Plenary Talk

Dr. Alexander Hoffmann, Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences (QCB) and the Department of Microbiology, Immunology and Molecular Genetics, UCLA

Abstract: Cellular responses to stress agents such as inflammatory cytokines or pathogens are mediated by transcription factors that exhibit complex dynamics. I will discuss our recent studies on whether these dynamics represent a signaling code that may specify cellular gene expression responses, and to what extent such a code may be harnessed to achieve greater specificity when targeting pleiotropic signaling hubs pharmacologically, or when identifying prognostic biomarkers to determine the course of treatment.

Faculty Given Talks:
 

1. Zhenbiao Yang

Title: Modeling polar cell growth in unicellular and multicellular plant systems

Abstract:  Plant cells contain high turgor pressure (>1 MPa), and thus cell expansion and cell shape in plants are regulated by the spatiotemporal pattern of the cell wall that encased plant cells.  A dynamic interface between cellular signaling and cell wall is believed to be critical for the regulation of cell expansion and shape formation in plants.  To understand the biochemical and biophysical mechanisms underlying the cytoplasm-cell wall interface, we use tip-growing pollen tubes as a unicellular system and leaf epidermal puzzle-piece shaped cells as a multicellular system.  The former is a good model system for the investigation of polar cell growth and penetrative cell growth into tissue such as penetration of host tissues by fungal pathogens, which also expand via tip growth.  The latter serve as a model for elucidating how cell growth and cell shape are coordinated between cells in a multicellular system by the biochemical-biophysical mechanism for the cytoplasm-cell wall interface.  Our current understanding of both systems by experimental and quantitative approaches will be discussed.

2. Weitao Chen

Title: Data-driven multiscale mathematical models of signaling in the maintenance oftranscription factor distribution in stem cell homeostasis

Abstract: The regulation and interpretation of transcription factor levels is critical in spatiotemporal regulation of gene expression in development biology. However, concentration-dependent transcriptional regulation, and the spatial regulation of transcription factor levels are poorly studied in plants. WUSCHEL, a stem cell-promoting homeodomain transcription factor was found to activate and repress transcription at lower and higher levels respectively. The differential accumulation of WUSCHEL in adjacent cells is critical for spatial regulation on the level of CLAVATA3, a negative regulator of WUSCHEL transcription, to establish the overall gradient. Experiments show that subcellular partitioning and protein destabilization control the WUSCHEL protein level and spatial distribution. Meanwhile the destabilization of WUSCHEL also depends on the protein concentration which in turn is influenced by intracellular processes. However, the roles of extrinsic spatial cues in maintaining differential accumulation of WUSCHEL are not well understood. We develop a 3D cell-based mathematical model which integrates sub-cellular partition with cellular concentration across the spatial domain to analyze the regulation of WUS and stem cell homeostasis in quantitative level. By using this model, we investigate the machinery of the maintenance of WUS gradient within the tissue.

3. Kurt Anderson

Title: Consumer-resource interactions on spatial networks: Dynamics and asynchrony

4. Tamar Shinar

Title: Computational Modeling of Cytoskeletal Phenomena

Abstract: All of the above-ground plant structures observed in higher plants are derived from a set of stem cells that reside within shoot apical meristems (SAM). WUSCHEL, a homeodomain transcription factor, is expressed within the deeper layers of the rib meristem and migrates into the overlying stem cells of the central zone region of Arabidopsis thaliana SAMs to repress the expression of genes involved in promoting differentiation. In order to balance and maintain the overall WUSCHEL gradient in the meristem that contributes to plant stem cell homeostasis, WUSCHEL itself regulates the expression of its negative-regulator, CLAVATA3, in a concentration-dependent manner to repress WUSCHEL expression to the rib meristem. However, even when WUSCHEL repression was lost in clavata3 null mutants, the unexpected low levels of the WUSCHEL protein led to a model where WUSCHEL activates the expression of its own transcriptional and post-translational regulator in a concentration-dependent context. Here we show that CLAVATA3 positively regulates WUSCHEL at the post-translational level, providing a dual role for the CLAVATA3 peptide signaling to negatively regulate WUSCHEL transcription while positively regulating the protein accumulation. At the molecular and subcellular level, we are exploring alternate models where CLAVATA3 likely functions through promoting protein stability or limiting export from the nucleus to increase WUSCHEL protein levels. Additionally, through combined experimental and modeling approaches, we investigate how CLAVATA3 signaling contributes to the regulation and maintenance of the WUSCHEL gradient in the SAM.

Graduate Student Talks: 

1. Alex Plong

Title: Multiscale analysis of the maintenance of WUSCHEL protein gradient

Abstract: All of the above-ground plant structures observed in higher plants are derived from a set of stem cells that reside within shoot apical meristems (SAM). WUSCHEL, a homeodomain transcription factor, is expressed within the deeper layers of the rib meristem and migrates into the overlying stem cells of the central zone region of Arabidopsis thaliana SAMs to repress the expression of genes involved in promoting differentiation. In order to balance and maintain the overall WUSCHEL gradient in the meristem that contributes to plant stem cell homeostasis, WUSCHEL itself regulates the expression of its negative-regulator, CLAVATA3, in a concentration-dependent manner to repress WUSCHEL expression to the rib meristem. However, even when WUSCHEL repression was lost in clavata3 null mutants, the unexpected low levels of the WUSCHEL protein led to a model where WUSCHEL activates the expression of its own transcriptional and post-translational regulator in a concentration-dependent context. Here we show that CLAVATA3 positively regulates WUSCHEL at the post-translational level, providing a dual role for the CLAVATA3 peptide signaling to negatively regulate WUSCHEL transcription while positively regulating the protein accumulation. At the molecular and subcellular level, we are exploring alternate models where CLAVATA3 likely functions through promoting protein stability or limiting export from the nucleus to increase WUSCHEL protein levels. Additionally, through combined experimental and modeling approaches, we investigate how CLAVATA3 signaling contributes to the regulation and maintenance of the WUSCHEL gradient in the SAM.

2. Mikahl Banwarth-Kuhn

Title: Novel subcellular element model of the generation and maintenance of the shape and structure of the shoot apical meristem of Arabidopsis thaliana

Abstract: One of the central problems in animal and plant developmental biology is deciphering how chemical and mechanical signals interact within a tissue to produce the final form, size and function of an organ. Cell walls in plants impose a unique constraint since cells are under turgor pressure and don't move relative to one another. Cell wall extensibility and distribution of stress on the wall contribute to determining rates of cell expansion and orientation of cell division. How cell wall mechanical properties influence cell behavior is still largely unknown. To address this problem, a novel multi-scale computational model of the stem cells of the shoot apical meristem (SAM) of Arabidopsis thaliana is developed and calibrated using experimental data. Novel biologically relevant features of the model include separate representations of the cell wall and cytoplasm as well as a detailed description of cell wall extensibility and average internal cellular pressure.  Model predictive simulations reveal relative impacts of cell wall mechanical properties, chemical signals controlling growth rates, and orientation of division on overall shape of SAM as well as corresponding distribution of internal pressure across stem cells.

3. Kevin Rodriguez

Abstract: Most of the homotypic cis regulatory modules (CRM) characterized so far across systems have been shown to activate transcription of target genes in response to increasing transcription factor (TF) levels. In contrast, our earlier work has shown that the CLAVATA3 (CLV3) enhancer region contains a WUSCHEL (WUS) binding homotypic CRM that activates CLV3 at lower WUS levels and repress at higher WUS levels. To understand how cis-elements collectively mediate a concentration-dependent transcriptional switch, we compared the intrinsic and collective roles of each cis-element. Analysis of reporter expression shows that intrinsically each cis-element can only activate CLV3 at higher WUS levels. However, the collective binding of all cis-elements leads to repression at higher WUS levels and activation at lower WUS levels. To understand the biochemical mechanisms of concentration dependent transcriptional discrimination we are analyzing WUS binding to individual cis-elements, local interactions among neighboring cis elements and long-range DNA looping. In collaboration with the Dr. Blaha’s group, we are working towards determining the structural features of WUS DNA binding and dimerization domains. In collaboration with the Dr. Mohideen’s group, we are employing biophysical methods to understand DNA looping and long range interactions. The combined approaches are expected to reveal the biochemical and biophysical mechanisms of WUS binding to the DNA, and the concentration-dependent transcriptional discrimination.

4. Samuel Britton.

Title: Computational study of remodeling of fibrin networks under compression

Abstract: Fibrin network is one of the major structural components of both physiological blood clots and pathological thrombi. Fibrin fiber mechanics underlie clot stability and macroscopic behavior of clots. Moreover, mechanical and structural properties of fibrin network contribute to clot mechanical stability and determine its deformation under pressure from blood flow. Fibrin polymers in the model to be described in the talk are represented using the Worm-Like-Chain (WLC) approach. The Langevin equations describe the motion of individual nodes. Computational study of dynamical deformations of fibrin networks under compression demonstrate that dramatic remodeling of a clot observed in experiments is based on bending and reorientation of individual fibers as well as on the fiber-fiber non-covalent linkage. Structures of the network used in model simulations are generated from the confocal microscopy images of in vitro fibrin clots. Upon network compression, non-covalent interactions between fibers result in dynamic variation of network architecture. These interactions significantly affect mechanical response of the network at high degrees of compression, ultimately resulting in clot stiffening. Simulation results match experimental data in both fiber linking rates and network densification under different compression rates. Finally, the model is used to predict how stress propagates through the network and how rearrangement and linking of fibrin fibers affects clot stiffening. Finally, the model can be extended for studying deformations of the fibrin-collagen composites.

 5. Nehemiah Zewde

Title: A Computational Model for the Evaluation of Complement System Regulation under Homeostasis, Disease, and Drug Intervention

Abstract: The complement system is an intricate defense network that rapidly removes invading pathogens. Although many complement regulators are present, the impairment of Factor H (FH) regulatory mechanism has been associated with several inflammatory diseases. To understand the dynamics involved in the pivotal balance in regulation, we have developed a comprehensive computational model of the alternative and classical pathways of the complement system. The model is composed of 290 ordinary differential equations with 142 kinetic parameters. We evaluated the state of the system by generating concentration-time profiles of biomarkers C3, C3a-desArg, C5, C5a-desArg, Factor B (FB), Ba, Bb, and fC5b-9 that are influenced by complement dysregulation. We show that FH disorder induces substantial levels of complement activation by generating reduced levels of C3 and FB, and to a lesser extent C5, and elevated levels of C3a-desArg, Ba, Bb, C5a-desArg, and fC5b-9. Furthermore, we introduced therapy states by modeling known inhibitors of the complement system, a compstatin variant (C3 inhibitor) and eculizumab (C5 inhibitor). Compstatin demonstrates strong restorative effects for early-stage biomarkers, such as C3a-desArg, FB, Ba, and Bb, and milder restorative effects for late-stage biomarkers, such as C5a-desArg and fC5b-9, whereas eculizumab has strong restorative effects on late-stage biomarkers, and negligible effects on early-stage biomarkers. These results highlight the need for patient-tailored therapies that target early complement activation at the C3 level, or late-stage propagation of the terminal cascade at the C5 level, depending on the specific FH-mediated disease and the manifestations of a patient’s genetic profile in complement regulatory function.

6. Rohith Mohan

Title: AESOP: A Python Library for Investigating Electrostatics in Protein Interactions

Abstract: Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool as an open-source and multiplatform framework in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association.

7. Bradley Hopp

Title: Investigating scorpion venom resistance in the pallid bat, Antrozous pallidus

Abstract: The pallid bat (Antrozous pallidus), a gleaning bat found in the western United States and Mexico, hunts a wide variety of ground-dwelling prey, including scorpions. Anecdotal evidence suggests that the pallid bat is resistant to scorpion venom, but no systematic study had been performed. We showed with behavioral measures and direct injection of venom that the pallid bat is resistant to venom of the Arizona bark scorpion, Centruroides sculpturatus. Our results showed that the pallid bat is stung multiple times during a hunt without any noticeable effect on behavior. In addition, direct injection of venom at mouse LD50 concentrations (1.5 mg/kg) had no effect on bat behavior. At the highest concentration tested (10 mg/kg), three out of four bats showed no effects. We are following up with increased doses of venom of 20 mg/kg in various populations of bats sympatric or allopatric to Centruroides. Scorpion venom is a cocktail of toxins, primarily activating voltage-gated sodium, potassium, or calcium ion channels to induce intense pain. Dorsal root ganglia (DRG) contain nociceptive neurons and are targets of scorpion venom toxins. To explore the venom resistance of the pallid bat we plan to perform Constellation Pharmacology, a high content screening of DRG neuron responses to a variety of chemicals such as menthol, capsaicin, ATP, etc. Once each cell is tested we can then observe how scorpion venom effects each class of cell and compare to mouse controls. This will lead us to receptors which grant venom resistance.

8. Reed Harrison

Title: Molecular Mechanisms of Macular Degeneration Associated with the Complement Factor H Y402H Single Nucleotide Polymorphism

Abstract: A single nucleotide polymorphism, tyrosine 402 to histidine (Y402H), within the gene encoding complement Factor H (FH) predisposes individuals to acquiring age-related macular degeneration (AMD) after aging. This polymorphism occurs in short consensus repeat (SCR) 7 of FH and results in decreased binding affinity of SCR 6-8 for heparin. As FH is responsible for regulating the complement system, decreased affinity for heparin results in decreased regulation on surfaces of self. To understand the involvement of the Y402H polymorphism in AMD, we leverage methods from bioinformatics and computational biophysics to quantify structural and dynamical differences between SCR7 isoforms that contribute to decreased pattern recognition in SCR7H402. Our data suggests a revised mechanism for decreased heparin binding where transient contacts between a coevolved pair involving Y402 and I412 in SCR7Y402 stabilize the molecule in a conformation that promotes association with heparin. We observe energy minima for sidechains of Y402 and R404 from SCR7Y402 that are predicted to associate with heparin at a rate constant faster than energy minima for sidechains of H402 and R404 from SCR7H402. As both carbohydrate density and degree of sulfation decrease with age in Bruch’s membrane of the macula, the decreased heparin recognition of SCR7H402 may contribute to the pathogenesis of AMD.

9. Holly Andrews

Title: Toward a spatiotemporal model of nutrient cycling in deserts

Abstract: Carbon and nitrogen cycling in deserts is highly heterogeneous in time and space, which may be a reason why global nutrient models tend to perform poorly over desert and other arid regions.  By combining Schlesinger’s “islands of fertility” hypothesis delineating the spatial arrangement of nutrients in deserts with Collins et al.’s pulse dynamics theory explaining desert nutrient fluxes in time, we aim to develop a more accurate spatiotemporal model of nutrient cycling in deserts.  In a well-studied desert in the UC Reserve System, Boyd Deep Canyon (BDC) Desert Research Center, we are tracking carbon and nitrogen pools and fluxes across the extremities of desert conditions in space (under shrub canopies vs. shrub interspaces) and time (peak wet season vs. peak dry season) to ideally capture the maximum amount of heterogeneity in the desert ecosystem.    Preliminary results suggest that fluxes of nitrogen trace gases in deserts vary widely across seasons.  Whereas previous studies at BDC observed dry-season emissions of nitrous oxide rivaling industrial agriculture emissions, we observed small fluxes of nitrous oxide uptake by BDC soils during this most recent wet season (February 2018).  We also observed higher nutrient cycling rates under shrub canopies compared to interspaces, further support for the “islands of fertility” hypothesis.  We look forward to returning to BDC in the 2018 dry season to spatially analyze what we expect to be high carbon and nitrogen emissions.  By capturing these spatiotemporal endmembers of desert heterogeneity, we can better inform future models of nutrient dynamics as well as contributions of ecosystems to climate change.