Motion artifact correction for cone beam CT stroke imaging: a prospective series.

BACKGROUND: Imaging assessment for acute ischemic stroke (AIS) patients in the angiosuite using cone beam CT (CBCT) has created increased interest since endovascular treatment became the first line therapy for proximal vessel occlusions. One of the main challenges of CBCT imaging in AIS patients is degraded image quality due to motion artifacts. This study aims to evaluate the prevalence of motion artifacts in CBCT stroke imaging and the effectiveness of a novel motion artifact correction algorithm for image quality improvement. METHODS: Patients presenting with acute stroke symptoms and considered for endovascular treatment were included in the study. CBCT scans were performed using the angiosuite X-ray system. All CBCT scans were post-processed using a motion artifact correction algorithm. Motion artifacts were scored before and after processing using a 4-point scale. RESULTS: We prospectively included 310 CBCT scans from acute stroke patients. 51% (n=159/310) of scans had motion artifacts, with 24% being moderate to severe. The post-processing algorithm improved motion artifacts in 91% of scans with motion (n=144/159), restoring clinical diagnostic capability in 34%. Overall, 76% of the scans were sufficient for clinical decision-making before correction, which improved to 93% (n=289/310) after post-processing with our algorithm. CONCLUSIONS: Our results demonstrate that CBCT motion artifacts are significantly reduced using a novel post-processing algorithm, which improved brain CBCT image quality and diagnostic assessment for stroke. This is an important step on the road towards a direct-to-angio approach for endovascular thrombectomy (EVT) treatment.

The butterfly effect: improving brain cone-beam CT image artifacts for stroke assessment using a novel dual-axis trajectory.

BACKGROUND: Cone-beam computed tomography (CBCT) imaging of the brain can be performed in the angiography suite to support various neurovascular procedures. Relying on CBCT brain imaging solely, however, still lacks full diagnostic confidence due to the inferior image quality compared with CT and various imaging artifacts that persist even with modern CBCT. OBJECTIVE: To perform a detailed evaluation of image artifact improvement using a new CBCT protocol which implements a novel dual-axis 'butterfly' trajectory. METHODS: Our study included 94 scans from 47 patients who received CBCT imaging for assessment of either ischemia or hemorrhage during a neurovascular procedure. Both a traditional uni-axis 'circular' and novel dual-axis 'butterfly' protocol were performed on each patient (same-patient control). Each brain scan was divided into six regions and scored out of 3 based on six artifacts originating from various physics-based and patient-based sources. RESULTS: The dual-axis trajectory produces CBCT images with significantly fewer image artifacts than the traditional circular scan (whole brain average artifact score, AS: 0.20 vs 0.33), with the greatest improvement in bone beam hardening (AS: 0.13 vs 0.78) and cone-beam artifacts (AS: 0.04 vs 0.55). CONCLUSIONS: Recent developments in CBCT imaging protocols have significantly improved image artifacts, which has improved diagnostic confidence for stroke and supports a direct-to-angiography suite transfer approach for patients with acute ischemic stroke.

Label-free 3D-CLEM Using Endogenous Tissue Landmarks.

Emerging 3D correlative light and electron microscopy approaches enable studying neuronal structure-function relations at unprecedented depth and precision. However, established protocols for the correlation of light and electron micrographs rely on the introduction of artificial fiducial markers, such as polymer beads or near-infrared brandings, which might obscure or even damage the structure under investigation. Here, we report a general applicable "flat embedding" preparation, enabling high-precision overlay of light and scanning electron micrographs, using exclusively endogenous landmarks in the brain: blood vessels, nuclei, and myelinated axons. Furthermore, we demonstrate feasibility of the workflow by combining in vivo 2-photon microscopy and focused ion beam scanning electron microscopy to dissect the role of astrocytic coverage in the persistence of dendritic spines.

Autophagy initiation by ULK complex assembly on ER tubulovesicular regions marked by ATG9 vesicles.

Autophagosome formation requires sequential translocation of autophagy-specific proteins to membranes enriched in PI3P and connected to the ER. Preceding this, the earliest autophagy-specific structure forming de novo is a small punctum of the ULK1 complex. The provenance of this structure and its mode of formation are unknown. We show that the ULK1 structure emerges from regions, where ATG9 vesicles align with the ER and its formation requires ER exit and coatomer function. Super-resolution microscopy reveals that the ULK1 compartment consists of regularly assembled punctate elements that cluster in progressively larger spherical structures and associates uniquely with the early autophagy machinery. Correlative electron microscopy after live imaging shows tubulovesicular membranes present at the locus of this structure. We propose that the nucleation of autophagosomes occurs in regions, where the ULK1 complex coalesces with ER and the ATG9 compartment.

Exometabolite niche partitioning among sympatric soil bacteria.

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.

FIB-SEM tomography of human skin telocytes and their extracellular vesicles.

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) - the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc.

3D Ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography.

The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.

A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria.

To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria.

The myosin-related motor protein Myo2 is an essential mediator of bud-directed mitochondrial movement in yeast.

The inheritance of mitochondria in yeast depends on bud-directed transport along actin filaments. It is a matter of debate whether anterograde mitochondrial movement is mediated by the myosin-related motor protein Myo2 or by motor-independent mechanisms. We show that mutations in the Myo2 cargo binding domain impair entry of mitochondria into the bud and are synthetically lethal with deletion of the YPT11 gene encoding a rab-type guanosine triphosphatase. Mitochondrial distribution defects and synthetic lethality were rescued by a mitochondria-specific Myo2 variant that carries a mitochondrial outer membrane anchor. Furthermore, immunoelectron microscopy revealed Myo2 on isolated mitochondria. Thus, Myo2 is an essential and direct mediator of bud-directed mitochondrial movement in yeast. Accumulating genetic evidence suggests that maintenance of mitochondrial morphology, Ypt11, and retention of mitochondria in the bud contribute to Myo2-dependent inheritance of mitochondria.

KMS1 and KMS2, two plant endoplasmic reticulum proteins involved in the early secretory pathway.

We have identified two endoplasmic reticulum (ER)-associated Arabidopsis proteins, KMS1 and KMS2, which are conserved among most species. Fluorescent protein fusions of KMS1 localised to the ER in plant cells, and over-expression induced the formation of a membrane structure, identified as ER whorls by electron microscopy. Hydrophobicity analysis suggested that KMS1 and KMS2 are integral membrane proteins bearing six transmembrane domains. Membrane protein topology was assessed by a redox-based topology assay (ReTA) with redox-sensitive GFP and confirmed by a protease protection assay. A major loop domain between transmembrane domains 2 and 3, plus the N- and C-termini were found on the cytosolic side of the ER. A C-terminal di(tri)-lysine motif is involved in retrieval of KMS1 and deletion led to a reduction of the GFP-KMS1 signal in the ER. Over-expression of KMS1/KMS2 truncations perturbed ER and Golgi morphology and similar effects were also seen when KMS1/KMS2 were knocked-down by RNA interference. Microscopy and biochemical experiments suggested that expression of KMS1/KMS2 truncations inhibited ER to Golgi protein transport.

A recycling-defective vacuolar sorting receptor reveals an intermediate compartment situated between prevacuoles and vacuoles in tobacco.

Plant vacuolar sorting receptors (VSRs) display cytosolic Tyr motifs (YMPL) for clathrin-mediated anterograde transport to the prevacuolar compartment. Here, we show that the same motif is also required for VSR recycling. A Y612A point mutation in Arabidopsis thaliana VSR2 leads to a quantitative shift in VSR2 steady state levels from the prevacuolar compartment to the trans-Golgi network when expressed in Nicotiana tabacum. By contrast, the L615A mutant VSR2 leaks strongly to vacuoles and accumulates in a previously undiscovered compartment. The latter is shown to be distinct from the Golgi stacks, the trans-Golgi network, and the prevacuolar compartment but is characterized by high concentrations of soluble vacuolar cargo and the rab5 GTPase Rha1(RabF2a). The results suggest that the prevacuolar compartment matures by gradual receptor depletion, leading to the formation of a late prevacuolar compartment situated between the prevacuolar compartment and the vacuole.

Biogenesis of the plant Golgi apparatus.

It has long been assumed that the individual cisternal stacks that comprise the plant Golgi apparatus multiply by some kind of fission process. However, more recently, it has been demonstrated that the Golgi apparatus can be experimentally disassembled and the reformation process from the ER (endoplasmic reticulum) monitored sequentially using confocal fluorescence and electron microscopy. Some other evidence suggests that Golgi stacks may arise de novo in cells. In the present paper, we review some of the more recent findings on plant Golgi stack biogenesis and propose a new model for their growth de novo from ER exit sites.

Inhibition of Golgi function causes plastid starch accumulation.

Little is known about possible interactions between chloroplasts and the Golgi apparatus, although there is increasing evidence for a direct Golgi to chloroplast transport pathway targeting proteins to their destinations within the membranes and stroma of plastids. Here data are presented showing that a blockage of secretion results in a significant increase of starch within plastids. Golgi disassembly promoted either by the secretory inhibitor brefeldin A or through an inducible Sar1-GTP system leads to dramatic starch accumulation in plastids, thus providing evidence for a direct interaction between plastids and Golgi activity. The possibility that starch accumulation is due either to elevated levels of cytosolic sugars because of loss of secretory Golgi activity or even to a blockage of amylase transport from the Golgi to the chloroplast is discussed.

Golgi membrane dynamics after induction of a dominant-negative mutant Sar1 GTPase in tobacco.

An inducible system has been established in Nicotiana tabacum plants allowing controlled expression of Sar1-GTP and thus the investigation of protein dynamics after inhibition of endoplasmic reticulum (ER) to Golgi transport. Complete Golgi disassembly and redistribution of Golgi markers into the ER was observed within 18-24h after induction. At the ultrastructural level Sar1-GTP expression led to a decrease in Golgi stack size followed by Golgi fragmentation and accumulation of vesicle remnants. Induction of Sar1-GTP resulted in redistribution of the green fluorescent protein (GFP)-tagged Arabidopsis golgins AtCASP and GC1 (golgin candidate 1, an Arabidopsis golgin 84 isoform) into the ER or cytoplasm, respectively. Additionally, both fusion proteins were observed in punctate structures, which co-located with a yellow fluorescent protein (YFP)-tagged version of Sar1-GTP. The Sar1-GTP-inducible system is compared with constitutive Sar1-GTP expression and brefeldin A treatment, and its potential for the study of the composition of ER exit sites and early cis-Golgi structures is discussed.

A missense mutation in the Arabidopsis COPII coat protein Sec24A induces the formation of clusters of the endoplasmic reticulum and Golgi apparatus.

How the endoplasmic reticulum (ER) and the Golgi apparatus maintain their morphological and functional identity while working in concert to ensure the production of biomolecules necessary for the cell's survival is a fundamental question in plant biology. Here, we isolated and characterized an Arabidopsis thaliana mutant that partially accumulates Golgi membrane markers and a soluble secretory marker in globular structures composed of a mass of convoluted ER tubules that maintain a connection with the bulk ER. We established that the aberrant phenotype was due to a missense recessive mutation in sec24A, one of the three Arabidopsis isoforms encoding the coat protomer complex II (COPII) protein Sec24, and that the mutation affects the distribution of this critical component at ER export sites. By contrast, total loss of sec24A function was lethal, suggesting that Arabidopsis sec24A is an essential gene. These results produce important insights into the functional diversification of plant COPII coat components and the role of these proteins in maintaining the dynamic identity of organelles of the early plant secretory pathway.

The syntaxins SYP31 and SYP81 control ER-Golgi trafficking in the plant secretory pathway.

Overexpression of the Golgi and endoplasmic reticulum (ER) syntaxins SYP31 and SYP81 strongly inhibits constitutive secretion. By comparing the secreted reporter alpha-amylase with the ER-retained reporter alpha-amylase-HDEL, it was concluded that SYP81 overexpression inhibits both retrograde and anterograde transport, while SYP31 overexpression mainly affected anterograde transport. Of the other interacting SNAREs investigated, only the overexpression of MEMB11 led to an inhibition of protein secretion. Although the position of a fluorescent tag does not influence the correct localization of the fusion protein, only N-terminal-tagged SYP31 retained the ability of the untagged SNARE to inhibit transport. C-terminal-tagged SYP31 failed to exhibit this effect. Overexpression of both wild-type and N-terminal-tagged syntaxins caused standard Golgi marker proteins to redistribute into the ER. Nevertheless, green fluorescent protein (GFP)-SYP31 was still visible as fluorescent punctae, which, unlike SYP31-GFP, were resistant to brefeldin A treatment. Immunogold electron microscopy showed that endogenous SYP81 is not only present at the ER but also in the cis Golgi, indicating that this syntaxin cycles between these two organelles. However, when expressed at non-inhibitory levels, YFP-SYP81 was seen to locate principally to subdomains of the ER. These punctate structures were physically separated from the Golgi, suggesting that they might possibly reflect the position of ER import sites.

The plant ER-Golgi interface.

The interface between the endoplasmic reticulum (ER) and the Golgi apparatus is a critical junction in the secretory pathway mediating the transport of both soluble and membrane cargo between the two organelles. Such transport can be bidirectional and is mediated by coated membranes. In this review, we consider the organization and dynamics of this interface in plant cells, the putative structure of which has caused some controversy in the literature, and we speculate on the stages of Golgi biogenesis from the ER and the role of the Golgi and ER on each other's motility.

Golgi regeneration after brefeldin A treatment in BY-2 cells entails stack enlargement and cisternal growth followed by division.

Brefeldin A (BFA) treatment stops secretion and leads to the resorption of much of the Golgi apparatus into the endoplasmic reticulum. This effect is reversible upon washing out the drug, providing a situation for studying Golgi biogenesis. In this investigation Golgi regeneration in synchronized tobacco BY-2 cells was followed by electron microscopy and by the immunofluorescence detection of ARF1, which localizes to the rims of Golgi cisternae and serves as an indicator of COPI vesiculation. Beginning as clusters of vesicles that are COPI positive, mini-Golgi stacks first become recognizable 60 min after BFA washout. They continue to increase in terms of numbers and length of cisternae for a further 90 min before overshooting the size of control Golgi stacks. As a result, increasing numbers of dividing Golgi stacks were observed 120 min after BFA washout. BFA-regeneration experiments performed on cells treated with BFA (10 microg mL(-1)) for only short periods (30-45 min) showed that the formation of ER-Golgi hybrid structures, once initiated by BFA treatment, is an irreversible process, the further incorporation of Golgi membranes into the ER continuing during a subsequent drug washout. Application of the protein kinase A inhibitor H-89, which effectively blocks the reassembly of the Golgi apparatus in mammalian cells, also prevented stack regeneration in BY-2 cells, but only at very high, almost toxic concentrations (>200 microm). Our data suggest that under normal conditions mitosis-related Golgi stack duplication may likely occur via cisternal growth followed by fission.