Porcine β1,4-Galactosyltransferase-I sequence and Expression

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REPRODUCTION IN DOMESTIC ANIMALS 2009年第2期44卷 228-234页

作者： Landers, E. A. Burkin, H. R. Bleck, G. T. Howell-Skalla, L. Miller, D. J. Univ Illinois Dept Anim Sci Urbana IL 61801 USA

beta 1,4-Galactosyltransferase-I (B4GALT1), one of seven beta 1,4-galactosyltransferases, is an enzyme commonly found in the trans-Golgi complex that adds galactose to oligosaccharides. In the three mammals studied to date, the B4GALT1 gene directs production of B4GALT1 protein using either of two transcription start sites. The product of the smaller transcript serves the traditional biosynthetic role in the Golgi. This form also complexes with alpha-lactalbumin, a mammary-specific protein, to form lactose synthase. In addition to a biosynthetic role, the protein translated from the longer transcript appears on the plasma membranes of some cells where it serves as a signalling receptor in cell-matrix interactions such as sperm-egg binding. The objective of this study was to sequence the protein-coding region of porcine B4GALT1 and examine the sequence for relationships to the bovine, human, murine and chicken B4GALT1 genes. The sequence for the 1203 base pair protein-coding region of porcine B4GALT1 was obtained. Analysis of the deduced protein sequences revealed that the transmembrane region displayed the highest identity between the four mammals. The catalytic domain was 84-88% identical between the porcine sequence and those of the bovine, human and mouse. The porcine protein had the lowest overall homology to the chicken amino acid sequence, 58% identity. Conservation of both transcription start sites in the porcine gene supports the existence of two isoforms. When compared to the other mammalian B4GALT1 genes, the porcine coding sequence contained a single threonine codon inserted into the region encoding the cytoplasmic domain. Two putative phosphorylation sites in the mouse cytoplasmic domain were conserved in the porcine sequence. Northern blots revealed a widely expressed 4.4 kb transcript that was more abundant in the mammary gland during lactation. These results are important for studies of the function of this unusual and important glycosyltransferase du

关键词： lactation coding sequence sperm-egg binding cell receptor Transcription Initiation Site Cytoplasmic Domain Amino Acid sequence Phosphorylation Site Lactation Golgi Apparatus B4GALT1 gene coding sequence Lactose Synthase

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Small RNA sequencing revealed dysregulated piRNAs in Alzheimer's disease and their probable role in pathogenesis

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MOLECULAR BIOSYSTEMS 2017年第3期13卷 565-576页

作者： Roy, Jyoti Sarkar, Arijita Parida, Sibun Ghosh, Zhumur Mallick, Bibekanand Natl Inst Technol Rourkela Dept Life Sci RNAi & Funct Genom Lab Rourkela 769008 Odisha India Bose Inst Bioinformat Ctr Kolkata 700054 India

PIWI-interacting RNAs (piRNAs), similar to 23-36 nucleotide-long small non-coding RNAs, earlier believed to be germline-specific, have now been identified in somatic cells including neural cells. However, piRNAs have not yet been studied in the human brain (HB) and Alzheimer's disease (AD)-affected brain. In this study, by next-generation small RNA sequencing, 564 and 451 piRNAs were identified in the HB and AD-affected brain respectively. The majority of the neuronal piRNAs have intronic origin wherein primary piRNAs are mostly from the negative strand. piRNAs originating from the coding sequence of mRNAs and tRNAs are highly conserved compared to other genomic contexts. We found 1923 mRNAs significantly downregulated in AD as the predicted targets of 125 up-regulated piRNAs. The filtering of targets based on our criteria coupled with pathway enrichment analysis of all the predicted targets resulted in five most significant AD-associated pathways enriched with four genes (CYCS, LIN7C, KPNA6, and RAB11A) found to be regulated by four piRNAs. The qRT-PCR study verified the reciprocal expression of piRNAs and their targets. This study provides the first evidence of piRNAs in the HB and AD which will provide the foundation for future studies to unravel the regulatory role of piRNAs in the human brain and associated diseases. The sequencing data have been submitted to the GEO database (Accession no. GSE85075).

关键词： Alzheimer Disease AD Cerebrum Targets CYCS gene wetware coding sequence Piwi-Interacting RNA Analyses, sequence RNA sequence pathogenesis

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THE sequence OF THE TMS TRANSCRIPT-2 LOCUS OF THE A-TUMEFACIENS PLASMID PTIA6 AND CHARACTERIZATION OF THE MUTATION IN PTIA66 THAT IS RESPONSIBLE FOR AUXIN ATTENUATION

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NUCLEIC ACIDS RESEARCH 1984年第3期12卷 1447-1461页

作者： SCIAKY, D THOMASHOW, MF WASHINGTON STATE UNIV DEPT BACTERIOL & PUBL HLTHPULLMANWA 99164

The incorporation of Ti plasmid sequences, the T-DNA, into the genomes of dicotyledenous plants causes the formation of tumors. Here we report the nucleotide sequence of one of the T-DNA“oncogenes”, the transcript 2 gene of pTiA6 and we further characterize the 2.7 Kb element that has spontaneously inserted into this gene in plasmid pTiA66. The results indicate that the transcript 2 portion of the T-DNA has an open reading frame that could encode a polypeptide of 49.8 Kd. The open reading frame is surrounded by sequences that typically have roles in eucaryotic gene expression. Nucleotide sequence and Southern blot analysis also indicates that the 2.7 Kb insert in the transcript 2 gene of pTiA66 i. located within the coding sequence of the gene and suggests that the element is an insertion sequence. We designate this element, 1

关键词： Auxins Camellia Mutation Southern blotting Genes T-DNA Plant Tumor-Inducing Plasmids sequences Elements Polypeptides Element Open Reading Frames transcript Base sequence coding sequence

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A Massive Proteogenomic Screen Identifies Thousands of Novel Peptides From the Human "Dark" Proteome

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MOLECULAR & CELLULAR PROTEOMICS 2024年第2期23卷 100719页

作者： Cao, Xiaolong Sun, Siqi Xing, Jinchuan Southern Med Univ Zhujiang Hosp Dept Anesthesiol Guangzhou Guangdong Peoples R China Rutgers State Univ Dept Genet Piscataway NJ 08854 USA Rutgers State Univ Human Genet Inst New Jersey Piscataway NJ 08854 USA

Although the human gene annotation has been continuously improved over the past 2 decades, numerous studies demonstrated the existence of a "dark proteome", consisting of proteins that were critical for biological processes but not included in widely used gene catalogs. The Genotype- Tissue Expression project generated more than 15,000 RNA-seq datasets from multiple tissues, which modeled 30 million transcripts in the human genome. To provide a resource of high-confidence novel proteins from the dark proteome, we screened 50,000 mass spectrometry runs from over 900 projects to identify proteins translated from the Genotype-Tissue Expression transcript model with proteomic support. We also integrated 3.8 million common genetic variants from the gnomAD database to improve peptide identification. As a result, we identified 170,529 novel peptides with proteomic evidence, of which 6048 passed the strictest standard we defined and were supported by Pep- Query. We provided a user-friendly website (https://ncorf. ***/) for researchers to check the evidence of novel peptides from their studies. The findings will improve our understanding of coding genes and facilitate genomic data interpretation in biomedical research.

关键词： proteogenomics noncanonical open reading frames novel proteoforms gene annotation GTEx CDS coding sequence circRNA circular RNA FDR false discovery rate gnomAD Genome Aggregation Database GTEx Genotype-Tissue Expression MS mass spectrometry MS/MS tandem mass spectrometry ncORF noncanonical open reading frame PRIDE PRoteomics IDEntification PSM peptide spectrum match QC quality control

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