Machine Learning for Enzyme Promiscuity

With the discovery of an increasing number of catalytically promiscuous enzymes, which are capable of catalyzing multiple reactions, the traditional view of enzymes as highly specific proteins has been brought into question. The significant implications of protein promiscuity for the theory of enzyme evolution suggest that this inherent feature can be utilized as the seed for engineering new functions in biotechnology and synthetic biology as well as in drug design. Therefore, understanding protein promiscuity is becoming even more important as it provides new insights into the evolutionary process that has led to such vast functional diversity. While there have been numerous efforts devoted to recognizing the determinants of promiscuity, till date, this pertinent question regarding the distinctions between specialized enzymes and promiscuous enzymes has remained unanswered. As an in silico approach, in this thesis, we attempt to find a predictive model which can accurately classify unseen proteins into catalytically promiscuous and non-promiscuous. To this end, we exploit different representations and properties of proteins, and adopt different computational approaches accordingly. The role of proteins sequences as indicators of promiscuity is investigated by means of the BLAST algorithm as well as string kernels. Additionally, to validate the interplay between proteins' three-dimensional structures and their promiscuous behaviors, we employ a novel method which is modeling the topological details of proteins as graphs. Graph kernel functions are then applied to measure the structural similarities between the 3D structures of proteins. The classification is performed using SVM as a kernel-based method. The results indicate that proteins' sequences have limited bearings on promiscuity. Conversely, proteins' 3D structures can reliably predict whether a protein has promiscuous activities with an accuracy of 96%. Our best results are achieved using the Weisfeiler-Lehman subtree graph kernel and the secondary structure information of proteins

Control/structure interaction during Space Station Freedom-Orbiter berthing

The berthing maneuver is essential for the construction and assembly of Space Station Freedom (SSF) and has a direct effect on the SSF assembly build up and SSF/Orbiter operations. The effects of flexible body dynamics coupled with the available control system may impose new requirements on the maneuver. The problem is further complicated by the effect of the SSF control system on the Shuttle Remote Manipulator System (SRMS). These effects will play a major role in the development of operational requirements which need to be identified and validated in order to assure total safety and maneuver execution during SSF construction. This paper presents the results of ongoing studies to investigate the Control/Structure Interaction (CSI) during the berthing operations. The problem is formulated in terms of multi-flex body equations of motion for SSF and the SRMS and on-orbit flight control systems for the SRMS and the SSF, which includes the Control Moment Gyro (CMG) and Reaction Control System (RCS) Attitude Control Systems (ACS). The SSF control system designs are based on the Preliminary Design Review (PDR) version of the Honeywell design. The simulation tool used for the analysis is briefly described and the CSI results are presented for given berthing scenarios

Sustainability assessment tools in higher education institutions: comprehensive analysis of the indicators and outlook

This chapter is structured as follows: Sections 8.2 provides an overview of sustainability assessment at HEIs and describes the existing tools in HEIs and the main gaps; Section 8.3 describes the methods and the steps of the analysis; Section 8.4 presents the results and comparative analysis; Section 8.5 provide the overall discussion and the future development of the research; and finally Section 8.6 concludes the chapter.info:eu-repo/semantics/publishedVersio

Waveguide Evanescent-Field Microscopy for Label-Free Monitoring of Biological Nanoparticles: Fabrication, Characterization and Application

The recent development of microscopy methods, biological assays and bioanalytical sensors has significantly advanced the understanding of biological systems. Surface-based bioanalytical sensors have in recent years gained increased interest thanks to improvements in sensitivity and simplicity to use. However, most of them, such as quartz crystal microbalance (QCM) and surface plasmon resonance (SPR), provide information based on ensemble averaging of biomolecular interactions. In contrast, with surface-sensitive microscopy methods, biological processes can be resolved down to the level of individual molecular interactions. Total internal reflection fluorescent microscopy is one commonly used surface-sensitive method, reaching sensitivities down to the level of single molecules, but it requires fluorescent labeling of at least one of the interaction partners and is often also hampered by photo bleaching processes.In this thesis, we introduce a new wide-field surface-sensitive microscopy platform, based on a nanofabricated planar optical waveguide design that is capable of label-free evanescent-field microscopy of biological nanoparticles well below 100\ua0nm in diameter. The waveguide generates an evanescent-field at the interface between the core of the waveguide and an aqueous solution, providing a thin sheet of illumination that offers imaging with low background disturbance. The device is presented in two designs, being compatible with either upright or inverted microscopes.The work presented demonstrates how simultaneous monitoring of fluorescence and scattering signals can offer new information about the relation between scattering intensity, refractive index and lipid content of biological nanoparticles, such as exosomes. Further, the microfluidic design allowed not only for convenient liquid handling with dead volumes of a few microliter, it is also showed to aid label-free investigations of the interaction between proteins and individual lipid vesicles, with the latter serving as cell-membrane mimic. With the device also being compatible with formation of fluid supported lipid bilayers, preliminary results suggest that the design will open up a possibility to simultaneously determine the size, scattering intensity and fluorescence emission at the level of individual biological nanoparticles. With this realized, we foresee a broad applicability of the microscopy platform as multidimensional characterization tool for biological nanoparticles and beyond

Comparing the predictions of a non-Schmid crystal plasticity model with phenomenological hardening and dislocation density hardening rules for superconducting cavities used in particle accelerators

High purity niobium is used to make superconducting radio frequency cavities. One potential fabrication method involves deep drawing cup-like shapes form slices of an ingot containing only a few grains. Thus, material models for large strain deformation of multicrystals are needed to predict conditions that lead to forming instabilities and to predict future responses to heat treatments to remove as many dislocations as possible. Deformation behavior of BCC materials does not follow the Schmid law. Therefore, the classical crystal plasticity cannot be used to predict their behavior. In BCC materials, core of screw dislocations expand on three different \u3c110\u3e planes, and influences from the stresses on each of these planes. This is known as non-Schmid behavior. In this study, a non-Schmid crystal plasticity model with a phenomenological hardening rule is developed and calibrated for single crystal niobium (Nb). The model accurately predicts the stress–strain response of Nb; however, the estimated crystal orientation evolution is not as accurate. A dislocation density hardening model is implemented to increase the accuracy of texture predictions. The results of these two hardening models are compared

Genetic and molecular analysis of trichome and root hair development in Arabis alpina

Evolutionary developmental (Evo-Devo) approaches are commonly used to compare homologous processes in closely related species. In this study, we use Arabis alpina, as a second model system of Brassicaceae to study trichome and root hair development and compare it to Arabidopsis thaliana. It has been shown previously that trichome and root hair pattern in A. alpina is different from A. thaliana. In Arabidopsis, trichomes are regularly spaced on the surface of the leaf and root hairs are found in single cell files (H-files) adjacent to the non-hair files (N-files). Arabis leaves are densely covered with small and big trichomes, and roots produce ectopic hairs in N file (Chopra et al. 2014). To understand the genetic basis of trihchome and root hair development in A. alpina, two EMS populations were screened. Mutants with defects in trichome (Chopra 2015, PhD thesis) and root hair patterning and morphology were selected. Screen results in A. alpina show a similar range of mutant phenotypes as known in A. thaliana. Mutants were then sequenced for candidate genes to find the specific mutant alleles in A. alpina. Mutations in Arabis TTG1 (Chopra et al. 2014) and TRY (Chopra 2015, PhD thesis) lead to the same phenotypes as expected from A. thaliana. However, Aagl3 mutants showed glabrous leaf and hairy root phenotype similar as the gl3 egl3 double mutant in A. thaliana. Moreover, overexpression of AaGL3 in A.alpina resulted in reduced number of trichomes; indicating an evolutionary change of the GL3 function. Similarly, Arabis GL2 function appears to be changed as it functions only in a subset of trichomes. I also present the identification of morphogenesis mutants affecting root hair development. Aakjk, Aacow1, Aascn1, Aaark1 and Aaspi are identified root hair mutants affecting root hair formation in A. alpina. Several morphology mutant alleles showing amino acid exchanges have been also identified

Manual da prosperidade

Esta apresentação inserem-se como recurso educativo no âmbito da Microcredêncial “Objetivos de Desenvolvimento Sustentável”Plano de Recuperação e resiliência (PRR) / União Europeiainfo:eu-repo/semantics/publishedVersio

Low-temperature fabrication and characterization of a symmetric hybrid organic–inorganic slab waveguide for evanescent light microscopy

Organic and inorganic solid materials form the building blocks for most of today\u27s high-technological instruments and devices. However, challenges related to dissimilar material properties have hampered the synthesis of thin-film devices comprised of both organic and inorganic films. We here give a detailed description of a carefully optimized processing protocol used for the construction of a three-layered hybrid organic–inorganic waveguide-chip intended for combined scattering and fluorescence evanescent-wave microscopy in aqueous environments using conventional upright microscopes. An inorganic core layer (SiO2 or Si3N4), embedded symmetrically in an organic cladding layer (CYTOP), aids simple, yet efficient in-coupling of light, and since the organic cladding layer is refractive index matched to water, low stray-light (background) scattering of the propagating light is ensured. Another major advantage is that the inorganic core layer makes the chip compatible with multiple well-established surface functionalization schemes that allows for a broad range of applications, including detection of single lipid vesicles, metallic nanoparticles or cells in complex environments, either label-free—by direct detection of scattered light—or by use of fluorescence excitation and emission. Herein, focus is put on a detailed description of the fabrication of the waveguide-chip, together with a fundamental characterization of its optical properties and performance, particularly in comparison with conventional epi illumination. Quantitative analysis of images obtained from both fluorescence and scattering intensities from surface-immobilized polystyrene nanoparticles in suspensions of different concentrations, revealed enhanced signal-to-noise and signal-to-background ratios for the waveguide illumination compared to the epi-illumination

Wild Australia, Meston's Wild Australia Show 1892-1893

In 1892 and 1893 a troupe of Aboriginal and Torres Strait Island performers was taken to Brisbane, Sydney and Melbourne to stage what was known as the 'Wild Australia' Show. The project was conceived and promoted by a Queensland journalist entrepreneur, Archibald Meston, who conscripted a junior partner, Brabazon Purcell as the manager of the troupe. This exhibition explores a brief period in the life of Archibald Meston, one of the most influential and controversial figures in Queensland Indigenous history. Meston attempted to portray a group of Aboriginal and Torres Strait Island people as “primitive savages” and marketed them as untouched by European influences. He attempted to profit financially from these performers and even though this ambitious plan soon failed, he continued to promote himself over the next decade as an expert in regard to Aboriginal people. Following this failed business venture Meston managed to position himself as one of the most influential advisors to the Queensland Government on Aboriginal issues and was very influential in the introduction of Queensland’s first Aboriginal protection policy that was introduced in 1897