Losing a loved one may speed up aging

Losing someone close, like a family member, can make you age faster, says a new study from Columbia University Mailman School of Public Health and the Butler Columbia Aging Center. The study found that people who lost a parent, partner, sibling, or child, showed signs of older biological age compared to those who hadn't experienced such losses. The research was published in JAMA Network Open.

Biological aging is the gradual decline in how well your cells, tissues, and organs function, leading to a higher risk of chronic diseases. Scientists measure this type of aging using DNA markers known as epigenetic clocks.

"Few studies have looked at how losing a loved one at different stages of life affects these DNA markers, especially in study samples that represent the U.S .population," said Allison Aiello, PhD, the James S. Jackson professor of health longevity in Epidemiology and the study's lead author. "Our study shows strong links between losing loved ones across the life course from childhood to adulthood and faster biological aging in the U.S."

The study, a collaboration with the Carolina Population Center at UNC Chapel Hill, suggests that the impact of loss on aging can be seen long before middle age and may contribute to health differences among racial and ethnic groups.

The researchers used data from the National Longitudinal Study of Adolescent to Adult Health, which started in 1994-95. It followed participants from their teenage years into adulthood.

To measure familial loss during childhood or adolescence from the longitudinal study, Aiello and colleagues followed participants through various waves, and aging timeframes. Wave I surveyed 20,745 adolescents in grades 7-12, most of whom were aged 12-19. Participants have been followed ever since. Wave V took place between 2016 and 2018 and completed interviews with 12,300 of the original participants. In the latest wave, between 2016 and 2018, participants were invited for an additional home exam where a blood sample of the nearly 4,500 visited was provided for DNA testing.

The study looked at losses experienced during childhood or adolescence (up to 18 years old) and adulthood (19 to 43 years old). They also examined the number of losses experienced across this time period. Biological aging data were assessed from blood DNA methylation using epigenetic clocks including DunedinPACE which was developed by by Aiello's Aging Center colleague and study co-author Dan Belsky and his collaborators at Duke University.

Nearly 40 percent of participants experienced at least one loss in adulthood between the ages of 33 and 43. Parental loss was more common in adulthood versus in childhood and adolescence (27 percent versus 6 percent). A larger proportion of Black (57 percent) and Hispanic (41 percent) participants experienced at least one loss compared to White participants (34 percent).

People who experienced two or more losses had older biological ages according to several epigenetic clocks. Experiencing two or more losses in adulthood was more strongly linked to biological aging than one loss and significantly more so than no losses.

"The connection between losing loved ones and health problems throughout life is well-established," Aiello noted. "But some stages of life might be more vulnerable to the health risks associated with loss and the accumulation of loss appears to be a significant factor."

For example, losing a parent or sibling early in life can be very traumatic, often leading to mental health issues, cognitive problems, higher risks of heart disease, and a greater chance of dying earlier. Losing a close family member at any age poses health risks, and repeated losses can increase the risks of heart disease, mortality, and dementia; and impacts may persist or become apparent long after the event.

Aiello and her co-authors emphasize that while loss at any age can have long-lasting health impacts, the effects might be more severe during key developmental periods like childhood or early adulthood. "We still don't fully understand how loss leads to poor health and higher mortality, but biological aging may be one mechanism as suggested in our study. Future research should focus on finding ways to reduce disproportionate losses among vulnerable groups. For those who experience loss, providing resources for coping and addressing the trauma is essential. ," Aiello concluded.

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Artificial cartilage with the help of 3D printing

Is it possible to grow tissue in the laboratory, for example to replace injured cartilage? At TU Wien (Vienna), an important step has now been taken towards creating replacement tissue in the lab -- using a technique that differs significantly from other methods used around the world.

A special high-resolution 3D printing process is used to create tiny, porous spheres made of biocompatible and degradable plastic, which are then colonized with cells.

These spheroids can then be arranged in any geometry, and the cells of the different units combine seamlessly to form a uniform, living tissue.

Cartilage tissue, with which the concept has now been demonstrated at TU Wien, was previously considered particularly challenging in this respect.

Tiny spherical cages as a scaffold for the cells

"Cultivating cartilage cells from stem cells is not the biggest challenge. The main problem is that you usually have little control over the shape of the resulting tissue," says Oliver Kopinski-Grünwald from the Institute of Materials Science and Technology at TU Wien, one of the authors of the current study.

"This is also due to the fact that such stem cell clumps change their shape over time and often shrink."

To prevent this, the research team at TU Wien is working with a new approach: specially developed laser-based high-resolution 3D printing systems are used to create tiny cage-like structures that look like mini footballs and have a diameter of just a third of a millimeter.

They serve as a support structure and form compact building blocks that can then be assembled into any shape.

Stem cells are first introduced into these football-shaped mini-cages, which quickly fill the tiny volume completely.

"In this way, we can reliably produce tissue elements in which the cells are evenly distributed and the cell density is very high. This would not have been possible with previous approaches," explains Prof.

Aleksandr Ovsianikov, head of the 3D Printing and Biofabrication research group at TU Wien.

Growing together perfectly

The team used differentiated stem cells -- i.e. stem cells that can no longer develop into any type of tissue, but are already predetermined to form a specific type of tissue, in this case cartilage tissue.

Such cells are particularly interesting for medical applications, but the construction of larger tissue is challenging when it comes to cartilage cells.

In cartilage tissue, the cells form a very pronounced extracellular matrix, a mesh-like structure between the cells that often prevents different cell spheroids from growing together in the desired way.

If the 3D-printed porous spheres are colonized with cells in the desired way, the spheres can be arranged in any desired shape.

The crucial question is now: do the cells of different spheroids also combine to form a uniform, homogeneous tissue?

"This is exactly what we have now been able to show for the first time," says Kopinski-Grünwald.

"Under the microscope, you can see very clearly: neighboring spheroids grow together, the cells migrate from one spheroid to the other and vice versa, they connect seamlessly and result in a closed structure without any cavities -- in contrast to other methods that have been used so far, in which visible interfaces remain between neighboring cell clumps."

The tiny 3D-printed scaffolds give the overall structure mechanical stability while the tissue continues to mature.

Over a period of a few months, the plastic structures degrade, they simply disappear, leaving behind the finished tissue in the desired shape.

First step towards medical application

In principle, the new approach is not limited to cartilage tissue, it could also be used to tailor different kinds of larger tissues such as bone tissue.

However, there are still a few tasks to be solved along the way -- after all, unlike in cartilage tissue, blood vessels would also have to be incorporated for these tissues above a certain size.

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Detailed map of the heart provides new insights into cardiac health and disease

In a new study, published today (12 July) in Nature, researchers have produced the most detailed and comprehensive human Heart Cell Atlas to date, including the specialised tissue of the cardiac conduction system -- where the heartbeat originates.

The multi-centre team is led by the Wellcome Sanger Institute and the National Heart and Lung Institute at Imperial College London, and has also presented a new drug-repurposing computational tool called Drug2cell, which can provide insights into the effects of drugs on heart rate.

This study is part of the international Human Cell Atlas* (HCA) initiative, which is mapping every cell type in the human body, to transform our understanding of health and disease, and will form the foundation for a fully integrated HCA Human Heart Cell Atlas.

Charting eight regions of the human heart, the work describes 75 different cell states including the cells of the cardiac conduction system -- the group of cells responsible for the heartbeat -- not understood at such a detailed level in humans before. The human cardiac conduction system, the heart's 'wiring', sends electrical impulses from the top to the bottom of the heart and coordinates the heartbeat.

By using spatial transcriptomics, which gives a "map" of where cells sit within a tissue, researchers were also able to understand how these cells communicate with each other for the first time. This map acts as a molecular guidebook, showing what healthy cells look like, and providing a crucial reference to understand what goes wrong in disease. The findings will help understand diseases such as those affecting the heart rhythm.

The assembly of a Human Heart Cell Atlas is key given that cardiovascular diseases are the leading cause of death globally. Around 20,000 electronic pacemakers are implanted each year in the UK for these disorders. These can be ineffective and are prone to complications and side-effects. Understanding the biology of the cells of the conduction system and how they differ from muscle cells paves the way to therapies to boost cardiac health and develop targeted treatments for arrhythmias.

The team also presents a new computational tool called Drug2cell. The tool can predict drug targets as well as drug side effects. It leverages single-cell profiles and the 19 million drug-target interactions in the EMBL-EBI ChEMBL database.

Unexpectedly, this tool identified that pacemaker cells express the target of certain medications, such as GLP1 drugs, which are used for diabetes and weight loss and are known to increase the heart rate as a side-effect, the mechanism of which was unclear. This study suggests that the increase in heart rate might be partly due to a direct action of these drugs on pacemaker cells, a finding the team also showed in an experimental stem cell model of pacemaker cells.

Dr James Cranley, joint first author, a cardiologist specialising in heart rhythm disorders and PhD student at the Wellcome Sanger Institute, said: "The cardiac conduction system is critical for the regular and coordinated beating of our hearts, yet the cells which make it up are poorly understood. This study sheds new light by defining the profiles of these cells, as well as the multicellular niches they inhabit. This deeper understanding opens the door to better, targeted anti-arrhythmic therapies in the future."

Dr Kazumasa Kanemaru, joint first author and Postdoctoral Fellow in the Gene Expression Genomics team at the Wellcome Sanger Institute, said: "The mechanism of activating and suppressing pacemaker cell genes is not clear, especially in humans. This is important for improving cell therapy to facilitate the production of pacemaker cells or to prevent the excessive spontaneous firing of cells. By understanding these cells at an individual genetic level, we can potentially develop new ways to improve heart treatments."

The study unearthed an unexpected discovery: a close relationship between conduction system cells and glial cells. Glial cells are part of the nervous system and are traditionally found in the brain. They have been explored very little in the heart. This research suggests that glial cells are in physical contact with conduction system cells and may play an important supporting role: communicating with the pacemaker cells, guiding nerve endings to them, and supporting their release of glutamate, a neurotransmitter.

Another key finding of the study is an immune structure on the heart's outer surface. This contains plasma cells, which release antibodies into the space around the heart to prevent infection from the nearby lungs. The researchers also identified a cellular niche enriching for a hormone that could be interpreted as an early warning sign of heart failure.

Dr Michela Noseda, senior Lecturer in Cardiac Molecular Pathology at the National Heart and Lung Institute, Imperial College London, a Coordinator of the Human Cell Atlas Heart BioNetwork and a lead author, said: "We often don't fully know what impact a new treatment will have on the heart and its electrical impulses -- this can mean a drug is withdrawn or fails to make it to the market. Our team developed the Drug2cell platform to improve how we evaluate new treatments and how they can affect our hearts, and potentially other tissues too. This could provide us with an invaluable tool to identify new drugs which target specific cells, as well as help to predict any potential side-effects early on in drug development."

Professor Metin Avkiran, Associate Medical Director at the British Heart Foundation, which part-funded the research with the German Centre for Cardiovascular Research (DZHK), said: "Using cutting-edge technologies, this research provides further intricate detail about the cells that make up specialised regions of the human heart and how those cells communicate with each other. The new findings on the heart's electrical conduction system and its regulation are likely to open up new approaches to preventing and treating rhythm disturbances that can impair the heart's function and may even become life-threatening."

"International collaboration is key to scientific progress. This impactful study and other discoveries from the broader Human Cell Atlas initiative are excellent examples of what can be achieved when the international research community works together across borders. Our combined efforts can ultimately produce better outcomes for patients worldwide."

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Eye color genes are critical for retinal health

Metabolic pathways consist of a series of biochemical reactions in cells that convert a starting component into other products. There is growing evidence that metabolic pathways coupled with external stress factors influence the health of cells and tissues. Many human diseases, including retinal or neurodegenerative diseases, are associated with imbalances in metabolic pathways.

Elisabeth Knust leads a team of researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, who describe an essential role for one such metabolic pathway in maintaining retinal health under conditions of stress. They studied the classic Drosophila genes cinnabar, cardinal, white, and scarlet, originally characterized decades ago and named due to their role in eye color pigmentation, in particular the formation of the brown pigment of the fly eye. These genes encode components of the kynurenine pathway, whose activity converts the amino acid tryptophan by various steps into other products. In this study, the authors have highlighted the function of this metabolic pathway in retinal health, independent of its role in pigment formation.

The Kynurenine pathway is an evolutionary conserved metabolic pathway that regulates a variety of biological processes. Its disruption can result in the buildup of either toxic or protective biomolecules or metabolites, which can worsen or improve, respectively, the health of the brain, including the retina. Knowledge on this important metabolic pathway was recently extended by the research team, led by Elisabeth Knust, Director Emerita at the MPI-CBG, in their publication in the journal Plos Genetics. Being aware of the remarkable conservation of this metabolic pathway and the genes that regulate it, they used flies as a model system to unravel the role of individual metabolites in retinal health. The researchers looked at four genes -- cinnabar, cardinal, white, and scarlet - named after abnormal eye colors following their loss in flies. "Since the Kynurenine pathway is conserved from flies to humans, we asked whether these genes regulate retinal health independent of their role in pigment formation," says Sarita Hebbar, one of the lead authors of the study.

To find this out, the scientists used a combination of genetics, dietary changes, and biochemical analysis of metabolites to study different mutations of the fruit fly, Drosophila melanogaster. Sofia Traikov, a co-author, developed a method for the biochemical analysis of the metabolites of the Kynurenine pathway. This allowed the researchers to link different metabolite levels to the health state of the retina. They found that one metabolite, 3-hydroxykynurenine (3OH-K), is damaging to the retina. More importantly, they could show that the degree of degeneration is influenced by the balance between toxic 3OH-K and protective metabolites, such as Kynurenic Acid (KYNA), and not just by their absolute amounts. Sarita continues: "We also fed two of these metabolites to normal (non-mutant) flies and found that 3OH-K enhanced stress-induced retinal damage, whereas KYNA protected the retina from stress-related damage." This means that retinal health in certain conditions can be improved by altering the ratio of metabolites of the Kynurenine pathway.

Furthermore, by targeting these four genes and therefore four distinct steps within the pathway, the researchers were able to demonstrate that not only the accumulation of 3OH-K as such, but also its location in the cell and hence its availability in further reactions, is important for retinal health.

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Salmonella exposure a risk for colon cancer

A new study published in the journal Cell Reports Medicine links exposure to salmonella bacteria to colon cancer risk.

The researchers, including a team led by Jun Sun from the University of Illinois Chicago, studied human colon cancer tissue samples and animal models and found that exposure to salmonella was linked with colon cancers that developed earlier and grew larger.

The study authors first looked at data from a Netherlands-based retrospective study of colon cancer patients that found tissue samples taken during routine colon cancer surgery with salmonella antibodies tended to be from people who had worse colon cancer outcomes.

Using salmonella strains isolated from these tissue samples, Sun and her U.S.-based team studied mice with colon cancer that had been exposed to the bacteria. They observed accelerated tumor growth and larger tumors in mice with salmonella exposure. They also saw that there was increased salmonella translocated to the tumors.

"During infection, salmonella hijacks essential host signaling pathways, and these molecular manipulations may cause oncogenic transformation. The current study tells us that more research is needed into the connection between salmonella exposure and colon cancer risk in the USA, and that simply by practicing safe food preparation, we can potentially help to protect ourselves," said Sun, UIC professor of medicine.

Sun's collaborators in the Netherlands also studied the bacteria in vitro. They combined human cancer cells and pre-cancer cells with the salmonella strain in the lab and measured any growth or changes in the tumor. They saw that even one infection caused transformation and that each salmonella infection exponentially increased the rate of cell transformation.

"The mouse and tissue culture experiments show that salmonella infection had a chronic effect to accelerate tumor growth," said Sun, who also is a member of the University of Illinois Cancer Center at UIC. "This evidence tells us that we need to look closer at salmonella exposure as an environmental risk factor for chronic diseases, such as colon cancer."

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New computational method builds detailed maps of human tissues

Weill Cornell Medicine researchers have developed a computational method to map the architecture of human tissues in unprecedented detail. Their approach promises to accelerate studies on organ-scale cellular interactions and could enable powerful new diagnostic strategies for a wide range of diseases.

The method, published Oct. 31 in Nature Methods, grew out of the scientists' frustration with the gap between classical microscopy and modern single-cell molecular analysis. "Looking at tissues under the microscope, you see a bunch of cells that are grouped together spatially -- you see that organization in images almost immediately," said lead author Junbum Kim, a graduate student in physiology and biophysics at Weill Cornell Medicine. "Now, cell biologists have gained the ability to examine individual cells in tremendous detail, down to which genes each cell is expressing, so they're focused on the cells instead of focusing on the tissue structure," he said.

However, "it's crucial for researchers to learn more about the details of tissue structure; fundamental changes in the relationships between cells within a tissue drive both healthy and diseased organ function," said senior author Dr. Olivier Elemento, director of the Englander Institute for Precision Medicine and a professor of physiology and biophysics and of computational genomics in computational biomedicine at Weill Cornell Medicine.

Manually combining single cell data with maps of tissue structure is slow and tedious, though. Machine learning algorithms have shown some potential for automating the process, but they're limited by the data used to train them. To address that, Kim and his colleagues developed an unsupervised computational strategy, using a combination of single-cell gene expression profiles and cells' locations to define structural regions within a tissue.

Co-senior author Dr. André Rendeiro, a postdoctoral fellow at Weill Cornell Medicine during the study and currently a principal investigator at the Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, Austria, compares the new method to mapping a city such as New York: "One way to go about it would be to go to every intersection and count each kind of building: is it residential, is it commercial … is it a shop or restaurant?" Putting all of those data into one matrix, and the buildings' locations into another, one could then combine the two matrices and look for patterns.

"Essentially, we could start to make a general statement about where the different neighborhoods are and where their borders are based on the abundance of, say, residential versus commercial buildings -- just as anyone walking through the Upper East Side, Midtown or Downtown would do based on their observations," said Dr. Rendeiro.

The researchers used the new method to generate detailed maps of several types of tissues, identifying and quantifying new aspects of microanatomy -- the patterns that emerge at small scale when cells interact and that determine the ultimate function of tissue. Collaborating with a colleague at the University of North Carolina at Chapel Hill who studies lung disease, they also demonstrated that their technique could draw fine shades of distinction between different disease states in a tissue.

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Turning the spotlight on cells in tissues so RNA can tell their story

A new advance overcomes present limitations in spatial transcriptomics with a DNA nanotechnology-driven method called 'Light-Seq.' Light-Seq allows researchers to 'geotag' the full repertoire of RNA sequences with unique DNA barcodes exclusive to a few cells of interest. These target cells are selected using light under a microscope via a fast and effective photocrosslinking process, and their RNAs made available to next-generation sequencing with the help of a new DNA nanotechnology-driven technique. This entire process can then be repeated for different cell populations in the same sample.

Under the microscope, researchers often observe different cell types organizing themselves in peculiar patterns within tissues, or sometimes a rare cell type that stands out by occupying a unique position, exhibiting an unusual shape, or expressing a specific biomarker molecule. To determine the deeper meaning of their observations, they have developed approaches to also access cells' gene expression patterns (transcriptomes) by analyzing the gene-derived RNA molecules present within them, which they can match with cells' shapes, spatial positions, and molecular biomarkers.

However, these "spatial transcriptomics" approaches still only capture a fraction of a cell's total RNA molecules, and cannot deliver the depth and quality of analysis provided by single-cell sequencing methods, which were developed to investigate the transcriptomes of individual cells isolated from tissues or biofluids via next-generation sequencing (NGS) techniques. Nor do they allow researchers to only home in on specific cells based on their location in a tissue, which would greatly facilitate the pursuit of disjointed cell populations, or rare, difficult-to-isolate cells like rare brain cells with unique functions, or immune cells that invade tumors. In addition, because the original tissue environment is disrupted, many spatial transcriptomics and all single-cell sequencing methods prevent researchers from revisiting their samples to perform follow-up analysis, and they are costly because they require specialized instruments or reagents.

A new advance made at the Wyss Institute for Biologically Inspired Engineering at Harvard University now overcomes these limitations with a DNA nanotechnology-driven method called "Light-Seq." Light-Seq allows researchers to "geotag" the full repertoire of RNA sequences with unique DNA barcodes exclusive to a few cells of interest. These target cells are selected using light under a microscope via a fast and effective photocrosslinking process.

With the help of a new DNA nanotechnology, the barcoded RNA sequences are then translated into coherent DNA strands, which can then be collected from the tissue sample and identified using NGS. The Light-Seq process can be repeated with different barcodes for different cell populations within the same sample, which is left intact for follow-up analysis. With a performance comparable to single-cell sequencing methods, it significantly broadens the depth and scope of investigations possible on a tissue sample. The method is published in Nature Methods[BB1] .

"Light-Seq's unique combination of features fills an unmet need: the ability to perform imaging-informed, spatially prescribed, deep-sequencing analysis of hard, if not impossible-to-isolate cell populations or rare cell types in preserved tissues, with one-to-one correspondence of their highly refined gene expression state with spatial, morphological, and potentially disease-relevant features," said Peng Yin, Ph.D., one of four corresponding authors and a Core Faculty member at the Wyss Institute, where his group developed Light-Seq. "It thus has potential to fast-forward the biological discovery process in various biomedical research areas." Yin is also a Professor of Systems Biology at Harvard Medical School (HMS).

From barcoding in situ to sequencing ex situ

The Light-Seq project was spearheaded by Jocelyn (Josie) Kishi, Ph.D., Sinem Saka, Ph.D., and Ninning Liu, Ph.D. in Yin's group at the Wyss, and Emma West, Ph.D. in Constance Cepko's lab at HMS. Previously, Kishi and Saka had developed SABER-FISH as a spatial transcriptomics method for imaging gene expression directly in intact tissues (in situ). "With SABER-FISH, we still were orders of magnitude away from capturing cells' complete gene expression programs, with many thousands of different RNA molecules per cell. RNA molecules are just too densely packed to be captured in their entirety using present imaging techniques," said co-first and co-corresponding author Kishi. "Light-Seq solves this problem by combining high-resolution barcode labeling with full-transcriptome sequencing via NGS, giving us the best of both worlds and additional key advantages." At the time of the study, Kishi was a Wyss Technology Development Fellow on Yin's team, and is now pursuing a path toward commercializing Light-Seq together with some of her co-authors.

"To specifically sequence the cells in custom-selected locations of intact tissue samples, we developed a new approach for photocrosslinking DNA barcodes to copies of RNA molecules, and a DNA nanotechnology-powered procedure that makes them and their attached RNA sequences readable by NGS," said co-first author Liu, a Postdoctoral Fellow in Yin's group who previously co-developed a parallelized DNA barcoding platform for a super-resolution imaging method called "Action-PAINT" that also became one of the core components of Light-Seq.

First, DNA primers "base-pair" with RNA molecules in cells, and are extended to create copies of the RNA sequences called complementary DNA sequences (cDNAs). Then, DNA barcode strands containing an ultrafast photocrosslinker nucleotide are in turn base-paired to the cDNAs in the cells. These become permanently linked together when a target cell is lit up under the microscope through a stencil-like optical device that keeps other, non-target cells in the microscopic field in the dark and thus spares them from the photocrosslinking reaction. After washing the barcoded DNA sequences out of cells that were not permanently linked in situ, the procedure can be repeated with different barcodes and light patterns to label more regions of interest.

"To be able to integrate this barcoding workflow with NGS, we engineered a new stitching reaction that is based on DNA nanotechnology. This innovation allows us to convert our barcoded cDNAs into contiguous readout sequences. We can then extract the complete collection of barcode-bearing cDNA sequences from the sample, and analyze them with standard NGS techniques," explained Saka, one of the study's corresponding authors who is currently a Group Leader at the European Molecular Biology Laboratory in Heidelberg, Germany. "Ultimately, each barcode traces the full transcriptome readout back to the pre-selected cells in the tissue sample, which remains intact for subsequent analyses. This provides us the unique chance to revisit the exact same cells after sequencing for validation or further exploration."

Eying complex tissues and rare cells

Following the first validation of Light-Seq in cultured cells, Yin's team wanted to apply it to a complex tissue and partnered up with the group of Constance Cepko, Ph.D. at HMS. Cepko is one of the study's corresponding authors and the Bullard Professor of Genetics and Neuroscience in the Blavatnik Institute at HMS, and investigates the development of the retina as a model of the nervous system. Kishi, Saka, and Liu joined forces with West in Cepko's group to apply Light-Seq to cross-sections of the mouse retina and profile three major layers with different functions. The researchers reached a sequence coverage comparable to single-cell sequencing methods, and found that thousands of RNAs were enriched between the retina's three major layers. They also showed that after sequence extraction, the tissue samples remained intact and could be further imaged for proteins and other biomolecules.

"Taking Light-Seq to the extreme, we were able to isolate the full transcriptome of a very rare cell type, known as 'dopaminergic amacrine cells' (DACs), which is extremely hard to isolate because of its intricate connections to other cells in the retina, by retrieving merely four to eight individually barcoded cells per cross-section," said West. DACs are involved in regulating the eye's circadian rhythm by fine-tuning visual perception to different light exposures during the day-night cycle. "Light-Seq also picked up RNAs that were specifically expressed in DACs at low levels, as well as dozens of DAC-specific biomarker RNAs that, to our knowledge, had not been described before, which opens new opportunities to study this rare cell type," added West, who at the time of the study was a graduate student and then Postdoctoral Fellow with Cepko, and has now joined Kishi in her Light-Seq commercialization effort.

Opening the field of spatial transcriptomics up to NGS also adds information on the level of a single RNA species. "Our sequencing data clearly showed that Light-Seq can determine natural variations in the structure of RNAs. Going forward, we're very interested in using Light-Seq to better understand the interplay between the immune system, disease-propagating cells, and different therapeutic strategies such as gene and cell therapy," said Kishi.

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Technology restores cell, organ function in pigs after death

Within minutes of the final heartbeat, a cascade of biochemical events triggered by a lack of blood flow, oxygen, and nutrients begins to destroy a body's cells and organs. But a team of Yale scientists has found that massive and permanent cellular failure doesn't have to happen so quickly.

Using a new technology they developed that delivers a specially designed cell-protective fluid to organs and tissues, the researchers restored blood circulation and other cellular functions in pigs a full hour after their deaths, they report in the Aug. 3 edition of the journal Nature.

The findings may help extend the health of human organs during surgery and expand availability of donor organs, the authors said.

"All cells do not die immediately, there is a more protracted series of events," said David Andrijevic, associate research scientist in neuroscience at Yale School of Medicine and co-lead author of the study. "It is a process in which you can intervene, stop, and restore some cellular function."

The research builds upon an earlier Yale-led project that restored circulation and certain cellular functions in the brain of a dead pig with technology dubbed BrainEx. Published in 2019, that study and the new one were led by the lab of Yale's Nenad Sestan, the Harvey and Kate Cushing Professor of Neuroscience and professor of comparative medicine, genetics, and psychiatry.

"If we were able to restore certain cellular functions in the dead brain, an organ known to be most susceptible to ischemia [inadequate blood supply], we hypothesized that something similar could also be achieved in other vital transplantable organs," Sestan said.

In the new study -- which involved senior author Sestan and colleagues Andrijevic, Zvonimir Vrselja, Taras Lysyy, and Shupei Zhang, all from Yale -- the researchers applied a modified version of BrainEx called OrganEx to the whole pig. The technology consists of a perfusion device similar to heart-lung machines -- which do the work of the heart and lungs during surgery -- and an experimental fluid containing compounds that can promote cellular health and suppress inflammation throughout the pig's body. Cardiac arrest was induced in anesthetized pigs, which were treated with OrganEx an hour after death.

Six hours after treatment with OrganEx, the scientists found that certain key cellular functions were active in many areas of the pigs' bodies -- including in the heart, liver, and kidneys -- and that some organ function had been restored. For instance, they found evidence of electrical activity in the heart, which retained the ability to contract.

"We were also able to restore circulation throughout the body, which amazed us," Sestan said.

Normally when the heart stops beating, organs begin to swell, collapsing blood vessels and blocking circulation, he said. Yet circulation was restored and organs in the deceased pigs that received OrganEx treatment appeared functional at the level of cells and tissue.

"Under the microscope, it was difficult to tell the difference between a healthy organ and one which had been treated with OrganEx technology after death," Vrselja said.

As in the 2019 experiment, the researchers also found that cellular activity in some areas of the brain had been restored, though no organized electrical activity that would indicate consciousness was detected during any part of the experiment.

The team was especially surprised to observe involuntary and spontaneous muscular movements in the head and neck areas when they evaluated the treated animals, which remained anesthetized through the entire six-hour experiment. These movements indicate the preservation of some motor functions, Sestan said.

The researchers stressed that additional studies are necessary to understand the apparently restored motor functions in the animals, and that rigorous ethical review from other scientists and bioethicists is required.

The experimental protocols for the latest study were approved by Yale's Institutional Animal Care and Use Committee and guided by an external advisory and ethics committee.

The OrganEx technology could eventually have several potential applications, the authors said. For instance, it could extend the life of organs in human patients and expand the availability of donor organs for transplant. It might also be able to help treat organs or tissue damaged by ischemia during heart attacks or strokes.

"There are numerous potential applications of this exciting new technology," said Stephen Latham, director of the Yale Interdisciplinary Center for Bioethics. "However, we need to maintain careful oversight of all future studies, particularly any that include perfusion of the brain."

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How the intestine replaces and repairs itself

To act as a robust barrier against pathogens while also absorbing needed nutrients, the lining of the intestines must regenerate on a daily basis to remain equal to the task. The intestine's resident stem cells are responsible for meeting this need for constant repair and replenishment, but each stem cell faces decisions that depend on the overall conditions of the intestine and the needs of the moment. Bad decisions and poor coordination could result in intestinal diseases or cancer.

A new study suggests that stem cells are able to integrate cues from their surroundings and coordinate their behavior across the tissue through networks of vasculature in their close vicinity.

Rockefeller scientists found that lymphatic capillaries -- fine vessels that transport immune cells and drain fluids from tissues -- represent a signaling hub that communicates with stem cells to regulate their activity. With molecular guidance from the lymphatics, the stem cells produce daughter cells to repopulate the intestinal lining or self-renew to restock the stem cell reserve.

The findings, published in the journal Cell Stem Cell, provide new insights about primary intestinal components whose disrupted communication may contribute to intestinal disorders, such as inflammatory bowel disease. "The key to treating these diseases will be to figure out who talks to whom in this ecosystem and how we can reset the communication networks," says Rachel Niec, a clinical scholar in the laboratory of Elaine Fuchs.

Communications in the crypt

The intestinal stem cells reside in so-called crypts, found at the base of densely packed indentations in the intestinal lining. The stem cells may renew and stay in the crypt, or differentiate into specialized cells, which then migrate out of the crypt to replenish the gut lining. "To understand how stem cells balance self-renewal with differentiation, we needed a more complete picture of crypt niches," says Marina Schernthanner, a graduate student in the Fuchs lab.

To zoom in on the crypt, the team used a suite of techniques, including single-cell and spatial transcriptomics, which allowed them to identify cell types at specific locations and study their signaling molecules. The results showed that lymphatic capillaries, which form an intimate connection with the stem cells in the crypt, produce a number of proteins known to be important for stem cell functioning.

One previously underappreciated protein, REELIN, emerged as a top candidate for mediating communications between lymphatics and stem cells. By manipulating the amount of REELIN in lab-grown intestinal organoid cultures in some experiments and genetically suppressing it in mice in others, the researchers found that REELIN directly governs the regenerative behavior of intestinal stem cells.

The involvement of the lymphatic system in stem cell functioning is a relatively new concept. A previous study by the Fuchs team revealed that lymphatics are also closely involved with stem cells of the skin and play a key role in hair regeneration. There, however, it is the hair follicle stem cells that signal to lymphatic capillaries. By controlling their interactions with lymphatics, the stem cells synchronize hair regeneration across the tissue. "This suggests that lymphatics may be a conserved feature of stem cell niches, but their relationship to stem cells are likely tailored around the needs of each tissue," Niec says.

From Science Daily

Octopus-like tentacles help cancer cells invade the body

With help from the best tweezers in the world a team of researchers from the University of Copenhagen has shed new light on a fundamental mechanism in all living cells that helps them explore their surroundings and even invade tissue. Their discovery could have implications for research into cancer, neurological disorders and much else.

Using octopus-like tentacles, a cell pushes toward its target, a bacterium, like a predator tracking down its prey. The scene could be playing out in a nature programme. Instead the pursuit is being observed at the nano-scale through a microscope at the University of Copenhagen's Niels Bohr Institute. The microscope recording shows a human immune cell pursuing and then devouring a bacterium.

With their new study, a team of Danish researchers has added to the world's understanding of how cells use octopus-like tentacles called filopodia to move around in our bodies. This discovery about how cells move had never been addressed. The study is being published today in the journal, Nature Communications.

"While the cell doesn't have eyes or a sense of smell, its surface is equipped with ultra-slim filopodia that resemble entangled octopus tentacles. These filopodia help a cell move towards a bacterium, and at the same time, act as sensory feelers that identify the bacterium as a prey," explains Associate Professor Poul Martin Bendix, head of the laboratory for experimental biophysics at the Niels Bohr Institute.

The discovery is not that filopodia act as sensory devices -- which was already well established -- but rather about how they can rotate and behave mechanically, which helps a cell move, as when a cancer cell invades new tissue.

"Obviously, our results are of interest to cancer researchers. Cancer cells are noted for their being highly invasive. And, it is reasonable to believe that they are especially dependent on the efficacy of their filopodia, in terms of examining their surroundings and facilitating their spread. So, it's conceivable that by finding ways of inhibiting the filopodia of cancer cells, cancer growth can be stalled," explains Associate Professor Poul Martin Bendix.

For this reason, researchers from the Danish Cancer Society Research Center are a part of the team behind the discovery. Among other things, the cancer researchers are interested in whether switching off the production of certain proteins can inhibit the transport mechanisms which are important for the filopodia of cancer cells.

The cell's engine and cutting torch

According to Poul Martin Bendix, the mechanical function of filopodia can be compared to a rubber band. Untwisted, a rubber band has no power. But if you twist it, it contracts. This combination of twisting and contraction helps a cell move directionally and makes the filopodia very flexible.

"They're able to bend -- twist, if you will -- in a way that allows them to explore the entire space around the cell, and they can even penetrate tissues in their environment," says lead author, Natascha Leijnse.

The mechanism discovered by the Danish researchers appears to be found in all living cells. Besides cancer cells, it is also relevant to study the importance of filopodia in other types of cells, such as embryonic stem cells and brain cells, which are highly dependent on filopodia for their development.

Studying cells with the best tweezers in the world

The project involved interdisciplinary collaboration at the Niels Bohr Institute, where Associate Professor Amin Doostmohammadi, who heads a research group that simulates biologically active materials, contributed with the modelling of filopodia behaviour.

"It is very interesting that Amin Doostmohammadi could simulate the mechanical movements we witnessed through the microscope, completely independent of chemical and biological details," explains Poul Martin Bendix.

The main reason that the team succeeded in being the first to describe the mechanical behaviour of filopodia is that NBI has unique equipment for this type of experiment, as well as skilled researchers with tremendous experience working with optical tweezers. When an object is extraordinarily small, holding onto it mechanically becomes impossible. However, it can be held and moved using a laser beam with a wavelength carefully calibrated to the object being studied. This is called an optical tweezers.

"At NBI, we have some of the world's best optical tweezers for biomechanical studies. The experiments require the use of several optical tweezers and the simultaneous deployment of ultra-fine microscopy," explains Poul Martin Bendix.

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Cell fusion ‘awakens’ regenerative potential of human retina

Fusing human retinal cells with adult stem cells could be a potential therapeutic strategy to treat retinal damage and visual impairment, according to the findings of a new study published in the journal eBioMedicine. The hybrid cells act by awakening the regenerative potential of human retinal tissue, previously only thought to be the preserve of cold-blood vertebrates.

Cell fusion events -- the combination of two different cells into one single entity -- are known to be a possible mechanism contributing to tissue regeneration. Though rare in humans, the phenomenon has been consistently detected in the liver, brain, and gastrointestinal tract.

A team led by ICREA Research Professor Pia Cosma at the Centre for Genomic Regulation (CRG) in Barcelona and funded by Fundació "la Caixa" has now found that cell fusion events also take place in the human retina.

The researchers tested whether cell fusion events could differentiate into cells that turn into neurons, which would show potential for tissue regeneration. The team fused Müller glia, cells that play a secondary but important role in maintaining the structure and function of the retina, with adult stem cells derived from human adipose tissue or bone marrow.

"We were able to carry out cell fusion in vitro,creating hybrid cells. Importantly, the process was more efficient in the presence of a chemical signal transmitted from the retina in response to damage, resulting in rates of hybridisation increasing twofold. This gave us an important clue for the role of cell fusion in the retina," says Sergi Bonilla, postdoctoral researcher at the CRG at the time of publication and first author of the study.

The hybrid cells were injected into a growing retinal organoid, a model that closely resembles the function of the human retina. The researchers found that the hybrid cells successfully engrafted into the tissue and differentiated into cells that closely resemble ganglion cells, a type of neuron essential for vision.

"Our findings are important because they show that the Müller Glia in the human retina have the potential to regenerate neurons," says Pia Cosma. "Salamanders and fish can repair damage caused to the retina thanks to their Müller glia, which differentiate into neurons that rescue or replace damaged neurons. Mammalian Müller glia have lost this regenerative capacity, which means retinal damage or degradation can lead to visual impairment for life. Our findings bring us one step closer to recovering this ability."

The authors caution that much work remains to be done before the development of any potential treatments. One of the next steps is understanding why hybrid cells -- with four complete sets of chromosomes -- don't result in chromosomal instability and cancer development. The authors of the study believe the retina may have a mechanism regulating chromosome segregation similar to the liver, which contains tetraploid cells that act as a genetic reservoir, undergoing mitosis in response to stress and injury.

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Complex three-dimensional kidney tissue generated in the lab from the scratch

A research team based in Kumamoto University (Japan) has created complex 3D kidney tissue in the lab solely from cultured mouse embryonic stem (ES) cells. These organoids could lead the way to better kidney research and, eventually, artificial kidneys for human transplant.

By focusing on an often-overlooked tissue type of organoid generation research, a type of organ tissue made up of various support and connective tissues called the stroma, Dr. Ryuichi Nishinakamura and his team were able to generate the last of a three-part puzzle that they had been working on for several years. Once the three pieces were combined, the resulting structure was found to be kidney-like in its architecture. The researchers believe that their work will be used to advance kidney research and even lead to a transplantable organ in the future.

The kidney is a very important organ for continued good health because it acts as a filter to extract waste and excess water from blood. It is a complex organ that develops from the combination of three components. Protocols have already been established by various research teams, including Dr. Nishinakamura's team at the Institute of Molecular Embryology and Genetics (IMEG) at Kumamoto University, to induce two of the components (the nephron progenitor and the ureteric bud) from mouse ES cells.

In this, their most recent work, the IMEG team has developed a method to induce the third and final component, kidney-specific stromal progenitor, in mice. Furthermore, by combining these three components in vitro, the researchers were able to generate a kidney-like 3D tissue, consisting of extensively branched tubules and several other kidney-specific structures.

The researchers believe that this is the first ever report on the in-lab generation of such a complex kidney structure from scratch. The IMEG team has already succeeded in inducing the first two components from human iPS cells. If this last component can also be generated from human cells, a similarly complex human kidney should be achievable.

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Blueprint reveals how plants build a sugar transport lane

A tiny region at the root tip has been found to be responsible for orchestrating the growth and development of the complex network of vascular tissues that transport sugars through plant roots.

In a paper published in Science today, an international team of scientists present a detailed blueprint of how plants construct phloem cells -- the tissue responsible for transporting and accumulating sugars and starch in the parts of the plant that we harvest (seeds, fruits and storage tubers) to feed much of the world.

This pivotal research reveals how global signals in root meristems coordinate distinct maturation phases of the phloem tissue.

Phloem is a highly specialised vascular tissue that forms an interconnected network of continuous strands throughout a plant's body. It transports sugars, nutrients and a range of signalling molecules between leaves, roots, flowers and fruits.

As a result, phloem is central to plant function. Understanding how the phloem network is initiated and develops is important for future applications in agriculture, forestry and biotechnology as it could reveal how to better transport this sugar energy to where it is needed.

How do plants build a sugar lane in a multi-lane highway?

Plant roots continue to grow throughout a plant's life. This phenomenon, known as indeterminate growth, means roots continually elongate as they add new tissues to the tip of the root -- like constructing a never-ending highway. A continuous file of specialised phloem cells running the length of roots (analogous to a lane on a highway) delivers the primary nutrient, sucrose, to the parts of the plant where it is needed for growth. To fulfil this vital role, phloem tissue must develop and mature rapidly so it can supply sugars to surrounding tissues -- akin to building a service lane that needs to be completed in the first stage of constructing a multi-lane highway.

The problem that has long puzzled plant scientists is how a single instructive gradient of proteins are able to stage the construction phases across all the different specialised cell files (highway lanes) that are present in roots. How does one cell type read the same gradient as its neighbours, but interprets it differently to stage its own specialised development is a question that plant scientists have been working to resolve.

Over the past 15 years, researchers in Yrjö Helariutta's teams at the University of Cambridge and University of Helsinkihave uncovered the central role of cell-to-cell communication and complex feedback-mechanisms involved in vascular patterning. This new research, undertaken with collaborators at New York University and North Carolina State University, reveals how this single lane of phloem cells is constructed independently of surrounding cells.

The Sainsbury/Helsinki group dissected each step in the construction of the phloem cell file (the sugar transport lane) in the model plant Arabidopsis thaliana using single-cell RNA-seq and live imaging. Their work showed how the proteins that control the broad maturation gradient of the root interact with the genetic machinery that specifically controls phloem development.

This is one mechanism that appears to help the phloem cell file to fast-track maturation using its own machinery to interpret the maturation cues. Dr Pawel Roszak, co-first-author of the study and researcher at the Sainsbury Laboratory Cambridge University (SLCU), explains: "We have shown how global signals in the root meristem interact with the cell type specific factors to determine distinct phases of phloem development at the cellular resolution. Using cell sorting followed by deep, high-resolution single-cell sequencing of the underlying gene regulatory network revealed a "seesaw" mechanism of reciprocal genetic repression that triggers rapid developmental transitions."

The group also showed how phloem development is staged over time, with early genetic programs inhibiting late genetic programs and vice versa -- just as the road asphalt-laying work crews' hand over construction to lane painters in the latter stages of highway construction. In addition, they showed how early phloem regulators instructed specific genes to split the phloem cells into two different subtypes -- like the construction of a fork in the road leading to two separate destinations.

Co-leader of the work, Professor Yrjö Helariutta, said his teams' reconstruction of the steps from birth to terminal differentiation of protophloem in the Arabidopsis root exposed the steps. Helariutta said: "Broad maturation gradients interfacing with cell-type specific transcriptional regulators to stage cellular differentiation is required for phloem development."

"By combining single-cell transcriptomics with live imaging, here we have mapped the cellular events from the birth of the phloem cell to its terminal differentiation into phloem sieve element cells. This allowed us to uncover genetic mechanisms that coordinate cellular maturation and connect the timing of the genetic cascade to broadly expressed master regulators of meristem maturation. The precise timing of developmental mechanisms was critical for proper phloem development, with apparent "fail safe" mechanisms to ensure transitions."

Read more at Science Daily

Radioactive radiation could damage biological tissue also via a previously unnoticed mechanism

When cells are exposed to ionizing radiation, more destructive chain reactions may occur than previously thought. An international team led by researchers from the Max Planck Institute for Nuclear Physics in Heidelberg has for the first time observed intermolecular Coulombic decay in organic molecules. This is triggered by ionizing radiation such as from radioactivity or from space. The effect damages two neighbouring molecules and ultimately leads to the breaking of bonds -- like the ones in DNA and proteins. The finding not only improves the understanding of radiation damage but could also help in the search for more effective substances to support radiation therapy.

Sometimes radioactive damage cannot be great enough -- especially when it comes to destroying tumour tissue with ionizing radiation. In radiation therapy, substances that specifically enhance the damage of the radiation in the tumour tissue are used. "The intermolecular Coulombic decay we found could help make such sensitizers more effective," says Alexander Dorn, who heads a research group at the Max Planck Institute for Nuclear Physics and was instrumental in the current study. His team's observations could also improve our understanding of how artificial or natural ionizing radiation damages the genetic material of healthy tissue.

Excess energy leads to a Coulomb explosion

The DNA double helix of the genome resembles a rope ladder with rungs of nucleic base pairs. "Because experiments with the free nucleic bases are difficult, we initially studied pairs of benzene molecules as a model system," explains Dorn. These hydrocarbon rings are connected in a similar way to the nucleic bases stacked on top of each other in a strand of DNA. The researchers bombarded the benzene pairs with electrons, thereby imitating radioactive radiation to a certain extent. When an electron hit a benzene molecule, it was ionized and charged with a lot of energy. The team has now observed that the molecule transferred some of this energy to its partner molecule. This energy boost was enough to ionize the second molecule as well. Both molecules were thus positively charged. Of course, that didn't last long. The two molecular ions repelled each other and flew apart in a Coulomb explosion.

Until now, scientists had assumed that ionizing radiation damages biomolecules mainly indirectly. The high-energy radiation also ionizes the water of which a cell is largely composed and which surrounds biomolecules such as DNA. The ionized water molecules -- especially hydroxide ions -- then attack the DNA. And if an electron of the beta radiation or a gamma quantum does hit a DNA molecule directly, the excess energy normally is dissipated by processes in the molecule itself. It thus remains intact. Or at least that was the assumption up to now. In any case, the weak bonds between different molecules or different parts of the molecule -- as they exist in DNA and proteins -- should not be affected by this either. However, in their reaction microscope, the researchers observed that radioactive radiation can indeed break such bonds. This instrument allows them not only to detect the two separating benzene molecules and measure their energy but also to characterize the electrons emitted.

Fatal consequences of multiple DNA breaks

"It is not yet clear how the intermolecular Coulombic decay affects the DNA strand," says Dorn. If a single strand in the DNA ladder breaks, the consequences should not be too serious. However, the mechanism observed also releases several electrons that can "blow up" further pairs of molecules. And if both strands of DNA are broken in the immediate vicinity, this could have fatal consequences.

Read more at Science Daily

Breakthrough in using CRISPR-Cas9 to target fat cells

Fat -- it is vital for life but too much can lead to a host of health problems. Studying how fat, or adipose, tissue functions in the body is critical for understanding obesity and other issues, yet structural differences in fat cells and their distribution throughout the body make doing so challenging.

"Fat cells are different from other cells in that they lack unique cell surface receptors and only account for a minority of the cells within fat tissue," said Steven Romanelli, Ph.D., a former member in the laboratory of Ormand MacDougald, Ph.D., in the Department of Molecular & Integrative Physiology.

In a new paper published in the Journal of Biological Chemistry, Romanelli, MacDougald and their colleagues describe a breakthrough using CRISPR-Cas9, a tool that has transformed molecular biological research, but whose use in the study of adipose tissue had been elusive.

"The biggest challenge in terms of adipose research to date has been that if you want to study a gene's function, you have to commit a considerable amount of time, resources and money into developing a transgenic mouse," said Romanelli.

The traditional way of developing mouse models involves breeding mice with a desired mutation to delete or introduce certain genes of interest, which Romanelli says can take more than a year and tens of thousands of dollars.

CRISPR-Cas9 has revolutionized this process. It's a gene editing technique comprised of an enzyme called Cas9 which can break strands of DNA and a piece of RNA that guides the Cas9 enzyme to a specific site in the genome for editing. This tool is packaged into a non-harmful virus for delivery to the cells being studied. The tool has been successfully used to study heart, liver, neurons, and skin cells to name a few, but never a certain type of adipose cells known as brown fat.

Using the technique, the team was able to successfully target brown fat, a specialized adipose tissue used to generate heat and protect core body temperature.

"What we've been able to do is take that whole process and distill it into anywhere from two weeks to a month to generate a transgenic mouse, reducing the cost to less than $2,000. Not only does it reduce time and cost, it democratizes the research so that any lab that is familiar with molecular biology techniques can adopt this method and do it themselves," said Romanelli.

They were also able to use this method to delete multiple genes simultaneously, a fact that could help researchers better understand important molecular pathways.

Using their adeno-associated virus CRISPR-Cas9 components, they were able to knockout the UCP1 gene that defines brown adipose and enables it to generate heat, in adult mice. They observed that the knockout mice were able to adapt to the loss of the gene and maintain their body temperature in cold conditions, hinting at other pathways involved in temperature homeostasis.

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Oxygen-delivering hydrogel accelerates diabetic wound healing

About one-fourth of people with diabetes develop painful foot ulcers, which are slow to heal due to low oxygen in the wound from impaired blood vessels and increased inflammation. These wounds can become chronic, leading to poor quality of life and potential amputation.

Jianjun Guan, a professor of mechanical engineering & materials science in the McKelvey School of Engineering at Washington University in St. Louis, has developed a hydrogel that delivers oxygen to a wound, which decreases inflammation, helps remodel tissue and accelerates healing. Results of the work, which were in a mouse model, are published Aug. 28 in Science Advances. Ya Guan, a doctoral student, and Hong Niu, a postdoctoral research associate, both in Guan's lab, are co-first authors.

"The oxygen has two roles: one, to improve skin cell survival under the low-oxygen condition of the diabetic wound; and two, oxygen can stimulate the skin cells to produce growth factors necessary for wound repair," Guan said.

Tissues in the body require oxygen to survive and need even more when tissue is injured. While there are several existing treatments for chronic wounds in people with diabetes, the most common treatment is dozens of sessions in a hyperbaric oxygen chamber, but its effectiveness is inconsistent and includes the risk of oxygen toxicity.

Guan's hydrogel delivers oxygen to the wound using microspheres that gradually release oxygen to interact with the cells through an enzyme on their surface that converts what is inside of the microsphere into oxygen. The oxygen is delivered to the wound over about a two-week period, and inflammation and swelling decrease, prompting healing.

In the mice, wounds treated with the hydrogel containing the oxygen-releasing microspheres had a greater rate of closure than wounds treated with only the gel or those with no treatment. By day 16, the wounds treated with the hydrogel had reduced to 10.7%. Those treated with the gel only were reduced to 30.4%, and those with no treatment had reduced to 52.2%.

In addition, the wounds treated with the hydrogel containing the oxygen-releasing microspheres had the thickest epidermis on day 8, but the thinnest by day 16, indicating the wound was healing and inflammation was reduced.

Over the past 14 years, Guan has been developing this type of gel, which has nearly 70 different functions and chemical structures.

"The gel is a liquid before we put it into the skin tissue, so it is easy to mix in the microspheres," he said. "Once we put the mixture of the gel and the microspheres into the wound, it becomes a solid because it is temperature-sensitive -- at lower temperatures it is a liquid, and at body temperature it's a solid."

One risk of delivering oxygen to wounds is delivering too much, which creates reactive oxygen species (ROS), which can damage or kill cells at elevated levels. Guan's hydrogel is able to scavenge for ROS content and destroy it, eliminating any risk.

Next, Guan's team plans to use the hydrogel in a large animal model with the expectation of future human clinical trials.

"This represents a new therapeutic approach to accelerating healing of chronic diabetic wounds without drugs," Guan said. "It also has the potential to treat other diseases in which oxygen is low, such as peripheral artery disease and coronary heart disease."

Read more at Science Daily

Major advance enables study of genetic mutations in any tissue

For the first time, scientists are able to study changes in the DNA of any human tissue, following the resolution of long-standing technical challenges by scientists at the Wellcome Sanger Institute. The new method, called nanorate sequencing (NanoSeq), makes it possible to study how genetic changes occur in human tissues with unprecedented accuracy.

The study, published today (28 April) in Nature, represents a major advance for research into cancer and ageing. Using NanoSeq to study samples of blood, colon, brain and muscle, the research also challenges the idea that cell division is the main mechanism driving genetic changes. The new method is also expected to allow researchers to study the effect of carcinogens on healthy cells, and to do so more easily and on a much larger scale than has been possible up until now.

The tissues in our body are composed of dividing and non-dividing cells. Stem cells renew themselves throughout our lifetimes and are responsible for supplying non-dividing cells to keep the body running. The vast majority of cells in our bodies are non-dividing or divide only rarely. They include granulocytes in our blood, which are produced in the billions every day and live for a very short time, or neurons in our brain, which live for much longer.

Genetic changes, known as somatic mutations, occur in our cells as we age. This is a natural process, with cells acquiring around 15-40 mutations per year. Most of these mutations will be harmless, but some of them can start a cell on the path to cancer.

Since the advent of genome sequencing in the late twentieth century, cancer researchers have been able to better understand the formation of cancers and how to treat them by studying somatic mutations in tumour DNA. In recent years, new technologies have also enabled scientists to study mutations in stem cells taken from healthy tissue.

But until now, genome sequencing has not been accurate enough to study new mutations in non-dividing cells, meaning that somatic mutation in the vast majority of our cells has been impossible to observe accurately.

In this new study, researchers at the Wellcome Sanger Institute sought to refine an advanced sequencing method called duplex sequencing1. The team searched for errors in duplex sequence data and realised that they were concentrated at the ends of DNA fragments, and had other features suggesting flaws in the process used to prepare DNA for sequencing.

They then implemented improvements to the DNA preparation process, such as using specific enzymes to cut DNA more cleanly, as well as improved bioinformatics methods. Over the course of four years, accuracy was improved until they achieved fewer than five errors per billion letters of DNA.

Dr Robert Osborne, an alumnus of the Wellcome Sanger Institute who led the development of the method, said: "Detecting somatic mutations that are only present in one or a few cells is incredibly technically challenging. You have to find a single letter change among tens of millions of DNA letters and previous sequencing methods were simply not accurate enough. Because NanoSeq makes only a few errors per billion DNA letters, we are now able to accurately study somatic mutations in any tissue."

The team took advantage of NanoSeq's improved sensitivity to compare the rates and patterns of mutation in both stem cells and non-dividing cells in several human tissue types.

Surprisingly, analysis of blood cells found a similar number of mutations in slowly dividing stem cells and more rapidly dividing progenitor cells2. This suggested that cell division is not the dominant process causing mutations in blood cells. Analysis of non-dividing neurons and rarely dividing cells from muscle also revealed that mutations accumulate throughout life in cells without cell division, and at a similar pace to cells in the blood.

Dr Federico Abascal, the first author of the paper from the Wellcome Sanger Institute, said: "It is often assumed that cell division is the main factor in the occurrence of somatic mutations, with a greater number of divisions creating a greater number of mutations. But our analysis found that blood cells that had divided many times more than others featured the same rates and patterns of mutation. This changes how we think about mutagenesis and suggests that other biological mechanisms besides cell division are key."

The ability to observe mutation in all cells opens up new avenues of research into cancer and ageing, such as studying the effects of known carcinogens like tobacco or sun exposure, as well as discovering new carcinogens. Such research could greatly improve our understanding of how lifestyles choices and exposures to carcinogens can lead to cancer.

A further benefit of the NanoSeq method is the relative ease with which samples can be collected. Rather than taking biopsies of tissue, cells can be collected non-invasively, such as by scraping the skin or swabbing the throat.

Read more at Science Daily