The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students

Undergraduate research. Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

In their 2012 report, the President\u27s Council of Advisors on Science and Technology advocated replacing standard science laboratory courses with discovery-based research courses -a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates

A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles

Photoreactivity of donor-acceptor stilbene complexes in a macrocyclic host

Host-guest 2:1 complexation of photoreactive alkene guests improves the selectivity of [2+2] photodimerizations by templating alkene orientation prior to irradiation. Host-guest chemistry can also provide 1:1:1 complexes through the inclusion of electronically complementary donor and acceptor guests, but the photoreactivity of such complexes has not been investigated. In this work, we investigated a series of donor and acceptor stilbenes and found 1:1:1 complexes with cucurbit[8]uril that exhibited charge-transfer (CT) absorption bands in the visible and near-IR regions. Irradiation of the CT band of an azastilbene, 4,4’-stilbenedicarboxylate, and cucurbit[8]uril ternary complex led to a selective cross-[2+2] photocycloaddition, while other substrate pairs exhibited no productive chemistry upon CT excitation. Using transient absorption (TA) spectroscopy, we were able to understand the variable photoreactivity of different stilbene donor-acceptor complexes. We found that the back electron transfer (BET) following CT excitation of the photoreactive complex is positioned deep in the Marcus inverted region due to electrostatic stabilization of the ground state, allowing [2+2] to effectively compete with this relaxation pathway. Control reactions revealed that the cucurbit[8]uril host not only serves to template the reaction from the ground state, but also protects the long-lived radical ions formed by CT from side reactions. This protective role of the host suggests that donor-acceptor host-guest ternary complexes could be used to improve existing CT-initiated photochemistry or access new reactivity

Light Directs Monomer Coordination in Catalyst-Free Grignard Photopolymerization

π-Conjugated polymers can serve as active layers in flexible and lightweight electronics, and are conventionally synthesized by transition-metal-mediated polycondensation at elevated temperatures. We recently reported a photopolymerization of electron-deficient heteroaryl Grignard monomers that enables the catalyst-free synthesis of n-type π-conjugated polymers. Herein we provide an experimental and computational investigation of the mechanism of this photopolymerization. Spectroscopic studies performed in situ and after quenching reveal that the propagating species is a radical anion with halide end groups. DFT calculations for model oligomers suggest a Mg-templated SRN1-type coupling, in which Grignard monomer coordination to the radical anion chain avoids the formation of free sp2 radicals and enables C–C bond formation with very low barriers. We find that light plays an unusual role in the reaction, photoexciting the radical anion chain to shift electron density to the termini and thus favor productive monomer binding

Tailoring Dynamic Hydrogels by Controlling Associative Exchange Rates

Dithioalkylidenes are a recently-developed class of conjugate acceptors that undergo thiol exchange via an associative mechanism and have been used for reprocessable vitrimers, amine sensors, and degradable networks. Here, we show that the exchange rate of the reaction in aqueous environments is highly sensitive to the structure of the acceptor and may be varied over four orders of magnitude. Cyclic acceptors exchange rapidly, from 0.95 to 15.6 M-1s-1, while acyclic acceptors exchange between 3.77x10-3 and 2.17x10-2 M-1s-1. Computational, spectroscopic, and structural data suggest that the cyclic acceptors are more reactive than their linear counterparts because of resonance stabilization of the tetrahedral intermediate. We leverage this insight to design a compound with reactivity intermediate to that of the cyclic and linear analogs. Lastly, we incorporate this dynamic bond into hydrogels and demonstrate that molecular kex correlates with the hydrogels characteristic stress relaxation time; furthermore, these values may be parametrized with respect to computed descriptors of the electrophilic site. This work opens new avenues to design and control hydrogel viscoelasticity with an associative exchange mechanism

Templated Synthesis of End-Functionalized Graphene Nanoribbons through Living Ring-Opening Alkyne Metathesis Polymerization.

Atomically precise bottom-up synthesized graphene nanoribbons (GNRs) are promising candidates for next-generation electronic materials. The incorporation of these highly tunable semiconductors into complex device architectures requires the development of synthetic tools that provide control over the absolute length, the sequence, and the end groups of GNRs. Here, we report the living chain-growth synthesis of chevron-type GNRs (cGNRs) templated by a poly-(arylene ethynylene) precursor prepared through ring-opening alkyne metathesis polymerization (ROAMP). The strained triple bonds of a macrocyclic monomer serve both as the site of polymerization and the reaction center for an annulation reaction that laterally extends the conjugated backbone to give cGNRs with predetermined lengths and end groups. The structural control provided by a living polymer-templated synthesis of GNRs paves the way for their future integration into hierarchical assemblies, sequence-defined heterojunctions, and well-defined single-GNR transistors via block copolymer templates

Templated Synthesis of End-Functionalized Graphene Nanoribbons through Living Ring-Opening Alkyne Metathesis Polymerization.

Atomically precise bottom-up synthesized graphene nanoribbons (GNRs) are promising candidates for next-generation electronic materials. The incorporation of these highly tunable semiconductors into complex device architectures requires the development of synthetic tools that provide control over the absolute length, the sequence, and the end groups of GNRs. Here, we report the living chain-growth synthesis of chevron-type GNRs (cGNRs) templated by a poly-(arylene ethynylene) precursor prepared through ring-opening alkyne metathesis polymerization (ROAMP). The strained triple bonds of a macrocyclic monomer serve both as the site of polymerization and the reaction center for an annulation reaction that laterally extends the conjugated backbone to give cGNRs with predetermined lengths and end groups. The structural control provided by a living polymer-templated synthesis of GNRs paves the way for their future integration into hierarchical assemblies, sequence-defined heterojunctions, and well-defined single-GNR transistors via block copolymer templates