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Tag dna [more than 800 articles]

 
Recent papers classified by the tag dna.
 

A magneto-DNA nanoparticle system for rapid detection and phenotyping of bacteria

  [CiTO]
Nature Nanotechnology, Vol. 8, No. 5. (05 May 2013), pp. 369-375, doi:10.1038/nnano.2013.70
posted to dna experiment lab-on-a-chip nanoparticles nmr by kristgy on 2013-05-24 13:19:28 **
 

Discrete-Time Signal Processing with DNA

  [CiTO]
ACS Synth. Biol., Vol. 2, No. 5. (12 March 2013), pp. 245-254, doi:10.1021/sb300087n
posted to circuits dna dna_computing synthetic_biology by pablocarb on 2013-05-24 09:40:39 **

Abstract

We present a methodology for implementing discrete-time signal processing operations, such as filtering, with molecular reactions. The reactions produce time-varying output quantities of molecules as a function of time-varying input quantities according to a functional specification. This computation is robust and independent of the reaction rates, provided that the rate constants fall within coarse categories. We describe two approaches: one entails synchronization with a clock signal, implemented through sustained chemical oscillations; the other is ?self-timed? or asynchronous. We illustrate the methodology ...

 

Nonresonant Confocal Raman Imaging of DNA and Protein Distribution in Apoptotic Cells

  [CiTO]
Biophysical Journal, Vol. 84, No. 6. (June 2003), pp. 3968-3981, doi:10.1016/s0006-3495(03)75124-8
posted to cell dna protein raman by suki_1 on 2013-05-23 14:44:11 **
 

Direct imaging of single UvrD helicase dynamics on long single-stranded DNA

  [CiTO]
Nature Communications, Vol. 4 (21 May 2013), 1878, doi:10.1038/ncomms2882
posted to bacteria dna helicase by jjray on 2013-05-22 17:04:54 **
 

On the N1–H and N3–H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study

  [CiTO]
J. Chem. Theory Comput., Vol. 8, No. 8. (12 July 2012), pp. 2769-2776, doi:10.1021/ct300153f
posted to attachment dissociative dna electron uracil by Xavi85 on 2013-05-20 11:32:23 *****

Abstract

The dissociative electron-attachment (DEA) phenomena at the N1?H and N3?H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence-bound π? and two dissociative σ? states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the π? and σ? are established as the structures which activate the DEA processes. The ...

 

Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge.

  [CiTO]
Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 50. (16 December 2008), pp. 19720-19725, doi:10.1073/pnas.0808296105
posted to dna by biblioteca_babel on 2013-05-19 13:07:46 ** along with 2 people jstapleton russell_aidan

Abstract

Both protein and solid-state nanopores are under intense investigation for the analysis of nucleic acids. A crucial advantage of protein nanopores is that site-directed mutagenesis permits precise tuning of their properties. Here, by augmenting the internal positive charge within the alpha-hemolysin pore and varying its distribution, we increase the frequency of translocation of a 92-nt single-stranded DNA through the pore at +120 mV by approximately ...

 

DNA-based programming of quantum dot valency, self-assembly and luminescence

  [CiTO]
Nat Nano, Vol. 6, No. 8. (August 2011), pp. 485-490, doi:10.1038/nnano.2011.100
posted to dna by biblioteca_babel on 2013-05-19 12:40:26 **
 

DNA charge transport over 34 nm

  [CiTO]
Nat Chem, Vol. 3, No. 3. (March 2011), pp. 228-233, doi:10.1038/nchem.982
posted to dna by biblioteca_babel on 2013-05-19 12:25:45 ** along with 1 person hanniy
 

Partial sequencing of a single DNA molecule with a scanning tunnelling microscope

  [CiTO]
Nat Nano, Vol. 4, No. 8. (05 August 2009), pp. 518-522, doi:10.1038/nnano.2009.155
posted to dna by biblioteca_babel  on 2013-05-19 12:25:06 ** along with 1 person alexknight

Abstract

The scanning tunnelling microscope is capable of the real-space imaging and spectroscopy of molecules on an atomic scale. Numerous attempts have been made to use the scanning tunnelling microscope to sequence single DNA molecules, but difficulties in preparing samples of long-chain DNA molecules on surfaces, and problems in reproducing results have limited these experiments1, 2, 3, 4, 5, 6. Here, we report single-molecule DNA sequencing with a scanning tunnelling microscope by using an oblique pulse-injection method to deposit the molecules onto ...

 

Nanomaterials: DNA brings quantum dots to order

  [CiTO]
Nat Nano, Vol. 6, No. 8. (August 2011), pp. 463-464, doi:10.1038/nnano.2011.126
posted to dna by biblioteca_babel on 2013-05-19 12:24:24 **
 

Scanning tunnelling microscopy: A DNA sequence scanned

  [CiTO]
Nat Nano, Vol. 4, No. 8. (August 2009), pp. 476-477, doi:10.1038/nnano.2009.212
posted to dna by biblioteca_babel on 2013-05-19 12:24:05 **
 

Solid-state nanopores

  [CiTO]
Nat Nano, Vol. 2, No. 4. (April 2007), pp. 209-215, doi:10.1038/nnano.2007.27
posted to dna by biblioteca_babel on 2013-05-19 12:23:16 **
 

Solid-state nanopore channels with DNA selectivity

  [CiTO]
Nat Nano, Vol. 2, No. 4. (April 2007), pp. 243-248, doi:10.1038/nnano.2007.78
posted to dna by biblioteca_babel on 2013-05-19 12:22:53 ** along with 1 person dna

Abstract

Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be determined by measuring how the forces on the DNA molecules, and also the ion currents through the nanopore, change as the molecules pass through the nanopore. Unlike their biological counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solutions and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a `probe' of hair-pin loop DNA ...

 

DNA sequencing: Read with quantum mechanics

  [CiTO]
Nat Nano, Vol. 5, No. 4. (April 2010), pp. 246-247, doi:10.1038/nnano.2010.72
posted to dna by biblioteca_babel on 2013-05-19 12:22:37 **
 

DNA nanotechnology: Geometrical self-assembly

  [CiTO]
Nat Chem, Vol. 3, No. 8. (August 2011), pp. 580-581, doi:10.1038/nchem.1097
posted to dna by biblioteca_babel on 2013-05-19 12:21:44 ** along with 1 person banannah
 

DNA Nanotechnology: A metamaterial with memory

  [CiTO]
Nat Nano, Vol. 7, No. 12. (December 2012), pp. 773-774, doi:10.1038/nnano.2012.221
posted to dna by biblioteca_babel on 2013-05-19 12:21:27 **
 

Folding and cutting DNA into reconfigurable topological nanostructures

  [CiTO]
Nat Nano, Vol. 5, No. 10. (October 2010), pp. 712-717, doi:10.1038/nnano.2010.193
posted to dna by biblioteca_babel  on 2013-05-19 12:20:51 ** along with 3 people and 1 group ibi001 Pedersen russell_aidan DNA nanotechnology
 

Single-molecule chemical reactions on DNA origami

  [CiTO]
Nat Nano, Vol. 5, No. 3. (28 March 2010), pp. 200-203, doi:10.1038/nnano.2010.5
posted to dna by biblioteca_babel  on 2013-05-19 12:20:29 ** along with 5 people and 1 group dna mkryj oteri Pedersen russell_aidan DNA nanotechnology

Abstract

DNA nanotechnology1, 2 and particularly DNA origami3, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures4, 5, 6, 7, 8, 9, 10. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged11, 12, 13. Here, we show that chemical reactions with ...

 

Challenges and opportunities for structural DNA nanotechnology

  [CiTO]
Nature Nanotechnology, Vol. 6, No. 12. (06 November 2011), pp. 763-772, doi:10.1038/nnano.2011.187
posted to dna by biblioteca_babel  on 2013-05-19 12:19:43 ** along with 3 people and 1 group heathervincent nsm120 Pedersen DNA nanotechnology
 

In Vivo Facilitated Diffusion Model

  [CiTO]
PLoS ONE, Vol. 8, No. 1. (18 January 2013), e53956, doi:10.1371/journal.pone.0053956
posted to biophysics brownian dna by parrot on 2013-05-19 04:42:47 **

Abstract

Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. ...

 

Nanoparticle assembly: DNA provides control

  [CiTO]
Nat Mater, Vol. 8, No. 5. (May 2009), pp. 365-366, doi:10.1038/nmat2436
posted to dna by biblioteca_babel on 2013-05-18 12:00:38 **
 

Electrically controlled DNA adhesion

  [CiTO]
Nat Nano, Vol. 5, No. 2. (20 February 2010), pp. 154-159, doi:10.1038/nnano.2009.377
posted to dna by biblioteca_babel  on 2013-05-18 11:49:08 ** along with 1 person quanwang

Abstract

The ability to control the interaction of polyelectrolytes, such as DNA or proteins, with charged surfaces is of pivotal importance for a multitude of biotechnological applications. Previously, we measured the desorption forces of single polymers on charged surfaces using an atomic force microscope. Here, we show that the adhesion of DNA on gold electrodes modified with self-assembled monolayers can be biased by the composition of the monolayer and externally controlled by means of the electrode potential. Positive potentials induced DNA adsorption ...

 

A Cationic Zinc Porphyrin as a Chiroptical Probe for Z-DNA

  [CiTO]
Angewandte Chemie International Edition, Vol. 44, No. 26. (27 June 2005), pp. 4006-4009, doi:10.1002/anie.200501149
posted to cd chirality dna porphyrins z-dna by amammana1 on 2013-05-17 20:23:22 **
 

Interactions of a Tetraanionic Porphyrin with DNA: from a Z-DNA Sensor to a Versatile Supramolecular Device

  [CiTO]
J. Am. Chem. Soc., Vol. 131, No. 6. (21 January 2009), pp. 2046-2047, doi:10.1021/ja808099u
posted to device dna porphyrins by amammana1 on 2013-05-17 20:21:24 *****

Abstract

The anionic nickel(II) porphyrin NiTPPS is able to selectively sense the spermine induced left-handed Z-form of DNA while it is completely silent in the presence of right-handed B-DNA. Interactions between the DNA and the porphyrin can be easily modulated by pH and temperature. The resulting Z-DNA?porphyrin?spermine complex behaves as a supramolecular reversible information storage system and as a reversible AND logic gate. ...

 

Role of Environmental Factors on the Structure and Spectroscopic Response of 5′-DNA–Porphyrin Conjugates Caused by Changes in the Porphyrin–Porphyrin Interactions

  [CiTO]
Chem. Eur. J., Vol. 15, No. 44. (9 November 2009), pp. 11853-11866, doi:10.1002/chem.200902029
posted to cd chirality circular dichroism dna porphyrins by amammana1 on 2013-05-17 20:08:16 **

Abstract

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin– and metalloporphyrin–oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found ...

 

A Chiroptical Photoswitchable DNA Complex

  [CiTO]
J. Phys. Chem. B, Vol. 115, No. 40. (31 August 2011), pp. 11581-11587, doi:10.1021/jp205893y

Abstract

The interesting structural, electronic, and optical properties of DNA provide fascinating opportunities for developing nanoscale smart materials by integrating DNA with opto-electronic components. In this article we demonstrate the electrostatic binding of an amine-terminated dithienylethene (DET) molecular switch to double-stranded synthetic polynucleotides. The DET switch can undergo photochemical ring-closure and opening reactions. Circular dichroism (CD) and UV?vis spectroscopy show that both the open, 1o, and the closed, 1c, forms of the switch bind to DNA. Upon addition of DNA to a ...

 

Complex Archimedean Tiling Self-Assembled from DNA Nanostructures

  [CiTO]
J. Am. Chem. Soc. (7 May 2013), doi:10.1021/ja4035957
posted to 23-05-13 2d_lattice dna by ts3435  on 2013-05-17 09:11:54 ** along with 1 person andrewhuynguyen

Abstract

Archimedean tilings are periodic polygonal tessellations that are created by placing regular polygons edge-to-edge around a vertex to fill the plane. Here we show that three- and four-arm DNA junction tiles with specifically designed arm lengths and intertile sticky-end interactions can be used to form sophisticated two-dimensional (2D) and three-dimensional (3D) tessellation patterns. We demonstrate two different complex Archimedean patterns, (33.42) and (32.4.3.4), and the formation of 2D lattices, 3D tubes, and sealed polygon-shaped pockets from the tessellations. The successful growth ...

 

TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models

  [CiTO]
Bioinformatics, Vol. 29, No. 10. (15 May 2013), pp. 1345-1347, doi:10.1093/bioinformatics/btt133
posted to dna rna by flbarroso on 2013-05-15 21:50:57 **

Abstract

Summary: The mesoscopic statistical physics models, known generically as Peyrard–Bishop (PB) models, have found many applications for the study of oligonucleotide properties. Unfortunately, PB models have not reached a wider non-specialized audience for the lack of freely available software implementations. Here we present an extensible C++ implementation of four variants of the PB model, which allows the user to calculate melting temperatures from tested model parameters. Even for a non-specialist, it should be straightforward to change these parameters to reflect different ...

 

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

  [CiTO]
Proceedings of the National Academy of Sciences, Vol. 110, No. 20. (14 May 2013), pp. 8290-8295, doi:10.1073/pnas.1300585110

Abstract

DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and ...

 

In vitro and in vivo expansion of hematopoietic stem cells

  [CiTO]
Oncogene, Vol. 23, No. 43. (Sep 2004), pp. 7223-32

Abstract

The capacity for sustained self-renewal膒the generation of daughter cells having the same regenerative properties as the parent cell膒is the defining feature of hematopoietic stem cells (HSCs). Strong evidence exists that self-renewal of HSC is under extrinsic biological control in vivo. A variety of cytokines, morphogenic ligands and associated signaling components influence self-renewal in culture and in vivo. Specific homeobox transcription factors act as powerful intrinsic agonists of HSC self-renewal in vitro and in vivo when supplied either as transduced cDNAs or ...

 

An ORC/Cdc6/MCM2-7 Complex Is Formed in a Multistep Reaction to Serve as a Platform for MCM Double-Hexamer Assembly.

  [CiTO]
Molecular cell (16 April 2013), doi:10.1016/j.molcel.2013.03.026
posted to dna dna_replication by cscweb on 2013-05-13 09:48:20 **

Abstract

In Saccharomyces cerevisiae and higher eukaryotes, the loading of the replicative helicase MCM2-7 onto DNA requires the combined activities of ORC, Cdc6, and Cdt1. These proteins load MCM2-7 in an unknown way into a double hexamer around DNA. Here we show that MCM2-7 recruitment by ORC/Cdc6 is blocked by an autoinhibitory domain in the C terminus of Mcm6. Interestingly, Cdt1 can overcome this inhibitory activity, ...

 

The plant genome's methylation status and response to stress: implications for plant improvement.

  [CiTO]
Curr Opin Plant Biol, Vol. 10, No. 3. (June 2007), pp. 317-322, doi:10.1016/j.pbi.2007.04.012

Abstract

Plant improvement depends on generating phenotypic variation and selecting for characteristics that are heritable. Classical genetics and early molecular genetics studies on single genes showed that differences in chromatin structure, especially cytosine methylation, can contribute to heritable phenotypic variation. Recent molecular genetic and genomic studies have revealed a new importance of cytosine methylation for gene regulation and have identified RNA interference (RNAi)-related proteins that are necessary for methylation. Methylation differences among plants can be caused by cis- or trans-acting DNA polymorphisms ...

 

Comparative Phosphoproteomic Analysis of Checkpoint Recovery Identifies New Regulators of the DNA Damage Response

  [CiTO]
Sci. Signal., Vol. 6, No. 272. (23 April 2013), rs9, doi:10.1126/scisignal.2003664
posted to checkpoint dna p53 repair by the_notch on 2013-05-11 19:38:08 **
 

The DNA sequence and biological annotation of human chromosome 1.

  [CiTO]
Nature, Vol. 441, No. 7091. (May 2006), pp. 315-321, doi:10.1038/nature04727

Abstract

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions ...

 

RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate

  [CiTO]
In Nature immunology, Vol. 10 (2009), 1065-72, doi:10.1038/ni.1779

Abstract

RNA is sensed by Toll-like receptor 7 (TLR7) and TLR8 or by the RNA helicases LGP2, Mda5 and RIG-I to trigger antiviral responses. Much less is known about sensors for DNA. Here we identify a novel DNA-sensing pathway involving RNA polymerase III and RIG-I. In this pathway, AT-rich double-stranded DNA (dsDNA) served as a template for RNA polymerase III and was transcribed into double-stranded RNA (dsRNA) containing a 5'-triphosphate moiety. Activation of RIG-I by this dsRNA induced production of type I ...

Note (first note only)

Ablasser, Andrea Bauernfeind, Franz Hartmann, Gunther Latz, Eicke Fitzgerald, Katherine A Hornung, Veit AI-065483/AI/NIAID NIH HHS/ AI-067497/AI/NIAID NIH HHS/ AI-083713/AI/NIAID NIH HHS/ Nat Immunol. 2009 Oct;10(10):1065-72. Epub 2009 Jul 16.

 

Optimized production and concentration of lentiviral vectors containing large inserts

  [CiTO]
In J Gene Med, Vol. 9 (2007), 579-84, doi:10.1002/jgm.1052

Abstract

Generation of high titer lentiviral stocks and efficient virus concentration are central to maximize the utility of lentiviral technology. Here we evaluate published protocols for lentivirus production on a range of transfer vectors differing in size (7.5-13.2 kb). We present a modified virus production protocol robustly yielding useful titers (up to 10(7)/ml) for a range of different transfer vectors containing packaging inserts up to 7.5 kb. Moreover, we find that virus recovery after concentration by ultracentrifugation depends on the size of ...

Note (first note only)

al Yacoub, Nadya Romanowska, Malgorzata Haritonova, Natalie Foerster, John eng England 2007/05/30 09:00 J Gene Med. 2007 Jul;9(7):579-84.

 

Inherited interleukin 12 deficiency in a child with bacille Calmette-Guerin and Salmonella enteritidis disseminated infection

  [CiTO]
In The Journal of clinical investigation, Vol. 102 (1998), 2035-40, doi:10.1172/JCI4950

Abstract

Interferon-gamma receptor ligand-binding chain (IFN-gammaR1) or signaling chain (IFN-gammaR2) deficiency, like interleukin 12 receptor beta1 chain (IL-12Rbeta1) deficiency, predispose to severe infections due to poorly virulent mycobacteria and salmonella. A child with bacille Calmette-Guerin and Salmonella enteritidis infection was investigated. Mutations in the genes for IFN-gammaR1, IFN-gammaR2, IL-12Rbeta1, and other molecules implicated in IL-12- or IFN-gamma-mediated immunity were sought. A large homozygous deletion within the IL-12 p40 subunit gene was found, precluding expression of functional IL-12 p70 cytokine by activated dendritic ...

Note (first note only)

Altare, F Lammas, D Revy, P Jouanguy, E Doffinger, R Lamhamedi, S Drysdale, P Scheel-Toellner, D Girdlestone, J Darbyshire, P Wadhwa, M Dockrell, H Salmon, M Fischer, A Durandy, A Casanova, J L Kumararatne, D S J Clin Invest. 1998 Dec 15;102(12):2035-40.

 

Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense

  [CiTO]
In PLoS Genet, Vol. 5 (2009), e1000562, doi:10.1371/journal.pgen.1000562

Abstract

Infectious diseases have been paramount among the threats to health and survival throughout human evolutionary history. Natural selection is therefore expected to act strongly on host defense genes, particularly on innate immunity genes whose products mediate the direct interaction between the host and the microbial environment. In insects and mammals, the Toll-like receptors (TLRs) appear to play a major role in initiating innate immune responses against microbes. In humans, however, it has been speculated that the set of TLRs could be ...

Note (first note only)

Barreiro, Luis B Ben-Ali, Meriem Quach, Helene Laval, Guillaume Patin, Etienne Pickrell, Joseph K Bouchier, Christiane Tichit, Magali Neyrolles, Olivier Gicquel, Brigitte Kidd, Judith R Kidd, Kenneth K Alcais, Alexandre Ragimbeau, Josiane Pellegrini, Sandra Abel, Laurent Casanova, Jean-Laurent Quintana-Murci, Lluis eng Howard Hughes Medical Institute/ Research Support, Non-U.S. Gov't 2009/07/18 09:00 PLoS Genet. 2009 Jul;5(7):e1000562. doi: 10.1371/journal.pgen.1000562. Epub 2009 Jul 17.

 

Quantification of viral DNA and liver enzymes in plasma improves early diagnosis and management of herpes simplex virus hepatitis

  [CiTO]
In Journal of viral hepatitis, Vol. 18 (2011), e160-6, doi:10.1111/j.1365-2893.2010.01352.x

Abstract

Herpes simplex virus (HSV) hepatitis is a rare and potential life-threatening disease. The diagnosis of HSV hepatitis is hampered by its indifferent clinical presentation, which necessitates confirmatory laboratory data to identify HSV in the affected liver. However, liver biopsies are often contraindicated in the context of coagulopathy, are prone to sampling errors and have low sensitivity in mild HSV hepatitis cases. There is an unmet need for less invasive diagnostic tools. The diagnostic and therapeutic value of HSV DNA load and ...

Note (first note only)

Beersma, M F C Verjans, G M G M Metselaar, H J Osterhaus, A D M E Berrington, W R van Doornum, G J K08 AI080952 01A1/AI/NIAID NIH HHS/ England J Viral Hepat. 2011 Apr;18(4):e160-6. doi: 10.1111/j.1365-2893.2010.01352.x. Epub 2010 Aug 12.

 

Clinical correlates of herpes simplex virus viremia among hospitalized adults

  [CiTO]
In Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, Vol. 49 (2009), 1295-301, doi:10.1086/606053

Abstract

BACKGROUND: Quantification of herpes simplex virus (HSV) DNA in the peripheral blood is often used to evaluate patients suspected of having disseminated HSV infection. Few studies have examined the clinical correlates of HSV viremia among adults. METHODS: We conducted a retrospective analysis of blood samples sent to a molecular virology reference laboratory at a university hospital for quantification of HSV DNA from October 2001 through June 2006. Medical records of patients with detectable HSV DNA were reviewed to abstract relevant clinical ...

Note (first note only)

Berrington, William R Jerome, Keith R Cook, Linda Wald, Anna Corey, Lawrence Casper, Corey AI-030731/AI/NIAID NIH HHS/ AI-07044/AI/NIAID NIH HHS/ AI-54162/AI/NIAID NIH HHS/ K08 AI080952-01A1/AI/NIAID NIH HHS/ K23 AI054162-01/AI/NIAID NIH HHS/ K23 AI054162-02/AI/NIAID NIH HHS/ K23 AI054162-03/AI/NIAID NIH HHS/ K23 AI054162-04/AI/NIAID NIH HHS/ K23 AI054162-05/AI/NIAID NIH HHS/ K24 AI-071113/AI/NIAID NIH HHS/ K24 AI071113-01/AI/NIAID NIH HHS/ K24 AI071113-02/AI/NIAID NIH HHS/ K24 AI071113-03/AI/NIAID NIH HHS/ K24 AI071113-04/AI/NIAID NIH HHS/ L30 AI075827-02/AI/NIAID NIH HHS/ P01 AI030731-18/AI/NIAID NIH HHS/ T32 AI007044-34/AI/NIAID NIH HHS/ Clin Infect Dis. 2009 Nov 1;49(9):1295-301.

 

The Legionella pneumophila icm locus: a set of genes required for intracellular multiplication in human macrophages

  [CiTO]
In Molecular microbiology, Vol. 14 (1994), 797-808

Abstract

Legionella pneumophila, the causative agent of Legionnaires' disease and related pneumonias, infects, replicates within and eventually kills human macrophages. A key feature of the intracellular life-style is the ability of the organism to replicate within a specialized phagosome which does not fuse with lysosomes or acidify. Avirulent mutants that are defective in intracellular multiplication and host-cell killing are unable to prevent phagosome-lysosome fusion. In a previous study, a 12 kb fragment of the L. pneumophila genome containing the icm locus (intracellular ...

Note (first note only)

Brand, B C Sadosky, A B Shuman, H A AI-08304/AI/NIAID NIH HHS/ AI-23549/AI/NIAID NIH HHS/ ENGLAND Mol Microbiol. 1994 Nov;14(4):797-808.

 

Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila

  [CiTO]
In Cellular microbiology, Vol. 8 (2006), 1228-40, doi:10.1111/j.1462-5822.2006.00703.x

Abstract

Adaptation to the host environment and exploitation of host cell functions are critical to the success of intracellular pathogens. Here, insight to these virulence mechanisms was obtained for the first time from the transcriptional program of the human pathogen Legionella pneumophila during infection of its natural host, Acanthamoeba castellanii. The biphasic life cycle of L. pneumophila was reflected by a major shift in gene expression from replicative to transmissive phase, concerning nearly half of the genes predicted in the genome. However, ...

Note (first note only)

Bruggemann, Holger Hagman, Arne Jules, Matthieu Sismeiro, Odile Dillies, Marie-Agnes Gouyette, Catherine Kunst, Frank Steinert, Michael Heuner, Klaus Coppee, Jean-Yves Buchrieser, Carmen England Cell Microbiol. 2006 Aug;8(8):1228-40.

 

Duplication and diversifying selection among termite antifungal peptides

  [CiTO]
In Mol Biol Evol, Vol. 21 (2004), 2256-64, doi:10.1093/molbev/msh236

Abstract

We have identified and analyzed the mRNA sequence of 20 new defensin-like peptides from 11 Australian termite species of Nasutitermes and from an outgroup, Drepanotermes rubriceps. The sequence was amplified by reverse transcriptase PCR with a degenerate primer designed from termicin, an antifungal peptide previously characterized from the termite Pseudocanthotermes spiniger. All 20 genes show high sequence identity with P. spiniger termicin and have duplicated repeatedly during the radiation of Nasutitermes. Comparison of the relative fixation rates of synonymous (silent) and ...

Note (first note only)

Bulmer, Mark S Crozier, Ross H eng Comparative Study Research Support, Non-U.S. Gov't 2004/08/20 05:00 Mol Biol Evol. 2004 Dec;21(12):2256-64. Epub 2004 Aug 18.

 

Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1

  [CiTO]
In Nature genetics, Vol. 30 (2002), 377-84, doi:10.1038/ng854

Abstract

Alteration of correct splicing patterns by disruption of an exonic splicing enhancer may be a frequent mechanism by which point mutations cause genetic diseases. Spinal muscular atrophy results from the lack of functional survival of motor neuron 1 gene (SMN1), even though all affected individuals carry a nearly identical, normal SMN2 gene. SMN2 is only partially active because a translationally silent, single-nucleotide difference in exon 7 causes exon skipping. Using ESE motif-prediction tools, mutational analysis and in vivo and in vitro ...

Note (first note only)

Cartegni, Luca Krainer, Adrian R Nat Genet. 2002 Apr;30(4):377-84. Epub 2002 Mar 4.

 

Definition of a bacterial type IV secretion pathway for a DNA substrate

  [CiTO]
In Science, Vol. 304 (2004), 1170-3, doi:10.1126/science.1095211

Abstract

Bacteria use conjugation systems, a subfamily of the type IV secretion systems, to transfer DNA to recipient cells. Despite 50 years of research, the architecture and mechanism of action of the channel mediating DNA transfer across the bacterial cell envelope remains obscure. By use of a sensitive, quantifiable assay termed transfer DNA immunoprecipitation (TrIP), we identify contacts between a DNA substrate (T-DNA) and 6 of 12 components of the VirB/D4 conjugation system of the phytopathogen Agrobacterium tumefaciens. Our results define the ...

Note (first note only)

Cascales, Eric Christie, Peter J GM48746/GM/NIGMS NIH HHS/ New York, N.Y. Science. 2004 May 21;304(5674):1170-3.

 

A commensal Helicobacter sp. of the rodent intestinal flora activates TLR2 and NOD1 responses in epithelial cells

  [CiTO]
In PloS one, Vol. 4 (2009), e5396, doi:10.1371/journal.pone.0005396

Abstract

Helicobacter spp. represent a proportionately small but significant component of the normal intestinal microflora of animal hosts. Several of these intestinal Helicobacter spp. are known to induce colitis in mouse models, yet the mechanisms by which these bacteria induce intestinal inflammation are poorly understood. To address this question, we performed in vitro co-culture experiments with mouse and human epithelial cell lines stimulated with a selection of Helicobacter spp., including known pathogenic species as well as ones for which the pathogenic potential ...

Note (first note only)

Chaouche-Drider, Nadia Kaparakis, Maria Karrar, Abdulgader Fernandez, Maria-Isabel Carneiro, Letitia A M Viala, Jerome Boneca, Ivo Gomperts Moran, Anthony P Philpott, Dana J Ferrero, Richard L Howard Hughes Medical Institute/ PLoS One. 2009;4(4):e5396. Epub 2009 Apr 29.

 

Salmonella spp. are cytotoxic for cultured macrophages

  [CiTO]
In Mol Microbiol, Vol. 21 (1996), 1101-15

Abstract

We have shown by a variety of microscopical and biochemical techniques that Salmonella spp. are cytotoxic for cultured J774A.1 and bone marrow-derived murine macrophages. The cytotoxicity is initially manifested by inhibition of membrane ruffling and macropinocytosis in infected macrophages, and is followed by cell death. Macrophages killed by Salmonella spp. exhibited features of apoptosis such as condensation and fragmentation of chromatin, membrane blebbing, and the presence of cytoplasmic nucleosomes and apoptotic bodies. Cytotoxicity does not require bacterial internalization as cytochalasin D, ...

Note (first note only)

Chen, L M Kaniga, K Galan, J E eng AI30492/AI/NIAID NIH HHS/ GM52543/GM/NIGMS NIH HHS/ Comparative Study Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. ENGLAND 1996/09/01 Mol Microbiol. 1996 Sep;21(5):1101-15.

 

RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway

  [CiTO]
In Cell, Vol. 138 (2009), 576-91, doi:10.1016/j.cell.2009.06.015

Abstract

Type I interferons (IFNs) are important for antiviral and autoimmune responses. Retinoic acid-induced gene I (RIG-I) and mitochondrial antiviral signaling (MAVS) proteins mediate IFN production in response to cytosolic double-stranded RNA or single-stranded RNA containing 5'-triphosphate (5'-ppp). Cytosolic B form double-stranded DNA, such as poly(dA-dT)*poly(dA-dT) [poly(dA-dT)], can also induce IFN-beta, but the underlying mechanism is unknown. Here, we show that the cytosolic poly(dA-dT) DNA is converted into 5'-ppp RNA to induce IFN-beta through the RIG-I pathway. Biochemical purification led to the ...

Note (first note only)

Chiu, Yu-Hsin Macmillan, John B Chen, Zhijian J R01 AI060919-05/AI/NIAID NIH HHS/ R01 GM063692-08/GM/NIGMS NIH HHS/ Cell. 2009 Aug 7;138(3):576-91. Epub 2009 Jul 23.

 

Characterization and treatment of chronic active Epstein-Barr virus disease: a 28-year experience in the United States

  [CiTO]
In Blood, Vol. 117 (2011), 5835-49, doi:10.1182/blood-2010-11-316745

Abstract

Chronic active EBV disease (CAEBV) is a lymphoproliferative disorder characterized by markedly elevated levels of antibody to EBV or EBV DNA in the blood and EBV RNA or protein in lymphocytes in tissues. We present our experience with CAEBV during the last 28 years, including the first 8 cases treated with hematopoietic stem cell transplantation in the United States. Most cases of CAEBV have been reported from Japan. Unlike CAEBV in Japan, where EBV is nearly always found in T or ...

Note (first note only)

Cohen, Jeffrey I Jaffe, Elaine S Dale, Janet K Pittaluga, Stefania Heslop, Helen E Rooney, Cliona M Gottschalk, Stephen Bollard, Catherine M Rao, V Koneti Marques, Adriana Burbelo, Peter D Turk, Siu-Ping Fulton, Rachael Wayne, Alan S Little, Richard F Cairo, Mitchell S El-Mallawany, Nader K Fowler, Daniel Sportes, Claude Bishop, Michael R Wilson, Wyndham Straus, Stephen E eng CA094237/CA/NCI NIH HHS/ P01 CA094237-09/CA/NCI NIH HHS/ P50 CA126752-04/CA/NCI NIH HHS/ P50CA126752/CA/NCI NIH HHS/ Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural 2011/04/02 06:00 Blood. 2011 Jun 2;117(22):5835-49. doi: 10.1182/blood-2010-11-316745. Epub 2011 Mar 31.

 

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

  [CiTO]
In Nat Genet, Vol. 42 (2010), 498-503, doi:10.1038/ng.590

Abstract

Mycobacterium tuberculosis is an obligate human pathogen capable of persisting in individual hosts for decades. We sequenced the genomes of 21 strains representative of the global diversity and six major lineages of the M. tuberculosis complex (MTBC) at 40- to 90-fold coverage using Illumina next-generation DNA sequencing. We constructed a genome-wide phylogeny based on these genome sequences. Comparative analyses of the sequences showed, as expected, that essential genes in MTBC were more evolutionarily conserved than nonessential genes. Notably, however, most of ...

Note (first note only)

Comas, Inaki Chakravartti, Jaidip Small, Peter M Galagan, James Niemann, Stefan Kremer, Kristin Ernst, Joel D Gagneux, Sebastien eng AI034238/AI/NIAID NIH HHS/ AI046097/AI/NIAID NIH HHS/ AI051242/AI/NIAID NIH HHS/ HHSN266200400001C/PHS HHS/ HHSN266200700022C/PHS HHS/ R01 AI046097/AI/NIAID NIH HHS/ R01 AI046097-10/AI/NIAID NIH HHS/ R01 AI051242/AI/NIAID NIH HHS/ R01 AI051242-08/AI/NIAID NIH HHS/ R01 AI051242-10/AI/NIAID NIH HHS/ R01 AI090928/AI/NIAID NIH HHS/ U117588500(88500)/Medical Research Council/United Kingdom Howard Hughes Medical Institute/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't 2010/05/25 06:00 Nat Genet. 2010 Jun;42(6):498-503. doi: 10.1038/ng.590. Epub 2010 May 23.

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