Evolutionary rate and expression noise of the static and dynamic modules

<p><b>Copyright information:</b></p><p>Taken from "Revealing static and dynamic modular architecture of the eukaryotic protein interaction network"</p><p></p><p>Molecular Systems Biology 2007;3():110-110.</p><p>Published online 24 Apr 2007</p><p>PMCID:PMC1865589.</p><p>Copyright © 2007, EMBO and Nature Publishing Group</p> Evolutionary rates of yeast proteins derived by were used. () Boxplot of evolutionary rates of family, party and date hubs. Family hubs are static hubs with neighborhood EVs of 0.45 and date hubs are those with neighborhood EV>0.3 and avPC

Supporting Information

This supporting information document links all the plant species codes used in the analysis with the full species names. It also includes attribute information for each of the species in the analysis (family, wetland status, etc.)

Cluster Analysis Data_herbaceous sqrt

This file contains the vegetation data from 15 riparian study reaches at Tejon Ranch, California. Reaches were sampled annually between 2013 and 2016. Columns are species, and rows are the plot_years. Values reported are absolute cover. All species in the "herbaceous canopy" (those not followed by "_Shrub" or "_Tree") have had their cover values square-root transformed. Definitions and attributes of of species codes are in the "Supporting Information" file

R Code for Riparian ESD:STM paper

This is the R code used to produce all the analyses in the paper (cluster analyses, indicator species analysis, CART analysis, and summary statistics). It requires that you install the packages loaded at the beginning of the script. If you don't want to run the code in R, but you do want to see the code and output, you can also look at the accompanying html file of the same name

R Code for Riparian ESD:STM paper.nb

This is the html output of the R script. It shows the code and the outputs from each step of the analysis

Pretreatment and intratumoral injections.

<p>(A) Mice were vaccinated 2 times and then injected with tumor cells 2 weeks later. (B) Tumors were allowed to grow to 100 mm³, and 3.5 x 10⁶ pfu/mouse in 25 ul of MVA, MVAmeso (meso) or MVAmesoA35Del (A35D) viruses were injected directly into tumors 3 times.</p

MVA kills Panc02 cells.

<p>Panc02 cells (10,000 cells/well) were plated in triplicate in a 96-well plate. MVA was added to the wells at an MOI of 0.5 or 5.0 pfu/cell. After 24 h, 10 ul MTS/PMS was added to each well, and the absorbance was read at 492 nm. Averages <u>+</u> SD error bars are shown. * p< 0.005. Media with no cells was used to define the background control level.</p

Mesothelin is expressed from MVAmeso viruses.

<p>BHK cells (2x10⁶ cells/well) were uninfected or infected with MVA, MVAmeso or MVAmesoA35Del. Cells were lysed and samples were loaded onto a pre-cast 4–20% gradient gel. Rabbit anti-mesothelin antibody and anti-rabbit IgG (Fc) AP Conjugate (Promega) detected mesothelin protein (arrow). HEK transected cells, previously described [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193131#pone.0193131.ref007" target="_blank">7</a>], were used as control.</p

MVA meso virus injections are safe.

<p>Female C57BL/6 mice (n = 5) were injected i.m. with PBS, MVA, MVAmeso or MVAmesoA35Del and monitored daily by body score condition (no change) and weight up to 125 days. No adverse effects were noted. Average weights are shown <u>+</u> SEM.</p

Treatment of tumor bearing mice.

<p>C57BL/6 mice were injected s.c. in one flank with 640,000 wild type Panc02 cells. At 11, 18, and 25 days (arrows) post tumor injection, mice were injected i.m. contralaterally with PBS or 7.6 x 10⁷ pfu/mouse of MVA, MVAmeso (Meso) or MVAmesoA35Del (A35D) viruses in 25 ul. (A) Tumor volumes were measured 3 times per week and survival (B) was monitored.</p