Recurrent Graph Convolutional Networks for Spatiotemporal Prediction of Snow Accumulation Using Airborne Radar

The accurate prediction and estimation of annual snow accumulation has grown in importance as we deal with the effects of climate change and the increase of global atmospheric temperatures. Airborne radar sensors, such as the Snow Radar, are able to measure accumulation rate patterns at a large-scale and monitor the effects of ongoing climate change on Greenland's precipitation and run-off. The Snow Radar's use of an ultra-wide bandwidth enables a fine vertical resolution that helps in capturing internal ice layers. Given the amount of snow accumulation in previous years using the radar data, in this paper, we propose a machine learning model based on recurrent graph convolutional networks to predict the snow accumulation in recent consecutive years at a certain location. We found that the model performs better and with more consistency than equivalent nongeometric and nontemporal models.Comment: Accepted to IEEE Radar Conference 2023. 6 pages, 4 figures, 2 table

Using Adobe Illustrator for mechanical engineering design

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 23-24).Sketching by hand is important in the creative process because it promotes reinterpretation through ambiguity. Adobe Illustrator is a valuable tool for an engineer to make professional-looking presentation drawings. The project conducted as this thesis was to create a website tutorial to teach students at Massachusetts Institute of Technology enrolled in 2.009, the senior capstone product design course, the basics of Illustrator. A study was conducted on two subjects to judge the effectiveness of the website tutorial project at teaching how to use Illustrator. The subjects had no previous experience with the program. Both of these subjects were able to learn the basics of Illustrator and create a simple logo design in under two hours. They reported that the tutorial gave them enough knowledge of the program to then experiment on their own to continue learning Illustrator. While this tutorial is not meant to teach all aspects of the program, it has been shown to be effective at teaching people with no Illustrator background how to create a simple but useful design that could function in the scope of 2.009.by Kim Zalatan.S.B

Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling

Engineering metabolism to efficiently produce chemicals from multi-step pathways requires optimizing multi-gene expression programs to achieve enzyme balance. CRISPR-Cas transcriptional control systems are emerging as important tools for programming multi-gene expression, but poor predictability of guide RNA folding can disrupt expression control. Here, we correlate efficacy of modified guide RNAs (scRNAs) for CRISPR activation (CRISPRa) in E. coli with a computational kinetic parameter describing scRNA folding rate into the active structure (rS = 0.8). This parameter also enables forward design of scRNAs, allowing us to design a system of three synthetic CRISPRa promoters that can orthogonally activate (>35-fold) expression of chosen outputs. Through combinatorial activation tuning, we profile a three-dimensional design space expressing two different biosynthetic pathways, demonstrating variable production of pteridine and human milk oligosaccharide products. This RNA design approach aids combinatorial optimization of metabolic pathways and may accelerate routine design of effective multi-gene regulation programs in bacterial hosts

Catalytic Nitrene Transfer To Alkynes: A Novel and Versatile Route for the Synthesis of Sulfinamides and Isothiazoles

A novel transformation is reported for the reaction of terminal or internal alkynes with the nitrene precursor PhI=NTs (Ts=p-toluenesulfonyl) in the presence of catalytic amounts of Tp(Br3)Cu(NCMe) (Tp(Br3)=hydrotris(3,4,5-tribromo-pyrazolylborate). Two products containing an imine functionality have been isolated from the reaction mixtures, identified as sulfinamides and isothiazoles. The former correspond to the formal reduction of the sulfone group into sulfoxide, whereas the latter involves the insertion of an alkyne carbon atom into the aromatic ring of the N-tosyl moiety.Support for this work was provided by the MINECO (CTQ2014-52769-C3-R-1, CTQ2014-57761-R, Severo Ochoa Excellence Accreditation 2014-2018 SEV-2013-0319, Red Intecat CTQ2014-52974-REDC) and by a FPU fellowship (M.R.R.). We thank Prof. Antonio Echavarren for helpful comments and discussions

Mammalian cell expression, purification, crystallization and microcrystal data collection of autotaxin/ENPP2, a secreted mammalian glycoprotein

Autotaxin, a four-domain ∼100 kDa mammalian glycoprotein, was expressed in stably transfected mammalian cells, purified from the medium and crystallized. Diffraction data from micrometre-thick crystal plates were collected on various European synchrotron beamlines and are presented and analysed

Multidimensional chemical control of CRISPR–Cas9

Cas9-based technologies have transformed genome engineering and the interrogation of genomic functions, but methods to control such technologies across numerous dimensions-including dose, time, specificity, and mutually exclusive modulation of multiple genes-are still lacking. We conferred such multidimensional controls to diverse Cas9 systems by leveraging small-molecule-regulated protein degron domains. Application of our strategy to both Cas9-mediated genome editing and transcriptional activities opens new avenues for systematic genome interrogation

Industrial systems biology and its impact on synthetic biology of yeast cell factories

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. (C) 2015 Wiley Periodicals, Inc

Enantioselective, intermolecular benzylic C–H amination catalysed by an engineered iron-haem enzyme

C–H bonds are ubiquitous structural units of organic molecules. Although these bonds are generally considered to be chemically inert, the recent emergence of methods for C–H functionalization promises to transform the way synthetic chemistry is performed. The intermolecular amination of C–H bonds represents a particularly desirable and challenging transformation for which no efficient, highly selective, and renewable catalysts exist. Here we report the directed evolution of an iron-containing enzymatic catalyst—based on a cytochrome P450 monooxygenase—for the highly enantioselective intermolecular amination of benzylic C–H bonds. The biocatalyst is capable of up to 1,300 turnovers, exhibits excellent enantioselectivities, and provides access to valuable benzylic amines. Iron complexes are generally poor catalysts for C–H amination: in this catalyst, the enzyme's protein framework confers activity on an otherwise unreactive iron-haem cofactor