Hexbyte Glen Cove Australian icebreaker maps deepsea mountain

Hexbyte Glen Cove

The seamount identified by satellites and partially mapped by RSV Nuyina. Credit: Pete Harmsen / AAD

The summit of an underwater mountain, higher than Mount Kosciuszko, has been mapped for the first time by the Australian icebreaker Research and Supply Vessel (RSV) Nuyina.

At 2500 meters high, 2900 meters wide and 4500 meters long, the seamount had been identified from satellites at about 50 degrees South, on the edge of the “Furious Fifties.”

While an earlier voyage had skimmed one side of the seamount, no detailed mapping at its summit had ever been done.

Data from the ship’s multibeam echosounder were used to create a map of the seamount topography, with high points in red and the seafloor (at about 3000 meters depth) in green. The highest point mapped so far was about 500 meters beneath the ocean’s surface. Credit: Pete Harmsen / AAD

Seamounts are usually formed from extinct volcanoes and can be biological hotspots, attracting plankton, corals, fish and marine mammals.

As Nuyina’s passage to Davis research station took the ship directly over the seamount, the onboard acoustics team took the opportunity to switch on the ship’s hull-mounted multibeam echosounder, to find out what lay beneath.

Senior Acoustics Officer Floyd Howard said the echosounder “sees” seafloor features by emitting pings of sound in a fan-like pattern beneath the ship.

When the sound hits an object or the seafloor, it bounces back towards the ship, allowing scientists to build a picture of the seafloor—similar to used by dolphins.

As the ship cruised at 8 knots over the seamount, its surface structure and height were gradually revealed, ping by colorful ping, with different colors representing different depths.

Approximate position of seamount mapping on 28 December during Nuyina’s first voyage to Antarctica. Credit: AAD

The excitement was palpable as people gathered to see just how high the mountain would rise from a base elevation of about 3000 meters.

“The highest point we reached was about 500 meters below the , so it’s a significant feature,” Mr Howard said.

The team has informally named the feature “Ridgy-Didge Seamount” until an official name can be bestowed upon it.

The information collected during the seamount pass, and future mapping efforts by Nuyina and other ships, will contribute to global efforts to map the world’s oceans by 2030.

Provided by
Australian Antarctic Program

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Hexbyte Glen Cove New study brings us one step closer to growing human organs for transplantation

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Credit: CC0 Public Domain

Realizing the vision of culturing organs for use in life-saving transplantation procedures is still a long way off. However, the work of Prof. Jacob Hanna on stem cells is paving the way for this to become a reality.

Hanna and his team from the Weizmann Institute of Science’s Molecular Genetics Department have found a way to culture human stem in a much earlier state than was previously possible. Not only that, the they created are far more competent, meaning that they are able to integrate more efficiently with their host environment. This substantially improves the chances of obtaining what is called a cross-species chimera—allowing cells from one creature to play a substantial role in the development of another.

The recently published findings demonstrate that very early human cells can be created and then successfully integrated into mice, owing to their undifferentiated (or “naïve”) state, wherein they can develop into any type of cell in the body, including other stem cells. Additionally, the researchers lay out a protocol for significantly increasing the efficiency (or competence) with which these cells can integrate. Improving our ability to create and study these cell types could be used in the future to transfer cells—if not organs—from one animal to another, humans included.

Hanna’s lab broke ground in 2013 when they were the first to inject human stem cells into mice and show that they can successfully integrate into the latter’s developing embryos. Eight years after this study was first published, Hanna and his team felt that they could go one step further by attempting to produce an even earlier, “fully” naïve form of stem cells for use in similar procedures. As they were mulling over the idea, Hanna knew that this might be nearly—if not altogether—impossible to achieve. “Our experience with producing similar cells in mice has taught us to expect challenging obstacles along the way,” says Hanna.

These cells normally suffer from genetic as well as epigenetic instability, and in the end they don’t differentiate too well, which is key to proper embryonic development and a prerequisite for their integration into another animal’s embryo. In fact, only about 1-3 percent of cells that have been transferred between species actually manage to integrate and contribute to development.

To boost these numbers, the researchers in the new study inhibited two additional signaling pathways to produce naïve human stem cells having a stable genome, relatively few gene regulation glitches, and most importantly, the ability to differentiate perfectly. The researchers also mutated an important gene that contributes to stability, which resulted in not only competent but also competitive stem cells that can integrate well without causing damage to the host. “We found a way to make human stem cells more competent, and competitive, increasing the chances for a successful transfer by about fivefold compared to what we were able to do in the past,” concludes Hanna.

While the previous study showed that human naïve stem cells can differentiate into primordial germ cells—the progenitors of egg or sperm cells—the fully naïve stem cells produced in the present study can also differentiate into extraembryonic tissues, the placenta and yolk sac cells that sustain the developing embryo. Such cells could be used, for example, as the source for developing synthetic embryos without the need for donor eggs. “Reaching this state with mouse stem cells is particularly difficult to accomplish,” Hanna explains, noting that “human cells are apparently different.”

This is perhaps the most surprising finding that the researchers made—highlighting the differences between the behavior of human and mouse stem cells, and between the different states of naïve cells. These differences expose the work that still needs to be done in making the dream of developing “made-to-order” organs a real-world actuality.

According to Hanna, understanding these differences will be pivotal for overcoming myriad issues still facing the field of stem cell research and application: “If in the future we should wish to grow a pancreas in pigs for human transplantation, for example, we will have to take into account these massive evolutionary differences between species, beginning with mice and humans.” For now, it would seem that Hanna and his team have taken a constructive leap in that direction.

More information:
Jonathan Bayerl et al, Principles of signaling pathway modulation for enhancing human naive pluripotency induction, Cell Stem Cell (2021). DOI: 10.1016/j.stem.2021.04.001

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Hexbyte Glen Cove High-resolution lab experiments show how cells ‘eat’

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Credit: CC0 Public Domain

A new study shows how cell membranes curve to create the “mouths” that allow the cells to consume things that surround them.

“Just like our eating habits basically shape anything in our body, the way cells ‘eat’ matters for the health of the cells,” said Comert Kural, associate professor of physics at The Ohio State University and lead author of the study. “And scientists did not, until now, understand the mechanics of how that happened.”

The study, published last month in the journal Developmental Cell, found that the intercellular machinery of a cell assembles into a highly curved basket-like structure that eventually grows into a closed cage. Scientists had previously believed that structure began as a flat lattice.

Membrane curvature is important, Kural said: It controls the formation of the pockets that carry substances into and out of a cell.

The pockets capture substances around the cell, forming around the extracellular substances, before turning into vesicles—small sacs one-one millionth the size of a red blood cell. Vesicles carry important things for a cell’s health—proteins, for example—into the cell. But they can also be hijacked by pathogens that can infect cells.

But the question of how those pockets formed from membranes that were previously believed to be flat had stymied researchers for nearly 40 years.

“It was a controversy in cellular studies,” Kural said. “And we were able to use super-resolution fluorescence imaging to actually watch these pockets form within live cells, and so we could answer that question of how they are created.

“Simply put, in contrast to the previous studies, we made high-resolution movies of cells instead of taking snapshots,” Kural said. “Our experiments revealed that protein scaffolds start deforming the underlying membrane as soon as they are recruited to the sites of vesicle formation.”

That contrasts with previous hypotheses that the protein scaffolds of a cell had to go through an energy-intensive reorganization in order for the membrane to curve, Kural said.

The way cells consume and expel vesicles plays a key role for living organisms. The process helps clear bad cholesterol from blood; it also transmits neural signals. The process is known to break down in several diseases, including cancer and Alzheimer’s disease.

“Understanding the origin and dynamics of membrane-bound vesicles is important—they can be utilized for delivering drugs for , but at the same time, hijacked by pathogens such as viruses to enter and infect ,” Kural said. “Our results matter, not only for our understanding of the fundamentals of life, but also for developing better therapeutic strategies.”

Emanuele Cocucci, an assistant professor in Ohio State’s College of Pharmacy, co-authored this study, along with researchers from UC Berkeley, UC Riverside, Iowa State University, Purdue University and the Chinese Academy of Sciences.

More information:
Nathan M. Willy et al, De novo endocytic clathrin coats develop curvature at early stages of their formation, Developmental Cell (2021). DOI: 10.1016/j.devcel.2021.10.019

High-resolution lab experiments show how cells ‘eat’ (2021, December 30)
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Hexbyte Glen Cove Speeding up directed evolution of molecules in the lab using a new robotic platform

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Bacteriophage Phi X 174 Electron micrograph. Credit: Wikipedia/CC BY-SA 4.0

Natural evolution is a slow process that relies on the gradual accumulation of genetic mutations. In recent years, scientists have found ways to speed up the process on a small scale, allowing them to rapidly create new proteins and other molecules in their lab.

This widely-used technique, known as directed evolution, has yielded new antibodies to treat cancer and other diseases, enzymes used in biofuel production, and imaging agents for magnetic resonance imaging (MRI).

Researchers at MIT have now developed a that can perform 100 times as many directed-evolution experiments in , giving many more populations the chance to come up with a solution, while monitoring their progress in real-time. In addition to helping researchers develop new molecules more rapidly, the technique could also be used to simulate natural evolution and answer fundamental questions about how it works.

“Traditionally, directed evolution has been much more of an art than a science, let alone an engineering discipline. And that remains true until you can systematically explore different permutations and observe the results,” says Kevin Esvelt, an assistant professor in MIT’s Media Lab and the senior author of the new study.

MIT graduate student Erika DeBenedictis and postdoc Emma Chory are the lead authors of the paper, which appears today in Nature Methods.

Rapid evolution

Directed evolution works by speeding up the accumulation and selection of novel mutations. For example, if scientists wanted to create an antibody that binds to a cancerous protein, they would start with a test tube of hundreds of millions of yeast cells or other microbes that have been engineered to express mammalian antibodies on their surfaces. These cells would be exposed to the cancer protein that the researchers want the antibody to bind to, and researchers would pick out those that bind the best.

Scientists would then introduce random into the antibody sequence and screen these new proteins again. The process can be repeated many times until the best candidate emerges.

About 10 years ago, as a graduate student at Harvard University, Esvelt developed a way to speed up directed evolution. This approach harnesses bacteriophages (viruses that infect bacteria) to help proteins evolve faster toward a desired function. The gene that the researchers hope to optimize is linked to a gene needed for bacteriophage survival, and the viruses compete against each other to optimize the protein. The selection process is run continuously, shortening each mutation round to the lifespan of the bacteriophage (which is about 20 minutes), and can be repeated many times, with no human intervention needed.

Using this method, known as phage-assisted continuous evolution (PACE), directed evolution can be performed 1 billion times faster than traditional directed evolution experiments. However, evolution often fails to come up with a solution, requiring the researchers to guess which new set of conditions will do better.

The technique described in the new Nature Methods paper, which the researchers have named phage and robotics-assisted near-continuous evolution (PRANCE), can evolve 100 times as many populations in parallel, using different conditions.

In the new PRANCE system, populations (which can only infect a specific strain of bacteria) are grown in wells of a 96-well plate, instead of a single bioreactor. This allows for many more evolutionary trajectories to occur simultaneously. Each viral population is monitored by a as it goes through the evolution process. When the virus succeeds in generating the desired protein, it produces a fluorescent protein that the robot can detect.

“The robot can babysit this population of viruses by measuring this readout, which allows it to see whether the viruses are performing well, or whether they’re really struggling and something needs to be done to help them,” DeBenedictis says.

If the viruses are struggling to survive, meaning that the target protein is not evolving in the desired way, the robot can help save them from extinction by replacing the bacteria they’re infecting with a different strain that makes it easier for the viruses to replicate. This prevents the population from dying out, which is a cause of failure for many directed evolution experiments.

“We can tune these evolutions in real-time, in direct response to how well these evolutions are occurring,” Chory says. “We can tell when an experiment is succeeding and we can change the environment, which gives us many more shots on goal, which is great from both a bioengineering perspective and a basic science perspective.”

Novel molecules

In this study, the researchers used their new platform to engineer a molecule that allows viruses to encode their in a new way. The genetic code of all living organisms stipulates that three DNA base pairs specify one amino acid. However, the MIT team was able to evolve several viral transfer RNA (tRNA) molecules that read four DNA base pairs instead of three.

In another experiment, they evolved a molecule that allows viruses to incorporate a synthetic amino acid into the proteins they make. All and living cells use the same 20 naturally occurring amino acids to build their proteins, but the MIT team was able to generate an enzyme that can incorporate an additional amino acid called Boc-lysine.

The researchers are now using PRANCE to try to make novel small-molecule drugs. Other possible applications for this kind of large-scale directed evolution include trying to evolve enzymes that degrade plastic more efficiently, or molecules that can edit the epigenome, similarly to how CRISPR can edit the genome, the researchers say.

With this system, scientists can also gain a better understanding of the step-by-step process that leads to a particular evolutionary outcome. Because they can study so many populations in parallel, they can tweak factors such as the mutation rate, size of original population, and environmental conditions, and then analyze how those variations affect the outcome. This type of large-scale, controlled experiment could allow them to potentially answer fundamental questions about how evolution naturally occurs.

“Our system allows us to actually perform these evolutions with substantially more understanding of what’s happening in the system,” Chory says. “We can learn about the history of the evolution, not just the end point.”

More information:
Erika A. DeBenedictis et al, Systematic molecular evolution enables robust biomolecule discovery, Nature Methods (2021). DOI: 10.1038/s41592-021-01348-4

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