Hot off the presses! Jun 01 Nat Meth

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Latest Articles Include:

• Mapping the money
  - Nat Meth 8(6):437 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• The author file
  - Nat Meth 8(6):439 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Color blindness
  - Nat Meth 8(6):441 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Database of NIH grants using machine-learned categories and graphical clustering
  - Nat Meth 8(6):443-444 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Predicting protein associations with long noncoding RNAs
  - Nat Meth 8(6):444-445 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Perfecting ChR2
  - Nat Meth 8(6):447 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• The right chromophore for the job
  - Nat Meth 8(6):448-449 (2011)
  Nature Methods | Research Highlights The right chromophore for the job * Daniel EvankoJournal name:Nature MethodsVolume: 8,Pages:448–449Year published:(2011)DOI:doi:10.1038/nmeth0611-448aPublished online27 May 2011 A normally undesirable property of chromophores is used in the creation of a genetically encoded tag for correlated light and electron microscopy. View full text Subject terms: * Sensors and probes Additional data Author Details * Daniel Evanko Search for this author in: * NPG journals * PubMed * Google Scholar
• From pseudogenes to proteins
  - Nat Meth 8(6):448-449 (2011)
  Nature Methods | Research Highlights From pseudogenes to proteins * Nicole RuskJournal name:Nature MethodsVolume: 8,Pages:448–449Year published:(2011)DOI:doi:10.1038/nmeth0611-448bPublished online27 May 2011 Combining proteome analysis with genome sequencing improves gene annotation and yields evidence that some genes presumed to be noncoding are actually expressed. View full text Subject terms: * Genomics Additional data Author Details * Nicole Rusk Search for this author in: * NPG journals * PubMed * Google Scholar
• News in brief
  - Nat Meth 8(6):449 (2011)
  Article preview View full access options Nature Methods | Research Highlights News in brief Journal name:Nature MethodsVolume: 8,Page:449Year published:(2011)DOI:doi:10.1038/nmeth0611-449Published online27 May 2011 Genome-wide map of the sixth base Although 5-hyrdoxymethyl-cytosine (5hmC) is thought to be important for genome function in certain cells, a lack of tools has made profiling difficult. Xu et al. used a 5hmC-specific antibody for methylated DNA immunoprecipitation (MeDIP) and found distinct genome-wide 5hmC patterns in the mouse. The researchers saw 5hmC enrichment in gene bodies rather than at promoters and in intergenic regions. They also uncovered a role for the ten-eleven translocation (Tet) family of 5mC hydroxylases. Xu, Y.et al. Mol. Cell. advance online publication (20 April 2011). Article preview Read the full article * FREE access with registration Register now * Already have a Nature.com account? Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Directed evolution made easy
  - Nat Meth 8(6):451 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• Resurrected enzymes
  - Nat Meth 8(6):452 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• DNA origami in 3D
  - Nat Meth 8(6):454 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• Microarrays, megasynthesis
  - Nat Meth 8(6):457-460 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Bringing fly brains in line
  - Nat Meth 8(6):461-463 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Channeling the data deluge
  - Nat Meth 8(6):463-465 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• All-in-one live: genes trapped, tagged and conditionally broken
  - Nat Meth 8(6):466-467 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Computational methods for transcriptome annotation and quantification using RNA-seq
  - Nat Meth 8(6):469-477 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Next-generation sequencing to generate interactome datasets
  - Nat Meth 8(6):478-480 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Combining quantitative proteomics data processing workflows for greater sensitivity
  - Nat Meth 8(6):481-483 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Analysis of repetitive DNA in chromosomes by flow cytometry
  - Nat Meth 8(6):484-486 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Adaptive informatics for multifactorial and high-content biological data
  - Nat Meth 8(6):487-492 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• BrainAligner: 3D registration atlases of Drosophila brains
  - Nat Meth 8(6):493-498 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Fast, three-dimensional super-resolution imaging of live cells
  - Nat Meth 8(6):499-505 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• In vivo protein trapping produces a functional expression codex of the vertebrate proteome
  - Nat Meth 8(6):506-512 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Sequence-based identification of 3D structural modules in RNA with RMDetect
  - Nat Meth 8(6):513-519 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data

Hot off the presses! Feb 01

The Feb 01 issue of the is now up on Pubget (About ): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• The scientist and the smartphone
  - Nature methods 7(2):87 (2010)
  Mobile computing platforms such as the iPhone are beginning to make inroads into the laboratory—serious prospect or fairy tale?
• The author file
  - Nature methods 7(2):89 (2010)
  Adapting optics: techniques for seeing stars scale to cells.
• Genome editing with modularly assembled zinc-finger nucleases
  - Nature methods 7(2):91 (2010)
  To the Editor: In a Correspondence in Nature Methods, some members of the Zinc Finger Consortium reported discouragingly high failure rates for the modular assembly of zinc-finger DNA-binding proteins and concluded that more time-consuming and labor-intensive selection-based methods were "the only publicly available alternatives for academic researchers interested in using ZFN technology". Zinc finger nucleases (ZFNs) are artificial restriction enzymes made by fusing reprogrammable zinc-finger DNA-binding units to the FokI nuclease domain, which efficiently induce, site-specific mutations in higher eukaryotic cells, and thus hold great promise in many fields.
• Reply to "Genome editing with modularly assembled zinc-finger nucleases"
  - Nature methods 7(2):91-92 (2010)
  Joung et al. reply: The publications cited by Kim et al. describing successful construction of zinc-finger nucleases (ZFNs) by modular assembly only further support our original conclusion that this method has a high failure rate for engineering functional zinc-finger arrays. Two of the three reports cited in their Correspondence provide data that enable calculation of failure rates for modular assembly.
• IntOGen: integration and data mining of multidimensional oncogenomic data
  - Nature methods 7(2):92-93 (2010)
  To the Editor: The use of high-throughput techniques has come to the fore in modern cancer research. Several projects collate and analyze multiple datasets from cancer gene studies.
• Systems biology: Big surprises in a little package
  - Nature methods 7(2):95 (2010)
  An in-depth, systems biology approach to analyzing a 'reduced genome' bacterium reveals startling complexity.
• Imaging and visualization: One-shot structure determination
  - Nature methods 7(2):96-97 (2010)
  By sampling a two-dimensional diffraction pattern on a spherical detector, three-dimensional structure determination of single molecules should be possible from a single measurement.
• Genomics: To each his own
  - Nature methods 7(2):96-97 (2010)
  De novo assembly of human genome sequences that are not currently included in the reference genome opens the possibility of a human pan-genome.
• News in brief
  - Nature methods 7(2):97 (2010)
  Gene regulation Mutagenesis screens in human cells The classical mutagenesis approach is a powerful method to determine the genes induced in various biological processes. However, the diploid nature of the human and other mammalian genomes has limited large-scale mutagenesis studies.
• Bioinformatics: Found in translation
  - Nature methods 7(2):98 (2010)
  Annotation of clinical databases using controlled vocabulary permits cross-species comparisons of phenotypes associated with human disease.
• Imaging and visualization: Taking imaging into the red
  - Nature methods 7(2):100 (2010)
  Subtle modifications to a red fluorescent protein make it highly effective for intravital imaging.
• Cell biology: Supporting actors
  - Nature methods 7(2):102 (2010)
  Two GFP-binding peptides, Enhancer and Minimizer, modulate GFP fluorescence and will enable a number of in vivo applications.
• Mind the gaps
  - Nature methods 7(2):105-106 (2010)
  Amid all the excitement about next-generation sequencing, scientists often neglect to mention the problems that are caused by short read lengths. Genome assemblies produced from short reads are far more fragmented than those produced from long reads, with many more gaps and with relatively poor long-range linking information.
• Advancing neurochemical monitoring
  - Nature methods 7(2):106-108 (2010)
  Identifying the neural basis of behavior is a core focus of neuroscience. One prominent methodology in this pursuit is monitoring the neurotransmitters that underlie communication between neurons.
• Correcting distorted optics: back to the basics
  - Nature methods 7(2):108-110 (2010)
  How can optical imperfections that cause image distortion be measured and corrected? This is an important problem in many fields, ranging from imaging very large structures as in astronomy down to the smallest as in high-resolution microscopy. Many often quite complicated ways have been invented to determine exactly how a given optical system differs from perfection.
• Target-enrichment strategies for next-generation sequencing
  - Nature methods 7(2):111-118 (2010)
  We have not yet reached a point at which routine sequencing of large numbers of whole eukaryotic genomes is feasible, and so it is often necessary to select genomic regions of interest and to enrich these regions before sequencing. There are several enrichment approaches, each with unique advantages and disadvantages. Here we describe our experiences with the leading target-enrichment technologies, the optimizations that we have performed and typical results that can be obtained using each. We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project.
• Parallel, tag-directed assembly of locally derived short sequence reads
  - Nature methods 7(2):119-122 (2010)
  We demonstrate subassembly, an in vitro library construction method that extends the utility of short-read sequencing platforms to applications requiring long, accurate reads. A long DNA fragment library is converted to a population of nested sublibraries, and a tag sequence directs grouping of short reads derived from the same long fragment, enabling localized assembly of long fragment sequences. Subassembly may facilitate accurate de novo genome assembly and metagenome sequencing.
• Two-color, two-photon uncaging of glutamate and GABA
  Kantevari S Matsuzaki M Kanemoto Y Kasai H Ellis-Davies GC - Nature methods 7(2):123-125 (2010)
  We developed a caged GABA (γ-aminobutyric acid), which, when combined with an appropriate caged glutamate, allows bimodal control of neuronal membrane potential with subcellular resolution using optically independent two-photon uncaging of each neurotransmitter. We used two-color, two-photon uncaging to fire and block action potentials from rat hippocampal CA1 neurons in brain slices with 720-nm and 830-nm light, respectively. Our method should be generalizable to other chemical messenger pairs.
• Chronic microsensors for longitudinal, subsecond dopamine detection in behaving animals
  Clark JJ Sandberg SG Wanat MJ Gan JO Horne EA Hart AS Akers CA Parker JG Willuhn I Martinez V Evans SB Stella N Phillips PE - Nature methods 7(2):126-129 (2010)
  Neurotransmission operates on a millisecond timescale but is changed by normal experience or neuropathology over days to months. Despite the importance of long-term neurotransmitter dynamics, no technique exists to track these changes in a subject from day to day over extended periods of time. Here we describe and characterize a microsensor that can detect the neurotransmitter dopamine with subsecond temporal resolution over months in vivo in rats and mice.
• FRT-seq: amplification-free, strand-specific transcriptome sequencing
  - Nature methods 7(2):130-132 (2010)
  We report an alternative approach to transcriptome sequencing for the Illumina Genome Analyzer, in which the reverse transcription reaction takes place on the flowcell. No amplification is performed during the library preparation, so PCR biases and duplicates are avoided, and because the template is poly(A)+ RNA rather than cDNA, the resulting sequences are necessarily strand-specific. The method is compatible with paired- or single-end sequencing.
• Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
  Gu H Bock C Mikkelsen TS Jäger N Smith ZD Tomazou E Gnirke A Lander ES Meissner A - Nature methods 7(2):133-136 (2010)
  Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation and describe a statistical method for assessing significance of altered DNA methylation patterns. Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples.
• Bright cyan fluorescent protein variants identified by fluorescence lifetime screening
  - Nature methods 7(2):137-139 (2010)
  Optimization of autofluorescent proteins by intensity-based screening of bacteria does not necessarily identify the brightest variant for eukaryotes. We report a strategy to screen excited state lifetimes, which identified cyan fluorescent proteins with long fluorescence lifetimes (>3.7 ns) and high quantum yields (>0.8). One variant, mTurquoise, was 1.5-fold brighter than mCerulean in mammalian cells and decayed mono-exponentially, making it an excellent fluorescence resonance energy transfer (FRET) donor.
• Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues
  Ji N Milkie DE Betzig E - Nature methods 7(2):141-147 (2010)
  Biological specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction–limited performance from a variety of biological and nonbiological samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resolution to depths of 400 μm.
• Systems analysis of EGF receptor signaling dynamics with microwestern arrays
  - Nature methods 7(2):148-155 (2010)
  We describe microwestern arrays, which enable quantitative, sensitive and high-throughput assessment of protein abundance and modifications after electrophoretic separation of microarrayed cell lysates. This method allowed us to measure 91 phosphosites on 67 proteins at six time points after stimulation with five epidermal growth factor (EGF) concentrations in A431 human carcinoma cells. We inferred the connectivities among 15 phosphorylation sites in 10 receptor tyrosine kinases (RTKs) and two sites from Src kinase using Bayesian network modeling and two mutual information-based methods; the three inference methods yielded substantial agreement on the network topology. These results imply multiple distinct RTK coactivation mechanisms and support the notion that small amounts of experimental data collected from phenotypically diverse network states may enable network inference.
• Mass spectrometry for biologists
  - Nature methods 7(2):157-161 (2010)
  Mass spectrometry–based proteomics is still rapidly expanding, not just in terms of the methods and instruments but also the biological questions.

Hot off the presses! Apr 01 Nature methods

The Apr 01 issue of the Nature methods is now up on Pubget (About Nature methods): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Cause and effect
  - Nature methods 7(4):243 (2010)
  The experimental tractability of biological systems makes it possible to explore the idea that causal relationships can be estimated from observational data.
• The author file: Philippe Bastiaens
  - Nature methods 7(4):245 (2010)
  Researchers watch proteins interact in real time.
• Predicting causal effects in large-scale systems from observational data
  - Nature methods 7(4):247-248 (2010)
  To the editor: Understanding cause-effect relationships between variables is of primary interest in many fields of science. The standard method for determining such relationships uses randomized controlled perturbation experiments.
• A method and server for predicting damaging missense mutations
  - Nature methods 7(4):248-249 (2010)
  To the editor: Applications of rapidly advancing sequencing technology exacerbate the need to interpret individual sequence variants. Sequencing of phenotyped clinical subjects will soon become a method of choice in studies of the genetic causes of Mendelian and complex diseases.
• Single-nucleotide evolutionary constraint scores highlight disease-causing mutations
  - Nature methods 7(4):250-251 (2010)
  To the editor: Identifying disease-causing genetic variants in individual human genomes is a major challenge, even in protein-coding exons (the 'exome'). Analysis of nucleotide-level sequence conservation may help address this challenge, on the assumption that purifying selection 'constrains' evolutionary divergence at phenotypically important nucleotides.
• Collective brain maps
  - Nature methods 7(4):253 (2010)
  A new study, pooling brain-imaging data from 35 centers across the world, shows the power of data sharing and demonstrates a universal architecture of functional connections in the human brain.
• The DNA-binding landscape
  - Nature methods 7(4):254-255 (2010)
  Visualizing binding data in the form of specificity landscapes yields new insight into the behavior of DNA-binding molecules.
• Fission yeast defies the code
  - Nature methods 7(4):254-255 (2010)
  A genome-wide map of nucleosome positions in Schizosaccharomyces pombe points to a positioning mechanism different from that of other organisms.
• News in brief
  - Nature methods 7(4):255 (2010)
  Stem cells From fibroblasts to neurons No biologist would be surprised these days if one cell type was converted to another by going through a pluripotent stage, nor if this reprogramming was done directly between two closely related cell lineages. But Vierbuchen et al. now demonstrate a way to directly convert fibroblasts into distantly related excitatory neurons.
• Glycan labeling, rerouted
  - Nature methods 7(4):256 (2010)
  Researchers develop a method to label GlcNAc residues of N-glycans in yeast with high specificity and efficiency.
• Tracking infection
  - Nature methods 7(4):258 (2010)
  A new cell-based fluorescent reporter system allows direct visualization of individual cells infected with hepatitis C virus in real time.
• Proteomics for exotic organisms
  - Nature methods 7(4):260 (2010)
  A creative application of protein labeling can probe uncharacterized genomes.
• Laser tricks without labels
  - Nature methods 7(4):261-266 (2010)
  Nonlinear optical microscopy lets researchers see chemical composition in living cells and organisms.
• The 'when and whereabouts' of injected pathogen effectors
  - Nature methods 7(4):267-269 (2010)
  Being in the right place at the right time is a straightforward recipe for success. This also holds true for many bacteria that use syringe-like injection devices, such as the type-3 secretion system (T3SS), to deliver into host cells cocktails of effector proteins that interfere with various cellular functions.
• Not all noise is waste
  - Nature methods 7(4):269-272 (2010)
  The dominance of deterministic thought in cell biology has obscured a fundamental property of living systems—variability. A cell population, however uniform, is ripe with heterogeneities.
• Toward atomic accuracy in RNA design
  - Nature methods 7(4):272-273 (2010)
  The amazingly diverse roles of RNA molecules in biology are attracting increasing attention. Their varied biological functions are a result of the diversity of three-dimensional structures they adopt.
• Probing cellular events, one quantum dot at a time
  - Nature methods 7(4):275-285 (2010)
  Monitoring the behavior of single molecules in living cells is a powerful approach to investigate the details of cellular processes. Owing to their optical, chemical and biofunctional properties, semiconductor quantum dot (QD) probes promise to be tools of choice in this endeavor. Here we review recent advances that allow ever more controlled experiments at the single-nanoparticle level in live cells. Several examples, related to membrane dynamics, cell signaling or intracellular transport, illustrate how single QD tracking can be readily used to decipher complex biological processes and address key concepts that underlie cellular organization and dynamics.
• Cell type–specific gene expression differences in complex tissues
  Shen-Orr SS Tibshirani R Khatri P Bodian DL Staedtler F Perry NM Hastie T Sarwal MM Davis MM Butte AJ - Nature methods 7(4):287-289 (2010)
  We describe cell type–specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.
• Atomic accuracy in predicting and designing noncanonical RNA structure
  Das R Karanicolas J Baker D - Nature methods 7(4):291-294 (2010)
  We present fragment assembly of RNA with full-atom refinement (FARFAR), a Rosetta framework for predicting and designing noncanonical motifs that define RNA tertiary structure. In a test set of thirty-two 6–20-nucleotide motifs, FARFAR recapitulated 50% of the experimental structures at near-atomic accuracy. Sequence redesign calculations recovered native bases at 65% of residues engaged in noncanonical interactions, and we experimentally validated mutations predicted to stabilize a signal recognition particle domain.
• Fluorescence fluctuations of quantum-dot sensors capture intracellular protein interaction dynamics
  Zamir E Lommerse PH Kinkhabwala A Grecco HE Bastiaens PI - Nature methods 7(4):295-298 (2010)
  We extend the in vitro principle of co-immunoprecipitation to quantify dynamic protein interactions in living cells. Using a multiresolution implementation of fluorescence correlation spectroscopy to achieve maximal temporal resolution, we monitored the interactions of endogenous bait proteins, recruited by quantum dots, with fluorescently tagged prey. With this approach, we analyzed the rapid physiological regulation of protein kinase A.
• Direct determination of molecular haplotypes by chromosome microdissection
  Ma L Xiao Y Huang H Wang Q Rao W Feng Y Zhang K Song Q - Nature methods 7(4):299-301 (2010)
  Direct observation of haplotypes is still technically challenging. Here we report a method for the determination of haplotypes through chromosome microdissection. We determined human long-range chromosomal haplotypes with more than 98.85% accuracy at 24,245 genome-wide heterozygous single-nucleotide polymorphism (SNP) loci.
• In vivo wide-area cellular imaging by side-view endomicroscopy
  Kim P Chung E Yamashita H Hung KE Mizoguchi A Kucherlapati R Fukumura D Jain RK Yun SH - Nature methods 7(4):303-305 (2010)
  In vivo imaging of small animals offers several possibilities for studying normal and disease biology, but visualizing organs with single-cell resolution is challenging. We describe rotational side-view confocal endomicroscopy, which enables cellular imaging of gastrointestinal and respiratory tracts in mice and may be extensible to imaging organ parenchyma such as cerebral cortex. We monitored cell infiltration, vascular changes and tumor progression during inflammation and tumorigenesis in colon over several months.
• Toxoplasma secreting Cre recombinase for analysis of host-parasite interactions
  Koshy AA Fouts AE Lodoen MB Alkan O Blau HM Boothroyd JC - Nature methods 7(4):307-309 (2010)
  We describe a Toxoplasma gondii strain that will permit the use of site-specific recombination to study the host-parasite interactions of this organism. This Toxoplasma strain efficiently injects a Cre fusion protein into host cells. In a Cre-reporter cell line, a single parasite invasion induced Cre-mediated recombination in 95% of infected host cells. By infecting Cre-reporter mice with these parasites, we also monitored host-cell infection in vivo.
• Identifying single-cell molecular programs by stochastic profiling
  Janes KA Wang CC Holmberg KJ Cabral K Brugge JS - Nature methods 7(4):311-317 (2010)
  Cells in tissues can be morphologically indistinguishable yet show molecular expression patterns that are remarkably heterogeneous. Here we describe an approach to comprehensively identify co-regulated, heterogeneously expressed genes among cells that otherwise appear identical. The technique, called stochastic profiling, involves repeated, random selection of very small cell populations via laser-capture microdissection followed by a customized single-cell amplification procedure and transcriptional profiling. Fluctuations in the resulting gene-expression measurements are then analyzed statistically to identify transcripts that are heterogeneously coexpressed. We stochastically profiled matrix-attached human epithelial cells in a three-dimensional culture model of mammary-acinar morphogenesis. Of 4,557 transcripts, we identified 547 genes with strong cell-to-cell expression differences. Clustering of this heterogeneous subset revealed several molecular 'programs' impl! icated in protein biosynthesis, oxidative-stress responses and NF-κB signaling, which we independently confirmed by RNA fluorescence in situ hybridization. Thus, stochastic profiling can reveal single-cell heterogeneities without the need to measure expression in individual cells.
• Protein folding stability and dynamics imaged in a living cell
  Ebbinghaus S Dhar A McDonald JD Gruebele M - Nature methods 7(4):319-323 (2010)
  Biomolecular dynamics and stability are predominantly investigated in vitro and extrapolated to explain function in the living cell. We present fast relaxation imaging (FreI), which combines fluorescence microscopy and temperature jumps to probe biomolecular dynamics and stability inside a single living cell with high spatiotemporal resolution. We demonstrated the method by measuring the reversible fast folding kinetics as well as folding thermodynamics of a fluorescence resonance energy transfer (FRET) probe-labeled phosphoglycerate kinase construct in two human cell lines. Comparison with in vitro experiments at 23–49 °C showed that the cell environment influences protein stability and folding rate. FReI should also be applicable to the study of protein-protein interactions and heat-shock responses as well as to comparative studies of cell populations or whole organisms.
• Imaging type-III secretion reveals dynamics and spatial segregation of Salmonella effectors
  Van Engelenburg SB Palmer AE - Nature methods 7(4):325-330 (2010)
  The type-III secretion system (T3SS) enables gram-negative bacteria to inject effector proteins into eukaryotic host cells. Upon entry, T3SS effectors work cooperatively to reprogram host cells, enabling bacterial survival. Progress in understanding when and where effectors localize in host cells has been hindered by a dearth of tools to study these proteins in the native cellular environment. We report a method to label and track T3SS effectors during infection using a split-GFP system. We demonstrate this technique by labeling three effectors from Salmonella enterica (PipB2, SteA and SteC) and characterizing their localization in host cells. PipB2 displayed highly dynamic behavior on tubules emanating from the Salmonella-containing vacuole labeled with both endo- and exocytic markers. SteA was preferentially enriched on tubules localizing with Golgi markers. This segregation suggests that effector targeting and localization may have a functional role during infection.