Pix3D: Dataset and Methods for Single-Image 3D Shape Modeling

We study 3D shape modeling from a single image and make contributions to it in three aspects. First, we present Pix3D, a large-scale benchmark of diverse image-shape pairs with pixel-level 2D-3D alignment. Pix3D has wide applications in shape-related tasks including reconstruction, retrieval, viewpoint estimation, etc. Building such a large-scale dataset, however, is highly challenging; existing datasets either contain only synthetic data, or lack precise alignment between 2D images and 3D shapes, or only have a small number of images. Second, we calibrate the evaluation criteria for 3D shape reconstruction through behavioral studies, and use them to objectively and systematically benchmark cutting-edge reconstruction algorithms on Pix3D. Third, we design a novel model that simultaneously performs 3D reconstruction and pose estimation; our multi-task learning approach achieves state-of-the-art performance on both tasks.Comment: CVPR 2018. The first two authors contributed equally to this work. Project page: http://pix3d.csail.mit.ed

Metabolic engineering of the L-phenylalanine pathway in Escherichia coli for the production of S- or R-mandelic acid

<p>Abstract</p> <p>Background</p> <p>Mandelic acid (MA), an important component in pharmaceutical syntheses, is currently produced exclusively via petrochemical processes. Growing concerns over the environment and fossil energy costs have inspired a quest to develop alternative routes to MA using renewable resources. Herein we report the first direct route to optically pure MA from glucose via genetic modification of the L-phenylalanine pathway in <it>E. coli</it>.</p> <p>Results</p> <p>The introduction of hydroxymandelate synthase (HmaS) from <it>Amycolatopsis orientalis </it>into <it>E. coli </it>led to a yield of 0.092 g/L S-MA. By combined deletion of competing pathways, further optimization of S-MA production was achieved, and the yield reached 0.74 g/L within 24 h. To produce R-MA, hydroxymandelate oxidase (Hmo) from <it>Streptomyces coelicolor </it>and D-mandelate dehydrogenase (DMD) from <it>Rhodotorula graminis </it>were co-expressed in an S-MA-producing strain, and the resulting strain was capable of producing 0.68 g/L R-MA. Finally, phenylpyruvate feeding experiments suggest that HmaS is a potential bottleneck to further improvement in yields.</p> <p>Conclusions</p> <p>We have constructed <it>E. coli </it>strains that successfully accomplished the production of S- and R-MA directly from glucose. Our work provides the first example of the completely fermentative production of S- and R-MA from renewable feedstock.</p

Pix3D: Dataset and Methods for Single-Image 3D Shape Modeling

We study 3D shape modeling from a single image and make contributions to it in three aspects. First, we present Pix3D, a large-scale benchmark of diverse image-shape pairs with pixel-level 2D-3D alignment. Pix3D has wide applications in shape-related tasks including reconstruction, retrieval, viewpoint estimation, etc. Building such a large-scale dataset, however, is highly challenging; existing datasets either contain only synthetic data, or lack precise alignment between 2D images and 3D shapes, or only have a small number of images. Second, we calibrate the evaluation criteria for 3D shape reconstruction through behavioral studies, and use them to objectively and systematically benchmark cutting-edge reconstruction algorithms on Pix3D. Third, we design a novel model that simultaneously performs 3D reconstruction and pose estimation; our multi-task learning approach achieves state-of-the-art performance on both tasks.Comment: CVPR 2018. The first two authors contributed equally to this work. Project page: http://pix3d.csail.mit.ed

A Pioneering Career in Catalysis: Manfred T. Reetz

In this invited Account, we highlight the enormous scientific breadth of our mentor Professor Manfred T. Reetz. It stretches from the development of organometallic reagents and transition metal catalysts to the adventurous idea of directed evolution of chemo-, stereo-, and regioselective enzymes, which he considered to be most important. We hope to show that Reetz did not consider these research areas to be totally unrelated realms, and attempt to reveal his transdisciplinary way of thinking about methodology development. Since biocatalysis has become crucial for chemical synthesis, we mainly focus on Reetz's contributions in this area. Some personal reflections from some of his former co-workers are also included, which reveal the stimulating atmosphere in the Reetz group in terms of science, career advice, and the importance of ethical considerations. </p

Peroxygenase-Catalyzed Selective Synthesis of Calcitriol Starting from Alfacalcidol

Calcitriol is an active analog of vitamin D3 and has excellent physiological activities in regulating healthy immune function. To synthesize the calcitriol compound, the concept of total synthesis is often adopted, which typically involves multiple steps and results in an overall low yield. Herein, we envisioned an enzymatic approach for the synthesis of calcitriol. Peroxygenase from Agrocybe aegerita (AaeUPO) was used as a catalyst to hydroxylate the C-H bond at the C-25 position of alfacalcidol and yielded the calcitriol in a single step. The enzymatic reaction yielded 80.3% product formation in excellent selectivity, with a turnover number up to 4000. In a semi-preparative scale synthesis, 72% isolated yield was obtained. It was also found that AaeUPO is capable of hydroxylating the C-H bond at the C-1 position of vitamin D3, thereby enabling the calcitriol synthesis directly from vitamin D3

A Pioneering Career in Catalysis: Manfred T. Reetz

In this invited Account, we highlight the enormous scientific breadth of our mentor Professor Manfred T. Reetz. It stretches from the development of organometallic reagents and transition metal catalysts to the adventurous idea of directed evolution of chemo-, stereo-, and regioselective enzymes, which he considered to be most important. We hope to show that Reetz did not consider these research areas to be totally unrelated realms, and attempt to reveal his transdisciplinary way of thinking about methodology development. Since biocatalysis has become crucial for chemical synthesis, we mainly focus on Reetz's contributions in this area. Some personal reflections from some of his former co-workers are also included, which reveal the stimulating atmosphere in the Reetz group in terms of science, career advice, and the importance of ethical considerations. BT/Biocatalysi

Multiparameter Optimization in Directed Evolution: Engineering Thermostability, Enantioselectivity, and Activity of an Epoxide Hydrolase

The challenge of optimizing several parameters in the directed evolution of enzymes remains a central issue. In this study we address the thermostability, enantioselectivity, and activity of limonene epoxide hydrolase (LEH) as the catalyst in the hydrolytic desymmetrization of cyclohexene oxide with formation of (<i>R</i>,<i>R</i>)- and (<i>S</i>,<i>S</i>)-cyclohexane-1,2-diol. Wild type LEH shows a thermostability of <i>T</i>₅₀³⁰ = 41 °C and an enanioselectivity of 2% ee (<i>S</i>,<i>S</i>). Two approaches are described herein. In one strategy, the mutations generated previously by Janssen, Baker, and co-workers for notably increased thermostability are combined with mutations evolved earlier for enhanced enantioselectivity. Although highly enantioselective <i>R</i>,<i>R</i> and <i>S</i>,<i>S</i> variants (92–93% ee) with increases in <i>T</i>₅₀³⁰ by 10–11 °C were obtained, relative to wild type LEH the tradeoff in activity was significant. The second strategy based on the simultaneous optimization of both parameters using iterative saturation mutagenesis (ISM) with minimized tradeoff in activity proved to be superior. Several notably improved variants were observed, a reasonable “compromise” being <i>R</i>,<i>R</i>- and <i>S</i>,<i>S</i>-selective LEH variants (80–94% ee) showing enhanced thermostability by 5–10 °C and still reasonable levels of activity. Analysis of the X-ray structure of the <i>S</i>,<i>S</i> variant (94% ee) with and without diol product sheds light on the origin of altered stereoselectivity