The Beckman Mentors: Description of Research Projects
Ball Laboratory: Metal-Catalyzed Incorporation of Sulfur Dioxide into Organic Molecules. The Ball Laboratory is interested in developing new metal-catalyzed/-mediated organic reactions. Our focus is to develop methodologies to make and activate sulfur(VI) fluorides. In particular we are interested in using sulfur (VI) fluorides as a more air and water stable alternative to traditional synthesis of sulfur-based organic molecules. Our strategy is to achieve this goal by metal-catalyzed activation of sulfur(VI) fluorides via sulfur-fluorine exchange (SuFEx) to make sulfonylated compounds. Additionally, we have interest in sulfur (VI) fluorides in cross-coupling chemistry.
Our research involves a two-step strategy: 1) development of new catalytic reactions, and 2) mechanistic investigations of these reactions with model organometallic complexes. Experiments and results from each component facilitate the innovation in the other providing an impactful, deeper understanding of the chemistry. The goals of this research for students is to learn how to turn theory into practice, to critically work through scientific challenges, and to understand and take ownership of their work. Most importantly, I want students to appreciate and develop a love for science!
Students will gain extensive experience in organic and inorganic synthesis, metal catalysis, NMR spectroscopy, and physical organic chemistry. Students with a wide variety of interests are welcomed into our lab! Please explore the links to learn more about the Ball Lab. Research theballlab.com
Our research involves a two-step strategy: 1) development of new catalytic reactions, and 2) mechanistic investigations of these reactions with model organometallic complexes. Experiments and results from each component facilitate the innovation in the other providing an impactful, deeper understanding of the chemistry. The goals of this research for students is to learn how to turn theory into practice, to critically work through scientific challenges, and to understand and take ownership of their work. Most importantly, I want students to appreciate and develop a love for science!
Students will gain extensive experience in organic and inorganic synthesis, metal catalysis, NMR spectroscopy, and physical organic chemistry. Students with a wide variety of interests are welcomed into our lab! Please explore the links to learn more about the Ball Lab. Research theballlab.com
Cavalcanti Laboratory: Computational analysis of ciliate evolution. Ciliates are unicellular eukaryotes that present nuclear dimorphism. We use computational simulations and mathematical modeling to study how this nuclear organization evolved and what are the consequences of this unique nuclear organization on the evolution, population dynamics, and aging of these organisms. A second project involves the study of fusion genes in eukaryotic genomes. We have developed software to detect fusion genes in sequenced genomes and are currently identifying and characterizing novel fusion genes in multiple genomes. Finally, my lab is involved in several microbiome projects to characterize the microbial communities in different environments, like hot springs, mud volcanoes, soils and rivers.
Crane Laboratory: Mechanisms of microbial elemental sulfur reduction at the community, cellular and enzymatic levels. Sulfur-based respiration has been proposed to be one of the earliest energy conserving pathways for life on earth, and the pathway remains important to the sulfur and other elemental cycles in oceans, the atmosphere, sediments and the deep subsurface. It is also of specific interest in petrochemical and other fields due to the extremely corrosive and toxic effect of microbially-produced sulfides. The mechanisms of microbial sulfur respiration have, however, only begun to be understood, and their contribution to sulfur cycling overall has been almost entirely overlooked. It is not at all clear which forms of sulfur contribute to this metabolism in situ or how, mechanistically, these enzymes carry out this transformation. The relative levels of sulfur-reducing enzymes and microbes in many environments remain unknown. These overarching questions will be approahced by focusing on a specific environment – a deep, hot hydrocarbon-rich reservoir – and integrate studies 1) at the level of the microbial community by characterizing the microbes in the deep, hot subsurface environment and identifying sulfur-reducing microbes and enzymes through metagenomic and metatranscriptomics, 2) at the enzymatic level by determining the mechanisms of sulfur-reducing enzymes by kinetic and structural techniques, and 3) at the geochemical level by using cyclic voltammetry to determine the chemical speciation of sulfur in situ and during reduction by microbes and enzymes. Each aspect of these studies depend on and drive each other.
Garza Laboratory: In Silico Studies for Prediction of Energy Transfer Reactions and Receptor-Ligand Interactions. Our lab utilizes a series of computational techniques, in connection with experimental results, to study two main areas. The first one is the study of diffusion-controlled reactions on catalytic surfaces with Euclidean or fractal surfaces to study energy transfer. An example is our study in dendrimer structures, which are novel systems, used in pharmaceuticals and energy storage. The second area of study in our lab is the prediction of binding-conformation of small ligands to appropriate target binding sites in a receptor. We complement the results of these simulations with molecular mechanics and/or molecular dynamics to estimate the strength of the intermolecular interactions between these small molecules and their biological targets. Some of these receptors or biological targets are responsible for specific neurological disorders (Alzheimer’s) and cancers (leukemia).
Glater Laboratory: Recognition of Natural Odor Blends and Neuronal Circuitry. In our laboratory, we study the neuronal circuitry underlying decision-making behavior in the free-living nematode, C. elegans. Specifically, we examine the preference of C. elegans for complex food odors and how genetic background and environment modify these preferences. Although a lot is known about how C. elegans responds to different pure odors, less is known about how C. elegans recognizes and discriminates among complex mixtures of volatile chemicals released by bacteria, their major food source. Does C. elegans use a single odorant or a bouquet of odorants to distinguish among different species of bacteria? We are identifying the attractive and repulsive odorants released by bacteria found in the natural habitat of C. elegans using solid-phase microextraction gas chromatography-mass spectrometry (SPME–GC-MS) in collaboration with Charles Taylor (Chemistry Department, Pomona College). We are also examining the neural machinery underlying bacterial preference among a diverse set of bacterial species found in the natural environment of C. elegans. Although the neurons required for the detection of specific food-odors have been well-defined, less is known about the sensory circuits underlying the discrimination among the mixtures of odors released by bacteria.
Johal Laboratory: Dual Polarization Interferometry (DPI) and Quartz Crystal Microbalance (QCM-D) Analysis of Ligand-Protein Interactions at the Solid-Aqueous Interface. The underlying theme of our research program is to take advantage of molecular self-assembly processes to construct functional nano-materials for optical and biosensing applications. Our research program primarily explores the electrostatic self-assembly (ESA) of novel polyelectrolytes, biological macromolecules, and ionic surfactants using layer-by-layer (LbL) methods, including direct adsorption and spin-assembly, to fabricate well-defined multilayer assemblies. Current work focuses on characterizing protein-drug and membrane-peptide antibiotic interactions at the solid-liquid interface, by using DPI and piezoelectric gravimetric QCM-D methods.
Johnson Laboratory: Molecular mechanisms of function of Syndecan. To build a functional nervous system, neurons must extend axons and build synaptic connections. The heparan sulfate proteoglycan (HSPG) Syndecan (Sdc) regulates axon guidance at the central nervous system midline by facilitating high affinity Slit/Robo interactions. In addition, Sdc works with the phosphatase LAR to control synapse formation at the neuromuscular junction. We determine how Sdc regulates CNS development by characterizing the interaction between Sdc and other HSPGs, conducting a structure/function analysis of Sdc in vivo, identifying binding partners for the cytoplasmic domains of Sdc, and elucidating the function of genes that interact with Sdc.
Karnovsky Laboratory: Students in my lab are engaged in ecological research focused on understanding anthropogenic impacts on the distribution, abundance and behavior of vertebrates. Recent research has included studies in the Arctic, the Bernard Field Station, and other areas in Southern California. We carry out research to answer questions such as 1) how are warmer temperatures impacting Arctic seabirds? 2) How are introduced species influencing native Western pond turtles? 3) How are windows and light pollution impacting migratory birds? 4)To what extent are Laysan albatross consuming plastic pollution in the Pacific Ocean? Research in my lab is highly collaborative with partners on campus, in the community, and abroad.
Liu Laboratory: Professor Liu’s research interests span three areas that all intersect chemistry and biology. (1) She investigates the persistence of Vibrio cholerae, the causative agent of cholera disease. An objective of this work is to elucidate the molecular mechanisms by which fluctuations in available sugars affect the physiology of V. cholerae. (2) Dr. Liu also aims to engineer novel biosensors. An objective of this work is to engineer riboswitch-based biosensors to monitor intracellular concentrations of endogenous small molecules. (3) Dr. Liu also engages students in discipline-based educational research, investigating how students learn chemistry and biochemistry.
Martinez Laboratory: Biology of ageing in Hydra. We are currently studying a species of Hydra, H. oligactis, which can be induced to age by exposure to low temperatures. One remarkable outcome was the discovery that aging in H. oligactis is reversible. These ‘revertant’ animals, are somehow able to escape the aging process and live indefinitely. We have been employing next- generation sequencing technologies to study aging in Hydra. We aim to sequence the transcriptomes of revertant (immortal) and non-revertant (mortal) Hydra, to identify what genes are allowing some individuals to escape the aging process and become immortal.
Meyer Laboratory: Students in my lab address a variety of ecological questions. However, most of my research is focused on understanding how to preserve biodiversity and ecosystem functioning in two biodiversity hotspots: southern California and Hawaii. Current research efforts are primarily focused on: (1) identifying important food resources for endangered Hawaiian land snails to enhance restoration and lab rearing efforts, (2) understanding factors that contribute to or prevent the re-establishment of the endangered sage scrub ecosystem following fire events, and (3) exploring how habitat modifications and fragmentation influence biodiversity and ecosystem services. However, I am open to students exploring questions not directly related to my primary research foci. For example, I have an on-going student-designed project examining how to best restore Mohave desert communities.
Negritto Laboratory: Our laboratory studies genome maintenance mechanisms, particularly mechanisms involved in the repair of double strand breaks and how these can affect genome instability.
Olson Laboratory: Development and Formation of Nematode Egg Shells. Our research focuses on the use of the nematode worm C. elegans, a roundworm, as a model organism to study how protective barriers form around embryos by using fluorescence microscopy, biochemistry, molecular biology and genetic approaches. Findings from this study could shed light on the early embryonic development in other species, including mammals. Another goal is to identify new drug targets to fight parasitic roundworm infection in humans, plants and animals. Parasitic worms affect people in developing countries in Africa, Central and South America and Southeast Asia. Their infections are a major burden that cause loss in agriculture, sickness in humans and loss of productivity. If we can figure out how the worm’s eggshell is built, we can also figure out how to destroy it in the parasitic worms.
Parfitt Laboratory: Our lab studies changes in synaptic transmission and memory that occur with Alzheimer’s Disease (AD). Many Alzheimer’s labs focus on the deleterious effects of beta amyloid (Aβ), a protein that is produced in excessive amounts in the Alzheimer’s brain. Excessive Aβ production leads to much less production of the protein secreted amyloid precursor protein-alpha, or sAPPα, because Aβ and sAPPα are made from the same precursor protein. Alzheimer’s patients have low levels of sAPPα, which is unfortunate because sAPPα has neuroprotective properties and can enhance neurogenesis. In a mouse model of AD, virus-mediated gene transfer of sAPPα can prevent development of memory deficits and can improve synaptic long term potentiation (LTP), a cellular model for memory. Furthermore, sAPPα can reverse LTP deficits when administered long after the deposition of beta amyloid (Aβ) plaques. We are currently studying the effects of drugs that enhance sAPPα concentrations in the mouse brain, or using shorter versions of the sAPPα protein, with an eye toward potential therapies for AD in humans.
Sazinsky Laboratory: Microbial Sulfur Metabolism & Protein Engineering. Our lab utilizes protein crystallography, enzymology and recombinant DNA technologies to study, engineer and predicrt protein function. Current efforts aim to explore (i) the reactivity and mechanism of enzymes involved in microbial sulfur respiration and biogeochemical sulfur cycling in collaboration with Professors Crane and Cavalcanti, (ii) glycosyl hydrolases that improve the bioavailability medicinally important natural compounds by removing rhamnose modifications, and (iii) machine learning as a means to predict sequence and structures of antibodies that target newly emerging antigens as a rapid response to pathogens. The latter project is in collaboration with researchers at KGI.
