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A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection

G3-GENES GENOMES GENETICS 2023年第7期13卷 jkad105页

作者： Weller, Benjamin Lin, Chung-Wen Pogoutse, Oxana Sauer, Mayra de la Rosa, Nora Strobel, Alexandra Young, Veronika Knapp, Jennifer J. Rayhan, Ashyad Falter, Claudia Kim, Dae-Kyum Roth, Frederick P. Falter-Braun, Pascal Helmholtz Zentrum Munchen Inst Network Biol INET Mol Targets & Therapeut Ctr MTTC German Res Ctr Environm Hlth Ingolstadter Landstr 1 D-85764 Neuherberg Germany Univ Toronto Donnelly Ctr Cellular & Biomol Res CCBR 160 Coll St Toronto ON M5S 3E1 Canada Univ Toronto Dept Mol Genet 1 Kings Coll Cir Toronto ON M5S 1A8 Canada Sinai Hlth Syst Lunenfeld Tanenbaum Res Inst LTRI 600 Univ Ave Toronto ON M5G 1X5 Canada Dana Farber Canc Inst Ctr Canc Syst Biol CCSB 450 Brookline Ave Boston MA 02215 USA Roswell Park Comprehens Canc Ctr Dept Canc Genet & Genom Elm & Carlton St Buffalo NY 14263 USA Univ Toronto Dept Comp Sci 40 St George St Toronto ON M5S 2E4 Canada Ludwig Maximilians Univ LMU Munchen Fac Biol Microbe Host Interact Grosshaderner Str 9 D-82152 Martinsried Germany Helmholtz Zentrum Munchen Inst Network Biol Ingolstadter Landstr 1 D-85764 Neuherberg Germany Univ Toronto Donnelly Ctr 160 Coll St Toronto ON M5S 3E1 Canada

The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.

关键词： coronavirus HCoV coding sequence SARS-CoV-2 OC43 MERS HKU1 229E NL63 Gateway Entry clone

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LMW-GS genes in Agropyron elongatum and their potential value in wheat breeding

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THEORETICAL AND APPLIED GENETICS 2005年第2期111卷 272-280页

作者： Luo, Z Chen, FG Feng, DS Xia, GM Shandong Univ Sch Life Sci Jinan 250100 Peoples R China

To study the usefulness of low-molecular-weight glutenin subunits (LMW-GS) of Agropyron elongatum (Host) Nevski to wheat (Triticum aestivum L.) quality improvement, we characterized LMW-GS genes of A. elongatum. Nine LMW-GS genes of A. elongatum, which were named AeL1 to AeL9, were cloned by genomic PCR. After sequencing, we obtained complete open reading frames from AeL2 to AeL8 and partial genes of AeL1 and AeL9. All nine sequences are homoeologous to those of wheat and related grasses. Comparison of the deduced amino acid sequences with those of published LMW-GS suggests that the basic structures of all the subunits are very similar. However, except for AeL4 and AeL5, which contain the identical N-terminal sequence with LMW-m, other LMW-GS sequences separated from A. elongatum cannot be classified according to previous criteria for the three types: LMW-m (methionine), LMW-s (serine), and LMW-i (isoleucine), and then 12 groups. In addition, there are some characters in the LMW-GS sequences of A. elongatum: AeL2, AeL3, and AeL6 involve a Cys residue in the signal peptide respectively, which is absent in most of LMW-GS;AeL3, AeL6, AeL8, and AeL9 start their first Cys residues in the N-terminal repetitive domains, respectively;both AeL2 and AeL5 have nine Cys residues, with an extra Cys residue in the N-terminal repetitive domain and the repetitive and glutamine-rich domain;AeL2, AeL3, AeL6, and AeL9 comprise long repetitive domains. Phylogenetic analysis indicates that there is a relatively weak sequence identity between the LMW-GS genes from A. elongatum cloned in this study and those reported from other plants. Three LMW-GS sequences, AeL2, AeL3, and AeL6, are clustered to Glu-A3 from wheat than to those from other plants. The possible use of these genes in relation to the high quality of hybrid wheat is discussed.

关键词： Agropyron elongatum somatic hybrid line LMW-GS coding sequence evolution wheat quality

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Generation, recognition and recoding of 64-chip bipolar optical code sequences using superstructured fibre Bragg gratings

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ELECTRONICS LETTERS 2001年第3期37卷 190-191页

作者： Teh, PC Petropoulos, P Ibsen, M Richardson, DJ Univ Southampton Optoelect Res Ctr Southampton SO17 1BJ Hants England

The generation, recognition and subsequent recoding of ac:hip. 160Gchip/s bipolar optical codes using superstructured fibre Bragg gratings is demonstrated. The results represent an eightfold increase in code length re... 详细信息

关键词： optical code code length coding sequence Fiber Bragg gratings ambipolar

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NEW TERNARY LINE CODES BASED ON TRELLIS STRUCTURE

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IEEE TRANSACTIONS ON COMMUNICATIONS 1993年第6期41卷 864-873页

作者： AYGOLU, U PANAYIRCI, E NEW JERSEY INST TECHNOL DEPT ELECT & COMP ENGNCTR COMMUN & SIGNAL PROCNEWARKNJ 07102

The trellis coding technique is applied to line-coded baseband digital transmission systems. For R = n/n + 1(n = 1, 2, 3) coding rates, a new codeword assignment model is proposed to accomplish basic requirements for line coding in which each length n binary data sequence is encoded into a length n + 1 ternary (+, 0, -) line codeword chosen among the code alphabet with 2n+2 elements. Assuming Viterbi decoding, the system error performance is improved by increasing the free Euclidean distance between coded sequences. A new algorithm is given for the calculation of the free distance between line-coded sequences so obtained. For R = 1/2 and R = 3/4 rates, the analytical error performance upper bounds are derived. The power spectral densities of the new line codes are also calculated and compared with those of known line codes.

关键词： codeword line code Codes Digital transmission systems Ternary Trellis codes GPR17 protein, human Euclidean distance error performance coding sequence

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PN-curve: A 3D graphical representation of DNA sequences and their numerical characterization

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CHEMICAL PHYSICS LETTERS 2007年第4-6期442卷 434-440页

作者： Qi, Zhao-Hui Fan, Tong-Rang Shijiazhuang Railway Inst Dept Comp & Informat Engn Shijiazhuang 050043 Hebei Peoples R China

We consider a novel 3D graphical representation of DNA sequences based on the pairs of nucleotides (PNs). The model avoids loss of information accompanying alternative 3D representations in which the curve standing for DNA sequence overlaps or intersects itself. The utility of the method can be illustrated by the examination of similarities/dissimilarities among the complete coding sequence part of beta globin gene of several different species. (c) 2007 Elsevier B.V. All rights reserved.

关键词： SIMILARITY/DISSIMILARITY SIMILARITY BASES Three Dimensions information loss coding sequence beta-Globins DNA sequence

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ANALYSIS OF A DIRECT-sequence CDMA MOBILE RADIO SYSTEM WITH REDUCED SET OF CODE sequenceS

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IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY 1995年第3期44卷 525-534页

作者： KIM, DI Department of Electronics Engineering Seoul City University Seoul South Korea

A code-division multiple-access scheme that requires a reduced set of code sequences, in which the size of the set is much less than the number of users in the system, is proposed for mobile radio communications, A direct-sequence spread-spectrum signaling is adopted to exploit the property of high time resolution and combat fading effects through multipath diversity reception. Theoretical performance of the proposed system is analyzed by deriving the collision-free path distribution and determining the proper size of the set without reducing the effect of multipath diversity, In connection with the proposed system, two combining schemes are investigated to characterize the effects of the primary and secondary user interferences and evaluate the behavior of the error rate when compared to the original CDMA system.

关键词： code division multiple access diversity reception fading land mobile radio multipath channels pseudonoise codes radiofrequency interference spread spectrum communication code sequences collision-free path distribution direct-sequence CDMA mobile radio sy Error analysis Codes coding sequence Code division multiple access pseudonoise codes Spread spectrum communication diversity reception fading color land mobile radio Direct-sequence code-division multiple access Mobile radio systems Radiofrequency interference Multipath channels

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FREQUENCY-HOPPING CODE sequence DESIGNS HAVING LARGE LINEAR SPAN

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IEEE TRANSACTIONS ON INFORMATION THEORY 1988年第1期34卷 146-151页

作者： KUMAR, PV NTT Media Intelligence Laboratories Tokyo Japan

In frequency-hopping spread-spectrum multiple-access communication systems, it is desirable to use sets of hopping patterns that, in addition to having good Hamming correlation properties and large period, are also derived from sequences having large linear span. Here, two such frequency hopping code sequence designs that are based on generalized bent functions and generalized bent sequences are presented. The Hamming correlation properties of the designs are optimal in the first case and close to optimal in the second. In terms of the alphabet size p (required to be prime in both cases), the period and family size of the two designs are given by (p/sup 2/, p) and (p/sup n/, p/sup n/2/+1) (n an even integer), respectively. The finite field sequences underlying the patterns in the first design have linear span exceeding p, whereas still larger linear spans (when compared to the sequence period) can be obtained using the second design method.

关键词： Optimal Family Size Agrostis Linear Long spans frequency hopping spread spectrum Prime multiple access communications coding sequence two-phase design Frequency hopping sequences

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Hidden Markov Model for Splicing Junction Sites Identification in DNA sequences

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CURRENT BIOINFORMATICS 2013年第3期8卷 369-379页

作者： Maji, Srabanti Garg, Deepak Thapar Univ Dept Comp Sci & Engn Patiala 147004 Punjab India

Identification of coding sequence from genomic DNA sequence is the major step in pursuit of gene identification. In the eukaryotic organism, gene structure consists of promoter, intron, start codon, exons and stop codon, etc. and to identify it, accurate labeling of the mentioned segments is necessary. Splice site is the 'separation' between exons and introns, the predicted accuracy of which is lower than 90% (in general) though the sequences adjacent to the splice sites have a high conservation. As the accuracy of splice site recognition has not yet been satisfactory (adequate), therefore, much attention has been paid to improve the prediction accuracy and improvement in the algorithms used is very essential element. In this manuscript, Hidden Markov Model (HMM) based splice sites predictor is developed and trained using Modified Expectation Maximization (MEM) algorithm. A 12 fold cross validation technique is also applied to check the reproducibility of the results obtained and to further increase the prediction accuracy. The proposed system can able to achieve the accuracy of 98% of true donor site and 93% for true acceptor site in the standard DNA (nucleotide) sequence.

关键词： Algorithms coding sequence cross validation gene finding hidden markov model modified expectation maximization (MEM) splice site

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ORGANIZATION AND CHROMOSOMAL LOCATIONS OF RAP1A/KREV sequenceS IN THE MOUSE

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MAMMALIAN GENOME 1992年第3期3卷 162-167页

作者： DOWER, NA SELDIN, MF PUGH, S STONE, JC UNIV ALBERTA DEPT PAEDIATEDMONTON T6G 2E1ALBERTACANADA DUKE UNIV MED CTRDEPT MEDDURHAMNC 27710 DUKE UNIV MED CTRDEPT MICROBIOLDURHAMNC 27710 UNIV ALBERTA DEPT BIOCHEMEDMONTON T6G 2E1ALBERTACANADA

The human RAP1A gene encodes a protein that apparently can antagonize the function of oncogenic ras genes in gene transfer experiments, but its normal function is unknown. To understand the function of this gene, we have undertaken a study of the mouse homolog, Rap1a. The complete coding sequence of a mouse Rap1a cDNA has been determined, and genomic clones representing three distinct Rap1a species were recovered. We find that Rap1a is located on distal mouse Chromosome (Chr) 3 near Nras, Ampd-1, Tshb, Ngfb, and Atp1a1. Two related sequences (Rap1a-rs1 and Rap1a-rs2) were also characterized. Rap1a-rs1, which was not localized, has a sequence very similar to the Rap1a cDNA, suggesting that it has been recently acquired by the mouse genome. Rap1a-rs2 is more distantly related to the gene sequence and is located on Chr 2 near Actc-1.

关键词： Organizations Chromosomes Molecular cloning Gene transfer Mouse sequences Gene function normal function Transgenes Mus Base sequence coding sequence Function

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THE COMPLETE DERIVED AMINO-ACID-sequence OF HUMAN LYSYL OXIDASE AND ASSIGNMENT OF THE GENE TO CHROMOSOME-5 - (EXTENSIVE sequence HOMOLOGY WITH THE MURINE RAS RECISION GENE)

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MATRIX 1992年第3期12卷 242-248页

作者： MARIANI, TJ TRACKMAN, PC KAGAN, HM EDDY, RL SHOWS, TB BOYD, CD DEAK, SB BOSTON UNIV SCH MEDDEPT BIOCHEMBOSTONMA 02118 ROSWELL PK CANC INST DEPT HUMAN GENETBUFFALONY 14263

Lysyl oxidase catalyzes the oxidation of lysine residues to alpha-aminoadipic-delta-semialdehyde. This is the first step in the covalent cross-linking of collagen and tropoelastin and results in the formation of insoluble collagen and elastic fibers in the extracellular matrix. We have characterized the complete nucleotide sequence of human lysyl oxidase (EC 1.4.3.13) and compared the derived amino acid sequence (417-amino acids) to rat lysyl oxidase and the mouse ras recision gene (rrg). 88% of amino acids and 83% of nucleotides were conserved between human and rat lysyl oxidase. The mouse ras recision gene demonstrated 89% conservation of amino acids with human lysyl oxidase. The sequence conservation was not evenly distributed along the molecule. The carboxy terminus of the protein, which contains the putative copper binding sites and is likely to be the catalytically active domain, was more highly conserved than the amino terminus. The 89% amino acid sequence similarity between the murine ras recision gene and human lysyl oxidase suggests that they are the same gene product. Therefore, in addition to cross linking of extracellular matrix proteins, lysyl oxidase may have a direct role in tumor suppression. Northern blot analysis of poly A + RNA from cultured skin fibroblasts revealed at least three-distinct transcripts, sized 4.8 kb, 3.8 kb and 2.0 kb. In addition, using a panel of human mouse cell hybrids, the lysyl oxidase gene was assigned to human chromosome 5.

关键词： coding sequence CHROMOSOME ASSIGNMENT HUMAN LYSYL OXIDASE RRG

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