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.
journal_name
Proc Natl Acad Sci U S Aauthors
Karlin S,Ladunga Idoi
10.1073/pnas.91.26.12832subject
Has Abstractpub_date
1994-12-20 00:00:00pages
12832-6issue
26eissn
0027-8424issn
1091-6490journal_volume
91pub_type
杂志文章abstract::Occurrence of the transversion mutation A.T to C.G is specifically enhanced in Escherichia coli mutT mutants. With the aid of the cloned mutT gene, the MutT protein, which has a molecular mass of 15 kilodaltons, was overproduced and purified to near homogeneity. The protein catalyzes hydrolysis of dGTP to dGMP. dGDP 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.86.11.3949
更新日期:1989-06-01 00:00:00
abstract::Although cells express hundreds of metalloenzymes, the mechanisms by which apoenzymes receive their metal cofactors are largely unknown. Poly(rC)-binding proteins PCBP1 and PCBP2 are multifunctional adaptor proteins that bind iron and deliver it to ferritin for storage or to prolyl and asparagyl hydroxylases to metall...
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.1402732111
更新日期:2014-06-03 00:00:00
abstract::Very little is known about how animals discriminate pathogens from innocuous microbes. To address this question, we examined infection-response gene induction in the nematode Caenorhabditis elegans. We focused on genes that are induced in C. elegans by infection with the bacterial pathogen Pseudomonas aeruginosa, but ...
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.0914643107
更新日期:2010-02-02 00:00:00
abstract::Nonribosomal peptide synthetases (NRPSs) and polyketide synthases are large, multidomain enzymes that biosynthesize a number of pharmaceutically important natural products. The recognition of biosynthetic intermediates, displayed via covalent attachment to carrier proteins, by catalytic domains is critical for NRPS an...
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.0601038103
更新日期:2006-04-04 00:00:00
abstract::The advent of molecular tension probes for real-time mapping of piconewton forces in living systems has had a major impact on mechanobiology. For example, DNA-based tension probes have revealed roles for mechanics in platelet, B cell, T cell, and fibroblast function. Nonetheless, imaging short-lived forces transmitted...
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.1904034116
更新日期:2019-08-20 00:00:00
abstract::Neutrophils are important effector cells in immunity to microorganisms, particularly bacteria. Here, we show that the process of neutrophil apoptosis is delayed in several inflammatory diseases, suggesting that this phenomenon may represent a general feature contributing to the development of neutrophilia, and, theref...
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.96.23.13330
更新日期:1999-11-09 00:00:00
abstract::Although advances in microfluidic technology have enabled increasingly sophisticated biosensing and bioassay operations to be performed at the microscale, many of these applications employ such small amounts of charged biomolecules (DNA, proteins, and peptides) that they must first be preconcentrated to a detectable l...
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.0506848103
更新日期:2006-03-28 00:00:00
abstract::Protein misfolding and deposition underlie an increasing number of debilitating human disorders. We have shown that model proteins unrelated to disease, such as the Src homology 3 (SH3) domain of the p58alpha subunit of bovine phosphatidyl-inositol-3'-kinase (PI3-SH3), can be converted in vitro into assemblies with st...
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.0308249101
更新日期:2004-05-11 00:00:00
abstract::Different strains of Newcastle disease virus vary in their ability to induce cell fusion. When administered to cells at high multiplicities of infection some strains induce cell fusion within three hours. This type of fusion is apparently caused by the virus particles in the inoculum, since it can be induced by noninf...
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.64.2.536
更新日期:1969-10-01 00:00:00
abstract::Opitz syndrome (OS) is a genetically heterogeneous disorder characterized by defects of the ventral midline, including hypertelorism, cleft lip and palate, heart defects, and mental retardation. We recently identified the gene responsible for X-linked OS. The ubiquitously expressed gene product, MID1, is a member of t...
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.96.6.2794
更新日期:1999-03-16 00:00:00
abstract::Reptiles and fish have robust regenerative powers for tooth renewal. However, extant mammals can either renew their teeth one time (diphyodont dentition) or not at all (monophyodont dentition). Humans replace their milk teeth with permanent teeth and then lose their ability for tooth renewal. Here, we study tooth rene...
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.1213202110
更新日期:2013-05-28 00:00:00
abstract::Toll-like receptors (TLRs) play key roles in detecting pathogens and initiating inflammatory responses that, subsequently, prime specific adaptive responses. Several mechanisms control TLR activity to avoid excessive inflammation and consequent immunopathology, including the anti-inflammatory cytokine IL-10. Recently,...
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.1219852110
更新日期:2013-07-09 00:00:00
abstract::Interleukin 3 (IL-3) is a hematopoietic growth factor that supports the proliferation and differentiation of early hematopoietic-lineage progenitors. By using growth factor-dependent cell lines, IL-3 has been shown to induce the appearance of several phosphotyrosine-containing proteins, including a 140-kDa cell surfac...
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.85.21.7982
更新日期:1988-11-01 00:00:00
abstract::Plant genetic engineering led to the production of plant-derived mAb (mAbP), which provides a safe and economically feasible alternative to the current methods of antibody production in animal systems. In this study, the heavy and light chains of human anti-rabies mAb were expressed and assembled in planta under 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.0832472100
更新日期:2003-06-24 00:00:00
abstract::Mutant alleles at the dilute unconventional myosin heavy chain locus cause diluted coat color, opisthotonic seizures, and death. The dilute coat color phenotype is caused by irregular clumping of pigment in the hair, but amounts of melanin are unchanged from wild-type controls. The melanocyte phenotype has been descri...
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.93.25.14554
更新日期:1996-12-10 00:00:00
abstract::The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown...
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.0501663102
更新日期:2005-04-26 00:00:00
abstract::The Prisoner's Dilemma (PD) is a widely employed metaphor for problems associated with the evolution of cooperative behavior. We have recently proposed an alternative approach to the PD, by exploring "spatial games" in which players--who are either pure cooperators, C, or pure defectors, D--interact with neighbors in ...
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.91.11.4877
更新日期:1994-05-24 00:00:00
abstract::Protein kinase A (PKA) is activated during sympathetic stimulation of the heart and phosphorylates key proteins involved in cardiac Ca(2+) handling, including the L-type Ca(2+) channel (Ca(V)1.2) and phospholamban (PLN). This results in acceleration and amplification of the beat-to-beat changes in cytosolic Ca(2+) in ...
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.1215219109
更新日期:2012-10-16 00:00:00
abstract::Expression of alphavbeta3- or alphavbeta5-integrins and selectins is widespread on blood cells and endothelial cells. Here we report that human tumor cells injected s.c. into mice lacking beta3- or beta3/beta5-integrins or various selectins show enhanced tumor growth compared with growth in control mice. There was inc...
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.0307289101
更新日期:2004-01-20 00:00:00
abstract::Seasonal cycles govern life on earth, from setting the time for the mating season to influencing migrations and governing physiological conditions like hibernation. The effect of such changing conditions on behavior is well-appreciated, but their impact on the brain remains virtually unknown. We investigate long-term ...
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.1922888117
更新日期:2020-12-15 00:00:00
abstract::A mol of creatine kinase (EC 2.7.3.2), an enzyme with two identical subunits can be titrated very rapidly and stoichiometrically with 2 mol of 2-chloromercuri-4-nitrophenol, an environmentally sensitive chromophoric probe specific for thiols. Chemical modification does not inactivate the enzyme nor can the reaction be...
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.70.10.2858
更新日期:1973-10-01 00:00:00
abstract::Growth hormone (GH) has previously been implicated in T-cell development, and here we test its efficacy in promoting T-lymphocyte engraftment in mice with severe combined immune deficiency (SCID). SCID mice receiving syngeneic thymocytes and treated with recombinant human GH (rhGH) had significantly better T-cell engr...
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.89.10.4481
更新日期:1992-05-15 00:00:00
abstract::Accumulative aggregation of mutant Huntingtin (Htt) is a primary neuropathological hallmark of Huntington's disease (HD). Currently, mechanistic understanding of the cytotoxicity of mutant Htt aggregates remains limited, and neuroprotective strategies combating mutant Htt-induced neurodegeneration are lacking. Here, 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.1904563116
更新日期:2019-09-17 00:00:00
abstract::Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor superfamily that act as ligand-dependent transcription factors. Here we identified the ten-eleven translocation protein 3 (TET3) as a TR interacting protein increasing cell sensitivity to T3. The interaction between TET3 and TRs is independent...
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.1702192114
更新日期:2017-08-01 00:00:00
abstract::Previous studies have shown that the immunosuppressive and carcinogenic polycyclic aromatic hydrocarbon 7,12-dimethylbenz(a)anthracene (DMBA) impairs Ca(2+)-dependent transmembrane signaling in human and murine lymphocytes. The purpose of the present studies was to analyze potential mechanisms of immunosuppression by ...
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.90.13.6105
更新日期:1993-07-01 00:00:00
abstract::In rod photoreceptors, several phototransduction components display light-dependent translocation between cellular compartments. Notably, the G protein transducin translocates from rod outer segments to inner segments/spherules in bright light, but the functional consequences of translocation remain unclear. We genera...
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.1222666110
更新日期:2013-07-23 00:00:00
abstract::A soluble 27-kDa protein from Saccharomyces cerevisiae specifically prevents the inactivation of various enzymes caused by a nonenzymatic Fe3+/O2/thiol mixed-function oxidation system but not by mixed-function oxidation systems in which the thiol component is replaced by another electron donor-e.g., ascorbate. In this...
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.86.16.6018
更新日期:1989-08-01 00:00:00
abstract::Recent excavations at Pre-Pottery Neolithic A (PPNA) WF16 in southern Jordan have revealed remarkable evidence of architectural developments in the early Neolithic. This sheds light on both special purpose structures and "domestic" settlement, allowing fresh insights into the development of increasingly sedentary comm...
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.1017642108
更新日期:2011-05-17 00:00:00
abstract::Precise spatiotemporal control of mRNA translation machinery is essential to the development of highly complex systems like the neocortex. However, spatiotemporal regulation of translation machinery in the developing neocortex remains poorly understood. Here, we show that an RNA-binding protein, Hu antigen R (HuR), re...
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.1408305111
更新日期:2014-09-09 00:00:00
abstract::In a passive dendritic tree, inhibitory synaptic inputs activating ionic conductances with an equilibrium potential near the resting potential can effectively veto excitatory inputs. Analog interactions of this type can be very powerful if the inputs are appropriately timed and occur at certain locations. We examine 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.80.9.2799
更新日期:1983-05-01 00:00:00