NSF REU Mentors and Projects

LIST OF PARTICIPANT MENTORS AND THEIR PROJECTS

Veronica Martinez Acosta, University of the Incarnate Word, TX: Research/Projects: Overall, my laboratory research utilizes a unique invertebrate model system, Lumbriculus variegatus, to study wound healing and regeneration within the central nervous system (CNS). Lumbriculus is capable of regenerating an entirely new worm from a fragment that is 1/50th the size of the original animal. Perhaps what sets Lumbriculus apart from other regenerating model systems is the ability to recover neural anatomy, physiology, and behavior following injury along any portion of the anterior-posterior body axis. Our overarching laboratory goal is to identify the cellular and molecular events triggered as a result of injury within the central nervous system (CNS) which promote regeneration and recovery of function versus deterioration. Most recently we have investigated the neuroanatomical and proteomic changes associated with regeneration in Lumbriculus. We have long focused on the basic cellular, physiological, and proteomic changes occurring in the regenerating worm fragment. Our current research focus is the investigation of regeneration and wound healing using traditional microscopy techniques, including transmission electron microscopy and fluorescence microscopy methods; proteomic approaches; and genetic approaches, in situ hybridization chain reaction. Ultimately, we would like to determine more precisely the location and timing of expression of specific signaling pathways triggered following wound formation in a system that is committed to successful regeneration and recovery of function.

Carrie Albertin, MBL: Research/Project: The Albertin lab studies how novelty arises over the course of evolution and development using cephalopods (squid, cuttlefish, and octopus) as models. We use diverse approaches, including comparative genomics, gene expression analyses, imaging, and functional genomics to study how developmental programs evolve. Projects in the lab include studying the expression and function of ancient developmental control genes (e.g. Hox genes and other transcription factors, as well as signaling ligands) in setting up cephalopod body plans and their nervous systems. We also study the function of cephalopod-specific genes in cephalopod genomes and the development and function of cephalopod novelties. Through these projects, we train students in basic molecular biology techniques (e.g. PCR, nucleic acid isolation and handling), staining (e.g. in situ hybridization, immunohistochemistry), confocal microscopy, image analysis, comparative genomics, phylogenetics, embryo handling and animal care, and experimental design.

Irina Arkhipova, MBL: Research/Project: Dr. Irina Arkhipova is a molecular evolutionary geneticist with a background in biochemistry and molecular biology. Her research deals withmobile DNA in its broader sense, including different types of transposable elements (TEs) that can move within and between genomes, their genomic impact, genetic and epigenetic regulation, evolutionary origins, and the mechanisms underlying their mobility.It is often driven by discoveries that were initially made in, but which are likely to have broader implications for eukaryotes in general. Her current research is focused on horizontally transferred genes, recruitment of transposable elements to perform host functions, and non-canonical mobile genetic elements. The overarching goal of her research is to obtain an integrated picture of mobile element structure, function and evolution, encompassing the widest spectrum of their interactions with host genomes, from deleterious to neutral to beneficial.

Scott Chimileski, MBL: Scott is a Research Scientist who works with Associate Scientist Jessica Mark Welch at the MBL. He is investigating structured microbial communities known as biofilms, formed by bacteria within the healthy human mouth (the oral microbiome), where hundreds of bacterial species live and interact. His research focuses on using advanced microscopy approaches to visualize the spatial organization of bacterial species within biofilms. Projects will work towards creating a new system for differentiating multiple species of bacteria from the human oral microbiome within living biofilms.

Karen Echeverri, MBL: Research/Project: “Molecular mechanisms of nerve regeneration” The lab focuses on: 1) understanding at the molecular and cellular level how salamanders can regenerate a fully functional spinal cord after injury. In particular, we focus on how the neural progenitor cells react to an injury and are activated to repair the lesion instead of forming inhibitory scar tissue. 2) identifying critical molecules, regulatory pathways and cellular processes underlying scar-free regeneration in the “axolotl” salamander. We use transcriptional profiling and in vivo imaging to understand which cells respond to the injury signal, what the potential of these cells is and where cells come from to heal the wounds. 3) evolution of regenerative ability. The sea anemone, Nematostella vectensis is used to elucidate and compare regulatory networks between invertebrates and vertebrates. Students will learn how to modulate and monitor pathways in vivo in live animals, by using antibody staining, in situs and fluorescence imaging. (2 students / 2 papers).

Kristin Gribble, MBL: In many animals, offspring from older mothers have shorter lifespan, lower reproduction, and decreased health than do offspring from young mothers. The cellular and molecular causes of these maternal effects on offspring are not understood, however. Our lab uses rotifers (microscopic, aquatic invertebrates) to study how a mother’s age and environment affects her offspring’s phenotype. We investigate the potential epigenetic and mitochondrial mechanisms of intergenerational and transgenerational inheritance. Potential projects in our lab include (1) investigating the effects of maternal age on offspring mitochondrial function, health, and reproductive success; (2) comparing maternal age effects on male and female offspring; and (3) examining differences maternal investment in offspring from young and old mothers. Students will learn to culture phytoplankton and zooplankton, measure hatching rate and lifespan, and will use microscopy, molecular biology, respirometry, and biochemistry methods.

Roger Hanlon, MBL: Research/Projects: “Rapid adaptive camouflage system of cephalopods.” The Hanlon lab studies sensory systems and behavior in cephalopods involving (i) rapid adaptive camouflage & communication in cuttlefish, squid and octopus and (ii) sensory capabilities of the octopus’ arms and suckers in relation to their peripheral vs. central brain control. The first system includes visual perception of backgrounds to determine which camouflage pattern to deploy; and a motor output system that produces a camouflaged body pattern. Behavioral experiments provide the experimental bioassay, and image analyses of the resultant camouflage body pattern provide a quantifiable proxy for motor output and pattern design. There is a refined neuromuscular control system of tens of thousands of pigmented chromatophore organs and iridescent cells in the skin to form the patterns, and we study these extraordinarily unique neuroanatomical and bio-optical mechanisms of dynamic pigmentary and structural coloration.

In the second project, we train octopuses to grab objects, then test chemical and tactile sensing of suckers by applying different textures and tastes to the object and perform neuroanatomical and neurophysiological studies of the arm and suckers. Students are exposed to neurobiology, sensory biology, anatomy, image analysis and ethology. In the broader context, students read experimental and theoretical papers related to this system, and discuss them in the context of their experiments to ensure that they understand why they are conducting these experiments, as opposed to solely learning how to conduct the experiment.

Marko Horb, MBL: “Genome editing in Xenopus”. Advances in genome editing have made it possible to generate mutant animals in almost any organism. The current focus of the Horb lab is to create Xenopus mutants to model human disease using CRISPR-Cas. Undergraduate students will be given the opportunity to create an F0 Xenopus mutant using CRISPR-Cas as well as learn to work with Xenopus embryos, including embryological and molecular biology techniques. Students will learn to navigate the Xenopus genome, identify specific target sites for generating mutants, inject Xenopus embryos and genotype the resulting embryos. Students should expect to learn, in detail, about genome editing and its applications.

Abhishek Kumar, MBL: Projects include:

Using advanced line-scanning confocal microscope to image cleared mouse brain

Many complex questions in neuroscience necessitate interdisciplinary collaborations to take advantage of advanced imaging technology and image analysis approaches. This project aims to utilize a home-built fast line-scanning confocal microscope for cleared whole brain imaging. Additionally, it involves use of custom designed image stitching, denoising and deblurring algorithms for image augmentation and analysis.During the progression of this project,students will learn about cutting edge home built line-scanning confocal and lightsheet microscopy and develop necessary skills in imaging and image analysis. Additionally, there will be opportunities to learn scientific computing for analyzing optical images.

Functional imaging during embryogenesis of C. elegans

We are interested in understanding the wiring of the brain inC. elegansembryos. To develop a comprehensive understanding, we are interested in functional imaging and correlating it with structural development of neuronsduring embryogenesis. This requires fast volumetric imaging of neurons which has been a challenge. The project entails imagingC. elegansembryos using a home-built dual-view lightsheet microscope and computationally fusing two views for better visualization of neurodevelopment.During the progression of this project,students will learn about cutting edge lightsheet microscopy and develop necessary skills in imaging and image analysis. Additionally, there will be opportunities to learn scientific computing for analyzing optical images.

Javier Lloret, MBL: Research/Project: Dr. Javier Lloret is an ecosystem scientist with a background in marine sciences, ecology and hydrology. His research focuses on the ecology and biogeochemistry of coastal wetlands and estuaries. Elucidating controls on coastal ecosystem functioning is critical because wetlands and estuaries play disproportionally important roles in the global cycling of elements such as carbon and nitrogen.Disturbances derived from the human occupation of the coast, overexploitation of natural resources, and pollution by excess nutrients and other substances, fundamentally alter how estuaries and wetlands function, and threaten the provision of valuable ecosystem services. Lloret is particularly interested in how these alterations are affecting and are affected by climate change. He uses a combination of field work, laboratory, mesocosm and landscape scale experiments, innovative biogeochemical tracers, and ecosystem modeling approaches to quantify pathways, transformations, and fate of pollutants in wetland and estuarine habitats, and evaluate the effects of human disturbances. He hopes to produce research that informs management and could help design better environmental policies.

Allen F. Mensinger, University of Minnesota at Duluth: “Multi-modal sensory integration in the toadfish.” The PI focuses on the neural mechanisms of behavior using the marine toadfish, Opsanus tau. He is investigating multi-modal sensory input of the auditory system and mechanosensory lateral line. Undergraduate students will be exposed to a wide range of skill sets before embarking on independent projects, including animal behavior, video imaging and analysis, microelectrode fabrication, neurophysiological data acquisition, neuroanatomy and histology. The student’s project may include: 1) Relative contribution of canal and superficial neuromast to sound localization: Students test female fish with intact or partially ablated lateral line during phonotaxis experiments. 2) Central projections of the lateral line and utricle: Students use neural tracers to label the lateral line and auditory nerves to determine if and where there is overlapping input in the brain. 3) The relative contribution of the auditory system and lateral line during sound localization. Students will record and analyze neural activity from fish with chronically implanted electrodes during sound presentation.

Jennifer R. Morgan, MBL: Research/Project:“Mechanisms of synaptic transmission in the vertebrate central nervous system.” Reliable neuron-to-neuron communication, or synaptic transmission, is fundamental to all nervous system functions, including movements, sensations, learning and memory, emotions, and cognition. The Morgan lab studies synaptic transmission using the lamprey as a model organism. The sealamprey (Petromyzon marinus) is a basal vertebrate that possesses large neurons and synapses that are amenable to the study of synaptic transmission using a variety of biochemical, imaging, physiology, and behavioral approaches. Current projects in the lab are focused onunderstanding the cellular and molecular mechanisms that support synaptic transmission under normal physiological conditions, as well as after disturbances such as injury or diseases, and during axon regeneration. These studies engage students in a wide array of topics ranging from basic cell and molecular biology to regenerative biology.

Nipam Patel, MBL: Currently the research of the lab focuses in three main areas: The role of Hox genes in arthropod development andevolution, the ability of Parhyale to regenerate its germline, and structural coloration and transparency in butterflies. Students would employ methods such as CRISPR genome editing, HCR in situ analysis, and confocal microscopy to address questions in one of these three areas. More information to follow regarding current projects.

Blair Paul, MBL: Research in the Paul Lab centers on understanding the significance of microbial genetic variation and hypermutation in shaping symbiotic interactions and response to environmental stress. We are also developing experimental approaches to determine functions and selective pressures that can be linked with dynamic processes in microbial genomes of bacteria and archaea. To this end, we apply a combination of computational, molecular, and geochemical tools to study molecular phenomena in microbes from a range of aquatic environments. Current projects in the lab include i) exploring the potential for adhesion/attachment proteins of viruses or microbial symbionts to be used as bait for enrichment and isolation of uncultivated hosts; ii) understanding the eco-evolutionary importance of hypermutation in aquatic bacteria and developing a model system for accelerated protein evolution.

Kate Rawlinson, MBL: Research/Project: The research of my lab focuses on the development, neurobiology and biological rhythms of parasitic and marine flatworms that impact human health and interests. We are currently working on the sensory biology and biological rhythms of the human blood flukeSchistosoma mansonito understand infection and host-parasite interactions. Students will learn techniques to investigate the expression of genes and proteins using immunofluorescence, in situ hybridization and imaging, as well as animal care and safe handling of parasites.

Loretta Roberson, MBL: Research/Project: I am interested in how organisms respond to anthropogenic impacts on coastal marine systems as well as ways to help mitigate or reduce those impacts. As more and more people move to coastal areas and global processes influence local conditions, more pressure is placed on these systems, often with devastating results like the. My lab has two main focus areas: (1) use of macroalgae as biomass for sustainable biofuel, valuable bioproduct production, biodiversity enhancement, and bioremediation and (2) understanding the mechanisms of calcification in corals and the role of symbiosis in response and resilience to climate change.

Joshua Rosenthal, MBL: Research/Project: The central dogma of biology maintains that genetic information passes faithfully from DNA to RNA to proteins; however, RNA editing by deamination of adenosine to inosine (A-to-I) alters genetic information. Unlike alternative splicing, which shuffles relatively large regions of RNA, the editing targets single bases. All multicellular animals, from cnidarians to mammals, express the underlying RNA editing enzymes (ADARs), but the extent to which they use them to recode is generally limited. Transcriptome-wide screens have only uncovered ~25 conserved recoding RNA editing sites in mammals, and several hundred in Drosophila. These studies have led to the assumption that recoding by RNA editing is extremely rare. My lab has shown that cephalopods break the rules and edit the majority of the messenger RNAs in their brains. This ability to alter genetic information is an intriguing innovation, is happening at unprecedented levels, and is used primarily in the nervous system to alter proteins directly involved in excitability. Projects in my lab include: 1) the use of CRISPR-Cas9 coupled with biochemical and cellular biology to explore the mechanistic underpinnings of high-level recoding in cephalopods; 2) the use of electrophysiological approaches to study how RNA editing affects protein function and electrical signaling; 3) the use of deep sequencing and computational approaches to study how RNA editing respond to environmental factors, particularly those that are being affected by human activities; 4) the use of evolutionary theory to understand how RNA editing sites evolve. To support these activities, the Rosenthal Lab is heavily invested in developing genetically tractable cephalopod research organisms.

S. Emil Ruff, MBL: Research focuses on microbial interactions and population dynamics as drivers of community function. To disentangle microbial food webs, Emil mainly studies ecosystems with reduced complexity, such as natural or laboratory enrichment cultures, microbial blooms or extreme habitats. His work has improved our understanding of the sources and sinks of the greenhouse gas methane in seafloor ecosystems and groundwater aquifers. Currently, he is investigating the effect of bioirrigation on the removal of methane from wetland sediments. More information to follow regarding current projects.

Michael Shribak, MBL: Research of the Shribak lab is focused on development of advanced light microscopy and computation imaging techniques, which should serve as advanced tools for biological discoveries and would answer to the live image challenges. More information to follow regarding current projects.

Mirta Teichberg, MBL: Research focuses on the response of aquatic macrophytes, including seagrass and macroalgae, to abiotic and biotic stressors in their environment and impacts on community structure and ecosystem function. Projects also include applied research on seagrass restoration to increase recovery of shallow water systems and restore ecosystem functions as well as to explore potential use for nature-based solutions.

The following mentors are visiting scientists. They have all mentored REU students previously. However, as the REU applications are processed prior to visiting scientist applications, we cannot guarantee they will be in residence in 2023.

Elizabeth Jonas, Yale University: “Synaptic plasticity, developmental and degenerative disease”. Dr. Jonas’ current research concentrates on understanding how mitochondria regulate synaptic function and decline; the lab focuses on normal neuronal development and synaptic plasticity (memory formation) and mechanisms of mitochondrial dysfunction in synapses within neurons undergoing developmental and neurodegenerative brain disorders. Projects in the laboratory for summer students have included measuring ATP levels in isolated hippocampal neurons using a FRET construct; measuring mitochondrial membrane potential; measuring Ca2+ uptake by mitochondria; immunocytochemistry to localize mitochondrial interacting proteins; use of specific therapeutic reagents to regulate mitochondrial function; measurements of synaptic plasticity in the setting of alterations in mitochondrial function; measurements of synaptic vesicle numbers and localization during synaptic plasticity. This summer of 2023 we will have two projects. One will focus on a mouse that has a mutation in the ATP synthase that makes ATP synthesis more efficient but that may derail normal brain development. The second project will focus on single molecule fluorescent imaging of ATP synthase in living neurons undergoing synaptic plasticity (stimulation of memory formation).