NSF REU Mentors and Projects
Veronica Martinez Acosta, University of the Incarnate Word, TX: Our laboratory utilizes an annelid 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 overall 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. We have investigated the neuroanatomical and proteomic changes associated with regeneration in Lumbriculus. While we will continue to characterize the regenerative process at the anatomical and proteomic levels, we would like to utilize transcriptomic data to clone and sequence candidate genes for use in genetic expression analyses in real time, including the use of RNA sequencing and in-situ hybridization. Our lab has successfully mentored primarily undergraduate students in the lab. Each student has the opportunity to be trained in confocal imaging, behavioral analysis, protein extraction, and genome level analysis in this unique model system.
Carrie Albertin, MBL: Research Interests: Octopuses are fantastically weird animals: they have flexible, sucker-lined arms, three hearts, blue blood, and skin that can change color and texture in the blink of an eye. They also have the largest invertebrate nervous system, and complex camera-type eyes to rival our own. To better understand how octopuses and their cephalopod cousins, the squid and the cuttlefish, make these amazing and strange bodies, we can dive into their DNA, looking for genes that may be responsible for different features. We can then study how these genes are expressed to better understand their role in building the body plan.
Irina Arkhipova, MBL: "Mobile DNA and horizontal gene transfer in eukaryotic genome function and evolution." Our lab investigates a variety of biological models, including bacteria, fungi, and rotifers. We apply advanced methods in molecular genetics, biochemistry, and bioinformatics to address fundamental questions in evolutionary biology and comparative genomics. Student projects in recent years included expression and purification of domesticated reverse transcriptases from bacteria and construction of their mutant versions; isolation and characterization of mutant strains from a Neurospora mutagenesis screen; studies of in vitro activity of hammerhead ribozyme motifs from rotifers; de novo identification and annotation of transposable elements in sequenced eukaryotic genomes; and studies of non-canonical rotifer methyltransferases. Future independent projects may include identification of extrachromosomal DNA forms corresponding to mobile genetic elements, strain-specific gene expression analysis, or comparative genomic studies of eukaryotic transposons. Prior experience with lab techniques such as basic microbiology, nucleic acid extraction, PCR, and gel electrophoresis is strongly preferred for a wet lab project; students with hands-on bioinformatic and programming skills can choose an independent dry lab project. Students will be fully engaged in the Bay Paul Center and the broader MBL scientific community, participating in lab meetings and in the end-of-summer MBL undergraduate symposium.
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.
Andrew Gillis, MBL: The Gillis lab is an interdisciplinary team of embryologists, physiologists, engineers and palaeontologists, with a shared aspiration to understand the development and evolution of the vertebrate body plan. We work extensively with embryos of cartilaginous fishes (sharks, skates and holocephalans), though our work is very comparative, and incorporates a wide range of emerging and established developmental model systems. Research projects in our lab would fall within one of the following broad areas:
- Development, growth and repair of cartilage: In mammals, cartilage is predominantly an embryonic tissue, forming a model of the future bony skeleton. Cartilage persists permanently in relatively few places within the adult mammalian skeleton (e.g. in the joints, as articular cartilage), and has a very poor capacity for spontaneous repair following injury. Sharks and skates, on the other hand, possess a skeleton that is composed entirely of cartilage, and that remains cartilaginous throughout life. We recently found that skates have the capacity to grow new cartilage throughout adulthood, and to spontaneously repair cartilage injury. Ongoing research in the lab aims to discover the cellular and molecular basis of adult cartilage growth and repair in the skate, to inform new strategies for articular cartilage repair in mammals.
- Diversity and evolution of neuroendocrine cell types: Neuroendocrine cells are a diffuse class of cells that release hormonal signals in response to neuronal input, and thus play a pivotal role at the interface of an organism’s nervous system, physiology and behavior. Vertebrates possess ~40 different neuroendocrine cell types, and these are dispersed among several major organ systems. We are taking a comparative approach to resolve the embryonic origin of neuroendocrine cell types in a range of vertebrate and invertebrate model systems, to test how neuroendocrine cell type diversification relates to life history evolution and anatomical novelty.
- Development and evolution of vertebrate pharyngeal arches: pharyngeal arches are paired columns of tissue that form on either side of the embryonic vertebrate head. In fishes, pharyngeal arches are the precursors of the jaws and gills, and are therefore central to the development of the craniofacial complex. Pharyngeal arches are composed of several embryonic tissue types, and interactions between these tissue types underlie the craniofacial growth and differentiation. Our lab is investigating the molecular basis of these pharyngeal arch tissues interactions, so that we may understand the developmental basis of craniofacial abnormalities, and how changes in pharyngeal arch tissue interactions have contributed to evolution of the vertebrate head.
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: “Rapid adaptive camouflage system of cephalopods.” The Hanlon lab studies sensory systems and behavior in cephalopods involving (i) rapid adaptive camouflage in cuttlefish 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 the gross and fine structure of these skin cells and organs. In the second project, we train octopuses to grab objects, then test chemo 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 in C. elegans embryos. To develop a comprehensive understanding, we are interested in functional imaging and correlating it with structural development of neurons during embryogenesis. This requires fast volumetric imaging of neurons which has been a challenge. The project entails imaging C. elegans embryos 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: Eutrophication and climate change in estuaries, ecology of estuarine plants and algae. Javier is interested in the interactions between human activities in land and their impact on relevant ecological processes in estuaries. Javier studies the sources, distribution and impacts of nutrient pollution and other environmental stressors across coastal ecosystems. He is also interested in how large-scale external drivers, including climate change, alter the functioning and health of estuarine habitats. Possible summer projects related to this work could be:
- Bioaccumulation and impacts of microplastics in estuarine organisms – Microplastics are accumulating in the environment, but the impacts of these particles on estuarine food webs are still unknown. We plan to extract and quantify microplastic particles from a variety of organisms inhabiting local estuaries in Cape Cod. Additionally, we also plan to carry out laboratory experiments using common estuarine invertebrates to determine organismal responses to microplastic exposure.
- Identify nitrogen pollution sources and effects in coastal ponds and assessing effectiveness of mitigation strategies – Nitrogen pollution of coastal ponds is a huge concern for coastal communities in Cape Cod and elsewhere. We will use stable isotopes as tools for identifying the location of watershed derived nitrogen hot-spots and evaluating the effectiveness of some management strategies in local ponds.
- Algal carbon stable isotopes as indicators of coastal eutrophication –When growing under nutrient-rich conditions, the bloom-forming macroalga Ulva displays a very marked shift in both carbon and nitrogen isotopic signatures. We plan to survey Ulva specimens in different estuaries of Cape Cod subject to different nutrient loads and characterize their isotopic signatures.
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: “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 lamprey is a basal vertebrate that possesses large neurons and synapses that are amenable to the study of synaptic transmission using a variety of molecular, imaging, physiology, and behavioral approaches. Current projects in the lab are focused on understanding the cellular and molecular mechanisms that support synaptic transmission under normal physiological conditions, as well as after disturbances such as injury or diseases. Students may engage in experiments of biomedical relevance, including mechanisms of axon and synapse regeneration after spinal cord injury. Other projects are focused on understanding how synaptic transmission is affected by Parkinson’s disease and how to correct the associated synaptic deficits. 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 and evolution, 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.
Loretta Roberson, MBL: “Understanding the mechanisms of calcification in corals and their responses to environmental stressors.” Despite the importance of coral reefs to tropical, marine ecosystems, the biological components of the calcification process are poorly understood. Evidence suggests that corals regulate the movement of ions such as bicarbonate, calcium, and hydrogen to facilitate calcification and that some species are more tolerant of changes in their environment, yet the mechanisms behind these important processes and their molecular components are unknown. In particular, the details of how the symbiotic dinoflagellates (Symbiodinacea) enhance calcification and their role in skeleton formation have not been identified to date. As threats such as climate change increase, understanding the mechanisms underlying coral calcification, and coral response to environmental change will be critical for the conservation of these fragile ecosystems. Interdisciplinary, multi-scale studies are therefore necessary to link molecular level changes to organismal and reef performance. For this study, students will be able to participate in and develop projects that include: population demographics of corals from Puerto Rico and Woods Hole, understanding temperature tolerance in temperate corals, the impact of environmental stressors on coral health and bleaching, changes in gene expression in response to environmental stressors, identification of genes involved in calcification, development of techniques for microscopic imaging of live corals and algal symbionts, developing treatments to enhance coral resilience to stress, and use of macroalgae to improve water quality on reefs.
Joshua Rosenthal, MBL: The central dogma of biology maintains that genetic information passes faithfully from DNA to RNA to proteins; however, with the help of diverse tools, sometimes it is modified within messenger RNA. RNA editing by deamination of adenosine to inosine (A-to-I) is a process used to alter genetic information. Unlike alternative splicing, which shuffles relatively large regions of RNA, editing targets single bases. Because inosine is interpreted as guanosine during translation, this process can recode codons. A-to-I RNA editing is catalyzed by the ADAR (adenosine deaminase that acts on RNA) family of enzymes. All multicellular animals, from cnidarians to mammals, express ADARs, but the extent to which they use them to recode is generally limited. In fact, transcriptome-wide screens have only uncovered about 25 conserved recoding RNA editing sites in mammals, and several hundred in Drosophila. These studies have led to the general assumption that recoding by RNA editing is extremely rare. Recent studies in my lab show that cephalopods break the rules. In fact, the behaviorally sophisticated Coleoids (squid, octopus and cuttlefish) edit the majority of their messenger RNAs. This ability to alter genetic information on the fly is an intriguing innovation. We know that it is happening at unprecedented levels, and that it is used primarily in the nervous system to alter proteins directly involved in neuronal signaling. Projects in my lab focus on five basic themes: 1) what are the mechanistic underpinnings of high-level RNA editing in cephalopods; 2) how does RNA editing affect protein function and electrical signaling; 3) does RNA editing respond to environmental factors, particularly those that are being affected by human activities; 4) how do RNA editing sites evolve. Students will be exposed to genome engineering, molecular biology, synthetic biology, cell physiology, and the bioinformatics associated with large DNA sequence data sets.
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).