Cryo-electron tomography (cryo-ET) allows researchers to image cells in their native, hydrated state at the highest resolution currently possible. The technique has several limitations, however, that make analyzing data it generates time-intensive and difficult. Hand segmenting a single tomogram can take from hours days, but microscope easily generate 50 or more tomograms day. Current deep learning segmentation programs for cryo-ET do exist, are limited one structure time. Here, multi-slice...

Nucleosome chains fold and self-associate to form higher-order structures whose internal organization is unknown. Here, cryoelectron tomography (cryo-ET) of native human chromatin reveals intrinsic folding motifs such as (1) non-uniform nucleosome stacking, (2) intermittent parallel perpendicular orientations adjacent planes, (3) a regressive chain path, which deviates from the direct zigzag topology seen in reconstituted nucleosomal arrays. By examining self-associated structures, we...

Deep learning excels at cryo-tomographic image restoration and segmentation tasks but is hindered by a lack of training data. Here we introduce cryo-TomoSim (CTS), MATLAB-based software package that builds coarse-grained models macromolecular complexes embedded in vitreous ice then simulates transmitted electron tilt series for tomographic reconstruction. We demonstrate the effectiveness these simulated datasets different deep use on real cryotomographic reconstructions. Computer-generated...

Abstract Deep learning excels at segmenting objects within noisy cryo-electron tomograms, but the approach is typically bottlenecked by access to ground truth training data. To address this issue we have developed CryoTomoSim (CTS), an open-source software package that builds coarse-grained models of macromolecular complexes embedded in vitreous ice and then simulates transmitted electron tilt series for tomographic reconstruction. Using CTS outputs, demonstrate effects key microscope...

Abstract Human papillomavirus (HPV)-positive head and neck cancers, predominantly oropharyngeal squamous cell carcinoma (OPSCC), exhibit epidemiologic, clinical, molecular characteristics distinct from those OPSCCs lacking HPV. We applied a combination of whole-genome sequencing optical genome mapping to interrogate the structure HPV-positive OPSCCs. found that virus had integrated in host two thirds tumors examined but resided solely extrachromosomally other third. Integration occurred at...

Parkinson's disease is marked clinically by motor dysfunction and pathologically dopaminergic cell loss in the substantia nigra iron accumulation nigra. The driver underlying remains unknown could be genetic or environmental. HFE protein critical for regulation of cellular uptake. Mutations within this are associated with increased including brain. We have focused on commonly occurring H63D variant gene as a modifier number neurodegenerative diseases. To investigate role genotype, we...

Cryo-electron tomography (cryo-ET) allows researchers to image cells in their native, hydrated state at the highest resolution currently possible. The technique has several limitations, however, that make analyzing data it generates time-intensive and difficult. Hand segmenting a single tomogram can take from hours days, but microscope easily generate 50 or more tomograms day. Current deep learning segmentation programs for cryo-ET do exist, are limited one structure time. Here, multi-slice...

Increased expression of the peptide hormone retinol-binding protein 4 (RBP4) has been implicated in development insulin resistance, type 2 diabetes, and visual dysfunction. Prior investigations mechanisms that influence RBP4 synthesis have focused solely on changes mRNA abundance. Yet, production many secreted proteins is controlled at level translation, as it allows for a rapid reversible change expression. Herein, we evaluated Rbp4 translation using sucrose density gradient centrifugation....

The H63D-HFE single nucleotide polymorphism (SNP) has been associated with brain iron dysregulation; however, the emergent role of this missense variant in structure and function yet to be determined. Previous work demonstrated that HFE SNP carriers have reduced white matter magnetic resonance imaging (MRI) proton relaxation rates. mechanism by which alterations perturb MRI is unknown as how these metrics are related myelin integrity.Fifteen subjects heterozygous for HFE-H63D 25 controls...

Cryo-electron tomography has seen an explosion in growth due to recent advances resolution, preparation workflows, and availability of TEM microscopes.Yet, these leaps data quantity, quality, diversity have not been matched with advancements analytical tools, especially considering the amount raw parse.Neural networks demonstrated capacity permit analysis tomograms excellent accuracy, but often significant startup investment barriers remain narrowly focused training requirements...

SUMMARY Nucleosome chains fold and self-associate to form higher order structures whose internal organization is unknown. Here, cryo-electron tomography (cryo-ET) of native human chromatin reveals novel folding motifs such as 1) non-uniform nucleosome stacking, 2) intermittent parallel perpendicular orientations adjacent planes, 3) an inverse zigzag chain path, which deviates from the direct topology seen in reconstituted nucleosomal arrays. By examining these self-associated structures, we...

Journal Article Phantoms Improve Robustness of Deep Learning Automated Segmentation in Cryotomography Get access Jessica Heebner, Heebner Pennsylvania State University College Medicine. Department Biochemistry and Molecular Biology Hershey, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Carson Purnell, Purnell Mike Marsh, Marsh Object Research Systems. Denver, CO, Matthew Swulius Corresponding Author: mts286@psu.edu Microscopy Microanalysis, Volume 28, Issue...

The loss of olfactory function is known to occur early in the development Alzheimer's disease (AD) prior clinical symptoms. cellular and neurological basis for involvement system remains unclear. 18F-fludeoxyglucose (FDG) positron emission tomography (PET) data from ADNI were analyzed characterize metabolism region AD (n=16), mild-cognitive impaired (MCI) (N=149), age-matched cognitively normal (CN) controls(N=80). In contrast medial temporal lobe FDG hypo-metabolism within default mode, a...

Abstract Cerebellar involvement in Alzheimer’s disease (AD) has not been studied to the extent that cortical neuropathological changes have. Historical and recent histopathological literature demonstrate cerebellar AD pathology while functional investigation demonstrated disrupted intrinsic – connectivity AD. Additionally, olfactory deficits occur early AD, prior onset of clinical symptoms. The neurological basis for cerebellum system course remain unclear. 18 F-fludeoxyglucose (FDG)...

Iron accumulation in the brain and oxidative stress are observed a number of neurodegenerative disorders such as Alzheimer's disease (AD). Common mutations that lead to high iron overload has been associated with two gene variants within HFE gene, C282Y H63D, transferrin (Tf) C2. Within these found increased frequency patients (estimates between 20-50%). The goal this work was understand how C2 effect transverse relaxation AD hypothesis will result rate brains C282Y, or carriers....

Iron accumulation in the brain and oxidative stress are observed a number of neurodegenerative disorders such as Alzheimer's disease (AD). Common mutations that lead to high iron overload has been associated with two gene variants within HFE gene, C282Y H63D, transferrin (Tf) C2. Within these found increased frequency patients (estimates between 20-50%). The goal this work was understand how C2 effect transverse relaxation AD hypothesis will result rate brains C282Y, or carriers....

Nucleosome chains fold and self-associate to form higher order structures whose internal organization is unknown. Here, cryo-electron tomography (cryo-ET) of native human chromatin reveals novel folding motifs such as 1) non-uniform nucleosome stacking, 2) intermittent parallel perpendicular orientations adjacent planes, 3) an inverse zigzag chain path, which deviates from the direct topology seen in reconstituted nucleosomal arrays. By examining these self-associated structures, we observed...