Towards Visual Proteomics at High Resolution

Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations. (C) 2021 Published by Elsevier Ltd

Polyglutamine inclusion body toxicity

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141741/1/mds27226_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141741/2/mds27226.pd

Teachers’ assessment of self-regulated learning: linking professional competences, assessment practices, and judgment accuracy

Self-regulated learning (SRL) is crucial for successful lifelong learning and an important educational goal. For students to develop SRL skills, they need appropriate SRL support from teachers in the classroom. Teachers, who are aware of their students’ strengths and weaknesses in SRL, can promote SRL more adaptively. This requires teachers to assess students’ SRL skills accurately. However, there is little research on teachers’ diagnostic competences in SRL. To address this research gap, the present exploratory study investigates teachers’ content knowledge about SRL, assessment activities, and accuracy in judging their students’ SRL. Furthermore, the study examines whether teachers’ characteristics and competences in SRL are associated with the accuracy of their judgments. The study included 41 lower secondary school teachers and their 173 students. The students completed metacognitive knowledge tests on several SRL skills while the teachers made predictions about the students’ metacognitive knowledge of those SRL skills. The results indicate that not all teachers were familiar with the assessment of SRL. Moreover, teachers exhibited greater familiarity with offline assessments of SRL than online assessments and a noteworthy proportion of teachers employed assessment activities that were not diagnostic of SRL. Low correlations between students’ actual test scores and teachers’ judgments generally revealed low accuracy for teachers in assessing their students’ metacognitive knowledge of various SRL skills. Teachers’ characteristics and competences in SRL were mainly uncorrelated with their judgment accuracy. Overall, these results highlight the need for further attention and support for teachers in developing their diagnostic competences in SRL

Investigating the Structure of Neurotoxic Protein Aggregates Inside Cells.

Neurodegenerative diseases affect the lives of millions of people across the world, being particularly prevalent in the aging population. Despite huge research efforts, conclusive insights into the disease mechanisms are still lacking. Therefore, therapeutic strategies are limited to symptomatic treatments. A common histopathological hallmark of many neurodegenerative diseases is the presence of large pathognomonic protein aggregates, but their role in the disease pathology is unclear and subject to controversy. Here, we discuss imaging methods allowing investigation of these structures within their cellular environment: conventional electron microscopy (EM), super-resolution light microscopy (SR-LM), and cryo-electron tomography (cryo-ET). Multidisciplinary approaches are key for understanding neurodegenerative diseases and may contribute to the development of effective treatments. For simplicity, we focus on huntingtin aggregates, characteristic of Huntington's disease. Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.Dedicated to the memory of Professor Dr. rer. nat. Edmund Bäuerlein (1932–2019)

Inertial focusing of a dilute suspension in pipe flow

The dynamics of rigid particle suspensions in a wall-bounded laminar flow present several non-trivial and intriguing features, including particle ordering, lateral transport, and the appearance of stable, preferential locations like the Segr\'e-Silberberg annulus. The formation of more than one annulus is a particularly puzzling phenomenon that is still not fully explained. Here, we present numerical simulation results of a dilute suspension of particles in (periodic) pipe flow based on the lattice Boltzmann and the discrete element methods (DEM). Our simulations provide access to the full radial position history of the particles while traveling downstream. This allows to accurately quantify the transient and steady states. We observe the formation of the secondary, inner annulus and show that its position invariably shifts toward the Segr\'e-Silberberg one if the channel is sufficiently long, proving that it is, in fact, a transient feature for Reynolds numbers (Re) up to 600. We quantify the variation of the channel focusing length ($L_s/2R$) with Re. Interestingly and unlike the theoretical prediction for a point-like particle, we observe that $L_s/2R$ increases with Re for both the single particle and the suspension

Asymmetrical flow field-flow fractionation hyphenated to Orbitrap high resolution mass spectrometry for the determination of (functionalised) aqueous fullerene aggregates

AbstractIn this short communication we report on the technical implementations of coupling an asymmetric flow field-flow fractionation (AF4) instrument to a high resolution mass spectrometer (Orbitrap) using an atmospheric photoionisation interface. This will allow for the first time online identification of different fullerenes in aqueous samples after their aggregates have been fractionated in the FFF channel. Quality parameters such as limits of detection (LODs), limits of quantification (LOQs) or linear range were evaluated and they were in the range of hundreds ng/L for LODs and LOQs and the detector response was linear in the range tested (up to ∼20μg/L). The low detection and quantification limits make this technique useful for future environmental or ecotoxicology studies in which low concentration levels are expected for fullerenes and common on-line detectors such as UV or MALS do not have enough sensitivity and selectivity

The Zebrafish Breathes new Life into the Study of Tuberculosis

Tuberculosis (TB) is a global health emergency. Up to one-third of the world’s population is infected with Mycobacterium tuberculosis, and the pathogen continues to kill 1.5 million people annually. Currently, the means for preventing, diagnosing, and treating TB are unsatisfactory. One of the main reasons for the poor progress in TB research has been a lack of good animal models to study the latency, dormancy, and reactivation of the disease. Although sophisticated in vitro and in silico methods suitable for TB research are constantly being developed, they cannot reproduce the complete vertebrate immune system and its interplay with pathogens and vaccines. However, the zebrafish has recently emerged as a useful alternative to more traditional models, such as mice, rabbits, guinea pigs, and non-human primates, for studying the complex pathophysiology of a mycobacterial infection. The model is based on the similarity between Mycobacterium marinum – a natural fish pathogen – and M. tuberculosis. In both zebrafish larvae and adult fish, an infection with M. marinum leads to the formation of macrophage aggregates and granulomas, which resemble the M. tuberculosis infections in humans. In this review, we will summarize the current status of the zebrafish model in TB research and highlight the advantages of using zebrafish to dissect mycobacterial virulence strategies as well as the host immune responses elicited against them. In addition, we will discuss the possibilities of using the adult zebrafish model for studying latency, dormancy, and reactivation in a mycobacterial infection