Functional Characterization of an Organ Specific Effector See1 of Ustilago Maydis

Ustilago maydis is the causative agent of the corn smut. This basidiomycetous fungus is a biotophic plant pathogen that succeeds by colonizing living tissue and establishes a biotrophic interaction which results in the formation of enormous tumors. This tumor formation is a result of efficient host immune suppression and nutrient efflux during disease progression. The fungus secretes several hundreds of effector proteins which are expressed at various stages of colonization to modulate the host. Previous studies have revealed that the effector proteins of U. maydis are acting in an organ specific manner and deletion of one organ specific effector does not hamper the symptom formation in non-target organ (Skibbe et al., 2010; Schilling et al., 2014). The previous study of Schilling et al., 2014 identified leaf specific effectors, which are induced in juvenile leaves. An interesting candidate among these that showed a perfect organ specificity was see1 (Seedling efficient effector 1, um02239), which is required in the colonized leaves. Deletion mutants for see1 are able to penetrate and colonize the seedling but fail to induce expansion of tumors. The deletion mutant is seen to be actively blocked in mesophyll and vascular cell layers of the leaf, which may indicate that the effector function may be confined to a specific cell or tissue type. In contrast, see1 deletion does not affect tumor formation in the floral parts of the host. Aim of this thesis was the functional characterization of See1. Monitoring of the DNA synthesis in host, showed that See1 is specifically required to induce DNA synthesis in colonized host cells and re-direct them to form tumors. Yeast-two-hybrid analysis showed that See1 interacts with a nucleo-cytoplasmic host protein SGT1, which is a cell cycle and immune response modulator and which also shows a leaf specific transcriptional regulation. Constitutive overexpression of see1 caused tassel base abnormality specifically showing tumors in the vegetative base of the tassel pointing towards an active role of see1 in inducing tumor in vegetative maize tissues. Electron microscopy showed that See1 is translocated to the plant cell and is localized in the cytoplasm and nucleus of the host cell. Furthermore, it was demonstrated that See1 blocks the phosphorylation of maize SGT1 at a monocot specific site which is necessary to activate the signaling cascade upon pathogen perception. Experiments indicate that see1 specifically activates the host cell cycle release thereby activating the colonized cells to undergo a tumor pathway. Hence organ specific effectors like see1, not only manipulate the defense responses, but also the metabolic state of the host cell leading to tumor development

CLAMP: A Contrastive Language And Molecule Pre-training Network

This paper highlights a shift in how to approach material generation. Instead of material-to-material, we propose a language-to-material generation architecture that utilizes millions of untapped data points. Using a web scraper to collect crystal text pairs from open-source research papers, a contrastive model can be trained using a convolutional graph neural network encoder and a language encoder. This would allow unsupervised zero-shot classification which can be trained by taking advantage of linguistic structure. Without any specific training data, an ~82\% accuracy was achieved and ~75\% accuracy for photocatalyst prediction with an extremely small dataset. This novel network could ideally be cross-applied to any reaction that can be described via text, opening completely new methods to think about 3D chemical framework generation. In the full experiment diffusion models would likely be incorporated to fully exploit the latent space.Comment: 3 pages, 1 figure, Presenting @ NeurIPS23 & Workshop - source @ https://github.com/neelr/clamp - dataset @ https://www.kaggle.com/datasets/programgeek01/cif-summary-dat

CarbNN: A Novel Active Transfer Learning Neural Network To Build De Novo Metal Organic Frameworks (MOFs) for Carbon Capture

Over the past decade, climate change has become an increasing problem with one of the major contributing factors being carbon dioxide (CO2) emissions; almost 51% of total US carbon emissions are from factories. Current materials used in CO2 capture are lacking either in efficiency, sustainability, or cost. Electrocatalysis of CO2 is a new approach where CO2 can be reduced and the components used industrially as fuel, saving transportation costs, creating financial incentives. Metal Organic Frameworks (MOFs) are crystals made of organo-metals that adsorb, filter, and electrocatalyze CO2. The current available MOFs for capture & electrocatalysis are expensive to manufacture and inefficient at capture. The goal therefore is to computationally design a MOF that can adsorb CO2 and catalyze carbon monoxide & oxygen with low cost. A novel active transfer learning neural network was developed, utilizing transfer learning due to limited available data on 15 MOFs. Using the Cambridge Structural Database with 10,000 MOFs, the model used incremental mutations to fit a trained fitness hyper-heuristic function. Eventually, a Selenium MOF (C18MgO25Se11Sn20Zn5) was converged on. Through analysis of predictions & literature, the converged MOF was shown to be more effective & more synthetically accessible than existing MOFs, showing the model had an understanding of effective electrocatalytic structures in the material space. This novel network can be implemented for other gas separations and catalysis applications that have limited training accessible datasets.Comment: 13 pages, 12 figures, presented at AAAI-23 orally & as a poste

Analysis and Control of Nonlinear Attitude Motion of Gravity-Gradient Stabilized Spacecraft via Lyapunov-Floquet Transformation and Normal Forms

This chapter demonstrates analysis and control of the attitude motion of a gravity-gradient stabilized spacecraft in eccentric orbit. The attitude motion is modeled by nonlinear planar pitch dynamics with periodic coefficients and additionally subjected to external periodic excitation. Consequently, using system state augmentation, Lyapunov-Floquet (L-F) transformation, and normal form simplification, we convert the unwieldy attitude dynamics into relatively more amenable schemes for motion analysis and control law development. We analyze the dynamical system’s periodicity, stability, resonance, and chaos via numerous nonlinear dynamic theory techniques facilitated by intuitive system state augmentation and Lyapunov-Floquet transformation. Versal deformation of the normal forms is constructed to investigate the bifurcation behavior of the dynamical system. Outcome from the analysis indicates that the motion is quasi-periodic, chaotic, librational, and undergoing a Hopf bifurcation in the small neighborhood of the critical point-engendering locally stable limit cycles. Consequently, we demonstrate the implementation of linear and nonlinear control laws (i.e., bifurcation and sliding mode control laws) on the relatively acquiescent transformed attitude dynamics. By employing a two-pronged approach, the quasiperiodic planar motion is independently shown to be stabilizable via the nonlinear control approaches

Characterization of Capacitive Comb-finger MEMS Accelerometers

This paper discusses various methods for testing the performance of MEMS capacitive comb-finger accelerometers manufactured by Sandia National Laboratories. The use of Capacitive MEMS devices requires complex circuits for measurement of capacitance. Sandia MEMS accelerometer’s capacitance changes in a very small femto-farad (fF) range. The performance of accelerometer is tested using Analog Devices AD7747 sigma-delta capacitance to digital converter. The response of a MEMS capacitive accelerometer to various tests is useful for testing and characterization and investigate it’s suitability for various application

Dynamics and Control of a Stop Rotor Unmanned Aerial Vehicle

The objective of this work was to develop a variety of control systems for a Stop-Rotor Unmanned Aerial Vehicle (UAV) in hover flight. The Stop-Rotor UAV has capabilities of Vertical Take-off and Landing (VTOL) like a helicopter and can convert from a helicopter mode to an airplane mode in mid-flight. Thus, this UAV can hover as a helicopter and achieve high mission range of an airplane. The stop-rotor concept implies that in mid-flight the thrust generating helicopter rotor stops and rotates the blades into airplane wings. The thrust in airplane mode is then provided by a pusher propeller. The aircraft configuration presents unique challenges in flight dynamics, modeling and control. In this paper a mathematical model is derived, and then the model is simulated with non-zero initial conditions. Various control systems are then implemented. The control techniques utilized are a linear control, optimal linear control and a nonlinear control with the objective of stabilizing the UAV in hover flight. Settling time and control effort are then compared across the different control systems.DOI:http://dx.doi.org/10.11591/ijece.v2i5.158

Bovine brain mitochondrial hexokinase: solubilization, purification, and role of sulfhydryl residues

Bovine brain mitochondrial hexokinase, type I, has been solubilized by extraction of the mitochondria in 0.2 m acetate buffer, pH 5.0, containing 0.9 m NaCl. The solubilized enzyme has been purified to apparent homogeneity as shown by ultracentrifugal and electrophoretic criteria. The purification procedure included fractionation of the solubilized enzyme with ammonium sulfate and two successive diethylaminoethyl cellulose chromatographic steps. The sedimentation coefficient, S20,w, was found to be 5.9 S at a protein concentration of 1.7 mg per ml. The approximate molecular weight as determined by gel filtration on Sephadex G-200 is 107,000. The enzyme has 11 to 13 sulfhydryl residues per mole as determined by reaction of the denatured enzyme with 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB). Almost all of these residues react with DTNB in the native enzyme though with differing degrees of reactivity. Reaction of the enzyme with excess DTNB caused its rapid inactivation. A comparison of the progress of this inactivation with the progress of the reaction of the sulfhydryl residues of the enzyme with DTNB showed that a maximum of only 2 residues could be involved in the inactivation process. If 2-mercaptoethanol is added to the enzyme immediately after complete inactivation, a rapid and total recovery of enzyme activity ensues. These results have been analyzed in terms of involvement of sulfhydryl residues, in the active conformation of the enzyme. Substrate glucose partially protects the enzyme against inactivation by DTNB and also modifies the reactivity of the sulfhydryl residues of the enzyme toward this reagent. MgATP, MgADP, and inorganic phosphate even at 10 mm concentration do not protect the enzyme against inactivation by DTNB. Product inhibitor glucose 6-phosphate affords a complete protection to the enzyme against inactivation by DTNB and drastically changes the reactivity of its sulfhydryl residues. Fructose 6-phosphate is without a comparable effect

A Conserved Microbial Motif ‘Traps’ Protease Activation in Host Immunity

A recent study (Misas-Villamil et al., Nat. Commun., 2019) reveals that Pit2, an apoplastic effector of the corn smut fungus Ustilago maydis, contains an embedded motif of 14 amino acids that binds to and inhibits plant cysteine proteases, thereby modulating host immunity. Intriguingly, the inhibitory motif acts by mimicking the protease substrate and is conserved across microbial kingdoms

Protecting normal cells from the cytotoxicity of chemotherapy

Comment on: van Leeuwen IMM, et al. Cell Cycle 2012; 11:1851-6