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 projects may include characterization of species-specific response to metal- induced stresses mediated by horizontally transferred genes; identification of rotifer extrachromosomal DNA forms corresponding to mobile genetic elements; and computational studies of eukaryotic transposons. Students gain experience in microbiology and aquatic culture, DNA/protein extraction and analysis, molecular cloning and biochemical assays, and cutting-edge high-throughput sequencing and bioinformatic methods. They will be co-mentored by the PI and resident research scientists in the lab and 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.
Karen Echeverri, MBL
The Echeverri lab focuses on elucidating the molecular mechanisms of regeneration Our group has two main areas of research; the first is to understand 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 signal and are activated to repair the lesion instead of forming inhibitory scar tissue. We aim to understand how these stem cells are guided to replace the correct number of lost neurons and reconnect the circuits to regain motor and sensory control. The second main focus of the lab is on scar free wound healing. Axolotls regenerate without the formation of scar tissue. Our longstanding work on the “axolotl” salamander, the champion among such species, is identifying critical molecules, regulatory pathways and cellular processes underlying scar-free regeneration. 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 scar free. These findings will pave the way to begin to elucidate regulatory networks necessary to initiate and terminate regenerative growth and shed light on why some species can regenerate and others cannot.
- Project titles:
- Molecular mechanisms of spinal cord regeneration in axolotl
- The role of axon derived signals in regeneration
André Fenton, New York University
The goal of my research is to identify the neurobiological mechanisms of persistent memory storage using approaches that integrate techniques and knowledge across multiple levels of biology. Undergraduate students can expect to understand the advantages and challenges of asking questions about biological mechanisms by simultaneously investigating multiple levels of biology, and have the opportunity to investigate memory persistence by conducting experiments that require techniques in computer-controlled mouse spatial behavior, animal sacrifice, brain removal, and the anatomically-precise tissue sampling required for region-specific transcriptomic and proteomic analyses. The students will have the opportunity to extract RNA from tissues, and single cell classes, and assess the electrophysiological functional properties of synapses within the entorhinal- hippocampus circuit. Students will have the opportunity to perform numerical bioinformatic analyses, to identify and compare correlation networks that are designed to identify the molecular mechanisms of memory persistence by determining the graph-theoretic inter-relationships between measures of memory as assessed by behavior, synaptic physiology, gene and protein expression.
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.
Elizabeth Jonas, Yale University
“Synaptic function, metabolic control and neuronal cell death”. Dr. Jonas’ current research concentrates on understanding synaptic function and neuronal cell death from the point of view of metabolic control, chiefly focusing on 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 2022 we will have two projects. One will focus on the role of mitochondria in learning and memory formation in the hippocampus. The second project will determine if a mutation affecting mitochondria will prevent ischemic cell death in hippocampal neurons during brain ischemia.
Abhishek Kumar, MBL
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
“Nutrients and eutrophication 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, modulate the functioning and health of estuarine habitats. Possible summer projects related to this work could be:
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 stable isotope contents. We plan to survey Ulva specimens in different estuaries of Cape Cod subject to different nutrient loads and characterize their isotopic signatures. We will also conduct laboratory experiments to examine the mechanisms responsible for this shift in isotopic contents.
Does eutrophication increase or decrease salt marsh accretion? – Nutrient enrichment fosters changes in plant productivity, and organic matter accumulation in salt marsh soils, therefore promoting changes in marsh platform vertical accretion. We plan to measure differences in salt marsh elevation in the Great Sippewissett Marsh experimental plots, a long-term (50+ years) salt marsh nutrient enrichment experiment.
Salt marsh vegetation responses to the combined effects of eutrophication and sea level rise – Long-term (50+ years) experimental nutrient enrichment has caused marked shifts in plant community composition in coastal salt marshes. In addition to that, the rates of sea level rise have accelerated in recent decades, and salt marsh vegetation is already displaying negative responses to these stressors. We plan to measure differences in salt marsh vegetation composition and assemblages in the Great Sippewissett Marsh experimental plots.
David Mark Welch, MBL
“Evolution of novel DNA repair and antioxidant defense genes.” The Mark Welch lab uses comparative genomics of rotifers, common marine and freshwater microinvertebrates, to study genome evolution, particularly neofunctionalization, subfunctionalization, and the evolution of novel function. Student projects combine aspects of evolutionary genomics, molecular biology, biochemistry, and bioinformatics. Our current focus is on exploring and characterizing systems involved in DNA repair, antioxidant defense, and redox maintenance in bdelloid rotifers, a group of animals that are highly resilient to desiccation and ionizing radiation, two environmental insults that cause extreme amounts of oxidative damage. Potential summer projects include examining the effect different of environmental conditions on the functions of a group of antioxidant enzymes unique to bdelloids, functional assays of genetically engineered variants of these proteins, and characterizing the function of a novel DNA repair gene.
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 regeneration in the vertebrate central nervous system.” The lamprey is a basal vertebrate that accomplishes full functional recovery (i.e. swimming) after a complete spinal cord injury. This functional recovery is supported by rapid wound healing and repair of the lesion scar, robust axon regeneration, and synaptic reconnections. Projects in the lab are focused on understanding the molecular mechanisms that support successful spinal cord regeneration, with an emphasis on identifying evolutionarily conserved genes and pathways promoting neural regeneration in the vertebrate CNS. Student projects involve a variety of approaches, including but not limited to: bioinformatics, molecular biology, biochemistry, immunofluorescence, and behavior. Ultimately, the goal is to discover relevant genes and pathways that when manipulated could improve CNS repair and regeneration in non-regenerative models and conditions. These studies engage students in a wide range of topics ranging from molecular evolution to conserved mechanisms of cell/tissue regeneration to neural control of behavior.
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.