PRUNET interface.

<p>The graphical user interface is organized in tabs, namely a welcome tab (<b>A</b>), input tab (<b>B</b>), options tab (<b>C</b>) and results tab (D). Both the input and results tab include a network visualizer to facilitate the interaction of the user with the program.</p

Comparison of PRUNET with similar available software.

<p>Scores represent the match between predicted and real phenotypes; a score of 1 represents a full agreement between training set and model predictions, while a score of 0.5 reflects a correct description of 50% of the training set.</p><p>Comparison of PRUNET with similar available software.</p

Validation of PRUNET using four biological examples.

<p>The scores obtained after the application of PRUNET to four biological examples, namely epithelial to mesenchymal transition (EMT), Th1-Th2 transdifferentiation (Th1-Th2), induced pluripotent stem cells (iPSC) and cardiomyocyte differention of human embryonic stem cells (hESC-cardiomyocyte), were compared with the scores obtained by a population of randomly generated subnetworks from the prior knowledge network. Green, orange and red lines represent the cumulative frequencies of scores obtained with training sets of a half, an intermediate number (different for each case) and all of the genes respectively, whereas the blue line represents the scores obtained from the population of subnetworks randomly generated from the prior knowledge network. The separation between blue and the other lines represents the contribution of PRUNET to the prior knowledge network in terms of describing the known phenotypes of different training set sizes.</p

HPLC profile and mass spectrum of synthesized amidated BMAP-28 peptides.

<p>The peptides (Sequence: GGLRSLGRKILRAWKKYGPIIVPIIRI-NH₂; M.W: 3131.92; Formula: C147H252N44O31) were isolated and purified by high-performance liquid chromatography (HPLC) to greater than 95% purity. The purity and molecular weight of the respective peptides were confirmed by matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry. Left panels: HPLC profile, right panels: mass spectrum. A) L-BMAP-28-NH₂, purity 95.64%; B) D-BMAP-28-NH₂, purity 95.35%; C) RI-BMAP-28-NH₂, purity 95.85%; D) Scrambled-BMAP-28-NH₂, purity 95.19%.</p

Replication Attempt: “Effect of BMAP-28 Antimicrobial Peptides on Leishmania Major Promastigote and Amastigote Growth: Role of Leishmanolysin in Parasite Survival”

<div><p>This study describes an attempt to replicate experiments from the paper “Effect of BMAP-28 Antimicrobial Peptides on <i>Leishmania major</i> Promastigote and Amastigote Growth: Role of Leishmanolysin in Parasite Survival,” which was submitted to the Reproducibility Initiative for independent validation. The cathelicidin bovine myeloid antimicrobial peptide 28 (BMAP-28) and its isomers were previously shown to have potent antiparasitic activity against <i>Leishmania major.</i> We tested the effectiveness of L-BMAP-28 and two of its isomers, the D-amino acid form (D-BMAP-28) and the retro-inverso form (RI-BMAP-28), in both unamidated and amidated forms, as anti-leishmanial agents against <i>Leishmania major</i> promastigotes <i>in vitro</i>. We observed that L-BMAP-28, as well as its D and RI isomers, demonstrate anti-leishmanial activity against <i>L. major</i> promastigotes <i>in vitro</i>. The inhibitory effect was lower than what was seen in the original study. At 2 µM of amidated peptides, the viability was 94%, 36%, and 66% with L-, D- and RI-peptides, versus 57%, 6%, and 18% in the original study.</p></div

Stable expression of luciferase after <i>in vitro</i> or <i>in vivo</i> passaging of <i>T. cruzi</i> trypomastigotes.

<p>Luciferase activity in 1×10⁵ epimastigotes (Epi) under continued drug selection (G418 200 µg/ml) (Epi); 1×10⁵ trypomastigotes (Tryp); 1×10⁵ trypomastigotes 2 weeks after differentiation into metacyclics, removal of drug selection and <i>in vitro</i> passage through LLCMK2 cells and subsequent <i>in vivo</i> passage in mice where luciferase activity was measured in 10⁵ trypomastigotes acquired from the blood of an infected 6 week-old Balb/c mouse 1 week post infection (<i>in vivo</i> trypo).</p

Color response of our SROFM device.

<p>Light transmission through a 27 µm channel containing different concentrations of Trypan blue dye. This figure demonstrates agreement with the Beer-Lambert law of light absorption, validating SROFM's color imaging capabilities.</p

Method for testing anti-<i>T.cruzi</i> compounds in mice.

<p>Groups of five mice were infected with <i>T. cruzi</i> trypomastigotes expressing luciferase and imaged on the indicated days after infection. Treatment with benznidazole (5 mg/kg/day, i.p.) started on day 4. (A) One representative mouse of each group is shown. (B) Quantification of luminescence signal from infected control or benznidazole treated mice. Results are expressed as average ± standard deviation (*, <i>P</i><0.05; **, <i>P</i><0.01).</p

HPLC profile and mass spectrum of synthesized unmodified BMAP-28 peptides.

<p>The peptides (Sequence: GGLRSLGRKILRAWKKYGPIIVPIIRIG; M.W: 3131.92; Formula: C147H252N44O31) were isolated and purified by high-performance liquid chromatography (HPLC) to greater than 95% purity. The purity and molecular weight of the respective peptides were confirmed by matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry. Left panels: HPLC profile, right panels: mass spectrum. A) L-BMAP-28, purity 95.61%; B) D-BMAP-28, purity 96.67%; C) RI-BMAP-28, purity 95.62%; D) Scrambled-BMAP-28, purity 95.34%.</p

Test for activity <i>in vivo</i> of compounds active <i>in vitro</i>.

<p>Groups of five mice were infected with <i>T. cruzi</i> and treated with different compounds following the protocol shown in (A). (B) Quantification of parasite infection levels in the groups of mice treated with the different compounds is expressed as <i>T. cruzi</i> index. Compounds are identified by their CID. Results are expressed as average ± standard deviation (*, <i>P</i><0.05). (C) One representative mouse of each group treated with compounds CID-12402750 and CID-24892493.</p