Karim AS, Dudley QM, Juminaga A, Yuan Y, Crowe SA, Heggestad JT, Garg S, Abdalla T, Grubbe WS, Rasor BJ, Coar DN, Torculas M, Krein M, Liew FE, Quattlebaum A, Jensen RO, Stuart JA, Simpson SD, Köpke M, and Jewett MC
Nature chemical biology [Nat Chem Biol] 2020 Jun 15. Date of Electronic Publication: 2020 Jun 15.
The design and optimization of biosynthetic pathways for industrially relevant, non-model organisms is challenging due to transformation idiosyncrasies, reduced numbers of validated genetic parts and a lack of high-throughput workflows. Here we describe a platform for in vitro prototyping and rapid optimization of biosynthetic enzymes (iPROBE) to accelerate this process. In iPROBE, cell lysates are enriched with biosynthetic enzymes by cell-free protein synthesis and then metabolic pathways are assembled in a mix-and-match fashion to assess pathway performance. We demonstrate iPROBE by screening 54 different cell-free pathways for 3-hydroxybutyrate production and optimizing a six-step butanol pathway across 205 permutations using data-driven design. Observing a strong correlation (r = 0.79) between cell-free and cellular performance, we then scaled up our highest-performing pathway, which improved in vivo 3-HB production in Clostridium by 20-fold to 14.63 ± 0.48 g l -1 . We expect iPROBE to accelerate design-build-test cycles for industrial biotechnology.
Geronazzo M, Vieira LS, Nilsson NC, Udesen J, and Serafin S
IEEE transactions on visualization and computer graphics [IEEE Trans Vis Comput Graph] 2020 May; Vol. 26 (5), pp. 1912-1922. Date of Electronic Publication: 2020 Feb 13.
Directivity and gain in microphone array systems for hearing aids or hearable devices allow users to acoustically enhance the information of a source of interest. This source is usually positioned directly in front. This feature is called acoustic beamforming. The current study aimed to improve users' interactions with beamforming via a virtual prototyping approach in immersive virtual environments (VEs). Eighteen participants took part in experimental sessions composed of a calibration procedure and a selective auditory attention voice-pairing task. Eight concurrent speakers were placed in an anechoic environment in two virtual reality (VR) scenarios. The scenarios were a purely virtual scenario and a realistic 360° audio-visual recording. Participants were asked to find an individual optimal parameterization for three different virtual beamformers: (i) head-guided, (ii) eye gaze-guided, and (iii) a novel interaction technique called dual beamformer, where head-guided is combined with an additional hand-guided beamformer. None of the participants were able to complete the task without a virtual beamformer (i.e., in normal hearing condition) due to the high complexity introduced by the experimental design. However, participants were able to correctly pair all speakers using all three proposed interaction metaphors. Providing superhuman hearing abilities in the form of a dual acoustic beamformer guided by head and hand movements resulted in statistically significant improvements in terms of pairing time, suggesting the task-relevance of interacting with multiple points of interests.
Rodallec A, Franco C, Robert S, Sicard G, Giacometti S, Lacarelle B, Bouquet F, Savina A, Lacroix R, Dignat-George F, Ciccolini J, Poncelet P, and Fanciullino R
Scientific reports [Sci Rep] 2020 Mar 05; Vol. 10 (1), pp. 4147. Date of Electronic Publication: 2020 Mar 05.
Developing targeted nanoparticles is a rising strategy to improve drug delivery in oncology. Antibodies are the most commonly used targeting agents. However, determination of their optimal number at the surface remains a challenging issue, mainly due to the difficulties in measuring precisely surface coating levels when prototyping nanoparticles. We developed an original quantitative assay to measure the exact number of coated antibodies per nanoparticle. Using flow cytometry optimized for submicron particle analysis and beads covered with known amounts of human IgG-kappa mimicking various amounts of antibodies, this new method was tested as part of the prototyping of docetaxel liposomes coated with trastuzumab against Her2+ breast cancer. This quantification method allowed to discriminate various batches of immunoliposomes depending on their trastuzumab density on nanoparticle surface (i.e., 330 (Immunoliposome-1), 480 (Immunoliposome-2) and 690 (Immunoliposome-3), p = 0.004, One-way ANOVA). Here we showed that optimal number of grafted antibodies on nanoparticles should be finely tuned and highest density of targeting agent is not necessarily associated with highest efficacy. Overall, this new method should help to better prototype third generation nanoparticles.