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Investigators form the Salk Institute for Biological Studies partnered with NCMIR to apply advanced EM techniques to study the connectivity of hypothalamic suprachiasmatic nucleus (SCN) neurons. The research reveals differences in synaptic input, dendritic network density, and criteria for identifying various axonic boutons within the SCN.

Investigators from Duke University leverage NCMIR’s expertise in multi-tilt STEM tomography to help characterize the ultrastructure and development of key constituents of retinal photoreceptor cells.

Professor George Spirou from the University of South Florida led an interdisciplinary consortium of investigators in the structural analysis of bushy cells in the mouse cochlear nucleus. The team, which included researchers from NCMIR, the University of North Carolina, and West Virginia University, combined advanced volume electron microscopy techniques with sophisticated computational modelling to predict heterogeneous bushy cell responses.

Scientists have long known that mitochondria, the "powerhouses" of cells, play a crucial role in the metabolism and energy production of cancer cells. However, until now, little was known about the relationship between the structural organization of mitochondrial networks and their functional bioenergetic activity at the level of whole tumors.

UCSD Investigators in the laboratory of Professor Takaki Komiyama partner with NCMIR to deepen understanding of the basics of information processing in the brain, and how such processing can flexibly change with learning.  Correlated light an electron microscopy was used to study the generation and development of learning-related dendritic spines, revealing new insight into the degree to which activity, location, and potentiation of existing spines affected the growth and maintenance of new spines.

NCMIR researchers join a consortium of investigators studying an autosomal dominant Alzheimer’s disease (ADAD) PSEN1 E280A carrier who was also homozygous for the APOE3 Christchurch (APOE3ch) variant and was protected against Alzheimer’s symptoms for almost three decades beyond the expected age of onset. Work reported in Acta Neuropathologica offers new insight into the Christchurch variant’s role in the distribution of tau pathology and the severity, progression, and clinical presentation of Alzheimer’s Disease, suggesting possible therapeutic strategies.

Mitochondria are known as the powerhouses of the cell, generating the energy that’s needed to fuel the functions that our cells carry out. Now, scientists at the Salk Institute and the National Center for Microscopy and Imaging Research (NCMIR) have taken a closer look at how mitochondria are maintained in nondividing cells, such as neurons, with the ultimate goal of developing a better understanding of how to prevent or treat age-related diseases. The researchers found that many of the proteins in mitochondria last much longer than expected, and that this stability likely protects them from damage. The findings were published October 28, 2021, in Developmental Cell.

Findings from a collaborative study conducted by scientists at the Gladstone Institutes, led by Senior Investigator Katerina Akassoglou, PhD, NCMIR and the University of Vienna, were recently published in the journal Brain.  This team explored the efficacy of drugs, currently in trials, for promoting the repair of myelin damage associated with multiple sclerosis. They identify a new line of therapeutics with the potential to stimulate myelin repair even in the presence of toxic blood leaks in the brain.

In the September 2018 issue of Nature Methods, NCMIR researchers debut a ready-to-use image segmentation solution for any lab.  The system, called CDeep3M, includes a pre-configured and publicly available deep convolutional neural network that can be run on the Amazon cloud compute platform.

In collaboration with Carl Zeiss Microscopy (www.zeiss.com), NCMIR researchers developed a new technology for improving the performance of serial blockface scanning EM (SBEM) using the Gatan 3View. This technology allows for the focused and synchronized delivery of nitrogen gas to the sample blockface during the imaging cycle to eliminate charging, greatly extending the utility of the volume imaging technique for even the most-charge-prone samples.

Scientists at The Scripps Research Institute (TSRI) and the National Center for Microscopy and Imaging Research (NCMIR) in La Jolla have revealed new clues to the wiring of the brain.  A team led by Associate Professor Anton Maximov, in collaboration with Dr. Mark Ellisman’s group, have found that neurons in brain regions that store memory can form networks in the absence of synaptic activity.

A team of researchers at the University of Wisconsin-Madison and UCSD/NCMIR  discovers that synapses in mouse cerebral cortex strengthen (grow larger) during wake to support learning but decline in strength (grow smaller) during sleep to consolidate memories and restore cellular function.

This method applied different lanthanides to label specific cellular components. The lanthanides’ electron energy-loss spectra were visualized, and the resulting elemental maps overlaid on a conventional greyscale EM image to “color-code” the labeled components and enable tracking of their movements over time across multiple images.

Applying a negative voltage to an SBEM stage creates a reversal potential that decreases the landing energy of probe-beam electrons. At a lower landing energy, probe electrons penetrate more shallowly, resulting in improved resolution. The reversal potential further accelerates backscattered electrons, leading to a large increase in their recorded signal by the detector.    

UCSD and NCMIR researchers introduce a powerful new approach for metabolic labeling and imaging of non-proteinaceous cellular components by light and electron microscopy.

Scientists at the National Center for Microscopy and Imaging Research (NCMIR) have summarized four recently developed, now widely used, electron microscopy (EM) probes (also called labels or tags) in a review to facilitate more general adoption of new probes and methods from the center.

Researchers at The Johns Hopkins University School of Medicine, the Hugo W. Moser Research Institute at Kennedy Krieger, Inc., and the National Center for Microscopy and Imaging Research demonstrated that, in a developing vertebrate ON, individual myelin segments can shorten in response to shortening in axon length, revealing a plasticity of myelin segments not previously known. Through volume EM-based quantification, the team further demonstrated that axon myelin segments shorten through selective astrocytic phagocytosis of small intra-segmental myelin dystrophies.

Researchers from UC San Francisco, the University of Freiburg (Germany), UC San Diego and its National Center for Microscopy and Imaging Research, the University of Glasgow (UK), King’s College London, and Stanford University team to establish a potential, previously unknown, mechanism by which the brain responds to injury.

Human memory can persist for a lifetime, yet the majority of synaptic proteins in the brain turn over at a rate of hours to days. Synthesizing, localizing, and stabilizing new protein copies at synapses are crucial factors in maintaining the synaptic changes required for storing long-term memories.  To gain insight into how long-lasting changes in synaptic strength are sustained, a research team from UC San Diego and the Howard Hughes Medical Institute investigated PKMζ and PKCλ stability in rat neurons.

A research team from the Howard Hughes Medical Institute, Harvard University, the National Center for Microscopy and Imaging Research, and UC San Diego developed a new method that combines 3D stochastic optical reconstruction microscopy (STORM) with several EM imaging modes, including protocols to image unembedded and embedded/sectioned samples. They applied the resulting protocols to several cellular and viral structures.

A research team from MIT, Massachusetts General Hospital, and UCSD in late November 2014 published a study in Nature Methods describing an electron microscopy tag, APEX2, which they developed for live-cell proteomics and genetic probe-based labeling for light and electron microscopy. Use of this tag enabled them to resolve a conflict between competing mechanistic models of regulation of the inner membrane channel through which calcium is supplied to mitochondria.

Electron microscopy is a very useful technique to analyze the form, distribution, and functional status of key organelle systems in various pathological processes including those associated with neurodegenerative diseases. Significantly, it has been used to provide important new insights into the mechanisms underlying diseases such as Parkinson’s and Alzheimer’s diseases and glaucoma.Moreover, recent advances in EM instrumentation are fueling a renaissance in the study of quantitative neuroanatomy. Data obtained from techniques such as serial block-face scanning electron microscopy (SBEM) provide unprecedented volumetric snapshots of the in-situ biological organization of the mammalian brain across a multitude of scales.

The recently developed 3D method of serial block-face scanning electron microscopy is rapidly establishing itself as a powerful imaging approach in the biological sciences research community. This approach is proving of great value for 3D visualization of nervous system ultrastructure, particularly when details of synaptic and other subcellular elements must be located and quantified. It is also important for constructing connectomic models of regional brain circuits. In addition, SBEM is increasingly used to perform nanohistology on a wide variety of tissue systems, including the lung, liver, tendons, kidney, and cell cultures.

Computational researchers, regardless of their disciplines, need software tools that save time, optimize and scale up computations, produce results faster, create an extensible platform, foster collaborations, effectively communicate the underlying science, and enable others to replicate the results. Some of the most effective tools are based on scientific workflows. A workflow is a software application that solves a scientific problem. It’s composed of computational steps and data manipulation tools that can scale up to run on high-performance computers, distributed environments, and commercial cloud systems. Workflows are used in all stages of the data lifecycle: generation and acquisition, analysis, comparison, publication, and archiving.

Fluorescent proteins are used commonly to tag components of interest in living cells for subsequent imaging. But there’s a cost: Their dim fluorescence, rapid photobleaching, and large size limit their utility, and they can disrupt protein folding and trafficking and/or impair protein function.Chemical fluorophores, by comparison, tend to be considerably smaller, brighter, and more photostable, characteristics that allow them to perform better in advanced biological imaging modalities such as single-molecule tracking and super-resolution microscopies. However, it is much more challenging to target them to specific cellular proteins inside living cells because they cannot be genetically encoded and have to target proteins post-translationally inside a complex cellular environment.

At the 2010 Microscopy and Microanalysis meeting in Portland, Oregon, NCMIR scientists presented their work "Enhancing Serial Block-Face Scanning Electron Microscopy to Enable High Resolution 3-D Nanohistology of Cells and Tissues," a collaboration with researchers Roger Tsien's laboratory at UCSD.