News
Katie Breuckman Accepted into NSF Graduate Research Traineeship Program in Biological Feedback Control
Katie Breuckman of the Hao and Khalil Labs was accepted as a trainee in the NSF Graduate Research Traineeship Program in Biological Feedback Control for the 2024-2025 academic year. This program is an NSF funded research traineeship combining the study of the engineering principles in feedback control with investigations of how biological systems self-regulate, adapt, heal and evolve. The NSF Research Traineeship (NRT) program seeks to provide effective training of STEM graduate students in high priority interdisciplinary or convergent research areas. Selected students participate in an industry internship, professional development events, and a co-mentored dissertation project in a breadth of topic areas including molecular level control algorithms, microbial feedback control systems, control of tissues homeostasis and regeneration, biohybrid and bioinspired engineered systems.
Katie is developing yeast-based selection methods for improving protease and nanobody specificity toward therapeutic targets. She aims to integrate laboratory evolution and scalable screening methods to rapidly, and cost-effectively produce bespoke therapeutics. Furthermore, through the NRT in Biological Feedback Control, she plans to develop mathematical models to predict evolutionary trajectories and computationally design improved starting points for further protein evolution. Through this work, Katie aims to enhance our grasp of feedback-based control for navigating protein fitness landscapes.
Congratulations, Katie!
Anna Berenson Receives 2024 Belamarich Award
Dr. Anna Berenson of the Fuxman Bass Lab was selected as the winner of the Biology Department's 2024 Belamarich Award for her doctoral dissertation in Molecular Biology, Cell Biology & Biochemistry titled “Paired Yeast One-Hybrid Assays to Detect DNA-Binding Cooperativity and Antagonism Across Transcription Factors.” The selection committee was impressed by the quality of Anna’s work, its combination of methods development, observational studies, and computational analyses, and its potential for informing future research in the field of gene regulation. More information about her research is below.
For her dissertation, Anna developed paired yeast one-hybrid (pY1H) assays to study interactions between pairs of transcription factor (TF) proteins and DNA regions of interest. In addition to identifying cooperative DNA binding of TF pairs, pY1H assays also revealed extensive DNA-binding antagonism between TFs, constituting a previously underappreciated mechanism to regulate TF-DNA binding. Anna further applied pY1H assays to study the role of TF-TF relationships in cytokine gene regulation, the effect of alternative TF isoform usage on these relationships, and the effect of viral proteins on human TF-DNA binding. This work contributes to our understanding of how TF-DNA interactions are specified and provides a useful method that can be applied to further elucidate TF-TF relationships and their role in transcriptional regulation.
Anna will be continuing her academic career as a postdoctoral researcher in the lab of Dr. Jef Boeke at the NYU Langone Health Institute for Systems Genetics.
Congratulations, Anna!
Michelle Teplensky Receives Beckman Young Investigator Award
Dr. Michelle Teplensky was recently named one of the 2024 Beckman Young Investigators. She and her team will receive $600,000 over four years to engineer versatile vaccine responses through nanomaterial design, with implications for the treatment of not only the flu but also other infectious diseases including the viruses that cause COVID-19, HIV, and more.
The Beckman Young Investigator (BYI) Program provides research support to the most promising young faculty members in the early stages of their academic careers in the chemical and life sciences, particularly to foster the invention of methods, instruments and materials that will open up new avenues of research in science.
Read a detailed announcement here.
Congratulations, Dr. Michelle Teplensky!
Jillian Ness Receives 2024 Marion R. Kramer Scholarship
Jillian Ness of the Wunderlich Lab is one of the recipients of the Biology Department's 2024 Marion R. Kramer Scholarship. Jillian and her team studied how enhancers work in development, focusing on redundant enhancers, or “shadow enhancers,” linked to developmental genes. These enhancers are remarkably abundant in animals and can compensate under conditions of stress to drive normal development.
She is exploring how these enhancers function, as well as how they are created and maintained in animal genomes. Her work involves creating simplified enhancer models in Drosophila and analyzing how they work. In parallel, she performs evolutionary studies on shadow enhancer sequences to understand genomic events from which the sequences originate. Ultimately, she aims to understand enhancer sequences to improve predictions of perturbations that lead to developmental disease in embryos.
Read the full announcement here.
Congratulations, Jillian!
Mandy Pinheiro Receives 2024 Belamarich Dissertation Writing Award
Mandy Pinheiro of the Naya Lab received the Biology Department's 2024 Belamarich Dissertation Writing Award. This award complements the Belamarich Award, and is given to support an outstanding PhD student through the dissertation writing stage.
Mandy’s research focuses on understanding how noncoding RNAs (ncRNAs) may be central to the coordination of metabolism and differentiation in skeletal muscle. The regulation of gene expression during cell state transitions is a complex and tightly controlled molecular process. One potential central regulator of myogenesis is the Dlk1-Dio3 ncRNA locus, the largest known mammalian cluster of ncRNAs. She used mouse skeletal muscle cells as a model system to investigate how this ncRNA cluster may coordinate metabolic and epigenetic changes that occur when proliferating myoblasts differentiate into mature myotubes.
Congratulations, Mandy!
Green Lab Publishes Patent for Detecting Nucleic Acids
Milad Babaei, MCBB PhD student of the Green Lab, and Dr. Zhaoqing Yan (GRS '23), along with their mentor, Dr. Alexander Green, are co-authors on a recently published patent. This patent, titled "Isothermal Nucleic Acid Detection Assays and Uses Thereof" by Green et al. (US Patent 2023/0313283, October 2, 2023), describes rapid methods for detecting nucleic acids, from viruses to circulating mRNAs, in low-cost portable formats.
Nucleic acids, such as DNA and RNA, play a crucial role in genetic information. "Isothermal" refers to processes that occur at a constant temperature. In the context of nucleic acid detection, isothermal assays are methods that allow the amplification and detection of nucleic acids at a constant temperature without the need for thermal cycling, as in PCR (Polymerase Chain Reaction).
The team is currently expanding its panel of detection by developing lateral flow strips that can spontaneously probe for multiple targets using multiple test lines. This capability is crucial for the future of detecting and analyzing nucleic acids, which are fundamental in various fields, including medical diagnostics, research, and biotechnology.
Congratulations, Dr. Alexander Green, Milad Babaei, and Dr. Zhaoqing Yan!
Michelle Teplensky Named AIChE’s 35 Under 35
Dr. Michelle Teplensky was recently named 2023 AIChE's (American Institute of Chemical Engineers) 35 under 35. AIChE honors 35 chemical engineering professionals who have mad great contributions to the field in seven categories, bioengineering, chemicals and materials, education and outreach, energy and environment, innovation and entrepreneurship, leadership. and safety. Teplensky was recognized under the bioengineering category.
Teplensky and her research group focuses on engineering nanotechnology to control immunological cell connectivity, processing, and communication by design. In doing so, they elucidate fundamentals about cellular events and leverage this knowledge to develop improved therapeutics and vaccines that can impact the treatment of cancer and infectious disease. Their work is highly interdisciplinary, and bridges the fields of engineering, chemistry, nanotechnology, immunology, and biomaterials. By sitting at this interface, we are able to develop and incorporate synthetic nanoscale advances to control immunological activity and elucidate design rules that have widespread impacts on therapeutic development. She hopes that the students trained in her lab enter their careers feeling inspired.
Teplensky loves to shop at Stew Leonard’s, and she has become an avid fan of Boston Univ.’s hockey team. Her family has a tradition of buying and completing a puzzle on every vacation.
Congratulations, Michelle Teplensky!
Anna Berenson Receives First Place in the PhD on Tap 3MT Competition
Anna Berenson, an MCBB PhD candidate of the Fuxman Bass Lab, received joint first place in the 2023 PhD on Tap 3MT Competition. The competition took place as part of PhD on Tap, which is a full day research showcase sponsored by the Office of the Associate Provost for Graduate Affairs and the Graduate School of Arts and Sciences.
In a project led by Anna, the Fuxman Bass Lab developed paired yeast one-hybrid assays to study DNA binding patterns of transcription factor pairs. Their work shows that extensive cooperativity and antagonism between transcription factors greatly affect their binding to gene promoters, and that viral proteins can modify the binding profiles of human transcription factors. You can check out their publication here.
Congratulations, Anna!
Alexander Green on Saliva Test for Soldiers, Athletes, and Others Aims to Predict Performance
Dr. Alexander Green, BU's Associate Professor in Biomedical Engineering, and his colleagues plan to develop a fast, portable saliva test that will analyze an assortment of biomarkers associated with performance on challenging tasks. This project is funded by the US Defense Projects Agency (DARPA), which aims to develop a test that will one day save lives and dollars by predicting soldiers' performance on missions.
With funding up to $17.7 million federal funds, Green and his team will start by testing volunteers as they undergo precise physiological tests. For example, the volunteers might be intensely exercising for multiple days with little rest, while the team will take samples to see how their performance might be associated with different biomarkers, such as testosterone, cortisol, and myoglobin.
Though this research will be a complex challenge, Green's long experience in developing paper-based testing systems will guide him through this research journey. You can read more about it here.
Congratulations, Dr. Alexander Green!
Summer Internship Roundup
Several MCBB students received internships this past summer; read below to learn more about their experiences!
 Maryam Dashtiahangar is a third-year PhD student in the Siggers Lab. Her PhD project involves characterizing the mechanisms of non-coding SNPs in autoimmune diseases using CASCADE, a protein binding microarray (PBM)-based technology developed by the Siggers Lab.
After completing three lab rotations in the first year of her PhD, she applied for the SB2 Fellowship, a 2-year Training Program in Synthetic Biology and Biotechnology founded by NIH. This program supports and funds students to undertake a summer internship between SB2 Year 1 and SB2 Year 2, providing valuable industry lab experience. For Maryam's internship, she chose to work with Pfizer. Over 12 weeks this summer, she focused on characterizing and developing a regulatory B cell assay. She's had the privilege of working with exceptional mentors and meeting brilliant people who are doing remarkable work. As Maryam wraps up her internship, she wants to express her gratitude to her Pfizer mentor, Dr. Joseph Brennan, and her PhD mentors, Dr. Trevor Siggers and Dr. Thomas Gilmore, for their support in making this internship possible. |
 Jillian Ness is a fourth year PhD student in the Wunderlich Lab. Dr. Wunderlich’s lab explores the design and evolvability of regulatory elements in the genome using Drosophila. Jillian's project investigates the role of redundancy in developmental gene programs; she employs computational and synthetic biology techniques to study and manipulate redundant regulatory elements.
Jillian had the opportunity to participate in the Synthetic Biology course at Cold Spring Harbor Laboratory located in Long Island, New York. Historically, this research institution has been home to some well-known and elegant science, and it was a wonderful opportunity to be on the campus. Through this intensive and highly collaborative course, industry and academic leaders introduced us to cutting-edge synthetic biology methods, while guiding us in designing and conducting research projects over the course's duration. Under their mentorship, Jillian chose to focus on computational modeling and in vitro programming of “gene neural networks.” This involved modeling and designing multi-layer gene regulatory networks to respond to specific inputs with an appropriate output according to the circuit design. This course was funded by a Kilachand travel scholarship. A big thanks to Dr. Thomas Gilmore for the support he provided. There are a multitude of excellent courses available at Cold Spring, as well as Marine Bio Labs, that she encourages MCBB students to investigate! |
 Mandy Pinheiro is a PhD Candidate in the Naya Lab. She studies the coordination of metabolism and differentiation through the Dlk1-Dio3 noncoding RNA cluster in skeletal muscle. As she plans her next steps after her PhD, she looks forward to pursuing a career in business development or venture capital/venture creation within the biotech and pharma ecosystem.
This summer Mandy worked as a Business Development and Licensing Innovation Intern at Mass General Brigham Innovation. She enjoyed getting exposed to a variety of technologies across different therapeutic areas and developing hands on experience at numerous stages in the commercialization process, from invention disclosure to licensing new technologies. Much of her work focused on invention triage and developing marketing materials for high value inventions. Mandy collaborated with colleagues across the organization to landscape the utility of Priority Review Vouchers (PRV) for groups working on PRV eligible diseases. This internship allowed her to play an active role in the commercialization of new technologies and to gain invaluable insights about business development strategies. |
Great work, Maryam, Jillian, and Mandy!