Empirical genome evolution models root the tree of life.


:A reliable phylogenetic reconstruction of the evolutionary history of contemporary species depends on a robust identification of the universal common ancestor (UCA) at the root of the Tree of Life (ToL). That root polarizes the tree so that the evolutionary succession of ancestors to descendants is discernable. In effect, the root determines the branching order and the direction of character evolution. Typically, conventional phylogenetic analyses implement time-reversible models of evolution for which character evolution is un-polarized. Such practices leave the root and the direction of character evolution undefined by the data used to construct such trees. In such cases, rooting relies on theoretic assumptions and/or the use of external data to interpret unrooted trees. The most common rooting method, the outgroup method is clearly inapplicable to the ToL, which has no outgroup. Both here and in the accompanying paper (Harish and Kurland, 2017) we have explored the theoretical and technical issues related to several rooting methods. We demonstrate (1) that Genome-level characters and evolution models are necessary for species phylogeny reconstructions. By the same token, standard practices exploiting sequence-based methods that implement gene-scale substitution models do not root species trees; (2) Modeling evolution of complex genomic characters and processes that are non-reversible and non-stationary is required to reconstruct the polarized evolution of the ToL; (3) Rooting experiments and Bayesian model selection tests overwhelmingly support the earlier finding that akaryotes and eukaryotes are sister clades that descend independently from UCA (Harish and Kurland, 2013); (4) Consistent ancestral state reconstructions from independent genome samplings confirm the previous finding that UCA features three fourths of the unique protein domain-superfamilies encoded by extant genomes.






Harish A,Kurland CG




Has Abstract


2017-07-01 00:00:00












  • 2-(4-methyl-1-piperazinylmethyl) acrylophenone dihydrochloride: a new antimicrotubular drug.

    abstract::With the relation between chemical structure and pharmacological activity as a guide, we have been for some time synthetizing a wide range of beta-amino-ketone derivatives. One of them, 2-(4-methyl-1-piperazinylmethyl) acrylophenone, MPMAP, possesses antimicrotubular activities. This product inhibits 50% of the microt...


    pub_type: 杂志文章


    authors: Mallevais ML,Delacourte A,Lesieur I,Lesieur D,Cazin M,Brunet C,Luyckx M

    更新日期:1984-06-01 00:00:00

  • [Influence of phosphatidylcholine/cholesterol molar ratios in liposomes on cholesterol reactivity with cholesterol:oxygen oxidoreductase].

    abstract::The reactivity of sonicated phosphatidylcholine-cholesterol liposomes with cholesterol : oxygene oxydoreductase, an enzyme which catalyses the oxidation of the 3 beta hydroxyl group of cholesterol to a ketone group, is compared with that of ternary system phosphatidylcholine-cholesterol-Thesit. Regardless to the phosp...


    pub_type: 杂志文章


    authors: Peynet J,Delattre J,Canal J,Rousselet F,Girard ML

    更新日期:1979-01-01 00:00:00

  • Elongating ribosomes in vivo are refractory to erythromycin.

    abstract::We have studied the kinetics of erythromycin inhibition of translation in growing bacteria. In order to simplify the interpretation of our data, we have used a mutant (envA), known to have an increased permeability to several antibiotics, including erythromycin. The data clearly show that an initial stage of translati...


    pub_type: 杂志文章


    authors: Andersson S,Kurland CG

    更新日期:1987-08-01 00:00:00

  • Conformational dynamics and enzyme activity.

    abstract::Conformational flexibility and structural fluctuations play an important role in enzyme activity. A great variety of internal motions ranging over different time scales and of different amplitudes are involved in the catalytic cycle. These different types of motions and their functional consequences are considered in ...


    pub_type: 杂志文章,评审


    authors: Yon JM,Perahia D,Ghélis C

    更新日期:1998-01-01 00:00:00

  • High altitude mediated skeletal muscle atrophy: Protective role of curcumin.

    abstract::Chronic hypobaric hypoxia induced muscle atrophy results in decreased physical performance at high altitude. Curcumin has been shown to have muscle sparing effects under cachectic conditions. However, the protective effects of curcumin under chronic hypobaric hypoxia have not been studied till now. Therefore, the pres...


    pub_type: 杂志文章


    authors: Chaudhary P,Sharma YK,Sharma S,Singh SN,Suryakumar G

    更新日期:2019-01-01 00:00:00

  • Structural and functional characterization of complex formation between two Kunitz-type serine protease inhibitors from Russell's Viper venom.

    abstract::Snake venom Kunitz-type serine protease inhibitors (KSPIs) exhibit various biological functions including anticoagulant activity. This study elucidates the occurrence and subunit stoichiometry of a putative complex formed between two KSPIs (Rusvikunin and Rusvikunin-II) purified from the native Rusvikunin complex of P...


    pub_type: 杂志文章


    authors: Mukherjee AK,Dutta S,Kalita B,Jha DK,Deb P,Mackessy SP

    更新日期:2016-09-01 00:00:00

  • Crystal structure of dihydroorotate dehydrogenase from Leishmania major.

    abstract::Dihydroorotate dehydrogenase (DHODH) is the fourth enzyme in the de novo pyrimidine biosynthetic pathway and has been exploited as the target for therapy against proliferative and parasitic diseases. In this study, we report the crystal structures of DHODH from Leishmania major, the species of Leishmania associated wi...


    pub_type: 杂志文章


    authors: Cordeiro AT,Feliciano PR,Pinheiro MP,Nonato MC

    更新日期:2012-08-01 00:00:00

  • Interaction of phosphonates related to glutathione with the rat kidney gamma-glutamylcysteine synthetase.

    abstract::Various phosphonic and sulfonic glutamate analogues as well as phosphonopeptides related to glutathione were studied for their interaction with rat kidney gamma-glutamylcysteine synthetase activity. We found, in all cases, that the presence of a phosphonic group increases the affinity for the enzyme. Among the tripept...


    pub_type: 杂志文章


    authors: Marche M,Basurko MJ,Cassaigne A

    更新日期:1987-05-01 00:00:00

  • Molecular characterization of BjussuSP-I, a new thrombin-like enzyme with procoagulant and kallikrein-like activity isolated from Bothrops jararacussu snake venom.

    abstract::A thrombin-like enzyme, named BjussuSP-I, isolated from Bothrops jararacussu snake venom, is an acidic single-chain glycoprotein with M(r)=61,000, pI approximately 3.8 and 6% sugar. BjussuSP-I shows high proteolytic activity upon synthetic substrates, such as S-2238 and S-2288. It also shows procoagulant and kallikrei...


    pub_type: 杂志文章


    authors: Sant'Ana CD,Bernardes CP,Izidoro LF,Mazzi MV,Soares SG,Fuly AL,Zingali RB,Magro AJ,Braz AS,Fontes MR,Stábeli RG,Sampaio SV,Soares AM

    更新日期:2008-03-01 00:00:00

  • Transposition of the Streptococcus lactis ssp. lactis Z270 lactose plasmid to pVA797: demonstration of an insertion sequence and its relationship to an inverted repeat sequence isolated by self-annealing.

    abstract::The lactose plasmid pUCL22 of the single plasmid strain Streptococcus lactis ssp. lactis Z270 was demonstrated to fuse with the heterologous conjugative plasmid pVA797. The fusion of pUCL22 with pVA797 occurred by recombination between a specific sequence of pUCL22 and different sites of pVA797. The cointegrates of pU...


    pub_type: 杂志文章


    authors: Novel M,Huang DC,Novel G

    更新日期:1988-04-01 00:00:00

  • Degradation of oxidized proteins by the 20S proteasome.

    abstract::Oxidatively modified proteins are continuously produced in cells by reactive oxygen and nitrogen species generated as a consequence of aerobic metabolism. During periods of oxidative stress, protein oxidation is significantly increased and may become a threat to cell survival. In eucaryotic cells the proteasome has be...


    pub_type: 杂志文章,评审


    authors: Davies KJ

    更新日期:2001-03-01 00:00:00

  • Unsolved issues related to human mitochondrial diseases.

    abstract::Human mitochondrial diseases, defined as the diseases due to a mitochondrial oxidative phosphorylation defect, represent a large group of very diverse diseases with respect to phenotype and genetic causes. They present with many unsolved issues, the comprehensive analysis of which is beyond the scope of this review. W...


    pub_type: 杂志文章,评审


    authors: Lombès A,Auré K,Bellanné-Chantelot C,Gilleron M,Jardel C

    更新日期:2014-05-01 00:00:00

  • [In vivo metabolism of rat submaxillary gland phospholipids].

    abstract::The metabolism of the phospholipids of the submaxillary gland are studied after intraperitoneal injections of [32P]-orthophosphate in several groups of rats. The gland contains mainly phosphatidylcholines and phosphatidylethanolamines and in smaller quantities phosphatidylinositols, phosphatidylserines, sphingomyelins...


    pub_type: 杂志文章


    authors: Leclercq C,Di Costanzo G

    更新日期:1976-01-01 00:00:00

  • Gamma-radiolysis study of the reductive activation of neocarzinostatin by the carboxyl radical.

    abstract::The activation of the antitumor protein antibiotic neocarzinostatin (NCS) by the carboxyl radical CO-2, a one-electron donor obtained selectively from gamma-ray irradiation of nitrous oxide-saturated formate buffer, has been investigated in the presence and in the absence of DNA at pH 4.7 and pH 7.0. The reaction of N...


    pub_type: 杂志文章


    authors: Favaudon V

    更新日期:1983-11-01 00:00:00

  • Development and preclinical evaluation of a new F(ab')₂ antitoxin against botulinum neurotoxin serotype A.

    abstract::Concern about the malicious applications of botulinum neurotoxin has highlighted the need for a new generation of safe and highly potent antitoxins. In this study, we developed and evaluated the preclinical pharmacology and safety of a new F(ab')₂ antitoxin against botulinum neurotoxin serotype A (BoNT/A). As an alter...


    pub_type: 杂志文章


    authors: Yu YZ,Zhang SM,Wang WB,Du Y,Zhu HQ,Wang RL,Zhou XW,Lin JB,Wang S,Yu WY,Huang PT,Sun ZW

    更新日期:2010-10-01 00:00:00

  • Secretome within the bone marrow microenvironment: A basis for mesenchymal stem cell treatment and role in cancer dormancy.

    abstract::The secretome produced by cells within the bone marrow is significant to homeostasis. The bone marrow, a well-studied organ, has multiple niches with distinct roles for supporting stem cell functions. Thus, an understanding of mediators involved in the regulation of stem cells could serve as a model for clinical probl...


    pub_type: 杂志文章,评审


    authors: Eltoukhy HS,Sinha G,Moore CA,Gergues M,Rameshwar P

    更新日期:2018-12-01 00:00:00

  • [Biosynthesis of phorcabiline, blue-green biliary pigment of Actias selene (Lepidoptera, Attacidae)].

    abstract::The blue-green bile pigments of Actias selene (Attacidae) have been investigated at different stages of its development. Coproporphyrinogen-14-C, protoporphyrin-IX3-H, and pterobilin-14-C, injected to larvae are metabolised into phorcabilin I, the main neopterobilin in this animal. It is concluded that phorcabilin I i...


    pub_type: 杂志文章


    authors: Choussy M,Barbier M,Vuillaume M

    更新日期:1975-01-01 00:00:00

  • Automatic identification of large collections of protein-coding or rRNA sequences.

    abstract::The number of available genomic sequences is growing very fast, due to the development of massive sequencing techniques. Sequence identification is needed and contributes to the assessment of gene and species evolutionary relationships. Automated bioinformatics tools are thus necessary to carry out these identificatio...


    pub_type: 杂志文章


    authors: Arigon AM,Perrière G,Gouy M

    更新日期:2008-04-01 00:00:00

  • Natural cysteine protease inhibitors in protozoa: Fifteen years of the chagasin family.

    abstract::Chagasin-type inhibitors comprise natural inhibitors of papain-like cysteine proteases that are distributed among Protist, Bacteria and Archaea. Chagasin was identified in the pathogenic protozoa Trypanosoma cruzi as an approximately 11 kDa protein that is a tight-binding and highly thermostable inhibitor of papain, c...


    pub_type: 杂志文章,评审


    authors: Costa TF,Lima AP

    更新日期:2016-03-01 00:00:00

  • Localization of defined carbohydrate epitopes in bovine polysialylated NCAM.

    abstract::Polysialylated neural cell adhesion molecule (NCAM) was immunoaffinity-purified from the brains of newborn calves. A degree of polymerization of up to 40 was chromatographically determined for released polysialic acid (PSA) chains. For characterization of N-glycan structures and attachment sites, PSA-NCAM was digested...


    pub_type: 杂志文章


    authors: Wuhrer M,Geyer H,von der Ohe M,Gerardy-Schahn R,Schachner M,Geyer R

    更新日期:2003-01-01 00:00:00

  • Exploiting the unique features of Zika and Dengue proteases for inhibitor design.

    abstract::Zika and Dengue viruses have attracted substantial attention from researchers in light of recent outbreaks of Dengue fever and increases in cases of congenital microcephaly in areas with Zika incidence. This review summarizes the current state of knowledge about Zika and Dengue proteases. These enzymes have several in...


    pub_type: 杂志文章,评审


    authors: Majerová T,Novotný P,Krýsová E,Konvalinka J

    更新日期:2019-11-01 00:00:00

  • Isolation and structure of a pseudopeptide gamma-L-glutamyl-L-aspartic acid from Datura stramonium that impairs learning retention in mice.

    abstract::Datura stramonium contains a compound that impairs learning retention in mice. It has been purified to homogeneity and its structure has been established as that of a gamma-L-glutamyl-L-aspartate. The biological activity of this pseudodipeptide has been found to be identical with that of the corresponding synthetic on...


    pub_type: 杂志文章


    authors: Schmitz-Bourgeois M,Amiri I,Reinbolt J,Boulanger Y,Ungerer A

    更新日期:1988-09-01 00:00:00

  • Differential contributions of recognition factors of two plant lectins -Amaranthus caudatus lectin and Arachis hypogea agglutinin, reacting with Thomsen-Friedenreich disaccharide (Galbeta1-3GalNAcalpha1-Ser/Thr).

    abstract::Previous reports on the carbohydrate specificities of Amaranthus caudatus lectin (ACL) and peanut agglutinin (PNA, Arachis hypogea) indicated that they share the same specificity for the Thomsen-Friedenreich (T(alpha), Galbeta1-3GalNAcalpha1-Ser/Thr) glycotope, but differ in monosaccharide binding--GalNAc>Gal (inactiv...


    pub_type: 杂志文章


    authors: Wu AM,Wu JH,Yang Z,Singh T,Goldstein IJ,Sharon N

    更新日期:2008-11-01 00:00:00

  • Characterization of papain-like isoenzymes from latex of Asclepias curassavica by molecular biology validated by proteomic approach.

    abstract::Latices from Asclepias spp are used in wound healing and the treatment of some digestive disorders. These pharmacological actions have been attributed to the presence of cysteine proteases in these milky latices. Asclepias curassavica (Asclepiadaceae), "scarlet milkweed" is a perennial subshrub native to South America...


    pub_type: 杂志文章


    authors: Obregón WD,Liggieri CS,Trejo SA,Avilés FX,Vairo-Cavalli SE,Priolo NS

    更新日期:2009-11-01 00:00:00

  • Crystal structure of the NADP-dependent mannitol dehydrogenase from Cladosporium herbarum: Implications for oligomerisation and catalysis.

    abstract::The ascomycete Cladosporium herbarum is a prominent fungal inducer of Type I allergy. The only major allergen identified so far is Cla h 8, a NADP-dependent mannitol dehydrogenase (MtDH). MtDH, a cytoplasmic protein of 28.5kDa, belongs to the Short chain Dehydrogenases/Reductases (SDR), acting as a NADP-dependent oxid...


    pub_type: 杂志文章


    authors: Nüss D,Goettig P,Magler I,Denk U,Breitenbach M,Schneider PB,Brandstetter H,Simon-Nobbe B

    更新日期:2010-08-01 00:00:00

  • One carbon metabolism and bone homeostasis and remodeling: A review of experimental research and population studies.

    abstract::Homocysteine (HCY) is a degradation product of the methionine pathway. The B vitamins, in particular vitamin B12 and folate, are the primary nutritional determinant of HCY levels and therefore their deficiencies result in hyperhomocysteinaemia (HHCY). Prevalence of hyperhomocysteinemia (HHCY) and related dietary defic...


    pub_type: 杂志文章,评审


    authors: Feigerlova E,Demarquet L,Guéant JL

    更新日期:2016-07-01 00:00:00

  • Role of nuclear architecture in the initiation of eukaryotic DNA replication.

    abstract::The eukaryotic genome is compacted in the cell nucleus, in a way that allows its faithful and ordered replication each cell cycle. Chromatin is organized into topologically constrained loops that are anchored to the nuclear matrix by specific attachment regions (SARs). Chromatin loops were proposed to correspond to re...


    pub_type: 杂志文章,评审


    authors: Hyrien O,Maric C,Lucas I

    更新日期:1997-10-01 00:00:00

  • Accurate estimation of inter-atomic distances in large proteins by NMR.

    abstract::Recently a method was proposed which permits the extraction of the exact interatomic distance information from the measurement of the evolution of a single cross-peak relative to the mixing time in a NOESY experiment. This is performed through a careful multi-exponential analysis allowing the extraction of the relaxat...


    pub_type: 杂志文章


    authors: Reisdorf C,Malliavin TE,Delsuc MA

    更新日期:1992-09-01 00:00:00

  • Homogeneity of lung tubulin isoforms during lung maturation.

    abstract::The rat and rabbit lung isoform pattern before (fetal) and after (adult) lung maturation has been analyzed by isoelectric focusing. This pattern has been compared to that of brain tubulin at the same developmental stages. No changes in the pattern of fetal and adult lung tubulin were found. However an increase in brai...


    pub_type: 杂志文章


    authors: Déiz JC,Avila J

    更新日期:1985-09-01 00:00:00

  • Localization of a segment of 16S RNA on the surface of the small ribosomal subunit by immune electron microscopy of complementary oligodeoxynucleotides.

    abstract::Oligonucleotides that complement Escherichia coli 16S ribosomal RNA residues 685-696 and 694-705 have been synthesized so as to incorporate antibody-recognizable markers: a 3'-terminal residue of N6-delta 2-isopentenyladenosine, a 5'-dinitrophenyl group, or both. Each oligonucleotide is able to bind RNA within the sma...


    pub_type: 杂志文章


    authors: McWilliams RA,Glitz DG

    更新日期:1991-07-01 00:00:00