63 research outputs found
A functional Bucky ball-GFP transgene visualizes germ plasm in living zebrafish
No full textIn many animals, the germline is specified by maternal RNA-granules termed germ plasm. The correct localization of germ plasm during embryogenesis is therefore crucial for the specification of germ cells. In zebrafish, we previously identified Bucky ball (Buc) as a key regulator of germ plasm formation. Here, we used a Buc antibody to describe its continuous germ plasm localization. Moreover, we generated a transgenic Buc-GFP line for live imaging, which visualizes germ plasm from its assembly during oogenesis up to the larval stages. Live imaging of Buc-GFP generated stunning movies, as they highlighted the dynamic details of germ plasm movements. Moreover, we discovered that Buc was still detected in primordial germ cells 2 days after fertilization. Interestingly, the transgene rescued buc mutants demonstrating genetically that the Buc-GFP fusion protein is functional. These results show that Buc-GFP exerts all biochemical interactions essential for germline development and highlight the potential of this line to analyze the molecular regulation of germ plasm formation. (C) 2015 Elsevier B.V. All rights reserved
Functional equivalence of germ plasm organizers
No full textThe proteins Oskar (Osk) in Drosophila and Bucky ball (Buc) in zebrafish act as germ plasm organizers. Both proteins recapitulate germ plasm activities but seem to be unique to their animal groups. Here, we discover that Osk and Buc show similar activities during germ cell specification. Drosophila Osk induces additional PGCs in zebrafish. Surprisingly, Osk and Buc do not show homologous protein motifs that would explain their related function. Nonetheless, we detect that both proteins contain stretches of intrinsically disordered regions (IDRs), which seem to be involved in protein aggregation. IDRs are known to rapidly change their sequence during evolution, which might obscure biochemical interaction motifs. Indeed, we show that Buc binds to the known Oskar interactors Vasa protein and nanos mRNA indicating conserved biochemical activities. These data provide a molecular framework for two proteins with unrelated sequence but with equivalent function to assemble a conserved core-complex nucleating germ plasm.</div
Functional conservation of germ plasm organizers Bucky ball in zebrafish and Drosophila Oskar
No full textThe reproductive cells of many animals are specified by a maternal determinant termed germ plasm. Cells inheriting germ plasm during embryogenesis will develop into primordial germ cells (PGCs), the precursors to eggs and sperm. Zebrafish specify their germ cells by deposition of germ plasm in the egg. To this end, only two proteins are known in the entire animal kingdom that program germ cell development in vivo: Oskar, which is specific to insects and Bucky ball (Buc), which our lab discovered in the zebrafish. Based on this unique activity, these two proteins are termed germ plasm organizers.
In my study, I show that the two germ plasm organizers transform a somatic cell into PGCs in zebrafish. This result indicates that both proteins act through a conserved biochemical network to specify germ cell fate. A comparison of the amino acid sequence of Drosophila Oskar and zebrafish Bucky Ball, showed no conserved domains to explain their similar function. Buc is a novel protein, whose protein sequence shows no homology to other known functional domains and hence, its biochemical activity is currently unknown. My analysis of the biochemical interaction network of Bucky ball revealed that it interacts with similar germ plasm factors as Oskar. These results suggest that germ plasm organizers form a common core complex to specify germ cells.
Nonetheless, Oskar and Bucky ball represent a deviation from the generally accepted sequence-structure-function paradigm. I therefore analyzed their biophysical properties and discovered that both encode intrinsically disordered proteins (IDPs). IDPs are known to quickly change their sequence during evolution, because their function is based on structural features. IDPs are known to assemble into hydrogels by liquid-liquid phase separation. Pharmacologically disrupting hydrogels fragmented Buc-complexes in zebrafish indicating their critical role during aggregation of germ plasm. These data suggest that Buc and Oskar exert their conserved role through similar biophysical and biochemical properties.
It has been frequently postulated in the literature that unrelated protein sequences perform the same function. To my knowledge, my data represents the first example of two proteins which were previously classified as “novel” or “species-specific”, but are indeed functionally conserved across distant species
Chern-Simons theory of magnetization plateaus on the kagome lattice
No full textFrustrated spin systems on Kagome lattices have long been considered to be a promising candidate for realizing exotic spin liquid phases. Recently, there has been a lot of renewed interest in these systems with the discovery of experimental materials such as Volborthite and Herbertsmithite that have Kagome like structures. In this thesis I will focus on studying frustrated spin systems on the Kagome lattice using a spin-1/2 antiferromagnetic XXZ Heisenberg model in the presence of an external magnetic field as well as other perturbations. Such a system is expected to give rise to magnetization platueaus which can exhibit topological characteristics in certain regimes.
We will first develop a flux-attachment transformation that maps the Heisenberg spins (hard-core bosons) onto a problem of fermions coupled to a Chern-Simons gauge field. This mapping relies on being able to define a consistent Chern-Simons term on the lattice. Using this newly developed mapping we analyse the phases/magnetization plateaus that arise at the mean-field level and also consider the effects of adding fluctuations to various mean-fi eld states. Along the way, we show how to discretize an abelian Chern-Simons gauge theory on generic 2D planar lattices that satisfy certain conditions. We find that as long as there exists a one-to-one correspondence between the vertices and plaquettes defined on the graph, one can write down a discretized lattice version of the abelian Chern-Simons gauge theory.
Using the newly developed flux attachment transformation, we show the existence of chiral spin liquid
states for various magnetization plateaus for certain range of parameters in the XXZ Heisenberg model in the presence of an external magnetic field. Speci cally, in the regime of XY anisotropy the ground states at the 1/3 and 2/3 plateau are equivalent to a bosonic fractional quantum Hall Laughlin state with filling fraction 1/2 and that the 5/9 plateau is equivalent to the first bosonic Jain daughter state at filling fraction 2/3.
Next, we also consider the effects of several perturbations: a) a chirality term, b) a Dzyaloshinskii-Moriya term, and c) a ring-exchange type term on the bowties of the kagome lattice, and inquire if they can also support chiral spin liquids as ground states. We find that the chirality term leads to a chiral spin liquid even in the absence of an uniform magnetic field, with an effective spin Hall conductance of 1/2 in the regime of XY anisotropy. The Dzyaloshinkii-Moriya term also leads a similar chiral spin liquid but only when this term is not too strong. An external magnetic field when combined with some of the above perturbations also has the possibility of giving rise to additional plateaus which also behave like chiral spin liquids in the XY regime. Under the in influence of a ring-exchange term we find that provided its coupling constant is large enough, it may trigger a phase transition into a chiral spin liquid by the spontaneous breaking of time-reversal invariance.
Finally, we also present some numerical results based on some exact diagonalization studies. Here, we specifically focus on the 2/3-magnetization plateau which we previously argued should be a chiral spin liquid with a spin hall conductance of 1/2 . Such a topological state has a non-trivial ground state degeneracy and it excitations are described by semionic quasiparticles. In the numerical analysis, we analyse the ground state degeneracy structure on various Kagome clusters of different sizes. We compute modular matrices from the resultant minimally entangled states as well as the Chern numbers of various eigenstates all of which provide strong evidence that the 2/3-magnetization plateau very closely resembles a chiral spin liquid state with the expected characteristics.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-12-01The student, Ponnuraj Krishnakumar, accepted the attached license on 2016-11-23 at 22:00.The student, Ponnuraj Krishnakumar, submitted this Dissertation for approval on 2016-11-23 at 22:29.This Dissertation was approved for publication on 2016-11-29 at 10:54.DSpace SAF Submission Ingestion Package generated from Vireo submission #10318 on 2017-02-28 at 14:36:45Made available in DSpace on 2017-03-01T16:36:55Z (GMT). No. of bitstreams: 2
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Previous issue date: 2016-11-29Embargo set by: Seth Robbins for item 98599
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Author response
No full textWe recently reported that the C2AB portion of Synaptotagmin 1 (Syt1) could selfassemble into Ca2+-sensitive ring-like oligomers on membranes, which could potentially regulate neurotransmitter release. Here we report that analogous ring-like oligomers assemble from the C2AB domains of other Syt isoforms (Syt2, Syt7, Syt9) as well as related C2 domain containing protein, Doc2B and extended Synaptotagmins (E-Syts). Evidently, circular oligomerization is a general and conserved structural aspect of many C2 domain proteins, including Synaptotagmins. Further, using electron microscopy combined with targeted mutations, we show that under physiologically relevant conditions, both the Syt1 ring assembly and its rapid disruption by Ca2+ involve the well-established functional surfaces on the C2B domain that are important for synaptic transmission. Our data suggests that ring formation may be triggered at an early step in synaptic vesicle docking and positions Syt1 to synchronize neurotransmitter release to Ca2+ influx.Fil: Zanetti, Maria Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Bello, Oscar Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Wang, Jing. University of Yale. School of Medicine; Estados UnidosFil: Coleman, Jeff. University of Yale. School of Medicine; Estados UnidosFil: Cai, Yiying. University of Yale. School of Medicine; Estados UnidosFil: Sindelar, Charles V.. University of Yale. School of Medicine; Estados UnidosFil: Rothman, James E.. University of Yale. School of Medicine; Estados UnidosFil: Krishnakumar, Shyam S.. University of Yale. School of Medicine; Estados Unido
Spatial, temporal and molecular hierarchies in the link between death, delamination and dorsal closure
No full textDead cells in most epithelia are eliminated by cell extrusion. Here, we explore whether cell delamination in the amnioserosa, a seemingly stochastic event that results in the extrusion of a small fraction of cells and known to provide a force for dorsal closure, is contingent upon the receipt of an apoptotic signal. Through the analysis of mutant combinations and the profiling of apoptotic signals in situ, we establish spatial, temporal and molecular hierarchies in the link between death and delamination. We show that although an apoptotic signal is necessary and sufficient to provide cell-autonomous instructions for delamination, its induction during natural delamination occurs downstream of mitochondrial fragmentation. We further show that apoptotic regulators can influence both delamination and dorsal closure cell non-autonomously, presumably by influencing tissue mechanics. The spatial heterogeneities in delamination frequency and mitochondrial morphology suggest that mechanical stresses may underlie the activation of the apoptotic cascade through their influence on mitochondrial dynamics. Our results document for the first time the temporal propagation of an apoptotic signal in the context of cell behaviours that accomplish morphogenesis during development. They highlight the importance of mitochondrial dynamics and tissue mechanics in its regulation. Together, they provide novel insights into how apoptotic signals can be deployed to pattern tissues.</jats:p
Modelling the Dynamic Nature of Networks, Enabling Smart Living
No full textHolons are universal and omni-present. They are organized in holarchies (hierarchical networks). Networks change continuously over time. At the aggregation level of the Sector Network and of the Telecom Network, diverse drivers cause changes. To provide for a better quality of life, trans-sector orchestration of change is required. Therefore, it is imperative to understand the sector network architecture, the major dilemmas, the drivers causing change and the interdependency with outer aggregation levels. In the Sector Network, households historically had a predominantly consumptive role. But they are increasingly becoming producers, or prosumers. Therefore, the introduction of the Smart Living concept into households will fuel the Sector Network evolution pro-foundly. Consequently, the infuence of the Smart Home on the Sector Network and its lower aggregates, like the Telecom Network, also will be signifcant. This thesis mainly investigates the drivers that infuence telecom transport network changes over time as well as the sector network dynamics over time, thereby providing insight into trans-sector orchestration over network evolution.Group of Networks and ServicesTelecommunicationsElectrical Engineering, Mathematics and Computer Scienc
Neural Ordinary Differential Equations for Frequency Security Assessment
No full textTo keep pace with increasing renewable energy penetration and consequent increase in inverter-based resources in the power grid, it is pertinent for present-day research to address the resulting drop in system inertia levels and its impact on frequency stability. With decreasing levels of inherent rotational inertia present in the system, any sudden disturbance causing an energy imbalance in the grid could lead to more drastic excursions of system frequency than those experienced hitherto. To ensure the resilience of the grid in such scenarios, advanced and competent frequency stability assessment and control methods are required. This thesis presents Neural Ordinary Differential Equations (NODE), a recently introduced family of neural networks, as an effective tool to achieve fast, real time estimates of the expected frequency response trajectory during an energy imbalance event. Since high-impact frequency instability events are sparse in reality, both real-world grid data and synthetically generated data corresponding to different inertial conditions are used to train predictive NODE models. Firstly, NODE is adapted to frequency prediction applications through relevant data processing steps, and modification of network parameters and algorithmic aspects pertaining to the predictive model definition. Secondly, patterns corresponding to specific sections of the frequency response curve are used to selectively train NODE models. Pattern-specific training methods exhibit better prediction performance when the NODE model encounters frequency behaviour similar to the one it initially trained on. Thirdly, a pre-training approach to cut short on the real-time training time required by NODE models to achieve desired levels of prediction performance is presented. Fast estimates of critical frequency stability parameters like nadir could act as potential triggers for early stability control actions to achieve a more controlled frequency response.Application of predictive NODE models for different frequency scenarios are presented using three test-cases: normal operating scenario, restoration post-system split scenario and synthetically generated high-impact frequency disturbance scenarios. Model tuning and training methods specific to each test-case are described, and prediction results are evaluated with relevant performance metrics. Finally, a comparison is made between the implementation of NODE among different test-cases and real-world implications of the frequency prediction outcomes from the test-cases are further discussed.Electrical Engineerin
Path Planning in Heterogenous Environments: A Combined Approach
No full textAutonomous vehicles are the inevitable future of the industry as theoretically they guarantee higher road throughput and a much safer means of transport compared to today’s ground vehicle. This has attracted the industries and universities making it a very important topic of research. The basic function of the autonomous vehicle boils down to transporting its passenger safety from door to door. This requires planning of a path that is obstacle free. Currently, sampling-based methods are widely used for path planning. Although these methods are proving to be successful in open environments, they are inefficient in heterogeneous environments. Planning in urban environments would be successful if this obstacle is tackled. In the current literature, it was found that there are many methods which focus on solving the path planning problem while planning around the obstruction, while there are other methods that focus on converging to optimal solutions. Hence, there is a need for methods that would plan optimal paths in heterogeneous environments. This thesis introduced a combined approach that shares elements of planning paths around obstacles and optimal path planning which are provided by the algorithms Adaptive RRT and Informed RRT* respectively. These methods are combined along with a Dubin’s motion model to simulate basic vehicle’s constraints. The proposed approach was compared with state of the art methods like RRT* to evaluate its performance via simulation. The simulation was carried out in three different scenarios with variable complexity depending upon the available free configuration space. The ability to find a solution and converge it were evaluated, an improvement of 50% was noticed in finding the initial solution and around 25% improvement was seen in convergence. This concluded that such a hybrid approach could be an important contribution to urban path planning.Mechanical Engineerin
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