2020 Beckman Symposium

During this seminar I will present details of my path from Beckman Scholar to MD-PhD, advanced training as a neurologist, then a neurointensivist, and the interleaving of additional research experience into this clinical training, eventually leading to my establishment of a wet bench laboratory and a paired human physiology laboratory in the intensive care unit. I will describe my group’s philosophy of bench-to-bedside translation, present one example of our work in this arena, and briefly highlight our current efforts to understand the mechanisms of traumatic brain injury and its links to Alzheimer’s disease.

Learning Objectives:

1. Understand the requirements of dual degree programs and elements of success as a physician-scientist

2. Understand the epidemiological and mechanistic connections between traumatic brain injury and Alzheimer’s disease

In this presentation Shameema Sikder will discuss her career trajectory starting as an undergraduate studying chemical engineering and biochemistry to an Associate Professor of Ophthalmology at Johns Hopkins leading initiatives to change cataract surgery training. She will highlight the impact of being a Beckman Scholar on her career path.

I will present how I came to choose the physician-scientist career pathway. I was inspired from an early age by stories about my great-grandfather, an academic surgeon who innovated gastric suction and is credited for saving thousands of lives. I became involved in research in high school and college, and continued my training in a combined MD/PhD program. As an MD/PhD student I was further inspired by the emerging data from the human genome project to develop tools to improve our understanding of gene functions. I found that the liver is amenable to genetic manipulation, and I focused my career around using genetic tools and methods to improve our understanding and treatment of human liver disease. My advice for budding scientists is to pursue whatever topic they find inspiring. This way, a long and sometimes toilsome career path will be interesting, fulfilling, and totally worth it.

This talk will touch on several key points: PhD (MD) important grounding in science; how to develop friendships, gather mentors and collaborators; keep up with the literature; look at evidence basis for medical practice; ask big questions, stay focused, and drill down; build your resume so that it holds together; and publish the highest level science (journals) you can. You need support at home: You will have kids during the training and there will be some down time; marriages can suffer so put effort into your relationship as well.

Learning Objectives:

1. How to do it all as a clinician scientist without burning out

2. How to have a wonderful time juggling a lot

The highly competitive nature of academic environments might seem to suggest that success can only be obtained at the cost of taking good care of oneself. However, sacrificing self‐care can be extremely harmful. This seminar will discuss ways that high performance and self‐care can be mutually reinforcing and produce long‐term success. A key goal is for each person to take away a set of practical strategies and habits they can employ to support their mental and physical health while also supporting their future success in research.

In this presentation, I will discuss my experiences leading to my current position as a scientist and team leader, focused on chemical biology and drug discovery in the pharmaceutical industry. This includes my undergraduate research as a Beckman Scholar at the University of Delaware and graduate work at Stony Brook University. Additionally, I will highlight the innovative chemistry, chemical biology and medicinal chemistry we are doing to support drug discovery at Pfizer Inc.

A career in science journalism may not be what you think. This talk is more than a rehash of one writer's career path (though there is a little of that). It explains where the majority of science writers work (hint: it's not at publications you can purchase at the newsstand). It also contains statistics about employment prospects and median salaries, and explains the skills and qualities that all science communicators share. This presentation is not only for researchers interested in exploring a career in science writing. It is for any scientist who'd like to be able to recognize a potential journalist among the people they mentor.

I will tell brief stories of experiences that have shaped my career, generalize the lessons learned, and translate them to three actionable items: (1) be careful with your pronouns, (2) embrace diversity of thinking, and (3) don't be duped. I'll conclude by suggesting a question that will help you know if you are on a successful career path: "Are you listening, learning and getting a little better every day?"

In the movie "Moana" the lead character sings the refrain, "There's no telling how far I'll go" before she heads off on the adventure of a lifetime. In this short talk, I will give a personal reflection of my own adventures in science, which started with telling my freshman advisor that I aspired to have a work-study position in a research lab. I was subsequently selected as part of the inaugural class of Beckman Scholars, and most recently, things have come full circle as I became co-Director of the Beckman Scholar Program at the University of Utah, where I am an associate professor of chemistry. My research has spanned the fields of chemical biology, synthetic biology, and microbiology, involved collaborations across the globe, and last year I led an experiment conducted on the International Space Station. In other words, I want to convey to current Beckman Scholars that an academic career is a "Choose Your Own Adventure" type of career, and there is no telling how far they will go!

Most researchers are curious about how to communicate their science to the media, yet they may also be worried that they'll be misquoted or misrepresented in an article. In an age where science and reason matter more than ever, researchers should empower themselves with techniques that will build collaborative relationships with reporters.

While media coverage is never a guarantee, this talk aims to boost researchers' chances of getting noticed by explaining where reporters look for story ideas, and which of those places are most within researchers' control. Strategies to put a project's real-world impact front and center will be discussed. And finally, the talk will offer tips for preparing for an interview with a member of the press.

Scientific posters haven't changed in 30 years, which should be alarming to you (nothing in science should be stagnant). And evidence suggests they are incredibly ineffective. In this talk, you will learn the evidence-based design principles that science has discovered in the last 30 years (since the birth of the Internet) and how you can apply them to create fully-modern scientific posters that transmit your knowledge much more effectively to other scientists, and help you and them have more fun at poster sessions too. As a bonus, these same principles apply to presentations, reports --- anything you design for people to use.

Learning Objectives:

1. Lowering interaction cost makes designs less effort to engage with

2. Increasing information scent by teaching instead of hinting boosts engagement

3. Triggering emotion is scientific and facilitates learning

RNA mediates essential biological processes in all organisms. These functions include catalysis of crucial biochemical reactions such as peptidyl transfer during translation and transesterification during RNA splicing, regulation of gene expression, and defense against foreign nucleic acids. A unifying characteristic of RNA-mediated cellular activities is that their function and specificity frequently depend on RNA secondary and tertiary structures which begin to fold during transcription. RNA sequence can therefore be constrained by its coding potential, by the architecture of its biochemically active folds, and by the requirements of co-transcriptional structure formation. Consequently, understanding the interdependence of these constraints is fundamental to predicting how changes in an RNA sequence affect its structure and biological function. As an Arnold O. Beckman Postdoctoral Fellow, my research has focused on addressing this fundamental challenge through the development and application of systematic in vitro methods for assessing cotranscriptional RNA structure and function. These studies have begun to expose the molecular details of cotranscriptional gene regulation in bacteria and have established a foundation for the continued development of quantitative experimental tools to understand how transcription and RNA folding are coordinated in biological systems.

Extrachromosomal circular DNA (eccDNA) comprises products of genomic recombination that cause somatic changes in gene length and sequence. These circular molecules are derived from canonical linear chromosomal loci, expanding the diversity in coding and regulatory capacity within eukaryotic genomes and transcriptomes. Using a brand-new multidisciplinary approach to investigate eccDNA-mediated allelic diversity, I have identified various coding regions of eccDNA biogenesis, such as Titin and Mucin loci. In order to systematically investigate the biological implications and mechanisms of eccDNA formation, this project will focus on Titin eccDNAs as a prototype for eccDNA-mediated chromosomal rearrangements. Titin (TTN) is an extremely large protein that is responsible for the passive elasticity of muscle, functioning as a molecular spring. This single gene (TTN) is expressed in various isoforms, each with its own associated “spring constant.” It has been assumed that Titin protein diversity results from complex mechanisms dependent on alternative RNA splicing. However, there is thus far no comprehensive alternative-RNA-splicing framework that accounts for the full spectrum of TTN diversity. Preliminary data obtained in the past years of support suggest a novel mechanism of TTN diversity involving circular-DNA excision that generates recombinant TTN loci at the genomic level. Here, I report TTN-eccDNA formation as a potential mechanism for modulating overall myofibrillar passive tension. Results from investigating this novel mechanism for the modulation of cardiovascular stiffness will revolutionize basic, clinical, and therapeutic approaches to cardiovascular diseases. The AOB Award has been instrumental in advancing the field of eccDNA, in general, and in providing a missing key element in DCM biology, consideration of which may drive a reevaluation of current therapies.

Current cancer management follows a multipronged approach that include surgery, radiation, and chemotherapy. There is a pressing need for a platform technology to provide precision chemotherapy screening, drug delivery detection, and real-time therapy efficacy monitoring. We have developed single walled carbon nanotube (SWNT) sensors for the detection of chemotherapeutics, more recently for temozolomide (TMZ) and its byproduct 5-Amino-4-imidazolecarboxamide (AIC) with sensitivity at 5-500 μM and in vitro viability up to 7 days in TMZ treated glioblastoma cells. Sensors for irinotecan, cisplatin, and lomustine were developed with sensitivities at 50 μM. H2O2 sensors were used to measure the therapy efficacy of gemcitabine and irinotecan in pancreatic ductal adenocarcinoma in vitro and in vivo. Multiplexing these sensors could yield insights into delivery, diffusion, metabolism, and efficacy of chemotherapeutics in hours or days. Other strategies are being developed such as ratiometric approaches and wavelength-induced frequency filtering to improve performance and sensitivity. A fiber optic platform was developed as a minimally invasive form factor to integrate the sensor hydrogel, optical waveguide, and detection system.

As a physician-scientist in NYC, my research rapidly shifted to the role of convalescent plasma (CP) in COVID-19. CP can be used to passively transfer antibodies from recently recovered patients to actively infected treatment-resistant patients. Initial studies revealed antibody neutralizing activity peaked at 31-35 days post symptom onset. Initial outcomes in severe and life-threatening COVID-19 hospitalized patients show CP as a potentially efficacious treatment for non-intubated patients. Retrospective study of 427 CP transfusion events yielded 12.9% of transfusion reaction rate with vast majority due to COVID-19 disease not CP. Increased risk was identified in patients with blood group B or cancer, and decreased risk for patients in their 80s

In the adult mammalian hippocampus, neurogenesis (in which new neurons are generated and integrated into the CNS) is believed to underlie learning and memory. Within the hippocampus, numerous cell types communicate via diverse signals. Some of these signals control neural stem and progenitor cells (NSPCs), which can divide or terminally differentiate into neurons, astrocytes, or oligodendrocytes, and then migrate and integrate into the existing brain circuitry. I have identified novel functions for a ligand-receptor pair, ephrin-A4 and EphA4, in this process. NSPCs express the receptor EphA4, while ephrin-A4 is predominately expressed by mature neurons. In cell culture studies, treating adult NSPCs with ephrin-A4 activated EphA4 and induced neuronal differentiation, and blocking EphA4 ligand-binding with an antagonist reversed these effects. Ephrin-A4/EphA4 signaling also regulated the migration of NSPCs. Finally, using AAV to deliver CRISPR/Cas9 into the brains of adult mice, I found that knocking out EphA4 or ephrin-A4 in select cell types alters neuronal differentiation and migration in vivo. These data thus support a significant role for ephrin-A4/EphA4 signaling in regulating adult neurogenesis.
 

The rodent visual system has attracted great interest in recent years, owing to its experimental tractability, but the fundamental mechanisms used by the mouse to represent the visual world remain unclear. One key step in representing the world in our visual system is that of perceptual organization, whereby individual objects are identified and segmented. An outstanding question is the extent to which perceptual organization is a common computational principle across mammalian visual systems. To answer this we looked for neural and behavioral evidence of such a process in the rodent. We find that mice can segment objects using contrast cues but fail to utilize motion cues. This is in contrast to primates who can use either cue. Lastly, we model the representations in the rodent visual cortex and find they are consistent with a feedforward cascade of computations. This work highlights both the strength and limits of the rodent as a model system for mid level vision.

Many experimental approaches rely on controlling gene expression in select subsets of cells within an individual animal. However, reproducibly targeting transgene expression to specific fractions of a genetically defined cell type is challenging. We developed Sparse Predictive Activity through Recombinase Competition (SPARC), a generalizable toolkit that can express any effector in precise proportions of post-mitotic cells in Drosophila. Using this approach, we demonstrate targeted expression of many effectors in several cell types and apply these tools to calcium imaging of individual neurons, optogenetic manipulation of sparse cell populations in vivo, and genomic profiling of mutant and control neuronal subtypes harvested from the same animals.

One of the most common pathologically relevant mutated variants of ALK-2 (activin receptor-like kinase-2) has a point mutation (R206H) in its Ser/Thr kinase domain that promotes uncontrolled signaling in rare diseases, namely Fibrodysplasia Ossificans Progressiva (FOP) and Diffuse Intrinsic Pontine Glioma (DIPG). Currently, there are no FDA approved drugs available for ALK-2 inhibition in these diseases. A computational platform has been developed for de novo design of similar dual inhibitors that can simultaneously engage other key targets – similarly augmented by protein-protein interactions. Employing this strategy and iterative modifications, a mutant-selective inhibitor for ALK-2 (R206H) has recently been identified that may have promise for the treatment of FOP and DIPG.
Eukaryotic protein kinases are induced to drive phosphorylation-initiated signal transduction via allosteric self-assembly. They explore a continuum of conformations that includes ensembles of ‘active state’ and ‘inactive state’ conformers. In the absence of a signaling stimulus, inactive state conformers dominate the continuum. When a signaling event is triggered by ligand binding (initiating self-assembly by homo- or hetero-oligomerization of kinase domains) or by recruitment of adapter proteins, the shift in the monomer/dimer equilibrium favors the active state conformers. We investigate the quantitative effects of patient-derived activating mutations on kinase domain dimerization strength (driving EGFR activation ‘from the inside’), activity of the kinase domain monomer and dimer, as well as structural dynamics of EGFR kinase domain activation and possible novel modes of disrupting this self assembly. Understanding the dynamics of constitutive allosteric activation in EGFR mutants seen in lung cancer patients, and how the mutations shift the equilibrium towards the active form of enzyme, are key steps in appreciating and combatting the origins of inhibitor resistance.

Natural light-harvesting systems, such as photosynthetic pigment-protein complexes, efficiently transfer energy through space with high efficiency. Ultimately, we would like to understand the design principles nature evolved to improve optoelectronic devices that rely on light harvesting and energy transfer, such as solar cells. We perform ultrafast 2D electronic spectroscopy measurements on a variety of systems ranging from the Fenna-Matthews-Olson antenna complex isolated from green sulfur bacteria to in vivo cyanobacteria. We observe larger amplitude coherences under reductive conditions that mimic the chemistry of the complex in vivo. We can use spectroscopic tools that allow us to follow the energy in both space and time. In particular we can correlate the existence of quantum coherences, particularly those involving excited electronic states, with faster, more efficient energy transfer, and assessing the role of the ground and excited states in the transfer process. Future work will look at the how changing light conditions influences the complex chemistry in the photosynthetic membranes, ultimately affecting the energy transfer processes.

This workshop will cover how to craft, organize, and deliver an engaging scientific talk. It will show you how to use various techniques to turn your research presentation into an engaging and repeatable story. Following the presentation, Bri will take notes as each 2017 Arnold O. Beckman Postdoctoral Fellow presents their own Beckman Briefing (lightning talk) to the group. After the workshop, Bri will offer helpful feedback, then meet with each fellow individually to give personalized feedback on how to improve their presentation.

Learning Objectives:

1. How to create a logical and repeatable presentation outline

2. How to effectively use imagery in your presentation

3. How to keep your audience engaged with your presentation

When I started my faculty job, I thought that just knowing the type of mentor I wanted to be and the lab culture that I wanted to create would be enough to make these things happen. I couldn't have been more wrong. Establishing and maintaining lab culture and mentoring practices doesn't have to be overly complicated, but it takes intentionality and communication. This workshop will explore approaches to designing and implementing systems and policies to support the lab environment that you want to cultivate.

In the battle between magnetism and superconductivity, magnetism wins so often that only a handful of magnetic superconductors are known. In this context, here we report our characterization of YbxPt5P, - providing experimental evidence for the possible coexistence of both magnetism and superconductivity in this material. Comparison of samples with different Yb stoichiometry shows that the relative strengths of magnetism and superconductivity can be tuned. The likely coexistence and tunability of such strongly competing electronic states, along with the presence of strong spin orbit coupling due to the large amount of Pt present, makes YbxPt5P a remarkable material and opens the door to a new family of magnetic superconductors.

Our work focuses on developing an optical brain-machine interface capable of interacting with neural activity in real-time. In this talk, I will describe our progress toward building the components that form such an interface. These components include protein sensors and actuators that interact with light to read and write neural activity, optical microscopes that can record neural activity from large volumes of brain tissue, and deep learning data processing algorithms that can calculate neural activity in real time. Together, these technology pieces will enable the next generation of neuroscientific experiments that control and investigate the cellular resolution response of the brain.

Carbon dioxide emissions, known to exacerbate climate change, have been increasing rapidly over the past century. One strategy to alleviate this issue is carbon capture and utilization (CCU), in which some of the abundant atmospheric CO₂ is used as a carbon source for the production of valuable compounds. An attractive target is sodium acrylate, the building block of superabsorbent sodium polyacrylate found in hygiene products and many other common goods. Currently, sodium acrylate is synthesized by sequential oxidations of propylene over heterogeneous catalysts at high temperatures. Researchers have instead sought a one-step process coupling CO₂ and ethylene, which is more sustainable and uses much less expensive starting materials. This method could consume a large quantity of atmospheric CO₂. However, coupling with ethylene is not spontaneous. Homogeneous nickel catalysts have shown great promise for enabling this reaction, but the reported systems suffer from low efficiency. The main obstacle is a very stable nickelalactone intermediate, which contains a rigid Ni–pre-acrylate ring that resists the release of free sodium acrylate from the catalyst. My project aims to develop nickel complexes which include an N-heterocyclic carbene (NHC) in a supporting bidentate ligand. The characteristic strong electron donation and steric imposition of NHCs are expected to destabilize nickelalactones and to promote ring-opening, thereby enabling efficient catalytic production of sodium acrylate. Initial results support the instability of a simple bis(NHC) nickelalactone, and experiments testing sodium acrylate production are underway. Computational investigation of NHC-containing ligands with varying electronic and steric effects also helps to elucidate their capability to support the target reaction. This family of ligands could be the key to efficient nickel catalysts coupling CO₂ and ethylene for sodium acrylate production, thus contributing to global CCU efforts.

Despite the increasing number of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Using our new cell-tracking pipeline called EllipTrack, we tracked the response of thousands of single melanoma cells to BRAF inhibitors and show that a subset of cells escapes drug within the first 3 days of treatment. These escapees cycle periodically in drug and out-proliferate non-escapees over extended treatment. Cell-cycle re-entry occurs via a nongenetic mechanism involving activation of ATF4, validated in ex vivo cultures of patient biopsies. Furthermore, escapees experience incomplete licensing of replication origins, leading to heightened DNA replication stress and DNA damage. Our work reveals a mutagenesis-prone, expanding subpopulation of early drug escapees that may represent a reservoir for the development of
permanent drug resistance.

Allenes, compounds containing two double bonds across three contiguous carbons, are versatile synthetic intermediates due to their substituent loading capacity and ability to generate one or more new stereogenic centers through axial-to-central chirality transfer. This structural motif is also present in over 150 natural products and a variety of bioactive molecules. Despite their prevalence and distinct reactivity, catalytic methods to access chiral 1,3-disubstituted allenes with high levels of selectivity from achiral starting materials remains a goal in chemical synthesis.

We have developed a mild and general strategy for the highly selective semi-reduction of prochiral 1,3-enynes. A diverse array of enantioenriched 1,3-disubstituted allenes are furnished in up to 98% yield and 99% enantioenrichment. This reaction is enabled by chiral copper hydride catalysts in the presence of water as a benign and abundant proton source. Additional applications of this method further illustrate the advantage of this simple protocol for the selective synthesis of mono-deuterated allenes and chiral 2,5-dihydropyrroles.

My lab is developing a bacterial strain that will catalyze the conversion of carbon dioxide to fuels and products using electrons from an electrode as the sole source of reducing power. This process would represent a new form of metabolism – electroautotrophy. Our platform for developing an electroautotrophic strain is Shewanella oneidensis, a metal-reducing bacterium that already possesses the capacity to exchange electrons with extracellular electrodes. The first key challenge in this project is to create an efficient pathway for electron flow from the electrode to intracellular electron carriers. This requires reversing the direction of electron flow through the native extracellular electron transfer pathway in S. oneidensis. We have demonstrated proof-of-concept for the inward electron transfer pathway by engineering S. oneidensis to catalyze the intracellular reduction of acetoin to 2,3-butanediol using an electrode as the electron source. We are currently working to improve flux through the inward electron transfer pathway by over-expressing the essential components. The second key challenge is to transplant a carbon fixation pathway into S. oneidensis, which is a heterotroph. We have expressed the missing components of the Calvin-Benson-Bassham cycle for carbon fixation in S. oneidensis and are currently working to functionalize the pathway through adaptive laboratory evolution. Moving forward, we will combine the modifications required for inward electron transfer and for carbon fixation to create the electroautotrophic strain.

Current cancer management follows a multipronged approach that include surgery, radiation, and chemotherapy. There is a pressing need for a platform technology to provide precision chemotherapy screening, drug delivery detection, and real-time therapy efficacy monitoring. We have developed single walled carbon nanotube (SWNT) sensors for the detection of chemotherapeutics, more recently for temozolomide (TMZ) and its byproduct 5-Amino-4-imidazolecarboxamide (AIC) with sensitivity at 5-500 μM and in vitro viability up to 7 days in TMZ treated glioblastoma cells. Sensors for irinotecan, cisplatin, and lomustine were developed with sensitivities at 50 μM. H2O2 sensors were used to measure the therapy efficacy of gemcitabine and irinotecan in pancreatic ductal adenocarcinoma in vitro and in vivo. Multiplexing these sensors could yield insights into delivery, diffusion, metabolism, and efficacy of chemotherapeutics in hours or days. Other strategies are being developed such as ratiometric approaches and wavelength-induced frequency filtering to improve performance and sensitivity. A fiber optic platform was developed as a minimally invasive form factor to integrate the sensor hydrogel, optical waveguide, and detection system. As a physician-scientist in NYC, my research rapidly shifted to the role of convalescent plasma (CP) in COVID-19. CP can be used to passively transfer antibodies from recently recovered patients to actively infected treatment-resistant patients. Initial studies revealed antibody neutralizing activity peaked at 31-35 days post symptom onset. Initial outcomes in severe and life-threatening COVID-19 hospitalized patients show CP as a potentially efficacious treatment for non-intubated patients. Retrospective study of 427 CP transfusion events yielded 12.9% of transfusion reaction rate with vast majority due to COVID-19 disease not CP. Increased risk was identified in patients with blood group B or cancer, and decreased risk for patients in their 80s.

In photosynthesis, solar energy capture to conversion occurs with a remarkable near-unity quantum efficiency through energy transport across a network of chromophore-containing proteins. Thermal fluctuations of these proteins lead to changes in the intermolecular interactions that drive energy transport. Despite this variation, high efficiency of transport is maintained. Both the extent to which the dynamics of energy transport vary and how the efficiency is robust to variation remain unclear. Previous measurements either lacked the temporal resolution required or the sensitivity to measure individual proteins, and thus averaged over the fluctuations. Here, we describe a new experiment, single-molecule pump-probe (SM2P) spectroscopy, that measures excited-state dynamics with femtosecond time resolution in single proteins. We demonstrate the power of this technique on cyanobacterial light-harvesting subunits. Our experiments reveal heterogeneous timescales of vibrational relaxation, yet a narrow distribution of energy transfer timescales. These results suggest the protein design serves to tightly regulate energy transfer despite fluctuations of its structure.

The Irvine CubeSat STEM Program (ICSP) is a collaboration between Irvine Public Schools Foundation, and Irvine and Tustin Unified school districts that provides teams of students from all six high schools in the City of Irvine the opportunity to assemble, test, and launch a nano-satellite (CubeSat) into low Earth orbit. The program aims to change the way students experience STEM education and inspire the next generation of innovative thinkers, makers, programmers, and explorers.

Teams work on different components of the satellite to gain advanced hands-on STEM experience, with mentorship from experts from JPL, NASA, and other industry leaders, before coming together to assemble the final project for launch. Last year, ICSP had two successful launches, making history as the first program to launch two all high school student-built CubeSat’s into orbit in less than a year.
 

The program aims to make STEM careers more accessible, especially to underrepresented groups including females and minorities. ICSP offers students the incredible opportunity to gain hands-on, real-world experience that will prepare them for success in college and beyond.

The Irvine CubeSat STEM Program (ICSP) is a collaboration between Irvine Public Schools Foundation, and Irvine and Tustin Unified school districts that provides teams of students from all six high schools in the City of Irvine the opportunity to assemble, test, and launch a nano-satellite (CubeSat) into low Earth orbit. The program aims to change the way students experience STEM education and inspire the next generation of innovative thinkers, makers, programmers, and explorers.

Teams work on different components of the satellite to gain advanced hands-on STEM experience, with mentorship from experts from JPL, NASA, and other industry leaders, before coming together to assemble the final project for launch. Last year, ICSP had two successful launches, making history as the first program to launch two all high school student-built CubeSat’s into orbit in less than a year.

The program aims to make STEM careers more accessible, especially to underrepresented groups including females and minorities. ICSP offers students the incredible opportunity to gain hands-on, real-world experience that will prepare them for success in college and beyond.

The Irvine CubeSat STEM Program (ICSP) is a collaboration between Irvine Public Schools Foundation, and Irvine and Tustin Unified school districts that provides teams of students from all six high schools in the City of Irvine the opportunity to assemble, test, and launch a nano-satellite (CubeSat) into low Earth orbit. The program aims to change the way students experience STEM education and inspire the next generation of innovative thinkers, makers, programmers, and explorers.

Teams work on different components of the satellite to gain advanced hands-on STEM experience, with mentorship from experts from JPL, NASA, and other industry leaders, before coming together to assemble the final project for launch. Last year, ICSP had two successful launches, making history as the first program to launch two all high school student-built CubeSat’s into orbit in less than a year.

The program aims to make STEM careers more accessible, especially to underrepresented groups including females and minorities. ICSP offers students the incredible opportunity to gain hands-on, real-world experience that will prepare them for success in college and beyond.

The Irvine CubeSat STEM Program (ICSP) is a collaboration between Irvine Public Schools Foundation, and Irvine and Tustin Unified school districts that provides teams of students from all six high schools in the City of Irvine the opportunity to assemble, test, and launch a nano-satellite (CubeSat) into low Earth orbit. The program aims to change the way students experience STEM education and inspire the next generation of innovative thinkers, makers, programmers, and explorers.

Teams work on different components of the satellite to gain advanced hands-on STEM experience, with mentorship from experts from JPL, NASA, and other industry leaders, before coming together to assemble the final project for launch. Last year, ICSP had two successful launches, making history as the first program to launch two all high school student-built CubeSat’s into orbit in less than a year.

The program aims to make STEM careers more accessible, especially to underrepresented groups including females and minorities. ICSP offers students the incredible opportunity to gain hands-on, real-world experience that will prepare them for success in college and beyond.

Infrared spectroscopy and microscopy directly couples to molecular functional groups, providing chemical information without extrinsic labels. However, conventional infrared spectroscopy and microscopy have two main limitations: lack of spatial resolution due to Abbe’s diffraction limit, and restriction of applications in the aqueous conditions due to strong infrared attenuation. On the other hand, many meaningful biological processes and chemical transformation happen in the liquid phase. The understanding of them requires insights from the nanoscale. With the support from Beckman Foundation, we have developed the liquid-phase peak force infrared (LiPFIR) microscopy to deliver both label-free super spatial resolution at 10 nm and compatibility with liquid-phase measurement. We have demonstrated the method on a range of samples, from tracking the surface re-organization of polymers in organic solvent, hydrogen-deuterium isotope exchange and ethanol-induced denaturation of proteins, to imaging of cellular structures in aqueous phases. The LiPFIR microscopy bypasses the two limitations of infrared spectroscopy and microscopy. It will enable label-free spectroscopic investigations of chemical reactions and biomolecular transformations from the tens of nanometer scale.

Primary metabolism supports essential chemical processes of living organisms, and is highly conserved among all life forms. In contrast, specialized metabolism contributes to the fitness of its host in specific abiotic and biotic environments, and distributes taxonomically along the evolving tree of life. We seek to understand how complex specialized metabolites are biosynthesized through an assembly line of specialized enzymes, why these specialized metabolic traits are relevant to their hosts under ecological niches, and how these complex pathways could have evolved in a Darwinian fashion. Exploration of the largely untapped eukaryotic specialized metabolic systems not only will advance our understanding of the chemistry of life processes, but also will empower synthetic biologists to engineer microbial production of those high-value natural products of eukaryotic origin in the near future.

Protein structural disorder helps avoid misfolding and aggregation, but in impeding protein folding might also impede function. The balance between these two selective pressures on protein biophysics might vary among species as a function of the effectiveness of weak selection.  We predicted the Intrinsic Structural Disorder (ISD) of Pfam domains across 118 fully-sequenced vertebrate species and estimated the effect of species identity on to control for differences in Pfam composition across species. We compared this to each species’ Codon Adaptation Index of Species (CAIS), a metric we developed to quantify for effectiveness of selection from synonymous codon usage, corrected for total genomic GC content and amino acid composition, to be comparable across species.
Simple correlations between ISD and CAIS indicate that well-adapted species tend to have high ISD (Spearman’s R = 0.67, p < 2e-16). To correct for phylogenetic confounding and resulting pseudoreplication, we transformed CAIS and ISD species effect data using Phylogenetic Independent Contrasts (PIC). Phylogenetically controlled linear models confirmed that better-adapted species have higher ISD (Spearman’s R = 0.43, p = 1.2e-7). This relationship is conserved across protein domains dated older than 2.1 Gya and protein domains dated younger than 1.5 Gya, though the relationship is stronger in recent domains than in ancient. This indicates selection for higher disorder, with the greater benefit to more recently emerged vertebrate protein domains.

Unique physical, chemical, and optical phenomena arise when materials are confined to the nanoscale. We are accustomed to making observations for the behavior of living systems on a macroscopic scale that is intuitive for the time and size scales of our day-to-day lives. However, the building blocks of life: proteins, nucleic acids, and cells, occupy different spatiotemporal scales. Our lab focuses on understanding and exploiting tunable optical and mechanical properties of nanomaterials to access information about biological systems stored at the nano-scale. In the context of leveraging nanomaterial optical properties, we present recent work on developing and implementing neuromodulator nanosensors to image serotonin or dopamine volume transmission in the extracellular space of the brain. We validate our dopamine nanosensor in acute striatal slices with electrical and optogenetic stimulation of dopamine release, and show disrupted dopamine release or reuptake kinetics when brain tissue is exposed to dopamine agonist or antagonist drugs. In the context of leveraging nanomaterial chemical properties, we also discuss how high aspect ratio nanomaterials can be synthesized to carry biomolecular cargo to living systems. In particular, genetic engineering of plants is at the core of environmental sustainability efforts, but the physical barrier presented by the cell wall has limited the ease and throughput with which exogenous biomolecules can be delivered to plants. We will describe how nanomaterials engineering principles can be leveraged to genetically manipulate living plants, without transgene integration, in efforts to reconcile the benefits of crop genetic engineering with the demand for non-GMO foods. Our work in the agricultural space provides a promising tool for species-independent, targeted, and passive delivery of genetic material, without transgene integration, into plant cells for rapid and parallelizable testing of plant genotype-phenotype relationships.

Effective locomotion in nature happens by transitioning between multiple modes (e.g., walk, run, climb, slither). Despite this, far more mechanistic understanding of terrestrial locomotion has been on how to generate and stabilize around near-steady-state movement in a single mode. Unlike flight and swimming with aero- and hydrodynamics, a major challenge in understanding terrestrial locomotor transitions is the lack of methods to measure and model how animals actively make use of physical interaction with complex terrain. As a result, robots cannot robustly traverse complex terrain, an ability required for critical applications like search and rescue in earthquake rubble and extraterrestrial exploration over Martian rocks. Our BYI work focuses on using an energy landscape approach to elucidate principles of terrestrial locomotor transitions via integration of biomechanics, sensorimotor control, and terrain physics. Recently, we discovered that an energy landscape approach helps understand probabilistic locomotor transitions. In complex terrain, animals’ and robots’ locomotor modes are attracted to basins of a potential energy landscape. We have been developing new methods to enable experiments and modeling of how animals and robots actively cross potential energy barriers and hop between basins to make locomotor transitions. These include: (1) terrain platforms and tracking techniques to quantify animal locomotor transitions and terrain interaction, (2) robots with animal-like motion as physical models, and (3) force sensors to measure physical interaction and understand provide feedback control. I will highlight two recent discoveries enabled by these tools: to make locomotor transitions and traverse complex terrain, (1) legged insects actively adjust head, body, and appendages to lower potential energy barriers; (2) besides vision, limbless snakes must use mechanical sensing to adjust body form and control terrain contact to maintain propulsion and stability.

Over 100 distinct alkane monooxygenase (AlkB) enzymes containing a covalently bound, or fused, rubredoxin domain were identified and analyzed using bioinformatic techniques. One such protein was cloned as a full-length protein and truncated with its rubredoxin domain deleted. Its catalytic activity was evaluated, and its interaction with exogenous electron transfer partners was examined. These experiments shed light on the diversity of AlkB structure and reactivity, and the interaction of AlkBs with electron transfer partners.

Recent advances in super-resolution fluorescence microscopy based on single-molecule imaging have led to ~10 nm spatial resolution and exciting science. We are developing new approaches to advance beyond the structural (shape) information offered by existing super-resolution methods, and reveal multidimensional information of intracellular functional parameters, including chemical polarity, diffusivity, and reactivity, with nanoscale resolution and single-molecule sensitivity. To this end, we have been developing new strategies to perform high-throughput, multidimensional single-molecule spectroscopy in the wide-field. In particular, with spectrally resolved SMLM, we encoded functional parameters into the emission spectra of single probe molecules, and so unveiled rich, nanoscale functional and compositional heterogeneities in the membranes of live mammalian cells and in phase-separated surface processes. With single-molecule displacement/diffusivity mapping (SMdM), we mapped out intracellular diffusivity with unprecedented spatial resolution and fidelity, and hence discovered that diffusion in the mammalian cytoplasm and nucleus are both spatially heterogeneous at the nanoscale, and identified the net charge of the diffuser as a previously overlooked, key determinant of diffusion rate. By adding remarkably rich functional dimensions to the already powerful super-resolution microscopy, we thus open up new ways to reveal fascinating local heterogeneities in both live cells and chemical systems.

Many experimental approaches rely on controlling gene expression in select subsets of cells within an individual animal. However, reproducibly targeting transgene expression to specific fractions of a genetically defined cell type is challenging. We developed Sparse Predictive Activity through Recombinase Competition (SPARC), a generalizable toolkit that can express any effector in precise proportions of post-mitotic cells in Drosophila. Using this approach, we demonstrate targeted expression of many effectors in several cell types and apply these tools to calcium imaging of individual neurons, optogenetic manipulation of sparse cell populations in vivo, and genomic profiling of mutant and control neuronal subtypes harvested from the same animals.

Auxin is a hormone crucial in nearly every aspect of plant growth and development. Advancing our understanding of auxin signaling in maize and other crop plants may provide needed tools for agricultural scientists to help feed a growing population in the face of global climate change. However, existing tools for detecting and measuring auxin level and location have significant shortcomings that can limit their utility in plants. We are working to build and test a novel auxin biosensor, ShadowAuxin, capable of accurate quantification and tracking of auxin in live plants. Our biosensor design relies on the dimerization of two fluorescent proteins (a donor and an acceptor) capable of Förster Resonance Energy Transfer (FRET) when in close proximity. Our biosensor utilizes a quenching fluorescent protein acceptor in the FRET pair; when this pair are held in close proximity by fused dimerization domains, the donor fluorescent signal should dim. Pilot experiments in yeast cells have shown that quenching FRET can be measured via fluorescence flow cytometry, and have revealed the importance of dimer-domain choice and carefully controlled protein expression level. A new pair of human-hormone inducible promoters has enabled us to precisely control the expression level of donor and acceptor proteins in order to maximize FRET quenching. This system allowed observation of quenching FRET without significant cellular toxicity; however we observed a maximum of only 12.9% decrease in fluorescent signal. This is likely due to off-target dimerization and imperfect intracellular stoichiometry of the fluorescent proteins. Therefore, current and future experiments focus on increasing FRET efficiency by adjusting promoter strength and testing new sets of heterodimerization domains. Ultimately, this quenching FRET system will be coupled to an auxin-sensing domain to generate a biosensor that relies on single-color fluorescence measurements and provides rapid response and wide dynamic range.

Why do some individuals live longer than others? Even identical twins have different lifespans, as do genetically identical model organisms raised in controlled laboratory environments. What then accounts for these differences? Random accumulation of damage, sudden exogenous insults, or internal biological processes that somehow diverge? We find strong evidence for the latter.

Using the nematode C. elegans, we find that prospectively long- vs. short-lived individuals are highly divergent in terms of gene regulation. Fully half of a library of promoter::GFP gene-expression reporters can effectively predict future lifespan. Moreover, these reporters represent diverse spatial and temporal expression patterns, suggesting that the regulatory states underlying long and short life are not specific to a particular tissue or a single regulatory process. Long- vs. short-lived individuals exhibit widespread, systematic, and organism-wide differences in gene regulation, well in advance of mortality.

Extrachromosomal circular DNA (eccDNA) comprises products of genomic recombination that cause somatic changes in gene length and sequence. These circular molecules are derived from canonical linear chromosomal loci, expanding the diversity in coding and regulatory capacity within eukaryotic genomes and transcriptomes. Using a brand-new multidisciplinary approach to investigate eccDNA-mediated allelic diversity, I have identified various coding regions of eccDNA biogenesis, such as Titin and Mucin loci. In order to systematically investigate the biological implications and mechanisms of eccDNA formation, this project will focus on Titin eccDNAs as a prototype for eccDNA-mediated chromosomal rearrangements. Titin (TTN) is an extremely large protein that is responsible for the passive elasticity of muscle, functioning as a molecular spring. This single gene (TTN) is expressed in various isoforms, each with its own associated “spring constant.” It has been assumed that Titin protein diversity results from complex mechanisms dependent on alternative RNA splicing. However, there is thus far no comprehensive alternative-RNA-splicing framework that accounts for the full spectrum of TTN diversity. Preliminary data obtained in the past years of support suggest a novel mechanism of TTN diversity involving circular-DNA excision that generates recombinant TTN loci at the genomic level. Here, I report TTN-eccDNA formation as a potential mechanism for modulating overall myofibrillar passive tension. Results from investigating this novel mechanism for the modulation of cardiovascular stiffness will revolutionize basic, clinical, and therapeutic approaches to cardiovascular diseases. The AOB Award has been instrumental in advancing the field of eccDNA, in general, and in providing a missing key element in DCM biology, consideration of which may drive a reevaluation of current therapies.