YouTube or You Lose: Grand Challenges Canada Explores Whether Scientists Are Ready for Web-Based Grant Competitions

It is not hard to trace the influence of technology on the way we read the literature or give scientific presentations. Not so long ago, chemists used hard copies of Chemical Abstracts to find papers and sticks of chalk to deliver talks. Only over the past decade have computer presentations become the norm. In contrast, the way that grants are evaluated has remained relatively unchanged: scientists submit written proposals that are then evaluated by committees of scientists in the field. Might this process soon change as well? The not-for-profit organization Grand Challenges Canada (GCC) recently sponsored a competition in which researchers presented audacious ideas to attack problems related to global health (Figure 1). In its search for bold ideas from scientists, the GCC organization tested a bold idea as well: each proposal had to be accompanied by a 2-min-long video for public consumption on the Internet. Web users were encouraged not only to view these video summaries but to participate in the evaluation of the proposals by means of clicking on a “thumbs up” button (similar to the “like” buttons found on YouTube and Facebook). The votes from the public video were used by GCC to evaluate each applicant’s ability to “engage the public and increase awareness in the grand challenges facing global health today”.^1 The competition collected over 180,000 votes and over 100,000 unique online visits from 156 countries in a mere 4 weeks—staggering statistics for scientific videos. While each applicant also submitted a written version of the proposal, which was privately evaluated by “standard” peer-review, the public video feature was one of the first direct implementations of Web 2.0 technology (user-interactive sites and applications) to evaluate scientific proposals. The competition raises an important question: to what extent, if any, should Web 2.0 technology or other direct evaluation by the public be used to determine the outcome of scientific grant proposals

Uniform Amplification of Phage with Different Growth Characteristics in Individual Compartments Consisting of Monodisperse Droplets

Jeder Klon zählt! Beim Phagen-Display gehen Klone, die das Phagenwachstum hemmende Liganden präsentieren, bei der Vervielfältigung verloren. In monodispersen Emulsionen, die mithilfe eines einfachen Mikrofluidiksystems erzeugt wurden, ist die Konkurrenz zwischen langsam (S) und schnell (R) wachsenden Phagen abgemildert, sodass das R/S-Verhältnis beibehalten bleibt. Die konkurrenzfreie Vervielfältigung von Phagen bewahrt Liganden, die im normalen Phagen-Display abhanden kommen.Chemistry and Chemical Biolog

Heat-enhanced peptide synthesis on Teflon-patterned paper

In this report, we describe the methodology for 96 parallel organic syntheses of peptides on Teflon-patterned paper assisted by heating with an infra-red lamp. SPOT synthesis is an important technology for production of peptide arrays on a paper-based support for rapid identification of peptide ligands, epitope mapping, and identification of bio-conjugation reactions. The major drawback of the SPOT synthesis methodology published to-date is suboptimal reaction conversion due to mass transport limitations in the unmixed reaction spot. The technology developed in this report overcomes these problems by changing the environment of the reaction from static to dynamic (flow-through), and further accelerating the reaction by selective heating of the reaction support in contact with activated amino acids. Patterning paper with Teflon allows for droplets of organic solvents to be confined in a zone on the paper array and flow through the paper at a well-defined rate and provide a convenient, power-free setup for flow-through solid-phase synthesis and efficient assembly of peptide arrays. We employed an infra-red (IR) lamp to locally heat the cellulosic support during the flow-through delivery of the reagents to each zone of the paper-based array. We demonstrate that IR-heating in solid phase peptide synthesis shortened the reaction time necessary for amide bond formation down to 3 minutes; in some couplings of alpha amino acids, conversion rates increased up to fifteen folds. The IR-heating improved the assembly of difficult sequences, such as homo-oligomers of all 20 natural amino acids

Reconfigurable Self-Assembly of Mesoscale Optical Components at a Liquid-Liquid Interface

Magnetic fields template the self-assembly of 2D mesoscale optical components consisting of magnetically responsive parts at a liquid–liquid interface. These optical components are tiles of reflective diffraction gratings. Their orientations, and the resulting optical effects, are reconfigurable by a change in the magnetic field. Transferring the assembled structure onto solid substrates generates optically functional coatings or films.Chemistry and Chemical Biolog

Towards purification of antibodies with light

One of the most common method to purify a particular antibody is done by affinity chromatography. Antibody binding proteins such as Protein A are used to purify antibody from the mixture of proteins and antibodies. The main objective of my project is to design a new method that utilizes light-responsive (LR) affinity-capture ligands for antibody purification. This would vastly improve the quality of purification of the antibodies. Using the LR affinity-capture ligands to purify the antibody can be widely applied to many fields related to biotechnology, life science industry, and pharmaceutical industry. To achieve this, we designed the LR cyclic peptide as affinity ligand that recognizes the constant region (Fc) of the antibody we want to purify. We began with octapeptide sequences that was known to have an affinity to the Fc region of IGg antibody. The octapeptide was attempted to react with the LR azobenzene linker 3,3’-bis(sulfonato)- 4,4’-bis(chloroacetamido)-azobenzene (BSBCA) to create a macrocyclic product, LR-macrocycle peptide. We hypothesized that the LR-macrocycle peptide will have two  geometric isomers: one isomer with higher affinity and one isomer with lower affinity towards the Fc region. The peptides were immobilized on paper for observing the affinity difference of  two isomers towards the Fc region of the antibody. The data obtained from preliminary study suggested that the LR-macrocycle peptides had different affinities between the two isomers. To further understanding the system, we will be validating the affinity differences of those ligands and will be optimizing the peptide sequences to increase the efficiency of the technique. *Indicates faculty mentor

Identification of chemical inducers of metastasis-related cell differentiation events using peptide microarrays

The epithelial-mesenchymal transition (EMT) is a key indicator of cancer progression and metastasis in vivo. The most important inducer of EMT is activation of the transforming growth factor beta (TGF-β) pathway. In addition to initiating EMT, TGF-β is able to cause cancer cells to switch cell states from the non-stem cancer cell (NSCC) to the more invasive and tumorigenic cancer stem cell (CSC) state. Investigation into factors that can activate the TGF-β pathway, and thereby initiate EMT or the NSCC-to-CSC conversion, is therefore of critical importance. It is well known that the chemical environment immediately surrounding the cell determines cell differentiation events. Small molecules such as peptides, then, can induce such events in cells that are bound to the peptides. In this project, we aimed to identify peptide ligands that were able to induce EMT in cells adhered to the peptide surface. Five peptides previously discovered through phage display (panning against MDA-MB-231 cells) along with three control peptides, were printed onto gold-coated glass slides in a patterned array using a DNA microarray printer and tested against NMuMG cells. The arrays of cells were then fixed and stained for eCadherin (an epithelial marker). We found that after four days of culture on the peptide-modified surfaces, eCadherin levels were decreased on two of the five test peptide surfaces, as well as in both of the positive control peptide surfaces, suggesting that those cell populations underwent EMT. Future studies will indicate whether these peptides can additionally induce the NSCC-to-CSC conversion. *Indicates faculty mentor

Continuously tunable microdroplet-laser in a microfluidic channel

This paper describes the generation and optical characterization of a series of dye-doped droplet-based optical microcavities with continuously decreasing radius in a microfluidic channel. A flow-focusing nozzle generated the droplets (~21 μm in radius) using benzyl alcohol as the disperse phase and water as the continuous phase. As these drops moved down the channel, they dissolved, and their size decreased. The emission characteristics from the drops could be matched to the whispering gallery modes from spherical micro-cavities. The wavelength of emission from the drops changed from 700 to 620 nm as the radius of the drops decreased from 21 μm to 7 μm. This range of tunability in wavelengths was larger than that reported in previous work on droplet-based cavities.Chemistry and Chemical Biolog

Reproducible Discovery of Cell-Binding Peptides “Lost” in Bulk Amplification via Emulsion Amplification in Phage Display Panning

Many pharmaceutically-relevant cell surface receptors are functional only in the context of intact cells. Phage display, while being a powerful method for the discovery of ligands for purified proteins often fails to identify a diverse set of ligands to receptors on a cell membrane mosaic. To understand this deficiency, we examined growth bias in naïve phage display libraries and observed that it fundamentally changes selection outcomes: The presence of growth-biased (parasite) phage clones in a phage library is detrimental to selection and cell-based panning of such biased libraries is poised to yield ligands from within a small parasite population. Importantly, amplification of phage libraries in water-oil emulsions suppressed the amplification of parasites and steered the selection of biased phage libraries away from parasite population. Attenuation of the growth bias through the use of emulsion amplification reproducibly discovers the ligands for cell-surface receptors that cannot be identified in screen that use conventional ‘bulk’ amplification

Platform for High-Throughput Testing of the Effect of Soluble Compounds on 3D Cell Cultures

In vitro 3D culture could provide an important model of tissues in vivo, but assessing the effects of chemical compounds on cells in specific regions of 3D culture requires physical isolation of cells and thus currently relies mostly on delicate and low-throughput methods. This paper describes a technique (“cells-in-gels-in-paper”, CiGiP) that permits rapid assembly of arrays of 3D cell cultures and convenient isolation of cells from specific regions of these cultures. The 3D cultures were generated by stacking sheets of 200-μm-thick paper, each sheet supporting 96 individual “spots” (thin circular slabs) of hydrogels containing cells, separated by hydrophobic material (wax, PDMS) impermeable to aqueous solutions, and hydrophilic and most hydrophobic solutes. A custom-made 96-well holder isolated the cell-containing zones from each other. Each well contained media to which a different compound could be added. After culture and disassembly of the holder, peeling the layers apart “sectioned” the individual 3D cultures into 200-μm-thick sections which were easy to analyze using 2D imaging (e.g., with a commercial gel scanner). This 96-well holder brings new utilities to high-throughput, cell-based screening, by combining the simplicity of CiGiP with the convenience of a microtiter plate. This work demonstrated the potential of this type of assays by examining the cytotoxic effects of phenylarsine oxide (PAO) and cyclophosphamide (CPA) on human breast cancer cells positioned at different separations from culture media in 3D cultures.Chemistry and Chemical Biolog

Deep Sequencing Analysis of Phage Libraries using Illumina Platform

This paper presents an analysis of phage-displayed libraries of peptides using Illumina. We describe steps for the preparation of short DNA fragments for deep sequencing and MatLab software for the analysis of the results. Screening of peptide libraries displayed on the surface of bacteriophage (phage display) can be used to discover peptides that bind to any target. The key step in this discovery is the analysis of peptide sequences present in the library. This analysis is usually performed by Sanger sequencing, which is labor intensive and limited to examination of a few hundred phage clones. On the other hand, Illumina deep-sequencing technology can characterize over 107 reads in a single run. We applied Illumina sequencing to analyze phage libraries. Using PCR, we isolated the variable regions from M13KE phage vectors from a phage display library. The PCR primers contained (i) sequences flanking the variable region, (ii) barcodes, and (iii) variable 5′-terminal region. We used this approach to examine how diversity of peptides in phage display libraries changes as a result of amplification of libraries in bacteria. Using HiSeq single-end Illumina sequencing of these fragments, we acquired over 2 × 107 reads, 57 base pairs (bp) in length. Each read contained information about the barcode (6 bp), one complimentary region (12 bp) and a variable region (36 bp). We applied this sequencing to a model library of 106 unique clones and observed that amplification enriches ∼150 clones, which dominate ∼20% of the library. Deep sequencing, for the first time, characterized the collapse of diversity in phage libraries. The results suggest that screens based on repeated amplification and small-scale sequencing identify a few binding clones and miss thousands of useful clones. The deep sequencing approach described here could identify under-represented clones in phage screens. It could also be instrumental in developing new screening strategies, which can preserve diversity of phage clones and identify ligands previously lost in phage display screens.Chemistry and Chemical Biolog