Evidence map›Paper›PMID 29243106›Full record

ArticleBrain structure & function2018

Quantitative validation of immunofluorescence and lectin staining using reduced CLARITY acrylamide formulations.

D M Krolewski, V Kumar, B Martin, R Tomer, K Deisseroth, R M Myers, A F Schatzberg, F S Lee, J D Barchas, W E Bunney and 2 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Brain structure & function, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
1.5field-weighted citation impact, top 13% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 6 institutions in 1 country.

D M KrolewskiMolecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Place, Ann Arbor, MI, 48109, USA. dkrolews@med.umich.edu.
V KumarMolecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
B MartinMolecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
R TomerDepartment of Biological Sciences, Columbia University, New York, NY, USA.
K DeisserothDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
R M MyersHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
A F SchatzbergPsychiatry and Behavioral Science, Stanford University, Stanford, CA, USA.
F S LeePsychiatry, Weill Cornell Medical College, Cornell University, New York, NY, USA.
J D BarchasPsychiatry, Weill Cornell Medical College, Cornell University, New York, NY, USA.
W E BunneyDepartment of Psychiatry, University of California, Irvine, CA, USA.
H AkilMolecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
S J WatsonMolecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
University of Michigan–Ann Arbor · USCornell University · USStanford University · USColumbia University · USHudsonAlpha Institute for Biotechnology · USUniversity of California, Irvine · US

Funding

Can Affective Resilience be Enhanced? A Developmental and Epigenetic ApproachR01MH104261 · NIMH · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI AKIL, HUDA, WATSON, STANLEY J · 2014 to 2018
$2.8M
National Institute of Mental Health R01MH104261NIMH NIH HHS R01 MH104261Office of Naval Research N00014-12-1-0366
6 · The paper itself

Abstract

The CLARITY technique enables three-dimensional visualization of fluorescent-labeled biomolecules in clarified intact brain samples, affording a unique view of molecular neuroanatomy and neurocircuitry. It is therefore, essential to find the ideal combination for clearing tissue and detecting the fluorescent-labeled signal. This method requires the formation of a formaldehyde-acrylamide fixative-generated hydrogel mesh through which cellular lipid is removed with sodium dodecyl sulfate. Several laboratories have used differential acrylamide and detergent concentrations to achieve better tissue clearing and antibody penetration, but the potential effects upon fluorescent signal retention is largely unknown. In an effort to optimize CLARITY processing procedures we performed quantitative parvalbumin immunofluorescence and lectin-based vasculature staining using either 4 or 8% sodium dodecyl sulfate detergent in combination with different acrylamide formulas in mouse brain slices. Using both confocal and CLARITY-optimized lightsheet microscope-acquired images, we demonstrate that 2% acrylamide monomer combined with 0.0125% bis-acrylamide and cleared with 4% sodium dodecyl sulfate generally provides the most optimal signal visualization amongst various hydrogel monomer concentrations, lipid removal times, and detergent concentrations.

Indexed as

AcrylamideAnimalsBrainDose-Response Relationship, DrugFluorescent Antibody TechniqueImaging, Three-DimensionalLectinsMaleMiceMice, Inbred C57BLMicroscopy, ConfocalParvalbuminsStaining and LabelingTime FactorsAcrylamideLectinsParvalbuminsCLARITYCortexImagingImmunofluorescenceVasculature

Identifiers

PMID29243106
PMCPMC5828880
OpenAlexW2774002483

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.