Scientists from Kumamoto University and The University of Tokyo, Japan have elucidated the control of cellular movement during blood vessel formation. Their findings show that cellular motion occurs not in only the direction toward the tip of the blood vessels, but in a dynamically changing manner!

Blood vessels form a large network with countless branches to supply sufficient oxygen and nutrients efficiently to all tissues within the body. Yet, both blood vessel growth and the formation of blood vessels from a collection of cells remains largely unknown.

Vessel growth was previously considered to occur in the direction of the tip of the blood vessel, stretching in a manner that left the lead cells behind. However, according to recent studies, it was realized that both tip cells and trailing cells move around at different speeds and directions, changing positions to extend the blood vessel through endothelial cell proliferation into the surrounding matrix.

Dr. Nishiyama of Kumamoto University, Mr. Sugihara and Dr. Kurihara of The University of Tokyo and their groups studied how to gain control of the complex cellular motion involved in blood vessel proliferation. They approached the problem by using a combination of biology, mathematical models and supercomputer simulations.

"We watched the movement of the vascular endothelial cells in real time, created a mathematical model of the movement and then performed simulations on a computer," explained Dr. Nishiyama, who led the study. "We found that we could reproduce blood vessel growth and the motion of the entire cellular structure by using only very simple cell-autonomous mechanisms. The mechanisms, such as speed and direction of movement, of every single cell change stochastically. It's really interesting."

Furthermore, Dr. Nishiyama and his team increased the accuracy of the simulation by adding a new rule to the mathematical model. This rule reduced the movement of cells at the tip of the vessel as the distance between cells at the tip and subsequent cells increased.

Additionally, they completed an experiment using actual cells to confirm whether the predicted cellular movement of the simulation was a feasible biological phenomena. They performed an operation to widen the distance between the tip cells and subsequent cells using a laser. The results showed that the forward movement of the tip cells was stopped in the same manner that was predicted by the mathematical model simulations.

"We found that complex cell motility, such as that seen during blood vessel growth, is a process in which coexisting cells successfully control themselves spontaneously and move in a coordinated manner through the influence of adjacent cells. The ability to directly control this phenomenon was made apparent in our study," said Dr. Nishiyama. "These results will add to the understanding of the formation of not only blood vessels but also various tissues and the fundamental mechanisms of the origins of the organism."

This study was published online in "Cell Reports" on November 19, 2015. "Autonomy and non-autonomy of angiogenic cell movements revealed by experiment-driven mathematical modeling"

CAPTION A visualization of one of the model cells simulated by researchers at the Georgia Institute of Technology in their study of macromolecule confinement in cells.

Using large-scale supercomputer modeling, researchers have shown the effects of confinement on macromolecules inside cells -- and taken the first steps toward simulating a living cell, a capability that could allow them to ask 'what-if' questions impossible to ask in real organisms. 

The work could help scientists better understand signaling between cells, and provide insights for designing new classes of therapeutics. For instance, the simulations showed that particles within the crowded cells tend to linger near cell walls, while confinement in the viscous liquid inside cells causes particles to move about more slowly than they would in unconfined spaces. 

The research is believed to be the first to consider the effects of confinement on intracellular macromolecular dynamics. Supported by the National Science Foundation, the results are reported Nov. 16 in the journal Proceedings of the National Academy of Sciences.

The research is an interdisciplinary collaboration between Edmond Chow, an associate professor in the Georgia Tech School of Computational Science and Engineering, and Jeffrey Skolnick, a professor in the Georgia Tech School of Biology. Their goal is to develop and study models for simulating the motions of molecules inside a cell, and also to develop advanced algorithms and computational techniques for performing large-scale simulations. 

"We are setting the stage for what we need to do to simulate a real cell," said Skolnick. "We would like to put enough of a real cell together to be able to understand all of the cellular biochemical principles of life. That would allow us to ask questions that we can't ask now."

Earlier simulations, which produced much less fidelity, had assumed that movement within a cell was the same as movement in an unconfined space. 

Skolnick compared the interior of a living cell to a large New Year's Eve party, perhaps even in Times Square.

"It's kind of like a crowded party that has big people and little people, snakes -- DNA strands -- running around, some really large molecules and some very small molecules," he said. "It's a very heterogeneous and dense environment with as much as 40 percent of the volume occupied."

The simulations showed that molecules near the cell walls tend to remain there for extended periods of time, just as a newcomer might be pushed toward the walls of the New Year's Eve party. Motions of nearby particles also tended to be correlated, and those correlations appeared linked to hydrodynamic forces.

"The lifetimes of these interactions get enhanced, and that is what's needed there for biological interactions to occur within the cell," said Skolnick. "This lingering near the wall could be important for understanding other interactions because if there are signaling proteins arriving from other cells, they would associate with those particles first. This could have important consequences for how signals are transduced."

For particles in the middle of the cell, however, things are different. These molecules interact primarily with nearby molecules, but they still feel the effects of the cell wall, even if it is relatively far away.

"Things move more slowly in the middle of the cell than they would if the cell were infinitely big," Skolnick said. "This may increase the likelihood of having metabolic fluxes because you have to bring molecules around partners. If they are moving slowly, they have more time to react because intimate interactions by accident are unavoidable."

While the rate of activity slows quantitatively, qualitatively it is the same kind of motion.

"Slowed motion is a double-edged sword," Skolnick explained. "If you happen to be nearby, it is likely that you are going to have interactions if you are slower. But if you are not nearby, being slower makes it difficult to be nearby, affecting potential interactions."

The researchers also compared the activities of systems of particles with different sizes, finding that having particles of different sizes didn't make an appreciable difference in the overall behavior of the molecules.

While the simulations didn't include the DNA strands or metabolite particles also found in cells, they did include up to a half-million objects. Using Brownian and Stokesian physics principles, Skolnick and Chow considered what the particles would do within the confined spherical cell a few microns in diameter.

"From the results of the computer simulations, we can measure things that we think might be interesting, such as the diffusion rates near the walls and away from the walls," said Chow. "We often don't know what we are looking for until we find something that forces us to ask more questions and analyze more data."

Such simulations take a lot of computational time, so the algorithms used must be efficient enough to be completed in a reasonable time. The 'art' of the algorithms is trading off fidelity with processing time. Even though the simulations were very large, they managed to study the actions of the confined particles for no more than milliseconds.

"Part of the art of this is guessing what will be a reasonable approximation that will mimic the system, but not be so simple to be trivial or too complicated that you can't take more than a few steps of the simulation," Chow explained.

Scientists, of course, can study real cells. But the simulation offers something the real thing can't do: The ability to turn certain forces on or off to isolate the effects of other processes. For instance, in the simulated cell Skolnick and Chow hope to build, they'll be able to turn on and off the hydrodynamic forces, allowing them to study the importance of these forces to the functioning of real cells.

Results from the simulation can suggest hypotheses to be confirmed or rejected by experiment, which can then lead to further questions and simulations.

"This becomes a tool you can use to understand real cells," said Chow. "It's a virtual system, and you can play all the games you want with it."

Researchers at North Carolina State University have used computational modelling to shed light on precisely how charged gold nanoparticles influence the structure of DNA and RNA – which may lead to new techniques for manipulating these genetic materials.

The work holds promise for developing applications that can store and transport genetic information, create custom scaffolds for bioelectronics and create new drug delivery technologies.

“In nature, meters of DNA are packed tightly into every living cell,” says Jessica Nash, a Ph.D. student at NC State and lead author of a paper on the work. “This is possible because the DNA is wrapped tightly around a positively charged protein called a histone. We’d like to be able to shape DNA using a similar approach that replaces the histone with a charged gold nanoparticle. So we used computational techniques to determine exactly how different charges influence the curvature of nucleic acids – DNA and RNA.”

In their model, the researchers manipulated the charge of the gold nanoparticles by adding or removing positively charged ligands – organic molecules attached to the surface of the nanoparticle. This allowed them to determine how the nucleic acid responded to each level of charge.

“This will let researchers know what to expect – how much charge they need in order to get the desired curvature in the nucleic acid,” says Yaroslava Yingling, an associate professor of materials science and engineering at NC State and corresponding author of the paper.

“We used ligands in the model, but there are other ways to manipulate the charge of the nanoparticles,” says Abhishek Singh, a postdoctoral researcher at NC State and co-author of the paper. “For example, if the nanoparticles and nucleic acid are in solution, you can change the charge by changing the pH of the solution.”

The work is also significant because it highlights how far computational research has come in materials science.

“Our large-scale models account for every atom involved in the process,” says Nan Li, a Ph.D. student at NC State and co-author of the paper. “This is an example of how we can use advanced computational hardware, such as the GPUs – or graphics processing units – developed for use in videogames, to conduct state-of-the-art scientific simulations.”

The research team is now building on these findings to design new nanoparticles with different shapes and surface chemistries to get even more control over the shape and structure of nucleic acids.

“No one has come close to matching nature’s efficiency when it comes to wrapping and unwrapping nucleic acids,” Yingling says. “We’re trying to advance our understanding of precisely how that works.”

Species interaction changed dramatically after the end of last ice age, the Pleistocene, some 11,000 years ago.

Researchers have found that the extinction of North America's megafauna, such as large mammal species including mammoths and saber-toothed cats, dramatically changed how species interacted after the end of last ice age, the Pleistocene, some 11,000 years ago.

The study, released recently in the journal Ecography, is among the first to examine how the extinction affected the distributions and interactions among surviving carnivores. The study focuses on the impacts on wolves, coyotes, foxes, and domestic dogs, collectively referred to as canids.

The research was led by Melissa Pardi, a doctoral candidate, and paleontologist at the University of New Mexico, along with Felisa Smith, a professor of Biology also at UNM.

For decades, paleontologists have debated the causes of the extinction of ice age megafauna, but more recently scientists have shifted their attention to the consequences. "Whatever the cause of the extinction, humans or climate, we are certain that the disappearance of millions of large mammals resulted in major ecosystem changes," said Pardi. "What we're trying to do is figure out what those changes were."

"What is so exciting about this project is that the animals we have today are the same species that interacted with extinct animals like dire wolves," said Pardi. The researchers wanted to know how smaller canids, like coyotes, responded to the extinction of large competitors. "It's tricky to predict," she said. "On the one hand, competition may have decreased. On the other hand, many prey species also went extinct and humans, which were probably hunting similar things, would have also been a significant challenge to contend with."

The researchers used the fossil record of each canid species from the past 20,000 years to build supercomputer models that predicted their expected distributions in the past. From those models, they were able to tell whether species were overlapping in space more or less than expected following the extinction. Increased overlap suggested that species were better able to share the same areas, whereas decreased overlap suggested that species were avoiding each other.

Researchers found that canid species began using different spatial areas and were probably avoiding each other following the Pleistocene extinction.

"After the extinction interactions between canids changed dramatically," said Smith, "and not always in the directions we would have predicted. The influx of a novel predator, humans, and their dogs, also seems to have impacted distributions"

Pardi and Smith hope more studies such as theirs will influence how conservation scientists view communities.

"When we see extinctions in modern ecosystems, we tend to only consider the individual species that go extinct," remarked Pardi, "what we often don't see are the changes in interactions throughout the rest of the community. We don't just lose species, we lose those connections."Survivors of the ice age extinction key to UNM researchSurvivors of the ice age extinction key to UNM research Survivors of the ice age extinction key to UNM research

UNC and UCSF labs create a new research tool to find homes for two orphan cell-surface receptors, a crucial step toward finding better therapeutics and causes of drug side effects

Our cells are constantly communicating, using neurotransmitters and hormones to signal to each other. Molecular receptors on each cell receive these chemical signals and allow cells to accomplish a task important for health. Astonishingly, for about half of these receptors, the chemical signals remain unknown. These "orphan receptors" are highly expressed in particular tissues but their functions remain a mystery. They are considered "dark" elements of the genome, and yet they hold great potential for drug development for a variety of diseases and conditions.

Now, scientists at the University of North Carolina School of Medicine (UNC) and University of California, San Francisco (UCSF) have created a general tool to probe the activity of these orphan receptors, illuminating their roles in behavior and making them accessible for drug discovery. The creation of the research tool - which involves supercomputer modeling, yeast- and mammalian cell-based molecular screening techniques, and mouse models - was published today in the journal Nature.

This work will help researchers learn how orphan receptors interact with molecules inside the body or with drugs. Specifically, the UNC and UCSF scientists used their new tool to find a novel probe molecule that can modulate the orphan G protein-coupled receptor 68 (GPR68, also known as OGR1), an orphan receptor that is highly expressed in the brain.

"GPCRs are the single most important family of therapeutic drug targets," said Brian Shoichet, PhD, professor of pharmaceutical chemistry at UCSF. "About 27 percent of FDA-approved drugs act through GPCRs. They are considered to be among the most useful targets for discovering new medications."

The new probe molecule, dubbed "ogerin," turns on GPR68, activating its signaling role. To understand how this activation of GPR68 affects brain function, the investigators gave it to mice and put them through a battery of behavioral tests. Mice that had been given ogerin were much less likely to learn to fear a specific stimulus. This "fear-conditioning" is controlled by the hippocampus, where GPR68 is highly expressed. But ogerin had no effect on mice that lacked this receptor.

To demonstrate general research applicability, the UNC and UCSF researchers also used their technique to find molecules that can modulate GPR65, another orphan receptor.

"We provide an integrated approach that we believe can be applied to many other receptors," said Bryan L. Roth, MD, PhD, co-senior author of the Nature paper and the Michael Hooker Distinguished Professor of Protein Therapeutics and Translational Proteomics in the Department of Pharmacology at UNC. "The goal is to quickly find drug-like compounds for these receptors. This should facilitate discovery of novel and safer therapeutics for a host of diseases."

Xi-Ping Huang, PhD, co-first author and research assistant professor at UNC, said, "We used yeast-based screening techniques to find compounds that activate an orphan receptor. Then [co-first author] Joel Karpiak, a graduate student in Shoichet's lab at UCSF, created a computer model and searched libraries of millions of compounds to find out what kind of molecular structure ensures proper binding and interaction with a specific receptor. Then, back in the lab, we tested new molecules and found a novel ligand."

A ligand is a chemical that binds to a specific part of a protein, such as a receptor.

"The fact that GPR68 is highly expressed in several tissues, especially the brain, and that it is a member of the large GPCR family, suggests that this discovery can be further leveraged for drug discovery," Shoichet said.

Currently, few drug developers would seek drugs for a target with an unknown role in human biology. With new evidence of the role of GPR68 - and a molecule that can modulate that role - the door has been opened for further research studies, both basic and applied.

"The druggable genome is an iceberg that is mostly submerged," Shoichet said. "This paper illuminates a small piece of it, providing new reagents to modulate a previously dark, unreachable drug target. Just as important, the strategy should be useful to many other dark targets in the genome."

Roth's lab is well known for developing technologies to probe biological function. His team developed DREADDS (Designer Receptors Exclusively Activated by Designer Drugs), for which he was given an NIH BRAIN Initiative grant. First results on work from that grant were reported earlier this year with the development of a second kind of DREADD.

For the Nature paper, Roth's lab teamed up with Shoichet lab, which developed the supercomputational method to screen more than 3.1 million molecules for potential activity on GPR68. The goal was to predict those very few molecules that could modulate the receptor. This eventually led them to the molecule ogerin. The same approach also helped the team discover compounds that activated or modulated GPR65, suggesting that the approach could help scientists discover ligands for other understudied and orphan G protein-coupled receptors.

"Orphan receptors could be a great source of therapeutics," Huang said. "But it has been difficult to study them. The research community has needed an approach that works, and that's why we put so much effort into this."

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