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  • 1
    Publication Date: 2011-02-28
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
    Publication Date: 2011-03-16
    Description: Cortical circuits perform the computations underlying rapid perceptual decisions within a few dozen milliseconds with each neuron emitting only a few spikes. Under these conditions, the theoretical analysis of neural population codes is challenging, as the most commonly used theoretical tool—Fisher information—can lead to erroneous conclusions about the optimality of different coding schemes. Here we revisit the effect of tuning function width and correlation structure on neural population codes based on ideal observer analysis in both a discrimination and a reconstruction task. We show that the optimal tuning function width and the optimal correlation structure in both paradigms strongly depend on the available decoding time in a very similar way. In contrast, population codes optimized for Fisher information do not depend on decoding time and are severely suboptimal when only few spikes are available. In addition, we use the neurometric functions of the ideal observer in the classification task to investigate the differential coding properties of these Fisher-optimal codes for fine and coarse discrimination. We find that the discrimination error for these codes does not decrease to zero with increasing population size, even in simple coarse discrimination tasks. Our results suggest that quite different population codes may be optimal for rapid decoding in cortical computations than those inferred from the optimization of Fisher information.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 3
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  • 5
    Publication Date: 2011-07-30
    Description: Plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. Pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. We generated an interaction network of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins, and ~8000 other Arabidopsis proteins. We noted convergence of effectors onto highly interconnected host proteins and indirect, rather than direct, connections between effectors and plant immune receptors. We demonstrated plant immune system functions for 15 of 17 tested host proteins that interact with effectors from both pathogens. Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170753/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170753/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukhtar, M Shahid -- Carvunis, Anne-Ruxandra -- Dreze, Matija -- Epple, Petra -- Steinbrenner, Jens -- Moore, Jonathan -- Tasan, Murat -- Galli, Mary -- Hao, Tong -- Nishimura, Marc T -- Pevzner, Samuel J -- Donovan, Susan E -- Ghamsari, Lila -- Santhanam, Balaji -- Romero, Viviana -- Poulin, Matthew M -- Gebreab, Fana -- Gutierrez, Bryan J -- Tam, Stanley -- Monachello, Dario -- Boxem, Mike -- Harbort, Christopher J -- McDonald, Nathan -- Gai, Lantian -- Chen, Huaming -- He, Yijian -- European Union Effectoromics Consortium -- Vandenhaute, Jean -- Roth, Frederick P -- Hill, David E -- Ecker, Joseph R -- Vidal, Marc -- Beynon, Jim -- Braun, Pascal -- Dangl, Jeffery L -- BB/E024815/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G015066/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- E024815/Biotechnology and Biological Sciences Research Council/United Kingdom -- F005806/Biotechnology and Biological Sciences Research Council/United Kingdom -- G015066/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM-066025/GM/NIGMS NIH HHS/ -- P50 HG004233/HG/NHGRI NIH HHS/ -- P50 HG004233-04/HG/NHGRI NIH HHS/ -- P50-HG004233/HG/NHGRI NIH HHS/ -- R01 GM066025/GM/NIGMS NIH HHS/ -- R01 GM066025-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 29;333(6042):596-601. doi: 10.1126/science.1203659.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21798943" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*immunology/*metabolism/microbiology ; Bacterial Proteins/metabolism ; Evolution, Molecular ; Genes, Plant ; *Host-Pathogen Interactions ; Immunity, Innate ; Oomycetes/pathogenicity ; Plant Diseases/*immunology ; *Plant Immunity ; Protein Interaction Mapping ; Pseudomonas syringae/pathogenicity ; Receptors, Immunologic/*metabolism ; Virulence Factors/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2011-05-10
    Description: 5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124347/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124347/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pastor, William A -- Pape, Utz J -- Huang, Yun -- Henderson, Hope R -- Lister, Ryan -- Ko, Myunggon -- McLoughlin, Erin M -- Brudno, Yevgeny -- Mahapatra, Sahasransu -- Kapranov, Philipp -- Tahiliani, Mamta -- Daley, George Q -- Liu, X Shirley -- Ecker, Joseph R -- Milos, Patrice M -- Agarwal, Suneet -- Rao, Anjana -- 1 R01 HD065812-01A1/HD/NICHD NIH HHS/ -- 1 UL1 RR 025758-02/RR/NCRR NIH HHS/ -- K08 HL089150/HL/NHLBI NIH HHS/ -- K08 HL089150-01A1/HL/NHLBI NIH HHS/ -- R01 AI044432/AI/NIAID NIH HHS/ -- R01 AI044432-10/AI/NIAID NIH HHS/ -- R01 AI44432/AI/NIAID NIH HHS/ -- R01 HD065812/HD/NICHD NIH HHS/ -- R01 HD065812-01A1/HD/NICHD NIH HHS/ -- RC1 DA028422/DA/NIDA NIH HHS/ -- RC1 DA028422-02/DA/NIDA NIH HHS/ -- UL1 RR025758/RR/NCRR NIH HHS/ -- England -- Nature. 2011 May 19;473(7347):394-7. doi: 10.1038/nature10102. Epub 2011 May 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21552279" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biotinylation ; Cell Line ; Cytosine/*analogs & derivatives/analysis/isolation & purification/metabolism ; DNA Methylation ; Embryonic Stem Cells/*metabolism ; Exons/genetics ; Gene Expression Regulation, Developmental/genetics ; Genome/*genetics ; Glucose/metabolism ; Mice ; Periodic Acid/metabolism ; Promoter Regions, Genetic/genetics ; Sequence Analysis, DNA/*methods ; Transcription Initiation Site ; Transcription, Genetic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2011-02-04
    Description: Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100360/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100360/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lister, Ryan -- Pelizzola, Mattia -- Kida, Yasuyuki S -- Hawkins, R David -- Nery, Joseph R -- Hon, Gary -- Antosiewicz-Bourget, Jessica -- O'Malley, Ronan -- Castanon, Rosa -- Klugman, Sarit -- Downes, Michael -- Yu, Ruth -- Stewart, Ron -- Ren, Bing -- Thomson, James A -- Evans, Ronald M -- Ecker, Joseph R -- 1U01ES017166-01/ES/NIEHS NIH HHS/ -- DK062434/DK/NIDDK NIH HHS/ -- P30 CA014195/CA/NCI NIH HHS/ -- U01 ES017166/ES/NIEHS NIH HHS/ -- U01 ES017166-01/ES/NIEHS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Mar 3;471(7336):68-73. doi: 10.1038/nature09798. Epub 2011 Feb 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21289626" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Differentiation/genetics ; Cell Line ; Cellular Reprogramming/*genetics ; CpG Islands/genetics ; DNA Methylation/*genetics ; Embryonic Stem Cells/cytology/metabolism ; Epigenomics ; Epistasis, Genetic/*genetics ; Fibroblasts/cytology/metabolism ; Genome, Human/*genetics ; Histones/metabolism ; Humans ; Induced Pluripotent Stem Cells/cytology/*metabolism ; Trophoblasts/cytology/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2011-09-17
    Description: Epigenetic information, which may affect an organism's phenotype, can be stored and stably inherited in the form of cytosine DNA methylation. Changes in DNA methylation can produce meiotically stable epialleles that affect transcription and morphology, but the rates of spontaneous gain or loss of DNA methylation are unknown. We examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants propagated by single-seed descent for 30 generations. We identified 114,287 CG single methylation polymorphisms and 2485 CG differentially methylated regions (DMRs), both of which show patterns of divergence compared with the ancestral state. Thus, transgenerational epigenetic variation in DNA methylation may generate new allelic states that alter transcription, providing a mechanism for phenotypic diversity in the absence of genetic mutation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210014/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210014/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmitz, Robert J -- Schultz, Matthew D -- Lewsey, Mathew G -- O'Malley, Ronan C -- Urich, Mark A -- Libiger, Ondrej -- Schork, Nicholas J -- Ecker, Joseph R -- F32 HG004830/HG/NHGRI NIH HHS/ -- F32 HG004830-01/HG/NHGRI NIH HHS/ -- F32 HG004830-02/HG/NHGRI NIH HHS/ -- F32 HG004830-03/HG/NHGRI NIH HHS/ -- F32-HG004830/HG/NHGRI NIH HHS/ -- R01 HG003523/HG/NHGRI NIH HHS/ -- R01 HG003523-01/HG/NHGRI NIH HHS/ -- R01 HG003523-02/HG/NHGRI NIH HHS/ -- R01 HG003523-03/HG/NHGRI NIH HHS/ -- UL1 RR025774/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Oct 21;334(6054):369-73. doi: 10.1126/science.1212959. Epub 2011 Sep 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921155" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/*genetics/metabolism ; *DNA Methylation ; DNA Transposable Elements ; DNA, Intergenic ; DNA, Plant/genetics/metabolism ; Dinucleoside Phosphates/metabolism ; *Epigenesis, Genetic ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Linear Models ; Mutation ; Polymorphism, Genetic ; Promoter Regions, Genetic ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2011-09-18
    Print ISSN: 1552-4450
    Electronic ISSN: 1552-4469
    Topics: Biology , Chemistry and Pharmacology
    Published by Springer Nature
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  • 10
    Publication Date: 2011-06-03
    Print ISSN: 1385-0237
    Electronic ISSN: 1573-5052
    Topics: Biology
    Published by Springer
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