Current SPROUT Projects

An Efficient and Low-cost Method for Annotation and Quantification of circRNAs

RNA
Sebastian Kadener, Ines Patop, Sinead Nguyen

 

Circular RNAs (circRNAs) are recently re-discovered types of highly abundant RNAs which are produced by circularization of exons present in protein coding genes.

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While the biological functionality of circRNAs is still under debate, their remarkable stability make them great candidates to biomark disease. Indeed, several studies have shown that they are very good biomarkers for different cancer types. An ongoing study from the Kadener lab is investigating whether they are also altered in Parkinson's disease and determining if their levels in blood can be used to biomark this disease. However, annotating and quantifying circRNAs is challenging. This is mainly because they share most of their sequence with their hosting linear RNAs, so their identification relies in a very short part of their sequence. Here the team proposes to utilize a specific RNA-seq library preparation approach together with Nanopore sequence technology to selectively amplify and sequence hundreds of circRNAs. The proposed approach is based on a strong expertise on circRNAs, RNA-seq and Nanopore and will allow to determine the levels of hundreds of cirRNAs simultaneously from dozens of samples at minimum cost. The project also includes the adaptation of a specific computational pipeline to analyze the data.

SciLinkR

public engagement platform
Anique Olivier-Mason, Seth Fraden, Avi Rodal, Irv Epstein, Ben Rogers, Jerald Dumas

 

SciLinkR is an online public engagement platform that will 1) connect scientists and engineers with educators and 2) document STEM outreach. The platform matches educators who need a scientist or engineer to come to their classrooms with STEM professionals looking to do outreach to schools and the community. It also provides STEM faculty with citable documenation of their outreach activities.

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When students interact with a working scientist or engineer, they get more curious and less intimidated about STEM, and so they are more likely to see themselves as future scientists. The problems are 1) that it is hard for scientists to connect with the public who needs them the most, and 2) it is not clear what the scientist should do to make the most impact. As a result, convenience and reinvention rule the day. SciLinkR will connect scientists and engineers with educators and simplify and enhance the outreach they are already doing. SciLinkR is still in a startup phase, but with a SPROUT award, they will be able to reach more scientists, engineers, teachers, librarians, museum educators, journalists, and ultimately, more children. With this funding, they will be able to grow the platform within the first year to >1000 profiles and >100 SciLinkReports. To accomplish this goal, they will present at national science and teacher conferences, co-host a launch party this fall with the Brandeis Library and the MakerLab, and be able to give away SciLinkR-branded promotional items to encourage more people to create profiles on the site.

Photo-switchable Adhesives

tape
Grace Han, Mihael Gerkman, Xiang Li, Eli Kengmana

 

Adhesives, from those on bandages, tape, and BBQ grill sealants, to epoxy used in the assembly of appliances and electronics, are an essential part of modern life. Removing them when no longer needed is a challenge. This new solution offers a way to remove adhesives more effectively.

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Various strategies and formulae have been developed to achieve high adhesive strengths suitable for a wide range of uses, but the selective and controlled removal of adhesives has remained a significant challenge. In order to tackle this prominent problem, the team employs a novel class of materials that have demonstrated their potential in applications that require quick adhesion and selective debonding. They envision a wide range of applications that will employ the photo-switchable adhesives, such as industrial usages, plus consumer applications such as bandages, surgical tape strips, and heavy-duty mounting tapes. They plan to further examine the potential of the photo-switchable adhesives by performing a systematic analysis of adhesive strengths and debonding conditions. The project will involve the synthesis of designed target molecules, fabrication of testing modules, and further mechanical analysis.

Functional Heat Storage Materials for Heating Engine Oil

oil
Grace Han, Yuran Shi, Mihael Gerkman, Jennifer Taufan
In areas where temperatures often drop below -20 °C (-4 °F), such as the northern US and Canada, cars have trouble starting up. At temperatures below 0 °C, the oil is thicker and denser than usual and increases friction wearing down the engine parts. Researchers in Grace Han's lab plan to replace the energy-inefficient block heaters with novel materials that store and release heat in response to changing environment.
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There is an obvious market for oil heating devices that warm up the oil pan in an engine using electricity. A standard oil pan heater is usually left on overnight and consumes several kWh of electricity, also overheating the engine oil. Grace Han's lab plans to replace the energy-inefficient block heaters with novel materials that store and release heat in response to changing environment. Their composites of phase-change materials and light- responsive molecules absorb the waste heat generated from a running engine, store the heat overnight, and release the heat instantly to warm up the engine once triggered by LED light. The team plans to develop an optimized and custom-designed oil heater, which provides an instant source of heat at almost zero cost by recycling the heat generated from a running engine.

Identification of Inhibitors Against Mycobacterium Tuberculosis IMPDH

diagram of lung
Liz Hedstrom, Michael Pepi

 

Each year there are more than 10 million new cases of TB which have lead to more than 1 million deaths. Lizbeth Hedstrom's lab has discovered two novel compounds, Q112 and Q200, with potent antibacterial activity and no cytotoxicity against mammalian cells in culture.

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Mycobacterium tuberculosis (Mtb) is a human pathogen and the main causative agent of tuberculosis (TB). Each year there are more than 10 million new cases of TB which have lead to more than 1 million deaths. Additionally, emergence of drug resistant strains has made the leading clinical drugs ineffective. New drugs and molecular targets are urgently needed to address the emergence and spread of drug-resistant tuberculosis. The Hedstrom laboratory has discovered two novel compounds, Q112 and Q200, with potent antibacterial activity versus Mtb and no cytotoxicity against mammalian cells in culture.  The next stage would be to test these compounds in an animal model.

Tuberculosis Drug Design

medicine
Liz Hedstrom, Xingyou Wang

 

The current therapy for TB typically requires 4 drugs and takes 6 months. Lizbeth Hedstrom's lab has identified a promising new target, IMPDH, for next-generation TB drugs that could reduce the number of drugs needed to treat TB and the amount of time patients require treatment.

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Tuberculosis (TB) is a disease caused by bacteria called Mycobacterium tuberculosis (Mtb). Each year there are more than 10 million new cases of TB and more than 1 million deaths. The current therapy for TB typically requires 4 drugs and takes 6 months. Besides, the emergence of drug resistant strains makes it necessary to identify better drugs to fight with Mtb. IMPDH is a key enzyme in de novo guanine nucleotide synthesis pathway and is a promising new target. The Hedstrom laboratory is working with Atomwise to identify new inhibitors of Mtb IMPDH. They will receive 72 potential inhibitors designed using Atomwise’s virtual screening technology. The next stage would be to test the inhibition of these compounds for both MtbIMPDH and human IMPDH and antibacterial activity against a nonpathogenic Mtb relative.

Sulfur-stabilized HIV Vaccine Antigens

vaccine
Isaac Krauss, Leiming Tian

 

Many antibodies that protect against HIV bind to carbohydrates on the HIV protein. Thus, Brandeis vaccine researchers are interested in using these carbohydrates as HIV vaccines. Isaac Krauss and Leiming Tian are working on a novel vaccine platform technology that may also have applications to other infectious diseases plus certain cancers.

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Isaac Krauss and his lab have recently shown that the existing designs of HIV vaccines are unstable in the bloodstream, and they stimulate antibodies that target the HIV virus inaccurately. Thus, the team proposes to make a stable version of the carbohydrates that target HIV and other diseases, leading potentially to improved vaccines.