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Biology subjects

Zwart, P. H.

Publications and source records attributed to Zwart, P. H..

5 recordsLinked to original sources

Hyperspectral Segmentation of Plants in Fabricated Ecosystems

Hyperspectral imaging provides a powerful tool for analyzing above-ground plant characteristics in fabricated ecosystems, offering rich spectral information across diverse wavelengths. This study presents an efficient workflow for hyperspectral data segmentation and subsequent data analytics, minimizing the need for user annotation through the use of ensembles of sparse mixed-scale convolution neural networks. The segmentation process leverages the diversity of ensembles to achieve high accuracy with minimal labeled data, reducing labor-intensive annotation efforts. To further enhance robustness, we incorporate image alignment techniques to address spatial variability in the dataset. Down-stream analysis focuses on using the segmented data for processing spectral data, enabling monitoring of plant health. This approach not only provides a scalable solution for spectral segmentation but also facilitates actionable insights into plant conditions in complex, controlled environments. Our results demonstrate the utility of combining advanced machine learning techniques with hyperspectral analytics for high-throughput plant monitoring.

plant biology↗

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Structure determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure but is constrained by the need for large, well-ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction, and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular weight threshold required by single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure determination methods. Here we present a data processing scheme that combines routines from X-ray crystallography and new algorithms we developed to solve structures from tomograms of nanocrystals. This pipeline handles image processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. We also assess the tolerance of this workflow to the effects of radiation damage. Our simulations indicate a trade-off between a wider tilt-range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors but not merging errors can be overcome with additional datasets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.

biophysics↗

Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens

The adaptive immune system is highly sensitive to arrayed antigens, and multivalent display of viral glycoproteins on symmetric scaffolds has been found to substantially increase the elicitation of antigen-specific antibodies. Motivated by the considerable promise of this strategy for next-generation anti-viral vaccines, we set out to design new self-assembling protein nanoparticles with geometries specifically tailored to scaffold ectodomains of different viral glycoproteins. We first designed and characterized homo-trimers from designed repeat proteins with N-terminal helices positioned to match the C termini of several viral glycoprotein trimers. Oligomers found to experimentally adopt the designed configuration were then used to generate nanoparticles with tetrahedral, octahedral, or icosahedral symmetry. Examples of all three target symmetries were experimentally validated by cryo-electron microscopy and several were assessed for their ability to display viral glycoproteins via genetic fusion. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles display conformationally intact native-like HIV-1 Env, influenza hemagglutinin, and prefusion RSV F trimers in the predicted geometries. This work demonstrates that novel nanoparticle immunogens can be designed from the bottom up with atomic-level accuracy and provides a general strategy for precisely controlling epitope presentation and accessibility.

synthetic biology↗

Evaluating crystallographic likelihood functions using numerical quadratures

Intensity-based likelihood functions in crystallographic applications have the potential to enhance the quality of structures derived from marginal diffraction data. Their usage however is complicated by the ability to efficiently compute these targets functions. Here a numerical quadrature is developed that allows for the rapid evaluation of intensity-based likelihood functions in crystallographic applications. By using a sequence of change of variable transformations, including a non-linear domain compression operation, an accurate, robust, and efficient quadrature is constructed. The approach is flexible and can incorporate different noise models with relative ease.

biophysics↗

Minimally disruptive optical control of protein tyrosine phosphatase 1B

Protein tyrosine phosphatases regulate a myriad of essential subcellular signaling events, yet they remain difficult to study in their native biophysical context. Here we develop a minimally disruptive optical approach to control protein tyrosine phosphatase 1B (PTP1B)--an important regulator of receptor tyrosine kinases and a therapeutic target for the treatment of diabetes, obesity, and cancer--and we use that approach to probe the intracellular function of this enzyme. Our conservative architecture for photocontrol, which consists of a protein-based light switch fused to an allosteric regulatory element, preserves the native structure, activity, and subcellular localization of PTP1B, affords changes in activity that match those elicited by post-translational modifications inside the cell, and permits experimental analyses of the molecular basis of optical modulation. Findings indicate, most strikingly, that small changes in the activity of PTP1B can cause large shifts in the phosphorylation states of its regulatory targets.

biochemistry↗