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ICGC Chronic Myeloid Disorders Group

  1. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Competing interests
No competing interests declared
  1. Luca Malcovati, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
  2. Sudhir Tauro, Division of Medial Sciences, University of Dundee, Dundee, UK
  3. Jacqueline Boultwood, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, UK

Author Details Person

Jenny Bloggs

  1. Evolutionary Studies Institute and Centre of Excellence in PalaeoSciences, University of the Witwatersrand, Johannesburg, South Africa
  2. School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
Present addresses
  1. Department of Inventive Inventions, Univertity of Wessex, Windowchester, Wessex
  2. Department of Underwater Basket Weaving, University of Somewhere
Contribution
Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents
Contributed equally with
  1. Francesca Smith
  2. Wendel Jakes III
For correspondence
  1. jenny@bloggs.com
  2. +1 555-4321-09876
Competing interests
No competing interests declared
ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3400-7927

Author Details Sub Group

ICGC Chronic Myeloid Disorders Group

  1. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Competing interests
No competing interests declared
Sub-group 1
  1. Luca Malcovati, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
  2. Sudhir Tauro, Division of Medial Sciences, University of Dundee, Dundee, UK
Sub-group 2
  1. Jacqueline Boultwood, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, UK

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Table 1 - source data 1.

Is the species name mentioned in the title, impact statement, abstract and digest of eLife papers (July–Sept 2014)?

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Many features are conserved between the mammalian nephron and planarian protonephridia.

(A) Image of a young adult C. elegans and schematic depicting the twelve pairs of sensory neurons in the anterior amphid individuals carrying a virus with k deleterious mutations at its endemic equilibrium. class carrying the fewest number of deleterious mutations is defined as mutation class k = 0. Inset: variation in the basic reproductive rate of infected individuals (gray histogram) and variation in the net reproductive rate R of infected individuals (brown histogram) resulting from variation in the number of deleterious mutations carried by circulating viruses.

Listed are, for each triplet of cell types, the probabilities of the four topologies for prior odds p(βi=1)p(βi=0)=0.05; the number of topologies that reach probability p(T | {giA,B,C})>0.6 for some value of p(βi=1)p(βi=0) between 10−6 and 102; the non-null topology that has the highest probability p(T | {giA,B,C}) over the range of prior odds (if the null topology is the most likely topology for the entire range of prior odds, the topology is marked ‘null’); and the value of highest probability p(T | {giA,B,C}) over the range of prior odds; the correct topology and triplet length in the traditional model; and the correct topology and triplet length in the Adolfsson model.

(A) Doxycycline-inducible gam-gfp fusion construct in the E. coli chromosome. Constitutively produced TetR protein represses the PN25tetO promoter, which produces GamGFP upon doxycycline induction. oriC, origin of replication; ter, replication terminus; arrows, directions of transcription. (B) Phage λ assay for end-blocking activity by Mu Gam and GamGFP. Rolling-circle replication of phage λred gam is inhibited by E. coli RecBCD, which causes small plaques of λred gam on wild-type E. coli (Smith, 1983). Mu Gam protein binds and protects DNA ends from RecBCD exonuclease activity (Akroyd and Symonds, 1986) and so is expected to allow rolling-circle replication of λred gam and therefore allow formation of large plaques. (C) λred gam plaques are small on recB+ (WT) and large on recB-deficient cells (recB-). Plaques produced on WT cells carrying gam and gam-gfp are small when Gam and GamGFP proteins are not produced (Uninduced). (D) λred gam produce large plaques on WT cells if Gam or GamGFP are produced (Induced). (E) UV sensitivity of E. coli recB-null mutant compared with recB+(WT), and uninduced gam and gam-gfp carrying cells. WT (), recB− (), WT GamGFP, (); WT Gam, (). (F) Induction of Gam or GamGFP with 200 ng/ml doxycycline causes UV sensitivity similar to that of recB-null mutant cells, indicating that Gam or GamGFP block RecBCD action on double-stranded DNA ends. WT, SMR14327; recB, SMR8350; WT GamGFP, SMR14334; WT Gam, SMR14333. Representative experiment performed three times with comparable results.

Code

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    <Sasa name=sasa confidence = 0/>
    <ShapeComplementarity name=shape verbose = 1 confidence = 0 jump = 1/> 
  </FILTERS>
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    <AtomTree name=docking_tree docking_ft = 1/>
    <DockSetupMover name=setup_dock/>
    <DockingProtocol name=dock docking_score_high=fullatom low_res_protocol_only = 0 docking_local_refine = 0 dock_min = 1 />
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  </APPLY_TO_POSE> 
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    <Add mover_name=setup_dock/> 
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    <Add filter_name=ddg/> 
    <Add filter_name=sasa/> 
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  </PROTOCOLS> 
</dock_design>

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Definition List

Research focus
Pre-mRNA splicing
post-transcriptional gene regulation
Experimental organism
Human
Mouse

Definition List Inline

Research focus
Pre-mRNA splicing
post-transcriptional gene regulation
Experimental organism
Human
Mouse

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https://doi.org/10.7554/eLife.16370

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https://doi.org/10.7554/eLife.16370

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https://doi.org/10.7554/eLife.16370

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doi: 10.7554/eLife.16370

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Math

Body Mass=0.060×FSTpr+13.856,SEE=6.78,r=0.50,p=<0.001.

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(7) y=β0+β1Choice+β2SVspend+β3SVsave+β4SeqSV+β5SeqLength+β6Cueposition+β7Left/right+β8Sequenceprogress+ϵ,

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(10) SVsaven= 1m−n∑i=n+1mSVspendi,

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  1. Schrenk F
  2. Bromage TG
  3. Betzler CG
  4. Ring U
  5. Juwayeyi YM
  6. Schrenk F
  7. Bromage TG
  8. Betzler CG
  9. Ring U
  10. Juwayeyi YM
  11. Schrenk F
  12. Bromage TG
  13. Betzler CG
  14. Ring U
  15. Juwayeyi YM
  16. Schrenk F
  17. Bromage TG
  18. Betzler CG
  19. Ring U
  20. Juwayeyi YM
  21. Schrenk F
  22. Bromage TG
  23. Betzler CG
  24. Ring U
  25. Juwayeyi YM
(1993)
Oldest Homo and Pliocene biogeography of the Malawi rift
Nature 365:833–836.
https://doi.org/10.1038/365833a0.1

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    Table

    F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)Partial η2Original effect size fReplication total sample sizeDetectable effect size f
    F(24,39) = 0.8678 (interaction)0.3481200.7307699169*0.3895070
    F(2,39) = 0.8075 (treatments)0.0397660.20350141690.2415459
    F(12,39) = 187.6811 (hematology parameters)0.9829787.599178169*0.3331365
    F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)F(Dfn, Dfd)Partial η2Original effect size fReplication total sample sizeDetectable effect size f
    F(24,39) = 0.8678 (interaction)0.3481200.7307699169*0.3895070
    F(2,39) = 0.8075 (treatments)0.0397660.2035014169*0.2415459
    F(12,39) = 187.6811 (hematology parameters)0.9829787.599178169*0.3331365
    1. *

      Footnote 1.

    2. The values in parenthesis refer to the highest resolution shell.

      *Rmerge=∑hkl∑i|I(hkl;i)−<I(hkl)>|∑hkl∑i(hkl;i) where I(hkl;i) is the intensity of an individual measurement of a reflection and <I(hkl)> is the average intensity of that reflection.

    Table Code Blocks

    data = {{x1,R1},{x2,R2},{x3,R3}...,{xm,Rm}};
    loglog=Function[{x,y},{Log[x/[C⁢a2+]0],Log[y]}];
    datalog=Apply[loglog,data,{1}];


    peakr = Function[{A,B,C,x},Piecewise[{{A+(1/2)*Log[1-(2/3)*B⁢x]
    +C*(1-(1-(2/3)*B⁢x)^(3/2),x<3/2/B,Infinity}}]];


    fit = NonlinearModelFit[datalog,{peakr[A,B,C,x],{A>0,B>0,C>0}},
    {{A,A0},{B,B0},{C,C0}},x,Method->NMinimize];
    fit['ParameterTable']

    1. Table with Code Blocks

    Table Equations

    Definitions of the simulated system
    TypeStatus
    Protein assembly occupancyk∈[1,Np]Pk∈{unbound,bound}
    Histonesi∈[1,N]Si∈{me0,me1,me2,me3}
    Regions of histonesRm={Histones[1,...,NNR]whenm=NR(nucleationregion)Histones[NNR+1,...,N]whenm=B(bodyregion),NB=N−NNRHistones[1,...,N]whenm=L(entireregion),NL=N

    1. Table with Equations

    Table Gene Sequences

    Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
    Recombinant DNA reagentsynthesized gene - mScarletIGenscriptactagtggtggttcaggaGTTTCAAAAGGTGAAGCCGTTATTAAAGAATTTATGAGATTCAAGGTTCACATGGAAGGAAGTATGAACGGTCATGAATTTGAGATTGAAGGAGAAGGTGAAGGTAGACCATATGAAGGCACCCAAACAGCTAAATTAAAAGTAACTAAAGGTGGTCCATTACCATTTAGTTGGGATATTTTATCTCCACAATTTATGTATGGTTCACGTGCTTTCAttAAACATCCAGCAGATATTCCAGATTATTATAAACAATCATTTCCAGAAGGTTTTAAATGGGAACGTGTCATGAACTTTGAAGATGGTGGAGCAGTTACAGTCACACAAGATACCTCATTAGAAGATGGTACATTAATATATAAAGTTAAATTACGTGGTACTAATTTTCCACCAGACGGTCCAGTAATGCAAAAAAAAACAATGGGCTGGGAAGCTAGTACAGAACGTTTATATCCTGAAGATGGTGTCCTTAAAGGCGATATAAAAATGGCCTTGAGATTAAAGGATGGTGGTAGGTATTTAGCAGATTTCAAAACCACTTATAAAGCAAAAAAACCAGTTCAAATGCCAGGTGCATATAATGTTGATAGAAAACTTGATATTACCAGTCATAATGAAGATTACACAGTTGTCGAACAATACGAACGTTCTGAAGGTCGTCATAGCACTGGTGGTATGGATGAATTATACAAATAAgctagcd
    Recombinant DNA reagentsynthesized gene - mNeonGenscriptactagtggtggttcaggaGTTTCAAAAGGTGAAGCCGTTATTAAAGAATTTATGAGATTCAAGGTTCACATGGAAGGAAGTATGAACGGTCATGAATTTGAGATTGAAGGAGAAGGTGAAGGTAGACCATATGAAGGCACCCAAACAGCTAAATTAAAAGTAACTAAAGGTGGTCCATTACCATTTAGTTGGGATATTTTATCTCCACAATTTATGTATGGTTCACGTGCTTTCAttAAACATCCAGCAGATATTCCAGATTATTATAAACAATCATTTCCAGAAGGTTTTAAATGGGAACGTGTCATGAACTTTGAAGATGGTGGAGCAGTTACAGTCACACAAGATACCTCATTAGAAGATGGTACATTAATATATAAAGTTAAATTACGTGGTACTAATTTTCCACCAGACGGTCCAGTAATGCAAAAAAAAACAATGGGCTGGGAAGCTAGTACAGAACGTTTATATCCTGAAGATGGTGTCCTTAAAGGCGATATAAAAATGGCCTTGAGATTAAAGGATGGTGGTAGGTATTTAGCAGATTTCAAAACCACTTATAAAGCAAAAAAACCAGTTCAAATGCCAGGTGCATATAATGTTGATAGAAAACTTGATATTACCAGTCATAATGAAGATTACACAGTTGTCGAACAATACGAACGTTCTGAAGGTCGTCATAGCACTGGTGGTATGGATGAATTATACAAATAAgctagc

    1. Table with Gene Sequences

    Table Inline Images

    unwindingturnover
    #Chemical drawingIC50[95%CI];µMIC50[95%CI];µM
    22.2
    [1.7–2.7]    		3.2
    [2.3–4.0]

    1. Table with inline images

    Table Long Url

    Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
    Software, algorithmMetamorphMetamorph vhttps://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/metamorph-microscopy#gref

    1. Table with long url

    Table Ordered List

    Factors classically associated with immune functions
    ProteinImmune system propertiesNervous system propertiesReferences
    Antimicrobial peptides(AMPs)

    1. Secreted by epithelial and phagocytic cells

    2. Disrupt microbial membranes leading to destruction of pathogen

    1. Antimicrobial in nervous system niches

    2. Control chemotaxis of immune cells and astroglia

    3. Mediate iron homeostasis

    4. Modulate nerve impulses

    5. Implicated in aging and neurodegeneration

    		Hanson et al., 2019;Lezi et al., 2018;Su et al., 2010;Zasloff, 2002

    1. Table with ordered list

    Table Unordered List

    Factors classically associated with immune functions
    ProteinImmune system propertiesNervous system propertiesReferences
    Antimicrobial peptides(AMPs)

    • Secreted by epithelial and phagocyticcells

    • Disrupt microbial membranes leading to destruction of pathogen

    • Antimicrobial in nervous system niches

    • Control chemotaxis of immune cells and astroglia

    • Mediate iron homeostasis

    • Modulate nerve impulses

    • Implicated in aging and neurodegeneration

    		Hanson et al., 2019;Lezi et al., 2018;Su et al., 2010;Zasloff, 2002

    1. Table with unordered list

    Term

    Title:
    Valuable: Summary
    • Valuable

    Term Significance

    Significance of the findings:
    Valuable: Contains findings that have theoretical or practical implications for a subfield.
    • Landmark
    • Fundamental
    • Important
    • Valuable
    • Useful

    Term Strength

    Strength of evidence:
    Solid: Methods, data and analyses broadly support the claims with only minor weaknesses.
    • Exceptional
    • Compelling
    • Convincing
    • Solid
    • Incomplete
    • Inadequate

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