Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons.

To unravel the complexity of biological processes, it is necessary to resolve the underlying protein organization down to single proteins. Here, we present a protocol for secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a DNA-PAINT-based super-resolution microscopy technique that is capable of resolving virtually unlimited protein species with single-protein resolution. We describe the steps to prepare neuronal cultures, troubleshoot and conduct SUM-PAINT experiments, and analyze the resulting feature-rich neuronal cell atlases using unsupervised machine learning approaches.

The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes.

DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a super-resolution fluorescence microscopy technique that achieves single-molecule 'blinking' by transient DNA hybridization. Despite blinking kinetics being largely independent of fluorescent dye choice, the dye employed substantially affects measurement quality. Thus far, there has been no systematic overview of dye performance for DNA-PAINT.

Spatial proteomics in neurons at single-protein resolution.

To understand biological processes, it is necessary to reveal the molecular heterogeneity of cells by gaining access to the location and interaction of all biomolecules. Significant advances were achieved by super-resolution microscopy, but such methods are still far from reaching the multiplexing capacity of proteomics. Here, we introduce secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a high-throughput imaging method that is capable of achieving virtually unlimited multiplexing at better than 15 nm resolution.

Advancing cell biology with nanoscale fluorescence imaging: essential practical considerations.

Recently, biologists have gained access to several far-field fluorescence nanoscopy (FN) technologies that allow the observation of cellular components with ~20 nm resolution. FN is revolutionizing cell biology by enabling the visualization of previously inaccessible subcellular details. While technological advances in microscopy are critical to the field, optimal sample preparation and labeling are equally important and often overlooked in FN experiments.

Independent, additive and interactive effects of acute normobaric hypoxia and cold on submaximal and maximal endurance exercise.

Purpose: To evaluate the independent and combined effects of hypoxia (FiO2 = 13.5%) and cold (- 20 °C) on physiological and perceptual responses to endurance exercise.

Methods: 14 trained male subjects ( O: 64 ± 5 mL/kg/min) randomly performed a discontinuous maximal incremental test to exhaustion on a motorized treadmill under four environmental conditions: Normothermic-Normoxia (N), Normothermic-Hypoxia (H), Cold-Normoxia (C) and Cold-Hypoxia (CH).

Age-dependent structural reorganization of utricular ribbon synapses.

In mammals, spatial orientation is synaptically-encoded by sensory hair cells of the vestibular labyrinth. Vestibular hair cells (VHCs) harbor synaptic ribbons at their presynaptic active zones (AZs), which play a critical role in molecular scaffolding and facilitate synaptic release and vesicular replenishment. With advancing age, the prevalence of vestibular deficits increases; yet, the underlying mechanisms are not well understood and the possible accompanying morphological changes in the VHC synapses have not yet been systematically examined.

A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy.

Imaging of living synapses has relied for over two decades on the overexpression of synaptic proteins fused to fluorescent reporters. This strategy alters the stoichiometry of synaptic components and ultimately affects synapse physiology. To overcome these limitations, here a nanobody is presented that binds the calcium sensor synaptotagmin-1 (NbSyt1).

Effects of low vs. moderate dose of recreational football on cardiovascular risk factors.

This study aimed to compare the effectiveness of recreational football performed once (LOW) vs. twice (MOD) a week on cardiovascular risk factors in healthy, sedentary men. Body composition, resting blood pressure, blood lipid profile and maximal oxygen consumption (VOmax) were measured at baseline, after a 12-week control and training period, using an interrupted time-series study (study 1,  = 18:  = 8, LOW and  = 10, MOD) nested in a randomized parallel trial (study 2,  = 34:  = 18 LOW and  = 16 MOD).

Protein lifetimes in aged brains reveal a proteostatic adaptation linking physiological aging to neurodegeneration.

Aging is a prominent risk factor for neurodegenerative disorders (NDDs); however, the molecular mechanisms rendering the aged brain particularly susceptible to neurodegeneration remain unclear. Here, we aim to determine the link between physiological aging and NDDs by exploring protein turnover using metabolic labeling and quantitative pulse-SILAC proteomics. By comparing protein lifetimes between physiologically aged and young adult mice, we found that in aged brains protein lifetimes are increased by ~20% and that aging affects distinct pathways linked to NDDs.

A Reliable Approach for Revealing Molecular Targets in Secondary Ion Mass Spectrometry.

Nano secondary ion mass spectrometry (nanoSIMS) imaging is a rapidly growing field in biological sciences, which enables investigators to describe the chemical composition of cells and tissues with high resolution. One of the major challenges of nanoSIMS is to identify specific molecules or organelles, as these are not immediately recognizable in nanoSIMS and need to be revealed by SIMS-compatible probes. Few laboratories have generated such probes, and none are commercially available.

In Vivo Protein Lifetime Measurements Across Multiple Organs in the Zebrafish.

Protein production and degradation are tightly regulated to prevent cellular structures from accumulating damage and to allow their correct functioning. A key aspect of this regulation is the protein half-life, corresponding to the time in which half of a specific protein population is exchanged with respect to its initial state. Proteome-wide techniques to investigate protein half-lives in vivo are emerging.

Monitoring mitochondrial translation in living cells.

Mitochondria possess a small genome that codes for core subunits of the oxidative phosphorylation system and whose expression is essential for energy production. Information on the regulation and spatial organization of mitochondrial gene expression in the cellular context has been difficult to obtain. Here we devise an imaging approach to analyze mitochondrial translation within the context of single cells, by following the incorporation of clickable non-canonical amino acids.

Talent Development in Young Cross-Country Skiers: Longitudinal Analysis of Anthropometric and Physiological Characteristics.

Very little is known about talent development and selection processes in young cross-country skiers. (1) to analyze the effect of age on anthropometric and physiological parameters in medium-to-high level cross-country skiers during the late teenage period; (2) to describe parameters' trend in selected talents after the late teenage period; (3) to define which characteristics during the late teenage period could discriminate against further talent selection. We found 14 male (M) and nine (F) athletes in our database, identified as talents by regional teams during the late teenage period, who performed the same diagonal-stride roller-skiing incremental test to exhaustion at 17 and 18 years old.

A comparative analysis of the mobility of 45 proteins in the synaptic bouton.

Many proteins involved in synaptic transmission are well known, and their features, as their abundance or spatial distribution, have been analyzed in systematic studies. This has not been the case, however, for their mobility. To solve this, we analyzed the motion of 45 GFP-tagged synaptic proteins expressed in cultured hippocampal neurons, using fluorescence recovery after photobleaching, particle tracking, and modeling.

A nanobody-based fluorescent reporter reveals human α-synuclein in the cell cytosol.

Aggregation and spreading of α-Synuclein (αSyn) are hallmarks of several neurodegenerative diseases, thus monitoring human αSyn (hαSyn) in animal models or cell cultures is vital for the field. However, the detection of native hαSyn in such systems is challenging. We show that the nanobody NbSyn87, previously-described to bind hαSyn, also shows cross-reactivity for the proteasomal subunit Rpn10.

The long noncoding RNA regulates presynaptic activity by interacting with the neurodegeneration-associated protein TDP-43.

The cellular and the molecular mechanisms by which long noncoding RNAs (lncRNAs) may regulate presynaptic function and neuronal activity are largely unexplored. Here, we established an integrated screening strategy to discover lncRNAs implicated in neurotransmitter and synaptic vesicle release. With this approach, we identified , a neuron-specific nuclear lncRNA conserved from rodents to humans.

A mass spectrometry workflow for measuring protein turnover rates in vivo.

Proteins are continually produced and degraded, to avoid the accumulation of old or damaged molecules and to maintain the efficiency of physiological processes. Despite its importance, protein turnover has been difficult to measure in vivo. Previous approaches to evaluating turnover in vivo have required custom labeling approaches, involved complex mass spectrometry (MS) analyses, or used comparative strategies that do not allow direct quantitative measurements.

The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain.

The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo.

Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions.

The turnover of brain proteins is critical for organism survival, and its perturbations are linked to pathology. Nevertheless, protein lifetimes have been difficult to obtain in vivo. They are readily measured in vitro by feeding cells with isotopically labeled amino acids, followed by mass spectrometry analyses.

Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission.

Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission.

BCAS1 expression defines a population of early myelinating oligodendrocytes in multiple sclerosis lesions.

Investigations into brain function and disease depend on the precise classification of neural cell types. Cells of the oligodendrocyte lineage differ greatly in their morphology, but accurate identification has thus far only been possible for oligodendrocyte progenitor cells and mature oligodendrocytes in humans. We find that breast carcinoma amplified sequence 1 (BCAS1) expression identifies an oligodendroglial subpopulation in the mouse and human brain.

Nonaqueous synthesis of TiO2 nanocrystals using TiF4 to engineer morphology, oxygen vacancy concentration, and photocatalytic activity.

Control over faceting in nanocrystals (NCs) is pivotal for many applications, but most notably when investigating catalytic reactions which occur on the surfaces of nanostructures. Anatase titanium dioxide (TiO(2)) is one of the most studied photocatalysts, but the shape dependence of its activity has not yet been satisfactorily investigated and many questions still remain unanswered. We report the nonaqueous surfactant-assisted synthesis of highly uniform anatase TiO(2) NCs with tailorable morphology in the 10-100 nm size regime, prepared through a seeded growth technique.