April 2009 Volume 6 Number 4, pp 237 - 311
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Programming antibodies to treat cancer and autoimmune diseases.
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Scripps researchers have devised a means of inducing antibodies by vaccine and then programming them with a target-specific molecule in vivo to treat mouse models of cancer. Programmed antibodies could also be used to treat autoimmune diseases, although it is not yet clear that they could treat infectious diseases. How does this approach change the landscape for conventional vaccine or infused antibody therapies?
Find out more by reading the first in-depth analysis of the scientific and commercial potential of the work in SciBX: Science-Business eXchange.
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EDITORIAL
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Defining the scientific method p237
The rise of 'omics' methods and data-driven research presents new
possibilities for discovery but also stimulates disagreement over how
science should be conducted and even how it should be defined.
doi:10.1038/nmeth0409-237
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CORRESPONDENCE
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The UCSC Cancer Genomics Browser pp239 - 240
Jingchun Zhu et al.
doi:10.1038/nmeth0409-239
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mzAPI: a new strategy for efficiently sharing mass spectrometry
data pp240 - 241
Manor Askenazi, Jignesh R Parikh and Jarrod A Marto
doi:10.1038/nmeth0409-240
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RESEARCH HIGHLIGHTS
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PALM reading p243
Super-resolution fluorescence microscopy gets a boost in axial
resolution from two groups of optics wizards.
Wayne Peng
doi:10.1038/nmeth0409-243
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Cheap third-generation sequencing p244
By covalently attaching cyclodextrin to a hemolysin nanopore,
researchers show single-molecule, label-free sequencing at very
high accuracy.
Nicole Rusk
doi:10.1038/nmeth0409-244a
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Deep sequencing of ribosome footprints p244
Combining ribosome profiling and deep sequencing, researchers present
a method to monitor protein translation genome-wide.
Natalie de Souza
doi:10.1038/nmeth0409-244b
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News in brief p245
doi:10.1038/nmeth0409-245
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Snapshots of proteins at work p246
Two groups extend the boundaries of in-cell nuclear magnetic
resonance spectroscopy.
Allison Doerr
doi:10.1038/nmeth0409-246
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Don't just stand there p248
A long-range magnetic resonance imaging platform promises
unprecedented capabilities for whole-organ visualization and
high-throughput sample analysis.
Michael Eisenstein
doi:10.1038/nmeth0409-248
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QPCR without the 'P' p250
With the addition of a ligand-sensing aptamer sequence, a
self-replicating RNA enzyme system enables general molecular
detection, analogous to that of quantitative PCR.
Irene Kaganman
doi:10.1038/nmeth0409-250
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NEWS AND VIEWS
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Questioning standardization in science pp253 - 254
Some scientists suggest that environmental standardization may
lead to spurious findings. The implication from this hypothesis
will likely be controversial.
Richard Paylor
doi:10.1038/nmeth0409-253
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Footprints by deep sequencing pp254 - 255
Deep sequencing of DNase I-treated yeast DNA yields genome-wide
information on chromatin transitions as well as protein binding
in these regions.
Gordon Hager
doi:10.1038/nmeth0409-254
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PERSPECTIVE
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Environmental standardization: cure or cause of poor reproducibility
in animal experiments? pp257 - 261
S Helene Richter, Joseph P Garner and Hanno Wurbel
doi:10.1038/nmeth.1312
Abstract: http://links.ealert.nature.com/ctt?kn=85&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Quantification of rare allelic variants from pooled genomic
DNA pp263 - 265
The base-calling algorithm SNPSeeker detects single-nucleotide
polymorphisms with frequencies that are below the error rate of
the sequencing platform. It is thus well suited to analyze data
from large pooled samples and find rare variants that may contribute
to diseases or complex traits.
Todd E Druley et al.
doi:10.1038/nmeth.1307
Abstract: http://links.ealert.nature.com/ctt?kn=108&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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Hematopoietic stem cell transplantation without
irradiation pp267 - 269
Long-term engraftment of hematopoietic stem cells into the bone
marrow of a recipient depends on immunological compatibility between
donor and host, or ablation of the host's immune system by
irradiation. A 'universal recipient' mouse model now shows that mice
that lack T, B and NK cells and bear mutations in the tyrosine kinase
Kit accept any donor HSC without irradiation.
Claudia Waskow et al.
doi:10.1038/nmeth.1309
Abstract: http://links.ealert.nature.com/ctt?kn=17&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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Neonatal desensitization allows long-term survival of neural
xenotransplants without immunosuppression pp271 - 273
Rats are desensitized to xenografts of human neural or embryonic
stem cell-derived cells by exposure to the xenogeneic cells during
the neonatal period. Brain grafts survive in immunocompetent rats
without chronic immunosuppression, allowing long-term studies.
Claire M Kelly et al.
doi:10.1038/nmeth.1308
Abstract: http://links.ealert.nature.com/ctt?kn=47&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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SUnSET, a nonradioactive method to monitor protein
synthesis pp275 - 277
As an alternative to the use of radioactively labeled amino acids,
incorporation of puromycin into proteins allows evaluation of
translation in heterogenous cell populations by flow cytometry
analysis after staining with an antibody to puromycin.
Enrico K Schmidt, Giovanna Clavarino, Maurizio Ceppi and Philippe
Pierre
doi:10.1038/nmeth.1314
Abstract: http://links.ealert.nature.com/ctt?kn=89&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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Nanoscale live-cell imaging using hopping probe ion conductance
microscopy pp279 - 281
Complex three-dimensional structures on cellular surfaces are often
damaged during high-resolution imaging of live cells. Now, hopping
probe scanning ion conductance microscopy-which uses a hopping
nanopipette that 'hops' instead of 'sliding'-protects surface
structures from probe-induced damage.
Pavel Novak et al.
doi:10.1038/nmeth.1306
Abstract: http://links.ealert.nature.com/ctt?kn=116&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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ARTICLES
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Global mapping of protein-DNA interactions in vivo by digital genomic
footprinting pp283 - 289
Dense mapping of DNase I cleavage sites across the whole yeast genome
by next-generation sequencing reveals a global view of the binding of
regulatory proteins to genomic DNA. The high resolution allows the
identification of new binding sites for known factors as well as the
de novo derivation of factor binding motifs.
Jay R Hesselberth et al.
doi:10.1038/nmeth.1313
Abstract: http://links.ealert.nature.com/ctt?kn=84&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=1&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
Amplification-free Illumina sequencing-library preparation
facilitates improved mapping and assembly of (G+C)-biased
genomes pp291 - 295
The PCR step in the preparation of sequencing libraries for the
Illumina Genome Analyzer can introduce coverage bias, especially
in very (A+T)-rich genomes. By directly annealing template DNA to
adapters with sequences needed for attachment in the flow cell, PCR
can be omitted as cluster amplification in the flow cell enriches for
fully ligated templates.
Iwanka Kozarewa et al.
doi:10.1038/nmeth.1311
Abstract: http://links.ealert.nature.com/ctt?kn=66&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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Automated monitoring and analysis of social behavior in
Drosophila pp297 - 303
An automated system to measure aggression and courtship in pairs
of interacting Drosophila is presented and should allow large-scale
screens of these behaviors in the future.
Heiko Dankert et al.
doi:10.1038/nmeth.1310
Abstract: http://links.ealert.nature.com/ctt?kn=61&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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TECHNOLOGY FEATURE
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Journeys across the membrane pp305 - 309
From high-throughput electroporation platforms capable of
transfecting thousands of different cells in a day, to nanowires
that puncture and deliver DNA to just a single cell, new technology
is emerging to help researchers with their changing gene delivery
needs.
Nathan Blow
doi:10.1038/nmeth0409-305
http://links.ealert.nature.com/ctt?kn=91&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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ERRATUM
----------------------
Erratum: Photoactivatable mCherry for high-resolution two-color
fluorescence microscopy p311
Fedor V Subach et al.
doi:10.1038/nmeth0409-311
http://links.ealert.nature.com/ctt?kn=99&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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APPLICATION NOTES
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Visualizing signal transduction pathways by quantifying
protein-protein interactions in native cells and tissue
Simon Fredriksson
Abstract: http://links.ealert.nature.com/ctt?kn=11&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=20&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiDTM
system
Anjali Shah
Abstract: http://links.ealert.nature.com/ctt?kn=65&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=115&m=32240862&r=MTc2NjExMzUwMAS2&b=2&j=NDcwMzUyOTMS1&mt=1&rt=0
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