Comparisons of eukaryotic genomic sequences.

Abstract:

:A method for assessing genomic similarity based on relative abundances of short oligonucleotides in large DNA samples is introduced. The method requires neither homologous sequences nor prior sequence alignments. The analysis centers on (i) dinucleotide (and tri- and tetra-) relative abundance extremes in genomic sequences, (ii) distances between sequences based on all dinucleotide relative abundance values, and (iii) a multidimensional partial ordering protocol. The emphasis in this paper is on assessments of general relatedness of genomes as distinguished from phylogenetic reconstructions. Our methods demonstrate that the relative abundance distances almost always differ more for genomic interspecific sequence comparisons than for genomic intraspecific sequence comparisons, indicating congruence over different genome sequence samples. The genomic comparisons are generally concordant with accepted phylogenies among vertebrate and among fungal species sequences. Several unexpected relationships between the major groups of metazoa, fungal, and protist DNA emerge, including the following. (i) Schizosaccharomyces pombe and Saccharomyces cerevisiae in dinucleotide relative abundance distances are as similar to each other as human is to bovine. (ii) S. cerevisiae, although substantially far from, is significantly closer to the vertebrates than are the invertebrates (Drosophila melanogaster, Bombyx mori, and Caenorhabditis elegans). This phenomenon may suggest variable evolutionary rates during the metazoan radiations and slower changes in the fungal divergences, and/or a polyphyletic origin of metazoa. (iii) The genomic sequences of D. melanogaster and Trypanosoma brucei are strikingly similar. This DNA similarity might be explained by some molecular adaptation of the parasite to its dipteran (tsetse fly) host, a host-parasite gene transfer hypothesis. Robustness of the methods may be due to a genomic signature of dinucleotide relative abundance values reflecting DNA structures related to dinucleotide stacking energies, constraints of DNA curvature, and mechanisms attendant to replication, repair, and recombination.

authors

Karlin S,Ladunga I

doi

10.1073/pnas.91.26.12832

subject

Has Abstract

pub_date

1994-12-20 00:00:00

pages

12832-6

issue

26

eissn

0027-8424

issn

1091-6490

journal_volume

91

pub_type

杂志文章
  • Topographically induced hierarchical assembly and geometrical transformation of focal conic domain arrays in smectic liquid crystals.

    abstract::Controlling topological defects in 3D liquid crystal phases is a crucial element in the development of novel devices, from blue-phase displays to passive biochemical sensors. However, it remains challenging to realize the 3D topological conditions necessary to robustly and arbitrarily direct the formation of defects. ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1214708109

    authors: Honglawan A,Beller DA,Cavallaro M Jr,Kamien RD,Stebe KJ,Yang S

    更新日期:2013-01-02 00:00:00

  • Long-range Pitx2c enhancer-promoter interactions prevent predisposition to atrial fibrillation.

    abstract::Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia, is associated with noncoding sequence variants located in proximity to PITX2 Cardiomyocyte-specific epigenomic and comparative genomics uncovered 2 AF-associated enhancers neighboring PITX2 w...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1907418116

    authors: Zhang M,Hill MC,Kadow ZA,Suh JH,Tucker NR,Hall AW,Tran TT,Swinton PS,Leach JP,Margulies KB,Ellinor PT,Li N,Martin JF

    更新日期:2019-11-05 00:00:00

  • Protein 4.1R-dependent multiprotein complex: new insights into the structural organization of the red blood cell membrane.

    abstract::Protein 4.1R (4.1R) is a multifunctional component of the red cell membrane. It forms a ternary complex with actin and spectrin, which defines the nodal junctions of the membrane-skeletal network, and its attachment to the transmembrane protein glycophorin C creates a bridge between the protein network and the membran...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0803225105

    authors: Salomao M,Zhang X,Yang Y,Lee S,Hartwig JH,Chasis JA,Mohandas N,An X

    更新日期:2008-06-10 00:00:00

  • Modification of DNA ends can decrease end joining relative to homologous recombination in mammalian cells.

    abstract::In animal cells, exogenous DNA recombines into random chromosomal sites much more frequently than it recombines into homologous sites. Free DNA ends are "recombinogenic" in both processes. To test the effects of specific ends on analogous extrachromosomal processes, we constructed a linear genome of simian virus 40 wi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.14.4959

    authors: Chang XB,Wilson JH

    更新日期:1987-07-01 00:00:00

  • Genome-wide RNAi screen identifies the Parkinson disease GWAS risk locus SREBF1 as a regulator of mitophagy.

    abstract::Genetic analysis of Parkinson disease (PD) has identified several genes whose mutation causes inherited parkinsonism, as well as risk loci for sporadic PD. PTEN-induced kinase 1 (PINK1) and parkin, linked to autosomal recessive PD, act in a common genetic pathway regulating the autophagic degradation of mitochondria, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1321207111

    authors: Ivatt RM,Sanchez-Martinez A,Godena VK,Brown S,Ziviani E,Whitworth AJ

    更新日期:2014-06-10 00:00:00

  • Oligonucleotide-directed mutagenesis as a general and powerful method for studies of protein function.

    abstract::We have used oligonucleotide-directed mutagenesis to make a specific change in the beta-lactamase (EC 3.5.2.6) (ampicillin resistance) gene of the plasmid pBR322. Evidence suggests that the active site for this enzyme may include a serine-threonine dyad (residues 70 and 71). By priming in vitro DNA synthesis with a ch...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.21.6409

    authors: Dalbadie-McFarland G,Cohen LW,Riggs AD,Morin C,Itakura K,Richards JH

    更新日期:1982-11-01 00:00:00

  • cAMP-PKA phosphorylation of tau confers risk for degeneration in aging association cortex.

    abstract::The pattern of neurodegeneration in Alzheimer's disease (AD) is very distinctive: neurofibrillary tangles (NFTs) composed of hyperphosphorylated tau selectively affect pyramidal neurons of the aging association cortex that interconnect extensively through glutamate synapses on dendritic spines. In contrast, primary se...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1322360111

    authors: Carlyle BC,Nairn AC,Wang M,Yang Y,Jin LE,Simen AA,Ramos BP,Bordner KA,Craft GE,Davies P,Pletikos M,Šestan N,Arnsten AF,Paspalas CD

    更新日期:2014-04-01 00:00:00

  • Modeling the status, trends, and impacts of wild bee abundance in the United States.

    abstract::Wild bees are highly valuable pollinators. Along with managed honey bees, they provide a critical ecosystem service by ensuring stable pollination to agriculture and wild plant communities. Increasing concern about the welfare of both wild and managed pollinators, however, has prompted recent calls for national evalua...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1517685113

    authors: Koh I,Lonsdorf EV,Williams NM,Brittain C,Isaacs R,Gibbs J,Ricketts TH

    更新日期:2016-01-05 00:00:00

  • A dual laminin/collagen receptor acts in peripheral nerve regeneration.

    abstract::A regeneration chamber was created in vivo by suturing a synthetic tube sealed at its distal end onto the proximal stump of a severed rat sciatic nerve. Nerves regenerated into tubes coated with laminin at a rate of 0.33 mm/day after a lag of about 2 days. At 25 days, regenerating nerves had extended 23% farther into ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.4.1319

    authors: Toyota B,Carbonetto S,David S

    更新日期:1990-02-01 00:00:00

  • S2 episome of maize mitochondria encodes a 130-kilodalton protein found in male sterile and fertile plants.

    abstract::The mitochondrial genome of the S-type male-sterile cytoplasm of maize contains two linear episomes, S1 (6397 base pairs) and S2 (5453 base pairs). The S2 episome contains two large unidentified open reading frames, URF1 (3512 base pairs) and URF2 (1017 base pairs). We have demonstrated that a polypeptide with an appa...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.22.7861

    authors: Zabala G,O'brien-Vedder C,Walbot V

    更新日期:1987-11-01 00:00:00

  • Nontypeable Haemophilus influenzae releases DNA and DNABII proteins via a T4SS-like complex and ComE of the type IV pilus machinery.

    abstract::Biofilms formed by nontypeable Haemophilus influenzae (NTHI) are central to the chronicity, recurrence, and resistance to treatment of multiple human respiratory tract diseases including otitis media, chronic rhinosinusitis, and exacerbations of both cystic fibrosis and chronic obstructive pulmonary disease. Extracell...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1705508114

    authors: Jurcisek JA,Brockman KL,Novotny LA,Goodman SD,Bakaletz LO

    更新日期:2017-08-08 00:00:00

  • Dinuclear nickel complexes modeling the structure and function of the acetyl CoA synthase active site.

    abstract::A dinuclear nickel complex with methyl and thiolate ligands, Ni(dadt(Et))Ni(Me)(SDmp) (2), has been synthesized as a dinuclear Ni(d)-Ni(p)-site model of acetyl-CoA synthase (ACS) (dadt(Et) is N,N'-diethyl-3,7-diazanonane-1,9-dithiolate; Dmp is 2,6-dimesitylphenyl). Complex 2 was prepared via 2 methods: (i) ligand subs...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900433106

    authors: Ito M,Kotera M,Matsumoto T,Tatsumi K

    更新日期:2009-07-21 00:00:00

  • Bird song syntax: learned intraspecific variation is meaningful.

    abstract::Song syntax, defined as orderly temporal arrangements of acoustic units within a bird song, is a conspicuous feature of the songs of many species of passerine birds. While syntactical features play a role in interspecific song recognition by males of many bird species, syntax variation within species and female respon...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.10.3657

    authors: Balaban E

    更新日期:1988-05-01 00:00:00

  • Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives.

    abstract::There has been much confusion recently about the relative merits of different approaches, osmotic stress, preferential interaction, and crowding, to describe the indirect effect of solutes on macromolecular conformations and reactions. To strengthen all interpretations of measurements and to forestall further unnecess...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.8.3987

    authors: Parsegian VA,Rand RP,Rau DC

    更新日期:2000-04-11 00:00:00

  • Proliferating cell nuclear antigen (PCNA)-associated KIAA0101/PAF15 protein is a cell cycle-regulated anaphase-promoting complex/cyclosome substrate.

    abstract::The anaphase-promoting complex/cyclosome (APC/C) is a cell cycle-regulated E3 ubiquitin ligase that controls the degradation of substrate proteins at mitotic exit and throughout the G1 phase. We have identified an APC/C substrate and cell cycle-regulated protein, KIAA0101/PAF15. PAF15 protein levels peak in the G2/M p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1106136108

    authors: Emanuele MJ,Ciccia A,Elia AE,Elledge SJ

    更新日期:2011-06-14 00:00:00

  • A pathogen-inducible endogenous siRNA in plant immunity.

    abstract::RNA interference, mediated by small interfering RNAs (siRNAs), is a conserved regulatory process that has evolved as an antiviral defense mechanism in plants and animals. It is not known whether host cells also use siRNAs as an antibacterial defense mechanism in eukaryotes. Here, we report the discovery of an endogeno...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0608258103

    authors: Katiyar-Agarwal S,Morgan R,Dahlbeck D,Borsani O,Villegas A Jr,Zhu JK,Staskawicz BJ,Jin H

    更新日期:2006-11-21 00:00:00

  • HSP90 is a chaperone for DLK and is required for axon injury signaling.

    abstract::Peripheral nerve injury induces a robust proregenerative program that drives axon regeneration. While many regeneration-associated genes are known, the mechanisms by which injury activates them are less well-understood. To identify such mechanisms, we performed a loss-of-function pharmacological screen in cultured adu...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1805351115

    authors: Karney-Grobe S,Russo A,Frey E,Milbrandt J,DiAntonio A

    更新日期:2018-10-16 00:00:00

  • Extranuclear estrogen receptor-alpha stimulates NeuroD1 binding to the insulin promoter and favors insulin synthesis.

    abstract::Estrogen receptors (ERs) protect pancreatic islet survival in mice through rapid extranuclear actions. ERalpha also enhances insulin synthesis in cultured islets. Whether ERalpha stimulates insulin synthesis in vivo and, if so, through which mechanism(s) remain largely unknown. To address these issues, we generated a ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0914501107

    authors: Wong WP,Tiano JP,Liu S,Hewitt SC,Le May C,Dalle S,Katzenellenbogen JA,Katzenellenbogen BS,Korach KS,Mauvais-Jarvis F

    更新日期:2010-07-20 00:00:00

  • Internal homologies in the two aspartokinase-homoserine dehydrogenases of Escherichia coli K-12.

    abstract::In Escherichia coli, AK I- HDH I and AK II- HDH II are two bifunctional proteins, derived from a common ancestor, that catalyze the first and third reactions of the common pathway leading to threonine and methionine. An extensive amino acid sequence comparison of both molecules reveals two main features on each of the...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.10.3019

    authors: Ferrara P,Duchange N,Zakin MM,Cohen GN

    更新日期:1984-05-01 00:00:00

  • Alzheimer beta/A4 amyloid precursor protein in human brain: aging-associated increases in holoprotein and in a proteolytic fragment.

    abstract::Alzheimer beta/A4 amyloid precursor protein (APP) has been suggested to play a central role in the pathogenesis of Alzheimer disease. We have measured the content of different species of APP holoprotein and carboxyl-terminal fragments in human brains from young individuals, nondemented aged individuals, and aged indiv...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.20.8910

    authors: Nordstedt C,Gandy SE,Alafuzoff I,Caporaso GL,Iverfeldt K,Grebb JA,Winblad B,Greengard P

    更新日期:1991-10-15 00:00:00

  • The delta isoform of CaM kinase II is required for pathological cardiac hypertrophy and remodeling after pressure overload.

    abstract::Acute and chronic injuries to the heart result in perturbation of intracellular calcium signaling, which leads to pathological cardiac hypertrophy and remodeling. Calcium/calmodulin-dependent protein kinase II (CaMKII) has been implicated in the transduction of calcium signals in the heart, but the specific isoforms o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0813013106

    authors: Backs J,Backs T,Neef S,Kreusser MM,Lehmann LH,Patrick DM,Grueter CE,Qi X,Richardson JA,Hill JA,Katus HA,Bassel-Duby R,Maier LS,Olson EN

    更新日期:2009-02-17 00:00:00

  • Changes in the three-dimensional structure of concanavalin A upon demetallization.

    abstract::When the Mn(2+) and Ca(2+) ions normally present in concanavalin A are removed, the protein becomes incapable of binding saccharides. To explore the structural differences between the native and demetallized forms and their effects on the saccharide-binding properties of the protein, we have refined and compared the c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.75.5.2286

    authors: Reeke GN Jr,Becker JW,Edelman GM

    更新日期:1978-05-01 00:00:00

  • Allozyme and restriction fragment length polymorphism analyses confirm Entomophaga maimaiga responsible for 1989 epizootics in North American gypsy moth populations.

    abstract::In 1989, populations of North American gypsy moth, Lymantria dispar, in seven contiguous northeastern states were severely reduced by a fungal pathogen. Based on morphology, development, and pathology, this organism appeared to be Entomophaga maimaiga. We have now used allozyme and restriction fragment length polymorp...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.18.6979

    authors: Hajek AE,Humber RA,Elkinton JS,May B,Walsh SR,Silver JC

    更新日期:1990-09-01 00:00:00

  • Isotopic evidence for large gaseous nitrogen losses from tropical rainforests.

    abstract::The nitrogen isotopic composition (15N/14N) of forested ecosystems varies systematically worldwide. In tropical forests, which are elevated in 15N relative to temperate biomes, a decrease in ecosystem 15N/14N with increasing rainfall has been reported. This trend is seen in a set of well characterized Hawaiian rainfor...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0510185103

    authors: Houlton BZ,Sigman DM,Hedin LO

    更新日期:2006-06-06 00:00:00

  • One-trial associative learning modifies food odor preferences of a terrestrial mollusc.

    abstract::We present evidence of rapid and reliable associative learning by the terrestrial mollusc, Limax maximus. Slugs were exposed once to a pairing of a highly attractive food odor (potato or carrot) and a saturated solution of quinidine sulfate, a bitter-tasting plant substance. In comparison with control slugs, the expos...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.1.640

    authors: Sahley C,Gelperin A,Rudy JW

    更新日期:1981-01-01 00:00:00

  • Ultraconserved words point to deep language ancestry across Eurasia.

    abstract::The search for ever deeper relationships among the World's languages is bedeviled by the fact that most words evolve too rapidly to preserve evidence of their ancestry beyond 5,000 to 9,000 y. On the other hand, quantitative modeling indicates that some "ultraconserved" words exist that might be used to find evidence ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.1218726110

    authors: Pagel M,Atkinson QD,S Calude A,Meade A

    更新日期:2013-05-21 00:00:00

  • Good genes sexual selection in nature.

    abstract::Whether the mate sampling and choice performed by females in nature influences offspring performance is a controversial issue in theory and an open empirical question. Pronghorn (Antilocapra americana) females engage in an obvious and energetically expensive mate sampling process to identify vigorous males. Although i...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0608184103

    authors: Byers JA,Waits L

    更新日期:2006-10-31 00:00:00

  • Rat skeletal muscle selenoprotein W: cDNA clone and mRNA modulation by dietary selenium.

    abstract::Rat skeletal muscle selenoprotein W cDNA was isolated and sequenced. The isolation strategy involved design of degenerate PCR primers from reverse translation of a partial peptide sequence. A reverse transcription-coupled PCR product from rat muscle mRNA was used to screen a muscle cDNA library prepared from selenium-...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.19.8749

    authors: Vendeland SC,Beilstein MA,Yeh JY,Ream W,Whanger PD

    更新日期:1995-09-12 00:00:00

  • SGTA antagonizes BAG6-mediated protein triage.

    abstract::The BAG6 complex was first identified as an upstream loading factor for tail-anchored membrane proteins entering the TRC40-dependent pathway for posttranslational delivery to the endoplasmic reticulum. Subsequently, BAG6 was shown to enhance the proteasomal degradation of mislocalized proteins by selectively promoting...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1209997109

    authors: Leznicki P,High S

    更新日期:2012-11-20 00:00:00

  • Cytological evidence for switches in polarity of chromosomal DNA.

    abstract::From the types of ring chromosomes induced in x-irradiated Chinese hamster ovary (CHO) cells, we deduce the existence of switches in the polarity of chromosomal DNA; if there is a continuous DNA double helix along the full length of the chromosome then the polarity switches imply 3'-3' and 5'-5' phosphodiester linkage...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.3.877

    authors: Wolff S,Lindsley DL,Peacock WJ

    更新日期:1976-03-01 00:00:00