#serial block-face scanning electron microscopy

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Powering Down Hearing

Your hearing depends on hair cells in your inner ear. When loud noises or ageing destroys these cells, it's their mitochondria – the powerhouses of your cells – that are involved in their downfall. Moreover, faults in over 30 genes key to mitochondrial activity are known to cause deafness. Yet little is known about hair cell mitochondria biology. Researchers now investigate in zebrafish. Using serial block-face scanning electron microscopy, they found mitochondria are more densely packed in hair cells (pictured, white) compared with support cells. These mitochondria also had a distinct architecture – multiple small mitochondria in the upper halves of cells and fine networks in the lower halves. In zebrafish with a faulty opa1 gene – a gene known to be mutated in human deafness – mitochondria function was disrupted. In mutants where hair cell mechanics were disrupted, so too was mitochondria architecture. This furthers our understanding of mitochondria-related deafness.

Written by Lux Fatimathas

Image from work by Andrea McQuate, Sharmon Knecht and David W Raible

Department of Biological Structure, University of Washington, Seattle, WA, USA

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in eLife, March 2023

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Image of the Week - February 5, 2018

CIL:50201 - http://www.cellimagelibrary.org/images/50201

Description: A longstanding limitation of imaging with serial block-face scanning electron microscopy is specimen surface charging. This charging is largely due to the difficulties in making biological specimens and the resins in which they are embedded sufficiently conductive. Local accumulation of charge on the specimen surface can result in poor image quality and distortions. Even minor charging can lead to misalignments between sequential images of the block-face due to image jitter. Typically, variable-pressure SEM is used to reduce specimen charging, but this results in a significant reduction to spatial resolution, signal-to-noise ratio and overall image quality. Here we show the development and application of a simple system that effectively mitigates specimen charging by using focal gas injection of nitrogen over the sample block-face during imaging. A standard gas injection valve is paired with a precisely positioned but retractable application nozzle, which is mechanically coupled to the reciprocating action of the serial block-face ultramicrotome. This system enables the application of nitrogen gas precisely over the block-face during imaging while allowing the specimen chamber to be maintained under high vacuum to maximise achievable SEM image resolution. The action of the ultramicrotome drives the nozzle retraction, automatically moving it away from the specimen area during the cutting cycle of the knife. The device described was added to a Gatan 3View system with minimal modifications, allowing high-resolution block-face imaging of even the most charge prone of epoxy-embedded biological samples.

Authors: Tom Deerinck, Tristan Shone, Eric Bushong, Ranjan Ramachandra,  Steven Peltier, and Mark Ellisman

Licensing: Public Domain: This image is in the public domain and thus free of any copyright restrictions. However, as is the norm in scientific publishing and as a matter of courtesy, any user should credit the content provider for any public or private use of this image whenever possible.

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Researchers used a newly developed imaging technique called serial block face scanning electron microscopy, to produce a digital reconstruction of eye tissues from the outer retina, at very high resolution. This is the first time this technology has been used to fully...

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Three-dimensional visualization and a deep-learning model reveal complex fungal parasite networks in behaviorally manipulated ants

Some microbes possess the ability to adaptively manipulate host behavior. To better understand how such microbial parasites control animal behavior, we examine the cell-level interactions between the species-specific fungal parasite Ophiocordyceps unilateralis sensu lato and its carpenter ant host (Camponotus castaneus) at a crucial moment in the parasite’s lifecycle: when the manipulated host fixes itself permanently to a substrate by its mandibles. The fungus is known to secrete tissue-specific metabolites and cause changes in host gene expression as well as atrophy in the mandible muscles of its ant host, but it is unknown how the fungus coordinates these effects to manipulate its host’s behavior. In this study, we combine techniques in serial block-face scanning-electron microscopy and deep-learning–based image segmentation algorithms to visualize the distribution, abundance, and interactions of this fungus inside the body of its manipulated host. Fungal cells were found throughout the host body but not in the brain, implying that behavioral control of the animal body by this microbe occurs peripherally. Additionally, fungal cells invaded host muscle fibers and joined together to form networks that encircled the muscles. These networks may represent a collective foraging behavior of this parasite, which may in turn facilitate host manipulation.

sooo... not so much zombified ants as sunken-placed ants

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How Does Sleeping Cause Your Brain to Shrink?

As it turns out, sleeping isn’t just for resting our tired bodies. A full night’s sleep is essential for many of the recharging processes, both in the body and in the brain. Just as we thought that we already know all about the benefits of getting eight hours of sleep, a new research study has revealed that our brains actually shrink when we sleep, and that this helps us prepare to learn new information.

The brain is an incredibly complex organ, and its capabilities are truly astounding. While we are awake, our brains constantly process the information from our environment, make new memories and direct our actions. There are billions of cells in the brain, otherwise known as neurons.Many previous scientific studies have already shown us that sleep plays a crucial role in memory consolidation, and that lack of sleep can cause memory impairments. But how exactly does sleep help us retain information?

In a recent study published in the journal Scienceby researchers of the University of Wisconsin-Madison Center for Sleep and Consciousness, scientists used a new, cutting edge technique called serial block-face scanning electron microscopy to take high resolution images of brain cells. The researchers made a surprising discovery: the synapses, or the connections between our brain cells, shrink by up to 20% during sleep [1].

During the day, we learn and makenew memories. In order for us to keep these memories, we have to make more connections in the brainand to increase the number of our synapses. According tobrain researchers, it is also necessary for the brain connections to shrink during sleep in order to reset, and to prevent overloading.Scientists call this theory “synaptic homeostasis hypothesis”. In addition, researchers believe that this type of scaling down of the brain connections helps to make room for new memories.

“Sleep is the perfect time to allow the synaptic renormalization to occur… because when we are awake, we are ‘slaves’ of the here and now, always attending some stimuli and learning something,” explained Dr. Chiara Cirelli, one of the study co-authors, in her interview with the science news website LiveScience [2]. “During sleep, we are much less preoccupied by the external world… and the brain can sample all of our synapses, and renormalize them in a smart way,” she added.

According to the synaptic homeostasis hypothesis, without synaptic downsizing, the synapses would reach their maximum size and capacity and we would not be able to continue to learn and consolidate our memories to retain them.

Interestingly, it was found that only the smaller connections were decreased in size, while the bigger synapses were not affected and stayed the same. The study authors suggest that the bigger synapses are more stable and contain important memories that the brain does not want to lose.

Another study recently published in Science provided some insight into the molecular process behind the synaptic downscaling. According to the findings, the shrinking of synapses is driven by the gene called Homer1a, and that this process is important for memory consolidation [3]. In this study, researchers found that sleepiness prompts brain cells to make Homer1A protein and to send it to their synapses. Then, during sleep, Homer1A activates the mechanisms responsible for “synaptic pruning”.

So does that mean that the main purpose of sleep is to “reset” our brains and prepare them for the next day? According to scientific studies, there are many important changes that take place both in our bodies and in our brains that occur during sleep.For example, people who are chronically sleep deprived are more likely to suffer from elevated blood pressure, type 2 diabetes, and depression; moreover, they have a higher risk for heart disease and stroke [4].

In his interview with New York Times, Dr. Markus H. Schmidt, another sleep researcher at the Ohio Sleep Medicine Institute, proposed that the shrinking of synapses is not necessarily the main reason that sleep exists. Referring to the new studies on synaptic downscaling, he said: “This work is great, but the question is, is this a function of sleep or is it the function?” [5].

A groundbreaking study published in 2013 has already shown us that as we sleep, the brain washes away waste and toxins that are built up during the day [6]. In this study, scientists found that some types of cells in the brain also shrink during sleep, allowing the spaces between cells to grow bigger. This allows more fluid to be pumped between brain cells, and to wash away more toxins.

In any case, we can conclude that sleep is an essential process that is important for learning and memory. In addition, the new studies help to explain why a lack of sleep can impair our memory and cognitive processes the next day: without shrinking during sleep, the synapses could not make room for new information

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Data Analysis for Three-dimensional Volume Scanning Electron Microscopy

 In recent years, three-dimensional (3D) scanning electron microscopy techniques have gained recognition in the biological sciences. In particular, array tomography, serial block face scanning electron microscopy (SBFSEM) and focused ion beam scanning electron microscopy (FIBSEM) (described in Three-Dimensional Scanning Electron Microscopy for Biology) have shown an increase in biological applications, elucidating ultrastructural details of cells […]

The post Data Analysis for Three-dimensional Volume Scanning Electron Microscopy appeared first on Bitesize Bio.

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Power Insight

The backs of our eyes are studded with millions of photoreceptors, cells in the retina triggered by light to help send electrical impulses to the brain. Differently-shaped ‘rod’ and ‘cone’ photoreceptors work to keep our vision precise and sensitive – and require a constant supply of energy. Here we see bundles cellular power stations – or mitochondria – highlighted in different colours around a single cone cell from a macaque monkey’s eye. To capture this level of detail, the retina was set in resin and a series of pictures taken while shaving away thin layers of tissue. The technique, called serial block face scanning electron microscopy, reveals the mitochondria have pointy 'tops' (left) and swollen bases (right), 10,000 times smaller than a bunch of asparagus. Researchers believe this arrangement helps with mitochondrial fusion – when the powerhouses join and rejuvenate, important to the health of retinal cells in monkeys and humans alike.

Written by John Ankers

Image from work by Matthew J. Hayes and colleagues

University College London Institute of Ophthalmology, London UK

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Scientific Reports, September 2021

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