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Sample records for acid-catalyzed bamberger rearrangement

  1. 75 FR 65226 - Establishment of Class E Airspace; Bamberg, SC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-22

    ... Register a notice of proposed rulemaking to establish Class E airspace at Bamberg, SC (75 FR 52654) Docket... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; Bamberg, SC AGENCY... establishes Class E airspace at Bamberg, SC. Lists of Subjects in 14 CFR Part 71 Airspace, Incorporation...

  2. Rearrangements of Cycloalkenyl Aryl Ethers.

    PubMed

    Törincsi, Mercedesz; Nagy, Melinda; Bihari, Tamás; Stirling, András; Kolonits, Pál; Novak, Lajos

    2016-01-01

    Rearrangement reactions of cycloalkenyl phenol and naphthyl ethers and the acid-catalyzed cyclization of the resulting product were investigated. Claisen rearrangement afforded 2-substituted phenol and naphthol derivatives. Combined Claisen and Cope rearrangement resulted in the formation of 4-substituted phenol and naphthol derivatives. In the case of cycloocthylphenyl ether the consecutive Claisen and Cope rearrangements were followed by an alkyl migration. The mechanism of this novel rearrangement reaction is also discussed. PMID:27104504

  3. 75 FR 57216 - Proposed Establishment of Class E Airspace; Bamberg, SC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-20

    ... Federal Aviation Administration 14 CFR Part 71 Proposed Establishment of Class E Airspace; Bamberg, SC...: This action proposes to establish Class E Airspace at Bamberg, SC, to accommodate the additional... Federal Regulations (14 CFR) part 71 to establish Class E airspace at Bamberg, SC to provide...

  4. 75 FR 52654 - Proposed Establishment of Class E Airspace; Bamberg, SC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-27

    ... Federal Aviation Administration 14 CFR Part 71 Proposed Establishment of Class E Airspace; Bamberg, SC...: This action proposes to establish Class E Airspace at Bamberg, SC, to accommodate the additional... Federal Regulations (14 CFR) part 71 to establish Class E airspace at Bamberg, SC to provide...

  5. Acid-catalyzed heterogeneous reaction of 3-methyl-2-buten-1-ol with hydrogen peroxide.

    PubMed

    Liu, Qifan; Wang, Weigang; Ge, Maofa

    2015-05-01

    Acid-catalyzed heterogeneous oxidation with hydrogen peroxide (H2O2) has been suggested to be a potential pathway for secondary organic aerosol (SOA) formation from isoprene and its oxidation products. However, knowledge of the chemical mechanism and kinetics for this process is still incomplete. 3-Methyl-2-buten-1-ol (MBO321), an aliphatic alcohol structurally similar to isoprene, is emitted by pine forests and widely used in the manufacturing industries. Herein the uptake of MBO321 into H2SO4-H2O2 mixed solution was investigated using a flow-tube reactor coupled to a mass spectrometer. The reactive uptake coefficients (γ) were acquired for the first time and were found to increase rapidly with increasing acid concentration. Corresponding aqueous-phase reactions were performed to further study the mechanism of this acid-catalyzed reaction. MBO321 could convert to 2-methyl-3-buten-2-ol (MBO232) and yield isoprene in acidic media. Organic hydroperoxides (ROOHs) were found to be generated through the acid-catalyzed route, which could undergo a rearrangement reaction and result in the formation of acetone and acetaldehyde. Organosulfates, which have been proposed to be SOA tracer compounds in the atmosphere, were also produced during the oxidation process. These results suggest that the heterogeneous acid-catalyzed reaction of MBO321 with H2O2 may contribute to SOA mass under certain atmospheric conditions.

  6. Acid-Catalyzed Isomerization of Carvone to Carvacrol

    ERIC Educational Resources Information Center

    Kjonaas, Richard A.; Mattingly, Shawn P.

    2005-01-01

    The acid-catalyzed isomerization of carvone to carvacrol, first reported by Ritter and Ginsburg, is especially well suited with a permanent-magnet FT instrument. The acid-catalyzed isomerization of carvone to carvacrol produced a 61% yield after a three hour reflux with 30% aqueous sulfuric acid.

  7. The Optical Transient Search in the Bamberg Plate Archive

    NASA Astrophysics Data System (ADS)

    Hudec, René; Kopel, Fabian; Krapp, Pedro; Heber, Ulrich; Cayé, Walter

    2011-08-01

    A substantial fraction of gamma-ray bursts is related to objects emitting temporarily optical light, i.e. optical afterglows and optical transients. So far, these phenomena (optical transients) were detected only after related gamma-ray satellite detection. However, taking into account their optical magnitudes at maximum light, these objects should be detectable in various historical and recent optical surveys, including photographic sky patrol. Here we report on an extended study based on blink-comparison of 5004 Bamberg Observatory Southern Sky Patrol Plates performed within a student project (Jugend Forscht).

  8. Boric acid catalyzed chemoselective esterification of alpha-hydroxycarboxylic acids.

    PubMed

    Houston, Todd A; Wilkinson, Brendan L; Blanchfield, Joanne T

    2004-03-01

    Boric acid catalyzes the selective esterification of alpha-hydroxycarboxylic acids without causing significant esterification to occur with other carboxylic acids. The procedure is simple, high-yielding, and applicable to the esterification of alpha-hydroxy carboxylates in the presence of other carboxylic acids including beta-hydroxyacids within the same molecule. [reaction: see text

  9. Acid-catalyzed dehydrogenation of amine-boranes

    DOEpatents

    Stephens, Frances Helen; Baker, Ralph Thomas

    2010-01-12

    A method of dehydrogenating an amine-borane using an acid-catalyzed reaction. The method generates hydrogen and produces a solid polymeric [R.sup.1R.sup.2B--NR.sup.3R.sup.4].sub.n product. The method of dehydrogenating amine-boranes may be used to generate H.sub.2 for portable power sources.

  10. Reactivity of Cations and Zwitterions Formed in Photochemical and Acid-Catalyzed Reactions from m-Hydroxycycloalkyl-Substituted Phenol Derivatives.

    PubMed

    Cindro, Nikola; Antol, Ivana; Mlinarić-Majerski, Kata; Halasz, Ivan; Wan, Peter; Basarić, Nikola

    2015-12-18

    Three m-substituted phenol derivatives, each with a labile benzylic alcohol group and bearing either protoadamantyl 4, homoadamantyl 5, or a cyclohexyl group 6, were synthesized and their thermal acid-catalyzed and photochemical solvolytic reactivity studied, using preparative irradiations, fluorescence measurements, nanosecond laser flash photolysis, and quantum chemical calculations. The choice of m-hydroxy-substitution was driven by the potential for these phenolic systems to generate m-quinone methides on photolysis, which could ultimately drive the excited-state pathway, as opposed to forming simple benzylic carbocations in the corresponding thermal route. Indeed, thermal acid-catalyzed reactions gave the corresponding cations, which undergo rearrangement and elimination from 4, only elimination from 5, and substitution and elimination from 6. On the other hand, upon photoexcitation of 4-6 to S1 in a polar protic solvent, proton dissociation from the phenol, coupled with elimination of the benzylic OH (as hydroxide ion) gave zwitterions (formal m-quinone methides). The zwitterions exhibit reactivity different from the corresponding cations due to a difference in charge distribution, as shown by DFT calculations. Thus, protoadamantyl zwitterion has a less nonclassical character than the corresponding cation, so it does not undergo 1,2-shift of the carbon atom, as observed in the acid-catalyzed reaction. PMID:26595342

  11. BAMBERGER REARRANGEMENT DURING TNT-METABOLISM BY CLOSTRIDIUM ACETORBUTYLICUM. (R825513C006)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  12. Methods of Comparative Androgogy: An International Expert Seminar (Bamberg, Germany, September 24-27, 1995).

    ERIC Educational Resources Information Center

    Charters, Margaret A.

    A seminar collected, shared, and discussed the consensus on definitions, standards, methods, and current problems in research methodology in comparative andragogy. Alfred Hierold opened the seminar with a brief history of the evolution of the University of Bamberg. The opening session focused on the importance of the researcher as a tool in…

  13. Solvent effects in acid-catalyzed biomass conversion reactions.

    PubMed

    Mellmer, Max A; Sener, Canan; Gallo, Jean Marcel R; Luterbacher, Jeremy S; Alonso, David Martin; Dumesic, James A

    2014-10-27

    Reaction kinetics were studied to quantify the effects of polar aprotic organic solvents on the acid-catalyzed conversion of xylose into furfural. A solvent of particular importance is γ-valerolactone (GVL), which leads to significant increases in reaction rates compared to water in addition to increased product selectivity. GVL has similar effects on the kinetics for the dehydration of 1,2-propanediol to propanal and for the hydrolysis of cellobiose to glucose. Based on results obtained for homogeneous Brønsted acid catalysts that span a range of pKa values, we suggest that an aprotic organic solvent affects the reaction kinetics by changing the stabilization of the acidic proton relative to the protonated transition state. This same behavior is displayed by strong solid Brønsted acid catalysts, such as H-mordenite and H-beta. PMID:25214063

  14. Photometric Study of the FU Orionis Object BBW 76 from the Bamberg Observatory Southern Sky Survey

    NASA Astrophysics Data System (ADS)

    Borisova, A.; Tsvetkova, K. P.; Tsvetkov, M. K.

    2006-04-01

    The Bamberg Observatory Southern Sky Survey provided 93 photographic plates with the FU Orionis object BBW 76, clearly detectable in the time interval 1963-1976. We perform aperture photometry of BBW 76 from the 2 x 2 degrees area near target star scanned with the Epson Expression 1640 XL flatbed scanner. For each plate a transformation of plate magnitude to the GSC 2.2 magnitudes in B photographic band was found out for selected reference stars, and used for deriving B magnitudes of BBW 76. The analysis of the photometric behaviour of BBW 76 is presented.

  15. Lewis Acid-Catalyzed Indole Synthesis via Intramolecular Nucleophilic Attack of Phenyldiazoacetates to Iminium Ions

    PubMed Central

    Zhou, Lei; Doyle, Michael P.

    2009-01-01

    Lewis acids catalyze the cyclization of methyl phenyldiazoacetates with an ortho-imino group, prepared from o-aminophenylacetic acid, to give 2,3-substituted indoles in quantitative yields. PMID:19904905

  16. Wagner–Meerwein-Type Rearrangements of Germapolysilanes - A Stable Ion Study

    PubMed Central

    2015-01-01

    The rearrangement of tris(trimethylsilyl)silyltrimethylgermane 1 to give tetrakis(trimethylsilyl)germane 2 was investigated as a typical example for Lewis acid catalyzed Wagner–Meerwein-type rearrangements of polysilanes and polygermasilanes. Direct 29Si NMR spectroscopic evidence is provided for several cationic intermediates during the reaction. The identity of these species was verified by independent synthesis and NMR characterization, and their transformation was followed by NMR spectroscopy. PMID:26294805

  17. Isoprene Epoxydiols as Precursors to Secondary Organic Aerosol Formation: Acid-Catalyzed Reactive Uptake Studies with Authentic Compounds

    PubMed Central

    Lin, Ying-Hsuan; Zhang, Zhenfa; Docherty, Kenneth S.; Zhang, Haofei; Budisulistiorini, Sri Hapsari; Rubitschun, Caitlin L.; Shaw, Stephanie L.; Knipping, Eladio M.; Edgerton, Eric S.; Kleindienst, Tadeusz E.; Gold, Avram; Surratt, Jason D.

    2011-01-01

    Isoprene epoxydiols (IEPOX), formed from the photooxidation of isoprene under low-NOx conditions, have recently been proposed as precursors of secondary organic aerosol (SOA) on the basis of mass spectrometric evidence. In the present study, IEPOX isomers were synthesized in high purity (> 99%) to investigate their potential to form SOA via reactive uptake in a series of controlled dark chamber studies followed by reaction product analyses. IEPOX-derived SOA was substantially observed only in the presence of acidic aerosols, with conservative lower-bound yields of 4.7–6.4% for β-IEPOX and 3.4–5.5% for δ-IEPOX, providing direct evidence for IEPOX isomers as precursors to isoprene SOA. These chamber studies demonstrate that IEPOX uptake explains the formation of known isoprene SOA tracers found in ambient aerosols, including 2-methyltetrols, C5-alkene triols, dimers, and IEPOX-derived organosulfates. Additionally, we show reactive uptake on the acidified sulfate aerosols supports a previously unreported acid-catalyzed intramolecular rearrangement of IEPOX to cis- and trans-3-methyltetrahydrofuran-3,4-diols (3-MeTHF-3,4-diols) in the particle phase. Analysis of these novel tracer compounds by aerosol mass spectrometry (AMS) suggests that they contribute to a unique factor resolved from positive matrix factorization (PMF) of AMS organic aerosol spectra collected from low-NOx, isoprene-dominated regions influenced by the presence of acidic aerosols. PMID:22103348

  18. Computational and experimental investigations of the formal dyotropic rearrangements of Himbert arene/allene cycloadducts.

    PubMed

    Pham, Hung V; Karns, Alexander S; Vanderwal, Christopher D; Houk, K N

    2015-06-01

    The fascinating intramolecular arene/allene cycloaddition discovered by Himbert affords dearomatized, polycyclic intermediates with sufficient strain energy to drive rearrangement processes of the newly formed ring system. We disclose a detailed examination of a thermally induced stepwise dyotropic skeletal rearrangement of these cycloadducts, a reaction also first described by Himbert. We offer computational evidence for a two-stage mechanism for this formal dyotropic rearrangement and provide rationalizations for the significant substitution-dependent rate differences observed in experiments. These investigations led to the development of a Lewis-acid-catalyzed rearrangement of precursors that were unreactive under simple thermal instigation. The isolation of the product of an "interrupted" rearrangement under Lewis acidic conditions provides further support for the proposed stepwise mechanism. Computational results also matched experiments in terms of regiochemical preferences in unsymmetrical rearrangement precursors and explained why lactam O-, S-, and C-heterologues do not easily undergo this rearrangement.

  19. Acid-Catalyzed Preparation of Biodiesel from Waste Vegetable Oil: An Experiment for the Undergraduate Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Bladt, Don; Murray, Steve; Gitch, Brittany; Trout, Haylee; Liberko, Charles

    2011-01-01

    This undergraduate organic laboratory exercise involves the sulfuric acid-catalyzed conversion of waste vegetable oil into biodiesel. The acid-catalyzed method, although inherently slower than the base-catalyzed methods, does not suffer from the loss of product or the creation of emulsion producing soap that plagues the base-catalyzed methods when…

  20. Optimizing the Acid Catalyzed Synthesis of Hyperbranched Poly(Glycerol-diacids) Oligomers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oligomeric pre-polymers were synthesized by the acid-catalyzed condensation of glycerol with succinic acid, glutaric acid and azelaic acid in dimethylsulfoxide (DMSO) or dimethylformamide (DMF). The prepolymers were obtained, on average in 84% yield, and were characterized by proton NMR, MALDI-TOF ...

  1. Brønsted acid-catalyzed Nazarov cyclization of pyrrole derivatives accelerated by microwave irradiation.

    PubMed

    Bachu, Prabhakar; Akiyama, Takahiko

    2009-07-15

    The Brønsted acid-catalyzed Nazarov cyclization of pyrrole derivatives was developed. Microwave irradiation accelerated the Nazarov cyclization significantly at 40 degrees C to give cyclopenta[b]pyrrole derivatives in excellent yields with high trans selectivity. PMID:19447615

  2. 4-Dimenthylaminopyridine or Acid-Catalyzed Synthesis of Esters: A Comparison

    ERIC Educational Resources Information Center

    van den Berg, Annemieke W. C.; Hanefeld, Ulf

    2006-01-01

    A set of highly atom-economic experiments was developed to highlight the differences between acid- and base-catalyzed ester syntheses and to introduce the principles of atom economy. The hydrochloric acid-catalyzed formation of an ester was compared with the 4-dimethylaminopyradine-catalyzed ester synthesis.

  3. Particle growth by acid-catalyzed heterogeneous reactions of organic carbonyls on preexisting aerosols.

    PubMed

    Jang, Myoseon; Carroll, Brian; Chandramouli, Bharadwaj; Kamens, Richard M

    2003-09-01

    Aerosol growth by the heterogeneous reactions of different aliphatic and alpha,beta-unsaturated carbonyls in the presence/absence of acidified seed aerosols was studied in a 2 m long flow reactor (2.5 cm i.d.) and a 0.5-m3 Teflon film bag under darkness. For the flow reactor experiments, 2,4-hexadienal, 5-methyl-3-hexen-2-one, 2-cyclohexenone, 3-methyl-2-cyclopentenone, 3-methyl-2-cyclohexenone, and octanal were studied. The carbonyls were selected based on their reactivity for acid-catalyzed reactions, their proton affinity, and their similarity to the ring-opening products from the atmospheric oxidation of aromatics. To facilitate acid-catalyzed heterogeneous hemiacetal/acetal formation, glycerol was injected along with inorganic seed aerosols into the flow reactor system. Carbonyl heterogeneous reactions were accelerated in the presence of acid catalysts (H2SO4), leading to higher aerosol yields than in their absence. Aldehydes were more reactive than ketones for acid-catalyzed reactions. The conjugated functionality also resulted in higher organic aerosol yieldsthan saturated aliphatic carbonyls because conjugation with the olefinic bond increases the basicity of the carbonyl leading to increased stability of the protonated carbonyl. Aerosol population was measured from a series of sampling ports along the length of the flow reactor using a scanning mobility particle sizer. Fourier transform infrared spectrometry of either an impacted liquid aerosol layer or direct reaction of carbonyls as a thin liquid layer on a zinc selenide FTIR disk was employed to demonstrate the direct transformation of chemical functional groups via the acid-catalyzed reactions. These results strongly indicate that atmospheric multifunctional organic carbonyls, which are created by atmospheric photooxidation reactions, can contribute significantly to secondary organic aerosol formation through acid-catalyzed heterogeneous reactions. Exploratory studies in 25- and 190-m3 outdoor chambers

  4. Brønsted Acid-Catalyzed Cascade Reactions Involving 1,2-Indole Migration.

    PubMed

    Álvarez, Estela; Nieto Faza, Olalla; Silva López, Carlos; Fernández-Rodríguez, Manuel A; Sanz, Roberto

    2015-09-01

    A cascade reaction of indoles with propargylic diols involving an unprecedented metal-free 1,2-indole migration onto an alkyne was carried out. DFT calculations support a mechanism consisting of a concerted nucleophilic attack of the indole nucleus with loss of water, followed by the 1,2-migration and subsequent Nazarov cyclization. This Brønsted acid-catalyzed protocol affords indole-functionalized benzofulvene derivatives in high yields. PMID:26211757

  5. On the Brønsted acid-catalyzed homogeneous hydrolysis of furans.

    PubMed

    Nikbin, Nima; Caratzoulas, Stavros; Vlachos, Dionisios G

    2013-11-01

    Furan affairs: Electronic structure calculations of the homogeneous Brønsted acid-catalyzed hydrolysis of 2,5-dimethylfuran show that proton transfer to the β-position is rate-limiting and provides support that the hydrolysis follows general acid catalysis. By means of projected Fukui indices, we show this to be the case for unsubstituted, 2-, and 2,5-substituted furans with electron-donating groups.

  6. Origins of Selectivity and General Model for Chiral Phosphoric Acid-Catalyzed Oxetane Desymmetrizations.

    PubMed

    Champagne, Pier Alexandre; Houk, K N

    2016-09-28

    The origins of the high enantioselectivity of chiral phosphoric acid-catalyzed oxetane desymmetrizations were investigated by density functional theory (DFT) calculations. Distortion of the catalyst structure, caused by steric crowding in the catalyst pocket of one enantiomeric transition state, is the main cause for stereochemical preference. A general model was developed to assist in the rational design of new catalysts for related transformations. PMID:27629045

  7. Acid-catalyzed autohydrolysis of wheat straw to improve sugar recovery.

    PubMed

    Ertas, Murat; Han, Qiang; Jameel, Hasan

    2014-10-01

    A comparison study of autohydrolysis and acid-catalyzed autohydrolysis of wheat straw was performed to understand the impact of acid addition on overall sugar recovery. Autohydrolysis combined with refining is capable of achieving sugar recoveries in the mid 70s. If the addition of a small amount of acid is capable of increasing the sugar recovery even higher it may be economically attractive. Acetic, sulfuric, hydrochloric and sulfurous acids were selected for acid-catalyzed autohydrolysis pretreatments. Autohydrolysis with no acid at 190 °C showed the highest total sugar in the prehydrolyzate. Enzymatic hydrolysis was performed for all the post-treated solids with and without refining at enzyme loadings of 4 and 10 FPU/g for 96 h. Acid-catalyzed autohydrolysis at 190 °C with sulfurous acid showed the highest total sugar recovery of 81.2% at 4 FPU/g enzyme charge compared with 64.3% at 190 °C autohydrolysis without acid.

  8. Synthesis of Fused Polycyclic Indoles by Brønsted Acid-Catalyzed Intramolecular Alkylation of Indoles with Alcohols.

    PubMed

    Suárez, Anisley; Gohain, Mukut; Fernández-Rodríguez, Manuel A; Sanz, Roberto

    2015-10-16

    An efficient methodology for the synthesis of a series of new fused polyclyclic indoles has been developed by Brønsted acid-catalyzed intramolecular Friedel-Crafts reactions of properly designed indolyl alcohols. PMID:26418556

  9. Eventorientierte Veranstaltungen und Lebensqualität innenstädtischer Wohnbevölkerung - Das Beispiel Bamberg

    NASA Astrophysics Data System (ADS)

    Redepenning, Marc; Rhein, Niklas; Sauerwald, David

    2016-09-01

    Events do have, in addition to economic effects, impact on the quality of life of the affected population. Using a case study from the city of Bamberg this article addresses the subjective contentment with larger events. The results show variation in the range of contentment depending on age and time of residency in the city. Furthermore, it becomes obvious that the particular expectation on "life in the inner city" shapes the contentment. Cities should pay attention to this social heterogeneity when deploying strategies of revitalisation through festivals and events. They should take it seriously by using tools of collaborative planning to preserve the multi-functionality of inner cities.

  10. Mechanism of the Fischer reaction. Effect of electronic factors on the kinetics of the rearrangement of m-substituted cyclohexanone arylhydrazones to tetrahydrocarbazoles

    SciTech Connect

    Przheval'skii, N.M.; Kostromina, L.Yu.; Grandberg, I.I.

    1986-03-01

    The kinetics of the thermal and acid-catalyzed Fischer indolization of m-substituted cyclohexanone arylhydrazones were studied. It was shown that substituents with different natures (-CH/sub 3/, -Cl) and the polarity of the solvent have little effect on the rate of the rearrangement. The results obtained were interpreted within the framework of the concerted mechanism for the formation of the carbon-carbon bond ((3,3)-sigmatropic rearrangement).

  11. Lewis Acid Catalyzed Selective Reactions of Donor-Acceptor Cyclopropanes with 2-Naphthols.

    PubMed

    Kaicharla, Trinadh; Roy, Tony; Thangaraj, Manikandan; Gonnade, Rajesh G; Biju, Akkattu T

    2016-08-16

    Lewis acid-catalyzed reactions of 2-substituted cyclopropane 1,1-dicarboxylates with 2-naphthols is reported. The reaction exhibits tunable selectivity depending on the nature of Lewis acid employed and proceed as a dearomatization/rearomatization sequence. With Bi(OTf)3 as the Lewis acid, a highly selective dehydrative [3+2] cyclopentannulation takes place leading to the formation of naphthalene-fused cyclopentanes. Interestingly, engaging Sc(OTf)3 as the Lewis acid, a Friedel-Crafts-type addition of 2-naphthols to cyclopropanes takes place, thus affording functionalized 2-naphthols. Both reactions furnished the target products in high regioselectivity and moderate to high yields. PMID:27391792

  12. Approach to Merosesquiterpenes via Lewis Acid Catalyzed Nazarov-Type Cyclization: Total Synthesis of Akaol A.

    PubMed

    Kakde, Badrinath N; Kumar, Nivesh; Mondal, Pradip Kumar; Bisai, Alakesh

    2016-04-15

    A Lewis acid catalyzed Nazarov-type cyclization of arylvinylcarbinol has been developed for the asymmetric synthesis of carbotetracyclic core of merosesquiterpenes. The reaction works only in the presence of 2 mol % of Sn(OTf)2 and Bi(OTf)3 in dichloroethane under elevated temperature. The methodology offers the synthesis of a variety of enantioenriched arylvinylcarbinols from commercially available (3aR)-sclareolide 9 in six steps with an eventual concise total synthesis of marine sesquiterpene quinol, akaol A (1a). PMID:27028314

  13. Sulfuric, hydrochloric, and nitric acid-catalyzed triacetone triperoxide (TATP) reaction mixtures: an aging study.

    PubMed

    Fitzgerald, Mark; Bilusich, Daniel

    2011-09-01

    The organic peroxide explosive triacetone triperoxide (TATP) is regularly encountered by law enforcement agents in various stages of its production. This study utilizes solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS) to examine sulfuric acid-, hydrochloric acid-, and nitric acid-catalyzed TATP syntheses during the initial 24 h of these reactions at low temperatures (5-9°C). Additionally, aging of the reaction mixtures was examined at both low and ambient temperatures (19-21°C) for a further 9 days. For each experiment, TATP could be readily identified in the headspace above the reaction mixture 1 h subsequent to the combination of reagents; at 24 h, TATP and diacetone diperoxide (DADP) were prominent. TATP degraded more rapidly than DADP. Additionally, chlorinated acetones chloroacetone and 1,1,-dichloroacetone were identified in the headspace above the hydrochloric acid-catalyzed TATP reaction mixture. These were not present when the catalyst was sulfuric acid or nitric acid. PMID:21595692

  14. Acid-catalyzed hot-water extraction of lipids from Chlorella vulgaris.

    PubMed

    Park, Ji-Yeon; Oh, You-Kwan; Lee, Jin-Suk; Lee, Kyubock; Jeong, Min-Ji; Choi, Sun-A

    2014-02-01

    Acid-catalyzed hot-water treatment for efficient extraction of lipids from a wet microalga, Chlorella vulgaris, was investigated. For an initial fatty acids content of 381.6mg/g cell, the extracted-lipid yield with no heating and no catalyst was 83.2mg/g cell. Under a 1% H2SO4 concentration heated at 120°C for 60min, however, the lipid-extraction yield was 337.4mg/g cell. The fatty acids content, meanwhile, was 935mg fatty acid/g lipid. According to the severity index formula, 337.5mg/g cell of yield under the 1% H2SO4 concentration heated at 150°C for 8min, and 334.2mg/g cell of yield under the 0.5% H2SO4 concentration heated at 150°C for 16min, were obtained. The lipids extracted by acid-catalyzed hot-water treatment were converted to biodiesel. The biodiesel's fatty acid methyl ester (FAME) content after esterification of the microalgal lipids was increased to 79.2% by the addition of excess methanol and sulfuric acid.

  15. Integrated Production of Xylonic Acid and Bioethanol from Acid-Catalyzed Steam-Exploded Corn Stover.

    PubMed

    Zhu, Junjun; Rong, Yayun; Yang, Jinlong; Zhou, Xin; Xu, Yong; Zhang, Lingling; Chen, Jiahui; Yong, Qiang; Yu, Shiyuan

    2015-07-01

    High-efficiency xylose utilization is one of the restrictive factors of bioethanol industrialization. However, xylonic acid (XA) as a new bio-based platform chemical can be produced by oxidation of xylose with microbial. So, an applicable technology of XA bioconversion was integrated into the process of bioethanol production. After corn stover was pretreated with acid-catalyzed steam-explosion, solid and liquid fractions were obtained. The liquid fraction, also named as acid-catalyzed steam-exploded corn stover (ASC) prehydrolyzate (mainly containing xylose), was catalyzed with Gluconobacter oxydans NL71 to prepare XA. After 72 h of bioconversion of concentrated ASC prehydrolyzate (containing 55.0 g/L of xylose), the XA concentration reached a peak value of 54.97 g/L, the sugar utilization ratio and XA yield were 94.08 and 95.45 %, respectively. The solid fraction was hydrolyzed to produce glucose with cellulase and then fermented with Saccharomyces cerevisiae NL22 to produce ethanol. After 18 h of fermentation of concentrated enzymatic hydrolyzate (containing 86.22 g/L of glucose), the ethanol concentration reached its highest value of 41.48 g/L, the sugar utilization ratio and ethanol yield were 98.72 and 95.25 %, respectively. The mass balance showed that 1 t ethanol and 1.3 t XA were produced from 7.8 t oven dry corn stover.

  16. Mechanisms and energetics for acid catalyzed β-D-glucose conversion to 5-hydroxymethylfurfurl.

    PubMed

    Qian, Xianghong

    2011-10-27

    Car-Parrinello based ab initio molecular dynamics (CPMD) coupled with metadynamics (MTD) simulations were carried out to investigate the mechanism and energetics for acid-catalyzed β-d-glucose conversion to 5-hydroxymethylfurfurl (HMF) in water. HMF is a critical intermediate for biomass conversion to biofuels. It was found that protonation of the C2-OH on glucose, the breakage of the C2-O2 bond, and the formation of the C2-O5 bond is the critical rate-limiting step for the direct glucose conversion to HMF without converting to fructose first, contrary to the wide-spread assumption in literature that fructose is the main intermediate for glucose conversion to HMF. The calculated reaction barrier of 30-35 kcal/mol appears to be solvent-induced and is in excellent agreement with experimental observations. PMID:21916465

  17. Solid acid-catalyzed depolymerization of barley straw driven by ball milling.

    PubMed

    Schneider, Laura; Haverinen, Jasmiina; Jaakkola, Mari; Lassi, Ulla

    2016-04-01

    This study describes a time and energy saving, solvent-free procedure for the conversion of lignocellulosic barley straw into reducing sugars by mechanocatalytical pretreatment. The catalytic conversion efficiency of several solid acids was tested which revealed oxalic acid dihydrate as a potential catalyst with high conversion rate. Samples were mechanically treated by ball milling and subsequently hydrolyzed at different temperatures. The parameters of the mechanical treatment were optimized in order to obtain sufficient amount of total reducing sugar (TRS) which was determined following the DNS assay. Additionally, capillary electrophoresis (CE) and Fourier transform infrared spectrometry (FT-IR) were carried out. Under optimal conditions TRS 42% was released using oxalic acid dihydrate as a catalyst. This study revealed that the acid strength plays an important role in the depolymerization of barley straw and in addition, showed, that the oxalic acid-catalyzed reaction generates low level of the degradation product 5-hydroxymethylfurfural (HMF). PMID:26859328

  18. Efficient Acid-catalyzed 18F/19F Fluoride Exchange of BODIPY Dyes

    PubMed Central

    Keliher, Edmund J.; Klubnick, Jenna A.; Reiner, Thomas; Mazitschek, Ralph

    2014-01-01

    Fluorine containing fluorochromes represent important validation agents for PET imaging agents as they can be easily rapidly validated in cells by fluorescence imaging. In particular, the 18F-labeled BODIPY-FL fluorophore has emerged as an important platform but little is known about alternative 18F-labeling strategies or labeling on red shifted fluorophores. Here we explore the acid-catalyzed 18F/19F exchange on a range of commercially available N-hydroxysuccinimidyl ester and maleimide BODIPY fluorophores. We show this method to be a simple and efficient 18F-labeling strategy for a diverse span of fluorescent compounds, including a BODIPY modified PARP-1 inhibitor, and amine- and thiol-reactive BODIPY fluorophores. PMID:24596307

  19. Lewis Acid Catalyzed Regiospecific Cross-Dehydrative Coupling Reaction of 2-Furylcarbinols with β-Keto Amides or 4-Hydroxycoumarins: A Route to Furyl Enols.

    PubMed

    Miao, Maozhong; Luo, Yi; Li, Hongli; Xu, Xin; Chen, Zhengkai; Xu, Jianfeng; Ren, Hongjun

    2016-06-17

    Lewis acid catalyzed directly dehydrative carbon-carbon bond formation reaction of 2-furylcarbinols with β-keto amides provides a straightforward method for regioselective synthesis of (Z)-furyl enols. Moreover, this Lewis acid catalyzed cross-coupling reaction can be extended to an interesting heterocyclic version featuring a functionalized 3-furyl-4-hydroxycoumarin synthesis. PMID:27224045

  20. Acid-catalyzed hydrothermal severity on the fractionation of agricultural residues for xylose-rich hydrolyzates.

    PubMed

    Lee, Ji Ye; Ryu, Hyun Jin; Oh, Kyeong Keun

    2013-03-01

    The objective of this work was to investigate the feasibility of acid-catalyzed hydrothermal fractionation for maximum solubilization of the hemicellulosic portion of three agricultural residues. The fractionation conditions converted into combined severity factor (CS) in the range of 1.2-2.9. The highest hemicellulose yield of 87.88% was achieved when barley straw was fractionated at a CS of 2.19. However, the maximum glucose release of 15.29% was achieved for the case of rice straw. The maximum productions of various by-products were observed with the fractionation of rape straw: 0.88 g/L of 5-hydroxymethylfurfural (5-HMF), 2.16 g/L of furfural, 0.44 g/L of levulinic acid, 1.59 g/L of formic acid, and 3.06 g/L of acetic acid. The highest selectivities, a criterion for evaluating the fractionation of 21.55 for fractionated solid and 7.48 for liquid hydrolyzate were obtained from barley straw.

  1. Three competitive transition states at the glycosidic bond of sucrose in its acid-catalyzed hydrolysis.

    PubMed

    Yamabe, Shinichi; Guan, Wei; Sakaki, Shigeyoshi

    2013-03-15

    The acid-catalyzed hydrolysis of sucrose to glucose and fructose was investigated by DFT calculations. Protonations to three ether oxygen atoms of the sucrose molecule, A, B, and (C, D), were compared. Three (B, the fructosyl-ring oxygen protonation; C, protonation to the bridge oxygen of the glycosidic bond for the glucosyl-oxygen cleavage; and D, protonation to that for the fructosyl-oxygen cleavage) gave the fragmentation. Paths B, C, and D were examined by the use of the sucrose molecule and H3O(+)(H2O)13. The path B needs a large activation energy, indicating that it is unlikely. The fragmentation transition state (TS1) of path C needs almost the same activation energy as that of path D. The isomerization TS of Int(C) → Int(D), TS(C → D), was also obtained as a bypass route. The present calculations showed that the path via the fructosyl-oxygen cleavage (D) is slightly (not absolutely) more favorable than that via the glucosyl-oxygen cleavage (C). PMID:23373870

  2. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zahn, Dirk

    2004-05-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C⋯O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate.

  3. Computational Mechanistic Studies of Acid-Catalyzed Lignin Model Dimers for Lignin Depolymerization

    SciTech Connect

    Kim, S.; Sturgeon, M. R.; Chmely, S. C.; Paton, R. S.; Beckham, G. T.

    2013-01-01

    Lignin is a heterogeneous alkyl-aromatic polymer that constitutes up to 30% of plant cell walls, and is used for water transport, structure, and defense. The highly irregular and heterogeneous structure of lignin presents a major obstacle in the development of strategies for its deconstruction and upgrading. Here we present mechanistic studies of the acid-catalyzed cleavage of lignin aryl-ether linkages, combining both experimental studies and quantum chemical calculations. Quantum mechanical calculations provide a detailed interpretation of reaction mechanisms including possible intermediates and transition states. Solvent effects on the hydrolysis reactions were incorporated through the use of a conductor-like polarizable continuum model (CPCM) and with cluster models including explicit water molecules in the first solvation shell. Reaction pathways were computed for four lignin model dimers including 2-phenoxy-phenylethanol (PPE), 1-(para-hydroxyphenyl)-2-phenoxy-ethanol (HPPE), 2-phenoxy-phenyl-1,3-propanediol (PPPD), and 1-(para-hydroxyphenyl)-2-phenoxy-1,3-propanediol (HPPPD). Lignin model dimers with a para-hydroxyphenyl ether (HPPE and HPPPD) show substantial differences in reactivity relative to the phenyl ether compound (PPE and PPPD) which have been clarified theoretically and experimentally. The significance of these results for acid deconstruction of lignin in plant cell walls will be discussed.

  4. Acid-catalyzed conversion of xylose, xylan and straw into furfural by microwave-assisted reaction.

    PubMed

    Yemiş, Oktay; Mazza, Giuseppe

    2011-08-01

    Furfural is a biomass derived-chemical that can be used to replace petrochemicals. In this study, the acid-catalyzed conversion of xylose and xylan to furfural by microwave-assisted reaction was investigated at selected ranges of temperature (140-190°C), time (1-30 min), substrate concentration (1:5-1:200 solid:liquid ratio), and pH (2-0.13). We found that a temperature of 180°C, a solid:liquid ratio of 1:200, a residence time of 20 min, and a pH of 1.12 gave the best furfural yields. The effect of different Brønsted acids on the conversion efficiency of xylose and xylan was also evaluated, with hydrochloric acid being found to be the most effective catalyst. The microwave-assisted process provides highly efficient conversion: furfural yields obtained from wheat straw, triticale straw, and flax shives were 48.4%, 45.7%, and 72.1%, respectively. PMID:21620690

  5. A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates

    SciTech Connect

    Netzel, D.A.

    1991-04-01

    Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center_dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

  6. A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates

    SciTech Connect

    Netzel, D.A.

    1991-04-01

    Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

  7. Potential of phosphoric acid-catalyzed pretreatment and subsequent enzymatic hydrolysis for biosugar production from Gracilaria verrucosa.

    PubMed

    Kwon, Oh-Min; Kim, Sung-Koo; Jeong, Gwi-Taek

    2016-07-01

    This study combined phosphoric acid-catalyzed pretreatment and enzymatic hydrolysis to produce biosugars from Gracilaria verrucosa as a potential renewable resource for bioenergy applications. We optimized phosphoric acid-catalyzed pretreatment conditions to 1:10 solid-to-liquid ratio, 1.5 % phosphoric acid, 140 °C, and 60 min reaction time, producing a 32.52 ± 0.06 % total reducing sugar (TRS) yield. By subsequent enzymatic hydrolysis, a 68.61 ± 0.90 % TRS yield was achieved. These results demonstrate the potential of phosphoric acid to produce biosugars for biofuel and biochemical production applications. PMID:27003825

  8. Potential of phosphoric acid-catalyzed pretreatment and subsequent enzymatic hydrolysis for biosugar production from Gracilaria verrucosa.

    PubMed

    Kwon, Oh-Min; Kim, Sung-Koo; Jeong, Gwi-Taek

    2016-07-01

    This study combined phosphoric acid-catalyzed pretreatment and enzymatic hydrolysis to produce biosugars from Gracilaria verrucosa as a potential renewable resource for bioenergy applications. We optimized phosphoric acid-catalyzed pretreatment conditions to 1:10 solid-to-liquid ratio, 1.5 % phosphoric acid, 140 °C, and 60 min reaction time, producing a 32.52 ± 0.06 % total reducing sugar (TRS) yield. By subsequent enzymatic hydrolysis, a 68.61 ± 0.90 % TRS yield was achieved. These results demonstrate the potential of phosphoric acid to produce biosugars for biofuel and biochemical production applications.

  9. Lewis acid catalyzed cascade reaction of 3-(2-benzenesulfonamide)propargylic alcohols to spiro[indene-benzosultam]s.

    PubMed

    Sun, Lang; Zhu, Yuanxun; Wang, Jing; Lu, Ping; Wang, Yanguang

    2015-01-16

    A highly efficient and convenient construction of the spiro[indene-benzosultam] skeleton from propargylic alcohols has been developed. The reaction proceeded in a Lewis acid catalyzed cascade process, including the trapping of allene carbocation with sulfonamide, electrophilic cyclization, and intramolecular Friedel-Crafts alkylation. In the presence of NIS or NBS, iodo/bromo-substituted spiro[indene-benzosultam]s could be prepared in excellent yields. PMID:25541815

  10. Mechanistic Investigation of Acid-Catalyzed Cleavage of Aryl-Ether Linkages: Implications for Lignin Depolymerization

    SciTech Connect

    Sturgeon, M. R.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2013-01-01

    Carbon-oxygen bonds are the primary inter-monomer linkages lignin polymers in plant cell walls, and as such, catalyst development to cleave these linkages is of paramount importance to deconstruct biomass to its constituent monomers for the production of renewable fuels and chemicals. For many decades, acid catalysis has been used to depolymerize lignin. Lignin is a primary component of plant cell walls, which is connected primarily by aryl-ether linkages, and the mechanism of its deconstruction by acid is not well understood, likely due to its heterogeneous and complex nature compared to cellulose. For effective biomass conversion strategies, utilization of lignin is of significant relevance and as such understanding the mechanisms of catalytic lignin deconstruction to constituent monomers and oligomers is of keen interest. Here, we present a comprehensive experimental and theoretical study of the acid catalysis of a range of dimeric species exhibiting the b-O-4 linkage, the most common inter-monomer linkage in lignin. We demonstrate that the presence of a phenolic species dramatically increases the rate of cleavage in acid at 150 degrees C. Quantum mechanical calculations on dimers with the para-hydroxyl group demonstrate that this acid-catalyzed pathway differs from the nonphenolic dimmers. Importantly, this result implies that depolymerization of native lignin in the plant cell wall will proceed via an unzipping mechanism wherein b-O-4 linkages will be cleaved from the ends of the branched, polymer chains inwards toward the center of the polymer. To test this hypothesis further, we synthesized a homopolymer of b-O-4 with a phenolic hydroxyl group, and demonstrate that it is cleaved in acid from the end containing the phenolic hydroxyl group. This result suggests that genetic modifications to lignin biosynthesis pathways in plants that will enable lower severity processes to fractionate lignin for upgrading and for easier access to the carbohydrate fraction of

  11. Acid-Catalyzed Conversion of Furfuryl Alcohol to Ethyl Levulinate in Liquid Ethanol

    PubMed Central

    González Maldonado, Gretchen M.; Assary, Rajeev S.; Dumesic, James; Curtiss, Larry A.

    2014-01-01

    Reaction pathways for the acid-catalyzed conversion of furfuryl alcohol (FAL) to ethyl levulinate (EL) in ethanol were investigated using liquid chromatography-mass spectrometry (LC-MS), 1D and 2D nuclear magnetic resonance (NMR) spectroscopy, and ab initio high-level quantum chemical (G4MP2) calculations. Our combined studies show that the production of EL at high yields from FAL is not accompanied by stoichiometric production of diethyl either (DEE), indicating that ethoxymethyl furan (EMF) is not an intermediate in the major reaction pathway. Several intermediates were observed using an LC-MS system, and three of these intermediates were isolated and subjected to reaction conditions. The structures of two intermediates were elucidated using 1D and 2D NMR techniques. One of these intermediates is EMF, which forms EL and DEE in a secondary reaction pathway. The second intermediate identified is 4,5,5-triethoxypentan-2-one, which is analogous to one of the intermediates observed in the conversion of FAL to LA in water (i.e. 4,5,5-trihydroxypentan-2-one). Furthermore, conversion of this intermediate to EL again involves the formation of DEE, indicating that it is also part of a secondary pathway. The primary pathway for production of EL involves solvent-assisted transfer of a water molecule from the partially detached protonated hydroxyl group of FAL to a ring carbon, followed by intra-molecular hydrogen shift, where the apparent reaction barrier for the hydrogen shift is relatively smaller in ethanol (21.1 kcal/mol) than that in water (26.6 kcal/mol). PMID:25035710

  12. Kinetics of acid-catalyzed degradation of cyclosporin A and its analogs in aqueous solution.

    PubMed

    Oliyai, R; Safadi, M; Meier, P G; Hu, M K; Rich, D H; Stella, V J

    1994-03-01

    The kinetics and mechanism of the degradation of cyclosporin A have been studied under aqueous acidic conditions. The rate of degradation was found to be specific acid-catalyzed over the pH range studied (1-4), with isocyclosporin A as the predominant degradation product. Selective reduction of the olefinic bond of the amino acid 2-N-methyl-(R)-((E)-2-butenyl)-4-methyl-L-threonine (MeBmt) did not affect the overall degradation kinetics and product distribution of cyclosporin A. These observations indicate that the alternative degradation pathway involving intramolecular alkoxy addition to the olefinic bond of amino acid MeBmt apparently does not significantly contribute to the overall degradation kinetics of cyclosporin A in the pH range 1-4. The chemical reactivity of O-acetyl-cyclosporin A was examined to probe the governing mechanism for the isomerization of cyclosporin A. Under identical conditions, O-acetyl-cyclosporin A showed a much greater chemical stability than cyclosporin A, consistent with a mechanism involving the hydroxyoxazolidine intermediate. The chemical stability of cyclosporin C, which contains two beta-hydroxyl groups, was also examined. The rate and product distribution for the degradation of cyclosporin C suggest that under aqueous acidic conditions it undergoes N,O-acyl migration solely at the amino acid residue MeBmt. Additionally, the impact of side-chain bulkiness of amino acid MeBmt was examined by studying the degradation kinetics of a series of cyclosporin A analogs.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. The Acid Catalyzed Nitration of Methanol: Formation of Methyl Nitrate via Aerosol Chemistry

    NASA Technical Reports Server (NTRS)

    Riffel, Brent G.; Michelsen, Rebecca R.; Iraci, Laura T.

    2004-01-01

    The liquid phase acid catalyzed reaction of methanol with nitric acid to yield methyl nitrate under atmospheric conditions has been investigated using gas phase infrared spectroscopy. This nitration reaction is expected to occur in acidic aerosol particles found in the upper troposphere/lower stratosphere as highly soluble methanol and nitric acid diffuse into these aerosols. Gaseous methyl nitrate is released upon formation, suggesting that some fraction of NO(x) may he liberated from nitric acid (methyl nitrate is later photolyzed to NO(x)) before it is removed from the atmosphere by wet deposition. Thus, this reaction may have important implications for the NO(x) budget. Reactions have been initiated in 45-62 wt% H2SO4 solutions at 10.0 C. Methyl nitrate production rates increased exponentially with acidity within the acidity regime studied. Preliminary calculations suggest that the nitronium ion (NO2(+) is the active nitrating agent under these conditions. The reaction order in methanol appears to depend on the water/methanol ratio and varies from first to zeroth order under conditions investigated. The nitration is first order in nitronium at all acidities investigated. A second order rate constant, kappa(sub 2), has been calculated to be 1 x 10(exp 8)/ M s when the reaction is first order in methanol. Calculations suggest the nitration is first order in methanol under tropospheric conditions. The infinitesimal percentage of nitric acid in the nitronium ion form in this acidity regime probably makes this reaction insignificant for the upper troposphere; however, this nitration may become significant in the mid stratosphere where colder temperatures increase nitric acid solubility and higher sulfuric acid content shifts nitric acid speciation toward the nitronium ion.

  14. Brönsted Acid-Catalyzed One-Pot Synthesis of Indoles from o-Aminobenzyl Alcohols and Furans

    PubMed Central

    Kuznetsov, Alexey; Makarov, Anton; Rubtsov, Alexandr E.; Butin, Alexander V.; Gevorgyan, Vladimir

    2013-01-01

    Brönsted acid-catalyzed one-pot synthesis of indoles from o-aminobenzyl alcohols and furans has been developed. This method operates via the in situ formation of aminobenzylfuran, followed by its recyclization into the indole core. The method proved to be efficient for substrates possessing different functional groups, including -OMe, -CO2Cy, and -Br. The resulting indoles can easily be transformed into diverse scaffolds, including 2,3- and 1,2-fused indoles, and indole possessing an α,β-unsaturated ketone moiety at the C-2 position. PMID:24255969

  15. Brønsted Acid Catalyzed Asymmetric Hydroamination of Alkenes: Synthesis of Pyrrolidines Bearing a Tetrasubstituted Carbon Stereocenter.

    PubMed

    Lin, Jin-Shun; Yu, Peng; Huang, Lin; Zhang, Pan; Tan, Bin; Liu, Xin-Yuan

    2015-06-26

    The first highly enantioselective Brønsted acid catalyzed intramolecular hydroamination of alkenes enables the efficient construction of a series of chiral (spirocyclic) pyrrolidines with an α-tetrasubstituted carbon stereocenter with excellent functional group tolerance. A unique feature of this strategy is the use of a thiourea group acting as both the activating and the directing group through cooperative multiple hydrogen bonding with a Brønsted acid and the double bond. The utility of this method is highlighted by the facile construction of chiral synthetic intermediates and important structural motifs that are widely found in organic synthesis.

  16. Microswelling-free negative resists for ArF excimer laser lithography utilizing acid-catalyzed intramolecular esterification

    NASA Astrophysics Data System (ADS)

    Hattori, Takashi; Tsuchiya, Yuko; Yokoyama, Yoshiyuki; Oizumi, Hiroaki; Morisawa, Taku; Yamaguchi, Atsuko; Shiraishi, Hiroshi

    1999-06-01

    We have examined alicyclic polymers with a (gamma) -hydroxy acid structure in order to investigate the properties of (gamma) -hydroxy acid and (gamma) -lactone as function groups of ArF negative resist materials. From the viewpoint of transparency and dry-etching resistance, (gamma) -hydroxy acid and (gamma) -lactone structure were found to be suitable for ArF negative resists materials. Surprisingly, the reactivity of the acid-catalyzed reaction of (gamma) -hydroxy acid is affected by the polymer structure. Using ArF excimer laser stepper, 0.20-micrometers line-and-space patterns without micro-swelling distortion were obtained from a negative resist consisting of alicyclic polymer with the (gamma) - hydroxy acid structure and a photoacid generator. Distortion was avoided because the number of carboxyl groups decreased drastically in the exposed area by the acid-catalyzed intramolecular esterification of (gamma) -hydroxy acid to (gamma) -lactone. As a result, (gamma) -hydroxy acid and (gamma) -lactone structure were found to be suitable function groups for ArF negative resist materials.

  17. The keto- and imine-epoxide rearrangements in the formation of substituted tetrahydrofurans and piperidines: Synthesis of ([+-])-teneraic acid; approahces to ([+-])-nemorensic acid and (+)-desoxoprosopinine

    SciTech Connect

    Kucharczyk, R.

    1992-01-01

    Previous work by Wasserman and co-workers showed that 2,7-dioxabicyclo-[2.21]heptanes can be formed via a thermal of Lewis acid-catalyzed rearrangement of 3,4-epoxy ketones. The author utilized this keto-epoxide rearrangement in the approach to the synthesis of nemorensic acid. A novel reaction of Grignard reagents with bicyclic acetals was developed permitting the stereoselective construction o9f highly substituted tetrahydrofurans. Thus, treatment of 1,4-dimethy1-2,7-dioxa-bicyclo[2.21]heptane with vinyl magnesium bromide resulted in Lewis acid-catalyzed acetal opening with subsequent chelation-controlled addition of the vinyl group to afford the tetrasubstituted tetrahydrofuran. Further functional group transformations demonstrated the feasibility of this approach in forming substituted tetrahydrofurans related to nemorensic acid. The carbonyl-epoxide rearrangement described above has been extended to imine epoxides in earlier work by Rusiecki. The resulting bicyclic oxazolidines can be stereoselectively reduced with hydride reagents to form substituted piperidines. The utility was demonstrated of this rearrangement/reduction methodology in the synthesis of [+-]-teneraic acid. The key steps in the synthesis were the formation of the bicyclic oxazolidine via the imine-epoxide rearrangement, and stereoselective hydride reduction to yield the trans piperidine. Oxidation of the t-butyloxycarbonyl-protected piperidine diol to the diacid, followed by deprotection of the amine, completed the synthesis of [+-]-teneraic acid. In seeking to apply the imine-epoxide rearrangement/reduction methodology in enantioselective syntheses, the author investigated an approach to the synthesis of (+)-desoxoprosopinine. This work has resulted in the successful construction of the desired intermediate keto epoxide which, with zinc chloride, rearranges cleanly to the corresponding bicyclic acetal. The corresponding imine-epoxide rearrangement has not been accomplished.

  18. Mechanism of the Fischer reaction. Rearrangement of cyclohexanone N-methylphenylhydrazone and N,N'-dimethyl-N-phenyl-N'-(1-cyclohexenyl)hydrazine to 9-methyl-1,2,3,4-tetrahydrocarbazole

    SciTech Connect

    Przheval'skii, N.M.; Kletskii, M.E.; Grandberg, I.I.; Kostromina, L.Yu.

    1985-12-01

    The kinetics of the thermal and acid-catalyzed Fischer reaction of cyclohexanone N-methylphenylhydrazone and N,N'-dimethyl-N-phenyl-N'-(1-cyclohexenyl)hydrazine were studied by a spectrophotometric method. Formation of the carbon-carbon bond proceeds by a (3,3)-sigmatropic shift mechanism. This conclusion was confirmed by MINDO/3 calculations of the rearrangement of a model divinylhydrazine.

  19. Enantiodivergent Atroposelective Synthesis of Chiral Biaryls by Asymmetric Transfer Hydrogenation: Chiral Phosphoric Acid Catalyzed Dynamic Kinetic Resolution.

    PubMed

    Mori, Keiji; Itakura, Tsubasa; Akiyama, Takahiko

    2016-09-12

    Reported herein is an enantiodivergent synthesis of chiral biaryls by a chiral phosphoric acid catalyzed asymmetric transfer hydrogenation reaction. Upon treatment of biaryl lactols with aromatic amines and a Hantzsch ester in the presence of chiral phosphoric acid, dynamic kinetic resolution (DKR) involving a reductive amination reaction proceeded smoothly to furnish both R and S isomers of chiral biaryls with excellent enantioselectivities by proper choice of hydroxyaniline derivative. This trend was observed in wide variety of substrates, and various chiral biphenyl and phenyl naphthyl adducts were synthesized with satisfactory enantioselectivities in enantiodivergent fashion. The enantiodivergent synthesis of synthetically challenging, chiral o-tetrasubstituted biaryls were also accomplished, and suggests high synthetic potential of the present method. PMID:27491630

  20. Kinetics and mechanism of the acid-catalyzed decomposition of omega-diazoacetophenones and their o-carbomethyoxy derivatives

    SciTech Connect

    Denisova, T.G.

    1988-01-01

    The kinetics of the acid-catalyzed decomposition of omega-diazoacetophenones and their o-carbomethoxy derivatives have been studied and their rate constants and activation energies measured in dioxane-H/sub 2/O (D/sub 2/O) and aqueous (D/sub 2/O)-dioxane mixtures (40:60 by volume) in the presence of H/sub 2/SO/sub 4/ (D/sub 2/SO/sub 4/), as well as in acetic and deuteroacetic acids, in the temperature range 290-328 K. Based on the results of k/sub H//k/sub D/ and ..delta..S not identical to measurements, assumptions have been made concerning the mechanism of the catalytic decomposition of the indicated diazoketones.

  1. Acid-catalyzed conversion of mono- and poly-sugars into platform chemicals: effects of molecular structure of sugar substrate.

    PubMed

    Hu, Xun; Wu, Liping; Wang, Yi; Song, Yao; Mourant, Daniel; Gunawan, Richard; Gholizadeh, Mortaza; Li, Chun-Zhu

    2013-04-01

    Hydrolysis/pyrolysis of lignocellulosic biomass always produces a mixture of sugars with distinct structures as intermediates or products. This study tried to elucidate the effects of molecular structure of sugars on their acid-catalyzed conversions in ethanol/water. Location of carbonyl group in sugars (fructose versus glucose) and steric configuration of hydroxyl groups (glucose versus galactose) significantly affected yields of levulinic acid/ester (fructose>glucose>galactose). The dehydration of fructose to 5-(hydroxymethyl)furfural produces much less soluble polymer than that from glucose and galactose, which results in high yields of levulinic acid/ester from fructose. Anhydrate sugar such as levoglucosan tends to undergo the undesirable decomposition to form less levulinic acid/ester. Catalytic behaviors of the poly-sugars (sucrose, maltose, raffinose, β-cyclodextrins) were determined much by their basic units. However, their big molecular sizes create the steric hindrance that significantly affects their followed conversion over solid acid catalyst. PMID:23454803

  2. Acid-catalyzed hydrolysis of lignin β-O-4 linkages in ionic liquid solvents: a computational mechanistic study.

    PubMed

    Janesko, Benjamin G

    2014-03-21

    This work presents a computational mechanistic study of the acid-catalyzed hydrolysis of lignin β-O-4 linkages in ionic liquid solvents. Model compound 2-hydroyxyethyl phenyl ether undergoes dehydration to vinyl phenyl ether followed by hydrolysis to phenol and "Hibbert's ketones". Larger model compound α-hydroxy-phenethyl phenyl ether illustrates an E1 dehydration mechanism involving resonance-stabilized carbocations. Continuum models for ionic liquid solvents indicate that solvation can significantly affect the reaction rates. The tested continuum ionic liquid solvents give similar results, and differ significantly from continuum organic solvents with comparable dielectric constants. The acidic ionic liquid cation 1-H-3-methylimidazolium has lower predicted catalytic activity than hydronium or HCl, consistent with the former's relatively small acid dissociation constant. Calculations with dispersion-corrected density functionals give similar behavior. Calculations on Lewis acidic metal chlorides used experimentally for lignin hydrolysis suggest that the metal chloride may participate in the initial dehydration. These results provide a baseline for future studies of improved hydrolysis catalysts. PMID:24509442

  3. Dietary phenolic acids and ascorbic acid: Influence on acid-catalyzed nitrosative chemistry in the presence and absence of lipids.

    PubMed

    Combet, Emilie; El Mesmari, Aziza; Preston, Tom; Crozier, Alan; McColl, Kenneth E L

    2010-03-15

    Acid-catalyzed nitrosation and production of potentially carcinogenic nitrosative species is focused at the gastroesophageal junction, where salivary nitrite, derived from dietary nitrate, encounters the gastric juice. Ascorbic acid provides protection by converting nitrosative species to nitric oxide (NO). However, NO may diffuse into adjacent lipid, where it reacts with O(2) to re-form nitrosative species and N-nitrosocompounds (NOC). In this way, ascorbic acid promotes acid nitrosation. Using a novel benchtop model representing the gastroesophageal junction, this study aimed to clarify the action of a range of water-soluble antioxidants on the nitrosative mechanisms in the presence or absence of lipids. Caffeic, ferulic, gallic, or chlorogenic and ascorbic acids were added individually to simulated gastric juice containing secondary amines, with or without lipid. NO and O(2) levels were monitored by electrochemical detection. NOC were measured in both aqueous and lipid phases by gas chromatography-tandem mass spectrometry. In the absence of lipids, all antioxidants tested inhibited nitrosation, ranging from 35.9 + or - 7.4% with gallic acid to 93 + or - 0.6% with ferulic acid. In the presence of lipids, the impact of each antioxidant on nitrosation was inversely correlated with the levels of NO they generated (R(2) = 0.95, p<0.01): gallic, chlorogenic, and ascorbic acid promoted nitrosation, whereas ferulic and caffeic acids markedly inhibited nitrosation.

  4. Acid-Catalyzed Multicomponent Tandem Double Cyclization: A One-pot, Metal-free Route to Synthesize Polyfunctional 4,9-Dihydropyrrolo[2,1-b]quinazolines.

    PubMed

    Cai, Qun; Li, Deng-Kui; Zhou, Rong-Rong; Zhuang, Shi-Yi; Ma, Jin-Tian; Wu, Yan-Dong; Wu, An-Xin

    2016-09-01

    An acid-catalyzed multicomponent tandem double cyclization protocol has been developed for the synthesis of polyfunctional 4,9-dihydropyrrolo[2,1-b]quinazolines from simple and readily available arylglyoxal monohydrates, 2-aminobenzylamine, and trans-β-nitrostyrenes. This practical and metal-free reaction proceeds through an imine formation/cyclization/Michael addition/Henry cyclization protocol, resulting in the construction of four new bonds and two ring moieties directly in one pot.

  5. Lewis acid catalyzed [2+2] cycloaddition of ynamides and propargyl silyl ethers: synthesis of alkylidenecyclobutenones and their reactivity in ring-opening and ring expansion.

    PubMed

    Chen, Ling; Cao, Jian; Xu, Zheng; Zheng, Zhan-Jiang; Cui, Yu-Ming; Xu, Li-Wen

    2016-07-21

    A family of four-membered enones, polysubstituted alkylidenecyclobutenones, were easily prepared by a Lewis acid catalyzed [2+2] cycloaddition of ynamides and propargyl silyl ethers. This challenging regioselective [2+2] cycloaddition enables the efficient construction and conversion of four-membered enones, which provides high-value and structurally diverse products through the unexpected ring-opening and ring expansion of alkylidenecyclobutenone with Grignard reagents, organolithium, primary amines, and water. PMID:27387596

  6. Suzuki–Miyaura cross-coupling reaction of 1-aryltriazenes with arylboronic acids catalyzed by a recyclable polymer-supported N-heterocyclic carbene–palladium complex catalyst

    PubMed Central

    Nan, Guangming; Ren, Fang

    2010-01-01

    Summary The Suzuki–Miyaura cross-coupling reaction of 1-aryltriazenes with arylboronic acids catalyzed by a recyclable polymer-supported Pd–NHC complex catalyst has been realized for the first time. The polymer-supported catalyst can be re-used several times still retaining high activity for this transformation. Various aryltriazenes were investigated as electrophilic substrates at room temperature to give biaryls in good to excellent yields and showed good chemoselectivity over aryl halides in the reactions. PMID:20703375

  7. Scope and limitations of aliphatic Friedel-Crafts alkylations. Lewis acid catalyzed addition reactions of alkyl chlorides to carbon-carbon double bonds

    SciTech Connect

    Mayr, H.; Striepe, W.

    1983-04-22

    Lewis acid catalyzed addition reactions of alkyl halides with unsaturated hydrocarbons have been studied. 1:1 addition products are formed if the addends dissociate faster than the corresponding products; otherwise, polymerization takes place. For reaction conditions under which these compounds exist mainly undissociated, solvolysis constants of model compounds can be used to predict the outcome of any such addition reactions if systems with considerable steric hindrance are excluded.

  8. Kinetics of Acid-Catalyzed Dehydration of Cyclic Hemiacetals in Organic Aerosol Particles in Equilibrium with Nitric Acid Vapor.

    PubMed

    Ranney, April P; Ziemann, Paul J

    2016-04-28

    Previous studies have shown that 1,4-hydroxycarbonyls, which are often major products of the atmospheric oxidation of hydrocarbons, can undergo acid-catalyzed cyclization and dehydration in aerosol particles to form highly reactive unsaturated dihydrofurans. In this study the kinetics of dehydration of cyclic hemiacetals, the rate-limiting step in this process, was investigated in a series of environmental chamber experiments in which secondary organic aerosol (SOA) containing cyclic hemiacetals was formed from the reaction of n-pentadecane with OH radicals in dry air in the presence of HNO3. A particle beam mass spectrometer was used to monitor the formation and dehydration of cyclic hemiacetals in real time, and SOA and HNO3 were quantified in filter samples by gravimetric analysis and ion chromatography. Measured dehydration rate constants increased linearly with increasing concentration of HNO3 in the gas phase and in SOA, corresponding to catalytic rate constants of 0.27 h(-1) ppmv(-1) and 7.0 h(-1) M(-1), respectively. The measured Henry's law constant for partitioning of HNO3 into SOA was 3.7 × 10(4) M atm(-1), ∼25% of the value for dissolution into water, and the acid dissociation constant was estimated to be <8 × 10(-4), at least a factor of 10(4) less than that for HNO3 in water. The results indicate that HNO3 was only weakly dissociated in the SOA and that dehydration of cyclic hemiacetals was catalyzed by molecular HNO3 rather than by H(+). The Henry's law constant and kinetics relationships measured here can be used to improve mechanisms and models of SOA formation from the oxidation of hydrocarbons in dry air in the presence of NOx, which are conditions commonly used in laboratory studies. The fate of cyclic hemiacetals in the atmosphere, where the effects of higher relative humidity, organic/aqueous phase separation, and acid catalysis by molecular H2SO4 and/or H(+) are likely to be important, is discussed. PMID:27043733

  9. Kinetics of Acid-Catalyzed Dehydration of Cyclic Hemiacetals in Organic Aerosol Particles in Equilibrium with Nitric Acid Vapor.

    PubMed

    Ranney, April P; Ziemann, Paul J

    2016-04-28

    Previous studies have shown that 1,4-hydroxycarbonyls, which are often major products of the atmospheric oxidation of hydrocarbons, can undergo acid-catalyzed cyclization and dehydration in aerosol particles to form highly reactive unsaturated dihydrofurans. In this study the kinetics of dehydration of cyclic hemiacetals, the rate-limiting step in this process, was investigated in a series of environmental chamber experiments in which secondary organic aerosol (SOA) containing cyclic hemiacetals was formed from the reaction of n-pentadecane with OH radicals in dry air in the presence of HNO3. A particle beam mass spectrometer was used to monitor the formation and dehydration of cyclic hemiacetals in real time, and SOA and HNO3 were quantified in filter samples by gravimetric analysis and ion chromatography. Measured dehydration rate constants increased linearly with increasing concentration of HNO3 in the gas phase and in SOA, corresponding to catalytic rate constants of 0.27 h(-1) ppmv(-1) and 7.0 h(-1) M(-1), respectively. The measured Henry's law constant for partitioning of HNO3 into SOA was 3.7 × 10(4) M atm(-1), ∼25% of the value for dissolution into water, and the acid dissociation constant was estimated to be <8 × 10(-4), at least a factor of 10(4) less than that for HNO3 in water. The results indicate that HNO3 was only weakly dissociated in the SOA and that dehydration of cyclic hemiacetals was catalyzed by molecular HNO3 rather than by H(+). The Henry's law constant and kinetics relationships measured here can be used to improve mechanisms and models of SOA formation from the oxidation of hydrocarbons in dry air in the presence of NOx, which are conditions commonly used in laboratory studies. The fate of cyclic hemiacetals in the atmosphere, where the effects of higher relative humidity, organic/aqueous phase separation, and acid catalysis by molecular H2SO4 and/or H(+) are likely to be important, is discussed.

  10. Claisen thermally rearranged (CTR) polymers

    PubMed Central

    Tena, Alberto; Rangou, Sofia; Shishatskiy, Sergey; Filiz, Volkan; Abetz, Volker

    2016-01-01

    Thermally rearranged (TR) polymers, which are considered the next-generation of membrane materials because of their excellent transport properties and high thermal and chemical stability, are proven to have significant drawbacks because of the high temperature required for the rearrangement and low degree of conversion during this process. We demonstrate that using a [3,3]-sigmatropic rearrangement, the temperature required for the rearrangement of a solid glassy polymer was reduced by 200°C. Conversions of functionalized polyimide to polybenzoxazole of more than 97% were achieved. These highly mechanically stable polymers were almost five times more permeable and had more than two times higher degrees of conversion than the reference polymer treated under the same conditions. Properties of these second-generation TR polymers provide the possibility of preparing efficient polymer membranes in a form of, for example, thin-film composite membranes for various gas and liquid membrane separation applications. PMID:27482538

  11. Claisen thermally rearranged (CTR) polymers.

    PubMed

    Tena, Alberto; Rangou, Sofia; Shishatskiy, Sergey; Filiz, Volkan; Abetz, Volker

    2016-07-01

    Thermally rearranged (TR) polymers, which are considered the next-generation of membrane materials because of their excellent transport properties and high thermal and chemical stability, are proven to have significant drawbacks because of the high temperature required for the rearrangement and low degree of conversion during this process. We demonstrate that using a [3,3]-sigmatropic rearrangement, the temperature required for the rearrangement of a solid glassy polymer was reduced by 200°C. Conversions of functionalized polyimide to polybenzoxazole of more than 97% were achieved. These highly mechanically stable polymers were almost five times more permeable and had more than two times higher degrees of conversion than the reference polymer treated under the same conditions. Properties of these second-generation TR polymers provide the possibility of preparing efficient polymer membranes in a form of, for example, thin-film composite membranes for various gas and liquid membrane separation applications. PMID:27482538

  12. Synthesis of oxacyclic scaffolds via dual ruthenium hydride/Brønsted acid-catalyzed isomerization/cyclization of allylic ethers.

    PubMed

    Ascic, Erhad; Ohm, Ragnhild G; Petersen, Rico; Hansen, Mette R; Hansen, Casper L; Madsen, Daniel; Tanner, David; Nielsen, Thomas E

    2014-03-17

    A ruthenium hydride/Brønsted acid-catalyzed tandem sequence is reported for the synthesis of 1,3,4,9-tetrahydropyrano[3,4-b]indoles (THPIs) and related oxacyclic scaffolds. The process was designed on the premise that readily available allylic ethers would undergo sequential isomerization, first to enol ethers (Ru catalysis), then to oxocarbenium ions (Brønsted acid catalysis) amenable to endo cyclization with tethered nucleophiles. This methodology provides not only an attractive alternative to the traditional oxa-Pictet-Spengler reaction for the synthesis of THPIs, but also convenient access to THPI congeners and other important oxacycles such as acetals. PMID:24616060

  13. Lewis Acid Catalyzed Formal Intramolecular [3 + 3] Cross-Cycloaddition of Cyclopropane 1,1-Diesters for Construction of Benzobicyclo[2.2.2]octane Skeletons.

    PubMed

    Ma, Weiwei; Fang, Jie; Ren, Jun; Wang, Zhongwen

    2015-09-01

    A novel Lewis acid catalyzed formal intramolecular [3 + 3] cross-cycloaddition (IMCC) of cyclopropane 1,1-diesters has been successfully developed. This supplies an efficient and conceptually new strategy for construction of bridged bicyclo[2.2.2]octane skeletons. This [3 + 3]IMCC could be run up to gram scale and from easily prepared starting materials. This [3 + 3]IMCC, together with our previously reported [3 + 2]IMCC strategy, can afford either the bicyclo[2.2.2]octane or bicyclo[3.2.1]octane skeletons from the similar starting materials by regulating the substituents on vinyl group.

  14. Brønsted Acid-Catalyzed Transfer Hydrogenation of Imines and Alkenes Using Cyclohexa-1,4-dienes as Dihydrogen Surrogates.

    PubMed

    Chatterjee, Indranil; Oestreich, Martin

    2016-05-20

    Cyclohexa-1,4-dienes are introduced to Brønsted acid-catalyzed transfer hydrogenation as an alternative to the widely used Hantzsch dihydropyridines. While these hydrocarbon-based dihydrogen surrogates do offer little advantage over established protocols in imine reduction as well as reductive amination, their use enables the previously unprecedented transfer hydrogenation of structurally and electronically unbiased 1,1-di- and trisubstituted alkenes. The mild procedure requires 5.0 mol % of Tf2NH, but the less acidic sulfonic acids TfOH and TsOH work equally well. PMID:27181437

  15. Immunoglobulin λ Gene Rearrangement Can Precede κ Gene Rearrangement

    DOE PAGES

    Berg, Jörg; Mcdowell, Mindy; Jäck, Hans-Martin; Wabl, Matthias

    1990-01-01

    Imore » mmunoglobulin genes are generated during differentiation of B lymphocytes by joining gene segments. A mouse pre-B cell contains a functional immunoglobulin heavy-chain gene, but no light-chain gene. Although there is only one heavy-chain locus, there are two lightchain loci: κ and λ .It has been reported that κ loci in the germ-line configuration are never (in man) or very rarely (in the mouse) present in cells with functionally rearranged λ -chain genes. Two explanations have been proposed to explain this: (a) the ordered rearrangement theory, which postulates that light-chain gene rearrangement in the pre-B cell is first attempted at the κ locus, and that only upon failure to produce a functional κ chain is there an attempt to rearrange the λ locus; and (b) the stochastic theory, which postulates that rearrangement at the λ locus proceeds at a rate that is intrinsically much slower than that at the κ locus. We show here that λ -chain genes are generated whether or not the κ locus has lost its germ-line arrangement, a result that is compatible only with the stochastic theory.« less

  16. Real and Virtual Heritage Historical Astronomical Plate Archives in Sonneberg, Bamberg and Hamburg Observatories, the Evolution of Astrophysics and their Influence on Human Knowledge and Culture

    NASA Astrophysics Data System (ADS)

    Kunzmann, Björn

    The rise of astrophysics around 1860 introduced new instruments, methods and research areas. Of course, the increasing number of foundations of new observatories around the world starting at that time was forced by that new scientific discipline, too, but especially by the usage of photographic instruments. At the end of the 19th century the formation and development of photographic methods and techniques had reached a level of sufficient stability for productive usage in astronomy and astrophysics, their new instrumrents, methods and goals. The fundamental meaning of star light analysis for astrophysics by increasing discoveries of Variable Stars and the Systematic search for moving Solar System objects had basically driven the beginning of large photographic sky patrols at that time, using photographic glass plates as detectors and information storages. Sky Patrols, especially systematic long-term monitoring of the whole sky or of well defined selected areas and Sky Surveys were (and still are) an important key method that forced the evolution and progress of astrophysics. Important scientific results by famous astronomers, for example Walter Baade, Cuno Hoffmeister and Harlow Shapley depended on the analysis of photographic plates. Today, there are around 50 photographic plate archives world-wide. Most of them, unfortunately, are in a quite poor condition and not yet digitized. Following Harvard College Observatory with an estimated total of 600,000 plates, Sonneberg observatory harbours the second largest archive world-wide (around 300,000 plates) among other large ones in Germany like Bamberg (40,000 plates) and Hamburg (35,000 plates). These plate archives form an important heritage with a total of roughly two million direct plates and some ten or hundred thousands of spectroscopic plates. A lot of progress has been made by transforming this real heritage to a virtual one by systematic digitisation of the plates, but perhaps only 15% of them have been

  17. Genome rearrangements: mother knows best!

    PubMed

    Chalker, Douglas L

    2005-10-25

    In Paramecium, developmentally programmed genome rearrangements can be altered by the presence of homologous sequences within the maternal somatic nucleus. Newly identified RNA-binding proteins appear to mediate the transfer of homologous sequence information from the maternal to the developing somatic nucleus, facilitating epigenetic regulation of this large-scale genome reorganization. PMID:16243019

  18. Biotransformation and Rearrangement of Laromustine.

    PubMed

    Nassar, Alaa-Eldin F; Wisnewski, Adam V; King, Ivan

    2016-08-01

    This review highlights the recent research into the biotransformations and rearrangement of the sulfonylhydrazine-alkylating agent laromustine. Incubation of [(14)C]laromustine with rat, dog, monkey, and human liver microsomes produced eight radioactive components (C-1 to C-8). There was little difference in the metabolite profile among the species examined, partly because NADPH was not required for the formation of most components, which instead involved decomposition and/or hydrolysis. The exception was C-7, a hydroxylated metabolite, largely formed by CYP2B6 and CYP3A4/5. Liquid chromatography-multistage mass spectrometry (LC-MS(n)) studies determined that collision-induced dissociation, and not biotransformation or enzyme catalysis, produced the unique mass spectral rearrangement. Accurate mass measurements performed with a Fourier-transform ion cyclotron resonance mass spectrometer (FTICR-MS) significantly aided determination of the elemental compositions of the fragments and in the case of laromustine revealed the possibility of rearrangement. Further, collision-induced dissociation produced the loss of nitrogen (N2) and methylsulfonyl and methyl isocyanate moieties. The rearrangement, metabolite/decomposition products, and conjugation reactions were analyzed utilizing hydrogen-deuterium exchange, exact mass, (13)C-labeled laromustine, nuclear magnetic resonance spectroscopy (NMR), and LC-MS(n) experiments to assist with the assignments of these fragments and possible mechanistic rearrangement. Such techniques produced valuable insights into these functions: 1) Cytochrome P450 is involved in C-7 formation but plays little or no role in the conversion of [(14)C]laromustine to C-1 through C-6 and C-8; 2) the relative abundance of individual degradation/metabolite products was not species-dependent; and 3) laromustine produces several reactive intermediates that may produce the toxicities seen in the clinical trials. PMID:27278961

  19. Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water

    SciTech Connect

    Caratzoulas, Stavros; Courtney, Timothy; Vlachos, Dionisios G.

    2011-01-01

    We use the conversion of protonated glycerol to acrolein for a case study of the mechanism of acid-catalyzed dehydration of polyols in aqueous environments. We employ hybrid Quamtum Mechanics/Molecular Mechanics Molecular Dynamics (QM/MM MD) simulations with biased sampling and perform free energy calculations for the elementary steps of the reaction. We investigate the effects of solvent dynamics and in particular the role of quantum mechanical water in the dehydration mechanism. We present results supporting a mechanism that proceeds via water-mediated proton transfers and thus through an enol intermediate. We find that the first dehydration may take place by two, low-energy pathways requiring, respectively, 20.9 and 18.8 kcal/mol of activation free energy. The second dehydration requires 19.9 kcal/mol of activation free energy while for the overall reaction we compute a free energy change of -8 kcal/mol.

  20. Difference analysis of the enzymatic hydrolysis performance of acid-catalyzed steam-exploded corn stover before and after washing with water.

    PubMed

    Zhu, Junjun; Shi, Linli; Zhang, Lingling; Xu, Yong; Yong, Qiang; Ouyang, Jia; Yu, Shiyuan

    2016-10-01

    The difference in the enzymatic hydrolysis yield of acid-catalyzed steam-exploded corn stover (ASC) before and after washing with water reached approximately 15 % under the same conditions. The reasons for the difference in the yield between ASC and washed ASC (wASC) were determined through the analysis of the composition of ASC prehydrolyzate and sugar concentration of enzymatic hydrolyzate. Salts produced by neutralization (CaSO4, Na2SO4, K2SO4, and (NH4)2SO4), sugars (polysaccharides, oligosaccharides, and monosaccharides), sugar-degradation products (weak acids and furans), and lignin-degradation products (ethyl acetate extracts and nine main lignin-degradation products) were back-added to wASC. Results showed that these products, except furans, exerted negative effect on enzymatic hydrolysis. According to the characteristics of acid-catalyzed steam explosion pretreatment, the five sugar-degradation products' mixture and salts [Na2SO4, (NH4)2SO4] showed minimal negative inhibition effect on enzymatic hydrolysis. By contrast, furans demonstrated a promotion effect. Moreover, soluble sugars, such as 13 g/L xylose (decreased by 6.38 %), 5 g/L cellobiose (5.36 %), 10 g/L glucose (3.67 %), as well as lignin-degradation products, and ethyl acetate extracts (4.87 %), exhibited evident inhibition effect on enzymatic hydrolysis. Therefore, removal of soluble sugars and lignin-degradation products could effectively promote the enzymatic hydrolysis performance. PMID:27277746

  1. Difference analysis of the enzymatic hydrolysis performance of acid-catalyzed steam-exploded corn stover before and after washing with water.

    PubMed

    Zhu, Junjun; Shi, Linli; Zhang, Lingling; Xu, Yong; Yong, Qiang; Ouyang, Jia; Yu, Shiyuan

    2016-10-01

    The difference in the enzymatic hydrolysis yield of acid-catalyzed steam-exploded corn stover (ASC) before and after washing with water reached approximately 15 % under the same conditions. The reasons for the difference in the yield between ASC and washed ASC (wASC) were determined through the analysis of the composition of ASC prehydrolyzate and sugar concentration of enzymatic hydrolyzate. Salts produced by neutralization (CaSO4, Na2SO4, K2SO4, and (NH4)2SO4), sugars (polysaccharides, oligosaccharides, and monosaccharides), sugar-degradation products (weak acids and furans), and lignin-degradation products (ethyl acetate extracts and nine main lignin-degradation products) were back-added to wASC. Results showed that these products, except furans, exerted negative effect on enzymatic hydrolysis. According to the characteristics of acid-catalyzed steam explosion pretreatment, the five sugar-degradation products' mixture and salts [Na2SO4, (NH4)2SO4] showed minimal negative inhibition effect on enzymatic hydrolysis. By contrast, furans demonstrated a promotion effect. Moreover, soluble sugars, such as 13 g/L xylose (decreased by 6.38 %), 5 g/L cellobiose (5.36 %), 10 g/L glucose (3.67 %), as well as lignin-degradation products, and ethyl acetate extracts (4.87 %), exhibited evident inhibition effect on enzymatic hydrolysis. Therefore, removal of soluble sugars and lignin-degradation products could effectively promote the enzymatic hydrolysis performance.

  2. An enantioselective strategy for the total synthesis of (S)-tylophorine via catalytic asymmetric allylation and a one-pot DMAP-promoted isocyanate formation/Lewis acid catalyzed cyclization sequence.

    PubMed

    Su, Bo; Zhang, Hui; Deng, Meng; Wang, Qingmin

    2014-06-14

    A new asymmetric total synthesis of a phenanthroindolizidine alkaloid (S)-tylophorine is reported, which features a catalytic asymmetric allylation of aldehydes and an unexpected one-pot DMAP promoted isocyanate formation and Lewis acid catalyzed intramolecular cyclization reaction. In addition, White's direct C-H oxidation catalyst system converting monosubstituted olefins to linear allylic acetates was also employed for late-stage transformation.

  3. Anionic Snieckus-Fries Rearrangement

    PubMed Central

    Riggs, Jason C.; Singh, Kanwal J.; Yun, Ma; Collum, David B.

    2009-01-01

    Lithiated aryl carbamates (ArLi) bearing methoxy or fluoro substituents in the meta position are generated from lithium diisopropylamide (LDA) in THF, n-BuOMe, Me2NEt, dimethoxyethane (DME), N,N,N’,N’-tetramethylethylenediamine (TMEDA), N,N,N’,N’-tetramethylcyclohexanediamine (TMCDA), and hexamethylphosphoramide (HMPA). The aryllithiums are shown with 6Li, 13C, and 15N NMR spectroscopies to be monomers, ArLi-LDA mixed dimers, and ArLi-LDA mixed trimers, depending on the choice of solvent. Subsequent Snieckus-Fries rearrangements afford ArOLi-LDA mixed dimers and trimers of the resulting phenolates. Rate studies of the rearrangement implicate mechanisms based on monomers, mixed dimers, and mixed trimers. PMID:18798619

  4. Programmed Genome Rearrangements in Tetrahymena.

    PubMed

    Yao, Meng-Chao; Chao, Ju-Lan; Cheng, Chao-Yin

    2014-12-01

    Ciliates are champions in programmed genome rearrangements. They carry out extensive restructuring during differentiation to drastically alter the complexity, relative copy number, and arrangement of sequences in the somatic genome. This chapter focuses on the model ciliate Tetrahymena, perhaps the simplest and best-understood ciliate studied. It summarizes past studies on various genome rearrangement processes and describes in detail the remarkable progress made in the past decade on the understanding of DNA deletion and other processes. The process occurs at thousands of specific sites to remove defined DNA segments that comprise roughly one-third of the genome including all transposons. Interestingly, this DNA rearranging process is a special form of RNA interference. It involves the production of double-stranded RNA and small RNA that guides the formation of heterochromatin. A domesticated piggyBac transposase is believed to cut off the marked chromatin, and the retained sequences are joined together through nonhomologous end-joining processes. Many of the proteins and DNA players involved have been analyzed and are described. This link provides possible explanations for the evolution, mechanism, and functional roles of the process. The article also discusses the interactions between parental and progeny somatic nuclei that affect the selection of sequences for deletion, and how the specific deletion boundaries are determined after heterochromatin marking.

  5. Programmed Rearrangement in Ciliates: Paramecium.

    PubMed

    Betermier, Mireille; Duharcourt, Sandra

    2014-12-01

    Programmed genome rearrangements in the ciliate Paramecium provide a nice illustration of the impact of transposons on genome evolution and plasticity. During the sexual cycle, development of the somatic macronucleus involves elimination of ∼30% of the germline genome, including repeated DNA (e.g., transposons) and ∼45,000 single-copy internal eliminated sequences (IES). IES excision is a precise cut-and-close process, in which double-stranded DNA cleavage at IES ends depends on PiggyMac, a domesticated piggyBac transposase. Genome-wide analysis has revealed that at least a fraction of IESs originate from Tc/mariner transposons unrelated to piggyBac. Moreover, genomic sequences with no transposon origin, such as gene promoters, can be excised reproducibly as IESs, indicating that genome rearrangements contribute to the control of gene expression. How the system has evolved to allow elimination of DNA sequences with no recognizable conserved motif has been the subject of extensive research during the past two decades. Increasing evidence has accumulated for the participation of noncoding RNAs in epigenetic control of elimination for a subset of IESs, and in trans-generational inheritance of alternative rearrangement patterns. This chapter summarizes our current knowledge of the structure of the germline and somatic genomes for the model species Paramecium tetraurelia, and describes the DNA cleavage and repair factors that constitute the IES excision machinery. We present an overview of the role of specialized RNA interference machineries and their associated noncoding RNAs in the control of DNA elimination. Finally, we discuss how RNA-dependent modification and/or remodeling of chromatin may guide PiggyMac to its cognate cleavage sites. PMID:26104450

  6. Transposable elements as catalysts for chromosome rearrangements.

    PubMed

    Zhang, Jianbo; Yu, Chuanhe; Krishnaswamy, Lakshminarasimhan; Peterson, Thomas

    2011-01-01

    Barbara McClintock first showed that transposable elements in maize can induce major chromosomal rearrangements, including duplications, deletions, inversions, and translocations. More recently, researchers have made significant progress in elucidating the mechanisms by which transposons can induce genome rearrangements. For the Ac/Ds transposable element system, rearrangements are generated when the termini of different elements are used as substrates for transposition. The resulting alternative transposition reaction directly generates a variety of rearrangements. The size and type of rearrangements produced depend on the location and orientation of transposon insertion. A single locus containing a pair of alternative transposition-competent elements can produce a virtually unlimited number of genome rearrangements. With a basic understanding of the mechanisms involved, researchers are beginning to utilize both naturally occurring and in vitro-generated configurations of transposable elements in order to manipulate chromosome structure. PMID:21181539

  7. Transposable elements as catalysts for chromosome rearrangements.

    PubMed

    Zhang, Jianbo; Yu, Chuanhe; Krishnaswamy, Lakshminarasimhan; Peterson, Thomas

    2011-01-01

    Barbara McClintock first showed that transposable elements in maize can induce major chromosomal rearrangements, including duplications, deletions, inversions, and translocations. More recently, researchers have made significant progress in elucidating the mechanisms by which transposons can induce genome rearrangements. For the Ac/Ds transposable element system, rearrangements are generated when the termini of different elements are used as substrates for transposition. The resulting alternative transposition reaction directly generates a variety of rearrangements. The size and type of rearrangements produced depend on the location and orientation of transposon insertion. A single locus containing a pair of alternative transposition-competent elements can produce a virtually unlimited number of genome rearrangements. With a basic understanding of the mechanisms involved, researchers are beginning to utilize both naturally occurring and in vitro-generated configurations of transposable elements in order to manipulate chromosome structure.

  8. The acid-catalyzed decompostion of phenacylcobalamin: evidence for the formation of an enol-Co(III) pi-complex intermediate.

    PubMed

    Brown, K L; Chu, M M; Ingraham, L L

    1976-04-01

    Phenacylcobalamin has been synthesized and characterized by thin-layer chromatography and uv-visible spectroscopy, as well as identification of the cobalt-containing and organic products of its cleavage in acid and base and by aerobic photolysis. The major organic product from all three cleavage reactions is acetophenone and the cobalt-containing product is aquacobalamin (or hydroxocobalamin, its conjugate base). In aqueous acidic solution (pH 0 to 7.3, ionic strength 1.0 M, and 25.0 degrees C), the kinetics of the formation of aquacobalamin are biphasic representing the linear sum of two exponential terms. The pH dependence of the first-order rate constant of both phases shows a first-order dependence on proton concentration but with an inflection point ot pH 3.55 for the faster phase and at pH 4.03 for the slower phase. This behavior is interpreted in terms of the specific acid catalyzed formation of an intermediate from both "base on" and "base off" phenacylcobalamin with different second-order rate constants for each form, followed by an intermediate decompotion step with a similar formal mechanism. The nature of the intermediate is discussed and it is concluded to be a pi-complex between cob(III)alamin and the enol of acetophenone. PMID:4086

  9. Acid catalyzed hydrocarbon conversion processes utilizing a catalyst comprising a group ivb, vb or vib metal oxide on an inorganic refractory oxide support

    SciTech Connect

    Grenoble, D.C.; Kim, C.J.; Murrell, L.L.

    1980-11-11

    It has been discovered and forms the basis of the disclosure that various acid catalyzed hydrocarbon conversion processes such as catalytic cracking of gas oil; xylene isomerization; toluene disproportionation; dealkylation of aromatics; ethylene, butylene , isobutylene, propylene polymerization; olefin isomerization; alcohol dehydration; olefin hydration; alkylation; heavy ends cat cracking, etc. are dramatically improved insofar as percent conversion, and selectivity are concerned by the use of a catalyst selected from the group consisting of the oxides of tungsten, niobium and mixtures thereof, and tungsten or niobium oxides in combination with one or more additional metal oxides selected from the group consisting of tantalum oxide, hafnium oxide, chromium oxide, titanium oxide and zirconium oxide, supported on an inorganic refractory oxide support. These catalysts may be prepared by the methods known in the art, I.E., incipient wetness, impregnation, coprecipitation, etc. Of the metal oxide precursor onto or with the supports followed by conversion into the oxide form. Before use, the metal oxide/support combination is preferably subjected to steaming at elevated temperatures either before introduction into the reactor or in situ in the process reactor. Conventional catalytic cracking catalysts are unstable at the elevated temperatures where the metal oxide/support combinations of the present invention are uniquely stable.

  10. Synthesis of a tricyclic lactam via Beckmann rearrangement and ring-rearrangement metathesis as key steps

    PubMed Central

    Ravikumar, Ongolu; Majhi, Jadab

    2015-01-01

    Summary A tricyclic lactam is reported in a four step synthesis sequence via Beckmann rearrangement and ring-rearrangement metathesis as key steps. Here, we used a simple starting material such as dicyclopentadiene. PMID:26425207

  11. Acid-, base-, and lewis-acid-catalyzed heterolysis of methoxide from an alpha-hydroxy-beta-methoxy radical: models for reactions catalyzed by coenzyme B12-dependent diol dehydratase.

    PubMed

    Xu, Libin; Newcomb, Martin

    2005-11-11

    [Reaction: see text].A model for glycol radicals was employed in laser flash photolysis kinetic studies of catalysis of the fragmentation of a methoxy group adjacent to an alpha-hydroxy radical center. Photolysis of a phenylselenylmethylcyclopropane precursor gave a cyclopropylcarbinyl radical that rapidly ring opened to the target alpha-hydroxy-beta-methoxy radical (3). Heterolysis of the methoxy group in 3 gave an enolyl radical (4a) or an enol ether radical cation (4b), depending upon pH. Radicals 4 contain a 2,2-diphenylcyclopropane reporter group, and they rapidly opened to give UV-observable diphenylalkyl radicals as the final products. No heterolysis was observed for radical 3 under neutral conditions. In basic aqueous acetonitrile solutions, specific base catalysis of the heterolysis was observed; the pK(a) of radical 3 was determined to be 12.5 from kinetic titration plots, and the ketyl radical formed by deprotonation of 3 eliminated methoxide with a rate constant of 5 x 10(7) s(-1). In the presence of carboxylic acids in acetonitrile solutions, radical 3 eliminated methanol in a general acid-catalyzed reaction, and rate constants for protonation of the methoxy group in 3 by several acids were measured. Radical 3 also reacted by fragmentation of methoxide in Lewis-acid-catalyzed heterolysis reactions; ZnBr2, Sc(OTf)3, and BF3 were found to be efficient catalysts. Catalytic rate constants for the heterolysis reactions were in the range of 3 x 10(4) to 2 x 10(6) s(-1). The Lewis-acid-catalyzed heterolysis reactions are fast enough for kinetic competence in coenzyme B12 dependent enzyme-catalyzed reactions of glycols, and Lewis-acid-catalyzed cleavages of beta-ethers in radicals might be applied in synthetic reactions.

  12. Rearrangement of sulfonamidyl radicals with hydrogen migration

    SciTech Connect

    Troyanskii, E.I.; Lazareva, M.I.; Nikishin, G.I.

    1987-01-20

    One-step outlying oxidative chlorination of alkanesulfonamides by the action of the Na/sub 2/S/sub 2/O/sub 8/-CuCl/sub 2/ system via intermediate sulfonamidyl radicals gives 3- and 4-chloroalkanesulfonamides. Rearrangements of sulfonamidyl radicals with H atom migration from the sulfonyl segment predominates over rearrangement with H atom migration from the amide segment.

  13. Rearrangements of organic peroxides and related processes

    PubMed Central

    Yaremenko, Ivan A; Vil’, Vera A; Demchuk, Dmitry V

    2016-01-01

    Summary This review is the first to collate and summarize main data on named and unnamed rearrangement reactions of peroxides. It should be noted, that in the chemistry of peroxides two types of processes are considered under the term rearrangements. These are conventional rearrangements occurring with the retention of the molecular weight and transformations of one of the peroxide moieties after O–O-bond cleavage. Detailed information about the Baeyer−Villiger, Criegee, Hock, Kornblum−DeLaMare, Dakin, Elbs, Schenck, Smith, Wieland, and Story reactions is given. Unnamed rearrangements of organic peroxides and related processes are also analyzed. The rearrangements and related processes of important natural and synthetic peroxides are discussed separately. PMID:27559418

  14. RET rearrangements in familial papillary thyroid carcinomas.

    PubMed

    Corvi, R; Lesueur, F; Martinez-Alfaro, M; Zini, M; Decaussin, M; Murat, A; Romeo, G

    2001-09-20

    Familial papillary thyroid carcinoma (FPTC) is an inherited tumor characterized by a more aggressive phenotype than that of its sporadic counterpart. Its mode of inheritance as well as its genetic and molecular bases are still poorly understood. On the contrary, genetic alterations in sporadic papillary thyroid carcinoma (PTC) are better characterized, the most common one involving the activation of the proto-oncogene RET through somatic rearrangements. In the present study, we investigated by interphase fluorescence in situ hybridization the presence of RET rearrangements in a series of 20 FPTC. We show that one FPTC and the adenoma from the same patient carry a RET rearrangement (type PTC1) and that this rearrangement is absent in the germline. Furthermore, we excluded a RET haplotype sharing in two brothers of the same family. These results show that RET rearrangements can indeed be found in FPTC and confirm that RET is not involved in the inherited predisposition to FPTC.

  15. Effect of acid-catalyzed formation rates of benzimidazole-linked polymers on porosity and selective CO2 capture from gas mixtures.

    PubMed

    Altarawneh, Suha; İslamoğlu, Timur; Sekizkardes, Ali Kemal; El-Kaderi, Hani M

    2015-04-01

    Benzimidazole-linked polymers (BILPs) are emerging candidates for gas storage and separation applications; however, their current synthetic methods offer limited control over textural properties which are vital for their multifaceted use. In this study, we investigate the impact of acid-catalyzed formation rates of the imidazole units on the porosity levels of BILPs and subsequent effects on CO2 and CH4 binding affinities and selective uptake of CO2 over CH4 and N2. Treatment of 3,3'-Diaminobenzidine tetrahydrochloride hydrate with 1,2,4,5-tetrakis(4-formylphenyl)benzene and 1,3,5-(4-formylphenyl)-benzene in anhydrous DMF afforded porous BILP-15 (448 m(2) g(-1)) and BILP-16 (435 m(2) g(-1)), respectively. Alternatively, the same polymers were prepared from the neutral 3,3'-Diaminobenzidine and catalytic amounts of aqueous HCl. The resulting polymers denoted BILP-15(AC) and BILP-16(AC) exhibited optimal surface areas; 862 m(2) g(-1) and 643 m(2) g(-1), respectively, only when 2 equiv of HCl (0.22 M) was used. In contrast, the CO2 binding affinity (Qst) dropped from 33.0 to 28.9 kJ mol(-1) for BILP-15 and from 32.0 to 31.6 kJ mol(-1) for BILP-16. According to initial slope calculations at 273 K/298 K, a notable change in CO2/N2 selectivity was observed for BILP-15(AC) (61/50) compared to BILP-15 (83/63). Similarly, ideal adsorbed solution theory (IAST) calculations also show the higher specific surface area of BILP-15(AC) and BILP-16(AC) compromises their CO2/N2 selectivity.

  16. Glycolytic regulation of cell rearrangement in angiogenesis.

    PubMed

    Cruys, Bert; Wong, Brian W; Kuchnio, Anna; Verdegem, Dries; Cantelmo, Anna Rita; Conradi, Lena-Christin; Vandekeere, Saar; Bouché, Ann; Cornelissen, Ivo; Vinckier, Stefan; Merks, Roeland M H; Dejana, Elisabetta; Gerhardt, Holger; Dewerchin, Mieke; Bentley, Katie; Carmeliet, Peter

    2016-01-01

    During vessel sprouting, endothelial cells (ECs) dynamically rearrange positions in the sprout to compete for the tip position. We recently identified a key role for the glycolytic activator PFKFB3 in vessel sprouting by regulating cytoskeleton remodelling, migration and tip cell competitiveness. It is, however, unknown how glycolysis regulates EC rearrangement during vessel sprouting. Here we report that computational simulations, validated by experimentation, predict that glycolytic production of ATP drives EC rearrangement by promoting filopodia formation and reducing intercellular adhesion. Notably, the simulations correctly predicted that blocking PFKFB3 normalizes the disturbed EC rearrangement in high VEGF conditions, as occurs during pathological angiogenesis. This interdisciplinary study integrates EC metabolism in vessel sprouting, yielding mechanistic insight in the control of vessel sprouting by glycolysis, and suggesting anti-glycolytic therapy for vessel normalization in cancer and non-malignant diseases. PMID:27436424

  17. The cytogenetics of mammalian autosomal rearrangements

    SciTech Connect

    Daniel, A. )

    1988-01-01

    This book is covered under the following topics: Ascertainment and risks of recombinant progeny; Infertility, gametic selection, and fetal loss; origin of chromosome rearrangements; and Some implications of chromosome breakpoints.

  18. Glycolytic regulation of cell rearrangement in angiogenesis

    PubMed Central

    Cruys, Bert; Wong, Brian W.; Kuchnio, Anna; Verdegem, Dries; Cantelmo, Anna Rita; Conradi, Lena-Christin; Vandekeere, Saar; Bouché, Ann; Cornelissen, Ivo; Vinckier, Stefan; Merks, Roeland M. H.; Dejana, Elisabetta; Gerhardt, Holger; Dewerchin, Mieke; Bentley, Katie; Carmeliet, Peter

    2016-01-01

    During vessel sprouting, endothelial cells (ECs) dynamically rearrange positions in the sprout to compete for the tip position. We recently identified a key role for the glycolytic activator PFKFB3 in vessel sprouting by regulating cytoskeleton remodelling, migration and tip cell competitiveness. It is, however, unknown how glycolysis regulates EC rearrangement during vessel sprouting. Here we report that computational simulations, validated by experimentation, predict that glycolytic production of ATP drives EC rearrangement by promoting filopodia formation and reducing intercellular adhesion. Notably, the simulations correctly predicted that blocking PFKFB3 normalizes the disturbed EC rearrangement in high VEGF conditions, as occurs during pathological angiogenesis. This interdisciplinary study integrates EC metabolism in vessel sprouting, yielding mechanistic insight in the control of vessel sprouting by glycolysis, and suggesting anti-glycolytic therapy for vessel normalization in cancer and non-malignant diseases. PMID:27436424

  19. Chiral Brønsted acid-catalyzed Friedel-Crafts alkylation of electron-rich arenes with in situ-generated ortho-quinone methides: highly enantioselective synthesis of diarylindolylmethanes and triarylmethanes.

    PubMed

    Saha, Satyajit; Alamsetti, Santosh Kumar; Schneider, Christoph

    2015-01-28

    We disclose herein a highly enantioselective protocol for the Brønsted acid-catalyzed addition of indoles and phenols to in situ-generated ortho-quinone methides which deliver broadly substituted diarylindolylmethanes and triarylmethanes, respectively, in a one-pot reaction under very mild conditions. A chiral phosphoric acid catalyst has been developed for this process serving to convert the starting ortho-hydroxybenzhydryl alcohols into the reactive ortho-quinone methides and to control the enantioselectivity of the carbon-carbon bond-forming event via hydrogen-bonding. PMID:25493449

  20. FLNA genomic rearrangements cause periventricular nodular heterotopia

    PubMed Central

    Clapham, K.R.; Yu, T.W.; Ganesh, V.S.; Barry, B.; Chan, Y.; Mei, D.; Parrini, E.; Funalot, B.; Dupuis, L.; Nezarati, M.M.; du Souich, C.; van Karnebeek, C.

    2012-01-01

    Objective: To identify copy number variant (CNV) causes of periventricular nodular heterotopia (PNH) in patients for whom FLNA sequencing is negative. Methods: Screening of 35 patients from 33 pedigrees on an Affymetrix 6.0 microarray led to the identification of one individual bearing a CNV that disrupted FLNA. FLNA-disrupting CNVs were also isolated in 2 other individuals by multiplex ligation probe amplification. These 3 cases were further characterized by high-resolution oligo array comparative genomic hybridization (CGH), and the precise junctional breakpoints of the rearrangements were identified by PCR amplification and sequencing. Results: We report 3 cases of PNH caused by nonrecurrent genomic rearrangements that disrupt one copy of FLNA. The first individual carried a 113-kb deletion that removes all but the first exon of FLNA. A second patient harbored a complex rearrangement including a deletion of the 3′ end of FLNA accompanied by a partial duplication event. A third patient bore a 39-kb deletion encompassing all of FLNA and the neighboring gene EMD. High-resolution oligo array CGH of the FLNA locus suggests distinct molecular mechanisms for each of these rearrangements, and implicates nearby low copy repeats in their pathogenesis. Conclusions: These results demonstrate that FLNA is prone to pathogenic rearrangements, and highlight the importance of screening for CNVs in individuals with PNH lacking FLNA point mutations. Neurology® 2012;78:269–278 PMID:22238415

  1. Crystal structure of 2α-(1,1-di­phenyl­eth­yl)-4-methyl-4α,5α-diphenyl-1,3-dioxolane: the result of a non-acid pinacol rearrangement

    PubMed Central

    Kirchner, Richard M.; Corfield, Peter W. R.; Annabi, Michelle; Regan, John; Speina, Kevin; DiProperzio, Anthony; Ciaccio, James A.; Capitani, Joseph F.

    2015-01-01

    The title compound, C30H28O2, was obtained during recrystallization of (±)-1,2-diphenyl-1,2-propane­diol in 1-butanol, from an unexpected non-acid-catalyzed pinacol rearrangement followed by acetal formation of the newly formed aldehyde with the diol. The tri-substituted dioxolane ring has a twist conformation on the C—O bond opposite the methyl-substituted C atom. There is an intra­molecular C—H⋯π inter­action present involving one of the di­phenyl­ethyl rings and an H atom of the phenyl ring in position 4 of the dioxolane ring. In the crystal, mol­ecules are linked by weak C—H⋯O hydrogen bonds, forming chains along [001]. The chains are linked by a second C—H⋯π inter­action, forming sheets parallel to the bc plane. PMID:26594491

  2. Cortical microtubule rearrangements and cell wall patterning

    PubMed Central

    Oda, Yoshihisa

    2015-01-01

    Plant cortical microtubules, which form a highly ordered array beneath the plasma membrane, play essential roles in determining cell shape and function by directing the arrangement of cellulosic and non-cellulosic compounds on the cell surface. Interphase transverse arrays of cortical microtubules self-organize through their dynamic instability and inter-microtubule interactions, and by branch-form microtubule nucleation and severing. Recent studies revealed that distinct spatial signals including ROP GTPase, cellular geometry, and mechanical stress regulate the behavior of cortical microtubules at the subcellular and supercellular levels, giving rise to dramatic rearrangements in the cortical microtubule array in response to internal and external cues. Increasing evidence indicates that negative regulators of microtubules also contribute to the rearrangement of the cortical microtubule array. In this review, I summarize recent insights into how the rearrangement of the cortical microtubule array leads to proper, flexible cell wall patterning. PMID:25904930

  3. Four mechanisms in the reactions of 3-aminopyrrole with 1,3,5-triazines: inverse electron demand Diels-Alder cycloadditions vs S(N)Ar reactions via uncatalyzed and acid-catalyzed pathways.

    PubMed

    De Rosa, Michael; Arnold, David; Hartline, Douglas

    2013-09-01

    Reaction of 3-aminopyrrole with seven 1,3,5-triazines was studied in a one-step reaction (in situ formation of 3-aminopyrrole) and a two-step reaction (using the tetraphenylborate salt and an amine base). An inverse-electron demand Diels-Alder reaction (IEDDA) was observed with R1 = CF3, CO2Et, and H with the formation of 5H-pyrrolo[3,2-d]pyrimidine derivatives. S(N)Ar was observed when 2,4,6-trifluoro- or 2,4,6-trichloro-1,3,5-triazine were used--1,3,5-triazines that had leaving groups. If excess 1,3,5-triazine was present the initial S(N)Ar product reacted further, in the presence of acid and water, with another equivalent of 1,3,5-triazine to give compounds containing three linked heterocyclic rings. No reaction was observed with R1 = C6H5 and OCH3. Four mechanisms are proposed to explain the experimental results: uncatalyzed and acid catalyzed inverse electron demand Diels-Alder cascades leading to cycloaddition, and uncatalyzed and acid-catalyzed S(N)Ar reactions leading, respectively, to single and double substitution products. Acid catalysis was a factor when there was reduced reactivity in either reactant.

  4. Osteosarcoma With Apparent Ewing Sarcoma Gene Rearrangement.

    PubMed

    Mathias, Melissa D; Chou, Alexander J; Meyers, Paul; Shukla, Neerav; Hameed, Meera; Agaram, Narasimhan; Wang, Lu; Berger, Michael F; Walsh, Michael; Kentsis, Alex

    2016-07-01

    Poorly differentiated round cell sarcomas present diagnostic challenges because of their variable morphology and lack of specific immunophenotypic markers. We present a case of a 15-year-old female with a tibial tumor that exhibited features of Ewing-like sarcoma, including apparent rearrangement of the EWSR1 gene. Hybridization capture-based next-generation DNA sequencing showed evidence of complex genomic rearrangements, absence of known pathogenic Ewing-like chromosome translocations, and deletions RB1, PTCH1, and ATRX, supporting the diagnosis of osteosarcoma. This illustrates the potential of clinical genomic profiling to improve diagnosis and enable specifically targeted therapies for cancers with complex pathologies. PMID:27352193

  5. Algorithm to search for genomic rearrangements

    NASA Astrophysics Data System (ADS)

    Nałecz-Charkiewicz, Katarzyna; Nowak, Robert

    2013-10-01

    The aim of this article is to discuss the issue of comparing nucleotide sequences in order to detect chromosomal rearrangements (for example, in the study of genomes of two cucumber varieties, Polish and Chinese). Two basic algorithms for detecting rearrangements has been described: Smith-Waterman algorithm, as well as a new method of searching genetic markers in combination with Knuth-Morris-Pratt algorithm. The computer program in client-server architecture was developed. The algorithms properties were examined on genomes Escherichia coli and Arabidopsis thaliana genomes, and are prepared to compare two cucumber varieties, Polish and Chinese. The results are promising and further works are planned.

  6. Tyrosine kinase gene rearrangements in epithelial malignancies.

    PubMed

    Shaw, Alice T; Hsu, Peggy P; Awad, Mark M; Engelman, Jeffrey A

    2013-11-01

    Chromosomal rearrangements that lead to oncogenic kinase activation are observed in many epithelial cancers. These cancers express activated fusion kinases that drive the initiation and progression of malignancy, and often have a considerable response to small-molecule kinase inhibitors, which validates these fusion kinases as 'druggable' targets. In this Review, we examine the aetiologic, pathogenic and clinical features that are associated with cancers harbouring oncogenic fusion kinases, including anaplastic lymphoma kinase (ALK), ROS1 and RET. We discuss the clinical outcomes with targeted therapies and explore strategies to discover additional kinases that are activated by chromosomal rearrangements in solid tumours.

  7. Tyrosine kinase gene rearrangements in epithelial malignancies

    PubMed Central

    Shaw, Alice T.; Hsu, Peggy P.; Awad, Mark M.; Engelman, Jeffrey A.

    2014-01-01

    Chromosomal rearrangements that lead to oncogenic kinase activation are observed in many epithelial cancers. These cancers express activated fusion kinases that drive the initiation and progression of malignancy, and often have a considerable response to small-molecule kinase inhibitors, which validates these fusion kinases as ‘druggable’ targets. In this Review, we examine the aetiologic, pathogenic and clinical features that are associated with cancers harbouring oncogenic fusion kinases, including anaplastic lymphoma kinase (ALK), ROS1 and RET. We discuss the clinical outcomes with targeted therapies and explore strategies to discover additional kinases that are activated by chromosomal rearrangements in solid tumours. PMID:24132104

  8. Facility rearrangement scoping study: Draft letter report

    SciTech Connect

    Not Available

    1987-04-17

    We assessed the feasibility of designing the salt repository layouts so that shafts, surface structures and facilities would be totally within the north-east (NE) and center-east (CE) (one square mile) sections of the 9 square mile Deaf Smith site. With the latest version of the SCP-Conceptual Design as the basis, rearrangement analyses were conducted for the surface and subsurface layouts. For the rearranged layouts that were workable, impact assessments, relative to the SCP-Conceptual Design, were performed. This study concluded that, on a qualitative basis, the salt repository surface facilities can be relocated to within the north-east and center-east sections of the site. A suitable subsurface layout can be designed to accommodate this rearrangement. The resultant surface rearrangement is depicted. The two study sections (NE and CE) are emphasized on this figure. For reference, the location of the surface facilities in the SCP-Conceptual Design is also shown. 11 refs., 1 tab.

  9. Deep cytoplasmic rearrangements in ventralized Xenopus embryos

    NASA Technical Reports Server (NTRS)

    Brown, E. E.; Denegre, J. M.; Danilchik, M. V.

    1993-01-01

    Following fertilization in Xenopus, dramatic rearrangements of the egg cytoplasm relocalize maternally synthesized egg components. During the first cell cycle the vegetal yolk mass rotates relative to the egg surface, toward the sperm entry point (SEP) (J. P. Vincent, G. F. Oster, and J. C. Gerhart, 1986, Dev. Biol. 113, 484-500), while concomitant deep cytoplasmic rearrangements occur in the animal hemisphere (M. V. Danilchik and J. M. Denegre, 1991, Development 111, 845-856). In this paper we examine the role of vegetal yolk mass rotation in producing the animal cytoplasmic rearrangements. We inhibited rotation by uv-irradiating embryos during the first cell cycle, a treatment that yields an extremely ventralized phenotype. Both uv-irradiated embryos and unirradiated control embryos show cytoplasmic rearrangements in the animal hemisphere during the first cell cycle. Cytoplasmic rearrangements on the SEP side of the embryo associated with the path of the sperm pronucleus, plus a swirl on the anti-SEP (dorsal) side, are seen, whether or not yolk mass rotation has occurred. This result suggests a role for the expanding sperm aster in directing animal hemisphere cytoplasmic movements. In unirradiated control embryos the anti-SEP (dorsal) swirl is larger than that in uv-irradiated embryos and often extends into the vegetal hemisphere, consistent with the animal cytoplasm having been pulled dorsally and vegetally by the sliding vegetal yolk mass. Thus the yolk mass rotation may normally enhance the dorsalward cytoplasmic movement, begun by the sperm aster, enough to induce normal axis formation. We extended our observations of unirradiated control and uv-irradiated embryos through early cleavages. The vegetal extent of the anti-SEP (dorsal) swirl pattern seen in control embryos persists through the early cleavage period, such that labeled animal cytoplasm extends deep into dorsal third-tier blastomeres at the 32-cell stage. Significantly, in uv-irradiated embryos

  10. Dynamics of genome rearrangement in bacterial populations.

    PubMed

    Darling, Aaron E; Miklós, István; Ragan, Mark A

    2008-01-01

    Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first

  11. Dynamics of Genome Rearrangement in Bacterial Populations

    PubMed Central

    Darling, Aaron E.; Miklós, István; Ragan, Mark A.

    2008-01-01

    Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of “symmetric inversions”—inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the

  12. Organometallic Enantiomeric Scaffolding: General Access to 2-Substituted Oxa- and Azabicyclo[3.2.1]octenes via a Brønsted Acid-catalyzed [5+2] Cycloaddition Reaction

    PubMed Central

    Garnier, Ethel C.; Liebeskind, Lanny S.

    2009-01-01

    6-Substituted TpMo(CO)2(η-2,3,4-pyranyl)- and TpMo(CO)2(η-2,3,4-pyridinyl) scaffolds (Tp = hydridotrispyrazolylborato) function as reaction partners in an efficient regio- and stereocontrolled synthesis of functionalized oxa- and azabicyclo[3.2.1]octenes through a novel Brønsted acid-catalyzed [5+2] cycloaddition reaction. Excellent exo-selectivities are obtained and the reaction gives products with complete retention of enantiomeric purity when carried out with chiral, non-racemic scaffolds. The substituent at C-6 of the η3-coordinated heterocyclic scaffold not only influences [5+2] reactivity but also plays a critical role in the demetalation step directing the reaction to only one of two possible products. PMID:18479131

  13. [Rearrangement and inference of chromosome structures].

    PubMed

    Gorbunov, K Yu; Gershgorin, R A; Lyubetsky, V A

    2015-01-01

    The chromosome structure is defined as a set of chromosomes that consist of genes assigned to one of the DNA strands and represented in a circular or linear arrangement. A widely investigated problem is to define the shortest algorithmic path of chromosome rearrangements that transforms one chromosome structure into another. When equal rearrangement costs and constant gene content are considered, the solution to the problem is known. In this work, a principally novel approach was developed that presents an exact algorithm with linear time complexity for both equal and unequal costs, in which chromosome structures defined on the same set of genes were considered. In addition, to solve the problem of the inference of ancestral chromosome structures containing different sets of genes when the original structures are fixed in leaves, exact and heuristic algorithms were developed.

  14. Enhancing bilinear subspace learning by element rearrangement.

    PubMed

    Xu, Dong; Yan, Shuicheng; Lin, Stephen; Huang, Thomas S; Chang, Shih-Fu

    2009-10-01

    The success of bilinear subspace learning heavily depends on reducing correlations among features along rows and columns of the data matrices. In this work, we study the problem of rearranging elements within a matrix in order to maximize these correlations so that information redundancy in matrix data can be more extensively removed by existing bilinear subspace learning algorithms. An efficient iterative algorithm is proposed to tackle this essentially integer programming problem. In each step, the matrix structure is refined with a constrained Earth Mover's Distance procedure that incrementally rearranges matrices to become more similar to their low-rank approximations, which have high correlation among features along rows and columns. In addition, we present two extensions of the algorithm for conducting supervised bilinear subspace learning. Experiments in both unsupervised and supervised bilinear subspace learning demonstrate the effectiveness of our proposed algorithms in improving data compression performance and classification accuracy.

  15. Catalytic synthesis of amides via aldoximes rearrangement.

    PubMed

    Crochet, Pascale; Cadierno, Victorio

    2015-02-14

    Amide bond formation reactions are among the most important transformations in organic chemistry because of the widespread occurrence of amides in pharmaceuticals, natural products and biologically active compounds. The Beckmann rearrangement is a well-known method to generate secondary amides from ketoximes. However, under the acidic conditions commonly employed, aldoximes RHC=NOH rarely rearrange into the corresponding primary amides RC(=O)NH2. In recent years, it was demonstrated that this atom-economical transformation can be carried out efficiently and selectively with the help of metal catalysts. Several homogeneous and heterogenous systems have been described. In addition, protocols offering the option to generate the aldoximes in situ from the corresponding aldehydes and hydroxylamine, or even from alcohols, have also been developed, as well as a series of tandem processes allowing the access to N-substituted amide products. In this Feature article a comprehensive overview of the advances achieved in this particular research area is presented.

  16. Sampling and counting genome rearrangement scenarios

    PubMed Central

    2015-01-01

    Background Even for moderate size inputs, there are a tremendous number of optimal rearrangement scenarios, regardless what the model is and which specific question is to be answered. Therefore giving one optimal solution might be misleading and cannot be used for statistical inferring. Statistically well funded methods are necessary to sample uniformly from the solution space and then a small number of samples are sufficient for statistical inferring. Contribution In this paper, we give a mini-review about the state-of-the-art of sampling and counting rearrangement scenarios, focusing on the reversal, DCJ and SCJ models. Above that, we also give a Gibbs sampler for sampling most parsimonious labeling of evolutionary trees under the SCJ model. The method has been implemented and tested on real life data. The software package together with example data can be downloaded from http://www.renyi.hu/~miklosi/SCJ-Gibbs/ PMID:26452124

  17. Genomic and functional overlap between somatic and germline chromosomal rearrangements.

    PubMed

    van Heesch, Sebastiaan; Simonis, Marieke; van Roosmalen, Markus J; Pillalamarri, Vamsee; Brand, Harrison; Kuijk, Ewart W; de Luca, Kim L; Lansu, Nico; Braat, A Koen; Menelaou, Androniki; Hao, Wensi; Korving, Jeroen; Snijder, Simone; van der Veken, Lars T; Hochstenbach, Ron; Knegt, Alida C; Duran, Karen; Renkens, Ivo; Alekozai, Najla; Jager, Myrthe; Vergult, Sarah; Menten, Björn; de Bruijn, Ewart; Boymans, Sander; Ippel, Elly; van Binsbergen, Ellen; Talkowski, Michael E; Lichtenbelt, Klaske; Cuppen, Edwin; Kloosterman, Wigard P

    2014-12-24

    Genomic rearrangements are a common cause of human congenital abnormalities. However, their origin and consequences are poorly understood. We performed molecular analysis of two patients with congenital disease who carried de novo genomic rearrangements. We found that the rearrangements in both patients hit genes that are recurrently rearranged in cancer (ETV1, FOXP1, and microRNA cluster C19MC) and drive formation of fusion genes similar to those described in cancer. Subsequent analysis of a large set of 552 de novo germline genomic rearrangements underlying congenital disorders revealed enrichment for genes rearranged in cancer and overlap with somatic cancer breakpoints. Breakpoints of common (inherited) germline structural variations also overlap with cancer breakpoints but are depleted for cancer genes. We propose that the same genomic positions are prone to genomic rearrangements in germline and soma but that timing and context of breakage determines whether developmental defects or cancer are promoted. PMID:25497101

  18. Structural analysis of a carcinogen-induced genomic rearrangement event

    SciTech Connect

    Barr, F.G.; Davis, R.J.; Eichenfield, L.; Emanuel, B.S. Univ. of Pennsylvania, Philadelphia )

    1992-02-01

    The authors have explored the mechanism of genomic rearrangement in a hamster fibroblast cell culture system in which rearrangements are induced 5{prime} to the endogenous thymidine kinase gene by chemical carcinogen treatment. The wild-type region around one rearrangement breakpoint was cloned and sequenced. With this sequence information, the carcinogen-induced rearrangement was cloned from the corresponding rearranged cell line by the inverse polymerase chain reaction. After the breakpoint fragment was sequenced, the wild-type rearrangement partner (RP15) was isolated by a second inverse polymerase chain reaction of unrearranged DNA. Comparison of the sequence of the rearrangement breakpoint with the wild-type RP15 and 5{prime} thymidine kinase gene regions revealed short repeats directly at the breakpoint, as well as nearby A+T-rich regions in rearrangement partner. Therefore, these studies reveal interesting sequence and chromatin features near the rearrangement breakpoints and suggest a role for nuclear organization in the mechanism of carcinogen-induced genomic rearrangement.

  19. A general heuristic for genome rearrangement problems.

    PubMed

    Dias, Ulisses; Galvão, Gustavo Rodrigues; Lintzmayer, Carla Négri; Dias, Zanoni

    2014-06-01

    In this paper, we present a general heuristic for several problems in the genome rearrangement field. Our heuristic does not solve any problem directly, it is rather used to improve the solutions provided by any non-optimal algorithm that solve them. Therefore, we have implemented several algorithms described in the literature and several algorithms developed by ourselves. As a whole, we implemented 23 algorithms for 9 well known problems in the genome rearrangement field. A total of 13 algorithms were implemented for problems that use the notions of prefix and suffix operations. In addition, we worked on 5 algorithms for the classic problem of sorting by transposition and we conclude the experiments by presenting results for 3 approximation algorithms for the sorting by reversals and transpositions problem and 2 approximation algorithms for the sorting by reversals problem. Another algorithm with better approximation ratio can be found for the last genome rearrangement problem, but it is purely theoretical with no practical implementation. The algorithms we implemented in addition to our heuristic lead to the best practical results in each case. In particular, we were able to improve results on the sorting by transpositions problem, which is a very special case because many efforts have been made to generate algorithms with good results in practice and some of these algorithms provide results that equal the optimum solutions in many cases. Our source codes and benchmarks are freely available upon request from the authors so that it will be easier to compare new approaches against our results. PMID:24969750

  20. Gene conversion in human rearranged immunoglobulin genes.

    PubMed

    Darlow, John M; Stott, David I

    2006-07-01

    Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V(H) segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V(H) replacements with no addition of untemplated nucleotides at the V(H)-V(H) joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V(H) replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion.

  1. Gene activation by induced DNA rearrangements

    SciTech Connect

    Schnipper, L.E.; Chan, V.; Sedivy, J.; Jat, P.; Sharp, P.A. )

    1989-12-01

    A murine cell line (EN/NIH) containing the retroviral vector ZIPNeoSV(x)1 that was modified by deletion of the enhancer elements in the viral long terminal repeats has been used as an assay system to detect induced DNA rearrangements that result in activation of a transcriptionally silent reporter gene encoded by the viral genome. The spontaneous frequency of G418 resistance is less than 10(-7), whereas exposure to the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) or the combination of UV irradiation plus TPA resulted in the emergence of drug resistant cell lines at a frequency of 5 per 10(6) and 67 per 10(6) cells, respectively. In several of the cell lines that were analyzed a low level of amplification of one of the two parental retroviral integrants was observed, whereas in others no alteration in the region of the viral genome was detected. To determine the effect of the SV40 large T antigen on induced DNA rearrangements, EN/NIH cells were transfected with a temperature sensitive (ts) mutant of SV40 T. Transfectants were maintained at the permissive temperature (33 degrees C) for varying periods of time (1-5 days) in order to vary SV40 T antigen exposure, after which they were shifted to 39.5 degrees C for selection in G418. The frequency of emergence of drug resistant cell clones increased with duration of exposure to large T antigen (9-52 per 10(6) cells over 1-5 days, respectively), and all cell lines analyzed demonstrated DNA rearrangements in the region of the neo gene. A novel 18-kilobase pair XbaI fragment was cloned from one cell line which revealed the presence of a 2.0-kilobase pair EcoRI segment containing an inverted duplication which hybridized to neo sequences. It is likely that the observed rearrangement was initiated by the specific binding of large T antigen to the SV40 origin of replication encoded within the viral genome.

  2. Rearranged hopanes in sediments and petroleum

    SciTech Connect

    Moldowan, J.M.; Fago, F.J.; Carlson, R.M.K. ); Young, D.C. ); Van Duyne, G.; Clardy, J. ); Schoell, M. ); Pilinger, C.T. ); Watt, D.S. )

    1991-11-01

    Two new rearranged hopanoid hydrocarbons have been isolated from a Prudhoe Bay crude, Alaska. 17{alpha}(H)-15{alpha}-methyl-27-norhopane was determined by X-ray crystallography. It is the first identified member of a new series of rearranged hopanes the authors propose to call 17{alpha}(H)-diahopanes. Analysis by gas chromatography-mass spectrometry-mass spectrometry (GC-MSS-MS) of the parents of m/z 191 in several crudes suggests that this compound is a member of a C{sub 29}-C{sub 34}series of 17{alpha}(H)-diahopanes common to many crude oils and sediments. In addition, a new member of the 18{alpha}(H)-neohopane series has also been elucidated. Determination of 18{alpha}(H)-17{alpha}-methyl-28,30-dinorhopane (18{alpha}(H)-30-norneohopane), which the authors propose to nickname C{sub 29}Ts, hinged upon advanced nuclear magnetic resonance (NMR) techniques (at 500 and 600 MHz) such as proton-detected {sup 1}H-13 correlated spectra for the C-skeleton and Rotating-frame Overhauser Enhancement Spectroscopy (ROESY) for stereochemistry, as well as several other two-dimensional (2D) NMR techniques. The structures of these rearranged hopanes are consistent with an origin by catalytic rearrangement from hopanes during early diagenesis. Carbon isotopic data collected on Ts, 17{alpha}(H)-diahopane, C{sub 29}Ts, 17{alpha}(H)-22,29,30-trisnorhopane (Tm), 17 {alpha}(H)-30-norhopane, and 17{alpha}(H)-hopane isolated from the Prudhoe Bay oil are in the {minus}27 to {minus}28% {delta}{sup 13}C range supporting mechanistic arguments based on structures that all are derived from common precursors. These {delta}{sup 13}C values are slightly more positive than the whole Prudhoe Bay oil ({minus}30.1%), suggesting that these hopanes may have been derived from heterotrophic or cyanobacteria in the paleoecosystem during deposition of its source rock.

  3. Molecular Cytogenetic Analysis of Telomere Rearrangements

    PubMed Central

    Martin, Christa Lese; Ledbetter, David H.

    2015-01-01

    Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several FISH-based methodologies that can be employed to study these unique regions of human chromosomes. It is a revision of the original version of the unit published in 2000, now including an introductory section describing advances in the discipline that have taken place since the original publication. PMID:25599669

  4. On the spot: very local chromosomal rearrangements

    PubMed Central

    Helsmoortel, Céline; Vandeweyer, Geert

    2012-01-01

    Over the last decade, the detection of chromosomal abnormalities has shifted from conventional karyotyping under a light microscope to molecular detection using microarrays. The latter technology identified copy number variation as a major source of variation in the human genome; moreover, copy number variants were found responsible for 10-20% of cases of intellectual disability. Recent technological advances in microarray technology have also enabled the detection of very small local chromosomal rearrangements, sometimes affecting the function of only a single gene. Here, we illustrate how high resolution microarray analysis has led to increased insights into the contribution of specific genes in disease. PMID:23189093

  5. Structures of Local Rearrangements in Soft Colloidal Glasses.

    PubMed

    Yang, Xiunan; Liu, Rui; Yang, Mingcheng; Wang, Wei-Hua; Chen, Ke

    2016-06-10

    We image local structural rearrangements in soft colloidal glasses under small periodic perturbations induced by thermal cycling. Local structural entropy S_{2} positively correlates with observed rearrangements in colloidal glasses. The high S_{2} values of the rearranging clusters in glasses indicate that fragile regions in glasses are structurally less correlated, similar to structural defects in crystalline solids. Slow-evolving high S_{2} spots are capable of predicting local rearrangements long before the relaxations occur, while fluctuation-created high S_{2} spots best correlate with local deformations right before the rearrangement events. Local free volumes are also found to correlate with particle rearrangements at extreme values, although the ability to identify relaxation sites is substantially lower than S_{2}. Our experiments provide an efficient structural identifier for the fragile regions in glasses and highlight the important role of structural correlations in the physics of glasses. PMID:27341261

  6. Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

    PubMed Central

    Hare, Stephanie R

    2016-01-01

    Summary This review describes unexpected dynamical behaviors of rearranging carbocations and the modern computational methods used to elucidate these aspects of reaction mechanisms. Unique potential energy surface topologies associated with these rearrangements have been discovered in recent years that are not only of fundamental interest, but also provide insight into the way Nature manipulates chemical space to accomplish specific chemical transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout. PMID:27340434

  7. Exceptional Complex Chromosomal Rearrangements in Three Generations

    PubMed Central

    Kartapradja, Hannie; Marzuki, Nanis Sacharina; Pertile, Mark D.; Francis, David; Suciati, Lita Putri; Anggaratri, Helena Woro; Ambarwati, Debby Dwi; Idris, Firman Prathama; Lesmana, Harry; Trimarsanto, Hidayat; Paramayuda, Chrysantine; Harahap, Alida Roswita

    2015-01-01

    We report an exceptional complex chromosomal rearrangement (CCR) found in three individuals in a family that involves 4 chromosomes with 5 breakpoints. The CCR was ascertained in a phenotypically abnormal newborn with additional chromosomal material on the short arm of chromosome 4. Maternal karyotyping indicated that the mother carried an apparently balanced CCR involving chromosomes 4, 6, 11, and 18. Maternal transmission of the derivative chromosome 4 resulted in partial trisomy for chromosomes 6q and 18q and a partial monosomy of chromosome 4p in the proband. Further family studies found that the maternal grandmother carried the same apparently balanced CCR as the proband's mother, which was confirmed using the whole chromosome painting (WCP) FISH. High resolution whole genome microarray analysis of DNA from the proband's mother found no evidence for copy number imbalance in the vicinity of the CCR translocation breakpoints, or elsewhere in the genome, providing evidence that the mother's and grandmother's CCRs were balanced at a molecular level. This structural rearrangement can be categorized as an exceptional CCR due to its complexity and is a rare example of an exceptional CCR being transmitted in balanced and/or unbalanced form across three generations. PMID:25722897

  8. Programmed genome rearrangements in the ciliate Oxytricha

    PubMed Central

    Yerlici, V. Talya; Landweber, Laura F.

    2015-01-01

    The ciliate Oxytricha is a microbial eukaryote with two genomes, one of which experiences extensive genome remodeling during development. Each round of conjugation initiates a cascade of events that construct a transcriptionally active somatic genome from a scrambled germline genome, with considerable help from both long and small noncoding RNAs. This process of genome remodeling entails massive DNA deletion and reshuffling of remaining DNA segments to form functional genes from their interrupted and scrambled germline precursors. The use of Oxytricha as a model system provides an opportunity to study an exaggerated form of programmed genome rearrangement. Furthermore, studying the mechanisms that maintain nuclear dimorphism and mediate genome rearrangement has demonstrated a surprising plasticity and diversity of non-coding RNA pathways, with new roles that go beyond conventional gene silencing. Another aspect of ciliate genetics is their unorthodox patterns of RNA-mediated, epigenetic inheritance, that rival Mendelian inheritance. This review takes the reader through the key experiments in a model eukaryote that led to fundamental discoveries in RNA biology and pushes the biological limits of DNA processing. PMID:26104449

  9. Dispersion-Energy-Driven Wagner–Meerwein Rearrangements in Oligosilanes

    PubMed Central

    2016-01-01

    The installation of structural complex oligosilanes from linear starting materials by Lewis acid induced skeletal rearrangement reactions was studied under stable ion conditions. The produced cations were fully characterized by multinuclear NMR spectroscopy at low temperature, and the reaction course was studied by substitution experiments. The results of density functional theory calculations indicate the decisive role of attractive dispersion forces between neighboring trimethylsilyl groups for product formation in these rearrangement reactions. These attractive dispersion interactions control the course of Wagner–Meerwein rearrangements in oligosilanes, in contrast to the classical rearrangement in hydrocarbon systems, which are dominated by electronic substituent effects such as resonance and hyperconjugation. PMID:27195490

  10. Cytoplasmic rearrangements associated with amphibian egg symmetrization

    NASA Technical Reports Server (NTRS)

    Malacinski, G. M.

    1984-01-01

    Cytoplasmic rearrangements which follow fertilization were mentioned in normal and inverted eggs. A set of yolk compartments was resolved by cytological analyses of both normally oriented and inverted eggs. Those compartments were characterized by their yolk platelet compositions and movement during egg inversion. It is found that during egg inversion the yolk compartments shift minor cytoplasmic compartments which line the egg cortex. Those yolk mass shifts occurred only after the inverted egg was activated. The direction of shift of the major yolk components, rather than the sperm entrance site, determines the dorsal/ventral polarity of the inverted egg. Among different spawnings the rate of shift varied. Eggs that displayed the fastest rate of shift exhibited the highest frequency of developmental abnormalities during organogenesis. Interpretation of novel observations on cytoplasmic organization provide criticism of some earlier models. A new density compartment model is presented as a coherent way to view the organization of the egg cytoplasm and the development of bilateral symmetry.

  11. New progress in snake mitochondrial gene rearrangement.

    PubMed

    Chen, Nian; Zhao, Shujin

    2009-08-01

    To further understand the evolution of snake mitochondrial genomes, the complete mitochondrial DNA (mtDNA) sequences were determined for representative species from two snake families: the Many-banded krait, the Banded krait, the Chinese cobra, the King cobra, the Hundred-pace viper, the Short-tailed mamushi, and the Chain viper. Thirteen protein-coding genes, 22-23 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNAPro gene were two notable features of the snake mtDNAs. These results from the gene rearrangement comparisons confirm the correctness of traditional classification schemes and validate the utility of comparing complete mtDNA sequences for snake phylogeny reconstruction. PMID:19479623

  12. Minimal distortion pathways in polyhedral rearrangements.

    PubMed

    Casanova, David; Cirera, Jordi; Llunell, Miquel; Alemany, Pere; Avnir, David; Alvarez, Santiago

    2004-02-18

    A definition of minimum distortion paths between two polyhedra in terms of continuous shape measures (CShM) is presented. A general analytical expression deduced for such pathways makes use of one parameter, the minimum distortion constant, that can be easily obtained through the CShM methodology and is herein tabulated for pairs of polyhedra having four to eight vertexes. The work presented here also allows us to obtain representative model molecular structures along the interconversion pathways. Several commonly used polytopal rearrangement pathways are shown to be in fact minimum distortion pathways: the spread path leading from the tetrahedron to the square, the Berry pseudorotation that interconverts a square pyramid and a trigonal bipyramid, and the Bailar twist for the interconversion of the octahedron and the trigonal prism. Examples of applications to the analysis of the stereochemistries of several families of metal complexes are presented. PMID:14871107

  13. Global alignment: Finding rearrangements during alignment

    SciTech Connect

    Brudno, Michael; Malde, Sanket; Poliakov, Alexander; Do, Chuong B.; Couronne, Olivier; Dubchak, Inna; Batzoglou, Serafim

    2003-01-06

    Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global alignment, where one string is transformed into the other, and local alignment, where all locations of similarity between the two strings are returned. Global alignments are less prone to demonstrating false homology as each letter of one sequence is constrained to being aligned to only one letter of the other. Local alignments, on the other hand, can cope with rearrangements between non-syntenic, orthologous sequences by identifying similar regions in sequences; this, however, comes at the expense of a higher false positive rate due to the inability of local aligners to take into account overall conservation maps.

  14. Androgen receptor gene mutation, rearrangement, polymorphism.

    PubMed

    Eisermann, Kurtis; Wang, Dan; Jing, Yifeng; Pascal, Laura E; Wang, Zhou

    2013-09-01

    Genetic aberrations of the androgen receptor (AR) caused by mutations, rearrangements, and polymorphisms result in a mutant receptor that has varied functions compared to wild type AR. To date, over 1,000 mutations have been reported in the AR with most of these being associated with androgen insensitivity syndrome (AIS). While mutations of AR associated with prostate cancer occur less often in early stage localized disease, mutations in castration-resistant prostate cancer (CRPC) patients treated with anti-androgens occur more frequently with 10-30% of these patients having some form of mutation in the AR. Resistance to anti-androgen therapy usually results from gain-of-function mutations in the LBD such as is seen with bicalutamide and more recently with enzalutamide (MDV3100). Thus, it is crucial to investigate these new AR mutations arising from drug resistance to anti-androgens and other small molecule pharmacological agents.

  15. A Novel synthesis of 2-functionalized benzofurans by palladium-catalyzed cycloisomerization of 2-(1-hydroxyprop-2-ynyl)phenols followed by acid-catalyzed allylic isomerization or allylic nucleophilic substitution.

    PubMed

    Gabriele, Bartolo; Mancuso, Raffaella; Salerno, Giuseppe

    2008-09-19

    A novel two-step synthesis of 2-hydroxymethylbenzofurans 3 and 2-alkoxymethylbenzofurans 4-6, based on palladium-catalyzed cycloisomerization of 2-(1-hydroxyprop-2-ynyl)phenols 1 under basic conditions to give 2-methylene-2,3-dihydrobenzofuran-3-ols 2, followed by acid-catalyzed isomerization or allylic nucleophilic substitution with alcohols as nucleophiles, is reported. Cycloisomerization reactions leading to 2 (80-98% yields) were carried out at 40 degrees C in MeOH as the solvent, in the presence of a base and catalytic amounts of PdX2 + 2KX (X = Cl, I). Isomerization reactions of 2 readily occurred at 25-60 degrees C in DME as the solvent, with H2SO4 as the proton source, to give 2-hydroxymethylbenzofurans 3 in 65-90% yields. In a similar manner, allylic nucleophilic substitution reactions of 2 with ROH as nucleophiles [carried out at 25-40 degrees C in ROH (R = Me) or ROH-DME mixtures (R = Bu, Bn) in the presence of H2SO4] afforded 2-alkoxymethylbenzofurans 4, 5, and 6 (R = Me, Bu, and Bn, respectively), in 65-98% yields.

  16. Synthesis of Methyl Cyclopentanecarboxylate: A Laboratory Experience in Carbon Rearrangement

    ERIC Educational Resources Information Center

    Orchard, Alexandra; Maniquis, Roxanne V.; Salzameda, Nicholas T.

    2016-01-01

    We present a novel guided inquiry second semester organic chemistry laboratory rearrangement experiment. Students performed the Favorskii Rearrangement to obtain methyl cyclopentanecarboxylate in good yields. The students learned about the individual steps of the Favorskii mechanism and were required to propose a complete reaction mechanism and…

  17. Enantioselective Claisen rearrangements with a hydrogen-bond donor catalyst.

    PubMed

    Uyeda, Christopher; Jacobsen, Eric N

    2008-07-23

    N,N'-Diphenylguanidinium ion associated with the noncoordinating BArF counterion is shown to be an effective catalyst for the [3,3]-sigmatropic rearrangement of a variety of substituted allyl vinyl ethers. Highly enantioselective catalytic Claisen rearrangements of ester-substituted allyl vinyl ethers are then documented using a new C2-symmetric guanidinium ion derivative. PMID:18576616

  18. Rate of accumulation of reproductive isolation by chromosome rearrangements

    SciTech Connect

    Walsh, J.B.

    1981-09-01

    The role of chromosome rearrangements as agents for rapid speciation has recently gained considerable support among evolutionary biologists, especially for the stasipatric model in which effective isolation is accomplished by fixation of a few strongly underdominant rearrangements. This support is, however, by no means universal, with critics citing the low probability of fixation of strongly underdominant rearrangements as a major problem of the stasipatric model. Population genetic considerations of the substitution rate of underdominant rearrangements in a finite population were examined by Lande, but as an estimator of long term effective deme size, rather than as a speciation model. The rate of accumulation of postzygotic isolation is analyzed for three models of underdominant rearrangements: strict underdominance; underdominance with the rearrangement homozygote being at a selective advantage; and underdominance with meiotic drive. It will be shown that reproductive isolation accumulates most rapidly in very small populations, but that strong homozygote advantage or drive can allow for fairly rapid speciation under certain conditions in large populations. Contrary to the stasipatric model, isolation usually proceeds most rapidly by fixation of a large number of weakly underdominant rearrangements even when moderate amounts of drive or homozygote advantage are allowed. Stasipatric speciation requires either the frequent occurrence of meiotically driven rearrangements or very small population sizes to operate in reasonable times.

  19. Uniparental disomy analysis in carriers of balanced chromosome rearrangements

    SciTech Connect

    May, K.M.; Pettay, D.; Muralidharan, K.

    1994-09-01

    Although most individuals who carry a balanced familial chromosome rearrangement are phenotypically normal, those who are clinically abnormal raise the question of whether or not the rearrangement plays a causative role. One possible mechanism involves meiotic segregation of a normal homolog along with the rearranged chromosome(s) such that a trisomic conception occurs. Subsequent loss by mitotic nondisjunction of the structurally normal chromosome contributed by the non-carrier parent would then result in uniparental disomy (UPD) in a conceptus carrying a balanced rearrangement. UPD for chromosomes 14 and 15 has been demonstrated in several clinically abnormal individuals who carry a familial Robertsonian translocation. We have extended this type of analysis to include other forms of balanced chromosome rearrangements. We report the results of UPD analysis of 14 families who have a phenotypically abnormal child with an apparently balanced rearrangement. The series includes 4 reciprocal translocations, 4 Robertsonian translocations, 2 X;autosome translocations, and 4 inversions. High resolution chromosomes were used to compare breakpoints between parent and offspring to exclude the possibility of further rearrangements. Parental origin of the chromosome(s) involved was determined by DNA polymorphism analysis using PCR or Southern blotting techniques. We found no evidence of UPD in any of the 14 cases. Our data suggest that UPD is not a common explanation for phenotypically abnormal carriers of balanced chromosome rearrangements.

  20. Analysis of genome rearrangement by block-interchanges.

    PubMed

    Lu, Chin Lung; Lin, Ying Chih; Huang, Yen Lin; Tang, Chuan Yi

    2007-01-01

    Block-interchanges are a new kind of genome rearrangements that affect the gene order in a chromosome by swapping two nonintersecting blocks of genes of any length. More recently, the study of such rearrangements is becoming increasingly important because of its applications in molecular evolution. Usually, this kind of study requires to solve a combinatorial problem, called the block-interchange distance problem, which is to find a minimum number of block-interchanges between two given gene orders of linear/circular chromosomes to transform one gene order into another. In this chapter, we shall introduce the basics of block-interchange rearrangements and permutation groups in algebra that are useful in analyses of genome rearrangements. In addition, we shall present a simple algorithm on the basis of permutation groups to efficiently solve the block-interchange distance problem, as well as ROBIN, a web server for the online analyses of block-interchange rearrangements.

  1. Energy barriers for cellular rearrangements in tissues

    NASA Astrophysics Data System (ADS)

    Bi, Dapeng; Lopez, J. H.; Schwarz, J. M.; Manning, M. Lisa

    2013-03-01

    The behavior of cellular aggregates strongly influences morphogenesis, cancer growth and wound healing. While single cell mechanics has been extensively studied, the collective dynamics of cells inside a tissue is not well understood. Recent experiments have shown cells in tissues behave like fluids on long timescales and solids on shorter timescales, and exhibit caging behavior at intermediate timescales as they are more tightly packed. These observations are reminiscent of dynamic slowing down and dynamical heterogeneities due to mutual confinement and crowding of particles glassy systems. A common and crucial feature of glassy systems is the existence of a Potential Energy Landscape (PEL) for local rearrangements. For thermal glassy materials, when these barriers are large compared to thermal fluctuations, its rheology is dependent on the PEL and external mechanical driving. In contrast, cells in a tissue are non-thermal and overcome energy barriers in the PEL mainly through local active processes, i.e. making new adhesions and cell shape changes. We numerically map the PEL of a confluent tissue as functions of different transition pathways and single cell properties. Analytical calculations are also performed to find the minimal energy shapes for 2-D confluent cell packings. J.H.L. and J.M.S. are supported by NSF-DMR-0645373.

  2. Human structural variation: mechanisms of chromosome rearrangements

    PubMed Central

    Weckselblatt, Brooke; Rudd, M. Katharine

    2015-01-01

    Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation. PMID:26209074

  3. Ants cushion applied stress by active rearrangements

    NASA Astrophysics Data System (ADS)

    Liu, Zhongyang; Hyatt, John; Mlot, Nathan; Gerov, Michael; Fernandez-Nieves, Alberto; Hu, David

    2013-11-01

    Fire ants, Solenopsis invicta, link their bodies together to form waterproof rafts, which in turn drip, spread, and coagulate, demonstrating properties of an active material that can change state from a liquid to a solid. This soft-matter phase transition is important when the raft interacts with environmental forces such as raindrops and crashing waves. We study this active behavior through plate-on-plate rheology on the ants, extracting the active components by comparison with the rheological behavior of a collection of dead ants. In controlled shear tests, both and live and dead ants show properties of a non-Newtonian fluid, specifically, shear-thinning behavior. In oscillatory tests, live ants exhibit a rare behavior in which their storage modulus (G') and loss modulus (G'') have approximately the same value over three orders magnitudes of frequency and two orders of magnitude of strain, indicating the ants are neither fluid nor solid. In comparison, dead ants are more solid-like, with a storage modulus twice as large as their loss modulus. This striking active behavior arises from rearrangement of their bodies and storage and dissipation of energy with the ants' muscles.

  4. : a database of ciliate genome rearrangements.

    PubMed

    Burns, Jonathan; Kukushkin, Denys; Lindblad, Kelsi; Chen, Xiao; Jonoska, Nataša; Landweber, Laura F

    2016-01-01

    Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The (http://oxytricha.princeton.edu/mds_ies_db) is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila.

  5. Developmentally Programmed, RNA-Directed Genome Rearrangement in Tetrahymena

    PubMed Central

    Mochizuki, Kazufumi

    2013-01-01

    Developmentally programmed genome rearrangement has been observed in a variety of eukaryotes from vertebrates to worms to protists, and it provides an interesting exception to the general rule of the constancy of the genome. DNA elimination in the ciliated protozoan Tetrahymena is one of the most well-characterized programmed genome rearrangement events. DNA elimination in the newly formed macronucleus of Tetrahymena is epigenetically regulated by the DNA sequence of the parental macronucleus. Dicer-produced, Piwi-associated small RNAs mediate this epigenetic regulation, probably through a whole-genome comparison of the germline micronucleus to the somatic macronucleus. However, a correlation between small RNAs and programmed genome rearrangement could not be detected in the worm Ascaris suum. Therefore, different types of eukaryotes may have developed unique solutions to perform genome rearrangement. PMID:22103557

  6. : a database of ciliate genome rearrangements

    PubMed Central

    Burns, Jonathan; Kukushkin, Denys; Lindblad, Kelsi; Chen, Xiao; Jonoska, Nataša; Landweber, Laura F.

    2016-01-01

    Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The (http://oxytricha.princeton.edu/mds_ies_db) is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila. PMID:26586804

  7. Developmentally programmed, RNA-directed genome rearrangement in Tetrahymena.

    PubMed

    Mochizuki, Kazufumi

    2012-01-01

    Developmentally programmed genome rearrangement has been observed in a variety of eukaryotes from vertebrates to worms to protists, and it provides an interesting exception to the general rule of the constancy of the genome. DNA elimination in the ciliated protozoan Tetrahymena is one of the most well-characterized programmed genome rearrangement events. DNA elimination in the newly formed macronucleus of Tetrahymena is epigenetically regulated by the DNA sequence of the parental macronucleus. Dicer-produced, Piwi-associated small RNAs mediate this epigenetic regulation, probably through a whole-genome comparison of the germline micronucleus to the somatic macronucleus. However, a correlation between small RNAs and programmed genome rearrangement could not be detected in the worm Ascaris suum. Therefore, different types of eukaryotes may have developed unique solutions to perform genome rearrangement.

  8. Somatic Rearrangement in B Cells: It's (Mostly) Nuclear Physics.

    PubMed

    Aiden, Erez Lieberman; Casellas, Rafael

    2015-08-13

    We discuss how principles of nuclear architecture drive typical gene rearrangements in B lymphocytes, whereas translocation hot spots and recurrent lesions reflect the extent of AID-mediated DNA damage and selection.

  9. Tetrasomy Y by structural rearrangement: clinical report.

    PubMed

    DesGroseilliers, Martin; Lemyre, Emmanuelle; Dallaire, Louis; Lemieux, Nicole

    2002-09-01

    Poly-Y karyotypes, except for 47,XYY, are rare events in humans. For instance, Y chromosome tetrasomy has been reported 10 times, 2 of which were by structural rearrangement. We present a 2-year-and-4-month-old boy who was referred for cytogenetic assessment because of global psychomotor delay. The GTG- and CBG-banded karyotypes on PHA-stimulated lymphocytes showed two cell populations, one of them contained two identical isodicentric Y chromosomes, which was seen in 93% of metaphases analyzed, and a 45,X cell line (7%). This was confirmed by FISH with probes DYZ3 (recognizing the centromeric region of the Y chromosome), 91H4.5 (recognizing Yp11.2), and DYZ1 (recognizing Y heterochromatin in Yq12). The breakpoint has occurred near the telomeric end of the heterochromatic region. Therefore, the karyotype is mos 47,X,idic(Y)(q12)x2[123]/45,X[9]. This is the second time that such a karyotype has been reported. This chromosomal anomaly was formed most likely by a U-type exchange. Clinical features included speech delay, short stature, brachycephaly, large ears, bilateral epicanthal folds, hypertelorism, delayed teeth eruption, bilateral radio-ulnar synostosis, bilateral fifth finger clinodactyly, normal external genitalia, and impulsive behavior. The father had normal phenotype and karyotype. A review of the tetrasomy Y patients is presented. All patients with Y chromosome tetrasomy exhibit some degree of mental retardation, various skeletal abnormalities, and facial dysmorphism. Nevertheless, the correlation between karyotype and phenotype is not yet well defined since few cases have been reported. This clinical report will be helpful in defining the phenotypic range associated with tetrasomy Y. PMID:12210299

  10. Rearrangement and annihilation in antihydrogen-atom scattering

    SciTech Connect

    Jonsell, Svante

    2008-08-08

    I review some results for annihilation and rearrangement processes in low-energy antihydrogen-hydrogen and antihydrogen-helium scattering. For the strong nuclear force results using a {delta}-function potential are compared to a scattering length approach. It is found that the {delta}-function potential does not give correct annihilation cross sections in the case of antihydrogen-helium scattering. Problem associated with the use of the Born-Oppenheimer approximation for rearrangement calculations are reviewed.

  11. Ultrafast infrared studies of complex ligand rearrangements in solution

    SciTech Connect

    Payne, Christine K.

    2003-05-31

    The complete description of a chemical reaction in solution depends upon an understanding of the reactive molecule as well as its interactions with the surrounding solvent molecules. Using ultrafast infrared spectroscopy it is possible to observe both the solute-solvent interactions and the rearrangement steps which determine the overall course of a chemical reaction. The topics addressed in these studies focus on reaction mechanisms which require the rearrangement of complex ligands and the spectroscopic techniques necessary for the determination of these mechanisms. Ligand rearrangement is studied by considering two different reaction mechanisms for which the rearrangement of a complex ligand constitutes the most important step of the reaction. The first system concerns the rearrangement of a cyclopentadienyl ring as the response of an organometallic complex to a loss of electron density. This mechanism, commonly referred to as ''ring slip'', is frequently cited to explain reaction mechanisms. However, the ring slipped intermediate is too short-lived to be observed using conventional methods. Using a combination of ultrafast infrared spectroscopy and electronic structure calculations it has been shown that the intermediate exists, but does not form an eighteen-electron intermediate as suggested by traditional molecular orbital models. The second example examines the initial steps of alkyne polymerization. Group 6 (Cr, Mo, W) pentacarbonyl species are generated photolytically and used to catalyze the polymerization of unsaturated hydrocarbons through a series of coordination and rearrangement steps. Observing this reaction on the femto- to millisecond timescale indicates that the initial coordination of an alkyne solvent molecule to the metal center results in a stable intermediate that does not rearrange to form the polymer precursor. This suggests that polymerization requires the dissociation of additional carbonyl ligands before rearrangement can occur. Overall

  12. Evolution of atomic rearrangements in deformation in metallic glasses.

    PubMed

    Shang, B S; Li, M Z; Yao, Y G; Lu, Y J; Wang, W H

    2014-10-01

    Atomic rearrangements induced by shear stress are fundamental for understanding deformation mechanisms in metallic glasses (MGs). Using molecular dynamic simulation, the atomic rearrangements characterized by nonaffine displacements (NADs) and their spatial distribution and evolution with tensile stress in Cu50Zr50 MG were investigated. It was found that in the elastic regime the atomic rearrangements with the largest NADs are relatively homogeneous in space, but exhibit strong spatial correlation, become localized and inhomogeneous, and form large clusters as strain increases, which may facilitate the so-called shear transformation zones. Furthermore, initially they prefer to take place around Cu atoms which have more nonicosahedral configurations. As strain increases, the preference decays and disappears in the plastic regime. The atomic rearrangements with the smallest NADs are preferentially located around Cu atoms, too, but with more icosahedral or icosahedral-like atomic configurations. The preference is maintained in the whole deformation process. In contrast, the atomic rearrangements with moderate NADs distribute homogeneously, and do not show explicit preference or spatial correlation, acting as matrix during deformation. Among the atomic rearrangements with different NADs, those with largest and smallest NADs are nearest neighbors initially, but separating with increasing strain, while those with largest and moderate NADs always avoid to each other. The correlations in the fluctuations of the NADs confirm the long-range strain correlation and the scale-free characteristic of NADs in both elastic and plastic deformation, which suggests a universality of the scaling in the plastic flow in MGs.

  13. Recurrent DNA inversion rearrangements in the human genome.

    PubMed

    Flores, Margarita; Morales, Lucía; Gonzaga-Jauregui, Claudia; Domínguez-Vidaña, Rocío; Zepeda, Cinthya; Yañez, Omar; Gutiérrez, María; Lemus, Tzitziki; Valle, David; Avila, Ma Carmen; Blanco, Daniel; Medina-Ruiz, Sofía; Meza, Karla; Ayala, Erandi; García, Delfino; Bustos, Patricia; González, Víctor; Girard, Lourdes; Tusie-Luna, Teresa; Dávila, Guillermo; Palacios, Rafael

    2007-04-10

    Several lines of evidence suggest that reiterated sequences in the human genome are targets for nonallelic homologous recombination (NAHR), which facilitates genomic rearrangements. We have used a PCR-based approach to identify breakpoint regions of rearranged structures in the human genome. In particular, we have identified intrachromosomal identical repeats that are located in reverse orientation, which may lead to chromosomal inversions. A bioinformatic workflow pathway to select appropriate regions for analysis was developed. Three such regions overlapping with known human genes, located on chromosomes 3, 15, and 19, were analyzed. The relative proportion of wild-type to rearranged structures was determined in DNA samples from blood obtained from different, unrelated individuals. The results obtained indicate that recurrent genomic rearrangements occur at relatively high frequency in somatic cells. Interestingly, the rearrangements studied were significantly more abundant in adults than in newborn individuals, suggesting that such DNA rearrangements might start to appear during embryogenesis or fetal life and continue to accumulate after birth. The relevance of our results in regard to human genomic variation is discussed.

  14. Divergence of gene regulation through chromosomal rearrangements

    PubMed Central

    2010-01-01

    Background The molecular mechanisms that modify genome structures to give birth and death to alleles are still not well understood. To investigate the causative chromosomal rearrangements, we took advantage of the allelic diversity of the duplicated p1 and p2 genes in maize. Both genes encode a transcription factor involved in maysin synthesis, which confers resistance to corn earworm. However, p1 also controls accumulation of reddish pigments in floral tissues and has therefore acquired a new function after gene duplication. p1 alleles vary in their tissue-specific expression, which is indicated in their allele designation: the first suffix refers to red or white pericarp pigmentation and the second to red or white glume pigmentation. Results Comparing chromosomal regions comprising p1-ww[4Co63], P1-rw1077 and P1-rr4B2 alleles with that of the reference genome, P1-wr[B73], enabled us to reconstruct additive events of transposition, chromosome breaks and repairs, and recombination that resulted in phenotypic variation and chimeric regulatory signals. The p1-ww[4Co63] null allele is probably derived from P1-wr[B73] by unequal crossover between large flanking sequences. A transposon insertion in a P1-wr-like allele and NHEJ (non-homologous end-joining) could have resulted in the formation of the P1-rw1077 allele. A second NHEJ event, followed by unequal crossover, probably led to the duplication of an enhancer region, creating the P1-rr4B2 allele. Moreover, a rather dynamic picture emerged in the use of polyadenylation signals by different p1 alleles. Interestingly, p1 alleles can be placed on both sides of a large retrotransposon cluster through recombination, while functional p2 alleles have only been found proximal to the cluster. Conclusions Allelic diversity of the p locus exemplifies how gene duplications promote phenotypic variability through composite regulatory signals. Transposition events increase the level of genomic complexity based not only on

  15. Chromosome Rearrangements That Involve the Nucleolus Organizer Region in Neurospora

    PubMed Central

    Perkins, D. D.; Raju, N. B.; Barry, E. G.; Butler, D. K.

    1995-01-01

    In ~3% of Neurospora crassa rearrangements, part of a chromosome arm becomes attached to the nucleolus organizer region (NOR) at one end of chromosome 2 (linkage group V). Investigations with one inversion and nine translocations of this type are reported here. They appear genetically to be nonreciprocal and terminal. When a rearrangement is heterozygous, about one-third of viable progeny are segmental aneuploids with the translocated segment present in two copies, one in normal position and one associated with the NOR. Duplications from many of the rearrangements are highly unstable, breaking down by loss of the NOR-attached segment to restore normal chromosome sequence. When most of the rearrangements are homozygous, attenuated strands can be seen extending through the unstained nucleolus at pachytene, joining the translocated distal segment to the remainder of chromosome 2. Although the rearrangements appear genetically to be nonreciprocal, molecular evidence shows that at least several of them are physically reciprocal, with a block of rDNA repeats translocated away from the NOR. Evidence that NOR-associated breakpoints are nonterminal is also provided by intercrosses between pairs of translocations that transfer different-length segments of the same donor-chromosome arm to the NOR. PMID:8582636

  16. Modeling of the primary rearrangement stage of liquid phase sintering

    NASA Astrophysics Data System (ADS)

    Malik Tahir, Abdul; Malik, Amer; Amberg, Gustav

    2016-10-01

    The dimensional variations during the rearrangement stage of liquid phase sintering could have a detrimental effect on the dimensional tolerances of the sintered product. A numerical approach to model the liquid phase penetration into interparticle boundaries and the accompanied dimensional variations during the primary rearrangement stage of liquid phase sintering is presented. The coupled system of the Cahn–Hilliard and the Navier–Stokes equations is used to model the penetration of the liquid phase, whereas the rearrangement of the solid particles due to capillary forces is modeled using the equilibrium equation for a linear elastic material. The simulations are performed using realistic physical properties of the phases involved and the effect of green density, wettability and amount of liquid phase is also incorporated in the model. In the first step, the kinetics of the liquid phase penetration and the rearrangement of solid particles connected by a liquid bridge is modeled. The predicted and the calculated (analytical) results are compared in order to validate the numerical model. The numerical model is then extended to simulate the dimensional changes during primary rearrangement stage and a qualitative match with the published experimental data is achieved.

  17. Topological rearrangements and local search method for tandem duplication trees.

    PubMed

    Bertrand, Denis; Gascuel, Olivier

    2005-01-01

    The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch . Many recent studies deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees. In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on duplication trees. We show that restricting the neighborhood defined by the SPR (Subtree Pruning and Regrafting) rearrangement to valid duplication trees, allows exploring the whole duplication tree space. We use these restricted rearrangements in a local search method which improves an initial tree via successive rearrangements. This method is applied to the optimization of parsimony and minimum evolution criteria. We show through simulations that this method improves all existing programs for both reconstructing the topology of the true tree and recovering its duplication events. We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our method than using any other program.

  18. Conditions for predicting quasistationary states by rearrangement formula

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Yoshiyuki Y.; Ogawa, Shun

    2015-10-01

    Predicting the long-lasting quasistationary state for a given initial state is one of central issues in Hamiltonian systems having long-range interaction. A recently proposed method is based on the Vlasov description and uniformly redistributes the initial distribution along contours of the asymptotic effective Hamiltonian, which is defined by the obtained quasistationary state and is determined self-consistently. The method, to which we refer as the rearrangement formula, was suggested to give precise prediction under limited situations. Restricting initial states consisting of a spatially homogeneous part and small perturbation, we numerically reveal two conditions that the rearrangement formula prefers: One is a no Landau damping condition for the unperturbed homogeneous part, and the other comes from the Casimir invariants. Mechanisms of these conditions are discussed. Clarifying these conditions, we validate to use the rearrangement formula as the response theory for an external field, and we shed light on improving the theory as a nonequilibrium statistical mechanics.

  19. Low-Temperature Cationic Rearrangement in a Bulk Metal Oxide.

    PubMed

    Li, Man-Rong; Retuerto, Maria; Stephens, Peter W; Croft, Mark; Sheptyakov, Denis; Pomjakushin, Vladimir; Deng, Zheng; Akamatsu, Hirofumi; Gopalan, Venkatraman; Sánchez-Benítez, Javier; Saouma, Felix O; Jang, Joon I; Walker, David; Greenblatt, Martha

    2016-08-16

    Cationic rearrangement is a compelling strategy for producing desirable physical properties by atomic-scale manipulation. However, activating ionic diffusion typically requires high temperature, and in some cases also high pressure in bulk oxide materials. Herein, we present the cationic rearrangement in bulk Mn2 FeMoO6 at unparalleled low temperatures of 150-300 (o) C. The irreversible ionic motion at ambient pressure, as evidenced by real-time powder synchrotron X-ray and neutron diffraction, and second harmonic generation, leads to a transition from a Ni3 TeO6 -type to an ordered-ilmenite structure, and dramatic changes of the electrical and magnetic properties. This work demonstrates a remarkable cationic rearrangement, with corresponding large changes in the physical properties in a bulk oxide at unprecedented low temperatures. PMID:27203790

  20. Genome rearrangements caused by interstitial telomeric sequences in yeast

    PubMed Central

    Aksenova, Anna Y.; Greenwell, Patricia W.; Dominska, Margaret; Shishkin, Alexander A.; Kim, Jane C.; Petes, Thomas D.; Mirkin, Sergei M.

    2013-01-01

    Interstitial telomeric sequences (ITSs) are present in many eukaryotic genomes and are linked to genome instabilities and disease in humans. The mechanisms responsible for ITS-mediated genome instability are not understood in molecular detail. Here, we use a model Saccharomyces cerevisiae system to characterize genome instability mediated by yeast telomeric (Ytel) repeats embedded within an intron of a reporter gene inside a yeast chromosome. We observed a very high rate of small insertions and deletions within the repeats. We also found frequent gross chromosome rearrangements, including deletions, duplications, inversions, translocations, and formation of acentric minichromosomes. The inversions are a unique class of chromosome rearrangement involving an interaction between the ITS and the true telomere of the chromosome. Because we previously found that Ytel repeats cause strong replication fork stalling, we suggest that formation of double-stranded DNA breaks within the Ytel sequences might be responsible for these gross chromosome rearrangements. PMID:24191060

  1. DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Neumann, Elizabeth K.; Solouki, Touradj

    2015-08-01

    Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine]- fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine]- and complementary y-B type product ions.

  2. Low-Temperature Cationic Rearrangement in a Bulk Metal Oxide.

    PubMed

    Li, Man-Rong; Retuerto, Maria; Stephens, Peter W; Croft, Mark; Sheptyakov, Denis; Pomjakushin, Vladimir; Deng, Zheng; Akamatsu, Hirofumi; Gopalan, Venkatraman; Sánchez-Benítez, Javier; Saouma, Felix O; Jang, Joon I; Walker, David; Greenblatt, Martha

    2016-08-16

    Cationic rearrangement is a compelling strategy for producing desirable physical properties by atomic-scale manipulation. However, activating ionic diffusion typically requires high temperature, and in some cases also high pressure in bulk oxide materials. Herein, we present the cationic rearrangement in bulk Mn2 FeMoO6 at unparalleled low temperatures of 150-300 (o) C. The irreversible ionic motion at ambient pressure, as evidenced by real-time powder synchrotron X-ray and neutron diffraction, and second harmonic generation, leads to a transition from a Ni3 TeO6 -type to an ordered-ilmenite structure, and dramatic changes of the electrical and magnetic properties. This work demonstrates a remarkable cationic rearrangement, with corresponding large changes in the physical properties in a bulk oxide at unprecedented low temperatures.

  3. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements

    PubMed Central

    Liu, Pengfei; Erez, Ayelet; Sreenath Nagamani, Sandesh C.; Dhar, Shweta U.; Kołodziejska, Katarzyna E.; Dharmadhikari, Avinash V.; Cooper, M. Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A.; Bacino, Carlos A.; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R.; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A.; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R.; McLean, Scott D.; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L.; Patel, Ankita; Cheung, Sau Wai; Hastings, P. J.; Stankiewicz, Paweł; Lupski, James R.; Bi, Weimin

    2011-01-01

    SUMMARY Complex genomic rearrangements (CGR) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated we observed localization and multiple copy number changes including deletions, duplications and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism’s life cycle. PMID:21925314

  4. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements.

    PubMed

    Liu, Pengfei; Erez, Ayelet; Nagamani, Sandesh C Sreenath; Dhar, Shweta U; Kołodziejska, Katarzyna E; Dharmadhikari, Avinash V; Cooper, M Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A; Bacino, Carlos A; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R; McLean, Scott D; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L; Patel, Ankita; Cheung, Sau Wai; Hastings, P J; Stankiewicz, Paweł; Lupski, James R; Bi, Weimin

    2011-09-16

    Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.

  5. Telomerase activation by genomic rearrangements in high-risk neuroblastoma

    PubMed Central

    Peifer, Martin; Hertwig, Falk; Roels, Frederik; Dreidax, Daniel; Gartlgruber, Moritz; Menon, Roopika; Krämer, Andrea; Roncaioli, Justin L.; Sand, Frederik; Heuckmann, Johannes M.; Ikram, Fakhera; Schmidt, Rene; Ackermann, Sandra; Engesser, Anne; Kahlert, Yvonne; Vogel, Wenzel; Altmüller, Janine; Nürnberg, Peter; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Mariappan, Aruljothi; Heynck, Stefanie; Mariotti, Erika; Henrich, Kai-Oliver; Glöckner, Christian; Bosco, Graziella; Leuschner, Ivo; Schweiger, Michal R.; Savelyeva, Larissa; Watkins, Simon C.; Shao, Chunxuan; Bell, Emma; Höfer, Thomas; Achter, Viktor; Lang, Ulrich; Theissen, Jessica; Volland, Ruth; Saadati, Maral; Eggert, Angelika; de Wilde, Bram; Berthold, Frank; Peng, Zhiyu; Zhao, Chen; Shi, Leming; Ortmann, Monika; Büttner, Reinhard; Perner, Sven; Hero, Barbara; Schramm, Alexander; Schulte, Johannes H.; Herrmann, Carl; O’Sullivan, Roderick J.; Westermann, Frank; Thomas, Roman K.; Fischer, Matthias

    2016-01-01

    Neuroblastoma is a malignant paediatric tumour of the sympathetic nervous system1. Roughly half of these tumours regress spontaneously or are cured by limited therapy. By contrast, high-risk neuroblastomas have an unfavourable clinical course despite intensive multimodal treatment, and their molecular basis has remained largely elusive2–4. Here we have performed whole-genome sequencing of 56 neuroblastomas (high-risk, n = 39; low-risk, n = 17) and discovered recurrent genomic rearrangements affecting a chromosomal region at 5p15.33 proximal of the telomerase reverse transcriptase gene (TERT). These rearrangements occurred only in high-risk neuroblastomas (12/39, 31%) in a mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumour type1,2,5. In an extended case series (n = 217), TERT rearrangements defined a subgroup of high-risk tumours with particularly poor outcome. Despite a large structural diversity of these rearrangements, they all induced massive transcriptional upregulation of TERT. In the remaining high-risk tumours, TERT expression was also elevated in MYCN-amplified tumours, whereas alternative lengthening of telomeres was present in neuroblastomas without TERT or MYCN alterations, suggesting that telomere lengthening represents a central mechanism defining this subtype. The 5p15.33 rearrangements juxtapose the TERT coding sequence to strong enhancer elements, resulting in massive chromatin remodelling and DNA methylation of the affected region. Supporting a functional role of TERT, neuroblastoma cell lines bearing rearrangements or amplified MYCN exhibited both upregulated TERT expression and enzymatic telomerase activity. In summary, our findings show that remodelling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumours. PMID:26466568

  6. Mycoreovirus genome rearrangements associated with RNA silencing deficiency

    PubMed Central

    Eusebio-Cope, Ana; Suzuki, Nobuhiro

    2015-01-01

    Mycoreovirus 1 (MyRV1) has 11 double-stranded RNA genome segments (S1 to S11) and confers hypovirulence to the chestnut blight fungus, Cryphonectria parasitica. MyRV1 genome rearrangements are frequently generated by a multifunctional protein, p29, encoded by a positive-strand RNA virus, Cryphonectria hypovirus 1. One of its functional roles is RNA silencing suppression. Here, we explored a possible link between MyRV1 genome rearrangements and the host RNA silencing pathway using wild-type (WT) and mutant strains of both MyRV1 and the host fungus. Host strains included deletion mutants of RNA silencing components such as dicer-like (dcl) and argonaute-like (agl) genes, while virus strains included an S4 internal deletion mutant MyRV1/S4ss. Consequently, intragenic rearrangements with nearly complete duplication of the three largest segments, i.e. S1, S2 and S3, were observed even more frequently in the RNA silencing-deficient strains Δdcl2 and Δagl2 infected with MyRV1/S4ss, but not with any other viral/host strain combinations. An interesting difference was noted between genome rearrangement events in the two host strains, i.e. generation of the rearrangement required prolonged culture for Δagl2 in comparison with Δdcl2. These results suggest a role for RNA silencing that suppresses genome rearrangements of a dsRNA virus. PMID:25800742

  7. Rearrangement and evolution of mitochondrial genomes in parrots.

    PubMed

    Eberhard, Jessica R; Wright, Timothy F

    2016-01-01

    Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One

  8. Oncogenic rearrangements driving ionizing radiation–associated human cancer

    PubMed Central

    Santoro, Massimo; Carlomagno, Francesca

    2013-01-01

    The Chernobyl nuclear disaster has caused a remarkable increase in radiation-induced papillary thyroid carcinoma in children and young adults. In this issue of the JCI, Ricarte-Filho and colleagues demonstrate that chromosomal rearrangements are the oncogenic “drivers” in most post-Chernobyl carcinomas and that they often lead to unscheduled activation of the MAPK signaling pathway. These findings represent a major step forward in our understanding of radiation-induced carcinogenesis and suggest various hypotheses about the mechanisms underlying the formation and selection of gene rearrangements during cancer cell evolution. PMID:24162670

  9. Submillisecond organic synthesis: Outpacing Fries rearrangement through microfluidic rapid mixing.

    PubMed

    Kim, Heejin; Min, Kyoung-Ik; Inoue, Keita; Im, Do Jin; Kim, Dong-Pyo; Yoshida, Jun-ichi

    2016-05-01

    In chemical synthesis, rapid intramolecular rearrangements often foil attempts at site-selective bimolecular functionalization. We developed a microfluidic technique that outpaces the very rapid anionic Fries rearrangement to chemoselectively functionalize iodophenyl carbamates at the ortho position. Central to the technique is a chip microreactor of our design, which can deliver a reaction time in the submillisecond range even at cryogenic temperatures. The microreactor was applied to the synthesis of afesal, a bioactive molecule exhibiting anthelmintic activity, to demonstrate its potential for practical synthesis and production.

  10. Enantioselective Oxidative Rearrangements with Chiral Hypervalent Iodine Reagents

    PubMed Central

    Brown, Michael; Kumar, Ravi; Rehbein, Julia

    2016-01-01

    Abstract A stereoselective hypervalent iodine‐promoted oxidative rearrangement of 1,1‐disubstituted alkenes has been developed. This practically simple protocol provides access to enantioenriched α‐arylated ketones without the use of transition metals from readily accessible alkenes. PMID:26800241

  11. Beckmann rearrangement of ketoximes to lactams by triphosphazene catalyst.

    PubMed

    Hashimoto, Masaharu; Obora, Yasushi; Sakaguchi, Satoshi; Ishii, Yasutaka

    2008-04-01

    Triphosphazene, 1,3,5-triazo-2,4,6-triphosphorine-2,2,4,4,6,6-chloride (TAPC), was found to be an efficient catalyst for the Beckmann rearrangement of cyclohexanone oxime and cyclododecanone oxime to epsilon-caprolactam and laurolactam, which are raw materials of nylon-6 and nylon-12, respectively.

  12. Computational Analysis of Stereospecificity in the Cope Rearrangement

    ERIC Educational Resources Information Center

    Glish, Laura; Hanks, Timothy W.

    2007-01-01

    The Cope rearrangement is a highly stereospecific, concerted reaction of considerable synthetic utility. Experimental product distributions from the reaction of disubstituted 1,5-hexadienes can be readily understood by computer modeling of the various possible transitions states. Semi-empirical methods give relative energies of transition states…

  13. The Basel Problem as a Rearrangement of Series

    ERIC Educational Resources Information Center

    Benko, David; Molokach, John

    2013-01-01

    We give an elementary solution to the famous Basel Problem, originally solved by Euler in 1735. We square the well-known series for arctan(1) due to Leibniz, and use a surprising relation among the re-arranged terms of this squared series.

  14. Radical [1,3] Rearrangements of Breslow Intermediates.

    PubMed

    Alwarsh, Sefat; Xu, Yi; Qian, Steven Y; McIntosh, Matthias C

    2016-01-01

    Breslow intermediates that bear radical-stabilizing N substituents, such as benzyl, cinnamyl, and diarylmethyl, undergo facile homolytic C-N bond scission under mild conditions to give products of formal [1,3] rearrangement rather than benzoin condensation. EPR experiments and computational analysis support a radical-based mechanism. Implications for thiamine-based enzymes are discussed.

  15. 10 CFR 2.909 - Rearrangement or suspension of proceedings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 1 2011-01-01 2011-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION RULES OF PRACTICE FOR DOMESTIC LICENSING PROCEEDINGS AND... the best interest of all parties and the public....

  16. 10 CFR 2.909 - Rearrangement or suspension of proceedings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 1 2014-01-01 2014-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION AGENCY RULES OF PRACTICE AND PROCEDURE Special Procedures... public interest. (c) Take such other action as he determines to be in the best interest of all...

  17. 10 CFR 2.909 - Rearrangement or suspension of proceedings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION RULES OF PRACTICE FOR DOMESTIC LICENSING PROCEEDINGS AND... the best interest of all parties and the public....

  18. 10 CFR 2.909 - Rearrangement or suspension of proceedings.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 1 2013-01-01 2013-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION AGENCY RULES OF PRACTICE AND PROCEDURE Special Procedures... public interest. (c) Take such other action as he determines to be in the best interest of all...

  19. 10 CFR 2.909 - Rearrangement or suspension of proceedings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 1 2012-01-01 2012-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION RULES OF PRACTICE FOR DOMESTIC LICENSING PROCEEDINGS AND... the best interest of all parties and the public....

  20. Ring Expansion and Rearrangements of Rhodium(II) Azavinyl Carbenes

    PubMed Central

    Selander, Nicklas; Worrell, Brady T.

    2013-01-01

    An efficient, regioselective and convergent method for the ring expansion and rearrangement of 1-sulfonyl-1,2,3-triazoles under rhodium(II)-catalyzed conditions is described. These denitrogenative reactions form substituted enaminone and olefin-based products, which in the former case can be further functionalized to unique products rendering the sulfonyl triazole traceless. PMID:23161725

  1. Stochastic rearrangement of immunoglobulin variable-region genes in chicken B-cell development.

    PubMed Central

    Benatar, T; Tkalec, L; Ratcliffe, M J

    1992-01-01

    The molecular mechanism by which immunoglobulin (Ig) gene rearrangement occurs is highly conserved between mammalian and avian species. However, in avian species, an equivalent to the mammalian pre-B cell, which has undergone Ig heavy-chain gene rearrangement and expresses mu heavy chains in the absence of Ig light-chain rearrangement, has not been convincingly demonstrated. It is consequently unclear whether an ordered progression of gene rearrangement events leading to functional Ig expression occurs in avian species. To examine the sequence of Ig gene rearrangement events in chicken B-cell development, we transformed day 12 embryo bursal cells with the REV-T(CSV) retrovirus. More than 100 clones were analyzed by Southern blotting and polymerase chain reaction for the presence of Ig gene rearrangements. The majority of these clones contained only germline Ig sequences. Several clones contained complete heavy- and light-chain rearrangements and 13 clones contained only heavy-chain rearrangements analogous to stages of mammalian B-cell development. However, 5 clones contained rearrangements of light-chain genes in the absence of complete heavy-chain rearrangement. Consequently, we conclude that rearrangement of chicken Ig light-chain genes does not require heavy-chain variable-region rearrangement. This observation suggests that chicken Ig gene rearrangement events required for Ig expression occur stochastically rather than sequentially. Images PMID:1502173

  2. The Manifestation of Chromosome Rearrangements in Unordered Asci of Neurospora

    PubMed Central

    Perkins, David D.

    1974-01-01

    Rapid, effective techniques have been developed for detecting and characterizing chromosome aberrations in Neurospora by visual inspection of ascospores and asci. Rearrangements that are detectable by the presence of deficient, nonblack ascospores in test crosses make up 5 to 10% of survivors after UV doses giving 10-55% survival. Over 135 rearrangements have been diagnosed by classifying unordered asci according to numbers of defective spores. (These include 15 originally identified or analyzed by other workers.) About 100 reciprocal translocations (RT's) have been confirmed and mapped genetically, involving all combinations of the seven chromosomes. Thirty-three other rearrangements generate viable nontandem duplications in meiosis. These consist of insertional translocations (IT's) (15 confirmed), and of rearrangements that involve a chromosome tip (10 translocations and 3 pericentric inversions). No inversion has been found that does not include the centromere. A reciprocal translocation was found within one population in nature. When pairs of RT's that involve the same two chromosome arms were intercrossed, viable duplications were produced if the breakpoints overlapped in such a way that pairing resembled that of insertional translocations (27 combinations).—The rapid analytical technique depends on the following. Deficiency ascospores are usually nonblack (W: "white") and inviable, while nondeficient ascospores, even those that include duplications, are black (B) and viable. Thus RT's typically produce 50% black spores, and IT's 75% black. Asci are shot spontaneously from ripe perithecia, and can be collected in large numbers as groups of eight ascospores representing unordered tetrads, which fall into five classes: 8B:0W; 6B:2W, 4B:4W, 2B:6B, 0B:8W. In isosequential crosses, 90-95% of tetrads are 8:0. When a rearrangement is heterozygous, the frequencies of tetrad classes are diagnostic of the type of rearrangement, and provide information also on the

  3. "Familial" versus "sporadic" intellectual disability: contribution of subtelomeric rearrangements

    PubMed Central

    2012-01-01

    Background Cryptic subtelomeric rearrangements have been proposed as a significant cause of sporadic intellectual disability (ID) but the role of such aberrations in familial ID has not yet been studied. As positive family history of ID had been proposed as an important and significant predicting factor of subtelomeric rearrangements, it was assumed that the contribution of subtelomeric aberrations in familial ID would be much more than the sporadic ones. Three hundred and twenty two patients from 102 unrelated families with more than two ID patients in the first degree relatives have been investigated. Assessment of subtelomeric rearrangements were carried out using Multiplex Ligation-Dependent Probe Amplification (MLPA) technique. Detected aberrations were then confirmed by Fluorescence in Situ Hybridization (FISH) method. Results Among the families studied, 27.4% had 4-12, 36.3% had 3 and 36.3% had 2 affected individuals in the first degree relatives. One unbalanced translocation and 4 polymorphic changes were detected. The prevalence of clinically significant subtelomeric rearrangements was 0.98%. Conclusion This is the first investigation of subtelomeric aberrations in a large sample set of familial ID patients. Our results show that the contribution of subtelomeric rearrangements to familial ID is not as much as what had been determined for sporadic ones in the literature. Moreover, this study shows that the positive family history by alone, cannot be the most important and determining indicator of subtelomeric aberrations while it would be a good predicting factor when associated with dysmorphism or congenital malformations. These findings propose that other cryptic chromosomal abnormalities or even single gene disorders may be the main cause of familial ID rather than subtelomeric aberrations. PMID:22260313

  4. Facilitating the Cope rearrangement by partial protonation: implications for synthesis and biosynthesis.

    PubMed

    Painter, Phillip P; Wong, Bonnie M; Tantillo, Dean J

    2014-09-19

    The theoretical investigation of concerted and stepwise Cope rearrangements of natural products led to the prediction that some concerted Cope rearrangements can be promoted by noncovalent association of their transition state structures with ammonium cations.

  5. Interspecific chromosomal rearrangements in monosomic addition lines of Allium.

    PubMed

    Barthes, L; Ricroch, A

    2001-10-01

    Monosomic alien addition lines (MAALs) are useful for assigning linkage groups to chromosomes. We examined whether the chromosomal rearrangements following the introduction of a single onion (Allium cepa) chromosome into the Allium fistulosum genome were produced by homeologous crossing over or by a nonreciprocal conversion event. Among the monosomic lines available, 17 were studied by fluorescent genomic in situ hybridisation, using total A. cepa genomic DNA as the probe and total A. fistulosum genomic DNA as the competitor. In this way, rearrangements such as chromosomal translocations between A. cepa and A. fistulosum were identified as terminal regions consisting of tandem DNA repeats. Homeologous crossing over between the two closely related genomes occurred in 4 of the 17 lines, suggesting that such events are not rare. On the basis of a detailed molecular cytogenetic characterisation, we identified true monosomic alien addition lines for A. cepa chromosomes 3, 4, 5, 7, and 8 that can reliably be used in genetic studies. PMID:11681618

  6. One-Step Generation of Chromosomal Rearrangements in Rice.

    PubMed

    Murata, Minoru; Kanatani, Asaka; Kashihara, Kazunari

    2016-01-01

    The combination of the DNA sequence-specific recombination system Cre/LoxP and the DNA transposon system Activator (Ac)/Dissociation (Ds) has been used for insertional and deletional mutagenesis, as well as for the generation of artificial ring chromosomes in model plants such as Arabidopsis and tobacco. However, it takes a long time to complete this process, even in Arabidopsis. To overcome this issue, a new binary vector, pDLHC, has been developed to induce chromosomal rearrangements for a short time in rice. pDLHC has been found to be effective in the induction of deletions between two LoxPs in the T2 generation of "Nihon bare" expressing Ac TPase. pDLHC has potential for the efficient generation of various types of chromosomal rearrangements including deletions, inversions, translocations and artificial ring chromosomes in plants, and the detailed protocol for rice is described here. PMID:27557686

  7. RNA-Mediated Epigenetic Programming of Genome Rearrangements

    PubMed Central

    Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F.

    2012-01-01

    RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha’s somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells. PMID:21801022

  8. Familial complex chromosomal rearrangement resulting in a recombinant chromosome.

    PubMed

    Berend, Sue Ann; Bodamer, Olaf A F; Shapira, Stuart K; Shaffer, Lisa G; Bacino, Carlos A

    2002-05-15

    Familial complex chromosomal rearrangements (CCRs) are rare and tend to involve fewer breakpoints and fewer chromosomes than CCRs that are de novo in origin. We report on a CCR identified in a child with congenital heart disease and dysmorphic features. Initially, the child's karyotype was thought to involve a straightforward three-way translocation between chromosomes 3, 8, and 16. However, after analyzing the mother's chromosomes, the mother was found to have a more complex rearrangement that resulted in a recombinant chromosome in the child. The mother's karyotype included an inverted chromosome 2 and multiple translocations involving chromosomes 3, 5, 8, and 16. No evidence of deletion or duplication that could account for the clinical findings in the child was identified.

  9. Chromosome-specific staining to detect genetic rearrangements

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

    2013-04-09

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  10. Recent applications of ring-rearrangement metathesis in organic synthesis

    PubMed Central

    Meshram, Milind; Khedkar, Priti; Banerjee, Shaibal; Deodhar, Deepak

    2015-01-01

    Summary Ring-rearrangement metathesis (RRM) involves multiple metathesis processes such as ring-opening metathesis (ROM)/ring-closing metathesis (RCM) in a one-pot operation to generate complex targets. RRM delivers complex frameworks that are difficult to assemble by conventional methods. The noteworthy point about this type of protocol is multi-bond formation and it is an atom economic process. In this review, we have covered literature that appeared during the last seven years (2008–2014). PMID:26664603

  11. Rearranging the exponential wall for large N-body systems.

    PubMed

    Watson, Deborah K; Dunn, Martin

    2010-07-01

    The work required to solve for the fully interacting N boson wave function, which is widely believed to scale exponentially with N, is rearranged so the problem scales order by order in a perturbation series as N0. The exponential complexity reappears in an exponential scaling with the order of our perturbation series allowing exact analytical calculations for very large N systems through low order. PMID:20867687

  12. Recent applications of ring-rearrangement metathesis in organic synthesis.

    PubMed

    Kotha, Sambasivarao; Meshram, Milind; Khedkar, Priti; Banerjee, Shaibal; Deodhar, Deepak

    2015-01-01

    Ring-rearrangement metathesis (RRM) involves multiple metathesis processes such as ring-opening metathesis (ROM)/ring-closing metathesis (RCM) in a one-pot operation to generate complex targets. RRM delivers complex frameworks that are difficult to assemble by conventional methods. The noteworthy point about this type of protocol is multi-bond formation and it is an atom economic process. In this review, we have covered literature that appeared during the last seven years (2008-2014).

  13. Recent applications of ring-rearrangement metathesis in organic synthesis.

    PubMed

    Kotha, Sambasivarao; Meshram, Milind; Khedkar, Priti; Banerjee, Shaibal; Deodhar, Deepak

    2015-01-01

    Ring-rearrangement metathesis (RRM) involves multiple metathesis processes such as ring-opening metathesis (ROM)/ring-closing metathesis (RCM) in a one-pot operation to generate complex targets. RRM delivers complex frameworks that are difficult to assemble by conventional methods. The noteworthy point about this type of protocol is multi-bond formation and it is an atom economic process. In this review, we have covered literature that appeared during the last seven years (2008-2014). PMID:26664603

  14. Quantifying stretching and rearrangement in epithelial sheet migration

    NASA Astrophysics Data System (ADS)

    Lee, Rachel M.; Kelley, Douglas H.; Nordstrom, Kerstin N.; Ouellette, Nicholas T.; Losert, Wolfgang

    2013-02-01

    Although understanding the collective migration of cells, such as that seen in epithelial sheets, is essential for understanding diseases such as metastatic cancer, this motion is not yet as well characterized as individual cell migration. Here we adapt quantitative metrics used to characterize the flow and deformation of soft matter to contrast different types of motion within a migrating sheet of cells. Using a finite-time Lyapunov exponent (FTLE) analysis, we find that—in spite of large fluctuations—the flow field of an epithelial cell sheet is not chaotic. Stretching of a sheet of cells (i.e. positive FTLE) is localized at the leading edge of migration and increases when the cells are more highly stimulated. By decomposing the motion of the cells into affine and non-affine components using the metric D_{\\min }^2 , we quantify local plastic rearrangements and describe the motion of a group of cells in a novel way. We find an increase in plastic rearrangements with increasing cell densities, whereas inanimate systems tend to exhibit less non-affine rearrangements with increasing density.

  15. Quantifying stretching and rearrangement in epithelial sheet migration

    NASA Astrophysics Data System (ADS)

    Lee, Rachel; Kelley, Douglas; Nordstrom, Kerstin; Ouellette, Nicholas; Losert, Wolfgang

    2013-03-01

    Although understanding the collective migration of cells, such as that seen in epithelial sheets, is essential for understanding diseases such as metastatic cancer, this motion is not yet as well characterized as individual cell migration. Here we adapt quantitative metrics used to characterize the flow and deformation of soft matter to contrast different types of motion within a migrating sheet of cells. Using a Finite-Time Lyapunov Exponent (FTLE) analysis, we find that - in spite of large fluctuations - the flow field of an epithelial cell sheet is not chaotic. Stretching of a sheet of cells (i.e., positive FTLE) is localized at the leading edge of migration. By decomposing the motion of the cells into affine and non-affine components using the metric Dmin2,we quantify local plastic rearrangements and describe the motion of a group of cells in a novel way. We find an increase in plastic rearrangements with increasing cell densities, whereas inanimate systems tend to exhibit less non-affine rearrangements with increasing density.

  16. Quantifying stretching and rearrangement in epithelial sheet migration.

    PubMed

    Lee, Rachel M; Kelley, Douglas H; Nordstrom, Kerstin N; Ouellette, Nicholas T; Losert, Wolfgang

    2013-02-25

    Although understanding the collective migration of cells, such as that seen in epithelial sheets, is essential for understanding diseases such as metastatic cancer, this motion is not yet as well characterized as individual cell migration. Here we adapt quantitative metrics used to characterize the flow and deformation of soft matter to contrast different types of motion within a migrating sheet of cells. Using a Finite-Time Lyapunov Exponent (FTLE) analysis, we find that - in spite of large fluctuations - the flow field of an epithelial cell sheet is not chaotic. Stretching of a sheet of cells (i.e., positive FTLE) is localized at the leading edge of migration and increases when the cells are more highly stimulated. By decomposing the motion of the cells into affine and non-affine components using the metric D(2)min , we quantify local plastic rearrangements and describe the motion of a group of cells in a novel way. We find an increase in plastic rearrangements with increasing cell densities, whereas inanimate systems tend to exhibit less non-affine rearrangements with increasing density.

  17. Quantifying stretching and rearrangement in epithelial sheet migration

    PubMed Central

    Lee, Rachel M.; Kelley, Douglas H.; Nordstrom, Kerstin N.; Ouellette, Nicholas T.; Losert, Wolfgang

    2013-01-01

    Although understanding the collective migration of cells, such as that seen in epithelial sheets, is essential for understanding diseases such as metastatic cancer, this motion is not yet as well characterized as individual cell migration. Here we adapt quantitative metrics used to characterize the flow and deformation of soft matter to contrast different types of motion within a migrating sheet of cells. Using a Finite-Time Lyapunov Exponent (FTLE) analysis, we find that - in spite of large fluctuations - the flow field of an epithelial cell sheet is not chaotic. Stretching of a sheet of cells (i.e., positive FTLE) is localized at the leading edge of migration and increases when the cells are more highly stimulated. By decomposing the motion of the cells into affine and non-affine components using the metric D2min, we quantify local plastic rearrangements and describe the motion of a group of cells in a novel way. We find an increase in plastic rearrangements with increasing cell densities, whereas inanimate systems tend to exhibit less non-affine rearrangements with increasing density. PMID:23599682

  18. Rapid identification of chromosomal rearrangements by PRINS technique

    SciTech Connect

    Pellestor, F.; Giradet, A.; Andreo, B.

    1994-09-01

    Chromosomal rearrangements contribute significantly to human reproductive failure, malformation/mental retardation syndromes and carcinogenesis. The variety of structural rearrangements is almost infinite and an identification by conventional cytogenetics is often labor intensive and may remain doubtful. Recent advances in molecular cytogenetics have provided new tools for detecting chromosomal abnormalities. The fluorescence in situ hybridization (FISH) procedure is actually the most employed technique and has led to numerous clinical applications. However, techniques required to produce suitable probes are time consuming and not accessible to all cytogenetics laboratories. The PRimed In Situ labeling (PRINS) method provides an alternate way for in situ chromosome screening. In this procedure, the chromosomal detection is performed by in situ annealing of a specific primer and subsequent primer extension by a Taq DNA polymerase in the presence of labeled nucleotides. Application of PRINS in clinical diagnosis is still limited. We have developed a semi-automatic PRINS protocol and used it to identify the origin of several chromosomal abnormalities. We report here the results of studies of three structural rearrangements: a translocation t(21;21), a supernumerary ring marker chromosome 18 and a complex chromosome 13 mosaicism involving a 13;13 Robertsonian translocation and a ring chromosome 13.

  19. Highly Variable Rates of Genome Rearrangements between Hemiascomycetous Yeast Lineages

    PubMed Central

    Fischer, Gilles; Rocha, Eduardo P. C; Brunet, Frédéric; Vergassola, Massimo; Dujon, Bernard

    2006-01-01

    Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage. PMID:16532063

  20. Extended Rearrangement Inequalities and Applications to Some Quantitative Stability Results

    NASA Astrophysics Data System (ADS)

    Lemou, Mohammed

    2016-09-01

    In this paper, we prove a new functional inequality of Hardy-Littlewood type for generalized rearrangements of functions. We then show how this inequality provides quantitative stability results of steady states to evolution systems that essentially preserve the rearrangements and some suitable energy functional, under minimal regularity assumptions on the perturbations. In particular, this inequality yields a quantitative stability result of a large class of steady state solutions to the Vlasov-Poisson systems, and more precisely we derive a quantitative control of the L 1 norm of the perturbation by the relative Hamiltonian (the energy functional) and rearrangements. A general non linear stability result has been obtained by Lemou et al. (Invent Math 187:145-194, 2012) in the gravitational context, however the proof relied in a crucial way on compactness arguments which by construction provides no quantitative control of the perturbation. Our functional inequality is also applied to the context of 2D-Euler systems and also provides quantitative stability results of a large class of steady-states to this system in a natural energy space.

  1. Mitochondrial DNA Rearrangement Spectrum in Brain Tissue of Alzheimer’s Disease: Analysis of 13 Cases

    PubMed Central

    Chen, Yucai; Liu, Changsheng; Parker, William Davis; Chen, Hongyi; Beach, Thomas G.; Liu, Xinhua; Serrano, Geidy E.; Lu, Yanfen; Huang, Jianjun; Yang, Kunfang; Wang, Chunmei

    2016-01-01

    Background Mitochondrial dysfunction may play a central role in the pathologic process of Alzheimer’s disease (AD), but there is still a scarcity of data that directly links the pathology of AD with the alteration of mitochondrial DNA. This study aimed to provide a comprehensive assessment of mtDNA rearrangement events in AD brain tissue. Patients and Methods Postmortem frozen human brain cerebral cortex samples were obtained from the Banner Sun Health Research Institute Brain and Body Donation Program, Sun City, AZ. Mitochondria were isolated and direct sequence by using MiSeq®, and analyzed by relative software. Results Three types of mitochondrial DNA (mtDNA) rearrangements have been seen in post mortem human brain tissue from patients with AD and age matched control. These observed rearrangements include a deletion, F-type rearrangement, and R-type rearrangement. We detected a high level of mtDNA rearrangement in brain tissue from cognitively normal subjects, as well as the patients with Alzheimer's disease (AD). The rate of rearrangements was calculated by dividing the number of positive rearrangements by the coverage depth. The rearrangement rate was significantly higher in AD brain tissue than in control brain tissue (17.9%versus 6.7%; p = 0.0052). Of specific types of rearrangement, deletions were markedly increased in AD (9.2% versus 2.3%; p = 0.0005). Conclusions Our data showed that failure of mitochondrial DNA in AD brain might be important etiology of AD pathology. PMID:27299301

  2. Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing

    PubMed Central

    Abel, Haley J.; Al-Kateb, Hussam; Cottrell, Catherine E.; Bredemeyer, Andrew J.; Pritchard, Colin C.; Grossmann, Allie H.; Wallander, Michelle L.; Pfeifer, John D.; Lockwood, Christina M.; Duncavage, Eric J.

    2015-01-01

    The identification of recurrent gene rearrangements in the clinical laboratory is the cornerstone for risk stratification and treatment decisions in many malignant tumors. Studies have reported that targeted next-generation sequencing assays have the potential to identify such rearrangements; however, their utility in the clinical laboratory is unknown. We examine the sensitivity and specificity of ALK and KMT2A (MLL) rearrangement detection by next-generation sequencing in the clinical laboratory. We analyzed a series of seven ALK rearranged cancers, six KMT2A rearranged leukemias, and 77 ALK/KMT2A rearrangement–negative cancers, previously tested by fluorescence in situ hybridization (FISH). Rearrangement detection was tested using publicly available software tools, including Breakdancer, ClusterFAST, CREST, and Hydra. Using Breakdancer and ClusterFAST, we detected ALK rearrangements in seven of seven FISH-positive cases and KMT2A rearrangements in six of six FISH-positive cases. Among the 77 ALK/KMT2A FISH-negative cases, no false-positive identifications were made by Breakdancer or ClusterFAST. Further, we identified one ALK rearranged case with a noncanonical intron 16 breakpoint, which is likely to affect its response to targeted inhibitors. We report that clinically relevant chromosomal rearrangements can be detected from targeted gene panel–based next-generation sequencing with sensitivity and specificity equivalent to that of FISH while providing finer-scale information and increased efficiency for molecular oncology testing. PMID:24813172

  3. Deep cytoplasmic rearrangements in axis-respecified Xenopus embryos

    NASA Technical Reports Server (NTRS)

    Denegre, J. M.; Danilchik, M. V.

    1993-01-01

    In fertilized eggs of the frog Xenopus, the vegetal yolk mass rotates away from the future dorsal side (J. P. Vincent and J. Gerhart, 1987, Dev. Biol. 123, 526-539), and a major rearrangement of the deep animal hemisphere cytoplasm produces a characteristic swirl in the prospective dorsal side (M. V. Danilchik and J. M. Denegre, 1991, Development 111, 845-856). The relationship between this swirl and determination of the dorsal-ventral axis was further investigated by attempting to experimentally separate the positions of the swirl and the dorsal-ventral axis. Eggs were obliquely oriented in the gravity field to respecify the direction of yolk mass rotation and the position of the dorsal-ventral axis. When yolk mass rotation occurred in the absence of a sperm, as in activated eggs, a swirl pattern formed on the side away from which the yolk mass had rotated. In fertilized eggs tipped with the sperm entry point (SEP) down or to the side, swirl patterns were always found to form on the side away from which the yolk mass was displaced. However, in eggs tipped SEP up, in which the yolk mass was forced to rotate away from the SEP, more complicated rearrangements were observed in addition to the rotation-oriented swirl. Because the direction of yolk mass rotation was found to be influenced by both gravity and the actual position of the SEP in obliquely oriented eggs (SEP to the side), such complicated rearrangement patterns may result from opposing forces generated by both yolk mass rotation and the expanding sperm aster. Thus, except in cases in which the influences of SEP position and unit gravity opposed each other, it was not possible to experimentally separate the position of the deep cytoplasmic swirl from the direction of yolk mass rotation, and therefore the position of the prospective dorsal side.

  4. Measurement of absolute T cell receptor rearrangement diversity.

    PubMed

    Baum, Paul D; Young, Jennifer J; McCune, Joseph M

    2011-05-31

    T cell receptor (TCR) diversity is critical for adaptive immunity. Existing methods for measuring such diversity are qualitative, expensive, and/or of uncertain accuracy. Here, we describe a method and associated reagents for estimating the absolute number of unique TCR Vβ rearrangements present in a given number of cells or volume of blood. Compared to next generation sequencing, this method is rapid, reproducible, and affordable. Diversity of a sample is calculated based on three independent measurements of one Vβ-Jβ family of TCR rearrangements at a time. The percentage of receptors using the given Vβ gene is determined by flow cytometric analysis of T cells stained with anti-Vβ family antibodies. The percentage of receptors using the Vβ gene in combination with the chosen Jβ gene is determined by quantitative PCR. Finally, the absolute clonal diversity of the Vβ-Jβ family is determined with the AmpliCot method of DNA hybridization kinetics, by interpolation relative to PCR standards of known sequence diversity. These three component measurements are reproducible and linear. Using titrations of known numbers of input cells, we show that the TCR diversity estimates obtained by this approach approximate expected values within a two-fold error, have a coefficient of variation of 20%, and yield similar results when different Vβ-Jβ pairs are chosen. The ability to obtain accurate measurements of the total number of different TCR gene rearrangements in a cell sample should be useful for basic studies of the adaptive immune system as well as in clinical studies of conditions such as HIV disease, transplantation, aging, and congenital immunodeficiencies. PMID:21385585

  5. Rearrangements of immunoglobulin genes during differentiation and evolution.

    PubMed

    Honjo, T; Nakai, S; Nishida, Y; Kataoka, T; Yamawaki-Kataoka, Y; Takahashi, N; Obata, M; Shimizu, A; Yaoita, Y; Nikaido, T; Ishida, N

    1981-01-01

    Immunoglobulin genes are shown to undergo dynamic rearrangements during differentiation as well as evolution. We have demonstrated that a complete immunoglobulin heavy chain gene is formed by at least two types of DNA rearrangement during B cell differentiation. The first type of rearrangement is V-D-J recombination to complete a variable region sequence and the second type is S-S recombination to switch a constant region sequence. Both types of recombination are accompanied by deletion of the intervening DNA segment. Structure and organization of CH genes are elucidated by molecular cloning and nucleotide sequence determination. Organization of H chain genes is summarized as VH-(unknown distance)-JH-(6.5 kb)-C mu-(4.5 kb)-C delta-(unknown distance)-C gamma 3-(34 kb)-C gamma 1-(21 kb)-C gamma 2b-(15 kb)-C gamma 2a-(14.5 kb)-C epsilon-(12.5 kb)-C alpha. The S-S recombination takes place at the S region which is located at the 5' side of each CH gene. Nucleotide sequence of the S region comprises tandem repetition of closely related sequences. The S-S recombination seems to be mediated by short common sequences shared among S regions. A sister chromatid exchange model was proposed as a mechanism for S-S recombination. Comparison of nucleotide sequences of CH genes indicates that immunoglobulin genes have scrambled by intervening sequence-mediated domain transfer during their evolution.

  6. [Clonality lymphoid study through rearrangement analysis of antigen receptor].

    PubMed

    Villamizar-Rivera, Nicolás; Olaya, Natalia

    2015-01-01

    As a rule, malignant lymphoid proliferations are clonal. While most of the time the biological potential can be established through routine pathologic examination and auxiliary techniques, some cases are difficult to classify. Moreover, there are situations in which there are dominant clones whose analysis are important, such as occur in autoimmune diseases and immunodeficiency. This paper presents in an understandable way the main techniques for the study of clonality in lymphoid lesions, i.e. the analysis of rearrangements of antigen receptor genes by multiplex polymerase chain reaction (PCR) based tests.

  7. Multiparty semiquantum secret sharing based on rearranging orders of qubits

    NASA Astrophysics Data System (ADS)

    Gao, Gan; Wang, Yue; Wang, Dong

    2016-04-01

    Based on the assumption of a perfect qubit, Boyer et al. proposed a novel semiquantum key distribution protocol [Phys. Rev. Lett. 99 (2007) 140501], in which quantum Alice shares a secret key with classical Bob. In this paper, we use Bell states to propose a multiparty semiquantum secret sharing (MSQSS) protocol, in which only the boss is quantum and all agents are classical. Classical agents are restricted to performing measurements in a computational basis and rearranging orders of qubits. Unless all classical agents collaborate, no subset of them can obtain the secret of the quantum boss. Also, we show that this proposed protocol is secure against eavesdropping.

  8. Absence of heterozygosity due to template switching during replicative rearrangements.

    PubMed

    Carvalho, Claudia M B; Pfundt, Rolph; King, Daniel A; Lindsay, Sarah J; Zuccherato, Luciana W; Macville, Merryn V E; Liu, Pengfei; Johnson, Diana; Stankiewicz, Pawel; Brown, Chester W; Shaw, Chad A; Hurles, Matthew E; Ira, Grzegorz; Hastings, P J; Brunner, Han G; Lupski, James R

    2015-04-01

    We investigated complex genomic rearrangements (CGRs) consisting of triplication copy-number variants (CNVs) that were accompanied by extended regions of copy-number-neutral absence of heterozygosity (AOH) in subjects with multiple congenital abnormalities. Molecular analyses provided observational evidence that in humans, post-zygotically generated CGRs can lead to regional uniparental disomy (UPD) due to template switches between homologs versus sister chromatids by using microhomology to prime DNA replication-a prediction of the replicative repair model, MMBIR. Our findings suggest that replication-based mechanisms might underlie the formation of diverse types of genomic alterations (CGRs and AOH) implicated in constitutional disorders. PMID:25799105

  9. Developmental arrest at early stages of Chinese hamster embryos homozygous for chromosomal rearrangements

    SciTech Connect

    Sonta, S.; Yamada, M.; Iida, T.; Ohashi, H. )

    1991-03-01

    Forty-three Chinese hamster stocks with autosomal rearrangements produced by X-irradiation were used. These rearrangements, 38 reciprocal translocations and 5 inversions, were chromosomally balanced. Heterozygotes for these rearrangements were all fertile and morphologically normal in both sexes except for one line with growth retardation. By crossing male and female heterozygotes for the same rearrangements, homozygotes were obtained in 37 lines. In the remaining 6 lines (5 with reciprocal translocations and 1 with an inversion), no homozygotes were viable. These 6 lines revealed arrested development of homozygous embryos at the two-cell stage, around the eight-cell stage, and after implantation, respectively. The bands of the breakpoints of rearrangements associated with lethality of homozygous embryos were different for each rearrangement. These results suggest that abnormal expression including embryonic lethality in homozygotes may be due to an influence of genes at the breakpoints.

  10. Diffusing Diffusivity: Survival in a Crowded Rearranging and Bounded Domain.

    PubMed

    Jain, Rohit; Sebastian, Kizhakeyil L

    2016-09-01

    We consider a particle diffusing in a bounded, crowded, rearranging medium. The rearrangement happens on a time scale longer than the typical time scale of diffusion of the particle; as a result, effectively, the diffusion coefficient of the particle varies as a stochastic function of time. What is the probability that the particle will survive within the bounded region, given that it is absorbed the first time it hits the boundary of the region in which it diffuses? This question is of great interest in a variety of chemical and biological problems. If the diffusion coefficient is a constant, then analytical solutions for a variety of cases are available in the literature. However, there is no solution available for the case in which the diffusion coefficient is a random function of time. We discuss a class of models for which it is possible to find analytical solutions to the problem. We illustrate the method for a circular, two-dimensional region, but our methods are easy to apply to diffusion in arbitrary dimensions and spherical/rectangular regions. Our solution shows that if the dimension of the region is large, then only the average value of the diffusion coefficient determines the survival probability. However, for smaller-sized regions, one would be able to see the effects of the stochasticity of the diffusion coefficient. We also give generalizations of the results to N dimensions. PMID:27478982

  11. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    PubMed

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing.

  12. RNA-directed epigenetic regulation of DNA rearrangements.

    PubMed

    Mochizuki, Kazufumi

    2010-09-20

    Ciliated protozoa undergo extensive DNA rearrangements, including DNA elimination, chromosome breakage and DNA unscrambling, when the germline micronucleus produces the new macronucleus during sexual reproduction. It has long been known that many of these events are epigenetically controlled by DNA sequences of the parental macronuclear genome. Recent studies in some model ciliates have revealed that these epigenetic regulations are mediated by non-coding RNAs. DNA elimination in Paramecium and Tetrahymena is regulated by small RNAs that are produced and operated by an RNAi (RNA interference)-related mechanism. It has been proposed that the small RNAs from the micronuclear genome can be used to identify eliminated DNAs by whole-genome comparison of the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the somatic parental macronuclear genome. These RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. The possible evolutionary benefits of these RNA-directed epigenetic regulations of DNA rearrangement in ciliates are discussed in the present chapter. PMID:20822488

  13. Transposon domestication versus mutualism in ciliate genome rearrangements.

    PubMed

    Vogt, Alexander; Goldman, Aaron David; Mochizuki, Kazufumi; Landweber, Laura F

    2013-01-01

    Ciliated protists rearrange their genomes dramatically during nuclear development via chromosome fragmentation and DNA deletion to produce a trimmer and highly reorganized somatic genome. The deleted portion of the genome includes potentially active transposons or transposon-like sequences that reside in the germline. Three independent studies recently showed that transposase proteins of the DDE/DDD superfamily are indispensible for DNA processing in three distantly related ciliates. In the spirotrich Oxytricha trifallax, high copy-number germline-limited transposons mediate their own excision from the somatic genome but also contribute to programmed genome rearrangement through a remarkable transposon mutualism with the host. By contrast, the genomes of two oligohymenophorean ciliates, Tetrahymena thermophila and Paramecium tetraurelia, encode homologous PiggyBac-like transposases as single-copy genes in both their germline and somatic genomes. These domesticated transposases are essential for deletion of thousands of different internal sequences in these species. This review contrasts the events underlying somatic genome reduction in three different ciliates and considers their evolutionary origins and the relationships among their distinct mechanisms for genome remodeling.

  14. FASEB Summer Research Conference. Genetic Recombination and Chromosome Rearrangements

    SciTech Connect

    Jinks-Robertson, Sue

    2002-02-01

    The 2001 meeting entitled ''Genetic Recombination and Genome Rearrangements'' was held July 21-26 in Snowmass, Colorado. The goal of the meeting was to bring together scientists using diverse approaches to study all aspects of genetic recombination. This goal was achieved by integrating talks covering the genetics, biochemistry and structural biology of homologous recombination, site-specific recombination, and nonhomologous recombination. The format of the meeting consisted of a keynote address on the opening evening, two formal plenary sessions on each of the four full meeting days, a single afternoon workshop consisting of short talks chosen from among submitted abstracts, and afternoon poster sessions on each of the four full meeting days. The eight plenary session were entitled: (1) Recombination Mechanisms, (2) Prokaryotic Recombination, (3) Repair and Recombination, (4) Site-specific Recombination and Transposition, (5) Eukaryotic Recombination I, (6) Genome Rearrangements, (7) Meiosis, and (8) Eukaryotic Recombination II. Each session included a mix of genetic, biochemical and structural talks; talks were limited to 20 minutes, followed by 10 minutes of very lively, general discussion. Much of the data presented in the plenary sessions was unpublished, thus providing attendees with the most up-to-date knowledge of this rapidly-moving field.

  15. Compositions and methods for detecting gene rearrangements and translocations

    DOEpatents

    Rowley, Janet D.; Diaz, Manuel O.

    2000-01-01

    Disclosed is a series of nucleic acid probes for use in diagnosing and monitoring certain types of leukemia using, e.g., Southern and Northern blot analyses and fluorescence in situ hybridization (FISH). These probes detect rearrangements, such as translocations involving chromosome band 11q23 with other chromosomes bands, including 4q21, 6q27, 9p22, 19p13.3, in both dividing leukemic cells and interphase nuclei. The breakpoints in all such translocations are clustered within an 8.3 kb BamHI genomic region of the MLL gene. A novel 0.7 kb BamH1 cDNA fragment derived from this gene detects rearrangements on Southern blot analysis with a single BamHI restriction digest in all patients with the common 11q23 translocations and in patients with other 11q23 anomalies. Northern blot analyses are presented demonstrating that the MLL gene has multiple transcripts and that transcript size differentiates leukemic cells from normal cells. Also disclosed are MLL fusion proteins, MLL protein domains and anti-MLL antibodies.

  16. Biogenetically Inspired Synthesis of Lingzhiol.

    PubMed

    Sharmah Gautam, Krishna; Birman, Vladimir B

    2016-04-01

    A concise stereo- and enantioselective synthesis of lingzhiol has been achieved featuring a biogenetically inspired Brønsted acid catalyzed semipinacol rearrangement of a glycidyl alcohol intermediate.

  17. Molecular screening of pituitary adenomas for gene mutations and rearrangements

    SciTech Connect

    Herman, V.; Drazin, N.Z.; Gonskey, R.; Melmed, S. )

    1993-07-01

    Although pituitary tumors arise as benign monoclonal neoplasms, genetic alterations have not readily been identified in these adenomas. The authors studied restriction fragment abnormalities involving the GH gene locus, and mutations in the p53 and H-, K-, and N-ras genes in 22 human GH cell adenomas. Twenty two nonsecretory adenomas were also examined for p53 and ras gene mutations. Seven prolactinoma DNA samples were tested for deletions in the multiple endocrine neoplasia-1 (MEN-1) locus, as well as for rearrangements in the hst gene, a member of the fibroblast growth factor family. In DNA from GH-cell adenomas, identical GH restriction patterns were detected in both pituitary and lymphocyte DNA in all patients and in one patient with a mixed GH-TSH cell adenoma. Using polymerase chain reaction (PCR)-single stranded conformation polymorphism analysis, no mutations were detected in exons 5, 6, 7 and 8 of the p53 gene in GH cell adenomas nor in 22 nonsecretory adenomas. Codons 12/13 and 61 of H-ras, K-ras, and N-ras genes were also intact on GH cell adenomas and in nonsecretory adenomas. Site-specific probes for chromosome 11q13 including, PYGM, D11S146, and INT2 were used in 7 sporadic PRL-secreting adenomas to detect deletions of the MEN-1 locus on chromosome 11. One patient was identified with a loss of 11p, and the remaining 6 patients did not demonstrate loss of heterozygosity in the pituitary 11q13 locus, compared to lymphocyte DNA. None of these patients demonstrated hst gene rearrangements which also maps to this locus. These results show that p53 and ras gene mutations are not common events in the pathogenesis of acromegaly and nonsecretory tumors. Although hst gene rearrangements and deletions of 11q13 are not associated with sporadic PRl-cell adenoma formation, a single patient was detected with a partial loss of chromosome 11, including the putative MEN-1 site. 31 refs., 5 figs., 2 tabs.

  18. CIC-rearranged Sarcomas: A Study of 20 Cases and Comparisons With Ewing Sarcomas.

    PubMed

    Yoshida, Akihiko; Goto, Keisuke; Kodaira, Makoto; Kobayashi, Eisuke; Kawamoto, Hiroshi; Mori, Taisuke; Yoshimoto, Seiichi; Endo, Otone; Kodama, Narihito; Kushima, Ryoji; Hiraoka, Nobuyoshi; Motoi, Toru; Kawai, Akira

    2016-03-01

    The CIC gene rearrangement exists in a subset of small round cell sarcomas. As the nosologic relationship of these sarcomas to Ewing sarcomas remains undetermined, we examined 20 CIC-rearranged sarcomas to compare their clinicopathologic features with those of Ewing sarcomas. The CIC-rearranged sarcomas were from a group of 14 men and 6 women with a median age of 24.5 years. The primary tumor sites included the limbs, trunk wall, internal trunk, lung, cerebrum, and pharynx. A comparison of the demographic and clinical characteristics of the 20 patients with CIC-rearranged sarcomas with those of the 53 near-consecutive patients with EWSR1-rarranged Ewing sarcomas showed that there were no differences with respect to their ages and sexes. Although none of the CIC-rearranged sarcomas arose in the bone, 40% of the Ewing sarcomas primarily affected the skeleton. The overall survival of patients with Ewing sarcomas was significantly better than that for patients with CIC-rearranged sarcomas. A histologic comparison of the CIC-rearranged sarcomas with 20 EWSR1-rearranged Ewing sarcomas showed significantly higher degrees of lobulation, nuclear pleomorphism, the prominence of the nucleoli, spindle cell elements, and myxoid changes in the CIC-rearranged sarcomas. Distinguishing immunohistochemical features included heterogenous CD99 reactivity, nuclear WT1 expression, and calretinin expression in the CIC-rearranged sarcomas and NKX2.2 expression in the Ewing sarcomas. CIC-rearranged sarcomas are distinct from Ewing sarcomas clinically, morphologically, and immunohistochemically, and they should be considered a separate entity rather than being grouped within the same family of tumors.

  19. [Transgene complete silencing may associate with rearrangement of retroviral vector].

    PubMed

    Wang, Dan; Xiao, Lejia; Ma, Qingxin; Zhai, Fen; Ren, Sichong; Li, Changlong

    2011-04-01

    Transgene silencing is one of two major obstacles in both basic biomedical research for transgene and clinical practice of gene therapy. Based on the model of HT1080 cell clones, which transduced single copy of retroviral vector MGPN2, the mechanism of transgene silencing was explored in this investigation by a serial molecular techniques. In the HT1080 cell clone that absence of GFP protein synthesized, no significant aberration of epigenetic modification was detected, but the transcript size and the sequence changed that resulted in the reading frame shift. In addition to chromosomal position effect leading to transgene silencing, the transcript reading frame shift associated with retroviral vector rearrangements could induce complete silencing of transgene.

  20. Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms

    NASA Astrophysics Data System (ADS)

    Calvo, Florent; Doye, Jonathan P. K.; Wales, David J.

    2012-02-01

    New experiments involving direct observation of colloidal clusters by optical microscopy promise to deliver a wealth of new information about such systems. Calculations suggest that some of the observable properties may be predicted using a simple pairwise potential to represent the interparticle forces, but in a range of parameter space that is distinctly different from previous representations of atomic clusters. The present contribution provides some benchmark calculations and predictions of structure, thermodynamics and rearrangement mechanisms for colloidal clusters containing up to 80 particles. The results suggest that distinct features characteristic of short-ranged interactions should be observable in terms of the structure, thermodynamics and dynamical properties. Analysis of a kinetic transition network for the 19-particle cluster reveals super-Arrhenius behaviour in the dynamics, analogous to a `fragile' glass-former.

  1. Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats.

    PubMed

    Karadjian, Gregory; Hassanin, Alexandre; Saintpierre, Benjamin; Gembu Tungaluna, Guy-Crispin; Ariey, Frederic; Ayala, Francisco J; Landau, Irene; Duval, Linda

    2016-08-30

    Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better understand the evolutionary history of Haemosporidia, which notably include the Plasmodium parasites, malaria's agents. We use next-generation sequencing to obtain the complete mitochondrial genome of Nycteria parasites from African Nycteris grandis (Nycteridae) and Rhinolophus alcyone (Rhinolophidae) and Asian Megaderma spasma (Megadermatidae). We report four complete mitochondrial genomes, including two rearranged mitochondrial genomes within Haemosporidia. Our results open outlooks into potentially undiscovered Haemosporidian diversity. PMID:27528689

  2. Structural rearrangements in self-assembled surfactant layers at surfaces

    SciTech Connect

    Sushko, Maria L.; Liu, Jun

    2010-03-25

    The transition from compact to extended configuration in ionic surfactant layers under the influence of salt, surfactant surface density and temperature is studied using the classical density functional theory (cDFT). The increase in ionic strength of aqueous salt solution or in surfactant surface density leads to the transition from the hemicylindrical to the perpendicular monolayer configuration of the molecules. Although producing the same structural rearrangement in the surfactant layer the origin of the effect of salt and surface density is different. While the addition of salt increases the out-of-plane attractive interactions with the solvent, the increase in density results in the increase in the in-plane repulsion in surfactant layer. The temperature effects are subtler and are mainly manifested in the reduction of the solution structuring at elevated temperatures.

  3. Enzymatic aerobic ring rearrangement of optically active furylcarbinols.

    PubMed

    Thiel, Daniel; Doknić, Diana; Deska, Jan

    2014-01-01

    Biogenic furans are currently discussed as highly attractive alternative feedstock in a post-fossil society; thus, also the creation of sustainable furan valorization pathways appears of great importance. Here an artificial Achmatowicz monooxygenase activity for the aerobic ring expansion of furans is achieved by the combination of commercial glucose oxidase as oxygen-activating biocatalyst and wild-type chloroperoxidase as oxygen-transfer mediator, providing a biological ready-to-use solution for this truly synthetic furan rearrangement. In concert with enzymatic transformations for the enantioselective preparation of optically active furylcarbinols, purely biocatalytic reaction cascades for the stereocontrolled construction of complex pyranones are obtained, exhibiting high functional group tolerance even to oxidation-sensitive moieties. PMID:25335580

  4. Somatic Engineering of Oncogenic Chromosomal Rearrangements: A Perspective.

    PubMed

    Maddalo, Danilo; Ventura, Andrea

    2016-09-01

    The ability to engineer specific mutations in mice has proven essential to advancing our understanding of the molecular basis of cancer. Chromosomal rearrangements, a common and clinically relevant class of cancer-causing mutations, have however remained difficult to faithfully recapitulate in vivo The development of genetic tools for in vivo somatic genome editing has recently overcome this limitation and led to the generation of more sophisticated and accurate preclinical models of human cancers. Here, we review the potential applications of these new technologies to the study of tumor biology and discuss their advantages over more conventional strategies, their limitations, and the remaining challenges. Cancer Res; 76(17); 4918-23. ©2016 AACR. PMID:27520450

  5. Rearrangement procedures in regenerative multibeammobile communications satellites with frequency reuse

    NASA Technical Reports Server (NTRS)

    Colombo, Gianni; Settimo, Franco; Vernucci, Antonio

    1988-01-01

    After a short overview on the European tendencies about a Land Mobile Satellite Service, this paper describes an advanced system architecture, based on multiple spot-beams and on-board processing, capable of providing message and voice services over a wide European coverage, including some North-Africa and Middle-East countries. A remarkable problem associated with spot-beam configurations is the requirement for flexibility in the capacity offer to the various coverage areas. This means incorporating procedures for changing the on-board modulator-to-spot associations, respecting the constraints imposed by frequency reuse. After discussing the requirements of the rearrangement procedure, an on-purpose algorithm is presented. This paper is derived from work performed on contract to the European Space Agency (ESA).

  6. Independent functions in rearrangement invariant spaces and the Kruglov property

    NASA Astrophysics Data System (ADS)

    Astashkin, S. V.

    2008-08-01

    Let X be a separable or maximal rearrangement invariant space on [0,1]. It is shown that the inequality \\displaystyle \\biggl\\Vert\\,\\sum_{k=1}^\\infty f_k\\biggr\\Vert _{X}\\le C\\biggl\\Vert\\biggl(\\,\\sum_{k=1}^\\infty f_k^2\\biggl)^{1/2}\\biggr\\Vert _Xholds for an arbitrary sequence of independent functions \\{f_k\\}_{k=1}^\\infty\\subset X, \\displaystyle\\int_0^1f_k(t)\\,dt=0, k=1,2,\\dots, if and only if X has the Kruglov property. As a consequence, it is proved that the same property is necessary and sufficient for a version of Maurey's well-known inequality for vector-valued Rademacher series with independent coefficients to hold in X.Bibliography: 24 titles.

  7. Rapid cloning of any rearranged mouse immunoglobulin variable genes

    SciTech Connect

    Dattamajumdar, A.K.; Jacobson, D.P.; Hood, L.E.; Osman, G.E.

    1996-12-31

    Immunoglobulins (Ig) have been the focus of extensive study for several decades and have become an important research area for immunologists and molecular biologists. The use of polymerase chain reaction (PCR) technology has accelerated the cloning, sequencing, and characterization of genes of the immune system. However, cloning and sequencing the Ig variable (V) genes using the PCR technology has been a challenging task, primarily due to the very diverse nature of Ig V region genes. We have developed a simple, rapid, and reproducible PCR-based technique to clone any rearranged mouse Ig heavy or light chain genes. A close examination of all Ig heavy and light chain V gene families has resulted in the design of 5{prime} and 3{prime} universal primers from regions that are highly conserved across all heavy or light chain V gene families, and the joining or constant regions, respectively. We present our strategy for designing universal primers for Ig V gene families. These primers were able to rapidly amplify the rearranged Ig V genes, belonging to diverse Ig V gene families from very different cell lines, i.e., J558, MOPC-21, 36-60, and a chicken ovalbumin specific B-cell hybridoma. In addition, the present study provides the complete alignment of nucleotide sequences of all heavy and light chain variable gene families. This powerful method of cloning Ig V genes, therefore, allows rapid and precise analysis of B-cell hybridomas, B-cell repertoire, and B-cell ontogeny. 55 refs., 5 figs., 2 tabs.

  8. Chromosomal rearrangement in autotetraploid plants of Arabidopsis thaliana.

    PubMed

    Weiss, H; Maluszynska, J

    2000-01-01

    Recent development of cytogenetic techniques has facilitated significant progress in Arabidopsis thaliana karyotype studies. Double-target FISH with rRNA genes provides makers that allow individual chromosome in the genome to be distinguished. Those studies have revealed that the number and position of rDNA loci is ecotype-specific. Arabidopsis is believed to be a true diploid (x = 5) with numerous ecotypes (accessions) and only a very few natural polyploid populations reported. Few studies were undertaken to induce polyploidy in Arabidopsis, however none of those gave the cytogenetic characteristics of polyploid plants. Our analysis of chromosome pairing of colchicine-induced autotetraploid Arabidopsis (Wilna ecotype) revealed preferential bivalent pairing in PMCs (pollen mother cells). In order to attempt to explain this phenomenon, first of all more detailed cytogenetic studies of autopolyploid plants have been undertaken. The localization of 45S and 5S rDNA loci in the diploid and autotetraploid plants revealed that Wilna ecotypes belongs to the group of Arabidopsis accessions with only two 5S rDNA loci present in a genome. Furthermore, the rearrangement of 45S rDNA locus in autopolyploid, when compared to the diploid plants of the same ecotype, was revealed. These results are interesting also in the context of the recently emphasised role of polyploidy in plant evolution and speciation. Arabidopsis, despite having small chromosomes, is a good system to study chromosome behaviour in relation to diploidization of autopolyploids and to evaluate the degree of chromosomal rearrangements during this process. PMID:11433970

  9. Mechanisms of chromosomal rearrangement in the human genome

    PubMed Central

    2010-01-01

    Many human cancers are associated with characteristic chromosomal rearrangements, especially hematopoietic cancers such as leukemias and lymphomas. The first and most critical step in the rearrangement process is the induction of two DNA double-strand breaks (DSB). In all cases, at least one of the two DSBs is generated by a pathologic process, such as (1) randomly-positioned breaks due to ionizing radiation, free radical oxidative damage, or spontaneous hydrolysis; (2) breaks associated with topoisomerase inhibitor treatment; or (3) breaks at direct or inverted repeat sequences, mediated by unidentified strand breakage mechanisms. In lymphoid cells, one of the two requisite DSBs is often physiologic, the result of V(D)J recombination or class switch recombination (CSR) at the lymphoid antigen receptor loci. The RAG complex, which causes the DSBs in V(D)J recombination, can cause (4) sequence-specific, pathologic DSBs at sites that fit the consensus of their normal V(D)J recombination signal targets; or (5) structure-specific, pathologic DSBs at regions of single- to double-strand transition. CSR occurs specifically in the B-cell lineage, and requires (6) activation-induced cytidine deaminase (AID) action at sites of single-stranded DNA, which may occur pathologically outside of the normal target loci of class switch recombination regions and somatic hypermutation (SHM) zones. Recent work proposes a seventh mechanism: the sequential action of AID and the RAG complex at CpG sites provides a coherent model for the pathologic DSBs at some of the most common sites of translocation in human lymphoma – the bcl-2 gene in follicular lymphoma and diffuse large B-cell lymphoma, and the bcl-1 gene in mantle cell lymphoma. PMID:20158866

  10. A rearranged junD transforms chicken embryo fibroblasts.

    PubMed

    Hartl, M; Vogt, P K

    1992-12-01

    A complementary DNA clone synthesized from the chicken junD mRNA, containing 5'- and 3'-untranslated sequences, was inserted in the retroviral expression vector RCAS to yield the construct JD. A second RCAS construct (DDDD) contained only the coding domains of JunD. DDDD did not transform upon primary transfection, but JD produced small numbers of transformed cell foci in chicken embryo fibroblast cultures. The virus recovered from these foci, JDV, was moderately transforming for chicken fibroblasts and weakly oncogenic in the animal. Its genome was rearranged, showing evidence for two recombination events. The first crossover was located between 5'-untranslated and coding sequences of junD and incorporated part of the 5'-untranslated region into an open reading frame. The second crossover occurred between junD and gag. The two crossovers generate a single open reading frame of 2064 nucleotides that encodes an 85 kilodalton protein in which sequences in the amino-terminal region of JunD are duplicated. This gag junD reading frame was recloned and then reconstituted into a replication-defective but transformation-competent retrovirus, indicating that the Gag-JunD fusion protein is the effector of transformation. A construct containing this rearranged coding sequence of JunD in Rc/RSV transactivated the collagenase promoter in chicken cells. Southern blot analysis of several independently isolated JunD transformants and deletion analysis of JDV indicated that duplication of a domain in the amino-terminal region of JunD is crucial for transformation and transactivation.

  11. Genome rearrangement affects RNA virus adaptability on prostate cancer cells

    PubMed Central

    Pesko, Kendra; Voigt, Emily A.; Swick, Adam; Morley, Valerie J.; Timm, Collin; Yin, John; Turner, Paul E.

    2015-01-01

    Gene order is often highly conserved within taxonomic groups, such that organisms with rearranged genomes tend to be less fit than wild type gene orders, and suggesting natural selection favors genome architectures that maximize fitness. But it is unclear whether rearranged genomes hinder adaptability: capacity to evolutionarily improve in a new environment. Negative-sense non-segmented RNA viruses (order Mononegavirales) have specific genome architecture: 3′ UTR – core protein genes – envelope protein genes – RNA-dependent RNA-polymerase gene – 5′ UTR. To test how genome architecture affects RNA virus evolution, we examined vesicular stomatitis virus (VSV) variants with the nucleocapsid (N) gene moved sequentially downstream in the genome. Because RNA polymerase stuttering in VSV replication causes greater mRNA production in upstream genes, N gene translocation toward the 5′ end leads to stepwise decreases in N transcription, viral replication and progeny production, and also impacts the activation of type 1 interferon mediated antiviral responses. We evolved VSV gene-order variants in two prostate cancer cell lines: LNCap cells deficient in innate immune response to viral infection, and PC-3 cells that mount an IFN stimulated anti-viral response to infection. We observed that gene order affects phenotypic adaptability (reproductive growth; viral suppression of immune function), especially on PC-3 cells that strongly select against virus infection. Overall, populations derived from the least-fit ancestor (most-altered N position architecture) adapted fastest, consistent with theory predicting populations with low initial fitness should improve faster in evolutionary time. Also, we observed correlated responses to selection, where viruses improved across both hosts, rather than suffer fitness trade-offs on unselected hosts. Whole genomics revealed multiple mutations in evolved variants, some of which were conserved across selective environments for a

  12. Chromosome 6p rearrangements appear to be secondary changes in various haematological malignancies.

    PubMed

    Huret, J L; Schoenwald, M; Brizard, A; Guilhot, F; Vilmer, E; Tanzer, J

    1989-01-01

    We report on six cases of 6p rearrangement in various haematological malignancies. On reviewing the literature, we assume 6p rearrangements to be secondary anomalies in both myeloid and lymphoid malignancies, and confirm it to be strongly associated with -5/del (5q) in myelodysplastic syndromes.

  13. Rearrangement and expression of T cell antigen receptor and gamma genes during thymic development

    PubMed Central

    1986-01-01

    Rearrangement and expression of the T cell antigen receptor and the gamma genes during T cell ontogeny is a regulated process; the gamma genes are rearranged and expressed first, followed by the beta and then the alpha genes. Expression of both functional alpha and beta gene RNA first occurs at day 17 of gestation, along with the expression of T3 delta chain RNA. T cell antigen receptor gene rearrangements occur primarily or exclusively in the thymus, although some gamma gene rearrangements occur outside the thymus in fetal liver cells that may be committed T cell progenitors. There is no gross difference in the extent of beta and gamma gene rearrangements in the adult thymocyte subpopulations that were analyzed, despite the fact that some of these populations cannot respond to antigen and never emigrate from the thymus. Quantitative analysis of rearrangements in total adult thymocyte DNA shows that beta gene rearrangements generally occur on both chromosomal homologs, and that rearrangements occur preferentially to the J beta 2 gene segment cluster. PMID:3487610

  14. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We identified complex genomic rearrangements consisting of intermixed duplications and triplications of genomic segments at the MECP2 and PLP1 loci. These complex rearrangements were characterized by a triplicated segment embedded within a duplication in 11 unrelated subjects. Notably, only two brea...

  15. Trifluoromethyl sulfoxides from allylic alcohols and electrophilic SCF3 donor by [2,3]-sigmatropic rearrangement.

    PubMed

    Maeno, Mayaka; Shibata, Norio; Cahard, Dominique

    2015-04-17

    An electrophilic trifluoromethylthiolation of allylic alcohols produces the corresponding allylic trifluoromethanesulfenates, which spontaneously rearrange into trifluoromethyl sulfoxides via a [2,3]-sigmatropic rearrangement. The reaction is straightforward and proceeds in good to high yields for the preparation of various allylic trifluoromethyl sulfoxides.

  16. Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease.

    PubMed

    Deakin, Janine E; Kruger-Andrzejewska, Maya

    2016-09-01

    Chromosome rearrangements have been implicated in diseases, such as cancer, and speciation, but it remains unclear whether rearrangements are causal or merely a consequence of these processes. Two marsupial families with very different rates of karyotype evolution provide excellent models in which to study the role of chromosome rearrangements in a disease and evolutionary context. The speciose family Dasyuridae displays remarkable karyotypic conservation, with all species examined to date possessing nearly identical karyotypes. Despite the seemingly high degree of chromosome stability within this family, they appear prone to developing tumours, including transmissible devil facial tumours. In contrast, chromosome rearrangements have been frequent in the evolution of the species-rich family Macropodidae, which displays a high level of karyotypic diversity. In particular, the genus Petrogale (rock-wallabies) displays an extraordinary level of chromosome rearrangement among species. For six parapatric Petrogale species, it appears that speciation has essentially been caught in the act, providing an opportunity to determine whether chromosomal rearrangements are a cause or consequence of speciation in this system. This review highlights the reasons that these two marsupial families are excellent models for testing hypotheses for hotspots of chromosome rearrangement and deciphering the role of chromosome rearrangements in disease and speciation. PMID:27255308

  17. A Prediction Model for ROS1-Rearranged Lung Adenocarcinomas based on Histologic Features

    PubMed Central

    Zheng, Jing; Kong, Mei; Sun, Ke; Wang, Bo; Chen, Xi; Ding, Wei; Zhou, Jianying

    2016-01-01

    Aims To identify the clinical and histological characteristics of ROS1-rearranged non-small-cell lung carcinomas (NSCLCs) and build a prediction model to prescreen suitable patients for molecular testing. Methods and Results We identified 27 cases of ROS1-rearranged lung adenocarcinomas in 1165 patients with NSCLCs confirmed by real-time PCR and FISH and performed univariate and multivariate analyses to identify predictive factors associated with ROS1 rearrangement and finally developed prediction model. Detected with ROS1 immunochemistry, 59 cases of 1165 patients had a certain degree of ROS1 expression. Among these cases, 19 cases (68%, 19/28) with 3+ and 8 cases (47%, 8/17) with 2+ staining were ROS1 rearrangement verified by real-time PCR and FISH. In the resected group, the acinar-predominant growth pattern was the most commonly observed (57%, 8/14), while in the biopsy group, solid patterns were the most frequently observed (78%, 7/13). Based on multiple logistic regression analysis, we determined that female sex, cribriform structure and the presence of psammoma body were the three most powerful indicators of ROS1 rearrangement, and we have developed a predictive model for the presence of ROS1 rearrangements in lung adenocarcinomas. Conclusions Female, cribriform structure and presence of psammoma body were the three most powerful indicator of ROS1 rearrangement status, and predictive formula was helpful in screening ROS1-rearranged NSCLC, especially for ROS1 immunochemistry equivocal cases. PMID:27648828

  18. Regioselective synthesis of heteroaryl triflones by LDA (lithium diisopropylamide)-mediated anionic thia-Fries rearrangement.

    PubMed

    Xu, Xiu-Hua; Wang, Xin; Liu, Guo-kai; Tokunaga, Etsuko; Shibata, Norio

    2012-05-18

    Novel heteroaryl triflones including oxindole, pyrazolone, pyridine, and quinoline derivatives have been regioselectively synthesized by LDA-mediated thia-Fries rearrangement for the first time. These reactions are also the first examples of the application of anionic thia-Fries rearrangement in heteroaromatic compounds.

  19. Recent applications of the divinylcyclopropane–cycloheptadiene rearrangement in organic synthesis

    PubMed Central

    Krüger, Sebastian

    2014-01-01

    Summary This review summarizes the application of the divinylcyclopropane–cycloheptadiene rearrangement in synthetic organic chemistry. A brief overview of the new mechanistic insights concerning the title reaction is provided as well as a condensed account on the biological relevance of the topic. Heteroatom variants of this rearrangement are covered briefly. PMID:24605138

  20. Dihydrothiophenes containing quaternary stereogenic centres by sequential stereospecific rearrangements and ring-closing metathesis.

    PubMed

    Mingat, Gaëlle; McDouall, Joseph J W; Clayden, Jonathan

    2014-06-28

    Stereospecific [3,3]-sigmatropic rearrangement of O-substituted thiocarbamate derivatives of enantiopure allylic alcohols provides allylic thiocarbamates as single enantiomers. Intramolecular arylation by rearrangement of their allyllithium derivatives provides allylic tertiary thiols. Allylation and ring-closing metathesis gives 2,5-dihydrothiophenes containing sulfur-bearing quaternary centres.

  1. Catalytic Rearrangement of 2-Alkoxy Diallyl Alcohols: Access to Polysubstituted Cyclopentenones.

    PubMed

    Lempenauer, Luisa; Duñach, Elisabet; Lemière, Gilles

    2016-03-18

    A catalytic rearrangement of diallyl alcohols comprising a cyclic enol ether has been developed using very mild conditions. Bismuth(III) triflate was found to be a very active catalyst for the ring rearrangement of a range of tertiary allylic alcohols to efficiently afford polysubstituted cyclopentenones with a high degree of diastereoselectivity. PMID:26927227

  2. On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

    PubMed Central

    Marques-Bonet, Tomàs; Sànchez-Ruiz, Jesús; Armengol, Lluís; Khaja, Razi; Bertranpetit, Jaume; Lopez-Bigas, Núria; Rocchi, Mariano; Gazave, Elodie; Navarro, Arcadi

    2007-01-01

    Background The role that chromosomal rearrangements might have played in the speciation processes that have separated the lineages of humans and chimpanzees has recently come into the spotlight. To date, however, results are contradictory. Here we revisit this issue by making use of the available human and chimpanzee genome sequence to study the relationship between chromosomal rearrangements and rates of DNA sequence evolution. Results Contrary to previous findings for this pair of species, we show that genes located in the rearranged chromosomes that differentiate the genomes of humans and chimpanzees, especially genes within rearrangements themselves, present lower divergence than genes elsewhere in the genome. Still, there are considerable differences between individual chromosomes. Chromosome 4, in particular, presents higher divergence in genes located within its rearrangement. Conclusion A first conclusion of our analysis is that divergence is lower for genes located in rearranged chromosomes than for those in colinear chromosomes. We also report that non-coding regions within rearranged regions tend to have lower divergence than non-coding regions outside them. These results suggest an association between chromosomal rearrangements and lower non-coding divergence that has not been reported before, even if some chromosomes do not follow this trend and could be potentially associated with a speciation episode. In summary, without excluding it, our results suggest that chromosomal speciation has not been common along the human and chimpanzee lineage. PMID:17971225

  3. Rearrangement hotspots in the sex chromosome of the Palearctic black fly Simulium bergi (Diptera, Simuliidae).

    PubMed

    Adler, Peter H; Yildirim, Alparslan; Onder, Zuhal; Tasci, G Taskin; Duzlu, Onder; Arslan, M Ozkan; Ciloglu, Arif; Sari, Baris; Parmaksizoglu, Nilgun; Inci, Abdullah

    2016-01-01

    An extreme example of nonrandom rearrangements, especially inversion breaks, is described in the polytene chromosomes of the black fly Simulium bergi Rubtsov, 1956 from Armenia and Turkey. A total of 48 rearrangements was discovered, relative to the standard banding sequence for the subgenus Simulium Latreille, 1802. One rearrangement, an inversion (IIS-C) in the short arm of the second chromosome, was fixed. Six (12.5%) of the rearrangements were autosomal polymorphisms, and the remaining 41 (85.4%) were sex linked. More than 40 X- and Y-linked rearrangements, predominantly inversions, were clustered in the long arm of the second chromosome (IIL), representing about 15% of the total complement. The pattern conforms to a nonrandom model of chromosome breakage, perhaps associated with an underlying molecular mechanism. PMID:27551350

  4. Rearrangement hotspots in the sex chromosome of the Palearctic black fly Simulium bergi (Diptera, Simuliidae)

    PubMed Central

    Adler, Peter H.; Yildirim, Alparslan; Onder, Zuhal; Tasci, G. Taskin; Duzlu, Onder; Arslan, M. Ozkan; Ciloglu, Arif; Sari, Baris; Parmaksizoglu, Nilgun; Inci, Abdullah

    2016-01-01

    Abstract An extreme example of nonrandom rearrangements, especially inversion breaks, is described in the polytene chromosomes of the black fly Simulium bergi Rubtsov, 1956 from Armenia and Turkey. A total of 48 rearrangements was discovered, relative to the standard banding sequence for the subgenus Simulium Latreille, 1802. One rearrangement, an inversion (IIS-C) in the short arm of the second chromosome, was fixed. Six (12.5%) of the rearrangements were autosomal polymorphisms, and the remaining 41 (85.4%) were sex linked. More than 40 X- and Y-linked rearrangements, predominantly inversions, were clustered in the long arm of the second chromosome (IIL), representing about 15% of the total complement. The pattern conforms to a nonrandom model of chromosome breakage, perhaps associated with an underlying molecular mechanism. PMID:27551350

  5. T cell receptor gamma and delta rearrangements in hematologic malignancies. Relationship to lymphoid differentiation.

    PubMed Central

    Griesinger, F; Greenberg, J M; Kersey, J H

    1989-01-01

    We have studied recombinatorial events of the T cell receptor delta and gamma chain genes in hematopoietic malignancies and related these to normal stages of lymphoid differentiation. T cell receptor delta gene recombinatorial events were found in 91% of acute T cell lymphoblastic leukemia, 68% of non-T, non-B lymphoid precursor acute lymphoblastic leukemia (ALL) and 80% of mixed lineage acute leukemias. Mature B-lineage leukemias and acute nonlymphocytic leukemias retained the T-cell receptor delta gene in the germline configuration. The incidence of T cell receptor gamma and delta was particularly high in CD10+CD19+ non-T, non-B lymphoid precursor ALL. In lymphoid precursor ALL, T cell receptor delta was frequently rearranged while T cell receptor gamma was in the germline configuration. This suggests that TCR delta rearrangements may precede TCR gamma rearrangements in lymphoid ontogeny. In T-ALL, only concordant T cell receptor delta and gamma rearrangements were observed. Several distinct rearrangements were defined using a panel of restriction enzymes. Most of the rearrangements observed in T-ALL represented joining events of J delta 1 to upstream regions. In contrast, the majority of rearrangements in lymphoid precursor ALL most likely represented D-D or V-D rearrangements, which have been found to be early recombinatorial events of the TCR delta locus. We next analyzed TCR delta rearrangements in five CD3+TCR gamma/delta+ ALL and cell lines. One T-ALL, which demonstrated a different staining pattern with monoclonal antibodies against the products of the TCR gamma/delta genes than the PEER cell line, rearranges J delta 1 to a currently unidentified variable region. Images PMID:2547833

  6. Solution (31)P NMR Study of the Acid-Catalyzed Formation of a Highly Charged {U24Pp12} Nanocluster, [(UO2)24(O2)24(P2O7)12](48-), and Its Structural Characterization in the Solid State Using Single-Crystal Neutron Diffraction.

    PubMed

    Dembowski, Mateusz; Olds, Travis A; Pellegrini, Kristi L; Hoffmann, Christina; Wang, Xiaoping; Hickam, Sarah; He, Junhong; Oliver, Allen G; Burns, Peter C

    2016-07-13

    The first neutron diffraction study of a single crystal containing uranyl peroxide nanoclusters is reported for pyrophosphate-functionalized Na44K6[(UO2)24(O2)24(P2O7)12][IO3]2·140H2O (1). Relative to earlier X-ray studies, neutron diffraction provides superior information concerning the positions of H atoms and lighter counterions. Hydrogen positions have been assigned and reveal an extensive network of H-bonds; notably, most O atoms present in the anionic cluster accept H-bonds from surrounding H2O molecules, and none of the surface-bound O atoms are protonated. The D4h symmetry of the cage is consistent with the presence of six encapsulated K cations, which appear to stabilize the lower symmetry variant of this cluster. (31)P NMR measurements demonstrate retention of this symmetry in solution, while in situ (31)P NMR studies suggest an acid-catalyzed mechanism for the assembly of 1 across a wide range of pH values.

  7. Bubble rearrangement dynamics and light transport in aqueous foams

    NASA Astrophysics Data System (ADS)

    Gittings, Alex St Clair

    The general scope of this work investigates two essential, yet surprisingly elusive, properties of aqueous foams. The first concerns how multiply scattered light is transported throughout the foam. The second concerns the dynamics of bubble rearrangement events for coarsening foams. The absorption of diffuse photons in aqueous foams is measured by adding a dye to the continuous liquid phase. For very wet and for dry foams, the absorption of the diffuse photons equals the absorption length of the liquid divided by the liquid volume fraction, indicating photons propagate by a random walk, sampling each phase in proportion to its volume. Foams of intermediate wetness, by contrast, absorb photons more strongly than expected, indicating photons have a higher probability for being transported in the network. This suggests novel transport effects such as photons that enter a border in a state that only allows internal reflection for the border length. We further investigate light transport in foams by considering a two-dimensional model foam with scattering described by geometric optics and the Fresnel equations. Here we develop theoretical results for bulk transport quantities, such as the scattering length, in terms of the basic microscopic structural elements of the foam. Results are compared with a computer simulation. Essential to this work is determining key quantities, such as the scattering length, for each phase separately. The transport quantity for the foam is then constructed from the phase dependant parts using probability weights. The probability weights represent the probability that a diffuse photon scatters at network and disperse incidence, and are determined simply in terms of the index of refraction for the liquid and gas. Study of bubble rearrangement dynamics for coarsening foams proceeds in two steps. First, simultaneous measurement of second and three-time temporal intensity correlations are performed to test the validity of Diffusing

  8. Bioactive montanine derivatives from halide-induced rearrangements of haemanthamine-type alkaloids. Absolute configuration by VCD.

    PubMed

    Cedrón, Juan C; Estévez-Braun, Ana; Ravelo, Angel G; Gutiérrez, David; Flores, Ninoska; Bucio, María A; Pérez-Hernández, Nury; Joseph-Nathan, Pedro

    2009-04-01

    An unexpected rearrangement of haemanthamine-type alkaloids in the presence of halogenating agents has been found. Rearranged compounds present the 5,11-methanomorphantridine framework characteristic of montanine-type alkaloids. These compounds are difficult to obtain because of their scarcity in natural sources and because the synthetic approaches developed so far require numerous steps. Vibrational circular dichroism (VCD) spectroscopy was used to determine the absolute configuration of one of the rearranged compounds. Several rearranged alkaloids showed antimalarial activity.

  9. Transmission of maize chromosome 9 rearrangements in oat-maize radiation hybrids.

    PubMed

    Vales, M Isabel; Riera-Lizarazu, Oscar; Rines, Howard W; Phillips, Ronald L

    2004-12-01

    Oat-maize radiation hybrids are oat (Avena sativa L.) plants carrying radiation-induced subchromosome fragments of a given maize (Zea mays L.) chromosome. Since first-generation radiation hybrids contain various maize chromosome rearrangements in a hemizygous condition, variation might be expected in the transmission of these rearrangements to subsequent generations. The transmission and integrity of maize chromosome 9 rearrangements were evaluated in progenies of 30 oat-maize radiation hybrids by using a series of DNA-based markers and by genomic in situ hybridization. Maize chromosome 9 rearrangements were reisolated by self-fertilization in 24 of the 30 radiation hybrid lineages. Normal and deleted versions of maize chromosome 9 were transmitted at similar frequencies of 9.1% and 7.6%, respectively, while intergenomic translocations were transmitted at a significantly higher frequency of 47.6%. Most lines (93%) that inherited a rearrangement had it in the hemizygous condition. Lines with a rearrangement in the homozygous state (7%) were only identified in lineages with intergenomic translocations. Homozygous lines are more desirable from the perspective of stock maintenance, since they may stably transmit a given rearrangement to a subsequent generation. However, their isolation is not strictly required, since hemizygous lines can also be used for genome mapping studies.

  10. The potential of clofarabine in MLL-rearranged infant acute lymphoblastic leukaemia.

    PubMed

    Stumpel, Dominique J P M; Schneider, Pauline; Pieters, Rob; Stam, Ronald W

    2015-09-01

    MLL-rearranged acute lymphoblastic leukaemia (ALL) in infants is the most difficult-to-treat type of childhood ALL, displaying a chemotherapy-resistant phenotype, and unique histone modifications, gene expression signatures and DNA methylation patterns. MLL-rearranged infant ALL responds remarkably well to nucleoside analogue drugs in vitro, such as cytarabine and cladribine, and to the demethylating agents decitabine and zebularine as measured by cytotoxicity assays. These observations led to the inclusion of cytarabine into the treatment regimens currently used for infants with ALL. However, survival chances for infants with MLL-rearranged ALL do still not exceed 30-40%. Here we explored the in vitro potential of the novel nucleoside analogue clofarabine for MLL-rearranged infant ALL. Therefore we used both cell line models as well as primary patient cells. Compared with other nucleoside analogues, clofarabine effectively targeted primary MLL-rearranged infant ALL cells at the lowest concentrations, with median LC50 values of ∼25 nM. Interestingly, clofarabine displayed synergistic cytotoxic effects in combination with cytarabine. Furthermore, at concentrations of 5-10nM clofarabine induced demethylation of the promoter region of the tumour suppressor gene FHIT (Fragile Histidine Triad), a gene typically hypermethylated in MLL-rearranged ALL. Demethylation of the FHIT promoter region was accompanied by subtle re-expression of this gene both at the mRNA and protein level. We conclude that clofarabine is an interesting candidate for further studies in MLL-rearranged ALL in infants.

  11. BRCA1 and BRCA2 rearrangements in Brazilian individuals with Hereditary Breast and Ovarian Cancer Syndrome.

    PubMed

    Ewald, Ingrid Petroni; Cossio, Silvia Liliana; Palmero, Edenir Inez; Pinheiro, Manuela; Nascimento, Ivana Lucia de Oliveira; Machado, Taisa Manuela Bonfim; Sandes, Kiyoko Abe; Toralles, Betânia; Garicochea, Bernardo; Izetti, Patricia; Pereira, Maria Luiza Saraiva; Bock, Hugo; Vargas, Fernando Regla; Moreira, Miguel Ângelo Martins; Peixoto, Ana; Teixeira, Manuel R; Ashton-Prolla, Patricia

    2016-01-01

    Approximately 5-10% of breast cancers are caused by germline mutations in high penetrance predisposition genes. Among these, BRCA1 and BRCA2, which are associated with the Hereditary Breast and Ovarian Cancer (HBOC) syndrome, are the most frequently affected genes. Recent studies confirm that gene rearrangements, especially in BRCA1, are responsible for a significant proportion of mutations in certain populations. In this study we determined the prevalence of BRCA rearrangements in 145 unrelated Brazilian individuals at risk for HBOC syndrome who had not been previously tested for BRCA mutations. Using Multiplex Ligation-dependent Probe Amplification (MLPA) and a specific PCR-based protocol to identify a Portuguese founder BRCA2 mutation, we identified two (1,4%) individuals with germline BRCA1 rearrangements (c.547+240_5193+178del and c.4675+467_5075-990del) and three probands with the c.156_157insAlu founder BRCA2 rearrangement. Furthermore, two families with false positive MLPA results were shown to carry a deleterious point mutation at the probe binding site. This study comprises the largest Brazilian series of HBOC families tested for BRCA1 and BRCA2 rearrangements to date and includes patients from three regions of the country. The overall observed rearrangement frequency of 3.44% indicates that rearrangements are relatively uncommon in the admixed population of Brazil. PMID:27303907

  12. BRCA1 and BRCA2 rearrangements in Brazilian individuals with Hereditary Breast and Ovarian Cancer Syndrome

    PubMed Central

    Ewald, Ingrid Petroni; Cossio, Silvia Liliana; Palmero, Edenir Inez; Pinheiro, Manuela; Nascimento, Ivana Lucia de Oliveira; Machado, Taisa Manuela Bonfim; Sandes, Kiyoko Abe; Toralles, Betânia; Garicochea, Bernardo; Izetti, Patricia; Pereira, Maria Luiza Saraiva; Bock, Hugo; Vargas, Fernando Regla; Moreira, Miguel Ângelo Martins; Peixoto, Ana; Teixeira, Manuel R.; Ashton-Prolla, Patricia

    2016-01-01

    Abstract Approximately 5-10% of breast cancers are caused by germline mutations in high penetrance predisposition genes. Among these, BRCA1 and BRCA2, which are associated with the Hereditary Breast and Ovarian Cancer (HBOC) syndrome, are the most frequently affected genes. Recent studies confirm that gene rearrangements, especially in BRCA1, are responsible for a significant proportion of mutations in certain populations. In this study we determined the prevalence of BRCA rearrangements in 145 unrelated Brazilian individuals at risk for HBOC syndrome who had not been previously tested for BRCA mutations. Using Multiplex Ligation-dependent Probe Amplification (MLPA) and a specific PCR-based protocol to identify a Portuguese founder BRCA2 mutation, we identified two (1,4%) individuals with germline BRCA1 rearrangements (c.547+240_5193+178del and c.4675+467_5075-990del) and three probands with the c.156_157insAlu founder BRCA2 rearrangement. Furthermore, two families with false positive MLPA results were shown to carry a deleterious point mutation at the probe binding site. This study comprises the largest Brazilian series of HBOC families tested for BRCA1 and BRCA2 rearrangements to date and includes patients from three regions of the country. The overall observed rearrangement frequency of 3.44% indicates that rearrangements are relatively uncommon in the admixed population of Brazil. PMID:27303907

  13. PDGFRA gene rearrangements are frequent genetic events in PDGFRA-amplified glioblastomas.

    PubMed

    Ozawa, Tatsuya; Brennan, Cameron W; Wang, Lu; Squatrito, Massimo; Sasayama, Takashi; Nakada, Mitsutoshi; Huse, Jason T; Pedraza, Alicia; Utsuki, Satoshi; Yasui, Yoshie; Tandon, Adesh; Fomchenko, Elena I; Oka, Hidehiro; Levine, Ross L; Fujii, Kiyotaka; Ladanyi, Marc; Holland, Eric C

    2010-10-01

    Gene rearrangement in the form of an intragenic deletion is the primary mechanism of oncogenic mutation of the epidermal growth factor receptor (EGFR) gene in gliomas. However, the incidence of platelet-derived growth factor receptor-α (PDGFRA) gene rearrangement in these tumors is unknown. We investigated the PDGFRA locus in PDGFRA-amplified gliomas and identified two rearrangements, including the first case of a gene fusion between kinase insert domain receptor (KDR) (VEGFRII) and the PDGFRA gene, and six cases of PDGFRA(Δ8, 9), an intragenic deletion rearrangement. The PDGFRA(Δ8, 9) mutant was common, being present in 40% of the glioblastoma multiformes (GBMs) with PDGFRA amplification. Tumors with these two types of PDGFRA rearrangement displayed histologic features of oligodendroglioma, and the gene products of both rearrangements showed constitutively elevated tyrosine kinase activity and transforming potential that was reversed by PDGFR blockade. These results suggest the possibility that these PDGFRA mutants behave as oncogenes in this subset of gliomas, and that the prevalence of such rearrangements may have been considerably underestimated. PMID:20889717

  14. Oxidative dehydrogenation of ethane on dynamically rearranging supported chloride catalysts.

    PubMed

    Gärtner, Christian A; van Veen, André C; Lercher, Johannes A

    2014-09-10

    Ethane is oxidatively dehydrogenated with a selectivity up to 95% on catalysts comprising a mixed molten alkali chloride supported on a mildly redox-active Dy2O3-doped MgO. The reactive oxyanionic OCl(-) species acting as active sites are catalytically formed by oxidation of Cl(-) at the MgO surface. Under reaction conditions this site is regenerated by O2, dissolving first in the alkali chloride melt, and in the second step dissociating and replenishing the oxygen vacancies on MgO. The oxyanion reactively dehydrogenates ethane at the melt-gas phase interface with nearly ideal selectivity. Thus, the reaction is concluded to proceed via two coupled steps following a Mars-van-Krevelen-mechanism at the solid-liquid and gas-liquid interface. The dissociation of O2 and/or the oxidation of Cl(-) at the melt-solid interface is concluded to have the lowest forward rate constants. The compositions of the oxide core and the molten chloride shell control the catalytic activity via the redox potential of the metal oxide and of the OCl(-). Traces of water may be present in the molten chloride under reaction conditions, but the specific impact of this water is not obvious at present. The spatial separation of oxygen and ethane activation sites and the dynamic rearrangement of the surface anions and cations, preventing the exposure of coordinatively unsaturated cations, are concluded to be the origin of the surprisingly high olefin selectivity. PMID:25118821

  15. Order and disorder control the functional rearrangement of influenza hemagglutinin

    PubMed Central

    Lin, Xingcheng; Eddy, Nathanial R.; Noel, Jeffrey K.; Whitford, Paul C.; Wang, Qinghua; Ma, Jianpeng; Onuchic, José N.

    2014-01-01

    Influenza hemagglutinin (HA), a homotrimeric glycoprotein crucial for membrane fusion, undergoes a large-scale structural rearrangement during viral invasion. X-ray crystallography has shown that the pre- and postfusion configurations of HA2, the membrane-fusion subunit of HA, have disparate secondary, tertiary, and quaternary structures, where some regions are displaced by more than 100 Å. To explore structural dynamics during the conformational transition, we studied simulations of a minimally frustrated model based on energy landscape theory. The model combines structural information from both the pre- and postfusion crystallographic configurations of HA2. Rather than a downhill drive toward formation of the central coiled-coil, we discovered an order-disorder transition early in the conformational change as the mechanism for the release of the fusion peptides from their burial sites in the prefusion crystal structure. This disorder quickly leads to a metastable intermediate with a broken threefold symmetry. Finally, kinetic competition between the formation of the extended coiled-coil and C-terminal melting results in two routes from this intermediate to the postfusion structure. Our study reiterates the roles that cracking and disorder can play in functional molecular motions, in contrast to the downhill mechanical interpretations of the “spring-loaded” model proposed for the HA2 conformational transition. PMID:25082896

  16. Complex chromosomal rearrangements induced in vivo by heavy ions.

    PubMed

    Durante, M; Ando, K; Furusawa, Y; Obe, G; George, K; Cucinotta, F A

    2004-01-01

    It has been suggested that the ratio complex/simple exchanges can be used as a biomarker of exposure to high-LET radiation. We tested this hypothesis in vivo, by considering data from several studies that measured complex exchanges in peripheral blood from humans exposed to mixed fields of low- and high-LET radiation. In particular, we studied data from astronauts involved in long-term missions in low-Earth-orbit, and uterus cancer patients treated with accelerated carbon ions. Data from two studies of chromosomal aberrations in astronauts used blood samples obtained before and after space flight, and a third study used blood samples from patients before and after radiotherapy course. Similar methods were used in each study, where lymphocytes were stimulated to grow in vitro, and collected after incubation in either colcemid or calyculin A. Slides were painted with whole-chromosome DNA fluorescent probes (FISH), and complex and simple chromosome exchanges in the painted genome were classified separately. Complex-type exchanges were observed at low frequencies in control subjects, and in our test subjects before the treatment. No statistically significant increase in the yield of complex-type exchanges was induced by the space flight. Radiation therapy induced a high fraction of complex exchanges, but no significant differences could be detected between patients treated with accelerated carbon ions or X-rays. Complex chromosomal rearrangements do not represent a practical biomarker of radiation quality in our test subjects. PMID:15162046

  17. Complex Chromosomal Rearrangements Induced in Vivo by Heavy Ions

    NASA Technical Reports Server (NTRS)

    Durante, M.; Ando, K.; Furusawa, G.; Obe, G.; George, K.; Cucinotta, F. A.

    2004-01-01

    It has been suggested that the ratio complex/simple exchanges can be used as a biomarker of exposure to high-LET radiation. We tested this hypothesis in vivo, by considering data from several studies that measured complex exchanges in peripheral blood from humans exposed to mixed fields of low- and high-LET radiation. In particular, we studied data from astronauts involved in long-term missions in low-Earth-orbit, and uterus cancer patients treated with accelerated carbon ions. Data from two studies of chromosomal aberrations in astronauts used blood samples obtained before and after space flight, and a third study used blood samples from patients before and after radiotherapy course. Similar methods were used in each study, where lymphocytes were stimulated to grow in vitro, and collected after incubation in either colcemid or calyculin A. Slides were painted with whole-chromosome DNA fluorescent probes (FISH), and complex and simple chromosome exchanges in the painted genome were classified separately. Complex-type exchanges were observed at low frequencies in control subjects, and in our test subjects before the treatment. No statistically significant increase in the yield of complex-type exchanges was induced by the space flight. Radiation therapy induced a high fraction of complex exchanges, but no significant differences could be detected between patients treated with accelerated carbon ions or X-rays. Complex chromosomal rearrangements do not represent a practical biomarker of radiation quality in our test subjects. Copyright 2003 S. Karger AG, Basel.

  18. Model of the cooperative rearranging region for polyhydric alcohols

    NASA Astrophysics Data System (ADS)

    Nakanishi, Masahiro; Nozaki, Ryusuke

    2011-07-01

    A simplified model of a hydrogen-bonding network is proposed in order to clarify the microscopic structure of the cooperative rearranging region (CRR) in Adam-Gibbs theory [G. Adam and J. H. Gibbs, J. Chem. Phys.JCPSA60021-960610.1063/1.1696442 43, 139 (1965)]. Our model can be solved analytically, and it successfully explains the reported systematic features of the glass transition of polyhydric alcohols. In this model, hydrogen bonding is formulated based on binding free energy. Assuming a cluster of molecules connected by double hydrogen bonds is a CRR and approximating the hydrogen-bonding network as a Bethe lattice in percolation theory, the temperature dependence of the structural relaxation time can be obtained analytically. Reported data on relaxation times are well described by the obtained equation. By taking the lower limit of the binding free energy with this equation, the Vogel-Fulcher-Tammann equation can be derived. Consequently, the fragility index and glass transition temperature can be expressed as functions of the number of OH groups in a molecule, and this relation agrees well with the reported experimental data.

  19. Ferrier rearrangement promoted by an electrochemically generated zirconium catalyst.

    PubMed

    Stevanović, Dragana; Pejović, Anka; Damljanović, Ivan; Minić, Aleksandra; Bogdanović, Goran A; Vukićević, Mirjana; Radulović, Niko S; Vukićević, Rastko D

    2015-04-30

    In situ generated zirconium catalyst from a sacrificial zirconium anode was successfully applied to promote Ferrier rearrangement of 3,4,5-tri-O-acetyl-D-glucal and 6-deoxy-3,4-di-O-acetyl-L-glucal (3,4-di-O-acetyl-L-rhamnal) in the presence of three thiols and eleven thiophenols as nucleophiles. A simple constant current electrolysis (20 mA, 0.4 F mol(-1)) of an acetonitrile solution of lithium perchlorate (0.1 M) containing the corresponding glycal and S-nucleophiles, using a zirconium anode and a platinum cathode resulted in the successful synthesis of the corresponding 2,3-unsaturated peracetylated thioglycosides (with an average anomer ratio α/β=4.129 in the case of peracetylated D-glucal and 8.740 in the case of L-rhamnal). The same procedure proved to be appropriate in synthesizing dihydropyran derivatives ('C-glycosides') using allyltrimethylsilane as the nucleophile (only 'α-anomers' were obtained). All new compounds were fully characterized by spectral data, whereas single-crystal X-ray analysis was performed for two thioglycosides.

  20. Characterization of the NTRK1 genomic region involved in chromosomal rearrangements generating TRK oncogenes

    SciTech Connect

    Greco, A.; Mariani, C.; Miranda, C.; Pagliardini, S.; Pierotti, M.A. )

    1993-11-01

    TRK oncogenes are created by chromosomal rearrangements linking the tyrosine-kinase domain of the NTRK1 gene (encoding one of the receptors for the nerve growth factor) to foreign activating sequences. TRK oncogenes are frequently detected in human papillary thyroid carcinoma, as a result of rearrangements involving at least three different activating genes. The authors have found that the rearrangements creating all the TRK oncogenes so far characterized fall within a 2.9-kb XbaI/SmaI restriction fragment of the NTRK1 gene. Here they report the nucleotide sequence and the exon organization of this fragment. 13 refs., 2 figs.

  1. Coupled-rearrangement-channels calculation of the three-body system under the absorbing boundary condition

    NASA Astrophysics Data System (ADS)

    Iwasaki, M.; Otani, R.; Ito, M.; Kamimura, M.

    2016-05-01

    We formulate the method of the absorbing boundary condition (ABC) in the coupled-rearrangement-channels variational method (CRCMV) for the three-body problem. In the present study, we handle the simple three-boson system, and the absorbing potential is introduced in the Jacobi coordinate in the individual rearrangement channels. The resonance parameters and the strength of the monopole breakup are compared with the complex scaling method (CSM). We have found that the CRCVM + ABC method nicely works in the threebody problem with the rearrangement channels.

  2. Premature termination of variable gene rearrangement in B lymphocytes from X-linked agammaglobulinemia.

    PubMed Central

    Schwaber, J; Chen, R H

    1988-01-01

    X-linked agammaglobulinemia (XLA) results from failure of B lymphocyte development. Immature B cells from a patient with XLA were found to produce truncated mu and delta immunoglobulin H chains encoded by D-JH-C (mu delta). The 5' terminal sequence of cDNA encoding the H chains is composed of D-JH with the characteristic GGTTTGAAG/CACTGTG consensus sequence utilized for VH gene rearrangement upstream, and a leader sequence that serves for translation of this intermediate stage of rearrangement. Failure of variable region gene rearrangement may underlie the failure of B lymphoid development in XLA. Images PMID:2838527

  3. Studies on immunoglobulin gene rearrangement in formalin-fixed, paraffin-embedded pathology specimens.

    PubMed

    Dubeau, L; Weinberg, K; Jones, P A; Nichols, P W

    1988-03-01

    Studies on immunoglobulin gene rearrangement in lymphoid lesions are an increasingly important application of molecular biology in diagnostic medicine. The authors have therefore examined the possibility of detecting such rearrangements in formalin-fixed, paraffin-embedded pathology specimens. Southern blots of DNA obtained from optimally fixed tissues were very similar to blots of unfixed material, except that the electrophoretic mobility of the fixed DNA fragments was sometimes slightly reduced. High-molecular-weight DNA was not recovered from suboptimally fixed partially autolysed samples. Increasing the time of exposure to formalin resulted in loss of hybridizable DNA. Monoclonal rearrangements of heavy and light chain immunoglobulin genes could be detected in formalin-fixed specimens provided that these fixation artifacts were taken into consideration. This technique expands the pool of material available for studies on gene rearrangement and should facilitate the use of such studies in clinical medicine.

  4. An efficient algorithm for the contig ordering problem under algebraic rearrangement distance.

    PubMed

    Lu, Chin Lung

    2015-11-01

    Assembling a genome from short reads currently obtained by next-generation sequencing techniques often results in a collection of contigs, whose relative position and orientation along the genome being sequenced are unknown. Given two sets of contigs, the contig ordering problem is to order and orient the contigs in each set such that the genome rearrangement distance between the resulting sets of ordered and oriented contigs is minimized. In this article, we utilize the permutation groups in algebra to propose a near-linear time algorithm for solving the contig ordering problem under algebraic rearrangement distance, where the algebraic rearrangement distance between two sets of ordered and oriented contigs is the minimum weight of applicable rearrangement operations required to transform one set into the other. PMID:26247343

  5. Complex structural rearrangement features suggesting chromoanagenesis mechanism in a case of 1p36 deletion syndrome.

    PubMed

    Zanardo, Évelin Aline; Piazzon, Flavia Balbo; Dutra, Roberta Lelis; Dias, Alexandre Torchio; Montenegro, Marília Moreira; Novo-Filho, Gil Monteiro; Costa, Thaís Virgínia Moura Machado; Nascimento, Amom Mendes; Kim, Chong Ae; Kulikowski, Leslie Domenici

    2014-12-01

    Genome rearrangements are caused by the erroneous repair of DNA double-strand breaks, leading to several alterations that result in loss or gain of the structural genomic of a dosage-sensitive genes. However, the mechanisms that promote the complexity of rearrangements of congenital or developmental defects in human disease are unclear. The investigation of complex genomic abnormalities could help to elucidate the mechanisms and causes for the formation and facilitate the understanding of congenital or developmental defects in human disease. We here report one case of a patient with atypical clinical features of the 1p36 syndrome and the use of cytogenomic techniques to characterize the genomic alterations. Analysis by multiplex ligation-dependent probe amplification and array revealed a complex rearrangement in the 1p36.3 region with deletions and duplication interspaced by normal sequences. We also suggest that chromoanagenesis could be a possible mechanism involved in the repair and stabilization of this rearrangement.

  6. Somatic Rearrangement in B cells: It’s (mostly) Nuclear Physics

    PubMed Central

    Aiden, Erez Lieberman; Casellas, Rafael

    2015-01-01

    We discuss how principles of nuclear architecture drive typical gene rearrangements in B lymphocytes, whereas translocation hotspots and recurrent lesions reflect the extent of AID-mediated DNA damage and selection. PMID:26276627

  7. Mycoreovirus genome alterations: similarities to and differences from rearrangements reported for other reoviruses.

    PubMed

    Tanaka, Toru; Eusebio-Cope, Ana; Sun, Liying; Suzuki, Nobuhiro

    2012-01-01

    The family Reoviridae is one of the largest virus families with genomes composed of 9-12 double-stranded RNA segments. It includes members infecting organisms from protists to humans. It is well known that reovirus genomes are prone to various types of genome alterations including intragenic rearrangement and reassortment under laboratory and natural conditions. Recently distinct genetic alterations were reported for members of the genus Mycoreovirus, Mycoreovirus 1 (MyRV1), and MyRV3 with 11 (S1-S11) and 12 genome segments (S1-S12), respectively. While MyRV3 S8 is lost during subculturing of infected host fungal strains, MyRV1 rearrangements undergo alterations spontaneously and inducibly. The inducible MyRV1 rearrangements are different from any other previous examples of reovirus rearrangements in their dependence on an unrelated virus factor, a multifunctional protein, p29, encoded by a distinct virus Cryphonectria parasitica hypovirus 1 (CHV1). A total of 5 MyRV1 variants with genome rearranged segments (S1-S3, S6 and S10) are generated in the background of a single viral strain in the presence of CHV1 p29 supplied either transgenically or by coinfection. MyRV1 S4 and S10 are rearranged, albeit very infrequently, in a CHV1 p29 independent fashion. A variant of MyRV1 with substantial deletions in both S4 and S10, generated through a combined reassortment and rearrangement approach, shows comparable replication levels to the wild-type MyRV1. In vivo and in vitro interactions of CHV1 p29 and MyRV1 VP9 are implicated in the induction of MyRV1 rearrangements. However, the mechanism underlying p29-mediated rearrangements remains largely unknown. MyRV1 S4 rearrangements spontaneously occurred independently of CHV1 p29. In the absence of reverse genetics systems for mycoreoviruses, molecular and biological characterization of these MyRV1 and MyRV3 variants contribute to functional analyses of the protein products encoded by those rearranged segments.

  8. ETV6 rearrangements are recurrent in myeloid malignancies and are frequently associated with other genetic events.

    PubMed

    Haferlach, Claudia; Bacher, Ulrike; Schnittger, Susanne; Alpermann, Tamara; Zenger, Melanie; Kern, Wolfgang; Haferlach, Torsten

    2012-04-01

    ETV6 (TEL) rearrangements are favorable in pediatric acute lymphoblastic leukemia but are less well characterized in myeloid malignancies. We investigated 9,550 patients with myeloid disorders for ETV6 rearrangements by chromosome banding analysis and interphase fluorescence in situ hybridization. ETV6 rearrangements were identified in 51 of 9,550 (0.5%) patients (range, 19.2-85.3 years). Frequencies were in detail: acute myeloid leukemia (AML): 40 of 3,798, 1.1%; myelodysplastic syndromes (MDS): 6 of 3,375, 0.2%; myeloproliferative neoplasms (MPNs): 5 of 1,720, 0.3%; MDS/MPN: 0 of 210; and chronic myelomonocytic leukemia: 0 of 447. Thirty-three different partner bands of ETV6 were identified, and most were recurrent: 3q26 (n = 10), 5q33 (n = 4), 17q11 (n = 3), 22q12 (n = 3), 5q31 (n = 2), and 2q31 (n = 2). Additional chromosomal abnormalities were identified in 29 of 51 (57%) ETV6 rearranged cases. In AML, ETV6 rearrangements were frequently associated with NPM1 (9/39, 23%) and RUNX1 mutations (6/31, 19%). The FAB M0 subtype was more frequent in ETV6 rearranged de novo AML than other AML (P < 0.001); expression of CD7 and CD34 by immunophenotyping was higher in ETV6 rearranged AML compared with other subgroups. Survival of 29 ETV6 rearranged de novo AML was compared with 818 AML from other cytogenetic subgroups. Median overall and event-free survival of ETV6 rearranged cases was similar to the intermediate-risk cohort (26.3 vs. 62.2 months and 14.0 vs. 15.4 months) defined according to Medical Research Council criteria. Our study confirms the variety of ETV6 rearrangements in AML, MDS, and MPNs often in association with other genetic events. Prognosis of ETV6 rearranged de novo AML seems to be intermediate, which should be independently confirmed. PMID:22162288

  9. Synthesis of novel boron chelate complexes and proposed mechanism of new rearrangement.

    PubMed

    Zhang, Rui-Zhe; Feng, Xiao; Liu, Ying; Wang, Sheng-Qing; Liu, Jin-Ting; Zhao, Bao-Xiang

    2015-03-15

    We synthesized novel boron chelate complexes by the reaction of pyrazoline derivatives and boron trifluoride diethyl etherate followed by a new rearrangement. The structures of the compounds were characterized by IR, NMR and HRMS, especially, a typical compound 3c was confirmed by X-ray single crystal analysis. We proposed a mechanism of the rearrangement. Moreover, the absorption and fluorescence spectroscopy of these compounds were measured.

  10. ROS1 rearranged non-small cell lung cancer brain metastases respond to low dose radiotherapy.

    PubMed

    Lukas, Rimas V; Hasan, Yasmin; Nicholas, Martin K; Salgia, Ravi

    2015-12-01

    We present a young woman with ROS1 gene rearranged non-small cell lung cancer (NSCLC) with brain metastases. ROS is a proto-oncogene tyrosine protein kinase. The patient received a partial course of whole brain radiation therapy and experienced a sustained partial response in the brain. We hypothesize that ROS1 rearranged NSCLC brain metastases may be particularly sensitive to radiation therapy.

  11. Thermal rearrangements in 1,2-poly/1,4-hexadiene/s

    NASA Technical Reports Server (NTRS)

    Golub, M. A.

    1978-01-01

    The work described was carried out to study the thermal rearrangements of two unsaturated diene polymers - 1,2-poly(cis-1,4-hexadiene) (CHD) and 1,2-poly(trans-1.4-hexadiene) (THD). It is shown that both CHD and THD have a predominatly 1,8 diene structure and seem to cyclize mainly by the (2 + 2) thermal cycloaddition of double bonds, and to a small extent also by sigmatropic rearrangement with hydrogen shift.

  12. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    SciTech Connect

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-09-18

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

  13. Chromosomal rearrangements directly cause underdominant F1 pollen sterility in Mimulus lewisii-Mimulus cardinalis hybrids.

    PubMed

    Stathos, Angela; Fishman, Lila

    2014-11-01

    Chromosomal rearrangements can contribute to the evolution of postzygotic reproductive isolation directly, by disrupting meiosis in F1 hybrids, or indirectly, by suppressing recombination among genic incompatibilities. Because direct effects of rearrangements on fertility imply fitness costs during their spread, understanding the mechanism of F1 hybrid sterility is integral to reconstructing the role(s) of rearrangements in speciation. In hybrids between monkeyflowers Mimulus cardinalis and Mimulus lewisii, rearrangements contain all quantitative trait loci (QTLs) for both premating barriers and pollen sterility, suggesting that they may have facilitated speciation in this model system. We used artificial chromosome doubling and comparative mapping to test whether heterozygous rearrangements directly cause underdominant male sterility in M. lewisii-M. cardinalis hybrids. Consistent with a direct chromosomal basis for hybrid sterility, synthetic tetraploid F1 s showed highly restored fertility (83.4% pollen fertility) relative to diploids F1 s (36.0%). Additional mapping with Mimulus parishii-M. cardinalis and M. parishii-M. lewisii hybrids demonstrated that underdominant male sterility is caused by one M. lewisii specific and one M. cardinalis specific reciprocal translocation, but that inversions had no direct effects on fertility. We discuss the importance of translocations as causes of reproductive isolation, and consider models for how underdominant rearrangements spread and fix despite intrinsic fitness costs.

  14. Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis

    PubMed Central

    Daveau, Romain; Combaret, Valérie; Pierre-Eugène, Cécile; Cazes, Alex; Louis-Brennetot, Caroline; Schleiermacher, Gudrun; Ferrand, Sandrine; Pierron, Gaëlle; Lermine, Alban; Frio, Thomas Rio; Raynal, Virginie; Vassal, Gilles; Barillot, Emmanuel; Delattre, Olivier; Janoueix-Lerosey, Isabelle

    2013-01-01

    Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis. PMID:23991058

  15. Rearrangement dynamics in colloidal particle packings identified through local structure and machine-learning

    NASA Astrophysics Data System (ADS)

    Davidson, Zoey S.; Still, Tim; Gratale, Matthew D.; Ma, Xiaoguang; Schoenholz, Samuel S.; Sussman, Daniel M.; Liu, A. J.; Yodh, A. G.

    We explore the connection between measures of local structure and particle rearrangements in soft thermal quasi-two-dimensional colloidal systems employing a machine learning approach. Local structure is characterized by two and three point structure functions that measure radial and angular distributions of particles, and rearrangements are identified by a measure of change in average colloidal particle position. By generating labeled training data, we can extract the features of these functions that contribute to the likelihood of a rearrangement. In particular, we use a machine-learning algorithm to construct a decision function in the form of a scalar field we call softness that with high accuracy labels regions of particles more likely to rearrange. Thus, we can predict dynamic rearrangements from the instantaneous local structure. The softness field remains a good predictor when we vary the packing fraction between training and test data sets. In glassy samples, the softness field can identify aging as particles become less likely to undergo cage rearrangements. We gratefully acknowledge financial support through NSF DMR12-05463, MRSEC DMR11-20901, NASA NNX08AO0G, and DE-FG02-05ER46199.

  16. Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.

    PubMed

    Boeva, Valentina; Jouannet, Stéphanie; Daveau, Romain; Combaret, Valérie; Pierre-Eugène, Cécile; Cazes, Alex; Louis-Brennetot, Caroline; Schleiermacher, Gudrun; Ferrand, Sandrine; Pierron, Gaëlle; Lermine, Alban; Rio Frio, Thomas; Raynal, Virginie; Vassal, Gilles; Barillot, Emmanuel; Delattre, Olivier; Janoueix-Lerosey, Isabelle

    2013-01-01

    Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis.

  17. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

    PubMed Central

    Ryan, Russell J.H.; Drier, Yotam; Whitton, Holly; Cotton, M. Joel; Kaur, Jasleen; Issner, Robbyn; Gillespie, Shawn; Epstein, Charles B.; Nardi, Valentina; Sohani, Aliyah R.; Hochberg, Ephraim P.; Bernstein, Bradley E.

    2015-01-01

    B-cell lymphomas frequently contain genomic rearrangements that lead to oncogene activation by heterologous distal regulatory elements. We utilized a novel approach, termed ‘Pinpointing Enhancer-Associated Rearrangements by Chromatin Immunoprecipitation’ or PEAR-ChIP, to simultaneously map enhancer activity and proximal rearrangements in lymphoma cell lines and patient biopsies. This method detects rearrangements involving known cancer genes, including CCND1, BCL2, MYC, PDCD1LG2, NOTCH1, CIITA, and SGK1, as well as novel enhancer duplication events of likely oncogenic significance. We identify lymphoma subtype-specific enhancers in the MYC locus that are silenced in lymphomas with MYC-activating rearrangements and are associated with germline polymorphisms that alter lymphoma risk. We show that BCL6-locus enhancers are acetylated by the BCL6-activating transcription factor MEF2B, and can undergo genomic duplication, or target the MYC promoter for activation in the context of a “pseudo-double-hit” t(3;8)(q27;q24) rearrangement linking the BCL6 and MYC loci. Our work provides novel insights regarding enhancer-driven oncogene activation in lymphoma. PMID:26229090

  18. Myosin II regulates actin rearrangement-related structural synaptic plasticity during conditioned taste aversion memory extinction.

    PubMed

    Bi, Ai-Ling; Wang, Yue; Zhang, Shuang; Li, Bo-Qin; Sun, Zong-Peng; Bi, Hong-Sheng; Chen, Zhe-Yu

    2015-03-01

    Similar to memory formation, memory extinction is also a new learning process that requires synaptic plasticity. Actin rearrangement is fundamental for synaptic plasticity, however, whether actin rearrangement in the infralimbic cortex (IL) plays a role in memory extinction, as well as the mechanisms underlying it, remains unclear. Here, using a conditioned taste aversion (CTA) paradigm, we demonstrated increased synaptic density and actin rearrangement in the IL during the extinction of CTA. Targeted infusion of an actin rearrangement inhibitor, cytochalasin D, into the IL impaired memory extinction and de novo synapse formation. Notably, we also found increased myosin II phosphorylation in the IL during the extinction of CTA. Microinfusion of a specific inhibitor of the myosin II ATPase, blebbistatin (Blebb), into the IL impaired memory extinction as well as the related actin rearrangement and changes in synaptic density. Moreover, the extinction deficit and the reduction of synaptic density induced by Blebb could be rescued by the actin polymerization stabilizer jasplakinolide (Jasp), suggesting that myosin II acts via actin filament polymerization to stabilize synaptic plasticity during the extinction of CTA. Taken together, we conclude that myosin II may regulate the plasticity of actin-related synaptic structure during memory extinction. Our studies provide a molecular mechanism for understanding the plasticity of actin rearrangement-associated synaptic structure during memory extinction.

  19. Somatosensory evoked potentials during natural and learning rearrangements of posture accompanied by limb elevation in dogs.

    PubMed

    Gavrilenko, T; Frolov, A G; Ioffe, M E; Ganchev, G N; Aleksandrov, A V; Pavlova, O G

    2002-01-01

    Changes in the functional state of the sensorimotor cortex associated with reorganization of the natural pattern of postural rearrangement before limb elevation (the "diagonal" patten and of an artificial rearrangement (the "unilateral" pattern) were studied in dogs. The state of cortical structures on postural rearrangement was assessed in terms of the pattern of somatosensory evoked potentials produced in response to stimulation of the forelimb during postural preparation of the animal for elevating the hindlimb (acquired avoidance response to a sound signal). Evoked potentials during the natural postural preparation (the "diagonal" pattern) were compared with those during the altered pattern of postural preparation (the "unilateral" pattern), this preparation taking place prior to elevation of the limb. Controls consisted of evoked potentials in the resting state. Decreases were seen in the latencies and amplitudes of most components of evoked potentials during postural rearrangement. In general, changes in evoked potentials were less marked in the "unilateral" pattern than in the "diagonal" pattern, though the differences were significant only for the amplitude of the first negative component. Changes in evoked potentials were similar regardless of whether the supporting forces of the limb to which the test stimulus was applied increased or decreased during postural rearrangement. It is suggested that differences in evoked potentials may reflect changes in the interaction between neuronal populations within the sensorimotor cortex during reorganization of the pattern of postural rearrangement associated with learning.

  20. Prevalence of chromosomal rearrangements involving non-ETS genes in prostate cancer.

    PubMed

    Kluth, Martina; Galal, Rami; Krohn, Antje; Weischenfeldt, Joachim; Tsourlakis, Christina; Paustian, Lisa; Ahrary, Ramin; Ahmed, Malik; Scherzai, Sekander; Meyer, Anne; Sirma, Hüseyin; Korbel, Jan; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Minner, Sarah

    2015-04-01

    Prostate cancer is characterized by structural rearrangements, most frequently including translocations between androgen-dependent genes and members of the ETS family of transcription factor like TMPRSS2:ERG. In a recent whole genome sequencing study we identified 140 gene fusions that were unrelated to ETS genes in 11 prostate cancers. The aim of the present study was to estimate the prevalence of non-ETS gene fusions. We randomly selected 27 of these rearrangements and analyzed them by fluorescence in situ hybridization (FISH) in a tissue microarray format containing 500 prostate cancers. Using break-apart FISH probes for one fusion partner each, we found rearrangements of 13 (48%) of the 27 analyzed genes in 300-400 analyzable cancers per gene. Recurrent breakage, often accompanied by partial deletion of the genes, was found for NCKAP5, SH3BGR and TTC3 in 3 (0.8%) tumors each, as well as for ARNTL2 and ENOX1 in 2 (0.5%) cancers each. One rearranged tumor sample was observed for each of VCL, ZNF578, IMMP2L, SLC16A12, PANK1, GPHN, LRP1 and ZHX2. Balanced rearrangements, indicating possible gene fusion, were found for ZNF578, SH3BGR, LPR12 and ZHX2 in individual cancers only. The results of the present study confirm that rearrangements involving non-ETS genes occur in prostate cancer, but demonstrate that they are highly individual and typically non-recurrent.

  1. Antibody repertoire development in fetal and neonatal piglets. XXII. Lambda rearrangement precedes kappa rearrangement during B-cell lymphogenesis in swine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PCR was used to detect VDJ and VJ rearrangement, expression of RAG-1, TdT and VpreB and the presence of signal joint circles (SJC) in an effort to identify sites of B cell lymphogenesis in tissue lysates and sorted leukocytes of fetal and newborn piglets. VDJ, VlambdaJlambda but not VkappaJkappa re...

  2. LEWIS ACID CATALYZED FORMATION OF TETRAHYDROPYRANS IN IONIC LIQUID

    EPA Science Inventory

    Tetrahydropyrans are integral moieties in innumerable natural products and have inspired the development of a variety of different methodologies. A Prins-type cyclization involving the coupling of a homoallylic alcohol and an aldehyde in the presence of catalytic scandium triflat...

  3. Acid-Catalyzed Enolization of [beta]-Tetralone

    ERIC Educational Resources Information Center

    Dewprashad, Brahmadeo; Nesturi, Anthony; Urena, Joel

    2008-01-01

    This experiment allows students to use [to the first power]H NMR to directly compare the relative initial rates of substitution of the benzylic and non-benzylic [alpha] hydrogens of [beta]-tetralone and correlate their findings with the predictions made by resonance theory. The experiment demonstrates that the benzylic hydrogens undergo [alpha]…

  4. Borinic Acid Catalyzed Stereo- and Regioselective Couplings of Glycosyl Methanesulfonates.

    PubMed

    D'Angelo, Kyan A; Taylor, Mark S

    2016-08-31

    In the presence of a diarylborinic acid catalyst, glycosyl methanesulfonates engage in regio- and stereoselective couplings with partially protected pyranoside and furanoside acceptors. The methanesulfonate donors are prepared in situ from glycosyl hemiacetals, and are coupled under mild, operationally simple conditions (amine base, organoboron catalyst, room temperature). The borinic acid catalyst not only influences site-selectivity via activation of 1,2- or 1,3-diol motifs, but also has a pronounced effect on the stereochemical outcome: 1,2-trans-linked disaccharides are obtained selectively in the absence of neighboring group participation. Reaction progress kinetic analysis was used to obtain insight into the mechanism of glycosylation, both in the presence of catalyst and in its absence, while rates of interconversion of methanesulfonate anomers were determined by NMR exchange spectroscopy (EXSY). Together, the results suggest that although the uncatalyzed and catalyzed reactions give rise to opposite stereochemical outcomes, both proceed by associative mechanisms. PMID:27533523

  5. Decomposition of peracetic acid catalyzed by vanadium complexes

    SciTech Connect

    Makarov, A.P.; Gekhman, A.E.; Moiseev, I.I.; Polotryuk, O.Y.

    1986-02-01

    This paper studies the decomposition of peracetic acid (AcOOH) in acetic acid (AcOH) catalyzed by vanadium complexes. It is shown that peractic acid in acetic acid solutions of ammonium anadate decomposes with the predominant formation of 0/sub 2/ and small amounts of CO/sub 2/, the yield of which increases with increasing temperature and peracetic acid concentration. Both reactions proceed without the formation of free radicals in amounts detectable by ESR spectroscopy. The rate of oxygen release under conditions in which the formation of CO/sub 2/ is insignificant obeys a kinetic equation indicating the intermediate formation of a complex between V/sup 5 +/ ions and peracetic acid and the slow conversion of this complex into the observed products.

  6. A Complex 6p25 Rearrangement in a Child With Multiple Epiphyseal Dysplasia

    PubMed Central

    Bedoyan, Jirair K.; Lesperance, Marci M.; Ackley, Todd; Iyer, Ramaswamy K.; Innis, Jeffrey W.; Misra, Vinod K.

    2015-01-01

    Genomic rearrangements are increasingly recognized as important contributors to human disease. Here we report on an 11½-year-old child with myopia, Duane retraction syndrome, bilateral mixed hearing loss, skeletal anomalies including multiple epiphyseal dysplasia, and global developmental delay, and a complex 6p25 genomic rearrangement. We have employed oligonucleotide-based comparative genomic hybridization arrays (aCGH) of different resolutions (44 and 244K) as well as a 1 M single nucleotide polymorphism (SNP) array to analyze this complex rearrangement. Our analyses reveal a complex rearrangement involving a ~2.21 Mb interstitial deletion, a ~240 kb terminal deletion, and a 70–80 kb region in between these two deletions that shows maintenance of genomic copy number. The interstitial deletion contains eight known genes, including three Forkhead box containing (FOX) transcription factors (FOXQ1, FOXF2, and FOXC1). The region maintaining genomic copy number partly overlaps the dual specificity protein phosphatase 22 (DUSP22) gene. Array analyses suggest a homozygous loss of genomic material at the 5′ end of DUSP22, which was corroborated using TaqMan® copy number analysis. It is possible that this homozygous genomic loss may render both copies of DUSP22 or its products non-functional. Our analysis suggests a rearrangement mechanism distinct from a previously reported replication-based error-prone mechanism without template switching for a specific 6p25 rearrangement with a 1.22 Mb interstitial deletion. Our study demonstrates the utility and limitations of using oligonucleotide-based aCGH and SNP array technologies of increasing resolutions in order to identify complex DNA rearrangements and gene disruptions. PMID:21204225

  7. Frequent PLAG1 gene rearrangements in skin and soft tissue myoepithelioma with ductal differentiation.

    PubMed

    Antonescu, Cristina R; Zhang, Lei; Shao, Sung Yun; Mosquera, Juan-Miguel; Weinreb, Ilan; Katabi, Nora; Fletcher, Christopher D M

    2013-07-01

    A subset of cutaneous and superficial soft tissue myoepithelial (ME) tumors displays a distinct ductal component and closely resembles mixed tumors/pleomorphic adenomas of salivary gland. As PLAG1 and HMGA2 rearrangements are the most common genetic events in pleomorphic adenomas, we sought to investigate if these abnormalities are also present in the skin/soft tissue ME lesions. In contrast, half of the deep-seated soft tissue ME tumors lacking ductal differentiation are known to be genetically unrelated, showing EWSR1 rearrangements. FISH analysis to detect PLAG1 and HMGA2 abnormalities was performed in 35 ME tumors, nine skin and 26 soft tissue, lacking EWSR1 and FUS rearrangements. For the PLAG1-rearranged tumors, FISH and RACE were performed to identify potential fusion partners, including CTNNB1 (beta-catenin) on 3p21 and LIFR (leukemia inhibitory factor receptor) on 5p13. Recurrent PLAG1 rearrangement by FISH was detected in 13 (37%) lesions, including three (33%) in the skin and 10 (38%) in the soft tissue. All were classified as benign and all except one showed abundant tubulo-ductal differentiation (comprising 12/24 [50%] of all tumors with ductal structures). A LIFR-PLAG1 fusion was detected by RACE and then confirmed by FISH in one soft tissue ME tumor with tubular formation. No CTNNB1 or LIFR abnormalities were detected in any of the remaining PLAG1-rearranged tumors. No structural HMGA2 abnormalities were detected in any of the 22 ME lesions tested. A subset of cutaneous and soft tissue ME tumors appears genetically linked to their salivary gland counterparts, displaying frequent PLAG1 gene rearrangements and occasionally LIFR-PLAG1 fusion.

  8. Ligand-Controlled Regiodivergence in the Copper-Catalyzed [2,3]- and [1,2]-Rearrangements of Iodonium Ylides.

    PubMed

    Xu, Bin; Tambar, Uttam K

    2016-09-21

    Despite the importance of allylic ylide rearrangements for the synthesis of complex molecules, the catalyst control of [2,3]- and [1,2]-rearrangements remains an unsolved problem. We developed the first regiodivergent [2,3]- and [1,2]-rearrangements of iodonium ylides that are controlled by copper catalysts bearing different ligands. In the presence of a 2,2'-dipyridyl ligand, diazoesters and allylic iodides react via a [2,3]-rearrangement pathway. Alternatively, a phosphine ligand favors the formation of the [1,2]-rearrangement product. A series of α-iodoesters containing a broad range of functional groups were obtained in high yields, regioselectivities, and diastereoselectivities. Deuterium-labeling studies suggest distinct mechanisms for the regioselective rearrangements. PMID:27603216

  9. Scoliosis and vertebral anomalies: additional abnormal phenotypes associated with chromosome 16p11.2 rearrangement.

    PubMed

    Al-Kateb, Hussam; Khanna, Geetika; Filges, Isabel; Hauser, Natalie; Grange, Dorothy K; Shen, Joseph; Smyser, Christopher D; Kulkarni, Shashikant; Shinawi, Marwan

    2014-05-01

    The typical chromosome 16p11.2 rearrangements are estimated to occur at a frequency of approximately 0.6% of all samples tested clinically and have been identified as a major cause of autism spectrum disorders, developmental delay, behavioral abnormalities, and seizures. Careful examination of patients with these rearrangements revealed association with abnormal head size, obesity, dysmorphism, and congenital abnormalities. In this report, we extend this list of phenotypic abnormalities to include scoliosis and vertebral anomalies. We present detailed characterization of phenotypic and radiological data of 10 new patients, nine with the 16p11.2 deletion and one with the duplication within the coordinates chr16:29,366,195 and 30,306,956 (hg19) with a minimal size of 555 kb. We discuss the phenotypical and radiological findings in our patients and review 5 previously reported patients with 16p11.2 rearrangement and similar skeletal abnormalities. Our data suggest that patients with the recurrent 16p11.2 rearrangement have increased incidence of scoliosis and vertebral anomalies. However, additional studies are required to confirm this observation and to establish the incidence of these anomalies. We discuss the potential implications of our findings on the diagnosis, surveillance and genetic counseling of patients with 16p11.2 rearrangement. PMID:24458548

  10. Analysis of Micro-Rearrangements in 25 Eukaryotic Species Pairs by SyntenyMapper

    PubMed Central

    Kaufmann, Stefanie; Frishman, Dmitrij

    2014-01-01

    High-quality mapping of genomic regions and genes between two organisms is an indispensable prerequisite for evolutionary analyses and comparative genomics. Existing approaches to this problem focus on either delineating orthologs or finding extended sequence regions of common evolutionary origin (syntenic blocks). We propose SyntenyMapper, a novel tool for refining predefined syntenic regions. SyntenyMapper creates a set of blocks with conserved gene order between two genomes and finds all minor rearrangements that occurred since the evolutionary split of the two species considered. We also present TrackMapper, a SyntenyMapper-based tool that allows users to directly compare genome features, such as histone modifications, between two organisms, and identify genes with highly conserved features. We demonstrate SyntenyMapper's advantages by conducting a large-scale analysis of micro-rearrangements within syntenic regions of 25 eukaryotic species. Unsurprisingly, the number and length of syntenic regions is correlated with evolutionary distance, while the number of micro-rearrangements depends only on the size of the harboring region. On the other hand, the size of rearranged regions remains relatively constant regardless of the evolutionary distance between the organisms, implying a length constraint in the rearrangement process. SyntenyMapper is a useful software tool for both large-scale and gene-centric genome comparisons. PMID:25375783

  11. Generation and Analysis of Transposon Ac/Ds-Induced Chromosomal Rearrangements in Rice Plants.

    PubMed

    Xuan, Yuan Hu; Peterson, Thomas; Han, Chang-Deok

    2016-01-01

    Closely-located transposable elements (TEs) have been known to induce chromosomal breakage and rearrangements via alternative transposition. To study genome rearrangements in rice, an Ac/Ds system has been employed. This system comprises an immobile Ac element expressed under the control of CaMV 35S promoter, and a modified Ds element. A starter line carried Ac and a single copy of Ds at the OsRLG5 (Oryza sativa receptor-like gene 5). To enhance the transpositional activity, seed-derived calli were cultured and regenerated into plants. Among 270 lines regenerated from the starter, one line was selected that contained a pair of inversely-oriented Ds elements at the OsRLG5 (Oryza sativa receptor-like gene 5). The selected line was again subjected to tissue culture to obtain a regenerant population. Among 300 regenerated plants, 107 (36 %) contained chromosomal rearrangements including deletions, duplications, and inversions of various sizes. From 34 plants, transposition mechanisms leading to such genomic rearrangements were analyzed. The rearrangements were induced by sister chromatid transposition (SCT), homologous recombination (HR), and single chromatid transposition (SLCT). Among them, 22 events (65 %) were found to be transmitted to the next generation. These results demonstrate a great potential of tissue culture regeneration and the Ac/Ds system in understanding alternative transposition mechanisms and in developing chromosome engineering in plants. PMID:27557685

  12. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project.

    PubMed

    Higgins, Anne W; Alkuraya, Fowzan S; Bosco, Amy F; Brown, Kerry K; Bruns, Gail A P; Donovan, Diana J; Eisenman, Robert; Fan, Yanli; Farra, Chantal G; Ferguson, Heather L; Gusella, James F; Harris, David J; Herrick, Steven R; Kelly, Chantal; Kim, Hyung-Goo; Kishikawa, Shotaro; Korf, Bruce R; Kulkarni, Shashikant; Lally, Eric; Leach, Natalia T; Lemyre, Emma; Lewis, Janine; Ligon, Azra H; Lu, Weining; Maas, Richard L; MacDonald, Marcy E; Moore, Steven D P; Peters, Roxanna E; Quade, Bradley J; Quintero-Rivera, Fabiola; Saadi, Irfan; Shen, Yiping; Shendure, Jay; Williamson, Robin E; Morton, Cynthia C

    2008-03-01

    Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.

  13. Generation and Analysis of Transposon Ac/Ds-Induced Chromosomal Rearrangements in Rice Plants.

    PubMed

    Xuan, Yuan Hu; Peterson, Thomas; Han, Chang-Deok

    2016-01-01

    Closely-located transposable elements (TEs) have been known to induce chromosomal breakage and rearrangements via alternative transposition. To study genome rearrangements in rice, an Ac/Ds system has been employed. This system comprises an immobile Ac element expressed under the control of CaMV 35S promoter, and a modified Ds element. A starter line carried Ac and a single copy of Ds at the OsRLG5 (Oryza sativa receptor-like gene 5). To enhance the transpositional activity, seed-derived calli were cultured and regenerated into plants. Among 270 lines regenerated from the starter, one line was selected that contained a pair of inversely-oriented Ds elements at the OsRLG5 (Oryza sativa receptor-like gene 5). The selected line was again subjected to tissue culture to obtain a regenerant population. Among 300 regenerated plants, 107 (36 %) contained chromosomal rearrangements including deletions, duplications, and inversions of various sizes. From 34 plants, transposition mechanisms leading to such genomic rearrangements were analyzed. The rearrangements were induced by sister chromatid transposition (SCT), homologous recombination (HR), and single chromatid transposition (SLCT). Among them, 22 events (65 %) were found to be transmitted to the next generation. These results demonstrate a great potential of tissue culture regeneration and the Ac/Ds system in understanding alternative transposition mechanisms and in developing chromosome engineering in plants.

  14. BCL-1 Gene Rearrangements in Iranian Non-Hodgkin Lymphoma Patients

    PubMed Central

    Tohidirad, Manoush; Estiar, Mehrdad Asghari; Rezamand, Azim; Ghorbian, Saeid; Andalib, Sasan; Jahanzad, Issa; Bahrami, Tayyeb; Sakhinia, Ebrahim

    2016-01-01

    In the present study, our aim was to assess the incidence of BCL-1 gene rearrangements in formalin-fixed paraffin embedded (FFPE) tissue in patients with non-Hodgkin lymphomas (NHL). The BIOMED-2 protocol was applied to assess the BCL-1 gene rearrangements in NHL patients. PCR amplification was carried out on FFPE in 100 patients with B-cell lymphoma including 89 cases with diffused large B-cell lymphoma (DLBCL) (15 cases under 18 years old) and 11 cases with mantle cell lymphoma (MCL). Out of the 100 patients, 19 cases (19%) were identified to have concurrent translocation involving BCL-1. The significant association was seen between BCL-1 gene rearrangements and the lymphomas in patients older than 55 years (P<0.05). Out of 100 cases, 80 cases were positive and 20 cases were negative regarding CD20. No significant association was found between DLBCL lymphoma in patients under 18 years old and BCL-1 gene rearrangements (P>0.05). In addition, the positive and negative expressions of LCA/CD45 marker were 76% (76/100) and 26% (26/100), respectively. Our findings revealed that BCL-1 gene rearrangement assays using BIOMED-2 protocol can be considered as a valuable approach in detection of the lymphomas. PMID:27045402

  15. Mosaic (MSC) cucumbers regenerated from independent cell cultures possess different mitochondrial rearrangements.

    PubMed

    Bartoszewski, Grzegorz; Malepszy, Stefan; Havey, Michael J

    2004-02-01

    Passage of the highly inbred cucumber ( Cucumis sativus L.) line B through cell culture produces progenies with paternally transmitted, mosaic (MSC) phenotypes. Because the mitochondrial genome of cucumber shows paternal transmission, we evaluated for structural polymorphisms by hybridizing cosmids spanning the entire mitochondrial genome of Arabidopsis thaliana L. to DNA-gel blots of four independently generated MSC and four wild-type cucumbers. Polymorphisms were identified by cosmids carrying rrn18, nad5-exon2, rpl5, and the previously described JLV5 deletion. Polymorphisms revealed by rrn18 and nad5-exon2 were due to one rearrangement bringing together these two coding regions. The polymorphism revealed by rpl5 was unique to MSC16 and was due to rearrangement(s) placing the rpl5 region next to the forward junction of the JLV5 deletion. The rearrangement near rpl5 existed as a sublimon in wild-type inbred B, but was not detected in the cultivar Calypso. Although RNA-gel blots revealed reduced transcription of rpl5 in MSC16 relative to wild-type cucumber, Western analyses revealed no differences for the RPL5 protein and the genetic basis of the MSC16 phenotype remains enigmatic. We evaluated 17 MSC and wild-type lines regenerated from independent cell-culture experiments for these structural polymorphisms and identified eight different patterns, indicating that the passage of cucumber through cell culture may be a unique mechanism to induce or select for novel rearrangements affecting mitochondrial gene expression.

  16. Rearrangement of immunoglobulin and T-cell receptor genes in Hodgkin's disease.

    PubMed Central

    Roth, M. S.; Schnitzer, B.; Bingham, E. L.; Harnden, C. E.; Hyder, D. M.; Ginsburg, D.

    1988-01-01

    The precise cellular origin of the malignant cell population in Hodgkin's disease (HD) is unknown. Recent application of Southern blotting techniques to detect clonal rearrangements of immunoglobulin (Ig) and T-cell receptor (TCR) genes has yielded conflicting results. The authors report the detailed analysis of tumor tissue DNA obtained from 18 cases of HD using Ig and TCR gene probes. The distribution of HD subtypes was similar to that in other series. Samples were examined for rearrangement by means of multiple restriction enzymes with specific probes for the Ig heavy chain, Ig kappa, Ig lambda, TCR beta, and TCR gamma loci. Only germline bands were detected in all 18 cases with the Ig gene probes and in 15 of 18 cases with the TCR probes. In 2 cases blot analysis suggested a predominance of polyclonal (or oligoclonal) T cells. In 1 case monoclonal rearrangement of the TCR beta gene was detected. Based on the intensity of the rearrangement and the small percentage of Reed-Sternberg (R-S) cells in this case, the clonal population detected was most likely not the R-S cell itself. The data do not support the frequent occurrence of Ig or TCR monoclonal gene rearrangement in HD. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:3358458

  17. Frequent occurrence of large duplications at reciprocal genomic rearrangement breakpoints in multiple myeloma and other tumors

    PubMed Central

    Demchenko, Yulia; Roschke, Anna; Chen, Wei-Dong; Asmann, Yan; Bergsagel, Peter Leif; Kuehl, Walter Michael

    2016-01-01

    Using a combination of array comparative genomic hybridization, mate pair and cloned sequences, and FISH analyses, we have identified in multiple myeloma cell lines and tumors a novel and recurrent type of genomic rearrangement, i.e. interchromosomal rearrangements (translocations or insertions) and intrachromosomal inversions that contain long (1–4000 kb; median ∼100 kb) identical sequences adjacent to both reciprocal breakpoint junctions. These duplicated sequences were generated from sequences immediately adjacent to the breakpoint from at least one—but sometimes both—chromosomal donor site(s). Tandem duplications had a similar size distribution suggesting the possibility of a shared mechanism for generating duplicated sequences at breakpoints. Although about 25% of apparent secondary rearrangements contained these duplications, primary IGH translocations rarely, if ever, had large duplications at breakpoint junctions. Significantly, these duplications often contain super-enhancers and/or oncogenes (e.g. MYC) that are dysregulated by rearrangements during tumor progression. We also found that long identical sequences often were identified at both reciprocal breakpoint junctions in six of eight other tumor types. Finally, we have been unable to find reports of similar kinds of rearrangements in wild-type or mutant prokaryotes or lower eukaryotes such as yeast. PMID:27353332

  18. Rapid, Nonradioactive Detection of Clonal T-Cell Receptor Gene Rearrangements in Lymphoid Neoplasms

    NASA Astrophysics Data System (ADS)

    Bourguin, Anne; Tung, Rosann; Galili, Naomi; Sklar, Jeffrey

    1990-11-01

    Southern blot hybridization analysis of clonal antigen receptor gene rearrangements has proved to be a valuable adjunct to conventional methods for diagnosing lymphoid neoplasia. However, Southern blot analysis suffers from a number of technical disadvantages, including the time necessary to obtain results, the use of radioactivity, and the susceptibility of the method to various artifacts. We have investigated an alternative approach for assessing the clonality of antigen receptor gene rearrangements in lymphoid tissue biopsy specimens. This approach involves the amplification of rearranged γ T-cell receptor genes by the polymerase chain reaction and analysis of the polymerase chain reaction products by denaturing gradient gel electrophoresis. By use of this approach, clonal rearrangements from neoplastic lymphocytes constituting as little as 0.1-1% of the total cells in the tissue are detected as discrete bands in the denaturing gel after the gel is stained with ethidium bromide and viewed under ultraviolet light. In contrast, polyclonal rearrangements from reactive lymphocytes appear as a diffuse smear along the length of the gel. Our findings suggest that polymerase chain reaction combined with denaturing gradient gel electrophoresis may offer a rapid, nonradioactive, and sensitive alternative to Southern blot analysis for the diagnostic evaluation of lymphoid tissue biopsy specimens.

  19. Strand breaks without DNA rearrangement in V(D)J recombination

    SciTech Connect

    Hendrickson, E.A.; Liu, V.F.; Weaver, D.T. )

    1991-06-01

    Somatic gene rearrangement of immunoglobulin and T-cell receptor genes (V(D)J recombination) is mediated by pairs of specific DNA sequence motifs termed signal sequences. In experiments described here, retroviral vectors containing V(D)J rearrangement cassettes in which the signal sequences had been altered were introduced into wild-type and scid (severe combined immune deficiency) pre-B cells and used to define intermediates in the V(D)J recombination pathway. The scid mutation has previously been shown to deleteriously affect the V(d)J recombination process. Cassettes containing a point mutation in one of the two cassettes with the characteristic scid deletional phenotype. Using these mutated templates, the authors identified junctional modifications at the wild-type signal sequences that had arisen from strand breaks which were not associated with overall V(D)J rearrangements. Neither cell type was able to rearrange constructs which contained only a single, nonmutated, signal sequence. Analysis of these signal sequence mutations has provided insights into intermediates in the V(D)J rearrangement pathway in wild-type and scid pre-B cells.

  20. Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae)

    PubMed Central

    Song, Fan; Li, Hu; Shao, Renfu; Shi, Aimin; Bai, Xiaoshuan; Zheng, Xiaorong; Heiss, Ernst; Cai, Wanzhi

    2016-01-01

    The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae. PMID:27180804

  1. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.

    PubMed

    Rausch, Tobias; Jones, David T W; Zapatka, Marc; Stütz, Adrian M; Zichner, Thomas; Weischenfeldt, Joachim; Jäger, Natalie; Remke, Marc; Shih, David; Northcott, Paul A; Pfaff, Elke; Tica, Jelena; Wang, Qi; Massimi, Luca; Witt, Hendrik; Bender, Sebastian; Pleier, Sabrina; Cin, Huriye; Hawkins, Cynthia; Beck, Christian; von Deimling, Andreas; Hans, Volkmar; Brors, Benedikt; Eils, Roland; Scheurlen, Wolfram; Blake, Jonathon; Benes, Vladimir; Kulozik, Andreas E; Witt, Olaf; Martin, Dianna; Zhang, Cindy; Porat, Rinnat; Merino, Diana M; Wasserman, Jonathan; Jabado, Nada; Fontebasso, Adam; Bullinger, Lars; Rücker, Frank G; Döhner, Konstanze; Döhner, Hartmut; Koster, Jan; Molenaar, Jan J; Versteeg, Rogier; Kool, Marcel; Tabori, Uri; Malkin, David; Korshunov, Andrey; Taylor, Michael D; Lichter, Peter; Pfister, Stefan M; Korbel, Jan O

    2012-01-20

    Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.

  2. Complex mitochondrial DNA rearrangements in individual cells from patients with sporadic inclusion body myositis

    PubMed Central

    Rygiel, Karolina A.; Tuppen, Helen A.; Grady, John P.; Vincent, Amy; Blakely, Emma L.; Reeve, Amy K.; Taylor, Robert W.; Picard, Martin; Miller, James; Turnbull, Doug M.

    2016-01-01

    Mitochondrial DNA (mtDNA) rearrangements are an important cause of mitochondrial disease and age related mitochondrial dysfunction in tissues including brain and skeletal muscle. It is known that different mtDNA deletions accumulate in single cells, but the detailed nature of these rearrangements is still unknown. To evaluate this we used a complementary set of sensitive assays to explore the mtDNA rearrangements in individual cells from patients with sporadic inclusion body myositis, a late-onset inflammatory myopathy with prominent mitochondrial changes. We identified large-scale mtDNA deletions in individual muscle fibres with 20% of cytochrome c oxidase-deficient myofibres accumulating two or more mtDNA deletions. The majority of deletions removed only the major arc but ∼10% of all deletions extended into the minor arc removing the origin of light strand replication (OL) and a variable number of genes. Some mtDNA molecules contained two deletion sites. Additionally, we found evidence of mitochondrial genome duplications allowing replication and clonal expansion of these complex rearranged molecules. The extended spectrum of mtDNA rearrangements in single cells provides insight into the process of clonal expansion which is fundamental to our understanding of the role of mtDNA mutations in ageing and disease. PMID:27131788

  3. Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation.

    PubMed

    Biller, Priscila; Guéguen, Laurent; Knibbe, Carole; Tannier, Eric

    2016-01-01

    Models of evolution by genome rearrangements are prone to two types of flaws: One is to ignore the diversity of susceptibility to breakage across genomic regions, and the other is to suppose that susceptibility values are given. Without necessarily supposing their precise localization, we call "solid" the regions that are improbably broken by rearrangements and "fragile" the regions outside solid ones. We propose a model of evolution by inversions where breakage probabilities vary across fragile regions and over time. It contains as a particular case the uniform breakage model on the nucleotidic sequence, where breakage probabilities are proportional to fragile region lengths. This is very different from the frequently used pseudouniform model where all fragile regions have the same probability to break. Estimations of rearrangement distances based on the pseudouniform model completely fail on simulations with the truly uniform model. On pairs of amniote genomes, we show that identifying coding genes with solid regions yields incoherent distance estimations, especially with the pseudouniform model, and to a lesser extent with the truly uniform model. This incoherence is solved when we coestimate the number of fragile regions with the rearrangement distance. The estimated number of fragile regions is surprisingly small, suggesting that a minority of regions are recurrently used by rearrangements. Estimations for several pairs of genomes at different divergence times are in agreement with a slowly evolvable colocalization of active genomic regions in the cell.

  4. Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints

    PubMed Central

    Skinner, B M; Griffin, D K

    2012-01-01

    It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intrachromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intrachromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250 kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one-third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination. PMID:22045382

  5. Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

    PubMed Central

    Biller, Priscila; Guéguen, Laurent; Knibbe, Carole; Tannier, Eric

    2016-01-01

    Models of evolution by genome rearrangements are prone to two types of flaws: One is to ignore the diversity of susceptibility to breakage across genomic regions, and the other is to suppose that susceptibility values are given. Without necessarily supposing their precise localization, we call “solid” the regions that are improbably broken by rearrangements and “fragile” the regions outside solid ones. We propose a model of evolution by inversions where breakage probabilities vary across fragile regions and over time. It contains as a particular case the uniform breakage model on the nucleotidic sequence, where breakage probabilities are proportional to fragile region lengths. This is very different from the frequently used pseudouniform model where all fragile regions have the same probability to break. Estimations of rearrangement distances based on the pseudouniform model completely fail on simulations with the truly uniform model. On pairs of amniote genomes, we show that identifying coding genes with solid regions yields incoherent distance estimations, especially with the pseudouniform model, and to a lesser extent with the truly uniform model. This incoherence is solved when we coestimate the number of fragile regions with the rearrangement distance. The estimated number of fragile regions is surprisingly small, suggesting that a minority of regions are recurrently used by rearrangements. Estimations for several pairs of genomes at different divergence times are in agreement with a slowly evolvable colocalization of active genomic regions in the cell. PMID:27190002

  6. Diverse, Biologically Relevant, and Targetable Gene Rearrangements in Triple-Negative Breast Cancer and Other Malignancies.

    PubMed

    Shaver, Timothy M; Lehmann, Brian D; Beeler, J Scott; Li, Chung-I; Li, Zhu; Jin, Hailing; Stricker, Thomas P; Shyr, Yu; Pietenpol, Jennifer A

    2016-08-15

    Triple-negative breast cancer (TNBC) and other molecularly heterogeneous malignancies present a significant clinical challenge due to a lack of high-frequency "driver" alterations amenable to therapeutic intervention. These cancers often exhibit genomic instability, resulting in chromosomal rearrangements that affect the structure and expression of protein-coding genes. However, identification of these rearrangements remains technically challenging. Using a newly developed approach that quantitatively predicts gene rearrangements in tumor-derived genetic material, we identified and characterized a novel oncogenic fusion involving the MER proto-oncogene tyrosine kinase (MERTK) and discovered a clinical occurrence and cell line model of the targetable FGFR3-TACC3 fusion in TNBC. Expanding our analysis to other malignancies, we identified a diverse array of novel and known hybrid transcripts, including rearrangements between noncoding regions and clinically relevant genes such as ALK, CSF1R, and CD274/PD-L1 The over 1,000 genetic alterations we identified highlight the importance of considering noncoding gene rearrangement partners, and the targetable gene fusions identified in TNBC demonstrate the need to advance gene fusion detection for molecularly heterogeneous cancers. Cancer Res; 76(16); 4850-60. ©2016 AACR. PMID:27231203

  7. A new approach to the elucidation of complex chromosome rearrangements illustrated by a case of Rieger syndrome.

    PubMed Central

    Ogilvie, C M; Raymond, F L; Harrison, R H; Scriven, P N; Docherty, Z

    1998-01-01

    A patient with a complex chromosome rearrangement and unilateral Rieger syndrome is presented. This rearrangement involves four chromosomes and six breakpoints, one of which is at 4q25, the candidate region for Rieger syndrome. We discuss a novel approach to the elucidation of this case using a multiprobe fluorescence in situ hybridisation method to show rearrangements unpredictable from G banded analysis, and the clear and unambiguous presentation of the karyotype using computer generated colour ideograms. Images PMID:9541109

  8. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia.

    PubMed

    Gröschel, Stefan; Sanders, Mathijs A; Hoogenboezem, Remco; de Wit, Elzo; Bouwman, Britta A M; Erpelinck, Claudia; van der Velden, Vincent H J; Havermans, Marije; Avellino, Roberto; van Lom, Kirsten; Rombouts, Elwin J; van Duin, Mark; Döhner, Konstanze; Beverloo, H Berna; Bradner, James E; Döhner, Hartmut; Löwenberg, Bob; Valk, Peter J M; Bindels, Eric M J; de Laat, Wouter; Delwel, Ruud

    2014-04-10

    Chromosomal rearrangements without gene fusions have been implicated in leukemogenesis by causing deregulation of proto-oncogenes via relocation of cryptic regulatory DNA elements. AML with inv(3)/t(3;3) is associated with aberrant expression of the stem-cell regulator EVI1. Applying functional genomics and genome-engineering, we demonstrate that both 3q rearrangements reposition a distal GATA2 enhancer to ectopically activate EVI1 and simultaneously confer GATA2 functional haploinsufficiency, previously identified as the cause of sporadic familial AML/MDS and MonoMac/Emberger syndromes. Genomic excision of the ectopic enhancer restored EVI1 silencing and led to growth inhibition and differentiation of AML cells, which could be replicated by pharmacologic BET inhibition. Our data show that structural rearrangements involving the chromosomal repositioning of a single enhancer can cause deregulation of two unrelated distal genes, with cancer as the outcome.

  9. Checkpoints are blind to replication restart and recombination intermediates that result in gross chromosomal rearrangements

    PubMed Central

    Mohebi, Saed; Mizuno, Ken’Ichi; Watson, Adam; Carr, Antony M.; Murray, Johanne M.

    2015-01-01

    Replication fork inactivation can be overcome by homologous recombination, but this can cause gross chromosomal rearrangements that subsequently missegregate at mitosis, driving further chromosome instability. It is unclear when the chromosome rearrangements are generated and whether individual replication problems or the resulting recombination intermediates delay the cell cycle. Here we have investigated checkpoint activation during HR-dependent replication restart using a site-specific replication fork-arrest system. Analysis during a single cell cycle shows that HR-dependent replication intermediates arise in S phase, shortly after replication arrest, and are resolved into acentric and dicentric chromosomes in G2. Despite this, cells progress into mitosis without delay. Neither the DNA damage nor the intra-S phase checkpoints are activated in the first cell cycle, demonstrating that these checkpoints are blind to replication and recombination intermediates as well as to rearranged chromosomes. The dicentrics form anaphase bridges that subsequently break, inducing checkpoint activation in the second cell cycle. PMID:25721418

  10. Marfan syndrome with a complex chromosomal rearrangement including deletion of the FBN1 gene

    PubMed Central

    2012-01-01

    Background The majority of Marfan syndrome (MFS) cases is caused by mutations in the fibrillin-1 gene (FBN1), mapped to chromosome 15q21.1. Only few reports on deletions including the whole FBN1 gene, detected by molecular cytogenetic techniques, were found in literature. Results We report here on a female patient with clinical symptoms of the MFS spectrum plus craniostenosis, hypothyroidism and intellectual deficiency who presents a 1.9 Mb deletion, including the FBN1 gene and a complex rearrangement with eight breakpoints involving chromosomes 6, 12 and 15. Discussion This is the first report of MFS with a complex chromosome rearrangement involving a deletion of FBN1 and contiguous genes. In addition to the typical clinical findings of the Marfan syndrome due to FBN1 gene haploinsufficiency, the patient presents features which may be due to the other gene deletions and possibly to the complex chromosome rearrangement. PMID:22260333

  11. Chromosomal Rearrangements in Salmonella enterica Serotype Typhi Affecting Molecular Typing in Outbreak Investigations

    PubMed Central

    Echeita, M. A.; Usera, M. A.

    1998-01-01

    Salmonella enterica serotype Typhi strains belonging to eight different outbreaks of typhoid fever that occurred in Spain between 1989 and 1994 were analyzed by ribotyping and pulsed-field gel electrophoresis. For three outbreaks, two different patterns were detected for each outbreak. The partial digestion analysis by the intron-encoded endonuclease I-CeuI of the two different strains from each outbreak provided an excellent tool for examining the organization of the genomes of epidemiologically related strains. S. enterica serotype Typhi seems to be more susceptible than other serotypes to genetic rearrangements produced by homologous recombinations between rrn operons; these rearrangements do not substantially alter the stability or survival of the bacterium. We conclude that genetic rearrangements can occur during the emergence of an outbreak. PMID:9650981

  12. Robust orthogonal recombination system for versatile genomic elements rearrangement in yeast Saccharomyces Cerevisiae

    PubMed Central

    Lin, Qiuhui; Qi, Hao; Wu, Yi; Yuan, Yingjin

    2015-01-01

    Rearrangement of genomic DNA elements in a dynamic controlled fashion is a fundamental challenge. Site-specific DNA recombinases have been tamed as a powerful tool in genome editing. Here, we reported a DNA element rearrangement on the basis of a pairwise orthogonal recombination system which is comprised of two site-specific recombinases of Vika/vox and Cre/loxp in yeast Saccharomyces Creevisiae. Taking the advantage of the robust pairwise orthogonality, we showed that multi gene elements could be organized in a programmed way, in which rationally designed pattern of loxP and vox determined the final genotype after expressing corresponding recombinases. Finally, it was demonstrated that the pairwise orthogonal recombination system could be utilized to refine synthetic chromosome rearrangement and modification by loxP-mediated evolution, SCRaMbLE, in yeast cell carrying a completely synthesized chromosome III. PMID:26477943

  13. Robust orthogonal recombination system for versatile genomic elements rearrangement in yeast Saccharomyces cerevisiae.

    PubMed

    Lin, Qiuhui; Qi, Hao; Wu, Yi; Yuan, Yingjin

    2015-01-01

    Rearrangement of genomic DNA elements in a dynamic controlled fashion is a fundamental challenge. Site-specific DNA recombinases have been tamed as a powerful tool in genome editing. Here, we reported a DNA element rearrangement on the basis of a pairwise orthogonal recombination system which is comprised of two site-specific recombinases of Vika/vox and Cre/loxp in yeast Saccharomyces Creevisiae. Taking the advantage of the robust pairwise orthogonality, we showed that multi gene elements could be organized in a programmed way, in which rationally designed pattern of loxP and vox determined the final genotype after expressing corresponding recombinases. Finally, it was demonstrated that the pairwise orthogonal recombination system could be utilized to refine synthetic chromosome rearrangement and modification by loxP-mediated evolution, SCRaMbLE, in yeast cell carrying a completely synthesized chromosome III.

  14. Synergistic Ion-Binding Catalysis Demonstrated via an Enantioselective, Catalytic [2,3]-Wittig Rearrangement

    PubMed Central

    2016-01-01

    Sigmatropic rearrangements number among the most powerful complexity-building transformations in organic synthesis but have remained largely insensitive to enantioselective catalysis due to the diffuse nature of their transition structures. Here, we describe a synergistic ion-binding strategy for asymmetric catalysis of anionic sigmatropic rearrangements. This approach is demonstrated with the enantioselective [2,3]-Wittig rearrangement of α-allyloxy carbonyl compounds to afford highly enantioenriched homoallylic alcohol products. Chiral thiourea catalysts are shown to engage reactive anions and their countercations through a cooperative set of attractive, noncovalent interactions. Catalyst structure–reactivity–selectivity relationship studies and computational analyses provide insight into catalyst–substrate interactions responsible for enantioinduction and allude to the potential generality of this catalytic strategy. PMID:27413786

  15. Rearrangement of a common cellular DNA domain on chromosome 4 in human primary liver tumors

    SciTech Connect

    Pasquinelli, C.; Garreau, F.; Bougueleret, L.; Cariani, E.; Thiers, V.; Croissant, O.; Hadchouel, M.; Tiollais, P.; Brechot, C. ); Grzeschik, K.H. )

    1988-02-01

    Hepatitis B virus (HBV) DNA integration has been shown to occur frequently in human hepatocellular carcinomas. The authors have investigated whether common cellular DNA domains might be rearranged, possibly by HBV integration, in human primary liver tumors. Unique cellular DNA sequences adjacent to an HBV integration site were isolated from a patient with hepatitis B surface antigen-positive hepatocellular carcinoma. These probes detected rearrangement of this cellular region of chromosomal DNA in 3 of 50 additional primary liver tumors studied. Of these three tumor samples, two contained HBV DNA, without an apparent link between the viral DNA and the rearranged allele; HBV DNA sequences were not detected in the third tumor sample. By use of a panel of somatic cell hybrids, these unique cellular DNA sequences were shown to be located on chromosome 4. Therefore, this region of chromosomal DNA might be implicated in the formation of different tumors at one step of liver cell transformation, possible related to HBV integration.

  16. Chromosomal rearrangements in Salmonella enterica serotype typhi affecting molecular typing in outbreak investigations.

    PubMed

    Echeita, M A; Usera, M A

    1998-07-01

    Salmonella enterica serotype Typhi strains belonging to eight different outbreaks of typhoid fever that occurred in Spain between 1989 and 1994 were analyzed by ribotyping and pulsed-field gel electrophoresis. For three outbreaks, two different patterns were detected for each outbreak. The partial digestion analysis by the intron-encoded endonuclease I-CeuI of the two different strains from each outbreak provided an excellent tool for examining the organization of the genomes of epidemiologically related strains. S. enterica serotype Typhi seems to be more susceptible than other serotypes to genetic rearrangements produced by homologous recombinations between rrn operons; these rearrangements do not substantially alter the stability or survival of the bacterium. We conclude that genetic rearrangements can occur during the emergence of an outbreak.

  17. SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges.

    PubMed

    Lin, Ying Chih; Lu, Chin Lung; Liu, Ying-Chuan; Tang, Chuan Yi

    2006-07-01

    SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any two input chromosomes for transforming one chromosome into another. The input of SPRING can be either bacterial-size sequences or gene/landmark orders. If the input is a set of chromosomal sequences then the SPRING will automatically search for identical landmarks, which are homologous/conserved regions shared by all input sequences. In particular, SPRING also computes the breakpoint distance between any pair of two chromosomes, which can be used to compare with the rearrangement distance to confirm whether they are correlated or not. In addition, SPRING shows phylogenetic trees that are reconstructed based on the rearrangement and breakpoint distance matrixes.

  18. Monoclonal γ-T-Cell Receptor Rearrangement in Vulvar Lichen Sclerosus and Squamous Cell Carcinomas

    PubMed Central

    Regauer, Sigrid; Reich, Olaf; Beham-Schmid, Christine

    2002-01-01

    Risk factors for vulvar squamous cell carcinoma (SCC) are human papilloma virus (HPV) infections and lichen sclerosus (LS). The significance of monoclonal γ-T-cell receptor (γ-TCR) rearrangement in the lymphoid infiltrate of LS and the consequence for vulvar carcinogenesis is unknown. One hundred sixty-one biopsies of vulvar LS and SCC, with and without LS, were examined for monoclonal γ-TCR rearrangement and HPV16 expression, and for the expression of B- and T-cell markers and fascin. Monoclonal γ-TCR rearrangement was identified in 8 of 17 patients with LS and 11 of 21 patients with SCC arising in LS with only occasional HPV16 DNA detection. None of the 19 SCC without LS showed monoclonal γ-TCR rearrangement, but 14 of 19 patients had strong HPV16 detection. The lichenoid infiltrate of LS with germline configuration consisted predominantly of T cells (CD8 > CD4), along with numerous B cells. However, in biopsies with monoclonally rearranged γ-TCR, CD4-positive T cells dominated along with B cells and fascin-positive cells in the lichenoid infiltrate and in deeply located lymphocyte aggregates (LAs). These LAs additionally contained fascin-positive dendritic cells with only individual CD8, CD57, and granzyme-positive cells. LAs in biopsies with germline configuration demonstrated numerous T cells (CD8 >CD4), but only single peripheral B cells, CD57, and fascin-positive lymphocytes. Our data suggest that monoclonal γ-TCR rearrangement is characteristic for and limited to LS and SCC arising in LS, raising the question for a LS-associated antigen. We interpret B cells, CD4-positive T cells, and fascin-expressing dendritic cells within LS as a cellular immune response to antigen or proliferating T-cell clones. The resulting local immune dysregulation in LS may provide a permissive environment for the development of a SCC. PMID:11891200

  19. A case report of CIC-rearranged undifferentiated small round cell sarcoma in the cerebrum.

    PubMed

    Ito, Mayumi; Ishikawa, Misawo; Kitajima, Masateru; Narita, Jun; Hattori, Shinya; Endo, Otone; Goto, Keisuke

    2016-10-01

    CIC-rearranged undifferentiated small round cell sarcoma (CIC-rearranged USRCS) is a recently established type of Ewing-like small round cell sarcomas, characterized by CIC gene rearrangement, most commonly CIC-DUX4 fusion. This report presents the second case of CIC-rearranged USRCS arising primarily in the cerebrum. A 64-year-old otherwise healthy woman presented with a 1 × 1 cm sized hemorrhagic subcortical tumor in the left temporo-parietal lobe. The tumor repeatedly recurred, and the patient underwent three surgeries, chemotherapy with doxorubicin and ifosfamide, and radiotherapy, as well as gamma knife surgery. Systemic examination revealed no other extracranial masses. Imprint cytology revealed small to moderate-sized round-to-ovoid tumor cells with mild pleomorphism and variations in size and shape. The nuclei contained finely granular chromatin, and some had easily-recognizable nucleoli. The tumor exhibited a mainly cytoplasmic pattern of CD99 immunostaining, rather than a diffuse membranous pattern. The tumor also exhibited diffuse positivity for calretinin and p16, as well as partial positivity for WT1 (nuclear and cytoplasmic staining pattern) and D2-40. FISH assessment showed CIC split signals. In conclusion, CIC-rearranged USRCSs can occur primarily in the cerebrum. It would be impossible to diagnose them through cytology alone, but cytology would be useful to rule out other small round cell brain tumors including gliomas, lymphomas, carcinomas, and germinoma. Immunohistochemical analysis including tests for CD99, calretinin, and WT1 would help to suggest CIC-rearranged USRCSs and distinguish them from Ewing sarcomas. Additionally, immunohistochemistry for p16 might be useful in the diagnosis. Diagn. Cytopathol. 2016;44:828-832. © 2016 Wiley Periodicals, Inc.

  20. Chromosomal Rainbows detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors

    SciTech Connect

    O'Brien, Benjamin; Jossart, Gregg H.; Ito, Yuko; Greulich-Bode, Karin M.; Weier, Jingly F.; Munne, Santiago; Clark, Orlo H.; Weier, Heinz-Ulrich G.

    2010-08-19

    Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'-end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners. We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabase-pair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of

  1. ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer

    PubMed Central

    Leeman-Neill, Rebecca J.; Kelly, Lindsey; Liu, Pengyuan; Brenner, Alina V.; Little, Mark P.; Bogdanova, Tetiana I.; Evdokimova, Viktoria; Hatch, Maureen; Zurnadzy, Liudmyla Y.; Nikiforova, Marina N.; Yue, Ning J.; Zhang, Miao; Mabuchi, Kiyohiko; Tronko, Mykola D.; Nikiforov, Yuri E.

    2013-01-01

    Background Our previous analysis of papillary thyroid carcinomas (PTC) from the Ukrainian-American cohort exposed to 131I from the Chernobyl accident found RET/PTC rearrangements and other driver mutations in 60% of tumors. Methods In this study, we analyzed the remaining, mutation-negative tumors using RNA-Seq and RT-PCR to identify novel chromosomal rearrangements and characterize their relationship with radiation dose. Results The ETV6-NTRK3 rearrangement was identified by RNA-Seq in a tumor from a patient who received a high 131I dose. Overall, it was detected in 9/62 (14.5%) of post-Chernobyl and in 3/151 (2%) of sporadic PTCs (p=0.019). The most common fusion type was between exon 4 of ETV6 and exon 14 of NTRK3. The ETV6-NTRK3 prevalence in post-Chernobyl PTCs was associated with increasing 131I dose, albeit at borderline significance (p=0.126). The group of rearrangement-positive PTCs (ETV6-NTRK3, RET/PTC, PAX8-PPARγ) was associated with significantly higher dose response compared to the group of PTCs with point mutations (BRAF, RAS) (p<0.001). In vitro exposure of human thyroid cells to 1 Gy of 131I and γ-radiation resulted in the formation of ETV6-NTRK3 with a rate of 7.9 × 10−6 and 3.0 ×10−6 cells, respectively. Conclusions We report here the occurrence of ETV6-NTRK3 rearrangements in thyroid cancer and show that this rearrangement is significantly more common in tumors associated with exposure to 131I and has a borderline significant dose response. Moreover, ETV6-NTRK3 can be directly induced in thyroid cells by ionizing radiation in vitro and therefore may represent a novel mechanism of radiation-induced carcinogenesis. PMID:24327398

  2. Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.

    PubMed

    Rogers, Rebekah L

    2015-12-01

    Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5'-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution.

  3. Durable Clinical Response to Entrectinib in NTRK1-Rearranged Non-Small Cell Lung Cancer

    PubMed Central

    Le, Long P.; Zheng, Zongli; Muzikansky, Alona; Drilon, Alexander; Patel, Manish; Bauer, Todd M.; Liu, Stephen V.; Ou, Sai-Hong I.; Jackman, David; Costa, Daniel B.; Multani, Pratik S.; Li, Gary G.; Hornby, Zachary; Chow-Maneval, Edna; Luo, David; Lim, Jonathan E.; Iafrate, Anthony J.; Shaw, Alice T.

    2015-01-01

    Introduction: Chromosomal rearrangements involving neurotrophic tyrosine kinase 1 (NTRK1) occur in a subset of non-small cell lung cancers (NSCLCs) and other solid tumor malignancies, leading to expression of an oncogenic TrkA fusion protein. Entrectinib (RXDX-101) is an orally available tyrosine kinase inhibitor, including TrkA. We sought to determine the frequency of NTRK1 rearrangements in NSCLC and to assess the clinical activity of entrectinib. Methods: We screened 1378 cases of NSCLC using anchored multiplex polymerase chain reaction (AMP). A patient with an NTRK1 gene rearrangement was enrolled onto a Phase 1 dose escalation study of entrectinib in adult patients with locally advanced or metastatic tumors (NCT02097810). We assessed safety and response to treatment. Results: We identified NTRK1 gene rearrangements at a frequency of 0.1% in this cohort. A patient with stage IV lung adenocrcinoma with an SQSTM1-NTRK1 fusion transcript expression was treated with entrectinib. Entrectinib was well tolerated, with no grade 3–4 adverse events. Within three weeks of starting on treatment, the patient reported resolution of prior dyspnea and pain. Restaging CT scans demonstrated a RECIST partial response (PR) and complete resolution of all brain metastases. This patient has continued on treatment for over 6 months with an ongoing PR. Conclusions: Entrectinib demonstrated significant anti-tumor activity in a patient with NSCLC harboring an SQSTM1-NTRK1 gene rearrangement, indicating that entrectinib may be an effective therapy for tumors with NTRK gene rearrangements, including those with central nervous system metastases. PMID:26565381

  4. Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.

    PubMed

    Rogers, Rebekah L

    2015-12-01

    Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5'-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution. PMID:26399483

  5. A case report of CIC-rearranged undifferentiated small round cell sarcoma in the cerebrum.

    PubMed

    Ito, Mayumi; Ishikawa, Misawo; Kitajima, Masateru; Narita, Jun; Hattori, Shinya; Endo, Otone; Goto, Keisuke

    2016-10-01

    CIC-rearranged undifferentiated small round cell sarcoma (CIC-rearranged USRCS) is a recently established type of Ewing-like small round cell sarcomas, characterized by CIC gene rearrangement, most commonly CIC-DUX4 fusion. This report presents the second case of CIC-rearranged USRCS arising primarily in the cerebrum. A 64-year-old otherwise healthy woman presented with a 1 × 1 cm sized hemorrhagic subcortical tumor in the left temporo-parietal lobe. The tumor repeatedly recurred, and the patient underwent three surgeries, chemotherapy with doxorubicin and ifosfamide, and radiotherapy, as well as gamma knife surgery. Systemic examination revealed no other extracranial masses. Imprint cytology revealed small to moderate-sized round-to-ovoid tumor cells with mild pleomorphism and variations in size and shape. The nuclei contained finely granular chromatin, and some had easily-recognizable nucleoli. The tumor exhibited a mainly cytoplasmic pattern of CD99 immunostaining, rather than a diffuse membranous pattern. The tumor also exhibited diffuse positivity for calretinin and p16, as well as partial positivity for WT1 (nuclear and cytoplasmic staining pattern) and D2-40. FISH assessment showed CIC split signals. In conclusion, CIC-rearranged USRCSs can occur primarily in the cerebrum. It would be impossible to diagnose them through cytology alone, but cytology would be useful to rule out other small round cell brain tumors including gliomas, lymphomas, carcinomas, and germinoma. Immunohistochemical analysis including tests for CD99, calretinin, and WT1 would help to suggest CIC-rearranged USRCSs and distinguish them from Ewing sarcomas. Additionally, immunohistochemistry for p16 might be useful in the diagnosis. Diagn. Cytopathol. 2016;44:828-832. © 2016 Wiley Periodicals, Inc. PMID:27324529

  6. 'Chromosomal Rainbows' Detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors.

    PubMed

    O'Brien, Benjamin; Jossart, Gregg H; Ito, Yuko; Greulich-Bode, Karin M; Weier, Jingly F; Munne, Santiago; Clark, Orlo H; Weier, Heinz-Ulrich G

    2010-01-01

    Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'- end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners.We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabasepair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of

  7. Normal Expression of a Rearranged and Mutated c-myc Oncogene after Transfection into Fibroblasts

    NASA Astrophysics Data System (ADS)

    Richman, Adam; Hayday, Adrian

    1989-10-01

    Expression of the c-myc oncogene is deregulated in a variety of malignancies. Rearrangement and mutation of the c-myc locus is a characteristic feature of human Burkitt's lymphoma. Whether deregulation is solely a result of mutation of c-myc or whether it is influenced by the transformed B cell context has not been determined. A translocated and mutated allele of c-myc was stably transfected into fibroblasts. The rearranged allele was expressed indistinguishably from a normal c-myc gene: it had serum-regulated expression, was transcribed with normal promoter preference, and was strongly attenuated. Thus mutations by themselves are insufficient to deregulate c-myc transcription.

  8. Azulenylcarbenes: Rearrangements on the C11 H8 Potential Energy Surface.

    PubMed

    Henkel, Stefan; Pollok, Corina H; Schleif, Tim; Sander, Wolfram

    2016-08-22

    Four isomeric azulenylcarbenes were synthesized in argon matrices by photolysis of the corresponding diazo precursors, and the photochemistry of these carbenes was studied. The carbenes and their rearranged products were characterized by IR, UV/Vis, and EPR spectroscopy, and the experimental data were compared to results from DFT calculations. While 2-, 5- and 6-azulenylcarbene show triplet ground states, 1-azulenylcarbene exhibits a singlet ground state, in accord with theoretical predictions. The rearrangements of the azulenylcarbenes give access to a number of unusual C11 H8 isomers, such as other carbenes and strained allenes. PMID:27404847

  9. 9;22 translocation and bcr rearrangements in chronic myelocytic leukemia patients among atomic bomb survivors.

    PubMed

    Tanaka, K; Takechi, M; Hong, J; Shigeta, C; Oguma, N; Kamada, N; Takimoto, Y; Kuramoto, A; Dohy, H; Kyo, T

    1989-12-01

    To elucidate the mechanism of leukemia induced by radiation, we studied both chromosome abnormalities and bcr rearrangements of seven CML patients with a history of atomic bomb exposure and 14 CML patients without the exposure. All patients, irrespective of radiation exposure, had 9;22 translocation and rearrangement of the bcr gene in the leukemic cells. Further analysis of breakpoints within the bcr gene demonstrated no distinct difference between the exposed and the non-exposed groups. The present study suggests that formation of the chimeric bcr-abl gene and its genetic products may play an important role in the development of leukemia in either radiation-induced or de novo CML.

  10. MYB-QKI rearrangements in Angiocentric Glioma drive tumorigenicity through a tripartite mechanism

    PubMed Central

    Bandopadhayay, Pratiti; Ramkissoon, Lori A.; Jain, Payal; Bergthold, Guillaume; Wala, Jeremiah; Zeid, Rhamy; Schumacher, Steven E.; Urbanski, Laura; O’Rourke, Ryan; Gibson, William J.; Pelton, Kristine; Ramkissoon, Shakti H.; Han, Harry J.; Zhu, Yuankun; Choudhari, Namrata; Silva, Amanda; Boucher, Katie; Henn, Rosemary E.; Kang, Yun Jee; Knoff, David; Paolella, Brenton R.; Gladden-Young, Adrianne; Varlet, Pascale; Pages, Melanie; Horowitz, Peleg M.; Federation, Alexander; Malkin, Hayley; Tracy, Adam; Seepo, Sara; Ducar, Matthew; Hummelen, Paul Van; Santi, Mariarita; Buccoliero, Anna Maria; Scagnet, Mirko; Bowers, Daniel C.; Giannini, Caterina; Puget, Stephanie; Hawkins, Cynthia; Tabori, Uri; Klekner, Almos; Bognar, Laszlo; Burger, Peter C.; Eberhart, Charles; Rodriguez, Fausto J.; Hill, D. Ashley; Mueller, Sabine; Haas-Kogan, Daphne A.; Phillips, Joanna J.; Santagata, Sandro; Stiles, Charles D.; Bradner, James E.; Jabado, Nada; Goren, Alon; Grill, Jacques; Ligon, Azra H.; Goumnerova, Liliana; Waanders, Angela J.; Storm, Phillip B.; Kieran, Mark W.; Ligon, Keith L.; Beroukhim, Rameen; Resnick, Adam C.

    2016-01-01

    Angiocentric gliomas are pediatric low-grade gliomas (PLGGs) without known recurrent genetic drivers. We performed genomic analysis of new and published data from 249 PLGGs including 19 Angiocentric Gliomas. We identified MYB-QKI fusions as a specific and single candidate driver event in Angiocentric Gliomas. In vitro and in vivo functional studies show MYB-QKI rearrangements promote tumorigenesis through three mechanisms: MYB activation by truncation, enhancer translocation driving aberrant MYB-QKI expression, and hemizygous loss of the tumor suppressor QKI. This represents the first example of a single driver rearrangement simultaneously transforming cells via three genetic and epigenetic mechanisms in a tumor. PMID:26829751

  11. High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer

    PubMed Central

    Pailler, E.; Auger, N.; Lindsay, C. R.; Vielh, P.; Islas-Morris-Hernandez, A.; Borget, I.; Ngo-Camus, M.; Planchard, D.; Soria, J.-C.; Besse, B.; Farace, F.

    2015-01-01

    Background Genetic aberrations affecting the c-ros oncogene 1 (ROS1) tyrosine kinase gene have been reported in a small subset of patients with non-small-cell lung cancer (NSCLC). We evaluated whether ROS1-chromosomal rearrangements could be detected in circulating tumor cells (CTCs) and examined tumor heterogeneity of CTCs and tumor biopsies in ROS1-rearranged NSCLC patients. Patients and methods Using isolation by size of epithelial tumor cells (ISET) filtration and filter-adapted-fluorescence in situ hybridization (FA-FISH), ROS1 rearrangement was examined in CTCs from four ROS1-rearranged patients treated with the ROS1-inhibitor, crizotinib, and four ROS1-negative patients. ROS1-gene alterations observed in CTCs at baseline from ROS1-rearranged patients were compared with those present in tumor biopsies and in CTCs during crizotinib treatment. Numerical chromosomal instability (CIN) of CTCs was assessed by DNA content quantification and chromosome enumeration. Results ROS1 rearrangement was detected in the CTCs of all four patients with ROS1 rearrangement previously confirmed by tumor biopsy. In ROS1-rearranged patients, median number of ROS1-rearranged CTCs at baseline was 34.5 per 3 ml blood (range, 24–55). In ROS1-negative patients, median background hybridization of ROS1-rearranged CTCs was 7.5 per 3 ml blood (range, 7–11). Tumor heterogeneity, assessed by ROS1 copy number, was significantly higher in baseline CTCs compared with paired tumor biopsies in the three patients experiencing PR or SD (P < 0.0001). Copy number in ROS1-rearranged CTCs increased significantly in two patients who progressed during crizotinib treatment (P < 0.02). CTCs from ROS1-rearranged patients had a high DNA content and gain of chromosomes, indicating high levels of aneuploidy and numerical CIN. Conclusion We provide the first proof-of-concept that CTCs can be used for noninvasive and sensitive detection of ROS1 rearrangement in NSCLC patients. CTCs from ROS1-rearranged

  12. [Analyses of the rearrangement of T-cell receptor- and immunoglobulin genes in the diagnosis of lymphoproliferative disorders].

    PubMed

    Griesser, D H

    1995-01-01

    Rearrangements are developmentally regulated genetic recombinations in T and B cells which generate functional T cell receptor (TcR) and immunoglobulin genes, respectively. Different variable, sometimes diversity, and joining gene segments which are discontinuously spread out within their chromosomal location in germline configuration, are randomly assembled in individual lymphocytes. These rearrangements can be detected by Southern Blot analysis if more than 5% of a total lymphocyte population in a biopsy specimen carries the same clonal rearrangement. We analyzed DNA from 324 snap-frozen biopsy specimens from lympho-proliferative disorders. None of the 20 reactive lesions and four malignant myelomonocytic tumors had a clonal antigen receptor gene rearrangement. All 117 malignant B cell lymphomas of different subtypes and 95 of 97 malignant T cell lymphomas showed a clonal gene rearrangement. Only two angioimmunoblastic lymphadenopathy(AILD)-type T cell lymphomas did not have immune receptor gene rearrangements. They were morphologically indistinguishable from the other 47 T/AILD lymphomas with clonal rearrangement patterns. In most cases TcR beta and immunoglobulin heavy chain (IgH) gene probes were sufficient for lineage assignment of the clonal T or B lymphocyte population. In 18% of B lymphomas, however, a cross-lineage rearrangement of TcR beta genes, and in 20% of the T cell lymphomas a clonal IgH gene rearrangement was detected. After exclusion of centrocytic, large cell anaplastic lymphomas (LCAL) of B-type, and T/AILD lymphomas which are overrepresented in our study, only 10% of the remaining 147 T and B cell lymphomas had aberrant rearrangements. TcR rearrangements other than those of the beta chain genes were extremely rare in B cell lymphomas, as were Ig kappa rearrangements in T lymphomas. Only two T/AILD lymphomas had IgH and Ig kappa rearrangement in addition to their clonal T cell receptor gene rearrangements. Both samples likely contain a clonal B

  13. The analysis of ALK gene rearrangement by fluorescence in situ hybridization in non-small cell lung cancer patients

    PubMed Central

    Krawczyk, Paweł Adam; Ramlau, Rodryg Adam; Szumiło, Justyna; Kozielski, Jerzy; Kalinka-Warzocha, Ewa; Bryl, Maciej; Knopik-Dąbrowicz, Alina; Spychalski, Łukasz; Szczęsna, Aleksandra; Rydzik, Ewelina; Milanowski, Janusz

    2013-01-01

    Introduction ALK gene rearrangement is observed in a small subset (3–7%) of non-small cell lung cancer (NSCLC) patients. The efficacy of crizotinib was shown in lung cancer patients harbouring ALK rearrangement. Nowadays, the analysis of ALK gene rearrangement is added to molecular examination of predictive factors. Aim of the study The frequency of ALK gene rearrangement as well as the type of its irregularity was analysed by fluorescence in situ hybridisation (FISH) in tissue samples from NSCLC patients. Material and methods The ALK gene rearrangement was analysed in 71 samples including 53 histological and 18 cytological samples. The analysis could be performed in 56 cases (78.87%), significantly more frequently in histological than in cytological materials. The encountered problem with ALK rearrangement diagnosis resulted from the scarcity of tumour cells in cytological samples, high background fluorescence noises and fragmentation of cell nuclei. Results The normal ALK copy number without gene rearrangement was observed in 26 (36.62%) patients ALK gene polysomy without gene rearrangement was observed in 25 (35.21%) samples while in 3 (4.23%) samples ALK gene amplification was found. ALK gene rearrangement was observed in 2 (2.82%) samples from males, while in the first case the rearrangement coexisted with ALK amplification. In the second case, signet-ring tumour cells were found during histopathological examination and this patient was successfully treated with crizotinib with partial remission lasting 16 months. Conclusions FISH is a useful technique for ALK gene rearrangement analysis which allows us to specify the type of gene irregularities. ALK gene examination could be performed in histological as well as cytological (cellblocks) samples, but obtaining a reliable result in cytological samples depends on the cellularity of examined materials. PMID:24592134

  14. Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing | Office of Cancer Genomics

    Cancer.gov

    Although exome sequencing data are generated primarily to detect single-nucleotide variants and indels, they can also be used to identify a subset of genomic rearrangements whose breakpoints are located in or near exons. Using >4,600 tumor and normal pairs across 15 cancer types, we identified over 9,000 high confidence somatic rearrangements, including a large number of gene fusions.

  15. New insights on human T cell development by quantitative T cell receptor gene rearrangement studies and gene expression profiling

    PubMed Central

    Dik, Willem A.; Pike-Overzet, Karin; Weerkamp, Floor; de Ridder, Dick; de Haas, Edwin F.E.; Baert, Miranda R.M.; van der Spek, Peter; Koster, Esther E.L.; Reinders, Marcel J.T.; van Dongen, Jacques J.M.; Langerak, Anton W.; Staal, Frank J.T.

    2005-01-01

    To gain more insight into initiation and regulation of T cell receptor (TCR) gene rearrangement during human T cell development, we analyzed TCR gene rearrangements by quantitative PCR analysis in nine consecutive T cell developmental stages, including CD34+ lin− cord blood cells as a reference. The same stages were used for gene expression profiling using DNA microarrays. We show that TCR loci rearrange in a highly ordered way (TCRD-TCRG-TCRB-TCRA) and that the initiating Dδ2-Dδ3 rearrangement occurs at the most immature CD34+CD38−CD1a− stage. TCRB rearrangement starts at the CD34+CD38+CD1a− stage and complete in-frame TCRB rearrangements were first detected in the immature single positive stage. TCRB rearrangement data together with the PTCRA (pTα) expression pattern show that human TCRβ-selection occurs at the CD34+CD38+CD1a+ stage. By combining the TCR rearrangement data with gene expression data, we identified candidate factors for the initiation/regulation of TCR recombination. Our data demonstrate that a number of key events occur earlier than assumed previously; therefore, human T cell development is much more similar to murine T cell development than reported before. PMID:15928199

  16. Oxidative allylic rearrangement of cycloalkenols: Formal total synthesis of enantiomerically pure trisporic acid B

    PubMed Central

    Dubberke, Silke; Abbas, Muhammad

    2011-01-01

    Summary Enantiomerically highly enriched unsaturated β-ketoesters bearing a quaternary stereocenter can be utilized as building blocks for the synthesis of natural occurring terpenes, i. a., trisporic acid and its derivatives. An advanced building block has been synthesized in a short reaction sequence, which involves an oxidative allylic rearrangement initiated by pyridinium dichromate (PDC) as the key step. PMID:21512603

  17. Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers.

    PubMed

    Paratala, Bhavna S; Dolfi, Sonia C; Khiabanian, Hossein; Rodriguez-Rodriguez, Lorna; Ganesan, Shridar; Hirshfield, Kim M

    2016-01-01

    Significant advances in our knowledge of cancer genomes are rapidly changing the way we think about tumor biology and the heterogeneity of cancer. Recent successes in genomically-guided treatment approaches accompanied by more sophisticated sequencing techniques have paved the way for deeper investigation into the landscape of genomic rearrangements in cancer. While considerable research on solid tumors has focused on point mutations that directly alter the coding sequence of key genes, far less is known about the role of somatic rearrangements. With many recurring alterations observed across tumor types, there is an obvious need for functional characterization of these genomic biomarkers in order to understand their relevance to tumor biology, therapy, and prognosis. As personalized therapy approaches are turning toward genomic alterations for answers, these biomarkers will become increasingly relevant to the practice of precision medicine. This review discusses the emerging role of genomic rearrangements in breast cancer, with a particular focus on fusion genes. In addition, it raises several key questions on the therapeutic value of such rearrangements and provides a framework to evaluate their significance as predictive and prognostic biomarkers. PMID:26917980

  18. Identification of archetype and rearranged forms of BK virus in leukocytes from healthy individuals.

    PubMed

    Chatterjee, M; Weyandt, T B; Frisque, R J

    2000-03-01

    BK virus (BKV) establishes a persistent, asymptomatic infection in more than 80% of the human population, and in immunocompromised individuals BKV causes acute urinary tract infections. Two forms of BKV, archetype and rearranged, have been recovered previously from urine samples. The rearranged form is believed to have emerged from the archetype form by the deletion and duplication of sequences within the transcriptional control region (TCR). We have PCR-amplified unique rearranged forms of the BKV TCR from peripheral blood leukocytes (PBLs) of healthy donors. By employing archetype-specific PCR primers, the archetype BKV TCR was also detected in PBLs. These findings are consistent with the hypotheses that PBLs transport BKV to different sites within the body and play a role in the TCR rearrangement process. BKV sequences were detected in 21 of 38 BKV-seropositive and 1 of 2 BKV-seronegative individuals. Because of recent suggestions that SV40 may circulate in the human population, the donors' sera were also examined for the presence of specific anti-SV40 antibodies. A high antibody titer to SV40 was detected in only 1 of the 40 donor specimens. This study is the first to characterize multiple BKV TCR variants in PBLs from healthy people and to correlate PCR and serological methods used to detect BKV infections.

  19. Electrophilic iodine(I) compounds induced semipinacol rearrangement via C-X bond cleavage.

    PubMed

    Tsuji, Nobuya; Kobayashi, Yusuke; Takemoto, Yoshiji

    2014-11-18

    Neutral electrophilic iodine(I) species proved to be efficient reagents for C-X bond cleavage of various cyclic and acyclic α-silyloxyhalides, and the induced desilylative semipinacol rearrangement provided the corresponding ketones in good yields. The reaction is operationally simple, and proceeds under mild conditions with good functional group compatibility. Mechanistic investigations, including computational studies, were also performed.

  20. Novel Cryptic Rearrangements in Adult B-Cell Precursor Acute Lymphoblastic Leukemia Involving the MLL Gene

    PubMed Central

    Othman, Moneeb A. K.; Grygalewicz, Beata; Pienkowska-Grela, Barbara; Rincic, Martina; Rittscher, Katharina; Melo, Joana B.; Carreira, Isabel M.; Meyer, Britta; Marzena, Watek

    2015-01-01

    MLL (mixed-lineage-leukemia) gene rearrangements are typical for acute leukemia and are associated with an aggressive course of disease, with a worse outcome than comparable case, and thus require intensified treatment. Here we describe a 69-year-old female with adult B cell precursor acute lymphoblastic leukemia (BCP-ALL) with hyperleukocytosis and immunophenotype CD10- and CD19+ with cryptic MLL rearrangements. G-banding at the time of diagnosis showed a normal karyotype: 46,XX. Molecular cytogenetics using multitude multicolor banding (mMCB) revealed a complex rearrangement of the two copies of chromosome 11. However, a locus-specific probe additionally identified that the MLL gene at 11q23.3 was disrupted, and that the 5′ region was inserted into the chromosomal sub-band 4q21; thus the aberration involved three chromosomes and five break events. Unfortunately, the patient died six months after the initial diagnosis from serious infections and severe complications. Overall, the present findings confirm that, by far not all MLL aberrations are seen by routine chromosome banding techniques and that fluorescence in situ hybridization (FISH) should be regarded as standard tool to access MLL rearrangements in patients with BCP-ALL. PMID:25699572

  1. TALEN-engineered AR gene rearrangements reveal endocrine uncoupling of androgen receptor in prostate cancer.

    PubMed

    Nyquist, Michael D; Li, Yingming; Hwang, Tae Hyun; Manlove, Luke S; Vessella, Robert L; Silverstein, Kevin A T; Voytas, Daniel F; Dehm, Scott M

    2013-10-22

    Androgen receptor (AR) target genes direct development and survival of the prostate epithelial lineage, including prostate cancer (PCa). Thus, endocrine therapies that inhibit the AR ligand-binding domain (LBD) are effective in treating PCa. AR transcriptional reactivation is central to resistance, as evidenced by the efficacy of AR retargeting in castration-resistant PCa (CRPC) with next-generation endocrine therapies abiraterone and enzalutamide. However, resistance to abiraterone and enzalutamide limits this efficacy in most men, and PCa remains the second-leading cause of male cancer deaths. Here we show that AR gene rearrangements in CRPC tissues underlie a completely androgen-independent, yet AR-dependent, resistance mechanism. We discovered intragenic AR gene rearrangements in CRPC tissues, which we modeled using transcription activator-like effector nuclease (TALEN)-mediated genome engineering. This modeling revealed that these AR gene rearrangements blocked full-length AR synthesis, but promoted expression of truncated AR variant proteins lacking the AR ligand-binding domain. Furthermore, these AR variant proteins maintained the constitutive activity of the AR transcriptional program and a CRPC growth phenotype independent of full-length AR or androgens. These findings demonstrate that AR gene rearrangements are a unique resistance mechanism by which AR transcriptional activity can be uncoupled from endocrine regulation in CRPC.

  2. A Girl with Pervasive Developmental Disorder and Complex Chromosome Rearrangement Involving 8p and 10p

    ERIC Educational Resources Information Center

    Zwaigenbaum, L; Sonnenberg, L. K.; Heshka, T.; Eastwood, S.; Xu, J.

    2005-01-01

    We report a 4-year-old girl with a "de novo", apparently balanced complex chromosome rearrangement. She initially presented for assessment of velopharyngeal insufficiency due to hypernasal speech. She has distinctive facial features (long face, broad nasal bridge, and protuberant ears with simplified helices), bifid uvula, strabismus, and joint…

  3. Oxidative rearrangement of cyclic tertiary allylic alcohols with IBX in DMSO.

    PubMed

    Shibuya, Masatoshi; Ito, Shinichiro; Takahashi, Michiyasu; Iwabuchi, Yoshiharu

    2004-11-11

    A practical and environmentally friendly method for oxidative rearrangement of five- and six-membered cyclic tertiary allylic alcohols to beta-disubstituted alpha,beta-unsaturated ketones by the IBX/DMSO reagent system is described. Several conventional protecting groups (e.g., Ac, MOM, and TBDPS) are compatible under the reaction conditions prescribed.

  4. Evidence for a gene involved in multiple and diverse rearrangements in the Drosophila genus.

    PubMed

    Puerma, Eva; Orengo, Dorcas J; Aguadé, Montserrat

    2014-11-01

    In Drosophila, chromosomes have been extensively reorganized during evolution, with most rearrangements affecting the gene order in chromosomal elements but not their gene content. The level of reorganization and the evidence for breakpoint reuse vary both between and within elements. The subito gene stands out as a gene involved in multiple rearrangements both because of its active single-gene transposition and because it is the nearest gene to diverse rearrangements breakpoints. Indeed, subito has undergone three single-gene transpositions and it is the nearest gene to the breakpoints of other single-gene transpositions and of two chromosomal inversions. Given that subito is involved in meiosis and therefore active in the female germ line, the high number of nearby fixed breakages might be related among others to the presumed high accessibility of the subito region to the machinery associated with double-strand breaks repair. A second important contributor would be the reduced and simple regulatory region of subito, which would imply that a fraction of the rearrangements originating from subito nearby breakages would have not affected either its pattern or timing of expression and would have, thus, not resulted in reduced fitness.

  5. Enantioselective total synthesis of (+)-Lingzhiol via tandem semipinacol rearrangement/Friedel-Crafts type cyclization.

    PubMed

    Chen, Dong; Xu, Wen-Dan; Liu, Hao-Miao; Li, Ming-Ming; Yan, Yong-Min; Li, Xiao-Nian; Li, Yan; Cheng, Yong-Xian; Qin, Hong-Bo

    2016-06-30

    Enantioselective total synthesis of (+)-Lingzhiol has been achieved. It is the first example of in tandem semipinacol rearrangement reactions, the migrated aryl group further reacting with the carbonyl oxonium electrophile to furnish a polycyclic skeleton. Our synthesis involves 13 steps and proceeds in 6% overall yield. PMID:27321202

  6. Total synthesis of (-)-dihydrosporothriolide utilizing an indium-mediated Reformatsky-Claisen rearrangement.

    PubMed

    Ishihara, Jun; Tsuru, Hiroaki; Hatakeyama, Susumi

    2014-06-20

    The asymmetric synthesis of (-)-dihydrosporothriolide (1), a biologically active bis-γ-butyrolactone, is described, that proceeds through a D-proline-catalyzed asymmetric aminooxylation, indium-mediated Reformatsky-Claisen rearrangement of an α,α-dibromoacetate derivative, and diastereoselective dihydroxylation. The route requires no protective group manipulation and allows the concise seven-step synthesis of 1 from n-octanal.

  7. Gold(I)-Catalyzed Dearomative Rautenstrauch Rearrangement: Enantioselective Access to Cyclopenta[b]indoles

    PubMed Central

    Zi, Weiwei; Wu, Hongmiao; Toste, F. Dean

    2016-01-01

    A highly enantioselective dearomative Rautenstrauch rearrangement catalyzed by cationic (S)-DTBM-Segphosgold(I) is reported. This reaction provides a straightforward method to prepare enantioenriched cyclopenta[b]indoles. These studies show vast difference in enantioselectivity in the reactions of propargyl acetates and propargyl acetals in the chiral ligand-controlled Rautenstrauch reaction. PMID:25710515

  8. The Ireland-Claisen rearrangement strategy towards the synthesis of the schizophrenia drug, (+)-asenapine.

    PubMed

    Anugu, Raghunath Reddy; Mainkar, Prathama S; Sridhar, Balasubramanian; Chandrasekhar, Srivari

    2016-01-28

    (±)-Asenapine, sold in the market as Saphris/Sycrest for the treatment of bipolar disorders, is synthesized in an optically pure form involving an Ireland-Claisen rearrangement as the key step. This approach allows access to all diastereomers. PMID:26659332

  9. Novel Cryptic Rearrangements in Adult B-Cell Precursor Acute Lymphoblastic Leukemia Involving the MLL Gene.

    PubMed

    Othman, Moneeb A K; Grygalewicz, Beata; Pienkowska-Grela, Barbara; Rincic, Martina; Rittscher, Katharina; Melo, Joana B; Carreira, Isabel M; Meyer, Britta; Marzena, Watek; Liehr, Thomas

    2015-05-01

    MLL (mixed-lineage-leukemia) gene rearrangements are typical for acute leukemia and are associated with an aggressive course of disease, with a worse outcome than comparable case, and thus require intensified treatment. Here we describe a 69-year-old female with adult B cell precursor acute lymphoblastic leukemia (BCP-ALL) with hyperleukocytosis and immunophenotype CD10- and CD19+ with cryptic MLL rearrangements. G-banding at the time of diagnosis showed a normal karyotype: 46,XX. Molecular cytogenetics using multitude multicolor banding (mMCB) revealed a complex rearrangement of the two copies of chromosome 11. However, a locus-specific probe additionally identified that the MLL gene at 11q23.3 was disrupted, and that the 5' region was inserted into the chromosomal sub-band 4q21; thus the aberration involved three chromosomes and five break events. Unfortunately, the patient died six months after the initial diagnosis from serious infections and severe complications. Overall, the present findings confirm that, by far not all MLL aberrations are seen by routine chromosome banding techniques and that fluorescence in situ hybridization (FISH) should be regarded as standard tool to access MLL rearrangements in patients with BCP-ALL. PMID:25699572

  10. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology.

    PubMed

    Blasco, Rafael B; Karaca, Elif; Ambrogio, Chiara; Cheong, Taek-Chin; Karayol, Emre; Minero, Valerio G; Voena, Claudia; Chiarle, Roberto

    2014-11-20

    Generation of genetically engineered mouse models (GEMMs) for chromosomal translocations in the endogenous loci by a knockin strategy is lengthy and costly. The CRISPR/Cas9 system provides an innovative and flexible approach for genome engineering of genomic loci in vitro and in vivo. Here, we report the use of the CRISPR/Cas9 system for engineering a specific chromosomal translocation in adult mice in vivo. We designed CRISPR/Cas9 lentiviral vectors to induce cleavage of the murine endogenous Eml4 and Alk loci in order to generate the Eml4-Alk gene rearrangement recurrently found in non-small-cell lung cancers (NSCLCs). Intratracheal or intrapulmonary inoculation of lentiviruses induced Eml4-Alk gene rearrangement in lung cells in vivo. Genomic and mRNA sequencing confirmed the genome editing and the production of the Eml4-Alk fusion transcript. All mice developed Eml4-Alk-rearranged lung tumors 2 months after the inoculation, demonstrating that the CRISPR/Cas9 system is a feasible and simple method for the generation of chromosomal rearrangements in vivo.

  11. Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers

    PubMed Central

    Paratala, Bhavna S.; Dolfi, Sonia C.; Khiabanian, Hossein; Rodriguez-Rodriguez, Lorna; Ganesan, Shridar; Hirshfield, Kim M.

    2016-01-01

    Significant advances in our knowledge of cancer genomes are rapidly changing the way we think about tumor biology and the heterogeneity of cancer. Recent successes in genomically-guided treatment approaches accompanied by more sophisticated sequencing techniques have paved the way for deeper investigation into the landscape of genomic rearrangements in cancer. While considerable research on solid tumors has focused on point mutations that directly alter the coding sequence of key genes, far less is known about the role of somatic rearrangements. With many recurring alterations observed across tumor types, there is an obvious need for functional characterization of these genomic biomarkers in order to understand their relevance to tumor biology, therapy, and prognosis. As personalized therapy approaches are turning toward genomic alterations for answers, these biomarkers will become increasingly relevant to the practice of precision medicine. This review discusses the emerging role of genomic rearrangements in breast cancer, with a particular focus on fusion genes. In addition, it raises several key questions on the therapeutic value of such rearrangements and provides a framework to evaluate their significance as predictive and prognostic biomarkers. PMID:26917980

  12. Sulfinyl-mediated stereoselective Overman rearrangements and Diels-Alder cycloadditions.

    PubMed

    Fernández de la Pradilla, Roberto; Colomer, Ignacio; Viso, Alma

    2012-06-15

    The Overman rearrangement of allylic sulfinyl trichloroacetimidates affords sulfinyl trichloroacetamides with high stereoselectivity and excellent yields. Bis-allylic substrates lead to amido 2-sulfinyl butadiene derivatives in excellent yields, with total chemo- and diastereoselectivity. The Diels-Alder cycloaddition of related dienes is controlled by the sulfoxide moiety.

  13. Bromine radical-mediated sequential radical rearrangement and addition reaction of alkylidenecyclopropanes.

    PubMed

    Kippo, Takashi; Hamaoka, Kanako; Ryu, Ilhyong

    2013-01-16

    Bromine radical-mediated cyclopropylcarbinyl-homoallyl rearrangement of alkylidenecyclopropanes was effectively accomplished by C-C bond formation with allylic bromides, which led to the syntheses of 2-bromo-1,6-dienes. A three-component coupling reaction comprising alkylidenecyclopropanes, allylic bromides, and carbon monoxide also proceeded well to give 2-bromo-1,7-dien-5-ones in good yield.

  14. Long-term rearrangements of hippocampal mossy fiber terminal connectivity in the adult regulated by experience.

    PubMed

    Galimberti, Ivan; Gogolla, Nadine; Alberi, Stefano; Santos, Alexandre Ferrao; Muller, Dominique; Caroni, Pico

    2006-06-01

    We investigated rearrangements of connectivity between hippocampal mossy fibers and CA3 pyramidal neurons. We found that mossy fibers establish 10-15 local terminal arborization complexes (LMT-Cs) in CA3, which exhibit major differences in size and divergence in adult mice. LMT-Cs exhibited two types of long-term rearrangements in connectivity in the adult: progressive expansion of LMT-C subsets along individual dendrites throughout life, and pronounced increases in LMT-C complexities in response to an enriched environment. In organotypic slice cultures, subsets of LMT-Cs also rearranged extensively and grew over weeks and months, altering the strength of preexisting connectivity, and establishing or dismantling connections with pyramidal neurons. Differences in LMT-C plasticity reflected properties of individual LMT-Cs, not mossy fibers. LMT-C maintenance and growth were regulated by spiking activity, mGluR2-sensitive transmitter release from LMTs, and PKC. Thus, subsets of terminal arborization complexes by mossy fibers rearrange their local connectivities in response to experience and age throughout life.

  15. Epoxide ring-opening and Meinwald rearrangement reactions of epoxides catalyzed by mesoporous aluminosilicates.

    PubMed

    Robinson, Mathew W C; Davies, A Matthew; Buckle, Richard; Mabbett, Ian; Taylor, Stuart H; Graham, Andrew E

    2009-06-21

    Mesoporous aluminosilicates efficiently catalyze the ring-opening of epoxides to produce beta-alkoxyalcohols in high yields under extremely mild reaction conditions. These materials also catalyze the corresponding Meinwald rearrangement in non-nucleophilic solvents to give aldehydes which can be trapped in situ to provide the corresponding acetals in an efficient tandem process.

  16. Non-coding RNAs mediate the rearrangements of genomic DNA in ciliates.

    PubMed

    Feng, Xuezhu; Guang, Shouhong

    2013-10-01

    Most eukaryotes employ a variety of mechanisms to defend the integrity of their genome by recognizing and silencing parasitic mobile nucleic acids. However, recent studies have shown that genomic DNA undergoes extensive rearrangements, including DNA elimination, fragmentation, and unscrambling, during the sexual reproduction of ciliated protozoa. Non-coding RNAs have been identified to program and regulate genome rearrangement events. In Paramecium and Tetrahymena, scan RNAs (scnRNAs) are produced from micronuclei and transported to vegetative macronuclei, in which scnRNA elicits the elimination of cognate genomic DNA. In contrast, Piwi-interacting RNAs (piRNAs) in Oxytricha enable the retention of genomic DNA that exhibits sequence complementarity in macronuclei. An RNA interference (RNAi)-like mechanism has been found to direct these genomic rearrangements. Furthermore, in Oxytricha, maternal RNA templates can guide the unscrambling process of genomic DNA. The non-coding RNA-directed genome rearrangements may have profound evolutionary implications, for example, eliciting the multigenerational inheritance of acquired adaptive traits. PMID:24008384

  17. Molecular Mechanisms and Diagnosis of Chromosome 22q11.2 Rearrangements

    ERIC Educational Resources Information Center

    Emanuel, Beverly S.

    2008-01-01

    Several recurrent, constitutional genomic disorders are present on chromosome 22q. These include the translocations and deletions associated with DiGeorge and velocardiofacial syndrome and the translocations that give rise to the recurrent t(11;22) supernumerary der(22) syndrome (Emanuel syndrome). The rearrangement breakpoints on 22q cluster…

  18. Complex polycyclic scaffolds by metathesis rearrangement of Himbert arene/allene cycloadducts.

    PubMed

    Lam, Jonathan K; Schmidt, Yvonne; Vanderwal, Christopher D

    2012-11-01

    The intramolecular arene/allene cycloaddition first described 30 years ago by Himbert and Henn permits rapid access to strained polycyclic compounds. Alkene metathesis processes cleanly rearrange appropriately substituted cycloadducts into complex, functional-group-rich polycyclic lactams of potential utility for natural product synthesis and medicinal chemistry.

  19. Iridium-Catalyzed Dynamic Kinetic Isomerization: Expedient Synthesis of Carbohydrates from Achmatowicz Rearrangement Products.

    PubMed

    Wang, Hao-Yuan; Yang, Ka; Bennett, Scott R; Guo, Sheng-rong; Tang, Weiping

    2015-07-20

    A highly stereoselective dynamic kinetic isomerization of Achmatowicz rearrangement products was discovered. This new internal redox isomerization provided ready access to key intermediates for the enantio- and diastereoselective synthesis of a series of naturally occurring sugars. The nature of the de novo synthesis also enables the preparation of both enantiomers.

  20. ROS1 rearrangements in lung adenocarcinoma: prognostic impact, therapeutic options and genetic variability

    PubMed Central

    Teixido, Cristina; Michels, Sebastian; Morales-Espinosa, Daniela; Viteri, Santiago; Hartmann, Wolfgang; Merkelbach-Bruse, Sabine; Fischer, Rieke; Schildhaus, Hans-Ulrich; Fassunke, Jana; Sebastian, Martin; Serke, Monika; Kaminsky, Britta; Randerath, Winfried; Gerigk, Ulrich; Ko, Yon-Dschun; Krüger, Stefan; Schnell, Roland; Rothe, Achim; Kropf-Sanchen, Cornelia; Heukamp, Lukas; Rosell, Rafael

    2015-01-01

    Background While recent data show that crizotinib is highly effective in patients with ROS1 rearrangement, few data is available about the prognostic impact, the predictive value for different treatments, and the genetic heterogeneity of ROS1-positive patients. Patients and Methods 1137 patients with adenocarcinoma of the lung were analyzed regarding their ROS1 status. In positive cases, next-generation sequencing (NGS) was performed. Clinical characteristics, treatments and outcome of these patients were assessed. Overall survival (OS) was compared with genetically defined subgroups of ROS1-negative patients. Results 19 patients of 1035 evaluable (1.8%) had ROS1-rearrangement. The median OS has not been reached. Stage IV patients with ROS1-rearrangement had the best OS of all subgroups (36.7 months, p < 0.001). 9 of 14 (64.2%) patients had at least one response to chemotherapy. Estimated mean OS for patients receiving chemotherapy and crizotinib was 5.3 years. Ten patients with ROS1-rearrangement (52.6%) harbored additional aberrations. Conclusion ROS1-rearangement is not only a predictive marker for response to crizotinib, but also seems to be the one of the best prognostic molecular markers in NSCLC reported so far. In stage IV patients, response to chemotherapy was remarkable high and overall survival was significantly better compared to other subgroups including EGFR-mutated and ALK-fusion-positive NSCLC. PMID:25868855

  1. Frequent rearrangements of rRNA-encoding chromosomes in Giardia lamblia.

    PubMed Central

    Le Blancq, S M; Korman, S H; Van der Ploeg, L H

    1991-01-01

    The ribosomal RNA (rRNA) genes in Giardia lamblia are present as short tandem arrays of a 5.6 Kb repeat unit on at least six telomeres. Four of these telomeres have the same overall organisation comprising a domain ranging in size from 25 to 300 Kb, delineated chromosome internally by a conserved island of restriction enzyme sites. Cloned lines of G. lamblia derived from the WB strain contain polymorphic subsets of chromosomes encoding rRNA genes. However, changes in the size of the rRNA telomere domains of these polymorphic chromosomes alone cannot account for the total size changes in the chromosomes. The rearrangement events are very frequent: 60% of subcloned lines had discrete rearranged karyotypes that differed from each other, suggesting either an estimated rearrangement rate that may be as high as 3% per division or a cloning-induced rearrangement event. The extreme plasticity of the genome has obvious implications for the maintenance of a functional genome and the control of gene expression in Giardia. Images PMID:1679533

  2. Isolation of Betulin and Rearrangement to Allobetulin: A Biomimetic Natural Product Synthesis

    ERIC Educational Resources Information Center

    Green, Brian; Bentley, Michael D.; Chung, Bong Y.; Lynch, Nicholas G.; Jensen, Bruce L.

    2007-01-01

    The triterpenes are a diverse class of widely distributed natural products derived from squalene. Various cyclization and subsequent rearrangement reactions produce many complex structural types. These compounds frequently display a wide divergence of biological properties. For example the pentacyclic triterpene, betulin, is isolated from white…

  3. Competition between Different Variegating Rearrangements for Limited Heterochromatic Factors in Drosophila Melanogaster

    PubMed Central

    Lloyd, V. K.; Sinclair, D. A.; Grigliatti, T. A.

    1997-01-01

    Position effect variegation (PEV) results from the juxtaposition of a euchromatic gene to heterochromatin. In its new position the gene is inactivated in some cells and not in others. This mosaic expression is consistent with variability in the spread of heterochromatin from cell to cell. As many components of heterochromatin are likely to be produced in limited amounts, the spread of heterochromatin into a normally euchromatic region should be accompanied by a concomitant loss or redistribution of the protein components from other heterochromatic regions. We have shown that this is the case by simultaneously monitoring variegation of a euchromatic and a heterochromatic gene associated with a single chromosome rearrangement. Secondly, if several heterochromatic regions of the genome share limited components of heterochromatin, then some variegating rearrangements should compete for these components. We have examined this hypothesis by testing flies with combinations of two or more different variegating rearrangements. Of the nine combinations of pairs of variegating rearrangements we studied, seven showed nonreciprocal interactions. These results imply that many components of heterochromatin are both shared and present in limited amounts and that they can transfer between chromosomal sites. Consequently, even nonvariegation portions of the genome will be disrupted by re-allocation of heterochromatic proteins associated with PEV. These results have implications for models of PEV. PMID:9093849

  4. Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants.

    PubMed

    Sandhu, Ajay Pal S; Abdelnoor, Ricardo V; Mackenzie, Sally A

    2007-02-01

    Stability of the mitochondrial genome is controlled by nuclear loci. In plants, nuclear genes suppress mitochondrial DNA rearrangements during development. One nuclear gene involved in this process is Msh1. Msh1 appears to be involved in the suppression of illegitimate recombination in plant mitochondria. To test the hypothesis that Msh1 disruption leads to the type of mitochondrial DNA rearrangements associated with naturally occurring cytoplasmic male sterility in plants, a transgenic approach for RNAi was used to modulate expression of Msh1 in tobacco and tomato. In both species, these experiments resulted in reproducible mitochondrial DNA rearrangements and a condition of male (pollen) sterility. The male sterility was, in each case, heritable, associated with normal female fertility, and apparently maternal in its inheritance. Segregation of the transgene did not reverse the male sterile phenotype, producing stable, nontransgenic male sterility. The reproducible transgenic induction of mitochondrial rearrangements in plants is unprecedented, providing a means to develop novel cytoplasmic male sterile lines for release as non-GMO or transgenic materials.

  5. Analyzing the CDR3 Repertoire with respect to TCR—Beta Chain V-D-J and V-J Rearrangements in Peripheral T Cells using HTS

    PubMed Central

    Ma, Long; Yang, Liwen; Bin Shi; He, Xiaoyan; Peng, Aihua; Li, Yuehong; Zhang, Teng; Sun, Suhong; Ma, Rui; Yao, Xinsheng

    2016-01-01

    V-D-J rearrangement of the TCR—beta chain follows the 12/23 rule and the beyond 12/23 restriction. Currently, the proportion and characteristics of TCR—beta chain V—J rearrangement is unclear. We used high-throughput sequencing to compare and analyze TCR—beta chain V-J rearrangement and V-D-J rearrangement in the CDR3 repertoires of T cells from the PBMCs of six volunteers and six BALB/c mice. The results showed that the percentage of V-J rearrangement of the volunteers was approximately 0.7%, whereas that of the mice was 2.2%. The clonality of mice V-J rearrangement was significantly reduced compared with the V-D-J rearrangement, whereas the clonality of human V-J rearrangement was slightly reduced compared with the V-D-J rearrangement. V-J rearrangement in CDR3 involved the significant usage of N, S, F and L, whereas V-D-J rearrangement in CDR3 involved the significant usage of R and G. The levels of V deletion and J deletion in V-J rearrangement were significantly reduced compared with V-D-J rearrangement. TRBD and TRBJ usage in V-J rearrangement differed from that of V-D-J rearrangement, including dominant usage of TRBV and TRBJ and their pairing. Taken together, these results provide new ideas and technology for studies of V-D-J rearrangement and V-J rearrangement in the CDR3 repertoire. PMID:27404392

  6. Analyzing the CDR3 Repertoire with respect to TCR-Beta Chain V-D-J and V-J Rearrangements in Peripheral T Cells using HTS.

    PubMed

    Ma, Long; Yang, Liwen; Bin Shi; He, Xiaoyan; Peng, Aihua; Li, Yuehong; Zhang, Teng; Sun, Suhong; Ma, Rui; Yao, Xinsheng

    2016-07-12

    V-D-J rearrangement of the TCR-beta chain follows the 12/23 rule and the beyond 12/23 restriction. Currently, the proportion and characteristics of TCR-beta chain V-J rearrangement is unclear. We used high-throughput sequencing to compare and analyze TCR-beta chain V-J rearrangement and V-D-J rearrangement in the CDR3 repertoires of T cells from the PBMCs of six volunteers and six BALB/c mice. The results showed that the percentage of V-J rearrangement of the volunteers was approximately 0.7%, whereas that of the mice was 2.2%. The clonality of mice V-J rearrangement was significantly reduced compared with the V-D-J rearrangement, whereas the clonality of human V-J rearrangement was slightly reduced compared with the V-D-J rearrangement. V-J rearrangement in CDR3 involved the significant usage of N, S, F and L, whereas V-D-J rearrangement in CDR3 involved the significant usage of R and G. The levels of V deletion and J deletion in V-J rearrangement were significantly reduced compared with V-D-J rearrangement. TRBD and TRBJ usage in V-J rearrangement differed from that of V-D-J rearrangement, including dominant usage of TRBV and TRBJ and their pairing. Taken together, these results provide new ideas and technology for studies of V-D-J rearrangement and V-J rearrangement in the CDR3 repertoire.

  7. Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

    PubMed Central

    Dunn, Barbara; Paulish, Terry; Stanbery, Alison; Piotrowski, Jeff; Koniges, Gregory; Kroll, Evgueny; Louis, Edward J.; Liti, Gianni; Sherlock, Gavin; Rosenzweig, Frank

    2013-01-01

    Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ∼1-kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5′ portion derives from S. cerevisiae and the 3′ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in

  8. Spatially rearranged object parts can facilitate perception of intact whole objects

    PubMed Central

    Cacciamani, Laura; Ayars, Alisabeth A.; Peterson, Mary A.

    2014-01-01

    The familiarity of an object depends on the spatial arrangement of its parts; when the parts are spatially rearranged, they form a novel, unrecognizable configuration. Yet the same collection of parts comprises both the familiar and novel configuration. Is it possible that the collection of familiar parts activates a representation of the intact familiar configuration even when they are spatially rearranged? We presented novel configurations as primes before test displays that assayed effects on figure-ground perception from memories of intact familiar objects. In our test displays, two equal-area regions shared a central border; one region depicted a portion of a familiar object. Previous research with such displays has shown that participants are more likely to perceive the region depicting a familiar object as the figure and the abutting region as its ground when the familiar object is depicted in its upright orientation rather than upside down. The novel primes comprised either the same or a different collection of parts as the familiar object in the test display (part-rearranged and control primes, respectively). We found that participants were more likely to perceive the familiar region as figure in upright vs. inverted displays following part-rearranged primes but not control primes. Thus, priming with a novel configuration comprising the same familiar parts as the upcoming figure-ground display facilitated orientation-dependent effects of object memories on figure assignment. Similar results were obtained when the spatially rearranged collection of parts was suggested on the groundside of the prime's border, suggesting that familiar parts in novel configurations access the representation of their corresponding intact whole object before figure assignment. These data demonstrate that familiar parts access memories of familiar objects even when they are arranged in a novel configuration. PMID:24904495

  9. Separate elements control DJ and VDJ rearrangement in a transgenic recombination substrate.

    PubMed Central

    Ferrier, P; Krippl, B; Blackwell, T K; Furley, A J; Suh, H; Winoto, A; Cook, W D; Hood, L; Costantini, F; Alt, F W

    1990-01-01

    We describe transgenic mice that carry an antigen receptor gene minilocus comprised of germline T cell receptor (TCR) beta variable gene elements (V, D and J) linked to an immunoglobulin (Ig) C mu constant region gene with or without a DNA segment containing the Ig heavy chain transcriptional enhancer (E mu). Transgenic constructs lacking the E mu-containing segment did not undergo detectable rearrangement in any tissue of six independent transgenic lines. In contrast, transgenic constructs containing this DNA segment underwent rearrangement at high frequency in lymphoid tissues, but not other tissues, of four independent lines. Analyses of purified B and T cells, as well as B and T cell lines, from transgenic animals demonstrated that the E mu-containing segment within the construct allowed partial TCR gene assembly (D to J) in both B and T cells. However, complete TCR gene rearrangement within the construct (V to DJ) occurred only in T cells. Therefore, we have demonstrated elements that can control two separate aspects of TCR beta VDJ rearrangement within this construct. One lies within the E mu-containing DNA segment and represents a dominant, cis-acting element that initiates lymphoid cell-specific D beta to J beta rearrangement; various considerations suggest this activity may be related to that of the E mu element. The second element provides T cell-specific control of complete (V beta to DJ beta) variable region gene assembly; it correlates in activity with expression of the unrearranged V beta segment. Images Fig. 1. Fig. 2. Fig. 4. Fig. 5. PMID:2153073

  10. Mechanism of the Fischer indole synthesis. Quantum-chemical interpretation of the rearrangement of substituted cyclohexanone arylhydrazones to tetrahydrocarbazoles

    SciTech Connect

    Vysotskii, Yu.B.; Przheval'skii, N.M.; Zemskii, B.P.; Grandberg, I.I.; Kostromina, L.Yu.

    1987-01-01

    Calculations of a number of model structures within the scheme of the Fischer indole synthesis were made on the basis of a bonding variant of perturbation theory in the self-consistent-field (SCF) MO LCAO method. A quantum-chemical interpretation of the effect of substituents on the course of the thermal process is given. The kinetics of the thermal and acid-catalyzed indolization of substituted cyclohexanone arylhydrazones to tetrahydrocarbazoles were studied by spectrophotometry. It was shown that the experimental data are in satisfactory agreement with the calculated values. It was concluded that a concerted mechanism (a (3,3)-sigma-tropic shift) for the step involving the formation of a carbon-carbon bond in the Fischer reaction is preferred.

  11. Targeted Next-Generation Sequencing at Copy-Number Breakpoints for Personalized Analysis of Rearranged Ends in Solid Tumors

    PubMed Central

    Lee, Kwang Man; Hwang, Hai-Li; Park, Seong-Yeol; Sorn, Sungbin; Chandra, Vishal; Kim, Kwang Gi; Yoon, Woong-Bae; Bae, Joon Seol; Shin, Hyoung Doo; Shin, Jong-Yeon; Seoh, Ju-Young; Kim, Jong-Il; Hong, Kyeong-Man

    2014-01-01

    Background The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS) for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs), which are abundant in solid tumors, can be utilized for identification of rearranged ends. Method As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB) in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP) microarray method entailing CNB-region refinement by competitor DNA. Result Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9%) were identified, and two polymerase chain reaction (PCR)-amplifiable rearrangements were obtained in six cases (66.7%). And significantly, TNGS-CNB, with its high positive identification rate (82.6%) of PCR-amplifiable rearrangements at candidate sites (19/23), just from filtering of aligned sequences, requires little effort for validation. Conclusion Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring. PMID:24937453

  12. Promiscuous Rearrangements of the MYC Locus Hijack Enhancers and Super-Enhancers to Dysregulate MYC Expression in Multiple Myeloma

    PubMed Central

    Affer, Maurizio; Chesi, Marta; Chen, Wei-Dong G.; Keats, Jonathan J.; Demchenko, Yulia N.; Roschke, Anna V.; Van Wier, Scott; Fonseca, Rafael

    2014-01-01

    MYC locus rearrangements – often complex combinations of translocations, insertions, deletions, and inversions - in multiple myeloma (MM) were thought to be a late progression event, which often did not involve immunoglobulin genes. Yet germinal center activation of MYC expression has been reported to cause progression to MM in an MGUS prone mouse strain. Although previously detected in 16% of MM, we find MYC rearrangements in nearly 50% of MM, including smoldering MM, and they are heterogeneous in some cases. Rearrangements reposition MYC near a limited number of genes associated with conventional enhancers, but mostly with super-enhancers (e.g., IGH, IGL, IGK, NSMCE2, TXNDC5, FAM46C, FOXO3, IGJ, PRDM1). MYC rearrangements are associated with a significant increase of MYC expression that is monoallelic, but MM tumors lacking a rearrangement have bi-allelic MYC expression at significantly higher levels than in MGUS. We also show that germinal center activation of MYC does not cause MM in a mouse strain that rarely develops spontaneous MGUS. It appears that increased MYC expression at the MGUS/MM transition usually is bi-allelic, but sometimes can be mono-allelic if there is a MYC rearrangement. Our data suggests that MYC rearrangements, regardless of when they occur during MM pathogenesis, provide one event that contributes to tumor autonomy. PMID:24518206

  13. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.

    PubMed

    Weng, Mao-Lun; Blazier, John C; Govindu, Madhumita; Jansen, Robert K

    2014-03-01

    Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed. PMID:24336877

  14. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements.

    PubMed

    D'Angelo, Carla S; Gajecka, Marzena; Kim, Chong A; Gentles, Andrew J; Glotzbach, Caron D; Shaffer, Lisa G; Koiffmann, Célia P

    2009-06-01

    The mechanisms involved in the formation of subtelomeric rearrangements are now beginning to be elucidated. Breakpoint sequencing analysis of 1p36 rearrangements has made important contributions to this line of inquiry. Despite the unique architecture of segmental duplications inherent to human subtelomeres, no common mechanism has been identified thus far and different nonexclusive recombination-repair mechanisms seem to predominate. In order to gain further insights into the mechanisms of chromosome breakage, repair, and stabilization mediating subtelomeric rearrangements in humans, we investigated the constitutional rearrangements of 1p36. Cloning of the breakpoint junctions in a complex rearrangement and three non-reciprocal translocations revealed similarities at the junctions, such as microhomology of up to three nucleotides, along with no significant sequence identity in close proximity to the breakpoint regions. All the breakpoints appeared to be unique and their occurrence was limited to non-repetitive, unique DNA sequences. Several recombination- or cleavage-associated motifs that may promote non-homologous recombination were observed in close proximity to the junctions. We conclude that NHEJ is likely the mechanism of DNA repair that generates these rearrangements. Additionally, two apparently pure terminal deletions were also investigated, and the refinement of the breakpoint regions identified two distinct genomic intervals ~25-kb apart, each containing a series of 1p36 specific segmental duplications with 90-98% identity. Segmental duplications can serve as substrates for ectopic homologous recombination or stimulate genomic rearrangements.

  15. Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize.

    PubMed

    Zhang, Jianbo; Yu, Chuanhe; Pulletikurti, Vinay; Lamb, Jonathan; Danilova, Tatiana; Weber, David F; Birchler, James; Peterson, Thomas

    2009-03-15

    Barbara McClintock reported that the Ac/Ds transposable element system can generate major chromosomal rearrangements (MCRs), but the underlying mechanism has not been determined. Here, we identified a series of chromosome rearrangements derived from maize lines containing pairs of closely linked Ac transposable element termini. Molecular and cytogenetic analyses showed that the MCRs in these lines comprised 17 reciprocal translocations and two large inversions. The breakpoints of all 19 MCRs are delineated by Ac termini and characteristic 8-base-pair target site duplications, indicating that the MCRs were generated by precise transposition reactions involving the Ac termini of two closely linked elements. This alternative transposition mechanism may have contributed to chromosome evolution and may also occur during V(D)J recombination resulting in oncogenic translocations. PMID:19299561

  16. Dynamic force measurement of rearrangements in a 2D network of droplets

    NASA Astrophysics Data System (ADS)

    Barkley, Solomon; Backholm, Matilda; Dalnoki-Veress, Kari

    2015-03-01

    The interaction between two liquid droplets in an immiscible liquid is well understood. However, the emulsions relevant to biological and industrial processes involve high concentrations of these droplets, and multi-body effects cannot be ignored. As droplets rearrange in response to a disturbance, the importance of individual pair-wise interactions between droplets changes with the geometry of neighbours. Here we report on an experimental setup consisting of a two- dimensional network of monodisperse droplets stabilized with a surfactant. The system is studied with micropipette deflection, which permits direct measurement of forces along with simultaneous imaging of the droplet network. One micropipette is used to apply a tensile or compressive force to the droplet cluster, while a second pipette acts as a force-transducing cantilever, deflecting in response to rearrangements of the droplets.

  17. The transcriptomic landscape and directed chemical interrogation of MLL-rearranged acute myeloid leukemias.

    PubMed

    Lavallée, Vincent-Philippe; Baccelli, Irène; Krosl, Jana; Wilhelm, Brian; Barabé, Frédéric; Gendron, Patrick; Boucher, Geneviève; Lemieux, Sébastien; Marinier, Anne; Meloche, Sylvain; Hébert, Josée; Sauvageau, Guy

    2015-09-01

    Using next-generation sequencing of primary acute myeloid leukemia (AML) specimens, we identified to our knowledge the first unifying genetic network common to the two subgroups of KMT2A (MLL)-rearranged leukemia, namely having MLL fusions or partial tandem duplications. Within this network, we experimentally confirmed upregulation of the gene with the most subtype-specific increase in expression, LOC100289656, and identified cryptic MLL fusions, including a new MLL-ENAH fusion. We also identified a subset of MLL fusion specimens carrying mutations in SPI1 accompanied by inactivation of its transcriptional network, as well as frequent RAS pathway mutations, which sensitized the leukemias to synthetic lethal interactions between MEK and receptor tyrosine kinase inhibitors. This transcriptomics-based characterization and chemical interrogation of human MLL-rearranged AML was a valuable approach for identifying complementary features that define this disease.

  18. Limited heterogeneity of rearranged T-cell receptor Vα transcripts in brains of multiple sclerosis patients

    NASA Astrophysics Data System (ADS)

    Oksenberg, Jorge R.; Stuart, Simon; Begovich, Ann B.; Bell, Robert B.; Erlich, Henry A.; Steinman, Lawrence; Bernard, Claude C. A.

    1990-05-01

    THE identification of activated ? cells in the brain of individuals with multiple sclerosis (MS) indicates that these cells are critical in the pathogenesis of this disease. In an attempt to elucidate the nature of the lymphocytic infiltration, we used the polymerase chain reaction to amplify T-cell antigen receptor (TCR) Vα sequences from transcripts derived from MS brain lesions. In each of three MS brains, only two to four rearranged TCR Vα transcripts were detected. No Vα transcripts could be found in control brains. Sequence analysis of transcripts encoded by the Vα 12.1 region showed rearrangements to a limited number of Jα region segments. These results imply that TCR Vα gene expression in MS brain lesions is restricted.

  19. Bioactive rearranged and halogenated semisynthetic derivatives of the marine natural product sarcophine.

    PubMed

    Sawant, Swapnali S; Sylvester, Paul W; Avery, Mitchell A; Desai, Prashant; Youssef, Diaa T A; El Sayed, Khalid A

    2004-12-01

    Cembranoids are natural diterpenes with 14-membered macrocyclic rings. The simplest natural cembranoid, (+)-cembrene, was isolated from pine oleoresin. Sarcophytols A and B are known cembranoids that inhibit tumor promotion. Sarcophine is a related cembranoid isolated from the Red Sea soft coral Sarcophyton glaucum. Sarcophine and its bioconversion products and semisynthetic derivatives are reported to possess cancer chemopreventive activity. Oxymercuration-demercuration of sarcophine using Hg(OAc)2 and NaBH4 afforded four new rearranged and hydroxylated products. Bromination of sarcophine with N-bromosuccinimide (NBS) furnished two new brominated and rearranged products. Reaction with iodine gave the known iso-sarcophinone and (+)-sarcophytoxin B. Structure elucidation was based on a combination of transition state modeling, molecular dynamics, mechanistic considerations, and 2D NMR data. The antiproliferative activity of the new products is also reported.

  20. Nascent Peptide Side-chains Induce Rearrangements in Distinct Locations of the Ribosomal Tunnel

    PubMed Central

    Lu, Jianli; Hua, Zhengmao; Kobertz, William R.; Deutsch, Carol

    2011-01-01

    Although we have numerous structures of ribosomes, none disclose side-chain rearrangements of the nascent peptide during chain elongation. This study reports for the first time that rearrangement of the peptide and/or tunnel occurs in distinct regions of the tunnel and is directed by the unique primary sequence of each nascent peptide. In the tunnel mid-region, the accessibility of an introduced cysteine to a series of novel hydrophilic maleimide reagents increases with increasing volume of the adjacent chain residue, a sensitivity not manifest at the constriction and exit port. This surprising result reveals molecular movements not yet resolvable from structural studies. These findings map solvent accessible volumes along the tunnel and provide novel insights critical to our understanding of allosteric communication within the ribosomal tunnel, translational arrest, chaperone interaction, folding, and rates of elongation. PMID:21663746

  1. Coupled-rearrangement-channels calculation of the three-body system under the absorbing boundary condition

    NASA Astrophysics Data System (ADS)

    Iwasaki, M.; Otani, R.; Ito, M.; Kamimura, M.

    2016-06-01

    We formulate the absorbing boundary condition (ABC) in the coupled rearrangement-channels variational method (CRCVM) for the three-body problem. The absorbing potential is introduced in the system of the identical three-bosons, on which the boson symmetry is explicitly imposed by considering the rearrangement channels. The resonance parameters and the strength of the monopole breakup are calculated by the CRCVM + ABC method, and the results are compared with the complex scaling method (CSM). We have found that the results of the ABC method are consistent with the CSM results. The effect of the boson symmetry, which is often neglected in the calculation of the triple α reactions, is also discussed.

  2. The Plastid Genome of Mycoheterotrophic Monocot Petrosavia stellaris Exhibits Both Gene Losses and Multiple Rearrangements

    PubMed Central

    Logacheva, Maria D.; Schelkunov, Mikhail I.; Nuraliev, Maxim S.; Samigullin, Tagir H.; Penin, Aleksey A.

    2014-01-01

    Plastid genomes of nonphotosynthetic plants represent a perfect model for studying evolution under relaxed selection pressure. However, the information on their sequences is still limited. We sequenced and assembled plastid genome of Petrosavia stellaris, a rare mycoheterotrophic monocot plant. After orchids, Petrosavia represents only the second family of nonphotosynthetic monocots to have its plastid genome examined. Several unusual features were found: retention of the ATP synthase genes and rbcL gene; extensive gene order rearrangement despite a relative lack of repeat sequences; an unusually short inverted repeat region that excludes most of the rDNA operon; and a lack of evidence for accelerated sequence evolution. Plastome of photosynthetic relative of P. stellaris, Japonolirion osense, has standard gene order and does not have the predisposition to inversions. Thus, the rearrangements in the P. stellaris plastome are the most likely associated with transition to heterotrophic way of life. PMID:24398375

  3. Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize.

    PubMed

    Zhang, Jianbo; Yu, Chuanhe; Pulletikurti, Vinay; Lamb, Jonathan; Danilova, Tatiana; Weber, David F; Birchler, James; Peterson, Thomas

    2009-03-15

    Barbara McClintock reported that the Ac/Ds transposable element system can generate major chromosomal rearrangements (MCRs), but the underlying mechanism has not been determined. Here, we identified a series of chromosome rearrangements derived from maize lines containing pairs of closely linked Ac transposable element termini. Molecular and cytogenetic analyses showed that the MCRs in these lines comprised 17 reciprocal translocations and two large inversions. The breakpoints of all 19 MCRs are delineated by Ac termini and characteristic 8-base-pair target site duplications, indicating that the MCRs were generated by precise transposition reactions involving the Ac termini of two closely linked elements. This alternative transposition mechanism may have contributed to chromosome evolution and may also occur during V(D)J recombination resulting in oncogenic translocations.

  4. Activation of lipid peroxidation as a mechanism of plant cell rearrangements under microgravity

    NASA Astrophysics Data System (ADS)

    Baranenko, V. V.

    Activation of the lipid peroxidation (LP) is a universal process perturbating cell membranes under different unfavourable conditions. It is suggested that the LP can be one of the important mechanisms of plant cell rearrangements under altered gravity as well. The purpose of this investigation is to study the LP intensity in pea leaves and chloroplasts under 7- and 14-day clinorotation. The intensification of the LP under both terms of clinorotation particularly under more prolonged, is detected. The adaptive increase in the unsaturated fatty acid content under 7-day clinorotation and their minor decrease under 14-day clinorotation are revealed. The lowering of electron transport rate in both photosystems, particularly in PSI, is established. The results confirm that the LPmay be one of the mechanisms of plant cell rearrangements under microgravity.

  5. T cell receptor rearrangements in a patient with γ-heavy chain disease: A case report

    PubMed Central

    ZHOU, HEBING; CHEN, WENMING; ZHANG, JUAN; ZENG, HUI; JIAN, YUAN; FU, CHENXIAO

    2016-01-01

    Heavy chain diseases (HCDs) are rare B cell lymphoplasma cell proliferative disorders that are characterized by the production of incomplete monoclonal immunoglobulin (Ig) heavy chains without the associated light chains. γ-HCD (IgG subtype) is a rare subtype, with ~150 cases reported in the literature to date; however, to the best of our knowledge, no reports of T cell receptor (TCR) gene rearrangement in γ-HCD exist in the literature. The present study reports the case of an 81-year-old man with γ-heavy chain disease associated with TCR gene rearrangement, identified in lymph node biopsy and bone marrow aspirate specimens. The present case revealed an alternative manifestation of γ-HCD, which may provide additional biological insights into this rare B cell disorder. PMID:27313757

  6. Cyclo-biphenalenyl biradicaloid molecular materials: conformation, rearrangement, magnetism, and thermochromism

    SciTech Connect

    Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent; Tian, Yong-Hui; Kertesz, Prof. Miklos

    2010-01-01

    Cyclo-biphenalenyl biradicaloid molecular materials with chair- and boat-conformations are studied by restricted and broken-symmetry DFT using the M06 family of meta-GGA functionals. The global minima of these molecular materials are magnetically silent due to the sigma-bond connecting the two phenalenyls, while the sigma-bond may undergo low-barrier sigmatropic rearrangements via pi-pi bonded paramagnetic intermediates. The validation of theory is performed for the chair-conformation by comparing the sigma-bonded structures and the rearrangement barriers with experimental data. The boat-conformation is then studied using the validated functional. The electronic spectra of both chair- and boat-conformations are calculated and their applications in thermochromism are discussed.

  7. Enantioselective Catalysis of the Aza-Cope Rearrangement by a Chiral Supramolecular Assembly

    SciTech Connect

    Brown, Casey J.; Bergman, Robert G.; Raymond, Kenneth N.

    2009-07-29

    The chiral supramolecular catalyst Ga{sub 4}L{sub 6} [L = 1,5-bis(2,3-dihydroxybenzoylamino)naphthalene] is a molecular tetrahedron that catalyzes the 3-aza-Cope rearrangement of allyl enammonium cations. This catalysis is accomplished by preorganizing the substrate in a reactive conformation within the host. This work demonstrates that through the use of enantiopure assembly, its chiral cavity is capable of catalyzing the 3-aza-Cope rearrangement enantioselectively, with yields of 21-74% and enantiomeric excesses from 6 to 64% at 50 C. At lower temperatures, the enantioselectivity improved, reaching 78% ee at 5 C. This is the highest enantioselectivity to date induced by the chiral cavity of a supramolecular assembly.

  8. Specific amplification by PCR of rearranged genomic variable regions of immunoglobulin genes from mouse hybridoma cells.

    PubMed

    Berdoz, J; Monath, T P; Kraehenbuhl, J P

    1995-04-01

    We have designed a novel strategy for the isolation of the rearranged genomic fragments encoding the L-VH-D-JH and L-V kappa/lambda-J kappa/lambda regions of mouse immunoglobulin genes. This strategy is based on the PCR amplification of genomic DNA from mouse hybridomas using multiple specific primers chosen in the 5'-untranslated region and in the intron downstream of the rearranged JH/J kappa/lambda sequences. Variable regions with intact coding sequences, including full-length leader peptides (L) can be obtained without previous DNA sequencing. Our strategy is based on a genomic template that produces fragments that do not need to be adapted for recombinant antibody expression, thus facilitating the generation of chimeric and isotype-switched immunoglobulins.

  9. Aza Cope Rearrangement of Propargyl Enammonium Cations Catalyzed By a Self-Assembled `Nanozyme

    SciTech Connect

    Hastings, Courntey J.; Fiedler, Dorothea; Bergman, Robert G.; Raymond, Kenneth N.

    2008-02-27

    The tetrahedral [Ga{sub 4}L{sub 6}]{sup 12-} assembly (L = N,N-bis(2,3-dihydroxybenzoyl)-1,5-diaminonaphthalene) encapsulates a variety of cations, including propargyl enammonium cations capable of undergoing the aza Cope rearrangement. For propargyl enammonium substrates that are encapsulated in the [Ga{sub 4}L{sub 6}]{sup 12-} assembly, rate accelerations of up to 184 are observed when compared to the background reaction. After rearrangement, the product iminium ion is released into solution and hydrolyzed allowing for catalytic turnover. The activation parameters for the catalyzed and uncatalyzed reaction were determined, revealing that a lowered entropy of activation is responsible for the observed rate enhancements. The catalyzed reaction exhibits saturation kinetics; the rate data obey the Michaelis-Menten model of enzyme kinetics, and competitive inhibition using a non-reactive guest has been demonstrated.

  10. Aniridia-associated cytogenetic rearrangements suggest that a position effect may cause the mutant phenotype.

    PubMed

    Fantes, J; Redeker, B; Breen, M; Boyle, S; Brown, J; Fletcher, J; Jones, S; Bickmore, W; Fukushima, Y; Mannens, M

    1995-03-01

    Current evidence suggests that aniridia (absence of iris) is caused by loss of function of one copy of the PAX6 gene, which maps to 11p13. We present the further characterisation of two aniridia pedigrees in which the disease segregates with chromosomal rearrangements which involve 11p13 but do not disrupt the PAX6 gene. We have isolated three human YAC clones which encompass the PAX6 locus and we have used these to show that in both cases the chromosomal breakpoint is at least 85 kb distal of the 3' end of PAX6. In addition, the open reading frame of PAX6 is apparently free of mutations. We propose that the PAX6 gene on the rearranged chromosome 11 is in an inappropriate chromatin environment for normal expression and therefore that a 'position effect' is the underlying mechanism of disease in these families.

  11. Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

    PubMed Central

    Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A.

    2016-01-01

    Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution. PMID:27363362

  12. Targeting brain metastases in ALK-rearranged non-small-cell lung cancer.

    PubMed

    Zhang, Isabella; Zaorsky, Nicholas G; Palmer, Joshua D; Mehra, Ranee; Lu, Bo

    2015-10-01

    The incidence of brain metastases has increased as a result of improved systemic control and advances in imaging. However, development of novel therapeutics with CNS activity has not advanced at the same rate. Research on molecular markers has revealed many potential targets for antineoplastic agents, and a particularly important aberration is translocation in the ALK gene, identified in non-small-cell lung cancer (NSCLC). ALK inhibitors have shown systemic efficacy against ALK-rearranged NSCLC in many clinical trials, but the effectiveness of crizotinib in CNS disease is limited by poor blood-brain barrier penetration and acquired drug resistance. In this Review, we discuss potential pathways to target ALK-rearranged brain metastases, including next generation ALK inhibitors with greater CNS penetration and mechanisms to overcome resistance. Other important mechanisms to control CNS disease include targeting pathways downstream of ALK phosphorylation, increasing the permeability of the blood-brain barrier, modifying the tumour microenvironment, and adding concurrent radiotherapy.

  13. To bridge or not to bridge: The role of sulfuric acid in the Beckmann rearrangement

    NASA Astrophysics Data System (ADS)

    Lin, Chester R.; Yu, Li-Juan; Li, Shuhua; Karton, Amir

    2016-08-01

    Based on ab initio calculations using the Gaussian-4 method, we propose a new catalytic mechanism for the Beckmann rearrangement in concentrated H2SO4. Our calculations suggest that H2SO4 catalyzes the 1,2-proton-shift step via a cyclic transition structure, in which H2SO4 acts as a proton-transfer bridge. The reaction barrier for this mechanism is lower by 48.1 kJ mol-1 than the barrier for the previously suggested catalytic mechanism, which involves a strained 3-memberd-ring transition structure. According to the previous mechanism the 1,2-proton shift has the highest activation energy, while in the revised mechanism the highest activation energy is obtained for the ensuing rearrangement/dehydration step.

  14. Gene rearrangements in the mitochondrial genome of Cynoglossus bilineatus (Pleuronectiformes: Cynoglossidae).

    PubMed

    Shi, Wei; Li, Dong-He; Kong, Xiao-Yu

    2016-05-01

    Cynoglossus bilineatus (Cynoglossidae, Soleoidei) is characterized by both eyes on the left side of the body and with a rounded snout and a short rostral hook. Here we first report the mitogenome of this tongue sole, which is 16,454 bp in length, and gene rearrangements have been observed. Particularly, the tRNA-Gln gene encoded by the light strand (L-strand) has translocated to the heavy strand (H-strand), along with the tRNA-Ile gene shuffling. In addition, the putative control region has translocated downstream to a position between the ND1 and tRNA-Gln genes, leaving a 26-bp intergenic spacer in its original position. However, the arrangement of the rest genes is identical to that of the typical teleost. This result could contribute to a better understanding the molecular mechanisms of gene rearrangement in fish mitogenome as well as phylogenetic study of Cynoglossidae and Pleuronectiformes.

  15. Hapmnioides A-C, Rearranged Labdane-Type Diterpenoids from the Chinese Liverwort Haplomitrium mnioides.

    PubMed

    Zhou, Jinchuan; Zhang, Jiaozhen; Li, Ruijuan; Liu, Jun; Fan, Peihong; Li, Yi; Ji, Mei; Dong, Yiwen; Yuan, Huiqing; Lou, Hongxiang

    2016-09-01

    Many exceptional labdane-type diterpenoids have been exclusively found in liverworts, which serve as taxonomic molecules or play important ecological roles in interactions among organisms. Three unprecedented labdane-type diterpenoids hapmnioides A (1), B (2), and C (3) formed through cascade rearrangement from the Chinese liverwort Haplomitrium mnioides are reported. Their structures were established by comprehensive spectroscopic analysis coupled with single-crystal X-ray diffraction, and their anti-inflammatory activities were also preliminarily tested. PMID:27513610

  16. Regioselective hypervalent iodine-induced Favorskii rearrangement of 3-oxo-5β-steroids.

    PubMed

    Viviano-Posadas, Alejandro O; Flores-Álamo, Marcos; Iglesias-Arteaga, Martín A

    2016-09-01

    Treatment of 3-oxo-5β-steroids with diacetoxyiodobenzene/KOH triggered a fast and regioselective Favorskii rearrangement that exclusively led to 3β-methoxycarbonyl-5β-4-norsteroids in good yields. The outcome of the reaction indicates that although both Cyclopropanone and Semi-benzylic pathways are possible, in the case of 3-oxo-5β-steroids, only the last participates. Unambiguous characterization of the products was achieved by NMR and X-ray Diffraction studies.

  17. Preparation and Reactivity of Acyclic Chiral Allylzinc Species by a Zinc-Brook Rearrangement.

    PubMed

    Leibeling, Markus; Shurrush, Khriesto A; Werner, Veronika; Perrin, Lionel; Marek, Ilan

    2016-05-10

    The zinc-Brook rearrangement of enantiomerically enriched α-hydroxy allylsilane produces a chiral allylzinc intermediate, which reacts with retention of configuration in the presence of an electrophile. Two remarkable features of this transformation are the stereochemical outcome during the formation of the allylzinc species and the complete stereocontrol in the organized six-membered transition state, which leads to an overall and complete transfer of chirality within the reaction sequence. PMID:27061357

  18. Brook Rearrangement as a Trigger for the Ring Opening of Strained Carbocycles.

    PubMed

    Zhang, Fa-Guang; Eppe, Guillaume; Marek, Ilan

    2016-01-11

    The combined regio- and stereoselective carbometalation of cyclopropenyl amides, followed by the addition of an acyl silane, led to the formation of polysubstituted cyclopropyl derivatives as unique diastereoisomers. Upon warming of the reaction mixture to room temperature, a Brook rearrangement proceeded with inversion of configuration to provide ready access to δ-ketoamides possessing a quaternary carbon center with high enantiomeric ratios through selective C-C bond cleavage of the ring. PMID:26663399

  19. Prospective screening for subtelomeric rearrangements in children with mental retardation of unknown aetiology: the Amsterdam experience

    PubMed Central

    van Karnebeek, C D M; Koevoets, C; Sluijter, S; Bijlsma, E; Smeets, D; Redeker, E; Hennekam, R; Hoovers, J

    2002-01-01

    Objective: The frequency of subtelomeric rearrangements in patients with unexplained mental retardation (MR) is uncertain, as most studies have been retrospective and case retrieval may have been biased towards cases more likely to have a chromosome anomaly. To ascertain the frequency of cytogenetic anomalies, including subtelomeric rearrangements, we prospectively screened a consecutive cohort of cases with unexplained MR in an academic tertiary centre. Methods: Inclusion criteria were: age <18 years at referral, IQ<85, no aetiological diagnosis after complete examination, which included karyotyping with high resolution banding (HRB). Results: In 266 karyotyped children, anomalies were detected in 20 (7.5%, seven numerical, 13 structural); 39 cases were analysed by FISH for specific interstitial microdeletions, and anomalies were found in nine (23%). FISH analyses for subtelomeric microdeletions were performed in 184 children (44% moderate-profound MR, 51% familial MR), and one rearrangement (0.5%) was identified in a non-familial MR female with mild MR (de novo deletion 12q24.33-qter). The number of probable polymorphisms was considerable: 2qter (n=7), Xpter (n=3), and Ypter (n=1). A significantly higher total number of malformations and minor anomalies was present in the cytogenetic anomaly group compared to the group without cytogenetic anomalies. Conclusions: The total frequency of cytogenetic anomalies in this prospective study was high (1:10), but the frequency of subtelomeric rearrangements was low. The most likely explanations are the high quality of HRB cytogenetic studies and the lack of clinical selection bias. Conventional cytogenetic analyses, combined with targeted microdeletion testing, remain the single most effective way of additional investigation in mentally retarded children, also in a tertiary centre. PMID:12161591

  20. Synthesis of the anti-HIV agent (-)-hyperolactone C by using oxonium ylide formation-rearrangement.

    PubMed

    Hodgson, David M; Man, Stanislav

    2011-08-22

    Starting from readily available (S)-styrene oxide an asymmetric synthesis is described of the naturally occurring anti-HIV spirolactone (-)-hyperolactone C, which possesses adjacent fully substituted stereocenters. The key step involves a stereocontrolled Rh(II) -catalysed oxonium ylide formation-[2,3] sigmatropic rearrangement of an α-diazo-β-ketoester bearing allylic ether functionality. From the resulting furanone, an acid-catalysed lactonisation and dehydrogenation gives the natural product. PMID:21766363

  1. Meiotic Recombination Analyses in Pigs Carrying Different Balanced Structural Chromosomal Rearrangements

    PubMed Central

    Mary, Nicolas; Barasc, Harmonie; Ferchaud, Stéphane; Priet, Aurélia; Calgaro, Anne; Loustau-Dudez, Anne-Marie; Bonnet, Nathalie; Yerle, Martine; Ducos, Alain; Pinton, Alain

    2016-01-01

    Correct pairing, synapsis and recombination between homologous chromosomes are essential for normal meiosis. All these events are strongly regulated, and our knowledge of the mechanisms involved in this regulation is increasing rapidly. Chromosomal rearrangements are known to disturb these processes. In the present paper, synapsis and recombination (number and distribution of MLH1 foci) were studied in three boars (Sus scrofa domestica) carrying different chromosomal rearrangements. One (T34he) was heterozygote for the t(3;4)(p1.3;q1.5) reciprocal translocation, one (T34ho) was homozygote for that translocation, while the third (T34Inv) was heterozygote for both the translocation and a pericentric inversion inv(4)(p1.4;q2.3). All three boars were normal for synapsis and sperm production. This particular situation allowed us to rigorously study the impact of rearrangements on recombination. Overall, the rearrangements induced only minor modifications of the number of MLH1 foci (per spermatocyte or per chromosome) and of the length of synaptonemal complexes for chromosomes 3 and 4. The distribution of MLH1 foci in T34he was comparable to that of the controls. Conversely, the distributions of MLH1 foci on chromosome 4 were strongly modified in boar T34Inv (lack of crossover in the heterosynaptic region of the quadrivalent, and crossover displaced to the chromosome extremities), and also in boar T34ho (two recombination peaks on the q-arms compared with one of higher magnitude in the controls). Analyses of boars T34he and T34Inv showed that the interference was propagated through the breakpoints. A different result was obtained for boar T34ho, in which the breakpoints (transition between SSC3 and SSC4 chromatin on the bivalents) seemed to alter the transmission of the interference signal. Our results suggest that the number of crossovers and crossover interference could be regulated by partially different mechanisms. PMID:27124413

  2. Sequential Multicomponent Reactions and a Cu-Mediated Rearrangement: Diastereoselective Synthesis of Tricyclic Ketones.

    PubMed

    Kröger, Denis; Franz, Max; Schmidtmann, Marc; Martens, Jürgen

    2015-12-01

    A novel Cu-mediated rearrangement reaction based on bisamides containing a thiazolidine substructure opens the possibility for diastereoselective synthesis toward a tricyclic annulated and bridged heterocyclic system. The required precursors are easily synthesizable by a two-step synthetic pathway using the concept of sequential multicomponent reactions, i.e. the Asinger and Ugi reactions. Due to this synthesis strategy, a number of unique tricyclic heterocycles, characterized by high diversity, are synthesized in an effective manner. PMID:26571048

  3. Prenatally diagnosed de novo complex chromosome rearrangements: Two new cases and review of the literature

    SciTech Connect

    Ruiz, C.; Grubs, R.E.; Jewett, T.

    1994-09-01

    Complex chromosome rearrangements (CCR) are rare structural rearrangements involving at least three chromosomes with three or more breakpoints. Although there have been numerous reports of individuals with CCR, most have been ascertained through the presence of multiple congenital anomalies, recurrent pregnancy loss, or infertility. Few cases have been ascertained prenatally. We present two new cases of prenatally ascertained CCR. In the first case, an amniocentesis revealed an apparently balanced de novo rearrangement in which chromosomes 5, 6 and 11 were involved in a three-way translocation: 46,XY,t(6;5)(5;11)(q23;p14.3;q15;p13). The pregnancy was unevenful. Recently, at the age of 9 months, a physical and developmental evaluation were normal but, height, weight, and head circumference were below the 5th percentile. In the second case an amniocentesis revealed an unbalanced de novo rearrangement involving separate translocations and an interstitial deletion: 46,XY,del(6)(q25.3q27),t(3;8)(p13;q21.3),t(6;18)(p11.2;q11.2). A meconium plug was present at birth and at 6 months of age surgery for Hirschsprung`s disease was required. Currently, at 10 months of age, the patient has hypotonia and developmental delay. The paucity of information regarding prenatally diagnosed CCR poses a problem in counseling families. Of the four prenatally diagnosed balanced de novo CCR cases, three had abnormal outcomes. In a review of the literature, approximately 70% of the postnatally ascertained balanced de novo CCR cases were associated with congenital anomalies, growth retardation and/or mental retardation. More information regarding the outcome of prenatally ascertained balanced de novo CCR is required for accurate risk assessment.

  4. Metal Free Bi(hetero)aryl Synthesis: A Benzyne Truce–Smiles Rearrangement

    PubMed Central

    Holden, Catherine M.; Sohel, Shariar M. A.

    2016-01-01

    Abstract A new benzyne transformation is described that affords versatile biaryl structures without recourse to transition‐metal catalysis or stoichiometric amounts of organometallic building blocks. Aryl sulfonamides add to benzyne upon fluoride activation, and then undergo an aryl Truce–Smiles rearrangement to afford biaryls with sulfur dioxide extrusion. The reaction proceeds under simple reaction conditions and has excellent scope for the synthesis of sterically hindered atropisomeric biaryl amines. PMID:26762551

  5. Metal Free Bi(hetero)aryl Synthesis: A Benzyne Truce-Smiles Rearrangement.

    PubMed

    Holden, Catherine M; Sohel, Shariar M A; Greaney, Michael F

    2016-02-12

    A new benzyne transformation is described that affords versatile biaryl structures without recourse to transition-metal catalysis or stoichiometric amounts of organometallic building blocks. Aryl sulfonamides add to benzyne upon fluoride activation, and then undergo an aryl Truce-Smiles rearrangement to afford biaryls with sulfur dioxide extrusion. The reaction proceeds under simple reaction conditions and has excellent scope for the synthesis of sterically hindered atropisomeric biaryl amines.

  6. MECP2 duplications in six patients with complex sex chromosome rearrangements

    PubMed Central

    Breman, Amy M; Ramocki, Melissa B; Kang, Sung-Hae L; Williams, Misti; Freedenberg, Debra; Patel, Ankita; Bader, Patricia I; Cheung, Sau Wai

    2011-01-01

    Duplications of the Xq28 chromosome region resulting in functional disomy are associated with a distinct clinical phenotype characterized by infantile hypotonia, severe developmental delay, progressive neurological impairment, absent speech, and proneness to infections. Increased expression of the dosage-sensitive MECP2 gene is considered responsible for the severe neurological impairments observed in affected individuals. Although cytogenetically visible duplications of Xq28 are well documented in the published literature, recent advances using array comparative genomic hybridization (CGH) led to the detection of an increasing number of microduplications spanning MECP2. In rare cases, duplication results from intrachromosomal rearrangement between the X and Y chromosomes. We report six cases with sex chromosome rearrangements involving duplication of MECP2. Cases 1–4 are unbalanced rearrangements between X and Y, resulting in MECP2 duplication. The additional Xq material was translocated to Yp in three cases (cases 1–3), and to the heterochromatic region of Yq12 in one case (case 4). Cases 5 and 6 were identified by array CGH to have a loss in copy number at Xp and a gain in copy number at Xq28 involving the MECP2 gene. In both cases, fluorescent in situ hybridization (FISH) analysis revealed a recombinant X chromosome containing the duplicated material from Xq28 on Xp, resulting from a maternal pericentric inversion. These cases add to a growing number of MECP2 duplications that have been detected by array CGH, while demonstrating the value of confirmatory chromosome and FISH studies for the localization of the duplicated material and the identification of complex rearrangements. PMID:21119712

  7. Structure of a frequently rearranged rRNA-encoding chromosome in Giardia lamblia.

    PubMed Central

    Hou, G; Le Blancq, S M; E, Y; Zhu, H; Lee, M G

    1995-01-01

    It has been shown previously that the rRNA encoding chromosomes in Giardia lamblia undergo frequent rearrangements with an estimated rate of approximately 1% per cell per division (Le Blancq et al., 1992, Nucleic Acids Res., 17, 4539-4545). Following these observations, we searched for highly recombinogenic regions in one of the frequently rearranged rRNA encoding chromosomes, that is chromosome 1, a small, 1.1 Mb chromosome. Chromosome 1 undergoes frequent rearrangements that result in size variation of 5-20%. We analyzed the structure of chromosome 1 in clonal lineages from the WB strain. The two ends of chromosome 1 comprise telomere repeat [TAGGG] arrays joined to a truncated rRNA gene and a sequence referred to as '4e', respectively. Comparison of the structure of four polymorphic versions of chromosome 1, resulting from independent rearrangement events in four cloned lines, located a single polymorphic region to the variable rDNA-telomere domain. Chromosome 1 is organized into two domains: a core region spanning approximately 850 kb that does not exhibit size heterogeneity among different chromosome 1 and a variable region that spans 185-450 kb and includes the telomeric rRNA genes, referred to as the variable rDNA-telomere domain. The core region contains a conserved region, spanning approximately 550 kb adjacent to the telomeric 4e sequence, which is only present in the 4e containing chromosomes and a 300 kb region of repetitive sequences that are also components of other chromosomes as well. Changes in the number of rDNA repeats accounted for some, but not all, of the size variation. Since there are four chromosomes that share the core region of chromosome 1, we suggest that the genome is tetraploid for this chromosome. Images PMID:7667108

  8. Brook Rearrangement as a Trigger for the Ring Opening of Strained Carbocycles.

    PubMed

    Zhang, Fa-Guang; Eppe, Guillaume; Marek, Ilan

    2016-01-11

    The combined regio- and stereoselective carbometalation of cyclopropenyl amides, followed by the addition of an acyl silane, led to the formation of polysubstituted cyclopropyl derivatives as unique diastereoisomers. Upon warming of the reaction mixture to room temperature, a Brook rearrangement proceeded with inversion of configuration to provide ready access to δ-ketoamides possessing a quaternary carbon center with high enantiomeric ratios through selective C-C bond cleavage of the ring.

  9. Preparation and Reactivity of Acyclic Chiral Allylzinc Species by a Zinc-Brook Rearrangement.

    PubMed

    Leibeling, Markus; Shurrush, Khriesto A; Werner, Veronika; Perrin, Lionel; Marek, Ilan

    2016-05-10

    The zinc-Brook rearrangement of enantiomerically enriched α-hydroxy allylsilane produces a chiral allylzinc intermediate, which reacts with retention of configuration in the presence of an electrophile. Two remarkable features of this transformation are the stereochemical outcome during the formation of the allylzinc species and the complete stereocontrol in the organized six-membered transition state, which leads to an overall and complete transfer of chirality within the reaction sequence.

  10. Computational strategies and improvements in the linear algebraic variational approach to rearrangement scattering

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Mladenovic, Mirjana; Zhao, Meishan; Truhlar, Donald G.; Sun, Yan

    1988-01-01

    The computational steps in calculating quantum mechanical reactive scattering amplitudes by the L2 generalized Newton variational principle are discussed with emphasis on computational strategies and recent improvements that make the calculations more efficient. Special emphasis is placed on quadrature techniques, storage management strategies, use of symmetry, and boundary conditions. It is concluded that an efficient implementation of these procedures provides a powerful algorithm for the accurate solution of the Schroedinger equation for rearrangements.

  11. Array-CGH and multipoint FISH to decode complex chromosomal rearrangements

    PubMed Central

    Darai-Ramqvist, Eva; de Ståhl, Teresita Diaz; Sandlund, Agneta; Mantripragada, Kiran; Klein, George; Dumanski, Jan; Imreh, Stefan; Kost-Alimova, Maria

    2006-01-01

    Background Recently, several high-resolution methods of chromosome analysis have been developed. It is important to compare these methods and to select reliable combinations of techniques to analyze complex chromosomal rearrangements in tumours. In this study we have compared array-CGH (comparative genomic hybridization) and multipoint FISH (mpFISH) for their ability to characterize complex rearrangements on human chromosome 3 (chr3) in tumour cell lines. We have used 179 BAC/PAC clones covering chr3 with an approximately 1 Mb resolution to analyze nine carcinoma lines. Chr3 was chosen for analysis, because of its frequent rearrangements in human solid tumours. Results The ploidy of the tumour cell lines ranged from near-diploid to near-pentaploid. Chr3 locus copy number was assessed by interphase and metaphase mpFISH. Totally 53 chr3 fragments were identified having copy numbers from 0 to 14. MpFISH results from the BAC/PAC clones and array-CGH gave mainly corresponding results. Each copy number change on the array profile could be related to a specific chromosome aberration detected by metaphase mpFISH. The analysis of the correlation between real copy number from mpFISH and the average normalized inter-locus fluorescence ratio (ANILFR) value detected by array-CGH demonstrated that copy number is a linear function of parameters that include the variable, ANILFR, and two constants, ploidy and background normalized fluorescence ratio. Conclusion In most cases, the changes in copy number seen on array-CGH profiles reflected cumulative chromosome rearrangements. Most of them stemmed from unbalanced translocations. Although our chr3 BAC/PAC array could identify single copy number changes even in pentaploid cells, mpFISH provided a more accurate analysis in the dissection of complex karyotypes at high ploidy levels. PMID:17196103

  12. Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi.

    PubMed

    Lavoie, Hugo; Hogues, Hervé; Whiteway, Malcolm

    2009-12-01

    Growing evidence suggests that transcriptional regulatory networks in many organisms are highly flexible. Here, we discuss the evolution of transcriptional regulatory networks governing the metabolic machinery of sequenced ascomycetes. In particular, recent work has shown that transcriptional rewiring is common in regulons controlling processes such as production of ribosome components and metabolism of carbohydrates and lipids. We note that dramatic rearrangements of the transcriptional regulatory components of metabolic functions have occurred among ascomycetes species.

  13. 1p/19q codeletion and RET rearrangements in small-cell lung cancer

    PubMed Central

    Lu, Hongyang; Xu, Haimiao; Xie, Fajun; Qin, Jing; Han, Na; Fan, Yun; Mao, Weimin

    2016-01-01

    The prognosis of small-cell lung cancer (SCLC) is poor despite reports suggesting modest improvement in survival. To date, chemotherapy remains the cornerstone treatment for SCLC patients, and many studies have focused on identifying the molecular characteristics of SCLC, which serve as the basis for precision treatments that improve the prognosis of SCLC. For instance, the therapeutic effect of temozolomide, recommended for patients with relapsed SCLC, is linked to 1p/19q codeletion in anaplastic oligodendroglial tumors. A subpopulation of SCLC patients may derive benefit from tyrosine kinase inhibitors targeting RET. In order to identify 1p/19q codeletion and RET rearrangement in SCLC patients, 32 SCLC resected specimens were retrospectively collected between 2008 and 2014 from the Zhejiang Cancer Hospital in People’s Republic of China. Fluorescence in situ hybridization was used to detect 1p/19q codeletion and RET rearrangement in the specimens. A 1p single deletion was detected in eight specimens, 19q single deletion was detected in three specimens, and only three specimens had a 1p/19q codeletion. None of the specimens had a RET rearrangement. The three patients whose specimens had a 1p/19q codeletion were alive after 58, 50, and 30 months of follow-up care. There was a trend toward prolonged overall survival for the patients with codeletion compared to no codeletion, 1p single deletion, 19q single deletion, and without 1p and 19q deletion (P=0.113, 0.168, 0.116, and 0.122, respectively). Our data showed that RET rearrangement may be not an ideal molecular target for SCLC therapies in People’s Republic of China. Instead, 1p/19q codeletion is a promising marker for a good prognosis and treatment with temozolomide in SCLC. PMID:27366094

  14. Provocative pattern of rearrangements of the genes for the gamma and beta chains of the T-cell receptor in human leukemias.

    PubMed Central

    Goorha, R; Bunin, N; Mirro, J; Murphy, S B; Cross, A H; Behm, F G; Quertermous, T; Seidman, J; Kitchingman, G R

    1987-01-01

    To examine the distribution of rearrangements of the gamma- and beta-chain T-cell receptor (TCR) genes in T- and non-T acute lymphoblastic leukemias (ALLs), and potentially to determine which genes rearrange first in ontogeny, we analyzed high molecular weight DNA from 102 patients with acute leukemia. Rearranged gamma- and beta-chain genes were found in all T-cell ALLs (22/22) examined. Overall, 27% (18/66) of B-lineage ALLs had beta-chain gene rearrangements, and 41% (24/58) had gamma-chain gene rearrangements, but the distribution of rearranged genes varied according to the stage of B-cell differentiation. The gamma-chain genes were rearranged in 11% (1/9) of the B-lineage patients negative for the common acute lymphoblastic leukemia antigen (cALLA) and 50% (23/46) of cALLA+ ALL patients, while the beta-chain genes were not rearranged in any of the 7 cALLA- ALL patients examined but were rearranged in 32% (18/56) of the cALLA+ patients. Neither TCR gene was found to be rearranged in acute nonlymphoid leukemia patients (0/12) or in patients with B-cell (surface immunoglobulin-positive) leukemia (0/3). Of the 44 cALLA+ patients in which a direct comparison of gamma- and beta-chain gene rearrangements could be made, 34% had both genes rearranged, 16% had only gamma-chain gene rearrangements, and the remaining 50% had both genes in the germ-line configuration. beta-Chain rearrangements have not been found in the absence of gamma-chain rearrangements, thus supporting a proposed hierarchy of TCR gene rearrangements. A provocative finding was that only a small percentage (11%) of the patients with cALLA- B precursor cell ALLs had rearranged TCR genes, while 50% of the cALLA+ leukemia patients had at least gamma-chain rearrangement, raising a question as to whether indeed cALLA- cells are precursors to cALLA+ cells. Interestingly, 18% (2/11) of the cytoplasmic immunoglobulin (cIg)-positive cALLA+ (pre-B) ALLs involved TCR gene rearrangements, compared to 60% (21/35) of

  15. 1,n-Rearrangement of allylic alcohols promoted by hot water: application to the synthesis of navenone B, a polyene natural product.

    PubMed

    Li, Pei-Fang; Wang, Heng-Lu; Qu, Jin

    2014-05-01

    It was reported for the first time that hot water as a mildly acidic catalyst efficiently promoted 1,n-rearrangement (n = 3, 5, 7, 9) of allylic alcohols. In some cases, the rearrangement reactions joined isolated C-C double or triple bonds to generate conjugated polyene or enyne structure motifs. We used the 1,3-rearrangement reaction of an allylic alcohol in hot water as part of an attractive new strategy for construction of the polyene natural product navenone B by iterative use of a Grignard reaction, a 1,3-rearrangement of the resulting allylic alcohol, and subsequent oxidation of the rearranged product. PMID:24716495

  16. Low-copy repeats at the human VIPR2 gene predispose to recurrent and nonrecurrent rearrangements

    PubMed Central

    Beri, Silvana; Bonaglia, Maria Clara; Giorda, Roberto

    2013-01-01

    Submicroscopic structural variations, including deletions, duplications, inversions and more complex rearrangements, are widespread in normal human genomes. Inverted segmental duplications or highly identical low-copy repeat (LCR) sequences can mediate the formation of inversions and more complex structural rearrangements through non-allelic homologous recombination. In a patient with 7q36 inverted duplication/terminal deletion, we demonstrated the central role of a pair of short inverted LCRs in the vasoactive intestinal peptide receptor gene (VIPR2)-LCRs in generating the rearrangement. We also revealed a relatively common VIPR2-LCR-associated inversion polymorphism disrupting the gene in almost 1% of healthy subjects, and a small number of complex duplications/triplications. In genome-wide studies of several thousand patients, a significant association of rare microduplications with variable size, all involving VIPR2, with schizophrenia was recently described, suggesting that altered vasoactive intestinal peptide signaling is likely implicated in the pathogenesis of schizophrenia. Genetic testing for VIPR2-LCR-associated inversions should be performed on available cohorts of psychiatric patients to evaluate their potential pathogenic role. PMID:23073313

  17. Carbamoyl Radical-Mediated Synthesis and Semipinacol Rearrangement of β-Lactam Diols

    PubMed Central

    Betou, Marie; Male, Louise; Steed, Jonathan W; Grainger, Richard S

    2014-01-01

    In an approach to the biologically important 6-azabicyclo[3.2.1]octane ring system, the scope of the tandem 4-exo-trig carbamoyl radical cyclization—dithiocarbamate group transfer reaction to ring-fused β-lactams is evaluated. β-Lactams fused to five-, six-, and seven-membered rings are prepared in good to excellent yield, and with moderate to complete control at the newly formed dithiocarbamate stereocentre. No cyclization is observed with an additional methyl substituent on the terminus of the double bond. Elimination of the dithiocarbamate group gives α,β- or β,γ-unsaturated lactams depending on both the methodology employed (base-mediated or thermal) and the nature of the carbocycle fused to the β-lactam. Fused β-lactam diols, obtained from catalytic OsO4-mediated dihydroxylation of α,β-unsaturated β-lactams, undergo semipinacol rearrangement via the corresponding cyclic sulfite or phosphorane to give keto-bridged bicyclic amides by exclusive N-acyl group migration. A monocyclic β-lactam diol undergoes Appel reaction at a primary alcohol in preference to semipinacol rearrangement. Preliminary investigations into the chemo- and stereoselective manipulation of the two carbonyl groups present in a representative 7,8-dioxo-6-azabicyclo[3.2.1]octane rearrangement product are also reported. PMID:24711140

  18. Unusual maternal uniparental isodisomic x chromosome mosaicism with asymmetric y chromosomal rearrangement.

    PubMed

    Lee, B Y; Kim, S Y; Park, J Y; Choi, E Y; Kim, D J; Kim, J W; Ryu, H M; Cho, Y H; Park, S Y; Seo, J T

    2014-01-01

    Infertile men with azoospermia commonly have associated microdeletions in the azoospermia factor (AZF) region of the Y chromosome, sex chromosome mosaicism, or sex chromosome rearrangements. In this study, we describe an unusual 46,XX and 45,X mosaicism with a rare Y chromosome rearrangement in a phenotypically normal male patient. The patient's karyotype was 46,XX[50]/45,X[25]/46,X,der(Y)(pter→q11.222::p11.2→pter)[25]. The derivative Y chromosome had a deletion at Yq11.222 and was duplicated at Yp11.2. Two copies of the SRY gene were confirmed by fluorescence in situ hybridization analysis, and complete deletion of the AZFb and AZFc regions was shown by multiplex-PCR for microdeletion analysis. Both X chromosomes of the predominant mosaic cell line (46,XX) were isodisomic and derived from the maternal gamete, as determined by examination of short tandem repeat markers. We postulate that the derivative Y chromosome might have been generated during paternal meiosis or early embryogenesis. Also, we suggest that the very rare mosaicism of isodisomic X chromosomes might be formed during maternal meiosis II or during postzygotic division derived from the 46,X,der(Y)/ 45,X lineage because of the instability of the derivative Y chromosome. To our knowledge, this is the first confirmatory study to verify the origin of a sex chromosome mosaicism with a Y chromosome rearrangement.

  19. Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers

    PubMed Central

    Harris, Faye R.; Kovtun, Irina V.; Smadbeck, James; Multinu, Francesco; Jatoi, Aminah; Kosari, Farhad; Kalli, Kimberly R.; Murphy, Stephen J.; Halling, Geoffrey C.; Johnson, Sarah H.; Liu, Minetta C.; Mariani, Andrea; Vasmatzis, George

    2016-01-01

    Recently, the use of a liquid biopsy has shown promise in monitoring tumor burden. While point mutations have been extensively studied, chromosomal rearrangements have demonstrated greater tumor specificity. Such rearrangements can be identified in the tumor and subsequently detected in the plasma of patients using quantitative PCR (qPCR). In this study we used a whole-genome mate-pair protocol to characterize a landscape of genomic rearrangements in the primary tumors of ten ovarian cancer patients. Individualized tumor-specific primer panels of aberrant chromosomal junctions were identified for each case and detected by qPCR within the cell-free DNA. Selected chromosomal junctions were detected in pre-surgically drawn blood in eight of the ten patients. Of these eight, three demonstrated the continued presence of circulating tumor DNA (ctDNA) post-surgery, consistent with their documented presence of disease, and in five ctDNA was undetectable in the post-surgical blood collection, consistent with their lack of detectable disease. The ctDNA fraction was calculated using a novel algorithm designed for the unique challenges of quantifying ctDNA using qPCR to allow observations of real-time tumor dynamics. In summary, a panel of individualized junctions derived from tumor DNA could be an effective way to monitor cancer patients for relapse and therapeutic efficacy using cfDNA. PMID:27436510

  20. Automation of ALK gene rearrangement testing with fluorescence in situ hybridization (FISH): a feasibility study.

    PubMed

    Zwaenepoel, Karen; Merkle, Dennis; Cabillic, Florian; Berg, Erica; Belaud-Rotureau, Marc-Antoine; Grazioli, Vittorio; Herelle, Olga; Hummel, Michael; Le Calve, Michele; Lenze, Dido; Mende, Stefanie; Pauwels, Patrick; Quilichini, Benoit; Repetti, Elena

    2015-02-01

    In the past several years we have observed a significant increase in our understanding of molecular mechanisms that drive lung cancer. Specifically in the non-small cell lung cancer sub-types, ALK gene rearrangements represent a sub-group of tumors that are targetable by the tyrosine kinase inhibitor Crizotinib, resulting in significant reductions in tumor burden. Phase II and III clinical trials were performed using an ALK break-apart FISH probe kit, making FISH the gold standard for identifying ALK rearrangements in patients. FISH is often considered a labor and cost intensive molecular technique, and in this study we aimed to demonstrate feasibility for automation of ALK FISH testing, to improve laboratory workflow and ease of testing. This involved automation of the pre-treatment steps of the ALK assay using various protocols on the VP 2000 instrument, and facilitating automated scanning of the fluorescent FISH specimens for simplified enumeration on various backend scanning and analysis systems. The results indicated that ALK FISH can be automated. Significantly, both the Ikoniscope and BioView system of automated FISH scanning and analysis systems provided a robust analysis algorithm to define ALK rearrangements. In addition, the BioView system facilitated consultation of difficult cases via the internet.

  1. Analysis of VH gene rearrangement and somatic hypermutation in type 1 autoimmune pancreatitis.

    PubMed

    Okumura, Fumihiro; Sakuma, Hidenori; Nakazawa, Takahiro; Hayashi, Kazuki; Naitoh, Itaru; Miyabe, Katsuyuki; Yoshida, Michihiro; Yamashita, Hiroaki; Ohara, Hirotaka; Inagaki, Hiroshi; Joh, Takashi

    2012-05-01

    Type 1 autoimmune pancreatitis (AIP) is the pancreatic manifestation of systemic fibroinflammatory disease called immunoglobulin G4-associated systemic disease. Although this inflammatory process is considered to be a disease with an autoimmune mechanism, its pathogenesis still remains unclear. To clarify the characteristics of B cells infiltrating the lesion, we analyzed the immunoglobulin heavy chain variable region (VH) gene rearrangement and somatic hypermutation of invasive lymphoid cells in type 1 AIP (n= 3), in comparison with obstructive pancreatitis (n= 3) as a control. DNA was extracted from the affected inflammatory lesions. After PCR amplification of the rearranged VH gene, the clones were subcloned, and recombinant clones were randomly selected and sequenced. More than 60 clones per case were analyzed. Monoclonal VH rearrangement was not detected in any of the cases examined. There was no VH family or VH fragment specific to type 1 AIP and obstructive pancreatitis. However, the rate of unmutated VH fragments in type 1 AIP (17%) was higher than that in obstructive pancreatitis (5.1%) (P= 0.010). Our study suggests that an increased rate of unmutated or less mutated VH genes may be characteristic of type 1 AIP and might play a role in the development of this disease.

  2. Wide Distribution of Mitochondrial Genome Rearrangements in Wild Strains of the Cultivated Basidiomycete Agrocybe aegerita

    PubMed Central

    Barroso, G.; Blesa, S.; Labarere, J.

    1995-01-01

    We used restriction fragment length polymorphisms to examine mitochondrial genome rearrangements in 36 wild strains of the cultivated basidiomycete Agrocybe aegerita, collected from widely distributed locations in Europe. We identified two polymorphic regions within the mitochondrial DNA which varied independently: one carrying the Cox II coding sequence and the other carrying the Cox I, ATP6, and ATP8 coding sequences. Two types of mutations were responsible for the restriction fragment length polymorphisms that we observed and, accordingly, were involved in the A. aegerita mitochondrial genome evolution: (i) point mutations, which resulted in strain-specific mitochondrial markers, and (ii) length mutations due to genome rearrangements, such as deletions, insertions, or duplications. Within each polymorphic region, the length differences defined only two mitochondrial types, suggesting that these length mutations were not randomly generated but resulted from a precise rearrangement mechanism. For each of the two polymorphic regions, the two molecular types were distributed among the 36 strains without obvious correlation with their geographic origin. On the basis of these two polymorphisms, it is possible to define four mitochondrial haplotypes. The four mitochondrial haplotypes could be the result of intermolecular recombination between allelic forms present in the population long enough to reach linkage equilibrium. All of the 36 dikaryotic strains contained only a single mitochondrial type, confirming the previously described mitochondrial sorting out after cytoplasmic mixing in basidiomycetes. PMID:16534984

  3. A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice.

    PubMed

    Yu, Chuanhe; Han, Fangpu; Zhang, Jianbo; Birchler, James; Peterson, Thomas

    2012-11-01

    The maize Activator (Ac)/Dissociation (Ds) transposable element system has been used in a variety of plants for insertional mutagenesis. Ac/Ds elements can also generate genome rearrangements via alternative transposition reactions which involve the termini of closely linked transposons. Here, we introduced a transgene containing reverse-oriented Ac/Ds termini together with an Ac transposase gene into rice (Oryza sativa ssp. japonica cv. Nipponbare). Among the transgenic progeny, we identified and characterized 25 independent genome rearrangements at three different chromosomal loci. The rearrangements include chromosomal deletions and inversions and one translocation. Most of the deletions occurred within the T-DNA region, but two cases showed the loss of 72 kilobase pairs (kb) and 79 kb of rice genomic DNA flanking the transgene. In addition to deletions, we obtained chromosomal inversions ranging in size from less than 10 kb (within the transgene DNA) to over 1 million base pairs (Mb). For 11 inversions, we cloned and sequenced both inversion breakpoints; in all 11 cases, the inversion junctions contained the typical 8 base pairs (bp) Ac/Ds target site duplications, confirming their origin as transposition products. Together, our results indicate that alternative Ac/Ds transposition can be an efficient tool for functional genomics and chromosomal manipulation in rice.

  4. QTAIM study on the degenerate cope rearrangements of 1,5-hexadiene and semibullvalene.

    PubMed

    Brown, Eric C; Bader, Richard F W; Werstiuk, Nick H

    2009-04-01

    Using the homotropylium cation (1) as an archetypal example of a homoaromatic molecule, we carried out a quantum theory of atoms-in-molecules (QTAIM) computational study--at DFT (density functional theory), CCSD (coupled cluster with singles and doubles), and CASSCF (complete active space self-consistent field) levels--on 1 and the degenerate Cope rearrangements of 1,5-hexadiene (2) and semibullvalene (3) including the evaluation of delocalization indexes and a visualization of atomic basins. This study yielded new insights into the factors determining the reaction barriers and the bonding of the ground and transitions states of 2 and 3. Contrary to conclusions reached in earlier studies, we found that the transition state for the degenerate rearrangement of 2 is not aromatic and that the driving force for the very facile Cope rearrangement of semibullvalene is caused by the stabilization of individual atoms as well as electronic delocalization, not by the release of strain in the three-membered ring. PMID:19275139

  5. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting

    PubMed Central

    Nie, W; Wang, J; Su, W; Wang, D; Tanomtong, A; Perelman, P L; Graphodatsky, A S; Yang, F

    2012-01-01

    Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species. PMID:22086079

  6. Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

    PubMed Central

    Beck, Christine R.; Carvalho, Claudia M. B.; Banser, Linda; Gambin, Tomasz; Stubbolo, Danielle; Yuan, Bo; Sperle, Karen; McCahan, Suzanne M.; Henneke, Marco; Seeman, Pavel; Hobson, Grace M.; Lupski, James R.

    2015-01-01

    Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication—inverted triplication—duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals—16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology—or homeology—driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model. PMID:25749076

  7. Nucleotide composition of CO1 sequences in Chelicerata (Arthropoda): detecting new mitogenomic rearrangements.

    PubMed

    Arabi, Juliette; Judson, Mark L I; Deharveng, Louis; Lourenço, Wilson R; Cruaud, Corinne; Hassanin, Alexandre

    2012-02-01

    Here we study the evolution of nucleotide composition in third codon-positions of CO1 sequences of Chelicerata, using a phylogenetic framework, based on 180 taxa and three markers (CO1, 18S, and 28S rRNA; 5,218 nt). The analyses of nucleotide composition were also extended to all CO1 sequences of Chelicerata found in GenBank (1,701 taxa). The results show that most species of Chelicerata have a positive strand bias in CO1, i.e., in favor of C nucleotides, including all Amblypygi, Palpigradi, Ricinulei, Solifugae, Uropygi, and Xiphosura. However, several taxa show a negative strand bias, i.e., in favor of G nucleotides: all Scorpiones, Opisthothelae spiders and several taxa within Acari, Opiliones, Pseudoscorpiones, and Pycnogonida. Several reversals of strand-specific bias can be attributed to either a rearrangement of the control region or an inversion of a fragment containing the CO1 gene. Key taxa for which sequencing of complete mitochondrial genomes will be necessary to determine the origin and nature of mtDNA rearrangements involved in the reversals are identified. Acari, Opiliones, Pseudoscorpiones, and Pycnogonida were found to show a strong variability in nucleotide composition. In addition, both mitochondrial and nuclear genomes have been affected by higher substitution rates in Acari and Pseudoscorpiones. The results therefore indicate that these two orders are more liable to fix mutations of all types, including base substitutions, indels, and genomic rearrangements.

  8. Rearrangement of MICU1 multimers for activation of MCU is solely controlled by cytosolic Ca(2.).

    PubMed

    Waldeck-Weiermair, Markus; Malli, Roland; Parichatikanond, Warisara; Gottschalk, Benjamin; Madreiter-Sokolowski, Corina T; Klec, Christiane; Rost, Rene; Graier, Wolfgang F

    2015-10-22

    Mitochondrial Ca(2+) uptake is a vital process that controls distinct cell and organelle functions. Mitochondrial calcium uptake 1 (MICU1) was identified as key regulator of the mitochondrial Ca(2+) uniporter (MCU) that together with the essential MCU regulator (EMRE) forms the mitochondrial Ca(2+) channel. However, mechanisms by which MICU1 controls MCU/EMRE activity to tune mitochondrial Ca(2+) signals remain ambiguous. Here we established a live-cell FRET approach and demonstrate that elevations of cytosolic Ca(2+) rearranges MICU1 multimers with an EC50 of 4.4 μM, resulting in activation of mitochondrial Ca(2+) uptake. MICU1 rearrangement essentially requires the EF-hand motifs and strictly correlates with the shape of cytosolic Ca(2+) rises. We further show that rearrangements of MICU1 multimers were independent of matrix Ca(2+) concentration, mitochondrial membrane potential, and expression levels of MCU and EMRE. Our experiments provide novel details about how MCU/EMRE is regulated by MICU1 and an original approach to investigate MCU/EMRE activation in intact cells.

  9. Extensive coronavirus-induced membrane rearrangements are not a determinant of pathogenicity

    PubMed Central

    Maier, Helena J.; Neuman, Benjamin W.; Bickerton, Erica; Keep, Sarah M.; Alrashedi, Hasan; Hall, Ross; Britton, Paul

    2016-01-01

    Positive-strand RNA (+RNA) viruses rearrange cellular membranes during replication, possibly in order to concentrate and arrange viral replication machinery for efficient viral RNA synthesis. Our previous work showed that in addition to the conserved coronavirus double membrane vesicles (DMVs), Beau-R, an apathogenic strain of avian Gammacoronavirus infectious bronchitis virus (IBV), induces regions of ER that are zippered together and tethered open-necked double membrane spherules that resemble replication organelles induced by other +RNA viruses. Here we compared structures induced by Beau-R with the pathogenic lab strain M41 to determine whether membrane rearrangements are strain dependent. Interestingly, M41 was found to have a low spherule phenotype. We then compared a panel of pathogenic, mild and attenuated IBV strains in ex vivo tracheal organ culture (TOC). Although the low spherule phenotype of M41 was conserved in TOCs, each of the other tested IBV strains produced DMVs, zippered ER and spherules. Furthermore, there was a significant correlation for the presence of DMVs with spherules, suggesting that these structures are spatially and temporally linked. Our data indicate that virus induced membrane rearrangements are fundamentally linked to the viral replicative machinery. However, coronavirus replicative apparatus clearly has the plasticity to function in different structural contexts. PMID:27255716

  10. Curtailing the hydroxylaminobarbituric acid-hydantoin rearrangement to favor HNO generation.

    PubMed

    Guthrie, Daryl A; Nourian, Saghar; Takahashi, Cyrus G; Toscano, John P

    2015-02-01

    Due to its inherent reactivity, HNO must be generated in situ through the use of donor compounds. One of the primary strategies for the development of new HNO donors has been modifying hydroxylamines with good leaving groups. A recent example of this strategy is the (hydroxylamino)barbituric acid (HABA) class of HNO donors. In this case, however, an undesired intramolecular rearrangement pathway to the corresponding hydantoin derivative competes with HNO formation, particularly in the absence of chemical traps for HNO. This competitive non-HNO-producing pathway has restricted the development of the HABA class to examples with fast HNO release profiles at physiological pH and temperature (t(1/2) < 1 min). Herein, the factors that favor the rearrangement pathway have been examined and two independent strategies that protect against rearrangement to favor HNO generation have been developed. The timecourse and stoichiometry for the in vitro conversion of these compounds to HNO (trapped as a phosphine aza-ylide) and the corresponding barbituric acid (BA) byproduct have been determined by (1)H NMR spectroscopy under physiologically relevant conditions. These results confirm the successful extension of the HABA class of pure HNO donors with half-lives at pH 7.4, 37 °C ranging from 19 to 107 min. PMID:25585151

  11. Palindrome-Mediated Translocations in Humans: A New Mechanistic Model for Gross Chromosomal Rearrangements

    PubMed Central

    Inagaki, Hidehito; Kato, Takema; Tsutsumi, Makiko; Ouchi, Yuya; Ohye, Tamae; Kurahashi, Hiroki

    2016-01-01

    Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure—single-stranded “hairpin” or double-stranded “cruciform”—has been extensively investigated in vitro, the existence of such unusual non-B DNA in vivo remains controversial. Here, we review palindrome-mediated gross chromosomal rearrangements possibly induced by non-B DNA in humans. Recent advances in next-generation sequencing have not yet overcome the difficulty of palindromic sequence analysis. However, a dozen palindromic AT-rich repeat (PATRR) sequences have been identified at the breakpoints of recurrent or non-recurrent chromosomal translocations in humans. The breakages always occur at the center of the palindrome. Analyses of polymorphisms within the palindromes indicate that the symmetry and length of the palindrome affect the frequency of the de novo occurrence of these palindrome-mediated translocations, suggesting the involvement of non-B DNA. Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements. Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined. Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms. PMID:27462347

  12. Pyrolysis of silica-immobilized benzyl phenyl ether: Competing radical rearrangement pathways under restricted diffusion

    SciTech Connect

    Buchanan, A.C. III; Britt, P.F.; Skeen, J.T.; Struss, J.A.; Elam, C.L.

    1998-12-25

    Pyrolysis studies of silica-immobilized benzyl phenyl ether ({approx}PhOCH{sub 2}Ph or {approx}BPE), a model for related ether structures in fuel resources, have been conducted at 275--325 C to examine the impact of restricted mass transport on the pyrolysis mechanism compared with previous studies in fluid phases. Significant rearrangement chemistry is observed for {approx}BPE occurring through two competitive free-radical pathways that are both promoted by the diffusional constraints. One path involves recombination of incipient benzyl and surface-bound phenoxy radicals to form benzylphenol isomers, 10. The second, previously unreported rearrangement path for {approx}BPE involves a 1,2-phenyl shift in an intermediate radical, {approx}PhOCH{center_dot}Ph, leading to formation of benzhydrol (8) and benzophenone (9) as principal products. The rearrangement products 8--10 typically account for ca. 50% of the pyrolysis products. However, the path selectivity is a sensitive function of {approx}BPE surface coverage and the presence of spacer molecules that either facilitate or hinder hydrogen atom transfer steps on the surface.

  13. Analysis of rearranged immunoglobulin genes indicating a process of clonal evolution in chronic lymphocytic leukaemia.

    PubMed

    Hakim, I; Rechavi, G; Brok-Simoni, F; Grossman, Z; Amariglio, N; Mandel, M; Ramot, B; Ben-Bassat, I; Katzir, N

    1993-07-01

    Chronic lymphocytic leukaemia (CLL) is known to be a stable monoclonal neoplasm. In contrast to early studies demonstrating no more than two hybridizing immunoglobulin heavy chain bands corresponding to the two expected alleles, we have demonstrated an unexpected multiband pattern when the HindIII-digested DNA samples from 38 CLL patients were analysed by Southern blot hybridization using JH and C mu gene probes. In order to characterize the genetic basis for the multiband pattern, we molecularly cloned the immunoglobulin heavy chain genes of one of the patients whose leukaemic DNA sample demonstrated three hybridizing JH bands and a loss of the germline band. The cloned rearranged immunoglobulin genes could be divided, based on the restriction mapping and the hybridization with the various probes, into two basic patterns representing two alleles. In one of the cloned rearranged immunoglobulin genes a secondary rearrangement occurred that resulted in the addition of 300 base-pair long sequence into the switch region, and the creation of a HindIII restriction site. The results of the study suggest that clonal evolution occurs in some CLL, and that many of these neoplasms are indeed oligoclonal due to the accumulation of secondary genetic changes.

  14. Clonal rearrangements of immunoglobulin genes and progression to B cell lymphoma in cutaneous lymphoid hyperplasia.

    PubMed

    Wood, G S; Ngan, B Y; Tung, R; Hoffman, T E; Abel, E A; Hoppe, R T; Warnke, R A; Cleary, M L; Sklar, J

    1989-07-01

    Cutaneous lymphoid hyperplasia (CLH) is a disorder characterized by the development of one or more skin lesions containing dense lymphoid infiltrates that exhibit the histopathologic features of a benign, reactive process. Nevertheless, some cases have been associated with the subsequent development of clinically overt lymphomas. This suggests that monoclonal populations may exist in some cases of CLH and that these cases may represent a subset more likely to evolve into lymphoma. To determine if such a subset of CLH can be distinguished, Southern blot analysis of DNA was used to study the immunogenotypic features of lesions from 14 patients with clinical, histopathologic, and immunopathologic findings characteristic of CLH. Five cases exhibited detectable clonal rearrangements of immunoglobulin genes. Furthermore, one of these five cases evolved into overt diffuse large cell lymphoma of B cell lineage during a 2-year follow-up of recurrent disease at the original cutaneous site. The immunoglobulin gene rearrangements of this lymphoma were identical to those of the prior CLH lesion. There was no evidence of detectable t(14;18) chromosomal translocations or clonal rearrangements of the beta gene of the T cell receptor in any case. It was concluded that CLH can be divided into two subsets based on the presence or absence of a clonal B cell population, and that overt lymphoma can arise from the former subset and contain the same B cell clone identified in the pre-existent CLH lesion.

  15. Molecular characterization of a balanced rearrangement of chromosome 12 in two siblings with Noonan syndrome.

    PubMed

    Yatsenko, Svetlana A; del Valle Torrado, Maria; Fernandes, Priscilla H; Wiszniewska, Joanna; Gallego, Marta; Herrera, Jorge; Bacino, Carlos A

    2009-12-01

    The etiology of Noonan syndrome (NS) has been greatly elucidated with the discovery of the disease causative genes PTPN11, KRAS, SOS1, and RAF1, all involved in the RAS/MAPK-signaling cascade. Given that overall mutations are identified in about 70% of patients, identification of other NS associated genes remains a high priority to fully understand the etiopathogenesis of the condition. We report two affected siblings with an apparently balanced rearrangement of chromosome 12 ins(12)(q12p11.2p12.3) which segregates with the Noonan phenotype. The rearrangement was inherited from the phenotypically normal mother who had mosaicism for the derivative chromosome 12. There were no mutations of PTPN11, KRAS, SOS1, or RAF1 genes detected in the probands. Using fluorescence in situ hybridization analysis we identified the three breakpoints involved at 12p12.3, 12p11.2, and 12q12. By microarray analysis, there were no gains or losses near the breakpoints. Neither, the PTPN11 or KRAS region on chromosome 12 was involved in the rearrangement. We hypothesize that other NS candidate gene(s) may be located in the breakpoint regions of chromosome 12 causing the Noonan phenotype in both of these children.

  16. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting.

    PubMed

    Nie, W; Wang, J; Su, W; Wang, D; Tanomtong, A; Perelman, P L; Graphodatsky, A S; Yang, F

    2012-01-01

    Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species.

  17. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.

    PubMed

    Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A

    2016-04-01

    Three-dimensional (3D) organization of genomes affects critical cellular processes such as transcription, replication, and deoxyribo nucleic acid (DNA) repair. While previous studies have investigated the natural role, the 3D organization plays in limiting a possible set of genomic rearrangements following DNA repair, the influence of specific organizational principles on this process, particularly over longer evolutionary time scales, remains relatively unexplored. In budding yeast S.cerevisiae, chromosomes are organized into a Rabl-like configuration, with clustered centromeres and telomeres tethered to the nuclear periphery. Hi-C data for S.cerevisiae show that a consequence of this Rabl-like organization is that regions equally distant from centromeres are more frequently in contact with each other, between arms of both the same and different chromosomes. Here, we detect rearrangement events in Saccharomyces species using an automatic approach, and observe increased rearrangement frequency between regions with higher contact frequencies. Together, our results underscore how specific principles of 3D chromosomal organization can influence evolutionary events.

  18. Uniform detection of immunoglobulin-gene rearrangement in benign lymphoepithelial lesions.

    PubMed

    Fishleder, A; Tubbs, R; Hesse, B; Levine, H

    1987-04-30

    The term "benign lymphoepithelial lesion" is used to describe the salivary-gland lymphocytic infiltration and epithelial changes typically found in association with Sjögren's syndrome. We used Southern blot hybridization techniques to examine the immunoglobulin genes in salivary-gland tissue derived from eight patients with benign lymphoepithelial lesions. Three of these patients had intrasalivary non-Hodgkin's lymphoma complicating the lesions, whereas the lesions in the remaining five were all histologically benign. Ten samples from the eight patients all revealed rearrangement of both the heavy-chain and light-chain immunoglobulin genes. In one of the patients in whom non-Hodgkin's lymphoma involved both the salivary-gland lesion and an ipsilateral lymph node, the rearrangements of the heavy-chain and light-chain immunoglobulin genes detected at the two sites were identical. One other patient had two distinct benign lymphoepithelial lesions removed two years apart. The rearrangements of the heavy-chain as well as the kappa light-chain genes detected in these two lesions were entirely different. These data suggest that B-cell clonal expansion has an integral role in the pathophysiology of the benign lymphoepithelial lesion and may explain the increased incidence of lymphoma noted in association with this disorder.

  19. Most human CD3+WT31- clones with T cell receptor C gamma 1 rearrangements show strong non-MHC-restricted cytotoxic activity in contrast to those with C gamma 2 rearrangements.

    PubMed

    Christmas, S E

    1989-04-01

    Clones expressing CD3 in the absence of WT31 expression were obtained by growing highly purified WT31- cells in the presence of interleukin 2 and phytohemagglutinin. Most clones showed rearrangements of T cell receptor (TcR) gamma genes on both chromosomes involving all five currently identified J gamma segments. About a third of these clones had a rearranged 12 kb Kpn I band with the J gamma probe, consistent with a V9JPC gamma 1 rearrangement. All clones with both chromosomes rearranged to C gamma 2 had low or intermediate cytotoxic activity while most of those with at least one chromosome rearranged to C gamma 1 had high cytotoxic activity against both natural killer-sensitive and natural killer-resistant targets. This applied both to clones with and without the V9JPC gamma 1 rearrangement. Of three clones with both C gamma 1 and C gamma 2 rearrangements two had high activity and the other was only weakly cytotoxic. In addition, most clones showed rearrangement of TcR beta genes. Some clones were capable of secreting levels of interferon-gamma and tumor necrosis factor-alpha which were as high as those produced by CD3+4+WT31+ T cell clones. The results suggest that most human CD3+WT31- clones expressing a disulfide-linked C gamma 1/delta heterodimer are capable of mediating strong non-major histocompatibility complex-restricted cytotoxicity whereas those expressing non-disulfide-linked C gamma 2/delta heterodimers are not.

  20. Expression of concern: A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones.

    PubMed

    Kelly, Richard

    2015-12-21

    Expression of concern for 'A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones' by Adán B. González-Pérez et al., Org. Biomol. Chem., 2014, 12, 7694-7701.

  1. Clonal rearrangement for immunoglobulin and T-cell receptor genes in systemic Castleman's disease. Association with Epstein-Barr virus.

    PubMed Central

    Hanson, C. A.; Frizzera, G.; Patton, D. F.; Peterson, B. A.; McClain, K. L.; Gajl-Peczalska, K. J.; Kersey, J. H.

    1988-01-01

    Castleman's disease is a morphologically and clinically heterogeneous lymphoproliferative disorder. Both a localized benign variant and an aggressive form with systemic manifestations have been described. To investigate the differences between these variants of Castleman's disease, the authors analyzed lymph node DNA from 4 patients with the localized type and 4 with the systemic type of Castleman's disease for immunoglobulin and T-cell receptor gene rearrangements. The role of Epstein-Barr virus (EBV) and cytomegalovirus (CMV) was also studied by viral genomic DNA probes. They detected clonal rearrangements in 3 of the 4 patients with the systemic variant of Castleman's; no patients with localized disease had rearrangements. Copies of EBV genome were also detected in 2 of the 3 patients with clonal rearrangements. These results suggest that systemic Castleman's disease is a disorder distinct from the classical localized variant in that it may evolve into a clonal lymphoproliferation. Images Figure 1 PMID:2833104

  2. Large genomic rearrangement of BRCA1 and BRCA2 genes in familial breast cancer patients in Korea.

    PubMed

    Cho, Ja Young; Cho, Dae-Yeon; Ahn, Sei Hyun; Choi, Su-Youn; Shin, Inkyung; Park, Hyun Gyu; Lee, Jong Won; Kim, Hee Jeong; Yu, Jong Han; Ko, Beom Seok; Ku, Bo Kyung; Son, Byung Ho

    2014-06-01

    We screened large genomic rearrangements of the BRCA1 and BRCA2 genes in Korean, familial breast cancer patients. Multiplex ligation-dependent probe amplification assay was used to identify BRCA1 and BRCA2 genomic rearrangements in 226 Korean familial breast cancer patients with risk factors for BRCA1 and BRCA2 mutations, who previously tested negative for point mutations in the two genes. We identified only one large deletion (c.4186-1593_4676-1465del) in BRCA1. No large rearrangements were found in BRCA2. Our result indicates that large genomic rearrangement in the BRCA1 and BRCA2 genes does not seem like a major determinant of breast cancer susceptibility in the Korean population. A large-scale study needs to validate our result in Korea.

  3. Appearance and evolution of the specific chromosomal rearrangements associated with malignant transformation of mouse m5S cells

    SciTech Connect

    Kodama, S.; Okumura, Y.; Komatsu, K.; Sasaki, M.S. )

    1991-06-01

    Chromosomal alterations were studied during the acquisition of malignant phenotypes in two karyotypically distinct cells isolated from transformed foci induced by x-irradiation in mouse m5S cells. Because the transformants, despite foci origin, showed low ability to grow in agar, they were cultured in vitro with serial transfer schedules to allow further cell generations and assayed for anchorage independence (AI) at each passage level. The AI frequency increased with the cell doubling numbers. Chromosome analysis showed that a focus was one cell origin, but the transformants showed karyotypic instability during cell proliferation, giving rise to the rearrangements clustered in the distal region of the specific chromosomes. These rearrangements appeared to be directed toward the acquisition of malignant phenotypes. Analysis of the types and sites of rearrangements indicated that a mechanism exists that induces frequent rearrangements of the specific region of a chromosome during the process of transformation into the malignant state.

  4. The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster

    SciTech Connect

    Wakimoto, B.T.; Hearn, M.G. )

    1990-05-01

    The light (lt) gene of Drosophila melanogaster is located at the base of the left arm of chromosome 2, within or very near centromeric heterochromatin (2Lh). Chromosome rearrangements that move the lt{sup +} gene from its normal proximal position and place the gene in distal euchromatin result in mosaic or variegated expression of the gene. The cytogenetic and genetic properties of 17 lt-variegated rearrangements induced by X radiation are described in this report. The authors show that five of the heterochromatic genes adjacent to lt are subject to inactivation by these rearrangements and that the euchromatic loci in proximal 2L are not detectably affected. The properties of the rearrangements suggest that proximity to heterochromatin is an important regulatory requirement for at least six 2Lh genes. They discuss how the properties of the position effects on heterochromatic genes relate to other proximity-dependent phenomena such as transvection.

  5. Complex chromosomal rearrangements leading to MECOM overexpression are recurrent in myeloid malignancies with various 3q abnormalities.

    PubMed

    Baldazzi, Carmen; Luatti, Simona; Zuffa, Elisa; Papayannidis, Cristina; Ottaviani, Emanuela; Marzocchi, Giulia; Ameli, Gaia; Bardi, Maria Antonella; Bonaldi, Laura; Paolini, Rossella; Gurrieri, Carmela; Rigolin, Gian Matteo; Cuneo, Antonio; Martinelli, Giovanni; Cavo, Michele; Testoni, Nicoletta

    2016-04-01

    Chromosomal rearrangements involving 3q26 are recurrent findings in myeloid malignancies leading to MECOM overexpression, which has been associated with a very poor prognosis. Other 3q abnormalities have been reported and cryptic MECOM rearrangements have been identified in some cases. By fluorescence in situ hybridization (FISH) analysis, we investigated 97 acute myeloid leukemia/myelodysplastic syndrome patients with various 3q abnormalities to determine the role and the frequency of the involvement of MECOM. We identified MECOM rearrangements in 51 patients, most of them showed 3q26 involvement by chromosome banding analysis (CBA): inv(3)/t(3;3) (n = 26) and other balanced 3q26 translocations (t(3q26)) (n = 15); the remaining cases (n = 10) showed various 3q abnormalities: five with balanced translocations involving 3q21 or 3q25; two with homogenously staining region (hsr) on 3q; and three with other various 3q abnormalities. Complex rearrangements with multiple breakpoints on 3q, masking 3q26 involvement, were identified in cases with 3q21/3q25 translocations. Furthermore, multiple breaks were observed in two cases with t(3q26), suggesting that complex rearrangement may also occur in apparently simple t(3q26). Intrachromosomal gene amplification was another mechanism leading to MECOM overexpression in two cases with hsr on 3q. In the last three cases, FISH analysis revealed 3q26 involvement that was missed by CBA because of metaphases' suboptimal quality. All cases with MECOM rearrangements showed overexpression by real-time quantitative PCR. Finally, MECOM rearrangements can occur in patients with 3q abnormalities even in the absence of specific 3q26 involvement, underlining that their frequency is underestimated. As MECOM rearrangement has been associated with very poor prognosis, its screening should be performed in patients with any 3q abnormalities.

  6. Curtius-like Rearrangement of an Iron-Nitrenoid Complex and Application in Biomimetic Synthesis of Bisindolylmethanes.

    PubMed

    Li, Dashan; Wu, Ting; Liang, Kangjiang; Xia, Chengfeng

    2016-05-01

    A Curtius-like rearrangement of hydroxamates to isocyanates was discovered. This reaction was initiated from an iron(II)-nitrenoid complex, which was generated by the iron(II)-catalyzed cleavage of N-O bonds of functionalized hydroxamates. To demonstrate the efficiency of this new Curtius-like rearrangement in synthetic chemistry, a biomimetic strategy for the one-pot preparation of bisindolylmethanes was developed. PMID:27116426

  7. Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations.

    PubMed

    Lorenz, Susanne; Barøy, Tale; Sun, Jinchang; Nome, Torfinn; Vodák, Daniel; Bryne, Jan-Christian; Håkelien, Anne-Mari; Fernandez-Cuesta, Lynnette; Möhlendick, Birte; Rieder, Harald; Szuhai, Karoly; Zaikova, Olga; Ahlquist, Terje C; Thomassen, Gard O S; Skotheim, Rolf I; Lothe, Ragnhild A; Tarpey, Patrick S; Campbell, Peter; Flanagan, Adrienne; Myklebost, Ola; Meza-Zepeda, Leonardo A

    2016-02-01

    In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2, and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies. PMID:26672768

  8. Complex chromosomal rearrangements leading to MECOM overexpression are recurrent in myeloid malignancies with various 3q abnormalities.

    PubMed

    Baldazzi, Carmen; Luatti, Simona; Zuffa, Elisa; Papayannidis, Cristina; Ottaviani, Emanuela; Marzocchi, Giulia; Ameli, Gaia; Bardi, Maria Antonella; Bonaldi, Laura; Paolini, Rossella; Gurrieri, Carmela; Rigolin, Gian Matteo; Cuneo, Antonio; Martinelli, Giovanni; Cavo, Michele; Testoni, Nicoletta

    2016-04-01

    Chromosomal rearrangements involving 3q26 are recurrent findings in myeloid malignancies leading to MECOM overexpression, which has been associated with a very poor prognosis. Other 3q abnormalities have been reported and cryptic MECOM rearrangements have been identified in some cases. By fluorescence in situ hybridization (FISH) analysis, we investigated 97 acute myeloid leukemia/myelodysplastic syndrome patients with various 3q abnormalities to determine the role and the frequency of the involvement of MECOM. We identified MECOM rearrangements in 51 patients, most of them showed 3q26 involvement by chromosome banding analysis (CBA): inv(3)/t(3;3) (n = 26) and other balanced 3q26 translocations (t(3q26)) (n = 15); the remaining cases (n = 10) showed various 3q abnormalities: five with balanced translocations involving 3q21 or 3q25; two with homogenously staining region (hsr) on 3q; and three with other various 3q abnormalities. Complex rearrangements with multiple breakpoints on 3q, masking 3q26 involvement, were identified in cases with 3q21/3q25 translocations. Furthermore, multiple breaks were observed in two cases with t(3q26), suggesting that complex rearrangement may also occur in apparently simple t(3q26). Intrachromosomal gene amplification was another mechanism leading to MECOM overexpression in two cases with hsr on 3q. In the last three cases, FISH analysis revealed 3q26 involvement that was missed by CBA because of metaphases' suboptimal quality. All cases with MECOM rearrangements showed overexpression by real-time quantitative PCR. Finally, MECOM rearrangements can occur in patients with 3q abnormalities even in the absence of specific 3q26 involvement, underlining that their frequency is underestimated. As MECOM rearrangement has been associated with very poor prognosis, its screening should be performed in patients with any 3q abnormalities. PMID:26815134

  9. Mass-spectrometric investigation of ortho-hydroxynitrosoarenes and their rearrangement products - /beta/(2-cyanoaryl)acrylic acids

    SciTech Connect

    Terent'ev, P.B.; Rakhimi, M.I.; Stankevichus, A.P.; Kalandarishvili, A.G.; Bundel', Yu.G.

    1988-06-20

    Comparative analysis of the mass spectra of 2-hydroxy-1-nitrosonaphthalene, its benzo-substituted derivatives, 2-hydroxy-1-nitrosoanthracene, 2-hydroxy-1-nitrosophenanthrene, and also the products from their Beckmann rearrangement of the second kind, i.e., ortho-cyanocinnamic (benzocinnamic) acids, shows that the molecular ions of the ortho-nitrosohydroxyarenes formed under electron impact largely retain the topology of the initial molecule and do not undergo a Beckmann rearrangement of the second kind to an appreciable degree.

  10. Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations

    PubMed Central

    Lorenz, Susanne; Barøy, Tale; Sun, Jinchang; Nome, Torfinn; Vodák, Daniel; Bryne, Jan-Christian; Håkelien, Anne-Mari; Fernandez-Cuesta, Lynnette; Möhlendick, Birte; Rieder, Harald; Szuhai, Karoly; Zaikova, Olga; Ahlquist, Terje C.; Thomassen, Gard O. S.; Skotheim, Rolf I.; Lothe, Ragnhild A.; Tarpey, Patrick S.; Campbell, Peter; Flanagan, Adrienne

    2016-01-01

    In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2, and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies. PMID:26672768

  11. Computational elucidation of the origins of reactivity and selectivity in non-aldol aldol rearrangements of cyclic epoxides.

    PubMed

    Wang, Hao; Houk, K N; Allen, Damian A; Jung, Michael E

    2011-06-17

    The non-aldol aldol reaction of the isomeric epoxy silyl ethers is controlled by the conformation of the transition states leading to an internal hydride shift. One isomer rearranges to the β-silyloxy ketone whereas the other isomer gives a β-elimination product. Theoretical calculations show that the substrates with substituents that favor the formation of the chairlike transition state rearrange normally while those that do not undergo elimination instead. PMID:21568276

  12. Direct Conversion of Aldehydes and Ketones to Allylic Halides by a NbX5-[3,3] Rearrangement

    PubMed Central

    Fleming, Fraser F.; Ravikumar, P. C.; Yao, Lihua

    2009-01-01

    Sequential addition of vinylmagnesium bromide and NbCl5, or NbBr5, to a series of aldehydes and ketones directly provides homologated, allylic halides. Transposition of the intermediate vinyl alkoxide is envisaged through a metalla-halo-[3,3] rearrangement with concomitant delivery of the halogen to the terminal carbon. The [3,3] rearrangement is equally effective for the conversion of a propargyllic alcohol to the corresponding allenyl bromide. PMID:20046989

  13. One-Pot Synthesis of Benzothiazole-Tethered Chromanones/Coumarins via Claisen Rearrangement Using the Solid State Melt Reaction.

    PubMed

    Bakthadoss, Manickam; Selvakumar, Raman

    2016-04-15

    A novel protocol has been successfully established for the efficient synthesis of benzothiazole-tethered chromanone/coumarin scaffolds via Claisen rearrangement using a solid state melt reaction in a one-pot manner. Benzothiazole formation and Claisen rearrangement involve the cleavage of S-S and C-O bonds and formation of C-S, C═N, and C-C bonds in a single operation without using a catalyst or solvent. PMID:26991666

  14. TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome

    PubMed Central

    Edison; Teo, Audrey S.M.; Madan, Babita; Zhang, Kang; Kohlmann, Wendy K.; Yao, Fei; Lee, Wah Heng; Hoi, Qiangze; Cai, Shaojiang; Woo, Xing Yi; Tan, Patrick; Jundt, Gernot; Smida, Jan; Nathrath, Michaela; Sung, Wing-Kin; Schiffman, Joshua D.; Virshup, David M.; Hillmer, Axel M.

    2015-01-01

    Somatic mutations of TP53 are among the most common in cancer and germline mutations of TP53 (usually missense) can cause Li-Fraumeni syndrome (LFS). Recently, recurrent genomic rearrangements in intron 1 of TP53 have been described in osteosarcoma (OS), a highly malignant neoplasm of bone belonging to the spectrum of LFS tumors. Using whole-genome sequencing of OS, we found features of TP53 intron 1 rearrangements suggesting a unique mechanism correlated with transcription. Screening of 288 OS and 1,090 tumors of other types revealed evidence for TP53 rearrangements in 46 (16%) OS, while none were detected in other tumor types, indicating this rearrangement to be highly specific to OS. We revisited a four-generation LFS family where no TP53 mutation had been identified and found a 445 kb inversion spanning from the TP53 intron 1 towards the centromere. The inversion segregated with tumors in the LFS family. Cancers in this family had loss of heterozygosity, retaining the rearranged allele and resulting in TP53 expression loss. In conclusion, intron 1 rearrangements cause p53-driven malignancies by both germline and somatic mechanisms and provide an important mechanism of TP53 inactivation in LFS, which might in part explain the diagnostic gap of formerly classified “TP53 wild-type” LFS. PMID:25762628

  15. LCR-initiated rearrangements at the IDS locus, completed with Alu-mediated recombination or non-homologous end joining.

    PubMed

    Oshima, Junko; Lee, Jennifer A; Breman, Amy M; Fernandes, Priscilla H; Babovic-Vuksanovic, Dusica; Ward, Patricia A; Wolfe, Lynne A; Eng, Christine M; Del Gaudio, Daniela

    2011-07-01

    Mucopolysaccharidosis type II (MPS II) is caused by mutations in the IDS gene, which encodes the lysosomal enzyme iduronate-2-sulfatase. In ∼20% of MPS II patients the disorder is caused by gross IDS structural rearrangements. We identified two male cases harboring complex rearrangements involving the IDS gene and the nearby pseudogene, IDSP1, which has been annotated as a low-copy repeat (LCR). In both cases the rearrangement included a partial deletion of IDS and an inverted insertion of the neighboring region. In silico analyses revealed the presence of repetitive elements as well as LCRs at the junctions of rearrangements. Our models illustrate two alternative consequences of rearrangements initiated by non-allelic homologous recombination of LCRs: resolution by a second recombination event (that is, Alu-mediated recombination), or resolution by non-homologous end joining repair. These complex rearrangements have the potential to be recurrent and may be present among those MSP II cases with previously uncharacterized aberrations involving IDS.

  16. Detection of archetype and rearranged variants of JC virus in multiple tissues from a pediatric PML patient.

    PubMed

    Newman, J T; Frisque, R J

    1997-07-01

    JC virus (JCV) establishes persistent infections in its human host, and in some immunocompromised individuals, the virus causes the fatal brain disease progressive multifocal leukoencephalopathy (PML). Two forms of the virus, archetype and rearranged, have been isolated, with the latter being derived from the archetype form by deletion and duplication of sequences within the viral transcriptional control region (TCR). We have used the PCR technique to amplify JCV TCR sequences present within multiple tissues of a pediatric PML patient and have cloned and sequenced the PCR products. Archetype JCV was readily detected in kidney tissue; this form of JCV was also identified for the first time in brain and lymph node tissue by employing archetype-specific PCR primers. In addition, several archetype-like variants containing small deletions within their regulatory regions were isolated from cardiac muscle and lung. Different, but related rearranged forms were detected in most of the tissue examined. Each of the rearranged TCRs lacked portions of a 66 base pair (bp) region found within the archetype promoter-enhancer but retained a 23 bp region that is deleted in the prototype (Mad 1) rearranged form of JCV. Although several rearranged forms of JCV were identified in this patient, the TCRs could be assigned to one of two groups based upon the deletion boundaries generated during the adaptation from archetype to rearranged JCV. This study is the first to characterize multiple JCV variants present in different tissues from a patient likely to have succumbed to PML during a primary infection.

  17. Characterization of gene rearrangements resulted from genomic structural aberrations in human esophageal squamous cell carcinoma KYSE150 cells.

    PubMed

    Hao, Jia-Jie; Gong, Ting; Zhang, Yu; Shi, Zhi-Zhou; Xu, Xin; Dong, Jin-Tang; Zhan, Qi-Min; Fu, Song-Bin; Wang, Ming-Rong

    2013-01-15

    Chromosomal rearrangements and involved genes have been reported to play important roles in the development and progression of human malignancies. But the gene rearrangements in esophageal squamous cell carcinoma (ESCC) remain to be identified. In the present study, array-based comparative genomic hybridization (array-CGH) was performed on the ESCC cell line KYSE150. Eight disrupted genes were detected according to the obviously distinct unbalanced breakpoints. The splitting of these genes was validated by dual-color fluorescence in-situ hybridization (FISH). By using rapid amplification of cDNA ends (RACE), genome walking and sequencing analysis, we further identified gene disruptions and rearrangements. A fusion transcript DTL-1q42.2 was derived from an intrachromosomal rearrangement of chromosome 1. Highly amplified segments of DTL and PTPRD were self-rearranged. The sequences on either side of the junctions possess micro-homology with each other. FISH results indicated that the split DTL and PTPRD were also involved in comprising parts of the derivative chromosomes resulted from t(1q;9p;12p) and t(9;1;9). Further, we found that regions harboring DTL (1q32.3) and PTPRD (9p23) were also splitting in ESCC tumors. The data supplement significant information on the existing genetic background of KYSE150, which may be used as a model for studying these gene rearrangements.

  18. TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome.

    PubMed

    Ribi, Sebastian; Baumhoer, Daniel; Lee, Kristy; Edison; Teo, Audrey S M; Madan, Babita; Zhang, Kang; Kohlmann, Wendy K; Yao, Fei; Lee, Wah Heng; Hoi, Qiangze; Cai, Shaojiang; Woo, Xing Yi; Tan, Patrick; Jundt, Gernot; Smida, Jan; Nathrath, Michaela; Sung, Wing-Kin; Schiffman, Joshua D; Virshup, David M; Hillmer, Axel M

    2015-04-10

    Somatic mutations of TP53 are among the most common in cancer and germline mutations of TP53 (usually missense) can cause Li-Fraumeni syndrome (LFS). Recently, recurrent genomic rearrangements in intron 1 of TP53 have been described in osteosarcoma (OS), a highly malignant neoplasm of bone belonging to the spectrum of LFS tumors. Using whole-genome sequencing of OS, we found features of TP53 intron 1 rearrangements suggesting a unique mechanism correlated with transcription. Screening of 288 OS and 1,090 tumors of other types revealed evidence for TP53 rearrangements in 46 (16%) OS, while none were detected in other tumor types, indicating this rearrangement to be highly specific to OS. We revisited a four-generation LFS family where no TP53 mutation had been identified and found a 445 kb inversion spanning from the TP53 intron 1 towards the centromere. The inversion segregated with tumors in the LFS family. Cancers in this family had loss of heterozygosity, retaining the rearranged allele and resulting in TP53 expression loss. In conclusion, intron 1 rearrangements cause p53-driven malignancies by both germline and somatic mechanisms and provide an important mechanism of TP53 inactivation in LFS, which might in part explain the diagnostic gap of formerly classified "TP53 wild-type" LFS. PMID:25762628

  19. HMGI-C rearrangements as the molecular basis for the majority of pulmonary chondroid hamartomas: a survey of 30 tumors.

    PubMed

    Kazmierczak, B; Rosigkeit, J; Wanschura, S; Meyer-Bolte, K; Van de Ven, W J; Kayser, K; Krieghoff, B; Kastendiek, H; Bartnitzke, S; Bullerdiek, J

    1996-02-01

    Pulmonary chondroid hamartomas (PCH) are benign tumors of the lung characterized by a more or less high degree of mesenchymal metaplasia. In our series we investigated 30 PCH by a combination of cytogenetic and molecular methods. 18 tumors (60%) had cytogenetically detectable aberrations involving either 12q14-15 or 6p21 with a clear predominance of chromosomal abnormalities involving 12q14-15 (15 tumors). As in subgroups of pleomorphic adenomas of the salivary glands, leiomyomas of the uterus, and lipomas with 12q14-15 abnormalities the HMGI-C gene is frequently rearranged we tested PCH with either 12q14-15 abnormalities or normal karyotype by FISH and 3' RACE experiments for rearrangements of HMGI-C. Rearrangements were found in all cases with chromosomal 12q14-15 abnormalities and further six cases with an apparently normal karyotype. By the combination of cytogenetics with molecular techniques the percentage of cases with intragenic rearrangements of HMGI-C or rearrangements of its immediate surrounding was thus increased to 70% (21/30 cases). Considering all types of aberrations within this series 80% (24/30) of all PCH were aberrant. This is the first report on a combined molecular and cytogenetic analysis of a large series of pulmonary chondroid hamartomas indicating that rearrangements of HMGI-C, a member of the high mobility group protein gene family, are the leading molecular events in the genesis of PCH.

  20. Reproductive Incompatibility Involving Senegalese Aedes aegypti (L) Is Associated with Chromosome Rearrangements.

    PubMed

    Dickson, Laura B; Sharakhova, Maria V; Timoshevskiy, Vladimir A; Fleming, Karen L; Caspary, Alex; Sylla, Massamba; Black, William C

    2016-04-01

    used to identify AT-rich regions, chromomycin A3 following pretreatment with barium hydroxide stained for GC-rich regions and stained the ribosomal RNA locus and YOYO-1 was used to test for differential staining. Chromosome patterns in SenAae strains revealed by these three stains differed from those in IB12. For FISH, 40 BAC clones previously physically mapped on Aaa chromosomes were used to test for chromosome rearrangements in SenAae relative to IB12. Differences in the order of markers identified two chromosomal rearrangements between IB12 and SenAae strains. The first rearrangement involves two overlapping pericentric (containing the centromere) inversions in chromosome 3 or an insertion of a large fragment into the 3q arm. The second rearrangement is close to the centromere on the p arm of chromosome 2. Linkage analysis of the SDL and the white-eye locus identified a likely chromosomal rearrangement on chromosome 1. The reproductive incompatibility observed within SenAae and between SenAae and Aaa may be generally associated with chromosome rearrangements on all three chromosomes and specifically caused by pericentric inversions on chromosomes 2 and 3.

  1. Reproductive Incompatibility Involving Senegalese Aedes aegypti (L) Is Associated with Chromosome Rearrangements

    PubMed Central

    Dickson, Laura B.; Sharakhova, Maria V.; Timoshevskiy, Vladimir A.; Fleming, Karen L.; Caspary, Alex; Sylla, Massamba; Black, William C.

    2016-01-01

    was used to identify AT-rich regions, chromomycin A3 following pretreatment with barium hydroxide stained for GC-rich regions and stained the ribosomal RNA locus and YOYO-1 was used to test for differential staining. Chromosome patterns in SenAae strains revealed by these three stains differed from those in IB12. For FISH, 40 BAC clones previously physically mapped on Aaa chromosomes were used to test for chromosome rearrangements in SenAae relative to IB12. Differences in the order of markers identified two chromosomal rearrangements between IB12 and SenAae strains. The first rearrangement involves two overlapping pericentric (containing the centromere) inversions in chromosome 3 or an insertion of a large fragment into the 3q arm. The second rearrangement is close to the centromere on the p arm of chromosome 2. Linkage analysis of the SDL and the white-eye locus identified a likely chromosomal rearrangement on chromosome 1. The reproductive incompatibility observed within SenAae and between SenAae and Aaa may be generally associated with chromosome rearrangements on all three chromosomes and specifically caused by pericentric inversions on chromosomes 2 and 3. PMID:27105225

  2. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes.

    PubMed

    Loo, Rachel R Ogorzalek; Loo, Joseph A

    2016-06-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ. PMID:27052739

  3. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes

    NASA Astrophysics Data System (ADS)

    Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2016-06-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes.

  4. TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.

    PubMed

    Maliszewska-Olejniczak, Kamila; Gruchota, Julita; Gromadka, Robert; Denby Wilkes, Cyril; Arnaiz, Olivier; Mathy, Nathalie; Duharcourt, Sandra; Bétermier, Mireille; Nowak, Jacek K

    2015-07-01

    Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs) in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline) nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs). Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium, and establishes for

  5. Metalloradical Complexes of Manganese and Chromium Featuring an Oxidatively Rearranged Ligand

    PubMed Central

    Çelenligil-Çetin, Remle; Paraskevopoulou, Patrina; Lalioti, Nikolia; Sanakis, Yiannis; Staples, Richard J.; Rath, Nigam P.; Stavropoulos, Pericles

    2009-01-01

    Redox events involving both metal and ligand sites are receiving increased attention since a number of biological processes direct redox equivalents toward functional residues. Metalloradical synthetic analogs remain scarce and require better definition of their mode of formation and subsequent operation. The trisamido-amine ligand [(RNC6H4)3N]3−, where R is the electron-rich 4-t-BuPh, is employed in this study to generate redox active residues in manganese and chromium complexes. Solutions of [(L1)Mn(II)–THF]− in THF are oxidized by dioxygen to afford [(L1re–1)Mn(III)–(O)2–Mn(III)(L1re–1)]2− as the major product. The rare dinuclear manganese (III,III) core is stabilized by a rearranged ligand that has undergone an one-electron oxidative transformation, followed by retention of the oxidation equivalent as a π radical in an o-diiminobenzosemiquinonate moiety. Magnetic studies indicate that the ligand-centered radical is stabilized by means of extended antiferromagnetic coupling between the S = ½ radical and the adjacent S = 2 Mn(III) site, as well as between the two Mn(III) centers via the dioxo bridge. Electrochemical and EPR data suggest that this system can store higher levels of oxidation potency. Entry to the corresponding Cr(III) chemistry is achieved by employing CrCl3 to access both [(L1)Cr(III)–THF] and [(L1re–1)Cr(III)–THF(Cl)], featuring the intact and the oxidatively rearranged ligands, respectively. The latter is generated by ligand-centered oxidation of the former compound. The rearranged ligand is perceived to be the product of an one-electron oxidation of the intact ligand to afford a metal-bound aminyl radical that subsequently mediates a radical 1,4-(N-to-N) aryl migration. PMID:18937446

  6. WIF1, an inhibitor of the Wnt pathway, is rearranged in salivary gland tumors.

    PubMed

    Queimado, Lurdes; Lopes, Carla S; Reis, Antonio M C

    2007-03-01

    Chromosome rearrangements involving 12q13-15 are frequent among several tumors, including pleomorphic adenomas. The common molecular target for these aberrations is the HMGA2 gene, but various fusion partners of HMGA2 have been reported in tumors. Here we report the identification of the WNT inhibitory factor 1 (WIF1) gene as a novel HMGA2 fusion partner in a salivary gland pleomorphic adenoma. In normal salivary gland tissue WIF1 is expressed at a high level and HMGA2 is not expressed. However, in the pleomorphic adenoma expressing the HMGA2/WIF1 fusion transcript, we observed re-expression of HMGA2 wild-type transcripts and very low levels of WIF1 expression. These data suggest a possible synergistic effect between upregulation of HMGA2 and downregulation of WIF1. We screened 13 additional benign and malignant salivary gland tumors and detected WIF1 rearrangement in one out of two carcinomas ex-pleomorphic adenoma analyzed. In this malignant tumor, the rearrangement of one WIF1 allele coexists with loss of the other allele, a classic signature of a tumor suppressor gene. WIF1 is an antagonist of the Wnt signaling pathway, which plays a critical role in human cancer. In transgenic mouse models, Wnt activation leads to a high frequency of benign and malignant salivary gland tumors. To our knowledge, this is the first report suggesting that WIF1 is a recurrent target in human salivary gland oncogenesis and that downregulation of WIF1 plays a role in the development and/or progression of pleomorphic adenomas.

  7. Genetic and clinical characterization of 45 acute leukemia patients with MLL gene rearrangements from a single institution.

    PubMed

    Cerveira, Nuno; Lisboa, Susana; Correia, Cecília; Bizarro, Susana; Santos, Joana; Torres, Lurdes; Vieira, Joana; Barros-Silva, João D; Pereira, Dulcineia; Moreira, Cláudia; Meyer, Claus; Oliva, Tereza; Moreira, Ilídia; Martins, Ângelo; Viterbo, Luísa; Costa, Vítor; Marschalek, Rolf; Pinto, Armando; Mariz, José M; Teixeira, Manuel R

    2012-10-01

    Chromosomal rearrangements affecting the MLL gene are associated with high-risk pediatric, adult and therapy-associated acute leukemia. In this study, conventional cytogenetic, fluorescence in situ hybridization, and molecular genetic studies were used to characterize the type and frequency of MLL rearrangements in a consecutive series of 45 Portuguese patients with MLL-related leukemia treated in a single institution between 1998 and 2011. In the group of patients with acute lymphoblastic leukemia and an identified MLL fusion partner, 47% showed the presence of an MLL-AFF1 fusion, as a result of a t(4;11). In the remaining cases, a MLL-MLLT3 (27%), a MLL-MLLT1 (20%), or MLL-MLLT4 (7%) rearrangement was found. The most frequent rearrangement found in patients with acute myeloid leukemia was the MLL-MLLT3 fusion (42%), followed by MLL-MLLT10 (23%), MLL-MLLT1 (8%), MLL-ELL (8%), MLL-MLLT4 (4%), and MLL-MLLT11 (4%). In three patients, fusions involving MLL and a septin family gene (SEPT2, SEPT6, and SEPT9), were identified. The most frequently identified chromosomal rearrangements were reciprocal translocations, but insertions and deletions, some cryptic, were also observed. In our series, patients with MLL rearrangements were shown to have a poor prognosis, regardless of leukemia subtype. Interestingly, children with 1 year or less showed a statistically significant better overall survival when compared with both older children and adults. The use of a combined strategy in the initial genetic evaluation of acute leukemia patients allowed us to characterize the pattern of MLL rearrangements in our institution, including our previous discovery of two novel MLL fusion partners, the SEPT2 and CT45A2 genes, and a very rare MLL-MLLT4 fusion variant. PMID:22846743

  8. RET/PTC rearrangements preferentially occurred in papillary thyroid cancer among atomic bomb survivors exposed to high radiation dose.

    PubMed

    Hamatani, Kiyohiro; Eguchi, Hidetaka; Ito, Reiko; Mukai, Mayumi; Takahashi, Keiko; Taga, Masataka; Imai, Kazue; Cologne, John; Soda, Midori; Arihiro, Koji; Fujihara, Megumu; Abe, Kuniko; Hayashi, Tomayoshi; Nakashima, Masahiro; Sekine, Ichiro; Yasui, Wataru; Hayashi, Yuzo; Nakachi, Kei

    2008-09-01

    A major early event in papillary thyroid carcinogenesis is constitutive activation of the mitogen-activated protein kinase signaling pathway caused by alterations of a single gene, typically rearrangements of the RET and NTRK1 genes or point mutations in the BRAF and RAS genes. In childhood papillary thyroid cancer, regardless of history of radiation exposure, RET/PTC rearrangements are a major event. Conversely, in adult-onset papillary thyroid cancer among the general population, the most common molecular event is BRAF(V600E) point mutation, not RET/PTC rearrangements. To clarify which gene alteration, chromosome aberration, or point mutation preferentially occurs in radiation-associated adult-onset papillary thyroid cancer, we have performed molecular analyses on RET/PTC rearrangements and BRAF(V600E) mutation in 71 papillary thyroid cancer cases among atomic bomb survivors (including 21 cases not exposed to atomic bomb radiation), in relation to radiation dose as well as time elapsed since atomic bomb radiation exposure. RET/PTC rearrangements showed significantly increased frequency with increased radiation dose (P(trend) = 0.002). In contrast, BRAF(V600E) mutation was less frequent in cases exposed to higher radiation dose (P(trend) < 0.001). Papillary thyroid cancer subjects harboring RET/PTC rearrangements developed this cancer earlier than did cases with BRAF(V600E) mutation (P = 0.03). These findings were confirmed by multivariate logistic regression analysis. These results suggest that RET/PTC rearrangements play an important role in radiation-associated thyroid carcinogenesis.

  9. Cooperative rearranging region size and free volume in As-Se glasses.

    PubMed

    Saiter, A; Saiter, J-M; Golovchak, R; Shpotyuk, M; Shpotyuk, O

    2009-02-18

    Glasses of the As-Se system have been used as model objects of the covalent disordered inorganic polymers to investigate the correlation between the cooperative rearranging region (CRR) size determined at the glass transition temperature and the free volume fraction in the glassy state. The CRR size has been determined using temperature modulated differential scanning calorimetry data according to Donth's approach, while the free volume fraction in the investigated materials has been estimated using positron annihilation lifetime spectroscopy data. The obtained results testify that the appearance of open-volume defects greater than 80 Å(3) leads to a significant decrease in the CRR size.

  10. Development of advanced zeolite catalysts for the vapor phase Beckmann rearrangement of cyclohexanone oxime

    NASA Astrophysics Data System (ADS)

    Dai, Lian-Xin; Iwaki, Yoshihide; Koyama, Katsuyuki; Tatsumi, Takashi

    1997-11-01

    The vapor phase Beckmann rearrangement of cyclohexanone oxime to ɛ-caprolactam catalyzed by various zeolites was studied. The catalytic performance was greatly affected by both the zeolite structure and diluent solvent. When 1-hexanol was used in place of benzene, the catalytic performance of all catalysts except silicalite-1 was greatly improved. In particular, the selectivity and stability of H-LTL and H-OFF-ERI zeolites remarkably increased; both catalysts exhibited ca. 100% oxime conversion and ɛ-caprolactam selectivity of >95% for 6 h.

  11. Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

    PubMed Central

    2013-01-01

    Background A skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes – the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass. Myctophids possess a unique communication system of species-specific photophore patterns and traditional intrafamilial classification has been established to reflect arrangements of photophores. Myctophids present the most diverse array of larval body forms found in fishes although this attribute has both corroborated and confounded phylogenetic hypotheses based on adult morphology. No molecular phylogeny is available for Myctophiformes, despite their importance within all ocean trophic cycles, open-ocean speciation and as an important part of neoteleost divergence. This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements. Results Mitogenomic evidence from DNA sequences and unique gene orders are highly congruent concerning phylogenetic resolution on several myctophiform classification levels, corroborating evidence from osteology, larval ontogeny and photophore patterns, although the lack of larval morphological characters within the subfamily Lampanyctinae stands out. Neoscopelidae is resolved as the sister family to myctophids with Solivomer arenidens positioned as a sister taxon to the remaining neoscopelids. The enigmatic Notolychnus valdiviae is placed as a sister taxon to all other myctophids and exhibits an unusual second copy of the tRNA-Met gene – a gene order rearrangement reminiscent of that found in

  12. Free electron laser-driven ultrafast rearrangement of the electronic structure in Ti

    PubMed Central

    Principi, E.; Giangrisostomi, E.; Cucini, R.; Bencivenga, F.; Battistoni, A.; Gessini, A.; Mincigrucci, R.; Saito, M.; Di Fonzo, S.; D'Amico, F.; Di Cicco, A.; Gunnella, R.; Filipponi, A.; Giglia, A.; Nannarone, S.; Masciovecchio, C.

    2015-01-01

    High-energy density extreme ultraviolet radiation delivered by the FERMI seeded free-electron laser has been used to create an exotic nonequilibrium state of matter in a titanium sample characterized by a highly excited electron subsystem at temperatures in excess of 10 eV and a cold solid-density ion lattice. The obtained transient state has been investigated through ultrafast absorption spectroscopy across the Ti M2,3-edge revealing a drastic rearrangement of the sample electronic structure around the Fermi level occurring on a time scale of about 100 fs. PMID:26798835

  13. Quantum description of coupling to neutron-rearrangement channels in fusion reactions near the Coulomb barrier

    SciTech Connect

    Samarin, V. V.

    2015-10-15

    The fusion cross sections for the {sup 17,18}O+{sup 27}Al, {sup 18}O+{sup 58}Ni, and {sup 6}He+{sup 197}Au reactions were calculated by the coupled-channel method. The radial dependence of matrices that describe coupling to valence-neutron-rearrangement channels was determined with the aid of two-center wave functions. The coupling-strength parameters were evaluated on the basis of numerically solving the time-dependent Schrödinger equation. Satisfactory agreement with experimental data was obtained.

  14. Toward Singlet-Triplet Bistable Nonalternant Kekulé Hydrocarbons: Azulene-to-Naphthalene Rearrangement.

    PubMed

    Das, Soumyajit; Wu, Jishan

    2015-12-01

    Recent developments of open-shell singlet diradicaloids motivated the search for stable singlet-triplet bistable nonalternant polycyclic hydrocarbons. During the synthesis of this type of molecule, such as the dibenzo-cyclohepta[def]fluorene 3, an unexpected azulene-to-naphthalene rearrangement was observed at room temperature, which resulted in new nonalternant hydrocarbons 8a/8b with a closed-shell singlet ground state. These studies provided insight into the unique chemistry of azulene and challenges for the synthesis of singlet-triplet bistable polycyclic hydrocarbons. PMID:26569547

  15. Actin cytoskeleton rearrangements in Arabidopsis roots under stress and during gravitropic response

    NASA Astrophysics Data System (ADS)

    Pozhvanov, Gregory; Medvedev, Sergei; Suslov, Dmitry; Demidchik, Vadim

    Among environmental factors, gravity vector is the only one which is constant in direction and accompanies the whole plant ontogenesis. That said, gravity vector can be considered as an essential factor for correct development of plants. Gravitropism is a plant growth response against changing its position relative to the gravity vector. It is well estableshed that gravitropism is directed by auxin redistribution across the gravistimulated organ. In addition to auxin, actin cytoskeleton was shown to be involved in gravitropism at different stages: gravity perception, signal transduction and gravitropic bending formation. However, the relationship between IAA and actin is still under discussion. In this work we studied rearrangements of actin cytoskeleton during root gravitropic response. Actin microfilaments were visualized in vivo in GFP-fABD2 transgenic Arabidopsis plants, and their angle distribution was acquired from MicroFilament Analyzer software. The curvature of actin microfilaments in root elongation zone was shown to be increased within 30-60 min of gravistimulation, the fraction of axially oriented microfilaments decreased with a concomitant increase in the fraction of oblique and transversally oriented microfilaments. In particular, the fraction of transversally oriented microfilaments (i.e. parallel to the gravity vector) increased 3-5 times. Under 10 min of sub-lethal salt stress impact, actin microfilament orientations widened from an initial axial orientation to a set of peaks at 15(°) , 45(°) and 90(°) . We conclude that the actin cytoskeleton rearrangements observed are associated with the regulation of basic mechanisms of cell extension growth by which the gravitropic bending is formed. Having common stress-related features, gravity-induced actin cytoskeleton rearrangement is slower but results in higher number of g-vector-parallel microfilaments when compared to salt stress-induced rearrangement. Also, differences in gravistimulated root

  16. Extraordinary number of gene rearrangements in the mitochondrial genomes of lice (Phthiraptera: Insecta).

    PubMed

    Covacin, C; Shao, R; Cameron, S; Barker, S C

    2006-02-01

    The arrangement of genes in the mitochondrial (mt) genomes of most insects is the same, or near-identical, to that inferred to be ancestral for insects. We sequenced the entire mt genome of the small pigeon louse, Campanulotes bidentatus compar, and part of the mt genomes of nine other species of lice. These species were from six families and the three main suborders of the order Phthiraptera. There was no variation in gene arrangement among species within a family but there was much variation in gene arrangement among the three suborders of lice. There has been an extraordinary number of gene rearrangements in the mitochondrial genomes of lice!

  17. The Amadori rearrangement as glycoconjugation method: Synthesis of non-natural C-glycosyl type glycoconjugates

    PubMed Central

    Adanitsch, Florian; Stütz, Arnold E

    2012-01-01

    Summary The Amadori rearrangement was investigated as a potential method for the conjugation of carbohydrate moieties to suitable amino components. Starting from selected aldoheptoses, which are readily available by means of the Kiliani–Fischer C-elongation reaction of the corresponding aldohexoses, glycoconjugates presenting D-gluco, D-manno and D-galacto as well as GlcNAc motifs have been synthesised. Following this strategy, non-natural C-glycosyl type glycoconjugates, which can be utilised as building blocks for the composition of larger molecular constructions, are available by a very short synthetic approach. PMID:23209494

  18. The Combined C—H Functionalization/Cope Rearrangement: Discovery and Applications in Organic Synthesis

    PubMed Central

    Davies, Huw M. L.; Lian, Yajing

    2012-01-01

    Conspectus The development of methods for the stereoselective functionalization of sp3 C–H bonds is a challenging undertaking. This Account describes the scope of the combined C–H functionalization/Cope rearrangement (CHCR), a reaction that occurs between rhodium-stabilized vinylcarbenoids and substrates containing allylic C–H bonds. Computational studies have shown that the CHCR reaction is initiated by a hydride transfer to the carbenoid from an allyl site of the substrate, which is then rapidly followed by C–C bond formation between the developing rhodium-bound allyl anion and the allyl cation. In principle, the reaction can proceed through four distinct orientations of the vinylcarbenoid and the approaching substrate. The early examples of the CHCR reaction were all highly diastereoselective, consistent with a reaction proceeding via a chair transition state with the vinylcarbenoid adopting an s-cis conformation. Recent computational studies have revealed that other transition state orientations are energetically accessible, and these results have guided the development of highly stereoselective CHCR reactions that proceed through a boat transition state with the vinylcarbenoid in an s-cis configuration. The CHCR reaction has broad applications in organic synthesis. In some new protocols, the CHCR reaction acts as a surrogate to some of the classic synthetic strategies in organic chemistry. The CHCR reaction has served as a synthetic equivalent of the Michael reaction, the vinylogous Mukaiyama aldol reaction, the tandem Claisen rearrangement/Cope rearrangement, and the tandem aldol reaction/siloxy-Cope rearrangement. In all of these cases, the products are generated with very high diastereocontrol. With a chiral dirhodium tetracarboxylate catalyst such as Rh2(S-DOSP)4 or Rh2(S-PTAD)4, researchers can achieve very high levels of asymmetric induction. Applications of the CHCR reaction include the effective enantiodifferentiation of racemic

  19. Formation of H3+ due to Intramolecular Bond Rearrangement in Doubly Charged Methanol

    NASA Astrophysics Data System (ADS)

    de, Sankar; Rajput, Jyoti; Roy, A.; Ghosh, P. N.; Safvan, C. P.

    2006-11-01

    We report the formation of H3+ by proton coagulation in methanol under the impact of low energy Ar8+ projectiles. Our time-of-flight coincidence measurements with CH3OD establish that the H3+ formation arises from intramolecular bond rearrangement of the methyl group. We have performed ab initio quantum chemical calculations that show the preferred pathway for C-H3 bond cleavage. Fragmentation of organic molecules like methanol under impact of highly charged ions is suggested as an alternative mechanism of H3+ formation in outer space.

  20. Molecular Rearrangement of an Aza-Scorpiand Macrocycle Induced by pH: A Computational Study.

    PubMed

    De Julián-Ortiz, Jesus Vicente; Verdejo, Begoña; Polo, Víctor; Besalú, Emili; García-España, Enrique

    2016-01-01

    Rearrangements and their control are a hot topic in supramolecular chemistry due to the possibilities that these phenomena open in the design of synthetic receptors and molecular machines. Macrocycle aza-scorpiands constitute an interesting system that can reorganize their spatial structure depending on pH variations or the presence of metal cations. In this study, the relative stabilities of these conformations were predicted computationally by semi-empirical and density functional theory approximations, and the reorganization from closed to open conformations was simulated by using the Monte Carlo multiple minimum method. PMID:27428955

  1. Rearranged Anaplastic Lymphoma Kinase (ALK) Gene in Adult-Onset Papillary Thyroid Cancer Amongst Atomic Bomb Survivors

    PubMed Central

    Mukai, Mayumi; Takahashi, Keiko; Hayashi, Yuzo; Nakachi, Kei; Kusunoki, Yoichiro

    2012-01-01

    Background We previously noted that among atomic bomb survivors (ABS), the relative frequency of cases of adult papillary thyroid cancer (PTC) with chromosomal rearrangements (mainly RET/PTC) was significantly greater in those with relatively higher radiation exposure than those with lower radiation exposure. In contrast, the frequency of PTC cases with point mutations (mainly BRAFV600E) was significantly lower in patients with relatively higher radiation exposure than those with lower radiation exposure. We also found that among ABS, the frequency of PTC cases with no detectable gene alterations in RET, neurotrophic tyrosine kinase receptor 1 (NTRK1), BRAF, or RAS was significantly higher in patients with relatively higher radiation exposure than those with lower radiation exposure. However, in ABS with PTC, the relationship between the presence of the anaplastic lymphoma kinase (ALK) gene fused with other gene partners and radiation exposure has received little study. In this study, we tested the hypothesis that the relative frequency of rearranged ALK in ABS with PTC, and with no detectable gene alterations in RET, NTRK1, BRAF, or RAS, would be greater in those having relatively higher radiation exposures. Methods The 105 subjects in the study were drawn from the Life Span Study cohort of ABS of Hiroshima and Nagasaki who were diagnosed with PTC between 1956 and 1993. Seventy-nine were exposed (>0 mGy), and 26 were not exposed to A-bomb radiation. In the 25 ABS with PTC, and with no detectable gene alterations in RET, NTRK1, BRAF, or RAS, we examined archival, formalin-fixed, paraffin-embedded PTC specimens for rearrangement of ALK using reverse transcription–polymerase chain reaction and 5′ rapid amplification of cDNA ends (5′ RACE). Results We found rearranged ALK in 10 of 19 radiation-exposed PTC cases, but none among 6 patients with PTC with no radiation exposure. In addition, solid/trabecular-like architecture in PTC was closely associated with ALK

  2. Kinase Expression and Chromosomal Rearrangements in Papillary Thyroid Cancer Tissues: Investigations at the Molecular and Microscopic Levels

    SciTech Connect

    Weier, Heinz-Ulrich; Kwan, Johnson; Lu, Chun-Mei; Ito, Yuko; Wang, Mei; Baumgartner, Adolf; Hayward, Simon W.; Weier, Jingly F.; Zitzelsberger, Horst F.

    2009-07-07

    Structural chromosome aberrations are known hallmarks of many solid tumors. In the papillary form of thyroid cancer (PTC), for example, activation of the receptor tyrosine kinase (RTK) genes, ret or the neurotrophic tyrosine kinase receptor type I (NTRK1) by intra- or interchromosomal rearrangements have been suggested as a cause of the disease. The 1986 accident at the nuclear power plant in Chernobyl, USSR, led to the uncontrolled release of high levels of radioisotopes. Ten years later, the incidence of childhood papillary thyroid cancer (chPTC) near Chernobyl had risen by two orders of magnitude. Tumors removed from some of these patients showed aberrant expression of the ret RTK gene due to a ret/PTC1 or ret/PTC3 rearrangement involving chromosome 10. However, many cultured chPTC cells show a normal G-banded karyotype and no ret rearrangement. We hypothesize that the 'ret-negative' tumors inappropriately express a different oncogene or have lost function of a tumor suppressor as a result of chromosomal rearrangements, and decided to apply molecular and cytogenetic methods to search for potentially oncogenic chromosomal rearrangements in Chernobyl chPTC cases. Knowledge of the kind of genetic alterations may facilitate the early detection and staging of chPTC as well as provide guidance for therapeutic intervention.

  3. Cytogenetic and molecular study of fifty constitutional rearrangements and fifteen couples with multiple miscarriages using TTAGGG sequence

    SciTech Connect

    Berube, D.; Matte, C.; Gagne, R.

    1994-09-01

    Telomeres have been extensively studied. In humans, they are constituted of a nonrandom mixture of at least three types of G-rich hexamere repeat units. The majority of telomeric repeat units are detected by the TTAGGG repeat. This sequence is highly conservated and seems to be essential for a normal cellular function. Investigators have studied this sequence in different rearrangements and have raised the intriguing possibility that specific telomere sequences could be involved in cryptic translocations. As telomeric sequences seem to play a primordial role in different rearrangements, we studied the presence of interstitial telomere sequences in 24 patients with a balanced translocation and a normal phenotype and 26 patients with unbalanced rearrangements and an abnormal phenotype. We also tested whether this telomere sequence occured with an increased frequency in couples with multiple miscarriages and without chromosomal abnormality. The data obtained in this study showed no significant telomere interstitial sequence in any patient analyzed as well in balanced and unbalanced rearrangements as in couples with multiple miscarriages. The results obtained from this experiment do not exclude the possibility that interstitial telomere sequences can exist and play a primordial role in cryptic translocations but it seems to be a rare and specific event. Presumably, this event may arise when a rearrangement involves several breaks.

  4. CRKL mediates EML4-ALK signaling and is a potential therapeutic target for ALK-rearranged lung adenocarcinoma

    PubMed Central

    Voeller, Donna; Gower, Arjan; Kim, In-Kyu; Zhang, Yu-Wen; Giaccone, Giuseppe

    2016-01-01

    Anaplastic lymphoma kinase (ALK) gene rearrangements are oncogenic drivers in a small subset of patients with non-small-cell lung cancer (NSCLC). The ALK inhibitors are highly effective in NSCLC patients harboring ALK rearrangements; however, most patients acquire resistance to the therapy following an initial response. Mechanisms of acquired resistance are complex. We used LC-MS/MS-based phosphotyrosine-peptide profiling in the EML4-ALK rearranged H3122 and H2228 cells treated with ALK inhibitors, to identify downstream effectors of ALK. We then used Western blot, siRNA experiments, cell proliferation, viability and migration assays to validate our findings. We identified CRKL as a novel downstream effector of ALK signaling. We demonstrated that CRKL tyrosine phosphorylation was repressed by pharmacological inhibition or small interfering RNA (siRNA) knockdown of ALK in the ALK-rearranged cells. More importantly, CRKL knockdown attenuated their cell proliferation, viability, and migration, but it had no effect on ALK phosphorylation and expression in these cells. Furthermore, CRKL tyrosine phosphorylation was inhibited by dasatinib (an inhibitor of ABL and SRC kinases), which in combination with the ALK inhibitor crizotinib displayed a synergistic inhibitory effect in vitro. In conclusion, our study suggests that CRKL is a key downstream effector of ALK, and combined inhibition of ALK and CRKL may represent an effective strategy for treating ALK-rearranged NSCLC patients. PMID:27078848

  5. Homeologous Recombination Plays a Major Role in Chromosome Rearrangements That Occur During Meiosis of Brassica napus Haploids

    PubMed Central

    Nicolas, Stéphane D.; Mignon, Guillaume Le; Eber, Frédérique; Coriton, Olivier; Monod, Hervé; Clouet, Vanessa; Huteau, Virginie; Lostanlen, Antoine; Delourme, Régine; Chalhoub, Boulos; Ryder, Carol D.; Chèvre, Anne Marie; Jenczewski, Eric

    2007-01-01

    Chromosomal rearrangements can be triggered by recombination between distinct but related regions. Brassica napus (AACC; 2n = 38) is a recent allopolyploid species whose progenitor genomes are widely replicated. In this article, we analyze the extent to which chromosomal rearrangements originate from homeologous recombination during meiosis of haploid B. napus (n = 19) by genotyping progenies of haploid × euploid B. napus with molecular markers. Our study focuses on three pairs of homeologous regions selected for their differing levels of divergence (N1/N11, N3/N13, and N9/N18). We show that a high number of chromosomal rearrangements occur during meiosis of B. napus haploid and are transmitted by first division restitution (FDR)-like unreduced gametes to their progeny; half of the progeny of Darmor-bzh haploids display duplications and/or losses in the chromosomal regions being studied. We demonstrate that half of these rearrangements are due to recombination between regions of primary homeology, which represents a 10- to 100-fold increase compared to the frequency of homeologous recombination measured in euploid lines. Some of the other rearrangements certainly result from recombination between paralogous regions because we observed an average of one to two autosyndetic A–A and/or C–C bivalents at metaphase I of the B. napus haploid. These results are discussed in the context of genome evolution of B. napus. PMID:17151256

  6. Study of particle rearrangement, compression behavior and dissolution properties after melt dispersion of ibuprofen, Avicel and Aerosil

    PubMed Central

    Mallick, Subrata; Kumar Pradhan, Saroj; Chandran, Muronia; Acharya, Manoj; Digdarsini, Tanmayee; Mohapatra, Rajaram

    2011-01-01

    Particle rearrangements, compaction under pressure and in vitro dissolution have been evaluated after melt dispersion of ibuprofen, Avicel and Aerosil. The Cooper–Eaton and Kuno equations were utilized for the determination of particle rearrangement and compression behavior from tap density and compact data. Particle rearrangement could be divided into two stages as primary and secondary rearrangement. Transitional tapping between the stages was found to be 20–25 taps in ibuprofen crystalline powder, which was increased up to 45 taps with all formulated powders. Compaction in the rearrangement stages was increased in all the formulations with respect to pure ibuprofen. Significantly increased compaction of ibuprofen under pressure can be achieved using Avicel by melt dispersion technique, which could be beneficial in ibuprofen tablet manufacturing by direct compression. SEM, FTIR and DSC have been utilized for physicochemical characterization of the melt dispersion powder materials. Dissolution of ibuprofen from compacted tablet of physical mixture and melt dispersion particles has also been improved greatly in the following order: Ibc

  7. Large BRCA1 and BRCA2 genomic rearrangements in Malaysian high risk breast-ovarian cancer families.

    PubMed

    Kang, Peter; Mariapun, Shivaani; Phuah, Sze Yee; Lim, Linda Shushan; Liu, Jianjun; Yoon, Sook-Yee; Thong, Meow Keong; Mohd Taib, Nur Aishah; Yip, Cheng Har; Teo, Soo-Hwang

    2010-11-01

    Early studies of genetic predisposition due to the BRCA1 and BRCA2 genes have focused largely on sequence alterations, but it has now emerged that 4-28% of inherited mutations in the BRCA genes may be due to large genomic rearrangements of these genes. However, to date, there have been relatively few studies of large genomic rearrangements in Asian populations. We have conducted a full sequencing and large genomic rearrangement analysis (using Multiplex Ligation-dependent Probe Amplification, MLPA) of 324 breast cancer patients who were selected from a multi-ethnic hospital-based cohort on the basis of age of onset of breast cancer and/or family history. Three unrelated individuals were found to have large genomic rearrangements: 2 in BRCA1 and 1 in BRCA2, which accounts for 2/24 (8%) of the total mutations detected in BRCA1 and 1/23 (4%) of the mutations in BRCA2 detected in this cohort. Notably, the family history of the individuals with these mutations is largely unremarkable suggesting that family history alone is a poor predictor of mutation status in Asian families. In conclusion, this study in a multi-ethnic (Malay, Chinese, Indian) cohort suggests that large genomic rearrangements are present at a low frequency but should nonetheless be included in the routine testing for BRCA1 and BRCA2. PMID:20617377

  8. Association between BRAF and RAS mutations, and RET rearrangements and the clinical features of papillary thyroid cancer

    PubMed Central

    Ming, Jie; Liu, Zeming; Zeng, Wen; Maimaiti, Yusufu; Guo, Yawen; Nie, Xiu; Chen, Chen; Zhao, Xiangwang; Shi, Lan; Liu, Chunping; Huang, Tao

    2015-01-01

    Objective: To evaluate the significance of BRAF V600E and Ras mutations, and RET rearrangements in papillary thyroid cancer (PTC) in the South central region of China. Methods: We included patients from Union hospital’s pathology archive diagnosed with PTC and meeting the criteria for BRAF mutation, RAS mutation, and RET rearrangement testing. Medical records were analyzed for BRAF and RAS mutation status, RET rearrangements (positive or negative), and a list of standardized clinicopathologic features. Results: Positive BRAF mutation was found to be significantly associated with age and extrathyroidal extension (P=0.011 and P=0.013, respectively). However, there was no significant association between BRAF mutation and sex, tumor size, histological subtype, multifocality, or accompanying nodular goiter and Hashimoto’s. On the other hand, none of these characteristics of PTC were been found to be associated with RAS mutation. Additionally, the frequency of RET rearrangements was higher in patients ≤45 years old than that in patients >45 years old. Conclusions: We demonstrated that the BRAF V600E mutation slightly correlated with the clinicopathological characteristics of PTC in the Han population. Furthermore, neither RAS mutation nor RET rearrangements were found to be associated with the clinicopathological characteristics of PTCs. Our work provides useful information on somatic mutations to predict the risk of PTC in different ethnic groups. PMID:26823860

  9. Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations

    PubMed Central

    Ma, Zhihong; Yang, Xuefen; Bercsenyi, Miklos; Wu, Junjie; Yu, Yongyao; Wei, Kaijian; Fan, Qixue; Yang, Ruibin

    2015-01-01

    To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species. PMID:26492246

  10. Large BRCA1 and BRCA2 genomic rearrangements in Malaysian high risk breast-ovarian cancer families.

    PubMed

    Kang, Peter; Mariapun, Shivaani; Phuah, Sze Yee; Lim, Linda Shushan; Liu, Jianjun; Yoon, Sook-Yee; Thong, Meow Keong; Mohd Taib, Nur Aishah; Yip, Cheng Har; Teo, Soo-Hwang

    2010-11-01

    Early studies of genetic predisposition due to the BRCA1 and BRCA2 genes have focused largely on sequence alterations, but it has now emerged that 4-28% of inherited mutations in the BRCA genes may be due to large genomic rearrangements of these genes. However, to date, there have been relatively few studies of large genomic rearrangements in Asian populations. We have conducted a full sequencing and large genomic rearrangement analysis (using Multiplex Ligation-dependent Probe Amplification, MLPA) of 324 breast cancer patients who were selected from a multi-ethnic hospital-based cohort on the basis of age of onset of breast cancer and/or family history. Three unrelated individuals were found to have large genomic rearrangements: 2 in BRCA1 and 1 in BRCA2, which accounts for 2/24 (8%) of the total mutations detected in BRCA1 and 1/23 (4%) of the mutations in BRCA2 detected in this cohort. Notably, the family history of the individuals with these mutations is largely unremarkable suggesting that family history alone is a poor predictor of mutation status in Asian families. In conclusion, this study in a multi-ethnic (Malay, Chinese, Indian) cohort suggests that large genomic rearrangements are present at a low frequency but should nonetheless be included in the routine testing for BRCA1 and BRCA2.

  11. Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.

    PubMed

    Rumpf, Tobias; Schiedel, Matthias; Karaman, Berin; Roessler, Claudia; North, Brian J; Lehotzky, Attila; Oláh, Judit; Ladwein, Kathrin I; Schmidtkunz, Karin; Gajer, Markus; Pannek, Martin; Steegborn, Clemens; Sinclair, David A; Gerhardt, Stefan; Ovádi, Judit; Schutkowski, Mike; Sippl, Wolfgang; Einsle, Oliver; Jung, Manfred

    2015-01-01

    Sirtuins are a highly conserved class of NAD(+)-dependent lysine deacylases. The human isotype Sirt2 has been implicated in the pathogenesis of cancer, inflammation and neurodegeneration, which makes the modulation of Sirt2 activity a promising strategy for pharmaceutical intervention. A rational basis for the development of optimized Sirt2 inhibitors is lacking so far. Here we present high-resolution structures of human Sirt2 in complex with highly selective drug-like inhibitors that show a unique inhibitory mechanism. Potency and the unprecedented Sirt2 selectivity are based on a ligand-induced structural rearrangement of the active site unveiling a yet-unexploited binding pocket. Application of the most potent Sirtuin-rearranging ligand, termed SirReal2, leads to tubulin hyperacetylation in HeLa cells and induces destabilization of the checkpoint protein BubR1, consistent with Sirt2 inhibition in vivo. Our structural insights into this unique mechanism of selective sirtuin inhibition provide the basis for further inhibitor development and selective tools for sirtuin biology. PMID:25672491

  12. Selective Sirt2 inhibition by ligand-induced rearrangement of the active site

    PubMed Central

    Rumpf, Tobias; Schiedel, Matthias; Karaman, Berin; Roessler, Claudia; North, Brian J.; Lehotzky, Attila; Oláh, Judit; Ladwein, Kathrin I.; Schmidtkunz, Karin; Gajer, Markus; Pannek, Martin; Steegborn, Clemens; Sinclair, David A.; Gerhardt, Stefan; Ovádi, Judit; Schutkowski, Mike; Sippl, Wolfgang; Einsle, Oliver; Jung, Manfred

    2015-01-01

    Sirtuins are a highly conserved class of NAD+-dependent lysine deacylases. The human isotype Sirt2 has been implicated in the pathogenesis of cancer, inflammation and neurodegeneration, which makes the modulation of Sirt2 activity a promising strategy for pharmaceutical intervention. A rational basis for the development of optimized Sirt2 inhibitors is lacking so far. Here we present high-resolution structures of human Sirt2 in complex with highly selective drug-like inhibitors that show a unique inhibitory mechanism. Potency and the unprecedented Sirt2 selectivity are based on a ligand-induced structural rearrangement of the active site unveiling a yet-unexploited binding pocket. Application of the most potent Sirtuin-rearranging ligand, termed SirReal2, leads to tubulin hyperacetylation in HeLa cells and induces destabilization of the checkpoint protein BubR1, consistent with Sirt2 inhibition in vivo. Our structural insights into this unique mechanism of selective sirtuin inhibition provide the basis for further inhibitor development and selective tools for sirtuin biology. PMID:25672491

  13. Molecular cytogenetic characterization of multiple intrachromosomal rearrangements in two representatives of the genus Turdus (Turdidae, Passeriformes).

    PubMed

    Kretschmer, Rafael; Gunski, Ricardo José; Garnero, Analía Del Valle; Furo, Ivanete de Oliveira; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A; de Oliveira, Edivaldo Herculano Corrêa

    2014-01-01

    Turdus rufiventris and Turdus albicollis, two songbirds belonging to the family Turdidae (Aves, Passeriformes) were studied by C-banding, 18S rDNA, as well as the use of whole chromosome probes derived from Gallus gallus (GGA) and Leucopternis albicollis (LAL). They showed very similar karyotypes, with 2n = 78 and the same pattern of distribution of heterochromatic blocks and hybridization patterns. However, the analysis of 18/28S rDNA has shown differences in the number of NOR-bearing chromosomes and ribosomal clusters. The hybridization pattern of GGA macrochromosomes was similar to the one found in songbirds studied by Fluorescent in situ hybridization, with fission of GGA 1 and GGA 4 chromosomes. In contrast, LAL chromosome paintings revealed a complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) on chromosome 2, which corresponds to GGA1q. The first inversion changed the chromosomal morphology and the second and third inversions changed the order of chromosome segments. Karyotype analysis in Turdus revealed that this genus has derived characteristics in relation to the putative avian ancestral karyotype, highlighting the importance of using new tools for analysis of chromosomal evolution in birds, such as the probes derived from L. albicollis, which make it possible to identify intrachromosomal rearrangements not visible with the use of GGA chromosome painting solely.

  14. Theoretical study of the mechanism of the rearrangement-cleavage reactions of allylenammonium salts

    SciTech Connect

    Kletskii, M.E.; Minkin, V.I.; Babayan, A.T.

    1988-03-10

    In a theoretical study of the mechanism of the rearrangement-cleavage of tetra-substituted ammonium salts containing 1,2- and 3,4-unsaturated groups using the CNDO/2 and MINDO/3 semiempirical methods, calculations were carried out to determine the electron density in trimethylvinylammonium, trimethylethynylammonium, and phosphonium cations and the minimal energy pathways for the 3,3-sigmatropic shift reactions in the vinylallylammonium cation and of the product of the /alpha/-addition of a hydride ion to it (nucleophilic catalysis model). According to the calculation data, the nucleophilic attack of enammonium compounds in basic media is directed toward the /alpha/-position of the 1,2-unsaturated group. The driving force for the rearrangement-cleavage is the attack of the /alpha/-position by the nucleophile which results in intramolecular C-alkylation by a concerted 3,3-sigmatropic shift mechanism. The calculated activation barrier of the catalyzed reaction (15.8 kcal/mole) is 7.4 kcal/mole lower than in the absence of nucleophilic action.

  15. Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase

    PubMed Central

    Klein, Tobias; Vajpai, Navratna; Phillips, Jonathan J.; Davies, Gareth; Holdgate, Geoffrey A.; Phillips, Chris; Tucker, Julie A.; Norman, Richard A.; Scott, Andrew D.; Higazi, Daniel R.; Lowe, David; Thompson, Gary S.; Breeze, Alexander L.

    2015-01-01

    Protein tyrosine kinases differ widely in their propensity to undergo rearrangements of the N-terminal Asp–Phe–Gly (DFG) motif of the activation loop, with some, including FGFR1 kinase, appearing refractory to this so-called ‘DFG flip'. Recent inhibitor-bound structures have unexpectedly revealed FGFR1 for the first time in a ‘DFG-out' state. Here we use conformationally selective inhibitors as chemical probes for interrogation of the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our detailed structural and biophysical insights identify contributions from altered dynamics in distal elements, including the αH helix, towards the outstanding stability of the DFG-out complex with the inhibitor ponatinib. We conclude that the αC-β4 loop and ‘molecular brake' regions together impose a high energy barrier for this conformational rearrangement, and that this may have significance for maintaining autoinhibition in the non-phosphorylated basal state of FGFR1. PMID:26203596

  16. Absence of subtelomeric rearrangements in selected patients with mental retardation as assessed by multiprobe T FISH

    PubMed Central

    2012-01-01

    Background Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening. Findings Fifteen patients (1–20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven. Conclusion In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR. PMID:23259705

  17. Novel CAD-ALK gene rearrangement is drugable by entrectinib in colorectal cancer

    PubMed Central

    Amatu, Alessio; Somaschini, Alessio; Cerea, Giulio; Bosotti, Roberta; Valtorta, Emanuele; Buonandi, Pasquale; Marrapese, Giovanna; Veronese, Silvio; Luo, David; Hornby, Zachary; Multani, Pratik; Murphy, Danielle; Shoemaker, Robert; Lauricella, Calogero; Giannetta, Laura; Maiolani, Martina; Vanzulli, Angelo; Ardini, Elena; Galvani, Arturo; Isacchi, Antonella; Sartore-Bianchi, Andrea; Siena, Salvatore

    2015-01-01

    Background: Activated anaplastic lymphoma kinase (ALK) gene fusions are recurrent events in a small fraction of colorectal cancers (CRCs), although these events have not yet been exploited as in other malignancies. Methods: We detected ALK protein expression by immunohistochemistry and gene rearrangements by fluorescence in situ hybridisation in the ALKA-372-001 phase I study of the pan-Trk, ROS1, and ALK inhibitor entrectinib. One out of 487 CRCs showed ALK positivity with a peculiar pattern that prompted further characterisation by targeted sequencing using anchored multiplex PCR. Results: A novel ALK fusion with the carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD) gene (CAD-ALK fusion gene) was identified. It resulted from inversion within chromosome 2 and the fusion of exons 1–35 of CAD with exons 20–29 of ALK. After failure of previous standard therapies, treatment of this patient with the ALK inhibitor entrectinib resulted in a durable objective tumour response. Conclusions: We describe the novel CAD-ALK rearrangement as an oncogene and provide the first evidence of its drugability as a new molecular target in CRC. PMID:26633560

  18. Comparative mapping identifies the fusion point of an ancient mammalian X-autosomal rearrangement

    SciTech Connect

    Wilcox, S.A.; Watson, J.M.; Spencer, J.A.

    1996-07-01

    Previous comparisons of gene location in the three major groups of mammals (eutherians, marsupials, and monotremes) have suggested that the long arm of the human X represents the ancestral mammalian X chromosome, whereas the short arm represents an autosomal region(s) recently added to the eutherian X chromosome. To identify the fusion point of this ancient X-autosome rearrangement, we have mapped four genes, three of which map near the centromere of the human Xp, in marsupials and in a monotreme. We found that ARAF1, and GATA1 are located on the X chromosome in marsupials, and ALA2 and GATA1 are also located on the X in the platypus. This implies that the proximal short arm of the human X chromosome, including the centromere, was part of the ancestral mammalian X chromosome. The fusion point between the conserved region and the recently added regions therefore maps to human Xp11.23, although gene order on the human X indicates that there has been some rearrangement of this region. 26 refs., 3 figs., 1 tab.

  19. Real-time 3D visualization of cellular rearrangements during cardiac valve formation.

    PubMed

    Pestel, Jenny; Ramadass, Radhan; Gauvrit, Sebastien; Helker, Christian; Herzog, Wiebke; Stainier, Didier Y R

    2016-06-15

    During cardiac valve development, the single-layered endocardial sheet at the atrioventricular canal (AVC) is remodeled into multilayered immature valve leaflets. Most of our knowledge about this process comes from examining fixed samples that do not allow a real-time appreciation of the intricacies of valve formation. Here, we exploit non-invasive in vivo imaging techniques to identify the dynamic cell behaviors that lead to the formation of the immature valve leaflets. We find that in zebrafish, the valve leaflets consist of two sets of endocardial cells at the luminal and abluminal side, which we refer to as luminal cells (LCs) and abluminal cells (ALCs), respectively. By analyzing cellular rearrangements during valve formation, we observed that the LCs and ALCs originate from the atrium and ventricle, respectively. Furthermore, we utilized Wnt/β-catenin and Notch signaling reporter lines to distinguish between the LCs and ALCs, and also found that cardiac contractility and/or blood flow is necessary for the endocardial expression of these signaling reporters. Thus, our 3D analyses of cardiac valve formation in zebrafish provide fundamental insights into the cellular rearrangements underlying this process.

  20. Chromodomain protein Tcd1 is required for macronuclear genome rearrangement and repair in Tetrahymena.

    PubMed

    Xu, Jing; Yuan, Yajing; Liang, Aihua; Wang, Wei

    2015-05-19

    The survival of an organism's progeny depends on the maintenance of its genome. Programmed DNA rearrangement and repair in Tetrahymena occur during the differentiation of the developing somatic macronuclear genome from the germ line micronuclear genome. Tetrahymena chromodomain protein (Tcd1) exhibited dynamic localization from the parental to the developing macronuclei. In the developing macronuclei, Tcd1 colocalized with Pdd1 and H3K9me3. Furthermore, Tcd1 colocalized with Pdd1 in the conjusome and "donut structure" of DNA elimination heterochromatin region. During the growth and conjugation stages, TCD1 knockout cells appeared normal and similar to wild-type strains. In addition, these knockout cells proceeded to the 2MAC-1MIC stage. However, the progeny of the TCD1 knockout cells did not grow upon return to SPP medium and eventually died. The deletion of the internal elimination sequence R element was partially disrupted in the developing new macronuclei. Gamma H2A staining showed that Tcd1 loss induced the accumulation of DNA double-strand breaks and the failure of genome repair. These results suggest that the chromodomain protein Tcd1 is required for the rearrangement and repair of new macronuclear genome in Tetrahymena.