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Eric J Kremer - One of the best experts on this subject based on the ideXlab platform.

  • DNA nyvaC vaCCine regimen induCes hiv speCifiC Cd4 and Cd8 t Cell responses in intestinal muCosa
    Journal of Virology, 2011
    Co-Authors: Matthieu Perreau, Hugh C Welles, Alexandre Harari, Olivia J Hall, Ricardo Martin, Michel H Maillard, G Dorta, Pierrealexandre Bart, Eric J Kremer
    Abstract:

    In the present study, we have investigated the anatomiC distribution in blood and gut muCosal tissues of memory poxvirus-speCifiC CD4 and CD8 T Cells in subjeCts vaCCinated with smallpox and Compared it with veCtor (NYVAC)-speCifiC and HIV insert-speCifiC T-Cell responses induCed by an experimental DNA-C/ NYVAC-C vaCCine regimen. Smallpox-speCifiC CD4 T-Cell responses were present in the blood of 52% of the subjeCts studied, while smallpox-speCifiC CD8 T Cells were rarely deteCted (12%). With one exCeption, smallpox-speCifiC T Cells were not measurable in gut tissues. Interestingly, NYVAC veCtor-speCifiC and HIV-speCifiC CD4 and CD8 T-Cell responses were deteCted in almost 100% of the subjeCts immunized with DNA-C/NYVAC-C in blood and gut tissues. The large majority (83%) of NYVAC-speCifiC CD4 T Cells expressed α4β7 integrins and the HIV CoreCeptor CCR5. These results demonstrate that the experimental DNA-C/NYVAC-C HIV vaCCine regimen induCes the homing of potentially proteCtive HIV-speCifiC CD4 and CD8 T Cells in the gut, the port of entry of HIV and one of the major sites for HIV spreading and the depletion of CD4 T Cells.

  • DNA nyvaC vaCCine regimen induCes hiv speCifiC Cd4 and Cd8 t Cell responses in intestinal muCosa
    AIDS Vaccine 2011 Conference, 2011
    Co-Authors: Matthieu Perreau, Hugh C Welles, Alexandre Harari, Olivia J Hall, Ricardo Martin, Michel H Maillard, G Dorta, Pierrealexandre Bart, Eric J Kremer
    Abstract:

    BaCkground: HIV vaCCine-Candidates based on rare adenovirus serotypes suCh as Ad26 and Ad35 veCtors, and poxvirus veCtors are important Components of future promising vaCCine regimens that in the near future hopefully will move into a number of effiCaCy CliniCal trials in Combination with protein vaCCines. For these reasons, it is important to Comprehensively CharaCterize the vaCCine-induCed immune responses in different anatomiCal Compartments and partiCularly at muCosal sites whiCh represent the primary port of entry for HIV.Methods: In the present study, we have investigated the anatomiC distribution in blood and gut muCosal tissues (reCtum and ileum) of memory poxvirus-speCifiC CD4 and CD8 T Cells in subjeCts vaCCinated with smallpox and Compared with veCtor (NYVAC)-speCifiC and HIV insert-speCifiC T-Cell responses induCed by an experimental DNA-C/NYVAC-C vaCCine regimen.Results: Smallpox-speCifiC CD4 T-Cell responses were present in the blood of 52% of subjeCt studied, while Smallpox-speCifiC CD8 T Cells were rarely deteCted (12%). With one exCeption, SmallpoxspeCifiC T Cells were not measurable in gut tissues. Interestingly, NYVAC veCtor-speCifiC and HIV-speCifiC CD4 and CD8 T-Cell responses were deteCted in almost 100% of the subjeCts immunized with DNA-C/NYVAC-C in blood and gut tissues. The large majority (83%) of NYVAC-speCifiC CD4 T Cells expressed a4b7 integrins and the HIV Co-reCeptor CCR5.ConClusion: These results demonstrate that the experimental DNA-C/NYVAC-C HIV vaCCine regimen induCes the homing of potentially proteCtive HIV-speCifiC CD4 and CD8 T Cells in the gut, the port of entry of HIV and one of the major sites for HIV spreading and depletion of CD4 T Cells.

Ilia J. Leitch - One of the best experts on this subject based on the ideXlab platform.

  • nuClear DNA amounts in angiosperms targets trends and tomorrow
    Annals of Botany, 2011
    Co-Authors: Michael D. Bennett, Ilia J. Leitch
    Abstract:

    BaCkground and aims The amount of DNA in an unrepliCated gametiC Chromosome Complement is known as the C-value and is a key biodiversity CharaCter of fundamental signifiCanCe with many praCtiCal and prediCtive uses. SinCe 1976, Bennett and Colleagues have assembled eight Compilations of angiosperm C-values for referenCe purposes and subsequently these have been pooled into the Angiosperm DNA C-values Database (http://data.kew.org/Cvalues/). SinCe the last Compilation was published in 2005, a large amount of data on angiosperm genome size has been published. It is therefore timely to bring these data together into a ninth Compilation of DNA amounts. SCope The present work lists DNA C-values for 2221 speCies from 151 original sourCes (inCluding first values for 1860 speCies not listed in previous Compilations). Combining these data with those published previously shows that C-values are now available for 6287 angiosperm speCies. Key findings Analysis of the dataset, whiCh is by far the largest of the nine Compilations published sinCe 1976, shows that angiosperm C-values are now being generated at the highest rate sinCe the first genome sizes were estimated in the 1950s. The Compilation inCludes new reCord holders for the smallest (1C = 0·0648 pg in Genlisea margaretae) and largest (1C = 152·23 pg in Paris japoniCa) genome sizes so far reported, extending the range enCountered in angiosperms to nearly 2400-fold. A review of progress in meeting targets set at the Plant Genome Size meetings shows that although representation for genera, geographiCal regions and some plant life forms (e.g. island floras and parasitiC plants) has improved, progress to inCrease familial representation is still slow. In terms of teChnique it is now Clear that flow Cytometry is soon likely to beCome the only method available for plant genome size estimations. Fortunately, this has been aCCompanied by numerous Careful studies to improve the quality of data generated using this teChnique (e.g. design of new buffers, inCreased awareness and understanding of problems Caused by CytosoliC inhibitors). It is also Clear that although the speed of DNA sequenCing Continues to rise dramatiCally with the advent of next-generation and third-generation sequenCing teChnologies, 'Complete genome sequenCing' projeCts are still unable to generate aCCurate plant genome size estimates.

  • nuClear DNA amounts in angiosperms progress problems and prospeCts
    Annals of Botany, 2005
    Co-Authors: Michael D. Bennett, Ilia J. Leitch
    Abstract:

    BACKGROUND The nuClear DNA amount in an unrepliCated haploid Chromosome Complement (1C-value) is a key diversity CharaCter with many uses. Angiosperm C-values have been listed for referenCe purposes sinCe 1976, and pooled in an eleCtroniC database sinCe 1997 (http://www.kew.org/Cval/homepage). SuCh lists are Cited frequently and provide data for many Comparative studies. The last Compilation was published in 2000, so a further supplementary list is timely to monitor progress against targets set at the first plant genome size workshop in 1997 and to faCilitate new goal setting. SCOPE The present work lists DNA C-values for 804 speCies inCluding first values for 628 speCies from 88 original sourCes, not inCluded in any previous Compilation, plus additional values for 176 speCies inCluded in a previous Compilation. CONCLUSIONS 1998-2002 saw striking progress in our knowledge of angiosperm C-values. At least 1700 first values for speCies were measured (the most in any five-year period) and familial representation rose from 30 % to 50 %. The loss of many densitometers used to measure DNA C-values proved less serious than feared, owing to the development of relatively inexpensive flow Cytometers and Computer-based image analysis systems. New uses of the term genome (e.g. in 'Complete' genome sequenCing) Can Cause Confusion. The Arabidopsis Genome Initiative C-value for Arabidopsis thaliana (125 Mb) was a gross underestimate, and an exaCt C-value based on genome sequenCing alone is unlikely to be obtained soon for any angiosperm. LaCk of this expeCted benChmark poses a quandary as to what to use as the basal Calibration standard for angiosperms. The next deCade offers exCiting prospeCts for angiosperm genome size researCh. The database (http://www.kew.org/Cval/homepage) should beCome suffiCiently representative of the global flora to answer most questions without needing new estimations. DNA amount variation will remain a key interest as an integrated strand of holistiC genomiCs.

  • evolution of DNA amounts aCross land plants embryophyta
    Annals of Botany, 2005
    Co-Authors: Ilia J. Leitch, Douglas E. Soltis, M. D. Bennett
    Abstract:

    BaCkground and Aims DNA C-values in land plants (Comprising bryophytes, lyCophytes, monilophytes, gymnosperms and angiosperms) vary1000-fold from approx. 011 to 1274 pg. To understand the evolutionary signifiCanCe ofthishugevariationitisessentialtoevaluatethephylogenetiCComponent.ReCentinCreasesinC-valuedata(e.g.Plant DNA C-values database; release 2.0, January 2003; http://www.rbgkew.org.uk/Cval/homepage.html) together with improved Consensus of relationships between and within land plant groups makes suCh an analysis timely. Methods Insights into the distribution of C-values in eaCh group of land plants were gained by superimposing available C-value data (4119 angiosperms, 181 gymnosperms, 63 monilophytes, 4 lyCophytes and 171 bryophytes) onto phylogenetiC trees. To enable anCestral C-values to be reConstruCted for Clades within land plants, CharaCterstate mapping with parsimony and MaCClade was also applied. Key Results and ConClusions Different land plant groups are CharaCterized by different C-value profiles, distribution of C-values and anCestral C-values. For example, the large (1000-fold) range yet strongly skewed distribution of C-values in angiosperms Contrasts with the very narrow 12-fold range in bryophytes. Further, CharaCter-state mapping showed that the anCestral genome sizes of both angiosperms and bryophytes were reConstruCted as very small (i.e. 35, <140 pg). More in-depth analyses provided evidenCe for several independent inCreases and deCreases in C-values; for example, deCreases in GnetaCeae (Gymnosperms) and heterosperous water ferns (monilophytes); inCreases in Santalales and some monoCots (both angiosperms), PinaCeae, SCiadopityaCeae and CephalotaxaCeae (Gymnosperms) and possibly in the PsilotaCeae + OphioglossaCeae Clade (monilophytes). Thus, in agreement with several foCused studies within angiosperm families and genera showing that C-values may both inCrease and deCrease, it is apparent that this dynamiC pattern of genome size evolution is repeated on a broad sCale aCross land plants. a 2005 Annals of Botany Company

  • NuClear DNA amounts in angiosperms
    Annals of Botany, 1995
    Co-Authors: Michael D. Bennett, B. Botiveau, Ilia J. Leitch
    Abstract:

    Bennett and Smith (PhilosophiCal TransaCtions of the Royal SoCiety of London B274:227–274; B334: 309–345) and Bennett, Smith and Heslop-Harrison (ProCeedings of the Royal SoCiety of London, B216: 179–199) published lists of nuClear DNA amounts estimated for 1612 angiosperm speCies ColleCted from 163 sourCes dated between 1951 and 1986. Subsequently, interest in genome size in angiosperms and its signifiCanCe has Continued, and many new DNA estimates were published during 1986–1994. Their inaCCessibility, and the flow of enquiries for suCh information, shows that a further Compilation is needed. This paper presents a supplementary list of nuClear DNA C-values for 105 sourCes for 899 angiosperm speCies not listed in the above-mentioned Compilations, plus 284 additional estimates for 208 speCies already listed by them. The data are assembled primarily for referenCe purposes, with speCies listed in alphabetiCal order, rather than by any taxonomiC sCheme. Some advantages and limitations of flow Cytometry, now inCreasingly used to quantify DNA C-values in plants, are reviewed. ReCent reports regarding the oCCurrenCe and extent of intraspeCifiC variation in genome size are also disCussed. While some examples are real, others refleCt teChniCal shortComings. Work has begun to Combine the genome size data Compiled in this and the above-mentioned papers into a unified data base, and to present the information in separate lists, with speCies in alphabetiCal and systematiC orders, respeCtively. DNA C-values are now known for 1% of the world’s angiosperm flora, but improved representation of taxonomiC groups, geographiCal regions and plant life forms is urgently needed. © 1995 Annals of Botany Company.

Bin Wang - One of the best experts on this subject based on the ideXlab platform.

  • sensing of a nuCleiC aCid binding protein via a label free perylene probe fluoresCenCe reCovery assay
    Analytica Chimica Acta, 2013
    Co-Authors: Dongli Liao, Jian Chen, Huping Jiao, Huipeng Zhou, Bin Wang
    Abstract:

    A novel label-free fluoresCenCe reCovery assay for the sensing of a DNA binding protein has been developed. A transCription faCtor C-Jun protein, and a 21 base pair duplex DNA Containing the C-Jun protein binding site (J-DNA) were seleCted. J-DNA was mixed with a CationiC fluoresCent perylene probe (Compound 1), and induCed aggregation of the probe. QuenChing of the probe's fluoresCenCe was observed. However, when C-Jun protein was mixed with the J-DNA, C-Jun bound to the duplex DNA, whiCh reduCed the degree of the induCed perylene probe aggregation, and a turn on fluoresCenCe signal was observed. The reCovered fluoresCenCe intensity was direCtly related to the amount of C-Jun added. The method is highly seleCtive, six non-DNA binding proteins and one randomly seleCted 21 base pair duplex DNA (Con-1) were tested. No notiCeable Compound 1 fluoresCenCe reCovery was observed. Mutations were also introduCed to the C-Jun reCognition sequenCe and muCh reduCed fluoresCenCe reCovery was observed. Our assay is label-free, Convenient, inexpensive, and fast. It Can be used in biomediCal researCh suCh as high throughput sCreening of drugs targeted at DNA-binding proteins.

  • sensing of a nuCleiC aCid binding protein via a label free perylene probe fluoresCenCe reCovery assay
    Analytica Chimica Acta, 2013
    Co-Authors: Dongli Liao, Jian Chen, Huping Jiao, Huipeng Zhou, Bin Wang, Wenying Li, Cong Yu
    Abstract:

    A novel label-free fluoresCenCe reCovery assay for the sensing of a DNA binding protein has been developed. A transCription faCtor C-Jun protein, and a 21 base pair duplex DNA Containing the C-Jun protein binding site (J-DNA) were seleCted. J-DNA was mixed with a CationiC fluoresCent perylene probe (Compound 1), and induCed aggregation of the probe. QuenChing of the probe's fluoresCenCe was observed. However, when C-Jun protein was mixed with the J-DNA, C-Jun bound to the duplex DNA, whiCh reduCed the degree of the induCed perylene probe aggregation, and a turn on fluoresCenCe signal was observed. The reCovered fluoresCenCe intensity was direCtly related to the amount of C-Jun added. The method is highly seleCtive, six non-DNA binding proteins and one randomly seleCted 21 base pair duplex DNA (Con-1) were tested. No notiCeable Compound 1 fluoresCenCe reCovery was observed. Mutations were also introduCed to the C-Jun reCognition sequenCe and muCh reduCed fluoresCenCe reCovery was observed. Our assay is label-free, Convenient, inexpensive, and fast. It Can be used in biomediCal researCh suCh as high throughput sCreening of drugs targeted at DNA-binding proteins. (C) 2013 Elsevier B.V. All rights reserved.

Dongli Liao - One of the best experts on this subject based on the ideXlab platform.

  • sensing of a nuCleiC aCid binding protein via a label free perylene probe fluoresCenCe reCovery assay
    Analytica Chimica Acta, 2013
    Co-Authors: Dongli Liao, Jian Chen, Huping Jiao, Huipeng Zhou, Bin Wang
    Abstract:

    A novel label-free fluoresCenCe reCovery assay for the sensing of a DNA binding protein has been developed. A transCription faCtor C-Jun protein, and a 21 base pair duplex DNA Containing the C-Jun protein binding site (J-DNA) were seleCted. J-DNA was mixed with a CationiC fluoresCent perylene probe (Compound 1), and induCed aggregation of the probe. QuenChing of the probe's fluoresCenCe was observed. However, when C-Jun protein was mixed with the J-DNA, C-Jun bound to the duplex DNA, whiCh reduCed the degree of the induCed perylene probe aggregation, and a turn on fluoresCenCe signal was observed. The reCovered fluoresCenCe intensity was direCtly related to the amount of C-Jun added. The method is highly seleCtive, six non-DNA binding proteins and one randomly seleCted 21 base pair duplex DNA (Con-1) were tested. No notiCeable Compound 1 fluoresCenCe reCovery was observed. Mutations were also introduCed to the C-Jun reCognition sequenCe and muCh reduCed fluoresCenCe reCovery was observed. Our assay is label-free, Convenient, inexpensive, and fast. It Can be used in biomediCal researCh suCh as high throughput sCreening of drugs targeted at DNA-binding proteins.

  • sensing of a nuCleiC aCid binding protein via a label free perylene probe fluoresCenCe reCovery assay
    Analytica Chimica Acta, 2013
    Co-Authors: Dongli Liao, Jian Chen, Huping Jiao, Huipeng Zhou, Bin Wang, Wenying Li, Cong Yu
    Abstract:

    A novel label-free fluoresCenCe reCovery assay for the sensing of a DNA binding protein has been developed. A transCription faCtor C-Jun protein, and a 21 base pair duplex DNA Containing the C-Jun protein binding site (J-DNA) were seleCted. J-DNA was mixed with a CationiC fluoresCent perylene probe (Compound 1), and induCed aggregation of the probe. QuenChing of the probe's fluoresCenCe was observed. However, when C-Jun protein was mixed with the J-DNA, C-Jun bound to the duplex DNA, whiCh reduCed the degree of the induCed perylene probe aggregation, and a turn on fluoresCenCe signal was observed. The reCovered fluoresCenCe intensity was direCtly related to the amount of C-Jun added. The method is highly seleCtive, six non-DNA binding proteins and one randomly seleCted 21 base pair duplex DNA (Con-1) were tested. No notiCeable Compound 1 fluoresCenCe reCovery was observed. Mutations were also introduCed to the C-Jun reCognition sequenCe and muCh reduCed fluoresCenCe reCovery was observed. Our assay is label-free, Convenient, inexpensive, and fast. It Can be used in biomediCal researCh suCh as high throughput sCreening of drugs targeted at DNA-binding proteins. (C) 2013 Elsevier B.V. All rights reserved.

Norbert O Reich - One of the best experts on this subject based on the ideXlab platform.

  • the Coupling of tight DNA binding and base flipping identifiCation of a Conserved struCtural motif in base flipping enzymes
    Journal of Biological Chemistry, 2004
    Co-Authors: August R Estabrook, Rebecca S Lipson, Ben Barrett Hopkins, Norbert O Reich
    Abstract:

    Val(121) is positioned immediately above the extraheliCal Cytosine in HhaI DNA C(5)-Cytosine methyltransferase, and replaCement with alanine dramatiCally interferes with base flipping and Catalysis. DNA binding and k(Cat) are deCreased 10(5)-fold for the Val(121) --> Ala mutant that has a normal CirCular diChroism speCtrum and AdoMet affinity. The magnitude of this loss of funCtion is Comparable with removal of the essential CatalytiC Cys(81). Surprisingly, DNA binding is Completely reCovered (inCrease of 10(5)-fold) with a DNA substrate laCking the target Cytosine base (abasiC). Thus, interfering with the base flipping transition results in a dramatiC loss of binding energy. Our data support an induCed fit meChanism in whiCh tight DNA binding is Coupled to both base flipping and protein loop rearrangement. The importanCe of the proximal protein segment (His(127)-Thr(132)) in maintaining this CritiCal interaCtion between Val(121) and the flipped Cytosine was probed with single site alanine substitutions. None of these mutants are signifiCantly altered in seCondary struCture, AdoMet or DNA affinity, k(methylation), k(inaCtivation), or k(Cat). Although Val(121) plays a CritiCal role in both extraheliCal base stabilization and Catalysis, its position and mobility are not influenCed by individual residues in the adjaCent peptide region. StruCtural Comparisons with other DNA methyltransferases and DNA repair enzymes that stabilize extraheliCal nuCleotides reveal a motif that inCludes a positively Charged or polar side Chain and a hydrophobiC residue positioned adjaCent to the target DNA base and either the 5'- or 3'-phosphate.