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1. Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

   https://doi.org/10.1002/anie.201915063  

   Zhang, Yingwei; Reinhardt, Aleks; Wang, Pengfei; Song, Jie; Ke, Yonggang (March 2020, Angewandte Chemie International Edition)

   Abstract Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures. 

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2. Novo&Stitch: accurate reconciliation of genome assemblies via optical maps

   https://doi.org/10.1093/bioinformatics/bty255  

   Pan, Weihua; Wanamaker, Steve I.; Ah-Fong, Audrey M. V.; Judelson, Howard S.; Lonardi, Stefano (June 2018, Bioinformatics)

   Abstract MotivationDe novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other. ResultsThe concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical maps to accurately carry out assembly reconciliation (assuming that the assembled contigs are sufficiently long to be reliably aligned to the optical maps, e.g. 50 Kbp or longer). Experimental results demonstrate that Novo&Stitch can double the contiguity (N50) of the input assemblies without introducing mis-joins or reducing genome completeness. Availability and implementationNovo&Stitch can be obtained from https://github.com/ucrbioinfo/Novo_Stitch. 

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3. Precision Evaluation of Large Payload SCARA Robot for PCB Assembly

   https://doi.org/10.1115/msec2022-85534  

   Nimon, Andrew S.; Sherehiy, Andriy; Alqatamin, Moath; Wei, Danming; Popa, Dan O. (June 2022, ASME 2022 17th International Manufacturing Science and Engineering Conference)

   Abstract The placement of SMD components is usually performed with Cartesian type robots, a task known as pick-and-place (P&P). Small Selective Compliance Articulated Robot Arm (SCARA) robots are also growing in popularity for this use because of their quick and accurate performance. This paper describes the use of the Lean Robotic Micromanufacturing (LRM) framework applied on a large, 10kg payload, industrial SCARA robot for PCB assembly. The LRM framework guided the precision evaluation of the PCB assembly process and provided a prediction of the placement precision and yield. We experimentally evaluated the repeatability of the system, as well as the resulting collective errors during the assembly. Results confirm that the P&P task can achieve the required assembly tolerance of 200 microns without employing closed-loop visual servoing, therefore considerably decreasing the system complexity and assembly time. 

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4. Self-assembly coupled to liquid-liquid phase separation

   https://doi.org/10.1371/journal.pcbi.1010652  

   Hagan, Michael F.; Mohajerani, Farzaneh (May 2023, PLOS Computational Biology)

   Zhou, Huan-Xiang (Ed.)

   Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications. 

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5. An autoinhibitory clamp of actin assembly constrains and directs synaptic endocytosis

   https://doi.org/10.7554/eLife.69597  

   Del Signore, Steven J; Kelley, Charlotte F; Messelaar, Emily M; Lemos, Tania; Marchan, Michelle F; Ermanoska, Biljana; Mund, Markus; Fai, Thomas G; Kaksonen, Marko; Rodal, Avital Adah (July 2021, eLife)

   Synaptic membrane-remodeling events such as endocytosis require force-generating actin assembly. The endocytic machinery that regulates these actin and membrane dynamics localizes at high concentrations to large areas of the presynaptic membrane, but actin assembly and productive endocytosis are far more restricted in space and time. Here we describe a mechanism whereby autoinhibition clamps the presynaptic endocytic machinery to limit actin assembly to discrete functional events. We found that collective interactions between theDrosophilaendocytic proteins Nwk/FCHSD2, Dap160/intersectin, and WASp relieve Nwk autoinhibition and promote robust membrane-coupled actin assembly in vitro. Using automated particle tracking to quantify synaptic actin dynamics in vivo, we discovered that Nwk-Dap160 interactions constrain spurious assembly of WASp-dependent actin structures. These interactions also promote synaptic endocytosis, suggesting that autoinhibition both clamps and primes the synaptic endocytic machinery, thereby constraining actin assembly to drive productive membrane remodeling in response to physiological cues. 

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