Brandeis UniversityBenjamin and Mae Volen NationalCenter for Complex Systems

October 2018

The M.R. Bauer Foundation Colloquium Series, Distinguished Lecturer Series, Annual Scientific Retreat, and Summer Science Research Fellowship

Table of Contents Introduction 3 The M.R. Bauer Colloquium Series Summaries

Introduction 5

Paola Arlotta, PhD 6ProfessorDepartment of Stem Cell and Regenerative Biology

Harvard University

Vivian Budnik, PhD 7Chair, ProfessorDepartment of Neurobiology

University of Massachusetts Medical School

Jeff Holt, PhD 8ProfessorDepartment Otolaryngology and Neurology

Boston Children’s Hospital

Antonio Giraldez, PhD 9Fergus F. Wallace Professor of Genetics, Chair of Genetics DepartmentDepartment of Genetics

Yale School of Medicine

Shawn Xu, PhD 10Bernard W. Agranoff Collegiate Pro-fessor of the Life SciencesDepartment of Molecular & Integrative Physiology

University of Michigan Sarah Ross, PhD 11Associate ProfessorDepartment of NeurobiologyUniversity of Pittsburgh

Laura Colgin, PhD 12Associate ProfessorDepartment of Neuroscience

University of Texas at Austin

The M.R. Bauer Foundation Colloquium Series, Distinguished Lecturer Series, Annual Scientific Retreat, and Summer Science Research Fellowship 2017-2018 Summary

Brandeis University

Benjamin and Mae Volen NationalCenter for Complex Systems

Volen National Center for Complex Systems Scientific Retreat 2016

Introduction 16

Schedule 17

John Lisman, PhD 18Zalman Abraham Kekst Professor of NeuroscienceDepartment of Biology

Brandeis University

Leslie Griffith, PhD 19Nancy Lurie Marks Professor of NeuroscienceDepartment of Biology

Brandeis University

Thomas Reese, M.D. 20Senior InvestigatorDepartment of Neurobiology

National Institutes of Health

Margaret Stratton, PhD 21Assistant ProfessorDepartment of Biochemistry and Molecular Biology

UMASS Amherst

The M.R. Bauer Distinguished Guest Lecturer Series Summaries

Introduction 13

Betty Eipper, PhD 14ProfessorDepartment of Molecular Biology and Biophysics

UCONN Health

Matteo Carandini, PhD 15ProfessorDepartment of Neuroscience

University College London

Roger Nicoll, M.D. 22ProfessorDepartment of Cellular MolecularPharmacology

University of California, San Francisco

Volen National Center for 23 Complex Systems Poster Session

The M.R. Bauer Foundation Summer Science Research Fellows 25

Alison Ma 26Oprian LabDepartment of Biochemistry

Brandeis University

Sophie Lis 27Turrigiano LabDepartment of Biology

Brandeis University

Muibat Yussuff 28Rosbash LabDepartment of Biology

Brandeis University

Kendrick Rubino 29Sengupta LabDepartment of Biology

Brandeis University

Lauren Hayashi 30Van Hooser LabDepartment of Biology

Brandeis University

Abigail Zeamer 31Nelson LabDepartment of Biology

Brandeis University

Chiquita McCoy-Crisp 32Kern LabDepartment of Biochemistry

Brandeis University

Alana Hodson 33Wingfield LabDepartment of Psychology

Brandeis University

Michael Hsiao 34Griffith LabDepartment of Biology

Brandeis University

Sam Lageson 35Dizio LabDepartment of Psychology

Brandeis University

Acknowledgements 36

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Basic science drives modern society. Advances in technology, medicine, health care, and other areas, made possible by investments in research, are entwined with our lives. There is much to marvel at and be amazed by.

But policies made far from campus may hamper our progress. The dramatic decline of federal support for basic science is affecting emerging and veteran researchers alike. There is urgency, since so much research, which can change entire sectors, is at stake. While our peers recognize the value of our work, decision makers increasingly undervalue the contributions of scientists. We must bridge that gap. Scientists cannot remain disengaged from the public discourse. We must educate government, industry, and the community about the importance of basic research.

Why? Because groundbreaking basic science has profound implications for human health. Last year, my Volen colleagues, Michael Rosbash and Jeffrey Hall, were awarded the Nobel Prize for their pioneering work on circadian rhythms. This work was done in the fruit fly but the findings allowed us to finally begin to understand the human clock. The full role of circadian rhythms in health and disease are just starting to be revealed, but it is clear that this basic science finding is going to bring important changes to the lives of many. The recognition of their work by the Nobel Committee should renew

The 2017-2018 M.R. Bauer FoundationColloquium Series, Distinguished Lecturer Series,Annual Scientific Retreat, and Summer Science Research Fellowship

Introduction

our joy in the process of discovery and the generation of new knowledge—and animate the public conversation.

There are other ways for us to gain inspiration. We are fortunate to have the support of the M.R. Bauer Foundation, which recognizes that the Colloquium Series, Distinguished Lecturer Series, and the Annual Retreat enable us to reflect and plan ahead. The Volen National Center for Complex Systems is richer for these gatherings, and it is clear that they stimulate our students, postdocs, staff and faculty in diverse ways.

Finally, we must redouble our efforts in training the next generation. Again, the M.R. Bauer Foundation, along with other generous donors, provide resources for undergraduate summer research fellowships. You may read about their experiences in this brochure, and they join me in encouraging you to be a mentor at your institutions. Student collaborations with Brandeis faculty prepare them to assume the mantle of leadership. These undergraduates, like the postdocs and other young scientists who were fortunate to join the Rosbash and Hall Labs, are ambassadors and are the future of science.

Leslie Griffith, M.D., PhDNancy Lurie Marks Professor of NeuroscienceDirector, Volen National Center for Complex Systems

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Imagine the moment a baby is born — the first bright lights, the first unmuffled sounds, the first feeling of cold rather than warm liquid. Imagine how overwhelming the onslaught of sensations must be! As we develop and learn, our senses help us to make sense of the world. Every image, sound, or smell offers information, information that is transduced to electrical signals that are then interpreted by the billions of neurons in the brain. These neurons communicate in multiple ways, electrical and chemical, to use that information to learn, form memories, and navigate the world. An understanding of the mechanics behind sensory processing and neuronal communication can lead to possible treatments for when those mechanics do not develop and function correctly.

The 2017-2018 M.R. Bauer Colloquium Series explored the many functions of sensory processing: how vision is used for navigation, how itch and pain are intensified, how neurons communicate on an individual or network level. The nine distinguished scientists included in this Series offered myriad insights into the mechanisms, development, and communication among sensory systems in the brain. Each speaker has presented a summary of their work, which is preceded by a brief introduction set in italics, explaining the presentation in a broader framework.

The M.R. Bauer Colloquium SeriesSummaries

Introduction

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Paola Arlotta, PhDProfessorDepartment of Stem Cell and Regenerative BiologyHarvard University(September 19, 2017)

Development of the Cerebral Cortex: From the Embryo To Brain Organoids

While science has made important steps towards an understanding of the functions and development of the brain, there is still a great deal to discover. The development of the brain, and the many ways that development can be altered, is still a main focus of research. Doctor Arlotta discussed her work using brain organoids (three-dimensional cell cultures that mimic the human brain) created with stem cells. These organoids are used by her lab to examine the basis of neurodevelopmental disorders.

Much remains to be understood regarding the cellular and molecular principles that govern the development of the mammalian brain, and how these events are affected in neurodevelopmental disease. Focusing on the cerebral cortex, Doctor Arlotta covered material on the identification of molecular mechanisms underlying developmental generation of neuronal diversity and discussed how diversification of cortical neurons plays a critical role in controlling cortical assembly, in vivo. Building on this developmental work in the mouse, she then introduced the challenges and opportunities of modeling human brain development in the dish, from pluripotent stem cells within 3-D human brain organoids, and the promise that organoids offer to understand complex neurodevelopmental disease. She discussed some recent work on the generation and long-term development of human brain organoids; their developmental trajectory, cellular diversity and neuronal network features.

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Vivian Budnik, PhDChair, ProfessorDepartment of NeurobiologyUniversity of Massachusetts Medical School(February 6, 2018)

Synaptic Communication Goes Viral

One of the central questions for neurobiology is how synapses are able to modulate the strength and location of their connections in response to stimuli. This phenomenon allows for synaptic plasticity in learning and sensory processing. Vivian Budnik is interested in the mechanisms of synaptic signaling, which may allow cells to communicate with each other and provoke plastic responses. Extracellular vesicles (EVs) are one such possible explanation Doctor Budnik poses for how trans-cellular communication can happen, via the transport of integral membrane proteins, non-diffusible signals, and even possibly neurotoxic prion-like proteins.

Initially, Doctor Budnik was interested in the way that synapses are formed. Using the Drosophila neuromuscular junction as a model, she observed that Wingless – a critical signaling molecule for synapse development – is released from the neuron to communicate with the postsynaptic muscle. She identified Evenness Interrupted (Evi) as being responsible for this release of Wingless. She then sought to determine how, mechanistically, Evi exerts control over Wingless release by first looking at larvae expressing neuronally-driven Evi-GFP to see where Evi resides. She observed Evi not only presynaptically, but also in small postsynaptic puncta. Thus, it appeared that Evi is trafficked into neuronally-derived EVs, and that it might affect Wingless’ ability to incorporate into these EVs. In fact, Doctor Budnik’s lab had been observing multi-vesicular bodies – the precursors of EVs – at synaptic

terminals by electron microscopy since the 90s but had always ignored them for lack of understanding what they might be there for. Doctor Budnik then conducted a screen to identify factors that could prevent release of these Evi-positive EVs and she identified Rab11, a critical regulator of the endosomal pathway. In the absence of Rab11, EV release is abolished.

Upon setting out to identify other EV cargoes, Doctor Budnik found mRNA encoding dARC, a protein that is considered the “master of synaptic plasticity” and that is enriched in EV’s. Furthermore, she found that there is a region of the dARC mRNA that is similar to a region of viral DNA, and found that the dARC protein is actually capable of associating with its own mRNA to form a “capsid”-like structure, suggesting that EVs may be able to transmit genetic material between cells in a way that is very similar to the way viruses transmit.

Doctor Budnik’s visit highlighted her impressive contributions to the fields of cellular biology and neuroscience by shedding light on the molecular mechanisms guiding EV formation as well as providing insight into the different purposes that these EVs may be able to serve in trans-cellular communication.

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Jeff Holt, PhDProfessorDepartment of Otolaryngology and NeurologyBoston Children’s Hospital(February 27, 2018)

Function, Dysfunction and Restoration of Auditory Sensory Transduction Channels

To further characterize TMC1, to investigate structure-function relationships in TMC1 and to identify a pore region in TMC1, Doctor Holt’s lab used cysteine substitution for several key TMC1 amino acids, selected as possible pore-lining residues. Application of cysteine modification reagents altered properties of hair cell sensory transduction in real-time, including current amplitudes and calcium selectivity. The data provide compelling evidence that these residues line the permeation pathway of sensory transduction channels in inner ear hair cells.

TMC1 is also a common target of genetic mutations that cause deafness in humans and mice. To investigate the possibility of restoring auditory function in mouse models of human deafness, they used wildtype TMC1 cDNA packaged into AAV vectors. The AAV-TMC1 vectors were injected into the inner ears of deaf TMC1 mutant mice. They found that the AAV-TMC1 vectors restored auditory function at the cellular level, the systems level and the behavioral level. He concluded that TMC1 gene therapy may be a viable strategy for translation to clinical application for the benefit of patients who suffer TMC1 deafness.

Hearing, like our other senses, is often taken for granted. It is something the body and brain seem to accomplish without effort. In reality, cells within the inner ear, the hair cells, convert sound information into electrical signals. Doctor Holt discussed his work identifying a key family of proteins that may form the channel for sound to be transduced to signal. Doctor Holt also discussed how targeting TMC1, a part of this protein family, using gene therapy restored hearing in a mouse model of TMC1 deafness. As this mutation also causes deafness in humans, gene therapy may be a potential treatment.

This seminar focused on the genes and proteins required for sensory transduction in the mammalian inner ear. The sensory cells of the inner ear, known as hair cells, convert mechanical information, such as sound, into electrical signals. The key protein at the center of the process is a mechanosensitive ion channel. The molecular identity of this ion channel has been a major focus of the ion channel field for the last several decades. Now, for the first time, a solid candidate has emerged, TMC1. TMC stands for Transmembrane Channel-like and includes a family of eight proteins, all with unknown function. TMC1 and closely related family member, TMC2, are expressed in inner ear hair cells and may form the elusive mechanosensory transduction channel.

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Antonio Giraldez, PhDFergus F. Wallace Professor of Genetics, Chair of Genetics DepartmentDepartment of GeneticsYale School of Medicine(March 6, 2018)

Deciphering the Regulatory Codes Shaping the Maternal to Zygotic Transition During Development

These approaches have provided three major insights into the regulatory landscape during embryogenesis. First, they determined that individual codons shape mRNA stability through deadenylation, an effect that is conserved from Drosophila to mammals during the maternal-to-zygotic transition. Second, they have identified common regulatory sequences in the 3’UTR and the CDS that have antagonistic effects in mRNA stability. They find that overall, 3’UTR regions confer stability, with the most prominent exception of miRNA target sites. In contrast, coding sequences confer destabilization. They showed that sequence bias composition explains part of this regulation, but in addition, identified motifs that are associated with increased and decreased stability of the mRNA in vivo. Finally, to define the set of regulatory proteins in vivo, they have undertaken interactome capture identifying 170 proteins that are associated with mRNAs during this transition. Parallel iClip analysis for 30 of these proteins revealed a binding map and their regulatory motifs in vivo. Comparing the iClip analysis with the identification of regulatory motifs in vivo revealed a combinatorial code that mediate mRNA stability and decay during the maternal to zygotic transition.

There are still many open questions about the genetics of early embryo development. Much depends on maternal RNA and its control over gene expression. The instructions provided by the RNA are a basic component of development. In his seminar, Doctor Giraldez discussed his work exploring what factors promote stability and what factors destabilize maternal RNA, and what proteins are involved in the transition from maternal RNA to embryo.

Post-transcriptional regulation plays a fundamental role in shaping gene expression after fertilization across animals, a period where the embryo is acquiring totipotency. To understand the post-transcriptional regulatory code that shapes mRNA decay and translation regulation during this maternal to zygotic transition his lab combined three approaches: i) RESA, a novel RNA Element Selection Assay which quantifies the regulatory activity of sequences in the 3’UTR and the CDS throughout the transcriptome in vivo. ii) Interactome capture, to identify the proteins involved and iii) Parallel iClip for 30 RNA binding proteins to define their regulatory targets and motifs during development.

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Shawn Xu, Ph.D.Bernard W. Agranoff Collegiate Professor of the Life SciencesDepartment of Molecular & Integrative PhysiologyUniversity of Michigan(March 20, 2018)

Eyeless But Not Blind: Photosensation In C. Elegans

Mammals make use of their senses (sight, hearing, taste, touch, and smell, as well as proprioception) to interact and navigate with their environment. Sensory input, such as sound, is transduced (or changed) into electrical signals. The worm C. elegans is a useful model system for studies on the molecular basis of how sensory inputs are transduced. Doctor Xu discussed his work examining how worms sense their world. His work has demonstrated that worms can sense and avoid light, mediated by a particular photoreceptor protein, LITE-1.

The Xu lab is a sensory neuroscience lab studying how animals interact and communicate with both the external and internal environments through the sensory systems, which are essential for survival and the quality of life. The questions they study in the lab include: i) Sensory transduction: how do sensory neurons/cells detect and distinguish different sensory cues and then transduce them into electric outputs? ii) Sensory processing: how do neural circuits process sensory information from sensory neurons to turn it into a behavioral output? iii) In addition to behavior, sensory stimuli also modulate other physiological processes such as aging and longevity, so they are also interested in characterizing how the sensory environment modulates aging. In his lecture, he covered only work on sensory transduction. There are five common senses in mammals: vision, hearing, smell, taste, and touch or somatosensation that includes temperature sensation, and a

sixth sense: propriopception, which is important for controlling body posture and balance during movement. Work from many labs have demonstrated that worms sense smell, tastants, touch, and temperature. The Xu lab has discovered a new sense in worms, proprioception, and found it requires a TRP channel. Instead of giving an overview of work on all these different kinds of sensory modalities, he focused on the sensing of light. C. elegans were thought be insensitive to light because they live in the dark soil. Interestingly, they found that worms are light sensitive as they avoid light, and engage in phototaxis behavior. This photoavoidance behavior is important for their survival and also provide a potential mechanism for keeping them in the dark. Worms are most sensitive to UV light, and they estimate that the amount of UV in the sunlight would be sufficient to drive this behavior. Through a combination of behavioral, genetic, functional imaging and electrophysiological studies, they have made a number of discoveries, which are summarized as follows: 1) worms sense light through a subset of ciliary photoreceptor neurons and engage in phototaxis behavior mediated by LITE-1. 2) LITE-1 is a new type of photoreceptor protein with an exceptionally high photon-capturing ability. 3) LITE-1 may not have a prosthetic chromophore and requires two tryptophan residues for photosensitivity. 4) Doctor Xu proposed that the two tryptophan residues participate the formation of the chromophore for LITE-1.

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Sarah Ross, PhDAssociate ProfessorDepartment of NeurobiologyUniversity of Pittsburgh (March 27, 2018)

The Neural Circuits of Itch and Pain

the role of KOR signaling in itch. These studies revealed that KOR signaling bidirectionally modulates itch sensitivity within the spinal cord: increasing kappa tone decreases itch, whereas decreasing kappa tone increases itch. Finally, their work provides evidence that B5-I neurons inhibit itch both through direct inhibition of spinal projection neurons, as well as by presynaptic opioid-mediated inhibition via release of dynorphin. These findings suggest the cellular basis through which counter-stimulation mediates the inhibition of itch.

One of the salient features of pain following injury is that nociceptive input becomes amplified. Though the spinal cord is thought to play a key role in the amplification of nociception, the specific microcircuits involved are poorly understood. Wind-up is a physiological mechanism of sensory amplification that may, under pathological conditions, contribute to hypersensitivity and allodynia. Although it is clear that wind-up is a network phenomenon, few studies have addressed the nature of such a network. Ross showed that one-fifth of lamina I spinoparabrachial (SPB) neurons undergo wind-up, and provide evidence that wind-up in these cells is mediated in part by a network of spinal excitatory neurotensin-expressing interneurons that show reverberating activity. These findings provide insight into a polysynaptic circuit of sensory augmentation that may contribute to the wind-up of pain’s unpleasantness.

We all know the annoyance of scratching a mosquito bite, only to have the itching get worse. But what about an itch or pain that is felt for no apparent reason? These can be debilitating problems that lower quality of life. Doctor Ross is examining the neuronal basis for persistent itch and pain. She discussed her work using a mouse model to locate molecular signals that modulate the intensity of pain or itch at the spinal cord.

Persistent pain and itch are widespread, debilitating conditions for which there is a pressing need for more effective treatments. Our approach to address this important health issue is to gain a better understanding of the underlying neural circuits. Towards this the Ross lab developed a novel approach allowing the manipulation of defined subsets of neurons within the context of semi-intact somatosensory preparation that is responsive to mechanical, thermal, and chemical stimulation of the skin and from which they can identify and record from spinal output neurons.

They found that mice lacking the transcription factor Bhlhb5 show elevated itch, and that this effect is caused by the loss of a specific population of spinal inhibitory neurons during development, which they termed B5-I neurons. Ross lab research revealed that B5-I neurons differentiate into two neurochemically distinct subsets of neurons in adult mice: dynorphin and nNOS subsets, which are lost in the dorsal horn of Bhlhb5 mutant mice. Since 80% of B5-I neurons express dynorphin, they also analyzed

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Laura Colgin, PhDAssociate ProfessorDepartment of Neuroscience University of Texas at Austin(April 24, 2018)

Gamma Oscillations in the Hippocampal Network

The formation and retrieval of memories is too complex for single neurons. The processes take a network of neurons functioning together. Networks of neurons firing in coordinated effort present as rhythms at different frequencies depending on the behavior. Gamma rhythms (at a frequency of roughly 8–100 Hz) are thought to reflect information flow in the hippocampus. Doctor Colgin discussed her work examining different gamma rhythm frequencies. Her research shows that fast and slow gamma rhythms may serve different purposes for memory encoding and retrieval.

How the brain stores and retrieves memories is one of the key questions in neuroscience. Isolated activity within individual brain cells, or “neurons”, cannot support complex cognitive operations such as learning and memory. Instead, groups of neurons must coordinate their activity to form functional networks that are capable of carrying out such high-level tasks. How is coordination of distributed neurons achieved in the brain? Brain rhythms reflect synchronized activity across large ensembles of neurons and are thought to be key for coordinating neurons during many cognitive tasks, including learning and memory.

The hippocampus is a brain area that is essential for creating and storing memories of events and experiences. Accordingly, rhythms in the hippocampal network are thought to play a role in learning and memory. Three major classes of rhythms are observed in the hippocampus: sharp wave-ripples (~200 Hz ripples

occurring on ~0.1-1 Hz sharp waves), theta rhythms (~8 Hz), and gamma rhythms (~25-100 Hz). Sharp wave-ripples occur during quiet wakefulness and slow-wave sleep and are thought to play a role in “offline” memory consolidation. In contrast, theta rhythms occur during active behaviors. Gamma rhythms occur during all behavioral states but are largest when they are nested within theta oscillations. The late John Lisman, a Brandeis faculty member, put forward several highly influential hypotheses about the function of theta-nested gamma rhythms. For example, he suggested that sequences of gamma cycles nested within a theta cycle serve to organize sequences of hippocampal “place cells”, neurons that fire selectively in specific spatial locations.

Much evidence now suggests that the class of oscillations traditionally known as gamma should be subdivided into distinct subtypes that exhibit different frequencies and reflect distinct streams of information flow in the hippocampal network. “Slow gamma” rhythms (~25-55 Hz) couple activity in hippocampal subfield CA1 to inputs from CA3, a neighboring subfield that is believed to be essential for retrieval of previously stored memories. In contrast, “fast gamma” rhythms (~65-100 Hz) link CA1 to inputs from superficial layers of medial entorhinal cortex that transmit current spatial information. The Colgin lab hypothesized that if slow and fast gamma rhythms constitute different oscillatory states of the hippocampal network, then hippocampal place cells should represent spatial information differently depending on whether slow

or fast gamma rhythms are present. In line with this hypothesis, they found that sequences of place cells represented relatively long paths in a temporally compressed manner during theta-nested slow gamma rhythms and accurately tracked ongoing trajectories in real-time during theta-nested fast gamma rhythms. They also obtained preliminary evidence suggesting that these different types of place cell ensemble firing patterns are differentially related to behavioral performance on a spatial memory task. The results suggest that distinct slow and fast gamma rhythms may prevent interference between memory encoding and retrieval operations in the hippocampal network.

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The M.R. Bauer Foundation Distinguished Guest Lecturer Series

Introduction

Every year the M.R. Bauer Distinguished Lecturer program brings to campus two distinguished visitors who spend a full week at Brandeis. These weeklong visitors present talks to small and large groups, visit Center laboratories, and engage students, postdoctoral fellows and faculty in informational and highly interactive conversations about shared areas of research interests. This year our distinguished lecturers were Betty Eipper from UCONN and Matteo Carandini from University College London.

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Betty Eipper, PhDProfessorDepartment of Molecular Biology and BiophysicsUCONN Health(October 31, 2017)

Using Neuropeptides to Communicate – Lessons Learned from A Single Cell Green Alga

Chemical signals, such as neurotransmitters and neuropeptides, are used by neurons for communication. This method must be adaptable and able to respond to different stimuli. Research has made clear that neuropeptides are of key importance, but many questions remain, including what peptides are necessary for what signal, and where and when they are used. In her seminar, Doctor Eipper discussed her work examining one enzyme, PAM, which plays an important role in neuropeptide function in single-celled green alga, as well as in mammals.

Neuropeptides (α-endorphin, vasopressin and cholecystokinin, for example) far outnumber the classical or small molecule neurotransmitters (glutamate, GABA, acetylcholine, biogenic amines and adenosine, for example). Flies, sea anemones and human neurons synthesize bioactive peptides in much the same way, utilizing the secretory pathway machinery used to produce membrane proteins and components of the extracellular matrix. It is now clear that most neurons utilize both classical transmitters and neuropeptides to communicate with their target tissues. Neuropeptides, acting almost entirely through G Protein Coupled Receptors, provide a great deal of plasticity to the nervous system: different neuropeptides can be targeted to axons vs dendrites; firing frequency and an array of environmental inputs can alter the transmitter mixture released. With the ability to activate specific subsets of peptidergic neurons, their role in circuit formation and function has become clear.

The ability of many neuropeptides to bind to their receptors requires that the readily ionizable carboxyl group at their

C-terminus be amidated, stabilizing the peptide and reducing any effect of modest changes in pH on its ionization. Following up on the observation that pituitary cells maintained in medium lacking serum retained the ability to produce peptide precursors and cleave them into the expected products, but were unable to amidate them, the Eipper lab purified and characterized the only enzyme known to catalyze this reaction, peptidylglycine α-amidating monooxygenase (PAM). This bifunctional type I integral membrane enzyme catalyzes the sequential conversion of peptidylglycine substrates into α-hydroxylated intermediates. Peptidylglycine α-hydroxylating monooxygenase (PHM), a copper, ascorbate (the component missing from serum-free media) and molecular oxygen dependent enzyme, first catalyzes the stereospecific hydroxylation of the α-carbon of the C-terminal glycine. Cleavage by peptidyl-α-hydroxyglycine α-amidating lyase (PAL) then releases the amidated peptide and glyoxylate. Its intrinsically disordered cytosolic domain governs PAM trafficking as it moves through the biosynthetic pathway, onto the plasma membrane and into the endocytic pathway, where it can be recycled to secretory granules or degraded. Strikingly, PHM is as sensitive to levels of molecular oxygen as the prolyl hydroxylases that control the stability of hypoxia inducible factor 1-α (HIF1-α), suggesting a cell non-autonomous role for peptide amidation in the response of different cells to hypoxia.

In both mice and flies, genetic elimination of PAM is lethal. The discovery of a highly homologous PAM gene in Chlamydomonas reinhardtii, a unicellular green alga, suggested the presence of a PAM-like gene in the last

eukaryotic common ancestor. Other genes known to play an essential role in nervous system function have also been found in organisms totally lacking a nervous system. CrPAM localizes to the Golgi region, as in mammalian neurons and endocrine cells. In addition, and unexpectedly, CrPAM also localizes to ciliary membranes; consistent with this observation, PAM activity is readily detectable in lysates of purified cilia. Never having looked before, they were quickly able to demonstrate the presence of PAM in both motile and sensory cilia in vertebrate systems.

Intrigued by a role for this copper, ascorbate and molecular oxygen dependent enzyme in cilia, they evaluated the effect of reducing the expression of CrPAM. Two independent CrPAM knockdown lines were unable to form cilia! No axoneme extended beyond the transition zone, which lacked Y-linkers. A conserved, but species-specific role for PAM in ciliogenesis was confirmed by examining the effects of reducing PAM expression in Schmidtea mediterranea, zebrafish and mice. Increased expression of CEP290 and NPHP4, components of the transition zone, in the CrPAM knockdown lines suggests changes in the signaling events involved in ciliogenesis. In addition, cargo-specific alterations in protein secretion were observed, consistent with the effects of PAM expression on secretory pathway function in mammalian cells.

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Matteo Carandini, PhDProfessorDepartment of NeuroscienceUniversity College London(January 30, 2018)

From Vision to Navigation: A Journey in the Cerebral Cortex

It happens to all of us at some point. If, while out walking or driving, we come to a supposedly familiar place from a different direction than usual, it can take a few minutes to reorient. This is accomplished with sight – our visual system helps us to make sense of our environment. Doctor Carandini investigates how visual signals are transformed into estimates of position. He has found that neurons in the mouse visual cortex show preference for certain spatial positions. This work highlights that more of the brain may be involved in navigation than previously expected.

The visual system and the navigational system are two of the most studied pathways in neuroscience. A key region of the visual system is the primary visual cortex, where myriad neurons deconstruct images into fragments and respond according to the fragment that falls in their receptive field. The navigational system, in turn, centers on a region of the hippocampus, where neurons exhibit place fields, i.e. are selective for the position that an animal occupies in the world. These notions are well understood, and their discoveries awarded with Nobel Prizes in 1981 and 2014.

These two systems, however, must talk to one another: a major role of vision is to guide navigation, and navigation is strongly driven by vision. How are visual signals transformed into estimates of position? To study this transformation, Doctor Carandini’s lab recorded from large populations of neurons in the cortex of mice that navigated environments in virtual

reality. To their surprise, they found that neurons as early as in primary visual cortex exhibit preferences for spatial position. These preferences strengthen as signals proceed towards parietal cortex, where responses become entirely related to navigation, coding for combinations of the animal’s position and heading direction.

Navigation signals in visual cortex correlate strongly with signals in the hippocampus, where cells have those well-known preferences for spatial position, and are closely related to the animal’s subjective estimate of location. Signals related to navigation, therefore, appear much earlier than expected in the visual system, and are intimately related to the animal’s own estimate of position in the world. The presence of such navigational signals as early as in a primary sensory area suggests that these signals permeate sensory processing in the cortex. The brain, or at least the brain of a mouse, may be devoted to navigation to a much larger extent than anticipated.

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The Volen National Center for Complex Systems Scientific Retreat 2017

Introduction

The Volen National Center for Complex Systems held its annual scientific retreat on October 12, 2017, at Brandeis University. This year we honored the pioneering work of Volen Center for Complex Systems faculty member John Lisman. The retreat, titled “Breakthroughs in understanding the role of CaMKII in synaptic function and memory,” brought together renowned researchers in the field of CaMKII and neural function. Volen Director Leslie Griffith started the day off and was followed by Thomas Reese of the NIH, Margaret Stratton from the University of Massachusetts, Amherst,

and Roger Nicoll from UCSF. John Lisman was our keynote speaker and presented an amazing summary of the field of CaMKII and its role in memory formation, including the pivotal work the Lisman Lab has contributed to this field of knowledge over the last forty years.

Scientists from across Brandeis departments attended to hear the lectures, share lunch, and attend the poster session for this day of science. The tribute to CaMKII and John Lisman’s contributions to the field are particularly poignant as, sadly, John passed away eight days after the retreat.

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The Volen National Center for Complex Systems Scientific Retreat

Schedule

October 12, 2017

8:00 a.m. Arrival and Check in

8:30 a.m.Leslie Griffith, Brandeis University“Local translation of CaMKII regulates plasticity of spontaneous release”

9:30 a.m.Thomas Reese, NIH“A structural view of CaMKII in the molecular organization of the PSD”

10:30 a.m. Break

11:00 a.m. Keynote SpeakerJohn Lisman, Brandeis University“The critical role of CaMKII in memory storage: 6 key physiological and behavioral tests”

12:00 p.m.Lunch

1:30 p.m.Margaret Stratton, University of Massachusetts, Amherst“Activation-triggered subunit exchange in CaMKII and its role in memory”

2:30 p.m.Roger Nicoll, University of California, San Francisco“The NMDAR/CaMKII complex is the master of the PSD universe”

3:30 p.m.Closing Discussion: John Lisman

4:00 p.m.Poster Session/Reception

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John Lisman PhDZalman Abraham Kekst Professor of Neuroscience Department of BiologyBrandeis University(October 12, 2017)

The Critical Role of CaMKII in Memory Storage: 6 Key Physiological and Behavioral Tests

Our memories are part of what defines us as individuals and thinking beings. How memory can be encoded in the wet-ware of the brain is a question that has occupied many scientists and philosophers. As our understanding of biology at the cellular and molecular level has progressed, the question of how memories are stored has taken on a more biochemical flavor. Beginning in the 1980s, work on CaMKII suggested that it might be a biochemical switch capable of holding memory.

In 1984 Francis Crick published an opinion piece laying out how the brain might get around the problem of molecular turnover (which occurs on a scale of days to weeks) for building a stable memory switch. The model he favored was one of a multimeric synaptic protein in which “memory” could be stored in a modification. The modified form of the protein could be maintained in the face of protein turnover by specifying that turnover occurred at the subunit level and that new subunits being incorporated into a holoenzyme could take on the memory state of the parent multimer. The next year, 1985, John Lisman published a model in PNAS showing that an autophosphorylating kinase/phosphatase pair could store memory indefinitely.

These two models gave a pretty decent description of CaMKII, an enzyme that was first discovered in the late ‘70s in Paul Greengard’s lab by Howard Schulman. The deep biochemical work on CaMKII from Mary Kennedy and a host of others showed that CaMKII is multimeric, autophosphorylating protein kinase that is localized to synaptic domains. Over the next two decades it was shown by the Lisman lab and others that its autophosphorylated state is associated with synaptic potentiation and memory. The one thing that was lacking was a demonstration that there could be subunit exchange and that has now been shown by Meg Stratton’s in vitro work. The Lisman lab’s most recent paper showing that a memory could be erased by flooding the synapse with a dead kinase argued that exchange is probably happening in vivo too and that it is critical to maintaining long-term memories.

Link to John’s talk.https://drive.google.com/file/d/0ByJ6rFh1CnizQkNfbnJya3ZJRGc/view?usp=sharing

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Leslie Griffith, M.D., PhDNancy Lurie Marks Professor of NeuroscienceDepartment of BiologyBrandeis University(October 12, 2017)

Local Translation of CaMKII Regulates Plasticity of Spontaneous Release

It has been known for many years that long-term memory requires the synthesis of new protein molecules at synapses. What these proteins are and how their function is specifically regulated by stimuli that drive formation of memory is still an open question.

CaMKII is required for memory formation in both rodents and the fruit fly Drosophila. To better understand the regulation of CaMKII synthesis, the Griffith lab generated null mutations in the CaMKII gene. These animals survived until pupation due to maternally deposited CaMKII mRNA and protein. Interestingly, the maternal CaMKII was not able to localize to synapses, suggesting that synaptic CaMKII, the pool most likely to be involved in plasticity and memory formation, required zygotically synthesized mRNA. A possible mechanism suggested itself when it was shown that the maternal mRNA lacked the long 3’UTR of the zygotic mRNA. This region of mRNAs is associated with translational regulation by microRNAs.

To test the role of local translation of the CaMKII mRNA, the Griffith lab utilized a plasticity paradigm that required local protein synthesis.

Spaced depolarization of the larval neuromuscular junction (NMJ) has a profound effect on the frequency of miniature end plate potentials (minis), which increase by 4-5X. They found that CaMKII mutant larva completely lacked this plasticity. Rescue of the mutant with a transgene that encoded a version of the CaMKII gene that lacked the long 3’UTR failed to rescue plasticity, whereas a transgene with the entire gene completely restored the increase in minis. Adults with these rescue constructs were tested for long-term memory in an odor-sugar appetitive associative memory assay. Only animals in which the transgene contained the long 3’UTR were able to form memory.

To test the role of microRNAs in plasticity, the Griffith lab overexpressed mir-289, a microRNA shown previously to regulate CaMKII at the larval NMJ. mir-289 also blocked mini plasticity when expressed in either the presynaptic or postsynaptic cell. In aggregate, these results suggest that local translation of CaMKII is critical to both synaptic plasticity and to memory formation.

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Thomas Reese, M.D.Senior InvestigatorDepartment of NeurobiologyNIH(October 12, 2017)

A Structural View of CaMKII in the Molecular Organization of the PSD

The formation of memories requires changes at the level of the synapse, changes to numbers of receptors, and changes to the shapes of dendritic spine synapses. Memory formation also requires certain enzymes, such as CaMKII. In his presentation, Doctor Reese discussed his research using electron microscopy to determine where CaMKII is localized in the core of the spine synapse, and how the positioning could affect memory formation.

The Reese laboratory investigates the molecular organization of synapses in the brain where memories are created and stored. Specifically, transmission of signals at these synapses depends on glutamate receptors, and changes in efficacy ensue when the numbers of spine receptors are adjusted up or down during synaptic activity. Changes in the numbers of receptors are accompanied by changes in the shapes of the spine synapses and they are interested in finding out what changes in the shapes, numbers and deployments of proteins in synaptic spines support the changes in efficacity.

John Lisman, whom we are honoring, made a major advance on this problem when he predicted and then demonstrated that an enzyme in the synaptic spine, CaMKII, undergoes dramatic changes during the first stages of learning, and that these changes are both necessary and sufficient for learning. Reese’s work

shows where CaMKII is localized in the spine so it can interact with receptors and the rest of the spine synaptic machinery.

In detail, he developed two methods to examine the distribution of CaMKII at spine synapses. The first involved biochemically isolating the cores of the spine synapse, known as the post synaptic density, or PSD. He then used a freeze dry/replica method that allowed him to use an antibody to attach gold particles to CaMKII molecules in the PSD, which show up clearly in the electron microscope. He found that much CaMKII forms large complexes clinging to the back surfaces of the PSDs, which may have a mechanical function or even buffer key control components such as calmodulin. Lisman was very intrigued with these CaMKII aggregates and many discussions of their function ensued.

CaMKII is an oligomer and has a 12-member ring at its base. Reese developed a method using a special negative stain to show these rings in the electron microscope and then we could use them to map the positions of CaMKII in the PSD. He found that a portion of the CaMKII in the PSD is situated in positions where it could regulate the function of receptors. Thus, this piece of the puzzle fell into place – we could see directly how CaMKII could affect the initiation of memories.

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Margaret Stratton, PhDAssistant ProfessorDepartment of Biochemistry and Molecular BiologyUniversity of Massachusetts, Amherst(October 12, 2017)

Activation-Triggered Subunit Exchange in CaMKII and Its Role in Memory

Memory formation, storage, and retrieval is a long-term process, and requires a cellular component, such as a protein, that can remain active over long periods of time. This has been an open question for many years, as most proteins degrade over time. Doctor Stratton’s research has demonstrated that CaMKII can produce long-term activation by the sharing of subunits (molecular components of the protein) with other CaMKII proteins. Doctor Stratton has determined that this sharing is activity-dependent. In this way, it is thought that CaMKII is in control of the persistent activity needed for memory formation.

Memories are stored and retrieved over a time-scale of decades while cellular components are degraded on a time-scale of minutes to days. Addressing this significant discrepancy is what drives the Stratton lab’s research. It was more than two decades ago that Francis Crick speculated that perhaps an oligomeric protein could solve this degradation paradox. He postulated that this oligomer could serve as a

molecular memory by sharing its activation state with newly synthesized proteins through subunit exchange. John Lisman later suggested that Ca2+-calmodulin dependent protein kinase II (CaMKII) is a good candidate for this ‘memory protein’. Stratton’s lab has recently shown, for the first time, that subunit exchange does occur between CaMKII holoenzymes. Importantly, this occurs only as a result of activation, and activation (phosphorylation in this case) is spread as a consequence of subunit exchange. This would be a mundane result if subunit exchange were not activation-dependent, since all protein oligomers disassemble and reassemble at some rate. It is exciting that there is something unique about the CaMKII assembly that allows this regulation. Long-term potentiation (LTP) requires persistent activity to sustain synaptic signaling over a long period of time (how long exactly remains unclear). She hypothesized that subunit exchange in CaMKII may be the key to this persistent activation.

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Roger Nicoll, M.D.ProfessorDepartment of Cellular Molecular PharmacologyUniversity of California, San Francisco(October 12, 2017)

The NMDAR/CaMKII Complex is the Master of the PSD Universe

The protein CaMKII is now understood to play a vital role in memory formation. Many questions remain, however, as to the full extent of its role in synaptic function. Doctor Nicoll discussed his work exploring how neurons function without CaMKII in its various forms. His work highlights the importance of CaMKII to the long-term activity needed for memory formation, and the importance of a particular receptor, the NMDAR, in this process.

CaMKII is one of the most studied synaptic proteins, but many critical issues regarding its function in baseline synaptic function and plasticity remain unresolved. Using a CRISPR based system to acutely delete CaMKII and replace it with mutated forms in single neurons, the Nicoll lab has comprehensively and rigorously

addressed its various synaptic roles. In brief, basal AMPAR and NMDAR synaptic transmission both require CaMKII, but not CaMKIIβ, indicating that, even in the adult, synaptic transmission is determined by the ongoing action of CaMKII. While AMPAR transmission requires kinase activity, NMDAR transmission does not, implying a scaffolding role for the CaMKII protein instead. LTP is abolished in the absence of CaMKII, CaMKIIβ and with the molecular replacement of the kinase dead mutant (T286A). Nicoll concludes that CaMKII fully accounts for NMDAR-dependent LTP. With the exception of NMDAR synaptic currents, all aspects of CaMKII signaling requires binding to the NMDAR, emphasizing the essential role of this receptor as a master synaptic signaling hub.

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Presenter Poster Title

Daniel Acker “Memory in structurally unstable neural networks”

Stephen Alkins “The long UTR mRNA of CaMKII is essential for translation-dependent plasticity of spontaneous release in Drosophila melanogaster”

Nicole Ayasse “The impact of context and competition on speech comprehension in younger and older adults revealed using eye-tracking and pupillometry”

Madelen Diaz “Allatostatin-C is a novel circadian neuropeptide in Drosophila melanogaster”

Johanna Flyer-Adams “Pigment dispersing factor (PDF): A novel circuit for memory regulation”

Josiah Herzog “TDP-43 misexpression causes defects in dendritic growth”

Alexis Johns “Misrecognizing spoken words: The time course of context effects, and why older adults are more susceptible to mishearing a word”

Katie Kimbrell “The role of Rem2 in conditioned taste aversion”

Aishwarya Krishnamoorthy “Neuronal functions of circular RNA”

Chelsea Groves Kuhnle “Temporal dynamics of acuity changes during monocular deprivation”

The Volen National Center for Complex Systems Poster Session

The Volen Retreat offers the opportunity for all Volen-affiliated faculty, postdoctoral fellows, graduate and undergraduate students to present a poster detailing their research. This is an opportunity for other members of the community to engage with their fellow scientists and exchange ideas. The face-to-face format of a poster session allows for direct and detailed discussion of data and techniques. This year 23 postdoctoral fellows and students presented posters at the Volen Retreat. The presenters and titles are below.

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Presenter Poster Title

The Volen National Center for Complex Systems Poster Session (Cont.)

Kang Liu “Physical principles for stable synaptic structure and long-term memory”

Jacqueline McDermott “The role of Class 4 Semaphorins and PlexinB receptors in GABAergic synapse formation”

Nate Miska “Brief visual deprivation shifts up excitation-inhibition ratio via selective depression at thalamocortical synapses onto PV+ interneurons”

Daniel Powell “Modulation of the pyrokinin-elicited gastric mill rhythm by an endogenous peptide hormone and a mechanosensory neuron”

Xiaodong Qu “A personalized reading coach using wearable EEG sensors”

Sarah Richards “Regulation of dendritic branching by sensory experience and the small GTPase Rem2”

Leandro de Oliveira Royer “The Ras-like GTPase Rem2 is a potent endogenous inhibitor of calcium/calmod-ulin-dependent kinase II activity”

Nadya Styczynski “Warmth and competence with motor resonance”

Stephen Thornquist “CaMKII measures the passage of time to coordinate motivational state”

ShiYu Wang “Molecular mechanisms of Sorting Nexin 16 (SNX16) on endosomes”

Timothy Wiggin “Mapping synapses between dorsal paired medial (DPM) and dopamine neurons in Drosophila melanogaster”

Weijin Xu “Reforming the TRIBE: a more efficient approach to identify RNA-binding protein targets”

Emmanuel Rivera-Rodriguez “Unraveling miR-190 and its role in sleep”

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The M.R. Bauer Foundation Summer Science Research Fellowships

Introduction

Benjamin Franklin said “Tell me and I forget. Teach me and I remember. Involve me and I learn.” Due to the gracious gift from the M.R. Bauer Foundation ten Brandeis undergraduates were able to learn science this summer. Sophie Lis, an undergraduate in the lab of Gina Turrigiano, expressed this best saying “I would like to sincerely thank the donors who made this opportunity possible for me and allowed me to do full-time research this summer without any barriers, and to really experience life as a scientist.” The experience of full time science for a summer is formative for these students and often solidifies their passion for science,

confidence in themselves as scientists, and desire to continue in research. The students present their science in poster format at the end of the summer during SciFest. Faculty, postdocs, graduate students, and research staff from the entire Division of Science attend SciFest and interact with the Bauer Fellows to learn about the science each student pursued. The following pages include the abstract from each of the M.R. Bauer Fellows’ posters and a personal statement expressing what this opportunity to do research in a Volen Center laboratory meant to them.

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Alison MaOprian LaboratoryDepartment of BiochemistryBrandeis University

Conformational Dynamics in Terpene Synthases

Poster AbstractTerpenes form the largest class of natural products. They provide a wide variety of uses with applications ranging from fragrances to therapeutics, to even serving as potential biofuels. Although thousands of different terpenes exist, all are derived from two 5-carbon universal precursors, dimethylallyl pyrophosphate (DMAPP) and isopentenyl pyrophosphate (IPP), linked head to tail to form C10 monoterpenes, C15 sesquiterpenes, and C20 diterpenes.

The committed step in all terpene biosynthetic pathways is catalyzed by a terpene synthase responsible for cyclization of the hydrocarbon product through intermediary generation and control of high energy carbenium intermediates. A firm mechanistic understanding of terpene synthase reactions is a prerequisite to exploitation of this remarkable class of proteins. Much is known about the carbocation cascade facilitated by terpene synthases, but insight into structural protein dynamics is lacking.

The focus of this project is on pentalenene synthase, the enzyme responsible for cyclization of farnesyl diphosphate to the sesquiterpene antibiotic precursor pentalenene. Solution NMR can be used to monitor conformational changes during the reaction and to follow dynamics of the enzyme during initial interaction with the farnesyl diphosphate substrate. Many terpene cyclases are too large for NMR spectroscopy or are dimers in solution, but pentalenene synthase is a 38kDa monomer, making it the perfect candidate for NMR studies (Cane, 1990; Christianson, 2017). In addition, the enzyme structure has been solved

by X-ray crystallography. These studies will elucidate the conformational landscape that pentalenene synthase navigates during catalysis and thus form the foundation for a mechanistic understanding of this important class of enzymes. Personal StatementThanks to the M.R. Bauer Foundation I was able to work full-time in the Oprian Lab on terpene synthases this summer. Although I had joined the lab the previous year, juggling academic coursework along with extracurricular activities and research made it difficult to really dive in to the experiments necessary for my projects. With the guidance of my mentor, I have been able to learn new skills and techniques while making significant strides in my project. Working in the lab this summer has made me more confident in troubleshooting problems and finding ways to overcome them when they inevitably arise. Furthermore, doing full-time research has given me an opportunity to understand what pursuing further education in the life sciences may be like after Brandeis. I am very thankful for this summer of research in which I not only got to work on my own project but also had the opportunity to develop critical thinking skills that I will be able to use both in and out of research.

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Sophie LisTurrigiano LaboratoryDepartment of BiologyBrandeis University

Applying Quality Control to Spike Sorting And Clustering Algorithm to Improve Data Analysis

Poster AbstractIn order to understand neuronal behavior in the living brain, scientific investigations rely on chronically implanted electrode arrays to track activity of single neurons over time. Resultant signals are analyzed via spike sorting and clustering algorithms, where waveforms are grouped into collections of spikes that putatively originate from the same neuron. However, successful single-unit identification during long-term implantation is error-prone due to electrode drift in neural tissue or background noise interference. This can result in the false splitting of spikes from one neuron into multiple clusters, or the merging of spikes from two neurons into one cluster, losing track of single-unit identity.

To evaluate the outcome of the present algorithm used in the Turrigiano lab, MATLAB was used to carry out quality control on given clusters as based on recordings from visual cortex (V1) in rats. A graphical user interface (GUI) was created to track hourly changes in each cluster to examine characteristics indicative of potential cluster errors. This allowed us to determine and isolate the presence of time points throughout the duration of the experiment where incorrect clustering occurred and to prevent the inclusion of this data in further analysis. This will allow for cleaner data analysis and will further future analysis of neuronal activity in visual cortex, as demonstrated with an example cluster. These outcomes will act as a grounding step for future re-evaluation and optimization of the present spike sorting and clustering algorithm in order to produce more reliable data analysis.

Personal StatementMy involvement in the lab this summer was a phenomenal opportunity to experience day-to-day life working in science and to carry out important research that positively affected data analysis in the Turrigiano lab. It was extremely important for me to be able allocate this time so as to make progress on my project and to make headway into aspects of research I had little time to explore during the school year. Thanks to very generous support of the M.R. Bauer Foundation, I was able to dedicate the entirety of these past ten weeks to building from head to toe graphical user interfaces (GUIs) to evaluate quality control of neural recordings. Most importantly, these tools were able to be implemented to identify location and types of errors during analysis, a major step in working to improve the way that neural recordings are analyzed to identify single cells followed over time.

These past few months have thus allowed me to reflect on my motivation to pursue scientific research and my future goals, as I enter my senior year at Brandeis and begin to think about next steps in my professional career. This experience has cemented my desire to seek positions in scientific programming or computational neuroscience following graduation, and to continue bettering my MATLAB skills and my ability to write clean, efficient code. I am extremely indebted to the M.R. Bauer Foundation for this chance to live out 9-5 life as a research assistant, especially given the financial difficulties I have experienced throughout my time at Brandeis. I would like to sincerely thank the donors who made this opportunity possible for me and allowed me to do full-time research this summer without any barriers, and to really experience life as a scientist.

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Muibat YussuffRosbash LaboratoryDepartment of BiologyBrandeis University

Investigation of CG17777 in the Circadian Clock of Drosophila Melanogaster

Poster AbstractCircadian rhythms are physiological and behavioral adaptations in an intrinsic 24-hour cycle. Circadian rhythms are highly conserved across species from bacteria to mammals, which makes the fruit fly a productive model system to investigate the mechanisms behind clock regulation. Approximately 150 neurons in the Drosophila brain function together to regulate circadian rhythms. Neuropeptides in these clock neurons play important roles in controlling both behaviors and physiological processes such as sleep, circadian rhythms, feeding, and mating. Although many neuropeptides are known to help maintain the circadian clock, it is still unclear how all of these clock neurons communicate with each other or outside of the clock circuit. In an effort to characterize additional neuropeptides that act within the circadian neuronal circuit, one of the five candidate neuropeptides from prior RNA sequencing results will be further investigated to determine their potential roles in the circadian clock. CC17777 is a particularly interesting candidate because previous RNA sequencing of the clock neurons showed that it is expressed in three distinct neuronal clock clusters, including the morning and evening pacemaker neurons. Circadian experiments show that CG17777 is necessary in the morning and evening pacemaker neurons to maintain rhythmicity, while sleep experiments show that CG17777 is required in a third clock cluster (DN1s) to inhibit daytime sleep. Together, this indicates that CG17777 plays different roles in the circadian clock. In the future, we will test if knocking-out CG17777 in different clock neurons lead to changes in sleep and locomotor activity.

Personal StatementI started working at the Rosbash lab in the spring of my sophomore year. I knew instantly that research was for me and it was something that I plan on doing for the rest of my life. This summer, I worked on continuing my research on investigating a candidate neuropeptide called CG17777 and identifying its role in the circadian clock. With the help of the M.R. Bauer Foundation, I was able to stay at the lab and work on a project I am extremely passionate about. I performed various circadian and sleep experiments using CG17777 knock-down flies to understand how their rhythmicity and sleep patterns are different from flies without the CG17777 knock-down. I also learned various new skills like brain dissections, different antibody staining protocols, and microscopy to visualize the clock neurons. I am very grateful to the foundation for giving me the opportunity to expand my knowledge outside the classroom. My experiences this summer have strengthened my passion for research and has driven me to pursue research in the future.

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Kendrick RubinoSengupta LaboratoryDepartment of BiologyBrandeis University

A role for the IFT-A complex in the TUBBY-dependent regulation of cilia membrane composition and cilia morphology in C. elegans

Poster AbstractPrimary cilia are cellular organelles that function as important signaling hubs for the cells to sense their external environment. Abnormal ciliary signaling in humans can cause disorders, termed ciliopathies. Proper ciliary signaling requires that many signaling molecules are trafficked to and within the cilia, but these trafficking mechanisms are not well characterized. The TUBBY family of proteins has been implicated in trafficking ciliary cargo into the cilia, but previous evidence suggests that these proteins function via different mechanisms in different cell types. Based on published work, I hypothesize that the C. elegans TUBBY family member, TUB-1, requires a motor protein adapter called the IFT-A complex to help TUB-1 shuttle ciliary cargo into the cilia. To determine if IFT-A plays a role in TUB-1 function I have shown that mutations in the IFT-A subunit daf-10 phenocopy tub-1 mutant phenotypes. This may suggest that TUB-1 and the DAF-10 subunit of the IFT-A complex function in the same genetic pathways. However, I have also determined that DAF-10 is not required for the correct localization of TUB-1 to the cilia and mutating the presumptive IFT-A binding sites within the TUB-1 protein can only rescue some of the tub-1 mutant phenotypes. Preliminarily, I have established that the human TULP1 construct that lacks a characterized IFT-A binding site shows a different localization pattern than TUB-1.

Personal StatementMy time in the lab this summer has been a great opportunity for me to be able to continue the research I began earlier this year. I was able to pursue the many questions I had in my research project and find conclusions. My time this summer also generated more questions for me to hopefully answer in the future. The Bauer Fellowship also gave me the opportunity to begin work on my senior thesis, which I will be completing over the upcoming school year. Also, this fellowship has given me the opportunity to work on projects that will soon be out for review and eventually published. Over this time in the fellowship, I became a much more confident scientist and I will look back on this fellowship as a time where I was able to gather my own data present it in front of a larger audience.

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Lauren HayashiVan Hooser LaboratoryDepartment of BiologyBrandeis University

Do Lgn Cells in Developing Ferrets Exhibit Directional Selectivity?

Poster AbstractDuring neural development, certain processes are dependent on sensory experience while others are innate. Development of directional selectivity in the primary visual cortex (V1) is an experience-based process, as selectivity is only exhibited post eye opening. The underlying mechanism of this development is yet unknown, and it is uncertain whether it is inherited from earlier points in the visual pathway, such as the lateral geniculate nucleus (LGN). We assess the LGN activity of visually naïve ferrets before and after presenting them with directional training stimuli in order to determine whether LGN neurons also gain directional selectivity from experience. As of now, data suggests that LGN cells are not tuned for orientation or direction.

Commercial 16-channel microwire brush-array electrodes are currently used to collect data, but work is being done to construct carbon fiber electrodes in-lab. This summer, we redesigned the 3D-printed jig that holds the electrode carbon fibers to a three-part model that provides ease when feeding fibers through and fire-polishing. Electrodes have not yet had satisfactory impedance measurements in all 16 channels, and our goal is to increase the number of successful channels before progressing to use in animals.

Personal StatementThis summer has gone by incredibly fast and I have gained so much through working in the Van Hooser lab. Though I officially joined the lab back in January, most of the experiences I had this summer were new, and I really got the chance to see what it would be like to work in a research lab full-time. I witnessed the bond between colleagues as I sat in on discussions about past, current, and future studies. In turn, I became much more comfortable around the other lab members and truly feel I could turn to them for support in my remaining time at Brandeis. This is especially true for my PI, and I have developed more confidence in approaching him for help or advice.

Over the past 10 weeks I was able to dedicate time to lab work in a way that is simply not possible during the school year, and I now have a whole new appreciation for the complexity and breadth of what we are studying. I found many opportunities to challenge myself: in thinking of ways to improve electrode construction, in taking on roles of responsibility during experiments, and in putting together a poster and presenting to fellow scientists and guests. I am so thankful to the M. R. Bauer Foundation for supporting me and my research this summer and allowing me to take full advantage of these opportunities.

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Abigail ZeamerNelson LaboratoryDepartment of BiologyBrandeis University

Cellular Quantification of Age-Related Transgene Silencing in the Mouse Brain

Poster AbstractGene regulation in the brain during sexual maturity is poorly understood. We have observed cell-type specific silencing in a set of tet-enhancer trap lines through loss of GFP expression during sexual maturation. To gain insight into the phenomena observed and potential molecular mechanisms, we identified and measured intensity values of individual cells in the occipital cortex of animals prior to, during and after sexual maturity. We found that cellular intensities and the number of detectable cells decrease with age in a progressive manner. Graded change in GFP expression at the cellular level hints towards the involvement of a dimmer switch-like mechanism in silencing.

Personal StatementMy curiosity has been a driving force since I was a child and would take apart my toys and attempt to rebuild them. In my first year of college, an intro biology class tapped into my curiosity and revealed my true passion, neurobiology. I discovered that complex circuits and pathway logic associated with underlying molecular interactions was incredibly fascinating to me. Throughout the school year, I manage a full-course load, a part-time job and lab work. The M.R. Bauer fellowship has allowed me to dive into my research this summer in a way that would not have been possible without the fellowship. This fellowship has given me the opportunity to explore what it means to truly do research full-time. Through the Bauer Fellowship, I have gained laboratory skills that will aid me in my future scientific pursuits and have been able to conduct research full time.

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Chiquita McCoy-CrispKern LaboratoryDepartment of BiochemistryBrandeis University

Illuminating Evolutionary Landscapes of Ancestral Enzymes Using a Custom Turbidostat

Poster AbstractDirected evolution is a powerful method for creating biocatalysts for use in the synthesis of pharmaceuticals. Engineering enzymes with increased specificity and higher efficiency is commonly practiced, generally successful, and environmentally friendly, but this method is not without limitations as many projects have hit plateaus in kinetic improvement. To combat this issue, we are utilizing ancestral sequence reconstruction (ASR) followed by directed evolution to see if enzymes that have not undergone billions of years of selective pressures are easier to evolve than extant enzymes. As a model system, we have resurrected ancestors of E. Coli adenylate kinase (ADK), an essential enzyme that regulates the concentrations of ATP, ADP and AMP within cells. We are utilizing a custom turbidostat capable of sustaining eight separate cultures at a constant temperature and cell density to grow bacteria containing variants of ADK for long periods of time. High-throughput, next-generation sequencing is being used to monitor the mutational diversity that occurs within the ADK gene when these organisms are subjected to the selective pressure of low temperatures. If these ancestors are able to adapt faster, it would indicate that ASR followed by directed evolution has strong potential in the creation of biocatalysts for drug synthesis.

Personal StatementMy experience in the Kern lab has shown me the value and excitement of research. One of the most fundamental skills I have gained from doing research is perseverance and the ability to stay focused on the goal of scientific discovery. Even though the question my project set out to answer is fairly simple, actually answering it has proven to be incredibly complex. It required the construction of an intricate device, which was a project unto itself and required me to learn a variety of new skills such as soldering, coding, and laser cutting. This showed me that in order to achieve a goal, in science and otherwise, you sometimes have to first create the tools you need.

Working in a lab this summer also compelled me to hone my time management skills and my ability to balance multiple tasks at the same time. I have had to integrate planning experiments in advance with being flexible when unexpected roadblocks occur, as they do quite often. These capabilities have not only made me a more competent scientist but have also translated to many other facets of my life, making me a better critical thinker and problem solver. I am incredibly thankful to have had the opportunity to continue my research this summer, and I will carry the skills I have learned from this experience with me into my future career.

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Alana HodsonWingfield LaboratoryDepartment of PsychologyBrandeis University

False Understanding: Strategies in Reducing Cognitive Effort During Language Processing As We Age

Poster AbstractAging can come with many disadvantages, among them being a decline in cognitive performance. However, even with this decline, language processing, one of the most cognitively taxing tasks, remains remarkably well preserved. Our aim is to investigate strategies, such as “good enough” processing, that may be used by older adults to maintain their high level of performance in language comprehension despite the increase burden on cognitive resources, especially when accompanied by mild to moderate hearing loss. Pupillometry was used to measure the cognitive effort expended by participants as they listened to 160 sentences that varied in syntactic complexity and answered comprehension questions. Preliminary data revealed that while a steady increase in pupillary response occurred for all three groups in the easier end of spectrum of sentence complexity, for both older adult groups the pupil response appeared to level off in the harder conditions. In a follow-up study, we will be further investigating this tail-end response by increasing the range of difficulty of the sentences by adding plausible and implausible conditions.

Personal StatementWhen I was first accepted to Brandeis, I had a clear path in mind — major in neuroscience, go on to medical school, and then become a neurologist. However, within my first few months at Brandeis, I quickly realized that there was a whole other side to neuroscience that I hadn’t considered — research. This area of academia intrigued me, and I joined the Memory and Cognition lab in the summer of my sophomore year.

I was incredibly fortunate to have joined a lab with such supportive and knowledgeable members, and I was taught more than just the basic theories in working memory and cognition. Among the most important, I learned to write code for data analysis, the ethics of working with human participants, the methods of designing an effective experiment, and how to analyze data with a critical eye. With the M. R. Bauer Fellowship, I was able to continue to expand my knowledge of neuroscience research as I designed the study that will become my senior honors research project. The poster on my work, presented at the annual SciFest event at the end of the summer, also granted me the opportunity to learn and practice another crucial skill — how to communicate my research effectively to other people. I’m grateful to the M.R. Bauer Foundation for giving me this opportunity to continue to conduct my research as I now walk down a new path, a path to graduate school and eventually heading my own lab at a university where I can impart my knowledge onto the next generation.

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Michael HsiaoGriffith LaboratoryDepartment of BiologyBrandeis University

Sleep is Essential for Appetitive Operant Learning in Drosophila Melanogaster

Poster AbstractLearning from experience takes place in our everyday lives. In classical conditioning, a neutral stimulus is paired with a reward or punishment, whereas in operant conditioning, a behavior is paired with a reward or punishment. Mutation of genes necessary for neuronal function is capable of disrupting both classical and operant learning. However, the neuronal basis for operant learning is still not yet known, even in simple model organisms like flies. Our approach is to use a Y-shaped maze to train flies to preferentially choose either the left or right arm of the maze when passing through the choice point by rewarding them with sugar each time they choose correctly. Our goal is to get a better understanding of how flies learn, as well as investigate connections between sleep and learning. We found that wild type (CS) flies that sleep early on in training learn significantly better than flies that don’t sleep. Furthermore, we found that wild type flies show a low preference index immediately before a sleep episode and a high preference index after a sleep episode, whereas this did not occur in mutant (dunce) flies known to be deficient in learning. With rising prevalence in mental illnesses such as anxiety disorders, where maladaptive operant learning such as avoidance and escape further worsens the condition, being able to identify the neurons responsible for operant learning could prove to be important.

Personal StatementHaving had the fortune to work in the Griffith Lab for over a year now, I was able to continue with my research over the summer with the help of the Bauer Foundation. Given the preliminary data that we had collected over the semester, our primary goal was to maximize data throughput. What I did in the first couple of weeks was nothing like what I had imagined I would to be doing in the laboratory environment, but nonetheless exciting and worthwhile. We spent days outside in the sun, building boxes in which our apparatus ended up residing. Perhaps not as pleasant of an experience as it sounds, it taught me more than I could ever ask for from a normal laboratory experience, with real life skills that I know I will end up using later on in life. Furthermore, it also fulfilled parts of my former aspiration to become an engineer, even though I have chosen to pursue a different career path. With what we have discovered about learning and sleep in flies, I hope to continue with the project over the semester and more than likely turning it into a thesis project.

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Sam LagesonDizio LaboratoryDepartment of PsychologyBrandeis University

Dyadic Control of a Simulated Inverted Pendulum

Poster AbstractThis experiment was designed to compare individual versus dyadic control of an inverted pendulum model of an unstable system as well as to provide a description of the shared manual interactions that might occur as the balancing task and the degree of shared control were varied. It was hypothesized that three outcomes were possible with respect to stability achieved, namely that individual control would be better than dyadic control, worse than dyadic control, or equal in performance to dyadic control. We designed the experiment to permit observation of how participants adjusted their motor control to stabilize the pendulum when sharing control. A computer-simulated inverted pendulum model was displayed to the participants with two possible difficulties and five possible shared control variations, ranging from full control for one participant to each participant sharing 50% control. We also included four pre- and post- trials where subjects performed alone. After compiling the data, an improvement in performance for both the 50%/50% and the 25%/75% conditions can be seen relative to the conditions in which one of the participants had full individual control over the pendulum. Further analysis is being performed to evaluate the specific manner in which participants controlled the pendulum in order to adapt to the additional input from the other participant that allowed the increase in performance.

Personal StatementThis summer has been a great opportunity for immersing myself in working with my professor and being able to focus solely on my research. Being from Portland, Oregon, I never would have been able to have this experience without the funding provided by the M.R. Bauer Foundation to assist with housing and living expenses. I have able to experience what it is like to do full time research and all that entails from designing the experiment, to getting the necessary paperwork, to then actually performing the experiment and analyzing the results. As much as I have appreciated and enjoyed this opportunity through every minute I am even more grateful for the experience because of how enlightening it has been. This summer has clarified my future career trajectory and I am grateful for the knowledge and understanding that their support has allowed me to gain.

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Acknowledgments

As always, we thank the speakers who came to the Brandeis campus this past year to share their research with us and to engage us in many hours of stimulating discussion and exchanges of ideas with Volen Center faculty, students, and postdoctoral fellows. We are also grateful to our visitors for forwarding to us their lecture summaries that form the basis of this report.

We especially acknowledge Kim MacKenzie, a past neuroscience PhD graduate, for her valuable contributions and editorial assistance in the preparation of this report.

The text of this summary of the Bauer Foundation series, along with summaries from previous years, can be found at www.bio.brandeis.edu/bauer.

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