Researchers uncover the physics behind formation of branching microtubules during cell division – News-Medical.net

As any cook knows, some liquids mix well with each other, but others do not. For example, when a tablespoon of vinegar is poured into water, a brief stir suffices to thoroughly combine the two liquids.

However, a tablespoon of oil poured into water will coalesce into droplets that no amount of stirring can dissolve. The physics that govern the mixing of liquids are not limited to mixing bowls; it also affects the behavior of things inside cells.

It's been known for several years that some proteins behave like liquids and that some liquid-like proteins don't mix together. However, very little is known about how these liquid-like proteins behave on cellular surfaces.

"The separation between two liquids that won't mix, like oil and water, is known as 'liquid-liquid phase separation', and it's central to the function of many proteins," said Sagar Setru, a 2021 Ph.D. graduate who worked with both Sabine Petry, a professor of molecular biology, and Joshua Shaevitz, a professor of physics and the Lewis-Sigler Institute for Integrative Genomics.

Such proteins do not dissolve inside the cell. Instead, they condense with themselves or with a limited number of other proteins, allowing cells to compartmentalize certain biochemical activities without having to wrap them inside membrane-bound spaces.

"In molecular biology, the study of proteins that form condensed phases with liquid-like properties is a rapidly growing field," said Bernardo Gouveia, a graduate student chemical and biological engineering, working with Howard Stone, the Donald R. Dixon '69 and Elizabeth W. Dixon Professor of Mechanical and Aerospace Engineering, and chair of the department. Setru and Gouveia collaborated as co-first authors on an effort to better understand one such protein.

"We were curious about the behavior of the liquid-like protein TPX2. What makes this protein special is that it does not form liquid droplets in the cytoplasm as had been observed before, but instead seems to undergo phase separation on biological polymers called microtubules," said Setru.

"TPX2 is necessary for making branched networks of microtubules, which is crucial for cell division. TPX2 is also overexpressed in some cancers, so understanding its behavior may have medical relevance."

Individual microtubules are linear filaments that are rod-like in shape. During cell division, new microtubules form on the sides of existing ones to create a branched network. The sites where new microtubules will grow are marked by globules of condensed TPX2. These TPX2 globules recruit other proteins that are necessary to generate microtubule growth.

The researchers were curious about how TPX2 globules form on a microtubule. To find out, they decided to try observing the process in action. First, they modified the microtubules and TPX2 so that each would glow with a different fluorescent color.

Next, they placed the microtubules on a microscope slide, added TPX2, and then watched to see what would happen. They also made observations at very high spatial resolution using a powerful imaging approach called atomic force microscopy.

"We found that TPX2 first coats the entire microtubule and then breaks up into droplets that are evenly spaced apart, similar to how morning dew coats a spider web and breaks up into droplets," said Gouveia.

Setru, Gouveia and colleagues found that this occurs because of something physicists call the Rayleigh-Plateau instability. Though non-physicists may not recognize the name, they will already be familiar with the phenomenon, which explains why a stream of water falling from a faucet breaks up into droplets, and why a uniform coating of water on a strand of spider web coalesces into separate beads.

"It is surprising to find such everyday physics in the nanoscale world of molecular biology," said Gouveia.

Extending their study, the researchers found that the spacing and size of TPX2 globules on a microtubule is determined by the thickness of the initial TPX2 coating -- that is, how much TPX2 is present. This may explain why microtubule branching is altered in cancer cells that overexpress TPX2.

We used simulations to show that these droplets are a more efficient way to make branches than just having a uniform coating or binding of the protein all along the microtubule."

Sagar Setru, 2021 PhD Graduate, Princeton University

"That the physics of droplet formation, so vividly visible to the naked eye, has a role to play down at the micrometer scales, helps establish the growing interface (no pun intended) between soft matter physics and biology," said Rohit Pappu, the Edwin H. Murty Professor of Engineering at Washington University in St. Louis, who was not involved in the study.

"The underlying theory is likely to be applicable to an assortment of interfaces between liquid-like condensates and cellular surfaces," adds Pappu. "I suspect we will be coming back to this work over and over again."

Source:

Journal reference:

Setru, S. U., et al. (2021) A hydrodynamic instability drives protein droplet formation on microtubules to nucleate branches. Nature Physics. doi.org/10.1038/s41567-020-01141-8.

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People in the News: New Appointments at Adaptive Biotechnologies, BD, Seven Bridges, More – GenomeWeb

Adaptive Biotechnologies: Mark Adams, Nancy Hill

Adaptive Biotechnologies has appointed Mark Adams as chief operating officer effective Jan. 25, 2021.Adams, 53, joined Adaptive in April 2020 as chief technical officer.

Adams holds a PhD in cell biology from Baylor College of Medicine and completed his postdoc in computational biology at Boston University.

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How Covid-19 mutations are changing the pandemic – BBC News

Early in its existence, Covid-19 gained an ability that would prove decisive in its relationship with human beings. The virus picked up a seemingly small change in its genetic code. It was likely an unfortunate accident a fragment of genetic information from another virus got muddled up with that of the coronavirus while they were both infecting a bat.

Included within this tiny piece of genome, however, were the instructions that altered a key part of the virus its spike protein. This important protein studs the outside of the coronavirus and is the part that attaches to the outside of cells, helping the rest of the virus to sneak inside where it can replicate.

This change to Covid-19's spike protein meant it could hijack an enzyme found in the human body called furin. This enzyme acts like a pair of molecular scissors, normally cutting open hormones and growth factors to activate them. But when furin snips part of the Covid-19 spike protein, which is normally folded in a series of loops on the outside of the virus, it opens like a hinge.

"This exposes a new sequence in the spike protein," says Yohei Yamauchi, a reader in viral cell biology at the University of Bristol, UK, who has been studying how this change may have led Covid-19 to become more infective in humans. "It is one of the changes that make this virus really different from previous coronaviruses that caused Sars and Mers."

This new mutation meant Covid-19 could suddenly latch onto an important molecule found scattered around the outside of human respiratory cells called Neuropilin 1. This molecule helps to transport material inside cells and deeper into tissues the mutation was like handing Covid-19 the keys to a new door into our cells and meant the virus could replicate in greater numbers in the human airways.

Although this mutation was just one in Covid-19's short existence, it proved to be important. Some researchers believe it may be one of the key mutations that allowed the coronavirus to jump species and begin causing a rapidly spreading disease in humans. But almost as soon as it did this, it began picking up other mutations.

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How Covid-19 mutations are changing the pandemic - BBC News

Cell Expansion Market: Ethical concerns regarding research in cell biology investigated in the latest research – WhaTech

The Global Cell Expansion Market size is estimated to be USD 14.9 billion in 2020 and projected to reach USD 30.1 billion by 2025, at a CAGR of 15.1%.

The Cell Expansion Market size is estimated to be USD 14.9 billion in 2020 and projected to reach USD 30.1 billion by 2025, at a CAGR of 15.1%.

Growth in this market is primarily driven by the increasing incidence of chronic diseases, government investments for cell-based research, growing focus on personalized medicine, increasing focus on R&D for cell-based therapies, and increasing GMP certifications for cell therapy production facilities.

The media segment accounted for the largest share of the consumables segment in the cell expansion market

Based on product type, consumables are segmented into media, reagents, sera, and disposables. The media segment accounted for the largest share of the consumables segment in the cell expansion market.

The large share of this segment can be attributed to its high requirement during the production of pharmaceutical products and rising R&D investments on cell-based therapies.

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Biotechnology & biopharmaceutical companies accounted for the fastest-growing end user segment of the cell expansion market

Based on end-users, the cell expansion industry market has been segmented into research institutes, biotechnology & biopharmaceutical companies, cell banks, and other end users (includes hospitals, diagnostic centers, and laboratories). In 2019, biotechnology & biopharmaceutical companies were the largest end-users in the cell expansion market, and the trend is the same throughout the forecast period.

North America accounted for the largest share of the cell expansion market

North America accounted for the largest share of the cell expansion industry market.

The large share of this segment can primarily be attributed to the rising incidence of cancer, increasing government funding, rising research activates on stem cell therapies, growing awareness regarding advanced treatment methods, increasing geriatric population, and the strong presence of industry players in the region.

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Leading Companies

Thermo Fisher Scientific, Inc. (US), Danaher (US), Becton, Dickinson and Company (US), Lonza (Switzerland), Corning, Inc. (US), Merck KGaA (Germany), Sartorius Stedim Biotech (France), Getinge AB (Sweden) Terumo Corporation (Japan), and Miltenyi Biotec (Germany)

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Protein identified that may help treat Parkinsons disease – Medical News Today

Scientists have identified a protein that can slow or stop some signs of Parkinsons disease in mice.

The team found that the bone morphogenetic proteins 5 and 7 (BMP5/7) can have these effects in a mouse model of the disease.

This research, which appears in the journal Brain, may be the first step toward developing a new treatment for Parkinsons disease.

This type of brain disorder typically affects people over the age of 60, and the symptoms worsen with time.

Common symptoms include stiffness, difficulty walking, tremors, and trouble with balance and coordination.

The disease can also affect the ability to speak and lead to mood changes, tiredness, and memory loss.

Parkinsons Foundation report that about 1 million people in the United States had the disease in 2020, with about 10 million affected globally.

Despite this prevalence, scientists are still unsure why Parkinsons disease affects some people and not others, and there is currently no cure.

The National Institute on Aging note that some cases of Parkinsons disease seem to be hereditary. In other words, the disease can emerge in different generations of a family but for many people with the disease, there appears to be no family history.

Researchers believe that multiple factors may affect a persons risk, including genetics, exposure to environmental toxins, and age.

Since there is currently no cure for Parkinsons disease, treatments typically focus on alleviating its symptoms.

Existing treatments can help alleviate of Parkinsons disease, such as stiffness. However, they may work less well, or not work, for others, such as tremors or a loss of coordination.

Though researchers are still unsure why some develop the disease and others do not, they understand what occurs in the brain of a person with Parkinsons.

The disease causes the neurons in the part of the brain that controls movement to stop working or die. The brain region, therefore, produces less of the chemical dopamine, which helps a person maintain smooth, purposeful movement, as the National Institute of Neurological Disorders and Stroke observe.

Also, Lewy bodies occur in the brains of some people with Parkinsons disease. These bodies are clumps primarily made up of misfolded forms of the protein alpha-synuclein.

In their recent study paper, the scientists refer to research suggesting that neurotrophic factors molecules that help neurons survive and thrive could, in theory, restore the function of neurons that produce dopamine. However, the clinical benefit of these factors had yet to be proven.

The team focused on bone morphogenetic proteins 5 and 7 (BMP5/7). They had previously shown that BMP5/7 has an important role in dopamine-producing neurons in mice.

In the latest study, the scientists wanted to see whether BMP5/7 could protect the neurons of mice against the damaging effects of misfolded alpha-synuclein proteins.

To do this, they injected one group of mice with a viral vector that caused misfolded alpha-synuclein proteins to form in their brains. They used other mice as a control group. The scientists then injected the mice with the BMP5/7 protein.

The researchers found that the BMP5/7 protein had a significant protective effect against the misfolded alpha-synuclein proteins.

According to senior study author Dr. Claude Brodski, of the Israel-based Ben-Gurion University of the Negevs Department of Physiology and Cell Biology, We found that BMP5/7 treatment can, in a Parkinsons disease mouse model, efficiently prevent movement impairments caused by the accumulation of alpha-synuclein and reverse the loss of dopamine-producing brain cells. He continues:

These findings are very promising, since they suggest that BMP5/7 could slow or stop Parkinsons disease progression. Currently, we are focusing all our efforts on bringing our discovery closer to clinical application.

The universitys technology transfer company, BGN Technologies, is currently looking to bring the development to the market.

Dr. Galit Mazooz-Perlmuter, the companys senior vice president of bio-pharma business development, notes that There is a vast need for new therapies to treat Parkinsons disease, especially in advanced stages of the disease.

Dr. Brodskis findings, although still in their early stages, offer a disease-modified drug target that will address this devastating condition. We are now seeking an industry partner for further development of this patent-pending invention.

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Unboxing: the Best Beauty Items We Tried in January – Prestige Online

Were starting the new year fresh with new skincare routines that help beat the harsh and dry winter, and beauty products to keep our glow on.Drunk ElephantThe Drunk Elephant Trunk 3.0 isnt exactly a new product. It came out in 2019, but the fully functional mini-fridge, which can chill (even warm!) your essential skincare products is still a favourite in our office. The trunk set comes with 10 best-selling, full-sized Drunk Elephant products, including the Sweet Biome Fermented Sake Spray.La MerLa Mers eye treatment combo is a lifesaver during the harsh winter days. The Eye Concentrate is a more advanced treatment that can help reduce dark circles and fine wrinkles even before visible damage begins. A pro tip: you could keep the eye treatment applicators in the fridge for a couple of minutes before you use them to massage the eye area for a quick microcirculation boost.DiorThe Dior Capture Totale Super Potent Rich Creme targets skin dryness with its heavily-researched science in mother cells and floral expertise. The rich creme combines bio-cellular technology with French peony oil extract.BenefitOur eyes and eyebrows are what most people tend to see these days, so its extremely pertinent that we keep our brows beautifully shaped and well-groomed. Benefits Brow Microfilling Pen mimics natural brow hair, comes in four versatile shades and is all-around the most essential beauty product you need these days.NarsNars is celebrating Chinese New Year with a new limited-edition collection that is beautifully packaged in a rich red floral design. To bring in good fortune for the Year of the Ox, the eyeshadow palette comes in soft neutral hues with a slight shimmer. There are two new shades of lipstick: Wen Wo (a brownish neutral shade) and China Rose (with a more rosy tint).TatchaTatchas Dewy Sin Creme is formulated with Hadasei-3, the brands proprietary complex of double-fermented Uji green tea, Akita rice and Mozuku algae. The result is super rich, smoothing cream that allows your make-up to glide on without a glitch.Laura MercierAlso perfect for Chinese New Year is Laura Merciers limited-edition beauty set, wrapped up in glorious shades of red and gold. The set comes with the Flawless Lumire Radiance-Perfecting Cushion, the Rouge Essentiel Silky Crme Lipstick, and the Translucent Loose Setting Powder that comes with a puff.YSL BeautyGlass skin was a term that came from K beauty to mean skin that appears poreless, luminous, clear as glass. YSL Beautys Soft Polish Double Essence is extremely gentle but comes with an effective peeling effect. Used alongside the Night Reboot serum and the Perfect Plumper Cream, glass skin is at your fingertips.AesopCold winter weather is not always the culprit sometimes, its the unpredictability of it, colder days and milder days, that disrupt our skin. Aesops latest winter skincare essentials are here to help. The selected products are gentle and nourishing on the skin, while keeping a balance, and comes in a range to suit different skin types.OribeOur focus is so often on skincare and make-up, but we shouldnt forget to care for our hair too. Available at Joyce Beauty, Oribes Signature Shampoo and Conditional set is a rich daily cleanser that is formulated to silken, detangle and protect.Este LauderThe Re-Nutriv Ultimate Diamond Transformative Eye Serum is part of Este Lauders premium line, and comes infused with Black Diamond Truffle Extract that lifts tired eyes instantly.Augustinus BaderFounded by Professor Augustinus Bader, globally recognized as one of the leaders in stem cell biology, theres no doubting the potency of the brands products. Its creams and oils are backed by 30 years of proprietary research, which resulted in its TFC8 complex, said to kickstart the skins natural abilities to rejuvenate itself. Available at Joyce Beauty.

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$25 Million Anonymous Gift Made to Brown for Brain Science Initiatives – GoLocalProv

Tuesday, January 26, 2021

GoLocalProv News Team

The university says the donation is intended to allow Brown to attract and retain world-class teachers and scholars, and it will endow an innovation awards program at the Universitys Robert J. and Nancy D. Carney Institute for Brain Science to provide seed funding for new high-impact research in computation and other areas of brain science.

This transformational gift recognizes the momentum that continues to build at Brown University, where our talented faculty are leading scientific discovery including in the rapidly emerging specialty of computational brain science, said Diane Lipscombe, director of the Carney Institute and a professor of neuroscience. This gift will allow us to sustain a culture of innovation, which has led to an impressive number of discoveries and returned countless new grants to Brown that forge new areas of research.

With more than 180 affiliated faculty members in 20 units and eight affiliated graduate programs, theCarney Instituteis pursuing research that has real-life, human applications, Lipscombe said. Core areas of research include work on innovative advances in computational brain science to investigate cognition, behavior and mood disorders; novel technologies to interface with the brain to understand brain circuits and restore lost functions; and research into the mechanisms of cell death to identify therapies for neurodegeneration, such as in amyotrophic lateral sclerosis (ALS) and Parkinsons and Alzheimers diseases.

This new $25 million gift is part of the Universitys $3-billionBrownTogethercampaign, which has raised $2.74 billion to date. It also builds upon significant philanthropic investment in Browns cutting-edge work in brain science of the total contributed by donors to date, more than $187 million has been raised to support research and education in brain science, including a$100 million giftthat named the institutein 2018. The gifts support a core research priority in BrownsBuilding on Distinctionstrategic plan: understanding the human brain.

In 2014, the Carney Institute launched aninnovation awards program to support early-stage research projects that are too new to attract external funding but have great potential to advance science and benefit society. The new gift will endow a similar innovation awards program, ensuring that the Carney Institute will be able to sustainably invest in innovation for years to come.

Ashley Webb, an assistant professor of molecular biology, cell biology and biochemistry at Brown, received an innovation award in 2019 to establish a new system to study how neurons age. She is developing a cell reprogramming platform, called direct reprogramming, to study aging in the hypothalamus brain region. The hypothalamus controls critical processes, such as sleep, temperature regulation, eating and metabolism, which can become dysregulated with aging. With direct reprogramming, Webb is able to convert a skin cell, for example, into a brain cell that maintains the hallmarks of aging.

Aging is the greatest risk factor for a number of diseases, including neurodegenerative diseases such as Alzheimers, Webb said. If we understand whats going wrong during aging, this will give us important insight into the mechanisms of disease. But right now, we dont have very good systems for studying these diseases in the context of aging. This is the problem we are working to solve.

Promoting computational brain science at Brown

According to Brown, the anonymous gift will allow Caarney to continue to lead in the emerging field of computational neuroscience. Last summer, Brownestablishedthe Center for Computational Brain Science at the institute to harness the Universitys expertise in computation, cognition and systems neuroscience. A portion of the new gift will support research in the center.

Computational neuroscience is a multidisciplinary field that seeks to understand the functions of the brain at all levels from cells to cognition using principles from physics, mathematics, engineering, computer science, biology, cognitive science and psychology. The center creates collaborations between basic brain science researchers and engineers, mathematicians and computer scientists, and brings computational neuroscience innovations to clinical applications and commercialization.

According to Michael Frank director of the Center for Computational Brain Science andthe recent recipientof the National Academy of Sciences Troland Award for early-career researchers the gift is a statement of support, confidence and appreciation for the contributions of computational neuroscientists at Brown. The $25 million gift will fuel the growing momentum to establish the newly minted computational brain science center as a world leader, he said.

It will expand the scope with which brain scientists can leverage powerful computational methods to understand neural mechanisms of complex behavior; to learn from, and reciprocally inspire, development in artificial intelligence; and to facilitate translation to improve brain health, Frank said.

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Medicine by Design researchers focus on promoting self-repair of the brain – News@UofT

If you asked Freda Miller 10 years ago if stem cells could be harnessed to repair brain injuries and disease, she would have said it was too early to tell.

Today, she describes the progress that she and other regenerative medicine experts have madein understanding what regulates populations of stem cells cells with the potential to turn into many different cell typesand the rapid advances those discoveries have driven.

The approaches were using allow us to find so much information on things we could only dream of before.

Miller, who is also a professor at the University of British Columbia, is leading a Medicine by Design-funded team with expertise in computational biology, neurobiology, bioengineering and stem cell biology that is investigating multiple strategies to recruit stem cells to promote self-repair in the brain and in muscle. If it succeeds, the research could improve treatments for diseases such as multiple sclerosis (MS) and cerebral palsy, as well as brain injury.

Millers team is one of 11 at U of T and its partner hospitals that are sharing nearly $21 million in funding from Medicine by Design over three years. Funded by a $114-million grant from the Canada First Research Excellence Fund, Medicine by Design is a strategic research initiative that is working at the convergence of engineering, medicine and science to catalyze transformative discoveries in regenerative medicine and accelerate them toward clinical impact.

This is the second round of large-scale, collaborative team projects that Medicine by Design has funded. The support builds on the progressmade in the first round of projects (2016-2019) and is spurring further innovation to push regenerative medicine forward. It alsoled to a 2017 publicationby many of the same researchers on Millers current project in Cell Reports that essentially provided a roadmap for how brain stem cells build the brain developmentally, and then persist to function in the adult brain.

Miller, a neuroscientist, has always been fascinated by the brain and neurons, the network of billions of nerve cells in the brain. Around 15 years ago, when she started to take an interest in the potential regenerative capabilities of stem cells, she began to wonder if she could use stem cells to treat brain injury or disease. Though too little was known about stem cells at the time, she knew that it was a question worth investigating. But she also realized that making and integrating new nerve cells, which are the working parts of brain circuits, would be a daunting task.

Even if you can convince the stem cells to make more neurons, those neurons then have to survive and they have to integrate into this really complex circuitry, says Miller. It just made sense to me that if were really going to test this idea of self-repair in the brain, we should go after something thats more achievable biologically.

So, Miller turned her attention to a substance called myelin, which covers nerves and allows nerve impulses to travel easily. In many nervous system diseases MS is a well-known example and brain injuries, damage to and loss of myelin is a main factor in debilitating symptoms. Thanks in part to the team project award from Medicine by Design, Miller leads a team that has a focus on recruiting stem cells to promote the generation of myelin.

Miller says repairing myelin, also called remyelination, will eventually help to better understand the effects of the target disease or injury, possibly even leading scientists to discover how to reverse it. Boosting myelin is a promising area of research, she adds, because its not an all-or-nothing situation.

Even a little bit of remyelination could have a big impact. You dont have to win the whole lottery; you dont have to have 100 per cent remyelination to have a measurable outcome.

The teams work is not limited to generating myelin to treat nervous system diseases or brain injury. They are also looking at how they could recruit stem cells to generate more muscle. They are specifically looking at muscular dystrophy, but Miller says the applications from that work can be used in other diseases or situations where damage to muscles has occurred, such as age-related disorders.

Millers team includes experts from diverse fields: Gary Bader, a professor at the Donnelly Centre for Cellular and Biomolecular Research and a computational biologist; bioengineers Alison McGuigan, a professor in the department of chemical engineering and applied chemistry in the Faculty of Applied Science & Engineering, and Penney Gilbert, an associate professor at the Institute of Biomedical Engineering; Sid Goyal, a professor at the department of physics in the Faculty of Arts & Science; ProfessorDavid Kaplan and Assistant ProfessorYun Li, both in the Temerty Faculty of Medicine and a senior scientist and a scientist, respectively, at SickKids; stem cell biologist Cindi Morshead, a professor and chair of the division of anatomy in the department of surgery in the Temerty Faculty of Medicine; and Peter Zandstra, a University Professor in the Faculty of Applied Science & Engineering and director of Michael Smith Laboratories at the University of British Columbia.

Miller says Medicine by Designs contribution in bringing teams like hers together is immeasurable.

There are tangible results you can measure like publications and other grants and clinical trials, Miller says. But there are a lot of intangible things Medicine by Design brings to the table like developing a culture of people from very diverse places and allowing them to do science together at a time when the biggest breakthroughs are going to be made by combining technological and biological approaches. Its hard to do that if youre on your own.

This large, interdisciplinary team effort combines data and computer modelling to look at individual stem cells in the brain and predict their behaviours. Through experimentation, they can then test if the cells behave the way they predicted, which Miller says they have had great success with. From there, the team casts a wide net, testing various ways to try to control cells behaviour with the end goal of convincing the stem cells to turn into cells that aid in healing and repair.

One approach they use is testing already approved pharmaceuticals to see if they have the desired effect on the stem cells behaviour. This approach has had success. In summer 2020, Morshead, Miller and their collaborators, led by Donald Mabbott, a SickKids senior scientist and professor in the department of psychology in the Faculty of Arts & Science, published a paper in Nature Medicine that showed that metformin, a common diabetes drug, has the potential to reverse brain injury in children who had had cranial radiation as a curative therapy for brain tumours.

Miller says that, to her knowledge, this is the first paper that demonstrates that this type of brain repair is possible in humans.

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RNA Molecules Are Masters of Their Own Destiny Regulating Their Own Production Through a Feedback Loop – SciTechDaily

A collaboration between biologists and physicists suggests that RNA is a feedback regulator of its own production. Low concentrations of RNA lead to the formation of transcriptional condensates (represented here as bubbles), and high levels lead to the dissolution of those condensates. Credit: Jennifer Cook-Chrysos/Whitehead Institute

Research suggests the products of transcription RNA molecules regulate their own production through a feedback loop.

At any given moment in the human body, in about 30 trillion cells, DNA is being read into molecules of messenger RNA, the intermediary step between DNA and proteins, in a process called transcription.

Scientists have a pretty good idea of how transcription gets started: Proteins called RNA polymerases are recruited to specific regions of the DNA molecules and begin skimming their way down the strand, synthesizing mRNA molecules as they go. But part of this process is less-well understood: How does the cell know when to stop transcribing?

Now, new work from the labs of Richard Young, Whitehead Institute for Biomedical Research member and MIT professor of biology, and Arup K. Chakraborty, professor of chemical engineering, physics, and chemistry at MIT, suggests that RNA molecules themselves are responsible for regulating their formation through a feedback loop. Too few RNA molecules, and the cell initiates transcription to create more. Then, at a certain threshold, too many RNA molecules cause transcription to draw to a halt.

The research, published in Cell, represents a collaboration between biologists and physicists, and provides some insight into the potential roles of the thousands of RNAs that are not translated into any proteins, called noncoding RNAs, which are common in mammals and have mystified scientists for decades.

Researchers formed these droplets in the lab to investigate the role of RNA in their formation and dissolution. Credit: Jon Henninger

Previous work in Youngs lab has focused on transcriptional condensates, small cellular droplets that bring together the molecules needed to transcribe DNA to RNA. Scientists in the lab discovered the transcriptional droplets in 2018, noticing that they typically formed when transcription began and dissolved a few seconds or minutes later, when the process was finished.

The researchers wondered if the force that governed the dissolution of the transcriptional condensates could be related to the chemical properties of the RNA they produced specifically, its highly negative charge. If this were the case, it would be the latest example of cellular processes being regulated via a feedback mechanism an elegant, efficient system used in the cell to control biological functions such as red blood cell production and DNA repair.

As an initial test, the researchers used an in vitro experiment to test whether the amount of RNA had an effect on condensate formation. They found that within the range of physiological levels observed in cells, low levels of RNA encouraged droplet formation and high levels of RNA discouraged it.

With these results in mind, Young lab postdocs and co-first authors Ozgur Oksuz and Jon Henninger teamed up with physicist and co-first author Krishna Shrinivas, a graduate student in Arup Chakrabortys lab, to investigate what physical forces were at play.

Shrinivas proposed that the team build a computational model to study the physical and chemical interactions between actively transcribed RNA and condensates formed by transcriptional proteins. The goal of the model was not to simply reproduce existing results, but to create a platform with which to test a variety of situations.

The way most people study these kinds of problems is to take mixtures of molecules in a test tube, shake it and see what happens, Shrinivas says. That is as far away from what happens in a cell as one can imagine. Our thought was, Can we try to study this problem in its biological context, which is this out-of-equilibrium, complex process?

Studying the problem from a physics perspective allowed the researchers to take a step back from traditional biology methods. As a biologist, its difficult to come up with new hypotheses, new approaches to understanding how things work from available data, Henninger says. You can do screens, you can identify new players, new proteins, new RNAs that may be involved in a process, but youre still limited by our classical understanding of how all these things interact. Whereas when talking with a physicist, youre in this theoretical space extending beyond what the data can currently give you. Physicists love to think about how something would behave, given certain parameters.

Once the model was complete, the researchers could ask it questions about situations that may arise in cells for instance, what happens to condensates when RNAs of different lengths are produced at different rates as time ensues? and then follow it up with an experiment at the lab bench. We ended up with a very nice convergence of model and experiment, Henninger says. To me, its like the model helps distill the simplest features of this type of system, and then you can do more predictive experiments in cells to see if it fits that model.

Through a series of modeling and experiments at the lab bench, the researchers were able to confirm their hypothesis that the effect of RNA on transcription is due to RNAs molecules highly negative charge. Furthermore, it was predicted that initial low levels of RNA enhance and subsequent higher levels dissolve condensates formed by transcriptional proteins. Because the charge is carried by the RNAs phosphate backbone, the effective charge of a given RNA molecule is directly proportional to its length.

In order to test this finding in a living cell, the researchers engineered mouse embryonic stem cells to have glowing condensates, then treated them with a chemical to disrupt the elongation phase of transcription. Consistent with the models predictions, the resulting dearth of condensate-dissolving RNA molecules increased the size and lifetime of condensates in the cell. Conversely, when the researchers engineered cells to induce the production of extra RNAs, transcriptional condensates at these sites dissolved. These results highlight the importance of understanding how non-equilibrium feedback mechanisms regulate the functions of the biomolecular condensates present in cells, says Chakraborty.

Confirmation of this feedback mechanism might help answer a longstanding mystery of the mammalian genome: the purpose of non-coding RNAs, which make up a large portion of genetic material. While we know a lot about how proteins work, there are tens of thousands of noncoding RNA species, and we dont know the functions of most of these molecules, says Young. The finding that RNA molecules can regulate transcriptional condensates makes us wonder if many of the noncoding species just function locally to tune gene expression throughout the genome. Then this giant mystery of what all these RNAs do has a potential solution.

The researchers are optimistic that understanding this new role for RNA in the cell could inform therapies for a wide range of diseases. Some diseases are actually caused by increased or decreased expression of a single gene, says Oksuz, a co-first author. We now know that if you modulate the levels of RNA, you have a predictable effect on condensates. So you could hypothetically tune up or down the expression of a disease gene to restore the expression and possibly restore the phenotype that you want, in order to treat a disease.

Young adds that a deeper understanding of RNA behavior could inform therapeutics more generally. In the past 10 years, a variety of drugs have been developed that directly target RNA successfully. RNA is an important target, Young says. Understanding mechanistically how RNA molecules regulate gene expression bridges the gap between gene dysregulation in disease and new therapeutic approaches that target RNA.

Reference: RNA-Mediated Feedback Control of Transcriptional Condensates by Jonathan E. Henninger, Ozgur Oksuz, Krishna Shrinivas, Ido Sagi, Gary LeRoy, Ming M. Zheng, J. Owen Andrews, Alicia V. Zamudio, Charalampos Lazaris, Nancy M. Hannett, Tong Ihn Lee, Phillip A. Sharp, Ibrahim I. Ciss, Arup K. Chakraborty and Richard A. Young, 16 December 2020, Cell.DOI: 10.1016/j.cell.2020.11.030

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RNA Molecules Are Masters of Their Own Destiny Regulating Their Own Production Through a Feedback Loop - SciTechDaily

The lymphatic system 5: vaccinations and immunological memory – Nursing Times

Vaccines use components of infectious agents such as bacteria and viruses to stimulate the bodys immune system to recognise and mark them for destruction, preventing the infectious agents from replicating and causing infection. This article is the fifth in a six-part series about the lymphatic system

This article, the fifth in a six-part series on the lymphatic system, examines the role of antibodies in developing immunity to infectious viruses and bacteria. It also summarises the history of vaccine development and explains how different vaccines stimulate an immune response.

Citation: Knight J, Nigam Y (2021) The lymphatic system 5: vaccinations and immunological memory. Nursing Times [online]; 117: 2, 38-42.

Authors: John Knight is associate professor in biomedical science; Yamni Nigam is professor in biomedical science; both at the College of Human and Health Sciences, Swansea University.

Vaccination is very much in the news as the first vaccines to combat SARS-Cov-2, the coronavirus responsible for Covid-19, gain regulatory approval. This article, the fifth in a six-part series on the lymphatic system, examines in greater detail the nature of antibody-mediated immunity discussed in part 3 and explores how vaccines can be used to prime the immune system against infectious diseases.

As highlighted in part 3, which discussed the role of the lymphatic system in developing immunity, antibodies are produced by B-lymphocytes when the body is exposed to foreign material. Any foreign material that can elicit a specific immune response and stimulate the production of antibodies is referred to as an antigen (Aryal, 2018). This article focuses on those associated with pathogens that cause infectious diseases. When antibodies are generated during infection their major role is to bind to the infectious agent, marking it for destruction by the immune system; this process is termed opsonisation (see part 3).

Antibodies (also known as immunoglobulins) are soluble globular proteins. The most abundant antibody circulating in the blood is immunoglobulin G (IgG), which accounts for around 10-20% of the total plasma protein content (Vidarsson et al, 2014).

Antibodies have a characteristic molecular configuration, often described as resembling the letter Y. Each molecule consists of four polypeptide (protein) chains, linked by disulphide bonds (Fig 1). Each antibody molecule consists of two heavy chains and two light chains in a Y shape (Fig 1a); the stem region is constant but the terminal ends of the arms are highly variable. These variable portions are the antigen-binding sites and resemble three-dimensional clefts or pockets into which the corresponding antigen will fit.

Antibody molecules are highly specific: each is usually only able to bind to a single antigen (Fig 1b). Just as a key will only fit one particular lock, an antigen will only fit into its complementary antibody by slotting into one of its antigen-binding sites this is essential to the way antibodies recognise and bind to foreign material.

When antibodies are generated against a pathogen, most bind to that pathogen alone, although some can bind to molecules with similar configurations as their original target antigen (Jain and Salunke, 2019). Such cross-reactivity is known to be associated with many autoimmune diseases, such as rheumatic fever.

The process of clonal selection (Fig 2) is at the heart of antibody-mediated immunity. B-cells (B-lymphocytes), which generate antibodies, circulate in the blood and are also present in lymphoid organs, such as the spleen, bone marrow and lymph nodes. A typical human body has billions of B-cells, with many displaying antibody molecules with unique antigen-binding sites.

The red circle in Fig 2 represents a particle of foreign material such as a bacterium or virus. When pathogens enter the body they typically circulate in the blood and lymph and through the lymphoid organs, and randomly come into contact with B-cells. The antigens on the surface of the pathogen will fit into the antigen-binding site of a complementary antibody molecule just like a key slotting into a lock (Fig 2). Once this occurs, clonal selection is deemed to have taken place; the B-cell will divide repeatedly, producing a large population of clones of the original B-cell (Silverstein, 2002). The majority of newly generated B-cell clones mature and enlarge into antibody-producing plasma cells, which release antibodies (IgG) into the blood (Fig 2). These will circulate throughout the body and bind to and opsonise the pathogen when they encounter it, marking it for destruction.

Not all B-cells generated by clonal selection mature into antibody-producing plasma cells. A significant proportion remain in the body for many years as memory cells (Ratajczak et al, 2018). These display the same antibody as the original B-cell clone and effectively hold a long-term memory of the encounter (Fig 2). If the pathogen is encountered again, these memory cells ensure clonal selection can occur quickly, allowing rapid killing of the pathogen before it can cause disease.

There are many different forms of vaccination, but all work on the same basic principle of priming the immune system against a potential infectious pathogen. This involves introducing a harmless form of the pathogen (or a component derived from it) to initiate clonal selection, antibody production and production of a pool of circulating memory cells.

Just as a key will only fit one particular lock, an antigen will only fit into its complementary antibody

English physician Edward Jenners use of a cowpox inoculation to provide immunity against the deadly smallpox virus is recognised as a key foundation in the newly emerging field of immunology and led to the development of the first effective and widely used vaccine. Jenner noted that milkmaids frequently contracted the relatively mild viral infection cowpox, which appeared to protect them against smallpox. He began using cowpox inoculation in 1796 but it was not until 1840 that widespread vaccination against smallpox using the cowpox vaccine became available (Riedel, 2005). International use of smallpox vaccines led to its global eradication in 1980 and it remains the only infectious disease to be completely eradicated through the use of vaccination. Following Jenners success, research into vaccines boomed and has continued since with key vaccines developed against some of the most virulent and deadly human pathogens, including those causing typhoid (1896), diphtheria (1942), polio (1956), measles (1968) and rubella (1970).

These are the earliest vaccines successfully used to confer immunity. They use micro-organisms that display limited pathogenicity in humans to stimulate the production of antibody and memory cells against highly pathogenic bacteria and viruses; because this is how Jenners original smallpox vaccine using cowpox functioned, these types of vaccines are often referred to as Jennerian vaccines (Esparza et al, 2018). With more advanced vaccine techniques now available, there are few pure heterologous vaccines that are in general use today, although the Bacillus Calmette-Gurin (BCG) vaccine, which provides protection against tuberculosis (TB), is an example of an attenuated heterologous vaccine.

These vaccines use live micro-organisms that have been rendered less pathogenic (attenuated) either by culturing and selecting for less virulent strains or by manipulating the biological properties of the pathogen. Once administered, the constituent micro-organisms replicate freely within the body, generating a natural immune response but without causing the disease. A major advantage of these vaccines is that they elicit a powerful immune response that closely mirrors that seen in people exposed to the disease-causing pathogen. They tend to generate high antibody titres (concentrations) and a large pool of circulating memory cells, meaning booster shots are not usually required.

Attenuated live vaccines are not usually offered to people with a weakened immune system because, in the absence of a normal immune response, the component pathogens can replicate quickly, potentially leading to serious systemic infection. People who are likely to be immunosuppressed include those with congenital immune deficiencies, those undergoing chemotherapy or radiotherapy, transplant recipients and patients using corticosteroids to manage chronic inflammatory or autoimmune disease (Arvas, 2014).

One of the first attenuated vaccines developed was the BCG vaccine, which is used to vaccinate against Mycobacterium tuberculosis, the bacterium causing TB. BCG uses the closely related pathogen M bovis, which causes TB in cattle and is a zoonotic bacterium (capable of crossing species barriers and infecting a variety of animals). It can also infect humans, causing zoonotic TB, which has symptoms often indistinguishable from those caused by M tuberculosis (World Health Organization, 2017).

In 1908 French microbiologists Albert Calmette and Camille Gurin began culturing M bovis isolated from an infected cow. After 11 years and over 230 subcultures, they isolated a strain that failed to cause TB in a variety of experimental animals. This attenuated strain was named Bacillus Calmette-Gurin (BCG) and was first used to vaccinate humans against TB in 1921. Initially the vaccine was given orally, before intradermal administration into the skin became commonplace (Luca and Mihaescu, 2013).

Early vaccinations proved successful in conferring immunity against TB, and many countries adopted BCG vaccination. However, in 1930 a batch of BCG vaccine contaminated with virulent bacteria caused the deaths of 73 infants in the German city of Lbeck. The so-called Lbeck disaster was caused by negligent production of the vaccine. It undermined confidence in the vaccine worldwide (Fox et al, 2016) and is generally recognised as the first major incident to cast global doubt on the safety of vaccines. It was not until the 1940s and 1950s, when TB infections increased significantly, that the BCG vaccine was used again in vaccination programmes and proven to be safe.

Recent evaluations suggest that BCG is 70-80% effective in protecting against severe forms of TB, although it is less effective in adults than in children. Its widespread use has dramatically reduced the incidence of TB in many countries, although infections have started to rise again in many regions, along with antibiotic-resistant strains of M tuberculosis. Due to its relatively low incidence in the UK, the BCG vaccine is only given on the NHS to children and adults at increased risk of TB (NHS, 2019a).

BCG remains one of the worlds most widely used vaccines and is also used as an immunotherapy to upregulate the immune system in the treatment of bladder cancer (see part 6). Modified forms are also used to enhance immune responses in the treatment of a variety of bacterial, viral and parasitic diseases (Zheng et al, 2015) and it is currently being evaluated for use in treating Covid-19 (Curtis and Sparrow, 2020).

Other attenuated vaccines used in the UK vaccination schedule include MMR (measles, mumps and rubella), nasal flu, shingles, chickenpox and rotavirus vaccines (Vaccine Knowledge Project, 2019).

These vaccines incorporate whole pathogens that have been killed, usually by heating or by exposing them to noxious chemicals or ionising radiation, rendering them unable to infect, replicate and cause disease. The current polio vaccine is an inactivated whole-pathogen vaccine; and is initially given as a component of the 6-in-1 vaccine, which also affords protection against diphtheria, hepatitis B, Haemophilus influenzae type b (Hib), tetanus and pertussis (whooping cough). The 6-in-1 vaccine is given as three doses at eight, 12 and 16 weeks of age (NHS, 2019b). Subsequent boosters are required at the age of:

Because inactivated whole-pathogen vaccines cannot replicate, they tend to elicit much weaker and shorter-lived immune responses than live attenuated vaccines. Repeated doses are required to generate an adequate immune response, followed by booster vaccinations to maintain immunity.

To help enhance the immune response to inactivated vaccines, the killed pathogen is usually suspended in a fluid containing irritants such as aluminium salts, which act as an adjuvant. When injected, adjuvants initiate an inflammatory response, increasing blood flow to the site to strengthen and amplify the immune response.

The inflammation initiated by adjuvants can result in tenderness and pain at the injection site, which usually resolves after a few days (Vaccine Knowledge Project, 2019). Because inactivated whole-pathogen vaccines contain no viable pathogen, they can usually be given safely to immunocompromised patients (Arvas, 2014). Other examples of inactivated whole-pathogen vaccines include the annual winter influenza vaccine and the rabies vaccine (Vaccine Knowledge Project, 2019).

Unlike inactivated whole-pathogen vaccines, subunit vaccines contain no intact bacterial or viral particles but use fragments of material derived from the target micro-organism. The pathogen-derived subunits chosen are typically components of bacterial cell walls and viral envelopes, as these are the natural antigens that would trigger clonal selection and antibody production during infection.

Today most subunit vaccines are made using recombinant DNA techniques. A good example is the vaccine for the hepatitis B virus (HBV); here the gene for an antigen on the HBV surface is inserted into brewers yeast. This genetically modified yeast can be cultured and will synthesise the HBV surface antigen, which can be harvested and purified for use in the HBV vaccine (Das et al, 2019). Subunit vaccines are particularly useful for highly pathogenic micro-organisms, as the lack of any intact viable pathogen ensures infection is impossible, even in severely immunocompromised patients.

Many of the vaccines currently being developed against SARS-Cov-2 are subunit vaccines using the surface spike protein that allows the virus to enter its target cells. The vaccine developed at the University of Oxford designated ChAdOx1 nCoV-19, which is currently being rolled out, takes the gene for the SARS-Cov-2 spike protein and inserts it into a non-pathogenic chimpanzee adenovirus. Following vaccination, the genetically modified adenovirus will infect target cells, which then synthesise large quantities of the SARS-Cov-2 spike protein, triggering antibody production. If the vaccinated patient comes into contact with SARS-Cov-2, their immune system will be able to target the virus and prevent infection (Mahase, 2020a).

The symptoms associated with many bacterial infections are caused by toxins produced by the pathogen. For example, Corynebacterium diphtheria (responsible for diphtheria) generates a powerful toxin that inhibits protein synthesis in the body, damaging the respiratory tract, nerves and heart (Murtaza et al, 2016). The diphtheria vaccine uses a modified version of this toxin, which has been inactivated with a chemical (usually formalin). The modified toxin is referred to as a toxoid (toxin-like molecule); because it is structurally almost identical to the original diphtheria toxin, it elicits antibody production when used in a vaccine. If a vaccine recipient becomes infected with diphtheria, these antibodies bind to and neutralise the diphtheria toxin reducing or eliminating symptoms. Although the pathogen itself is not being targeted, eventually the persons immune system can target and eliminate the C diphtheria bacterium itself.

Some antigens on the surface of pathogens do not naturally elicit a strong immune response when used in vaccines. Conjugated vaccines can improve immune responses to these relatively weak antigens by linking (conjugating) them to other molecules, such as bacterial toxoids, which generate more robust immune reactions. The Hib vaccine is a good example of a conjugated vaccine. Hib is unrelated to viral influenza; it is a bacterial infection that typically infects babies and young children, causing potentially life-threating septicaemia and bacterial meningitis. The Hib vaccine takes portions of the bacterial cell wall and conjugates them to toxoids (commonly tetanus or diphtheria toxoids) to render them more powerful elicitors of antibody production (Heath and McVernon, 2002).

With recent advances in molecular biology allowing the rapid sequencing and manipulation of DNA, attention has turned to using this technology to design and produce a new generation of vaccines. DNA and RNA vaccines use the bodys own cells to make antigenic components of bacteria and viruses to trigger an immune response. For example, a DNA vaccine can be created by inserting the sequence of a viral protein into a small, ring-shaped piece of DNA called a plasmid, which is then injected into a muscle. The muscle cells take up the plasmid and use the information encoded in its sequences to make the viral protein; this stimulates the production of antibodies via normal clonal selection.

Although DNA vaccines are already licensed for veterinary use, none are yet licenced for use in humans. However, clinical trials are exploring their use against a variety of human pathogens, including the Ebola, Marburg and Zika viruses. Early results have been encouraging, with boostable antibody production reported (Liu, 2019).

The current coronavirus pandemic has advanced novel vaccine development: one of the first SARS-Cov-2 vaccines to undergo clinical trials was an RNA-based vaccine developed in the US. This uses messenger RNA (mRNA) sequences that code for the SARS-Cov-2 spike protein (Fig3); these are enveloped in a lipid coating and injected into the deltoid muscle. The mRNA will then initiate production of the spike protein in human cells, stimulating production of antibodies against the virus. Initial findings reported in July 2020 indicated the vaccine is effective in producing specific immune responses against SARS-Cov-2 without any trial-limiting safety concerns (Jackson et al, 2020). The vaccine, now known as the Moderna vaccine, was approved for use in the US in December 2020; earlier that month a similar RNA vaccine, developed by Pfizer and BioNTech, became the first SARS-Cov-2 vaccine to receive regulatory approval in the UK (Mahase, 2020b).

The anti-vaccination movement is as old as modern vaccination itself. When the effectiveness of Jenners smallpox vaccine became apparent, the Vaccination Act in 1840 made it mandatory for parents in the UK to vaccinate their children. This led to significant public opposition and the formation of the Anti-Vaccination League, which successfully campaigned for removal of penalties and for parents right to conscientiously object to vaccination (Hussain et al, 2018). Although the contaminated BCG vaccine that led to the Lbeck disaster shook public confidence in early TB vaccination programmes, the effectiveness of successive new vaccines against a variety of deadly diseases ensured that vaccine uptake was maintained at a high level.

The modern anti-vaccination movement was given great impetus by a paper published in The Lancet that linked the MMR vaccine with the development of autism in young children (Wakefield et al, 1998). Despite being widely criticised in the scientific community, and later retracted by The Lancet, there was widespread loss of public confidence in the vaccine. In the UK, uptake of the MMR vaccine dropped from 92% in 1996 to 84% in 2002 and in parts of London to as low as 61% which is far below the threshold required for herd immunity against measles. Unsurprisingly, cases increased significantly and in 2008 measles was declared endemic in the UK for the first time in 14 years (Hussain et al, 2018).

MMR vaccination has recovered in recent years and, currently, scheduled childhood vaccine uptake in the UK remains high. However, there is a major concern that increased use of the internet and social media to promote anti-vaccination messages will further undermine confidence in the safety of vaccines and reduce uptake (Gilroy, 2019).

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The lymphatic system 5: vaccinations and immunological memory - Nursing Times