http://blogs.nature.com/methagora a blog from Nature Methods Mon, 24 Oct 2016 13:51:32 +0000 hourly 1 http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/-yIcWFDEqhY/database-under-maintenance.html http://blogs.nature.com/methagora/2016/08/database-under-maintenance.html#comments Thu, 01 Jan 1970 01:00:00 +0000 tal-nawy http://blogs.nature.com/methagora/?p=2631 Read more]]> here.]]> http://blogs.nature.com/methagora/2016/08/database-under-maintenance.html/feed/ 0 http://blogs.nature.com/methagora/2016/08/database-under-maintenance.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/EMJEcJ2-57g/building-core-strength.html http://blogs.nature.com/methagora/2016/07/building-core-strength.html#comments Thu, 01 Jan 1970 01:00:00 +0000 nicole-rusk http://blogs.nature.com/methagora/?p=2625 Read more]]> here) in this month’s editorial.]]> http://blogs.nature.com/methagora/2016/07/building-core-strength.html/feed/ 0 http://blogs.nature.com/methagora/2016/07/building-core-strength.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/qMlOaWzRhdk/private-funding-for-science.html http://blogs.nature.com/methagora/2016/06/private-funding-for-science.html#comments Thu, 01 Jan 1970 01:00:00 +0000 Natalie-de-Souza http://blogs.nature.com/methagora/?p=2609 Read more]]> Here is this month's editorial, in which we discuss the role of private sources of funding for scientific research, and outline some steps researchers might consider in order to find and obtain such resources.]]> http://blogs.nature.com/methagora/2016/06/private-funding-for-science.html/feed/ 0 http://blogs.nature.com/methagora/2016/06/private-funding-for-science.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/-PyW0CMlCYE/dont-forget-the-methods-in-human-embryo-research.html http://blogs.nature.com/methagora/2016/06/dont-forget-the-methods-in-human-embryo-research.html#comments Thu, 01 Jan 1970 01:00:00 +0000 Natalie-de-Souza http://blogs.nature.com/methagora/?p=2569 Read more]]> here.]]> http://blogs.nature.com/methagora/2016/06/dont-forget-the-methods-in-human-embryo-research.html/feed/ 0 http://blogs.nature.com/methagora/2016/06/dont-forget-the-methods-in-human-embryo-research.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/wFeX20DI4lc/glycoscience-a-tea-party-no-longer.html http://blogs.nature.com/methagora/2016/05/glycoscience-a-tea-party-no-longer.html#comments Thu, 01 Jan 1970 01:00:00 +0000 nicole-rusk http://blogs.nature.com/methagora/?p=2541 Read more]]> his recent work, published the June issue of Nature Methods, the Cummings lab uses household bleach to release glycans from tissue and cells. He started this research at Emory School of Medicine and continued at his new lab at Harvard Medical School. He also directs the Center for Functional Glycomics, a virtual center that he already led at Emory and that is funded by the National Institutes of Health to explore protein-glycan interactions and to develop new tools and technologies to explore glycoconjugate functions. When people now stop by the Cummings lab they can, for example, leave with four grams of carbohydrates in a 50ml tube full of white powder. “Those are all the carbohydrate structures in the pig lung,” he says. With this material on hand scientists can use nuclear magnetic resonance techniques for glycan analysis. Cummings and his team want to enable more labs around the world to study glycoscience by shipping material to colleagues upon request. - Hear Rick Cummings talk about the offer here (14 seconds) [audio m4a="http://blogs.nature.com/methagora/files/2016/05/rick_two-audio.m4a"][/audio] - Glycans are difficult to synthesize but now it is possible to harvest them from natural sources such as eggs, meat or plants. “We can make them at such large scale now, we‘re going to just give them away,” he says. Once purified, glycans can be archived, printed on microarrays to explore glycan recognition by lectins, antibodies, bacteria or viruses, or sequenced with mass spectrometry, nuclear magnetic resonance techniques or other methods. As researchers become aware of the role of carbohydrates in health and disease, the field of glycoscience is broadening, says Cummings. Glycans are being recognized as one of the four major classes of macromolecules, alongside nucleic acids, proteins and lipids. In the 1970s and 1980s, this field was just getting its start and it was considered merely another part of biochemistry. When carbohydrate researchers got together at meetings, it was more like “tea parties” with 50 to 100 attendees, says Cummings. Glycoscience was far from the spotlight. The community began using the term glycobiology, which Raymond Dwek coined in 1985 and which resonated with researchers. And then, he says,  “all of us kind of chose the term glycomics at some point to distinguish ourselves scientifically from proteomics and the other ‘omics.” - Hear Rick Cummings talk about the history of the field here (40 seconds) [audio mp3="http://blogs.nature.com/methagora/files/2016/10/rick_history.mp3.mp3"][/audio] - Studying glycan function preceded the study of carbohydrate structure, says Cummings, a situation not unlike molecular biology. For example, work by the chemist Linus Pauling on sickle cell disease occurred before the responsible mutation had been identified and before it was possible to sequence DNA. “We really didn’t know the gene until years later,” says Cummings. The molecular biology arena exploded when it became possible to clone and to synthesize oligonucleotides. “We’re at that point now in glyco-science,” he says. These days it’s increasingly difficult for scientists to overlook glycans, says Cummings. Access and collaboration are what is needed next to grow the field now that researchers are more than willing to, as he says, “dip their little toes in the glycoscience waters.” That being said, he does still hear disparaging comments about glycoscience, but he takes the remarks as a matter of pride. “So you can think of glycans as being like that little awkward kid on the playground who grew up to be a sizable individual whom no one bullies anymore.”]]> http://blogs.nature.com/methagora/2016/05/glycoscience-a-tea-party-no-longer.html/feed/ 0 http://blogs.nature.com/methagora/2016/05/glycoscience-a-tea-party-no-longer.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/54PcRZIUfLk/sharing-data-to-advance-structural-biology.html http://blogs.nature.com/methagora/2016/04/sharing-data-to-advance-structural-biology.html#comments Thu, 01 Jan 1970 01:00:00 +0000 Natalie-de-Souza http://blogs.nature.com/methagora/?p=2537 Read more]]> editorial, we highlight two new archives: for raw X-ray crystallography (the Structural Biology Data Grid, or SBDG) and for cryo-EM (EMPIAR). These archives join the long-established Biological Magnetic Resonance Data Bank, or BMRB (which hosts biomolecular NMR spectral data) as important resources which will facilitate greater transparency and accelerate progress in structural biology. Note that neither archive is intended as a “data dump”: datasets in the SBDG must be tied to a journal publication and must be sponsored by the principle investigator of the work, and datasets in EMPIAR must be tied to an Electron Microscopy Data Bank (EMDB) EM density map entry. Though we do not mandate raw X-ray or cryo-EM data deposition at this time, we applaud these efforts and welcome feedback from the structural biology community about how these archives are bolstering community needs.]]> http://blogs.nature.com/methagora/2016/04/sharing-data-to-advance-structural-biology.html/feed/ 0 http://blogs.nature.com/methagora/2016/04/sharing-data-to-advance-structural-biology.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/cd-Uw8IhvuU/preprints-in-biology.html http://blogs.nature.com/methagora/2016/04/preprints-in-biology.html#comments Thu, 01 Jan 1970 01:00:00 +0000 Natalie-de-Souza http://blogs.nature.com/methagora/?p=2529 Read more]]> We remind our readers about our policies on the use of preprints: in short, we support them. A Nature Methods author can post a preprint prior to submission without fearing a penalty. The full editorial is here.]]> http://blogs.nature.com/methagora/2016/04/preprints-in-biology.html/feed/ 0 http://blogs.nature.com/methagora/2016/04/preprints-in-biology.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/UQAlRONwNWw/an-archive-for-raw-em-data.html http://blogs.nature.com/methagora/2016/03/an-archive-for-raw-em-data.html#comments Thu, 01 Jan 1970 01:00:00 +0000 allison-doerr http://blogs.nature.com/methagora/?p=2517 Read more]]> Correspondence describing EMPIAR, a public archive for raw 2D electron microscopy (EM) image data. While the established Electron Microscopy Data Bank (EMDB) hosts the 3D EM map data required by most journals for publication, the EM community has long been calling for an archive to host the raw 2D image data underlying the 3D maps, as highlighted in our Method of the Year 2015 feature. EMPIAR, a pilot project from the Protein Data Bank in Europe (PDBe), now fills this need. At Nature Methods we support this archive as a welcome development in the rapidly growing 3D EM field that will enhance transparency, reproducibility, and facilitate the development and refinement of data analysis tools. Though we do not require that our authors deposit their 2D EM image data in EMPIAR, we do encourage it. We urge researchers to make use of the archive and provide feedback to the developers in order to ensure that it is meeting the needs of the field. Any interested readers without a subscription or site license may read the full text of the Correspondence here.]]> http://blogs.nature.com/methagora/2016/03/an-archive-for-raw-em-data.html/feed/ 0 http://blogs.nature.com/methagora/2016/03/an-archive-for-raw-em-data.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/vEBZbYqC7U4/debates-on-genomic-footprinting.html http://blogs.nature.com/methagora/2016/03/debates-on-genomic-footprinting.html#comments Thu, 01 Jan 1970 01:00:00 +0000 Natalie-de-Souza http://blogs.nature.com/methagora/?p=2513 … Read more]]> here The papers we refer to in this editorial are: Genomic footprinting Genome-wide footprinting: ready for prime time? Analysis of computational footprinting methods for DNase sequencing experiments]]> http://blogs.nature.com/methagora/2016/03/debates-on-genomic-footprinting.html/feed/ 0 http://blogs.nature.com/methagora/2016/03/debates-on-genomic-footprinting.html http://feedproxy.google.com/~r/nmeth/rss/methagora_with_comments/~3/wSBO653SvbI/methods-and-probes-for-cleared-tissue-an-imperfect-table.html http://blogs.nature.com/methagora/2016/02/methods-and-probes-for-cleared-tissue-an-imperfect-table.html#comments Fri, 01 Nov 8611 14:56:42 +0000 Natalie-de-Souza http://blogs.nature.com/methagora/?p=2391 Read more]]> {credit}Digital Vision/Punchstock {/credit}[/caption] In the March issue of Nature Methods, the technology feature explores some ways that labs are optimizing probes to image cleared tissue. As we interviewed scientists, we learned about published work and ongoing unpublished experiences. Here is a snapshot of how some probes work with some clearing methods. It’s an imperfect table and is likely to evolve as research continues. We welcome your comments. We know there are different viewpoints and varying experiences and we hope it will be helpful to others to hear about them. We wish this could be a wiki page, then again that might deprive you of your nighttime rest, as you edit one another’s entries. This way, your comments can be seen by all.  

An imperfect table about some labels that have been used in cleared tissue

Probe	Labeling shown in large samplesb	Labeling shown in small samples	Does not work well?
Genetically encoded fluorescent proteins	3DISCO (signal quenched after a few days), CLARITY, CUBIC, ExM (variant)a, PACT/PARS (signal retained 6 months and longer)a, sDISCOa	BABB (signal quenched after a few hours), ClearT2, ExM (variant)a , ExM/ePACTa , ScaleA2, ScaleS, SeeDB, Sucrose, TDE
Immunolabels	3DISCO, CLARITY, iDISCO, iDISCO+a, iSeeDB, PACT/PARS, Sucrose, SWITCH	BABB, ClearT, ClearT2, CUBIC, SeeDB, SeeDB2a (in press) Sucrose, TDE, ExM
Specific nucleic acid detection	EDC-CLARITY	CLARITY, ExM (variant)a, PACT/PARS
Dyes and stains
Congo Red	3DISCO
Lipophilic dyes such as DiI, Sudan Black	PACT/PARS (Sudan Black), SWITCH (DiI)	ClearT, ScaleS, SeeDB
Nuclear stains such as DAPI, DRAQ5, SYTO and PI	CUBIC, ExM (variant)a, PACT/PARS, SWITCH	SeeDB, SeeDB2a
SNAP-tags with SiR probes	PACT/PARS, BABB, Scale	SeeDB

Clearing method: Solvent-based; simple immersion; hyperhydration; hydrogel-based. ^aUnpublished information ^bIndicates larger samples such as whole organs Sources: E. Boyden, MIT; K. Chung, MIT, K. Deisseroth, Stanford University; H-U. Dodt, Vienna University of Technology/Medical University of Vienna; V. Gradinaru, Caltech; P. Heppenstall, EMBL; Takeshi Imai, RIKEN; ­­K. Johnsson, EPFL; J. Lichtman, D. Richardson, Harvard University; A. Miyawaki, RIKEN; M. Tessier-Lavigne, N. Renier, Rockefeller University. * Glossary of some tissue clearing agent acronyms 3DISCO :  Three-dimensional imaging of solvent-cleared organs sDISCO: Stabilized three-dimensional imaging of solvent-cleared organs BABB :  Benzyl alcohol and benzyl-benzoate CLARITY : Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ hybridization-compatible Tissue-hYdrogel CUBIC : Clear unobstructed brain imaging cocktails and computational analysis EDC-CLARITY : 1-Ethyl-3-3-dimethyl-aminopropyl carbodiimide-CLARITY ePACT: PACT-based expansion clearing. iDISCO : Immunolabeling-enabled 3D imaging of solvent-cleared organs iDISCO+ : Immunolabeling-enabled 3D imaging of solvent-cleared organs plus PACT :  Passive Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ hybridization-compatible Tissue-hYdrogel PARS : Perfusion-assisted agent release in situ SeeDB : See Deep Brain Spalteholz’s preparation :  Benzylbanzoate/methylsalicate TDE  : 2,2′-thiodiethanol   Some lab resource pages Chung lab resources – Literature, protocols, videos and discussion pages from the MIT lab of Kwanghun Chung related to SWITCH, electrostochastic transport and CLARITY. CLARITY Resources – Protocols, literature, data and videos related to CLARITY, developed in the lab of Karl Deisseroth at Stanford University. Links to CLARITY Wiki and CLARITY Forum Expansion microscopy resources – Literature and protocols related to expansion microscopy developed in the MIT lab of Edward Boyden. iDISCO resources – Literature, protocols and information about validated antibodies related to iDISCO SeeDB Resources – Protocols, literature videos related to SeeDB developed in the RIKEN lab of Takeshi Imai.]]> http://blogs.nature.com/methagora/2016/02/methods-and-probes-for-cleared-tissue-an-imperfect-table.html/feed/ 0 http://blogs.nature.com/methagora/2016/02/methods-and-probes-for-cleared-tissue-an-imperfect-table.html