Alignment of a 1.2-Mb chromosomal region from three strains of Rhodobacter capsulatus reveals a significantly mosaic structure.

Abstract:

:High-resolution physical maps of the genomes of three Rhodobacter capsulatus strains, derived from ordered cosmid libraries, were aligned. The 1.2-Mb segment of the SB1003 genome studied here is adjacent to a 1-Mb region analyzed previously [Fonstein, M., Nikolskaya, T. & Haselkorn, H. (1995) J. Bacteriol. 177, 2368-2372]. Probes derived from the ordered cosmid set of R. capsulatus SB1003 were used to link cosmids from the St. Louis and 2.3.1 strain libraries. Cosmids selected this way did not merge into a single contig but formed several unlinked groups. EcoRV restriction maps of the ordered cosmids were then constructed using lambda terminase and fused to derive fragments of the chromosomal map. In order to link these fragments, their ends were transcribed to produce secondary probes for hybridization to gridded cosmid libraries of the same strains. This linking reduced the number of subcontigs to three for the St. Louis strain and one for the 2.3.1 strain. Hybridization of the same probes back to the ordered cosmid set of SB1003 positioned the subcontigs on the high-resolution physical map of SB1003. The final alignment of the restriction maps shows numerous large and small translocations in this 1.2-Mb chromosomal region of the three Rhodobacter strains. In addition, the chromosomes of the three strains, whose fine-structure maps can now be compared over 2.2 Mb, are seen to contain regions of 15-80 kb in which restriction sites are highly polymorphic, interspersed among regions in which the positions of restriction sites are highly conserved.

authors

Nikolskaya T,Fonstein M,Haselkorn R

doi

10.1073/pnas.92.23.10609

subject

Has Abstract

pub_date

1995-11-07 00:00:00

pages

10609-13

issue

23

eissn

0027-8424

issn

1091-6490

journal_volume

92

pub_type

杂志文章
  • Cloning and sequencing of parafusin, a calcium-dependent exocytosis-related phosphoglycoprotein.

    abstract::A cDNA for parafusin, an evolutionarily conserved phosphoglycoprotein involved in exocytosis, has been cloned and sequenced from a unicellular eukaryote, Paramecium tetraurelia. A Paramecium cDNA library was screened with an oligonucleotide probe synthesized to an internal amino acid sequence of isolated parafusin. Th...

    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.91.21.9832

    authors: Subramanian SV,Wyroba E,Andersen AP,Satir BH

    更新日期:1994-10-11 00:00:00

  • Viral particles are required for infection in neurodegenerative Creutzfeldt-Jakob disease.

    abstract::Several models have been proposed for the infectious agents that cause human Creutzfeldt-Jakob disease (CJD) and sheep scrapie. Purified proteins and extracted nucleic acids are not infectious. To further identify the critical molecular components of the CJD agent, 120S infectious material with reduced prion protein (...

    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.92.11.5124

    authors: Manuelidis L,Sklaviadis T,Akowitz A,Fritch W

    更新日期:1995-05-23 00:00:00

  • Spreading of differentiating human monocytes is associated with a major increase in membrane-bound CDC42.

    abstract::In a search for a model cell system that might allow studies of the function of the Rho-related GTPase CDC42Hs in human cells, we measured the content and distribution of CDC42Hs in monocytes that were differentiating into macrophages. The total content of this protein increased 5- to 6-fold in phorbol ester-treated h...

    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.91.10.4263

    authors: Aepfelbacher M,Vauti F,Weber PC,Glomset JA

    更新日期:1994-05-10 00:00:00

  • Molecular analysis of chromosome 11 deletions in aniridia-Wilms tumor syndrome.

    abstract::We describe five individuals who have constitutional deletions of the short arm of one chromosome 11, including all or part of the band p13. All of these individuals suffer from aniridia; two have had a Wilms tumor removed. We have established lymphoblastoid cell lines from these and in three cases constructed somatic...

    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.82.24.8592

    authors: van Heyningen V,Boyd PA,Seawright A,Fletcher JM,Fantes JA,Buckton KE,Spowart G,Porteous DJ,Hill RE,Newton MS

    更新日期:1985-12-01 00:00:00

  • Thymic output in aged mice.

    abstract::Using GFP to mark recent thymic emigrants (RTEs) in mice carrying a GFP transgene driven by the recombination-activating gene 2 promoter, we demonstrate that RTEs are readily detectable even in 2-year-old mice, despite the fact that the proportion of the peripheral T cell pool comprised of RTEs declines with age. Alth...

    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.0601040103

    authors: Hale JS,Boursalian TE,Turk GL,Fink PJ

    更新日期:2006-05-30 00:00:00

  • Chloride uptake into cultured airway epithelial cells from cystic fibrosis patients and normal individuals.

    abstract::The chloride permeability of airway and sweat ductal epithelium of cystic fibrosis (CF) patients is decreased. This abnormality could represent an intrinsic characteristic of the epithelial cell or the response to a tonic extrinsic stimulus, in vivo. We cultured airway epithelial cells derived from CF and non-CF 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.82.19.6677

    authors: Stutts MJ,Cotton CU,Yankaskas JR,Cheng E,Knowles MR,Gatzy JT,Boucher RC

    更新日期:1985-10-01 00:00:00

  • Dynamic periplasmic chaperone reservoir facilitates biogenesis of outer membrane proteins.

    abstract::Outer membrane protein (OMP) biogenesis is critical to bacterial physiology because the cellular envelope is vital to bacterial pathogenesis and antibiotic resistance. The process of OMP biogenesis has been studied in vivo, and each of its components has been studied in isolation in vitro. This work integrates paramet...

    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.1601002113

    authors: Costello SM,Plummer AM,Fleming PJ,Fleming KG

    更新日期:2016-08-16 00:00:00

  • Effect of controlled adventitial heparin delivery on smooth muscle cell proliferation following endothelial injury.

    abstract::Continuous intravenous infusion of heparin suppresses smooth muscle cell proliferation in rats after endothelial injury but may lead to hemorrhage and other complications. The anticoagulant property has been removed from chemically modified heparin without loss of antiproliferative effect but use of such compounds is ...

    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.87.10.3773

    authors: Edelman ER,Adams DH,Karnovsky MJ

    更新日期:1990-05-01 00:00:00

  • Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus.

    abstract::The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from Thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits I and II. R...

    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.1107345109

    authors: Chang HY,Choi SK,Vakkasoglu AS,Chen Y,Hemp J,Fee JA,Gennis RB

    更新日期:2012-04-03 00:00:00

  • A phosphatidylinositol 3-kinase/Akt/mTOR pathway mediates and PTEN antagonizes tumor necrosis factor inhibition of insulin signaling through insulin receptor substrate-1.

    abstract::Tyrosine phosphorylation of insulin receptor substrate-1 (IRS-1) by the insulin receptor permits this docking protein to interact with signaling proteins that promote insulin action. Serine phosphorylation uncouples IRS-1 from the insulin receptor, thereby inhibiting its tyrosine phosphorylation and insulin signaling....

    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.051042298

    authors: Ozes ON,Akca H,Mayo LD,Gustin JA,Maehama T,Dixon JE,Donner DB

    更新日期:2001-04-10 00:00:00

  • Search for mutations affecting protein structure in children of atomic bomb survivors: preliminary report.

    abstract::A total of 289,868 locus tests, based on 28 different protein phenotypes and using one-dimensional electrophoresis to detect variant proteins, has yielded one probable mutation in the offspring of "proximally exposed" parents, who received an estimated average gonadal exposure of 31 to 39 rem in the atomic bombings of...

    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.77.7.4221

    authors: Neel JV,Satoh C,Hamilton HB,Otake M,Goriki K,Kageoka T,Fujita M,Neriishi S,Asakawa J

    更新日期:1980-07-01 00:00:00

  • Prior expectations induce prestimulus sensory templates.

    abstract::Perception can be described as a process of inference, integrating bottom-up sensory inputs and top-down expectations. However, it is unclear how this process is neurally implemented. It has been proposed that expectations lead to prestimulus baseline increases in sensory neurons tuned to the expected stimulus, which ...

    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.1705652114

    authors: Kok P,Mostert P,de Lange FP

    更新日期:2017-09-26 00:00:00

  • Cotranslational folding cooperativity of contiguous domains of α-spectrin.

    abstract::Proteins synthesized in the cell can begin to fold during translation before the entire polypeptide has been produced, which may be particularly relevant to the folding of multidomain proteins. Here, we study the cotranslational folding of adjacent domains from the cytoskeletal protein α-spectrin using force profile 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.1909683117

    authors: Kemp G,Nilsson OB,Tian P,Best RB,von Heijne G

    更新日期:2020-06-23 00:00:00

  • Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.

    abstract::Eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria. Hamiltonella defensa, an endosymbiont of aphids and other sap-feeding insects, protects its aphid host from attack by parasitoid wasps. Thus H. defensa is only conditionally beneficial to hosts, unlike ancient nutritional symbio...

    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.0900194106

    authors: Degnan PH,Yu Y,Sisneros N,Wing RA,Moran NA

    更新日期:2009-06-02 00:00:00

  • Directional selection is the primary cause of phenotypic diversification.

    abstract::Selection is widely accepted as the principal force shaping phenotypic variation within populations. Its importance in speciation and macroevolution has been questioned, however, because phenotypic differences between species or higher taxa sometimes appear to be nonadaptive. Here, we use the quantitative trait locus ...

    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.192360899

    authors: Rieseberg LH,Widmer A,Arntz AM,Burke JM

    更新日期:2002-09-17 00:00:00

  • An inherited p53 mutation that contributes in a tissue-specific manner to pediatric adrenal cortical carcinoma.

    abstract::The incidence of pediatric adrenal cortical carcinoma (ACC) in southern Brazil is 10-15 times higher than that of pediatric ACC worldwide. Because childhood ACC is associated with Li-Fraumeni syndrome, we examined the cancer history and p53 status of 36 Brazilian patients and their families. Remarkably, 35 of 36 patie...

    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.161479898

    authors: Ribeiro RC,Sandrini F,Figueiredo B,Zambetti GP,Michalkiewicz E,Lafferty AR,DeLacerda L,Rabin M,Cadwell C,Sampaio G,Cat I,Stratakis CA,Sandrini R

    更新日期:2001-07-31 00:00:00

  • Global human mandibular variation reflects differences in agricultural and hunter-gatherer subsistence strategies.

    abstract::Variation in the masticatory behavior of hunter-gatherer and agricultural populations is hypothesized to be one of the major forces affecting the form of the human mandible. However, this has yet to be analyzed at a global level. Here, the relationship between global mandibular shape variation and subsistence economy ...

    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.1113050108

    authors: von Cramon-Taubadel N

    更新日期:2011-12-06 00:00:00

  • Somatostatin: an endogenous peptide in the toad urinary bladder inhibits vasopressin-stimulated water flow.

    abstract::Somatostatin (somatotropin release-inhibiting factor; SRIF) is a tetradecapeptide present in brain, pancreas, gastrointestinal tract, and thyroid that inhibits the secretion or action of several hormones in these tissues. We observed that the toad urinary bladder contains concentrations of endogenous somatostatin (8.0...

    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.77.8.4984

    authors: Forrest JN Jr,Reichlin S,Goodman DB

    更新日期:1980-08-01 00:00:00

  • X-raying galaxies: a Chandra legacy.

    abstract::This presentation reviews Chandra's major contribution to the understanding of nearby galaxies. After a brief summary on significant advances in characterizing various types of discrete x-ray sources, the presentation focuses on the global hot gas in and around galaxies, especially normal ones like our own. The hot ga...

    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.0914255107

    authors: Wang QD

    更新日期:2010-04-20 00:00:00

  • Potential downside of high initial visual acuity.

    abstract::Children who are treated for congenital cataracts later exhibit impairments in configural face analysis. This has been explained in terms of a critical period for the acquisition of normal face processing. Here, we consider a more parsimonious account according to which deficits in configural analysis result from 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.1800901115

    authors: Vogelsang L,Gilad-Gutnick S,Ehrenberg E,Yonas A,Diamond S,Held R,Sinha P

    更新日期:2018-10-30 00:00:00

  • Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish.

    abstract::The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh...

    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.93.23.13036

    authors: Zardoya R,Abouheif E,Meyer A

    更新日期:1996-11-12 00:00:00

  • Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer.

    abstract::The Escherichia coli RuvA and RuvB protein complex promotes branch migration of Holliday junctions during recombinational repair and homologous recombination and at stalled replication forks. The RuvB protein belongs to the AAA(+) (ATPase associated with various cellular activities) ATPase family and forms a hexameric...

    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.0403584101

    authors: Hishida T,Han YW,Fujimoto S,Iwasaki H,Shinagawa H

    更新日期:2004-06-29 00:00:00

  • Kidney-specific inactivation of the KIF3A subunit of kinesin-II inhibits renal ciliogenesis and produces polycystic kidney disease.

    abstract::Polycystic kidney disease (PKD) is the most common genetic cause of renal failure in humans. Several proteins that are encoded by genes associated with PKD have recently been identified in primary cilia in renal tubular epithelia. These findings have suggested that abnormalities in cilia formation and function may pla...

    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.0836980100

    authors: Lin F,Hiesberger T,Cordes K,Sinclair AM,Goldstein LS,Somlo S,Igarashi P

    更新日期:2003-04-29 00:00:00

  • Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine.

    abstract::DNA containing 5-azacytosine (azaC) has previously been shown to be a potent inhibitor of DNA-cytosine methyltransferases. In this report, we describe experiments which demonstrate that azaC-DNA forms a covalent complex with Hpa II methylase, a bacterial enzyme that methylates the internal C of C-C-G-G sequences. 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.81.22.6993

    authors: Santi DV,Norment A,Garrett CE

    更新日期:1984-11-01 00:00:00

  • A rodent model for Wilms tumors: embryonal kidney neoplasms induced by N-nitroso-N'-methylurea.

    abstract::Embryonal kidney cell tumors develop in rats given the alkylating agent N-nitroso-N'-methylurea as neonates. These tumors resemble the childhood Wilms tumors in their histopathology. Deletions and mutations in the Wilms tumor suppressor gene, WT1, are present in up to 6% of childhood nephroblastomas. To investigate th...

    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.91.21.9931

    authors: Sharma PM,Bowman M,Yu BF,Sukumar S

    更新日期:1994-10-11 00:00:00

  • High-pressure transformations in xenon hydrates.

    abstract::A high-pressure investigation of the Xe*H(2)O chemical system was conducted by using diamond-anvil cell techniques combined with in situ Raman spectroscopy, synchrotron x-ray diffraction, and laser heating. Structure I xenon clathrate was observed to be stable up to 1.8 GPa, at which pressure it transforms to a new Xe...

    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.221602698

    authors: Sanloup C,Mao Hk HK,Hemley RJ

    更新日期:2002-01-08 00:00:00

  • Stimulus repetition modulates gamma-band synchronization in primate visual cortex.

    abstract::When a sensory stimulus repeats, neuronal firing rate and functional MRI blood oxygen level-dependent responses typically decline, yet perception and behavioral performance either stay constant or improve. An additional aspect of neuronal activity is neuronal synchronization, which can enhance the impact of neurons on...

    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.1309714111

    authors: Brunet NM,Bosman CA,Vinck M,Roberts M,Oostenveld R,Desimone R,De Weerd P,Fries P

    更新日期:2014-03-04 00:00:00

  • Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation.

    abstract::The mechanisms ensuring balanced growth remain a critical question in developmental biology. In plants, this balance relies on spatiotemporal integration of hormonal signaling pathways, but the understanding of the precise contribution of each hormone is just beginning to take form. Brassinosteroid (BR) hormone is sho...

    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.1417947112

    authors: Vragović K,Sela A,Friedlander-Shani L,Fridman Y,Hacham Y,Holland N,Bartom E,Mockler TC,Savaldi-Goldstein S

    更新日期:2015-01-20 00:00:00

  • Mitogen-activated protein kinase kinase 3 is a pivotal pathway regulating p38 activation in inflammatory arthritis.

    abstract::p38 mitogen-activated protein kinase (MAPK) regulates cytokines in arthritis and is, in turn, regulated by MAPK kinase (MKK) 3 and MKK6. To modulate p38 function but potentially minimize toxicity, we evaluated the utility of targeting MKK3 by using MKK3(-/-) mice. These studies showed that TNF-alpha increased phosphor...

    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.0509188103

    authors: Inoue T,Boyle DL,Corr M,Hammaker D,Davis RJ,Flavell RA,Firestein GS

    更新日期:2006-04-04 00:00:00

  • Solar thermal desalination as a nonlinear optical process.

    abstract::The ever-increasing global need for potable water requires practical, sustainable approaches for purifying abundant alternative sources such as seawater, high-salinity processed water, or underground reservoirs. Evaporation-based solutions are of particular interest for treating high salinity water, since conventional...

    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.1905311116

    authors: Dongare PD,Alabastri A,Neumann O,Nordlander P,Halas NJ

    更新日期:2019-07-02 00:00:00