Automated identification of elemental ions in macromolecular crystal structures.

Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed

Phosphoproteomics analysis of Alzheimer's disease

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, February, 2021Cataloged from the official PDF version of thesis.Includes bibliographical references (pages [137]-[153]).Alzheimer's disease (AD) is a form of dementia characterized by the appearance of amyloid-[beta] plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Despite numerous clinical trials, a limited understanding of disease pathogenesis has prevented the development of effective therapies. Several lines of genetic and biomolecular evidence indicate that AD progression involves cellular signaling through neuronal and glial protein phosphorylation networks. In order to understand which phosphorylation networks are dysregulated, I use mass spectrometry to characterize the phosphoproteome of post-mortem brain tissue from AD patients and multiple mouse models of AD. Using computational analysis, I identified several signaling pathways that are dysregulated before neurodegeneration occurs. Many of these signaling factors were expressed primarily in non-neuronal cell types, including microglia, astrocytes, and oligodendrocytes.My results highlight potential therapeutic targets in the signaling responses of glial cells and are split into two parts. In the first part of this thesis, I have quantified the phosphoproteome of the CK-p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. I identified a shared response involving Siglec-F which was upregulated on a subset of reactive microglia. The human paralog Siglec-8 was also found to be upregulated on microglia in AD. Siglec-F and Siglec-8 were upregulated following microglial activation with interferon gamma (IFN[gamma]) in BV-2 cell line and human stem-cell derived microglia models. Siglec-F overexpression activates an endocytic and pyroptotic inflammatory response in BV-2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine-based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV-2 cells.Collectively, my results point to an important role for mouse Siglec-F and human Siglec-8 in regulating microglial activation during neurodegeneration. In the second part of this thesis, I performed a combined analysis of the tyrosine, serine, and threonine phosphoproteome, and proteome of temporal cortex tissue from AD patients and aged matched controls. I identified several co-correlated peptide modules that were associated with varying levels of Tau, oligodendrocyte, astrocyte, microglia, and neuronal pathologies in different patients. I observed phosphorylation sites on known Tau-kinases and other novel signaling factors that were correlated these peptide modules. Finally, I used a data-driven statistical modeling approach to identify individual peptides and co-correlated signaling networks that were predictive of AD pathologies. Together, these results build a map of pathology-associated phosphorylation signaling events occurring in AD.by Nader Francis Morshed.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Biological Engineerin

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network

Obesity-associated type 2 diabetes and accompanying diseases have developed into a leading human health risk across industrialized and developing countries. The complex molecular underpinnings of how lipid overload and lipid metabolites lead to the deregulation of metabolic processes are incompletely understood. We assessed hepatic post-translational alterations in response to treatment of cells with saturated and unsaturated free fatty acids and the consumption of a high-fat diet by mice. These data revealed widespread tyrosine phosphorylation changes affecting a large number of enzymes involved in metabolic processes as well as canonical receptor-mediated signal transduction networks. Targeting two of the most prominently affected molecular features in our data, SRC-family kinase activity and elevated reactive oxygen species, significantly abrogated the effects of saturated fat exposure in vitro and high-fat diet in vivo. In summary, we present a comprehensive view of diet-induced alterations of tyrosine signaling networks, including proteins involved in fundamental metabolic pathways.National Institutes of Health (U.S.) (Grant DK090963

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network

Abstract Obesity‐associated type 2 diabetes and accompanying diseases have developed into a leading human health risk across industrialized and developing countries. The complex molecular underpinnings of how lipid overload and lipid metabolites lead to the deregulation of metabolic processes are incompletely understood. We assessed hepatic post‐translational alterations in response to treatment of cells with saturated and unsaturated free fatty acids and the consumption of a high‐fat diet by mice. These data revealed widespread tyrosine phosphorylation changes affecting a large number of enzymes involved in metabolic processes as well as canonical receptor‐mediated signal transduction networks. Targeting two of the most prominently affected molecular features in our data, SRC‐family kinase activity and elevated reactive oxygen species, significantly abrogated the effects of saturated fat exposure in vitro and high‐fat diet in vivo. In summary, we present a comprehensive view of diet‐induced alterations of tyrosine signaling networks, including proteins involved in fundamental metabolic pathways

Phlya/adjustText: 1.0.1

<p>Ship necessary interval overlap code from bioframe, remove bioframe dependency</p&gt

Phlya/adjustText: 1.0.2

<p>Fix packaging</p&gt

Phlya/adjustText: 1.0.0

<p>Major release with the new engine and breaking API changes. Everything should be much faster! Also bugfixes and small improvements.</p> <h2>What's Changed</h2> <ul> <li>Fix using correct canvas for drawing and input empty list by @oscargus in https://github.com/Phlya/adjustText/pull/141</li> <li>Add a bit of info to setup.py by @oscargus in https://github.com/Phlya/adjustText/pull/142</li> <li>Implement new engine! by @Phlya in https://github.com/Phlya/adjustText/pull/139</li> <li>New get_renderer() function that should function with more backends and matplotlib versions by @oliver-s-lee in https://github.com/Phlya/adjustText/pull/149</li> <li>Fix docstring typos and defaults by @nvaulin in https://github.com/Phlya/adjustText/pull/150</li> <li>Fix long_description for PyPI upload by @penguinpee in https://github.com/Phlya/adjustText/pull/160</li> <li>Add <code>iter_lim</code> to <code>adjust_text()</code> function argument by @136s in https://github.com/Phlya/adjustText/pull/165</li> </ul> <h2>New Contributors</h2> <ul> <li>@oscargus made their first contribution in https://github.com/Phlya/adjustText/pull/141</li> <li>@oliver-s-lee made their first contribution in https://github.com/Phlya/adjustText/pull/149</li> <li>@nvaulin made their first contribution in https://github.com/Phlya/adjustText/pull/150</li> <li>@penguinpee made their first contribution in https://github.com/Phlya/adjustText/pull/160</li> <li>@136s made their first contribution in https://github.com/Phlya/adjustText/pull/165</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/Phlya/adjustText/compare/0.8.0...v1.0</p&gt

Phlya/adjustText: 1.0.4

<p>Minor changes, removed unnecessary pandas import.</p&gt

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration

Alzheimer’s disease (AD) is characterized by the appearance of amyloid-β plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Using mass spectrometry, we have quantified the phosphoproteome of the CK-p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. We identified a shared response involving Siglec-F which was upregulated on a subset of reactive microglia. The human paralog Siglec-8 was also upregulated on microglia in AD. Siglec-F and Siglec-8 were upregulated following microglial activation with interferon gamma (IFNγ) in BV-2 cell line and human stem cell-derived microglia models. Siglec-F overexpression activates an endocytic and pyroptotic inflammatory response in BV-2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine-based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV-2 cells. Collectively, our results point to an important role for mouse Siglec-F and human Siglec-8 in regulating microglial activation during neurodegeneration.NIH (Grants T32GM008334, U54-CA210180, R37-NS051874 and RF1-AG054321