Syracuse physicists develop the first simulations capturing how cells containing the protein vimentin move through body tissue

The process of normal cell division in the human body is quite simple: start dividing in response to a signal such as a wound and stop when enough cells have been produced and the skin is healed. But cancerous cells ignore the stop signs. They grow and spread rapidly, proliferating even in cramped locations. Similar to navigating through a large crowd of people, moving through dense tissue is no easy task. Any normal cell would die during the process, but many cancerous cells have a cage-like protein that helps them protect their nucleus and DNA. That protein, called vimentin, is often expressed in intermediate filaments (one of the three structural elements of the cell) during cell movement. And now, A&S researchers are finding out more about this protein, which could eventually help with cancer treatment or wound healing. The protein vimentin (green) helps protect a cell’s nucleus and DNA during migration. (Image courtesy of Maxx Swoger)

In the past, the role of vimentin remained largely unclear, but researchers in Syracuse University's College of Arts and Sciences have developed one of the first models that capture the dynamics of confined cell motility and show how vimentin helps protect the cell’s nucleus during migration. The team, which includes lead author Sarthak Gupta, a graduate student in physics, Alison Patteson, assistant professor of physics, and Jennifer Schwarz, professor of physics, recently had their results published in the New Journal of Physics. Their model sheds light on the function of a protein that is a major player in cancer growth, and their results could one day help researchers determine better ways to stop the spread of cancer.

Cell migration is a fundamental process that contributes to building and maintaining tissue. During wound healing and cancer metastasis, two instances when cells are known to be on the move, they depend on the skeleton of the cell, known as the cytoskeleton, for protection and to generate force. The cytoskeleton is made up of a network of proteins, and one in particular – vimentin – is often present when cells decide that they want to travel.

“When a cell is stationary, it is known that the vimentin protein expression is very minimal,” says Gupta. “Conversely, when the cells become migratory, expression of this protein increases.”

In Patteson’s lab, researchers have been recreating what a cell goes through as it migrates to observe how vimentin plays into the process. By squeezing cells with and without vimentin through narrow microchannels on collagen gels, they mimic in 3D the way cells navigate through small pores in real tissue. In their observations, they found that the presence of vimentin in the cytoskeleton was crucial for the survival of cells moving through 3D space, something that researchers were previously unable to detect using traditional two-dimensional experiments on glass or plastic.

Using Patteson’s experimental results, Gupta and Schwarz developed a model that captures the effects of the vimentin protein on the cell’s cytoskeleton and the nucleus. That model enables the team to regulate the forces that the cell generates and the stiffness of the nucleus, providing visual proof of Patteson’s lab experiments.

“Without vimentin, we found that the cells are very soft and the nucleus becomes deformed as it moves,” says Gupta. “In the simulation with vimentin, the cell is much more resistant to deformation and the inside of the nucleus and its DNA is protected.”

By understanding vimentin’s role in protecting cancerous cells as they spread through the body, Patteson says their research could help pinpoint drugs that could slow its growth.

“In theory treating cancer with drugs that target vimentin could be an option,” says Patteson. “By targeting vimentin, the cell will not be able to go from one place to another efficiently, stopping the spread of cancer in its tracks.”

The team says another possible application could be with wound healing, where drugs that stimulate vimentin expression could be administered to speed up the movement of cells to the wound area, essentially accelerating the tissue restoration process.

Read the team’s full paper in the New Journal of Physics.

Arizona researcher finds slower ocean circulation as the result of climate change could intensify extreme cold weather in the U.S.

Throughout Earth's oceans runs a conveyor belt of water. Its churning is powered by differences in the water's temperature and saltiness, and weather patterns around the world are regulated by its activity.

A pair of researchers studied the Atlantic portion of this worldwide conveyor belt called the Atlantic Meridional Overturning Circulation, or AMOC, and found that winter weather in the United States critically depends on this conveyor belt-like system. As the AMOC slows because of climate change, the U.S. will experience more extreme cold winter weather.

The study, published in the journal Communications Earth & Environment was led by Jianjun Yin, an associate professor in the University of Arizona Department of Geosciences, and co-authored by Ming Zhao, a physical scientist at the National Oceanic and Atmospheric Administration's Geophysical Fluid Dynamics Laboratory.

AMOC works like this: Warm water travels north in the upper Atlantic Ocean and releases heat into the atmosphere at high latitudes. As the water cools, it becomes denser, which causes it to sink into the deep ocean where it flows back south.

"This circulation transports an enormous amount of heat northward in the ocean," Yin said. "The magnitude is on the order of 1 petawatt, or 10 to the 15 power watts. Right now, the energy consumption by the entire world is about 20 terawatts or 10 to 12 power watts. So, 1 petawatt is enough to run about 50 civilizations."

But as the climate warms, so does the ocean surface. At the same time, the Greenland ice sheet experiences melting, which dumps more freshwater into the ocean. Both warming and freshening of the water can reduce surface water density and inhibit the sinking of the water, slowing the AMOC. If the AMOC slows, so does the northward heat transport.

This is important because the equator receives more energy from the sun than the poles. Both the atmosphere and ocean work to transport energy from low latitudes to high latitudes. If the ocean can't transport as much heat northward, then the atmosphere must instead transport more heat through more extreme weather processes at mid-latitudes. When the atmosphere moves heat northward, cold air is displaced from the poles and pushed to lower latitudes, reaching places as far south as the U.S. southern border.

"Think of it as two highways connecting two big cities," Yin said. "If one is shut down, the other one gets more traffic. In the atmosphere, the traffic is the daily weather. So, if the ocean heat transport slows or shuts down, the weather becomes more extreme."

Yin said the study was motivated by the extreme cold weather Texas experienced in February.

"In Houston, the daily temperature dropped to 40 degrees Fahrenheit below the normal," Yin said. "That's the typical range of a summer/winter temperature difference. It made Texas feel like the Arctic. This kind of extreme winter weather happened several times in the U.S. during recent years, so the scientific community has been working to understand the mechanism behind these extreme events."

The crisis in Texas caused widespread and catastrophic power outages, and the National Oceanic and Atmospheric Administration estimated that socioeconomic damages totaled $20 billion. Yin was curious about the role the ocean played in extreme weather events.

Yin and Zhao used a state-of-the-art, high-resolution global climate model to measure the influence of the AMOC on U.S. extreme cold weather.

They ran the model twice, first looking at today's climate with a functioning AMOC. They then adjusted the model by inputting enough freshwater into the high-latitude North Atlantic to shut down the AMOC. The difference revealed the role of the AMOC in extremely cold weather. They found that without the AMOC and its northward heat transport, extremely cold winter weather intensifies in the U.S.

According to recent observational studies, the AMOC has weakened in the past decades. Climate models project it will get even weaker in response to increased greenhouse gases in the atmosphere.

"But there is uncertainty about the magnitude of the weakening because, at this point, we don't know exactly how much the Greenland ice sheet will melt," Yin said. "How much it melts depends on the greenhouse gas emissions."

The researchers also didn't take into account in their model the effects of human-caused global warming, but that's an area of interest for the future, Yin said.

"We just turn off the AMOC (in the model) to look at the response by extreme weather," he said. "Next, we want to factor in the greenhouse gases and look at the combined effects of the AMOC slowdown and global warming on extreme cold weather."

Datadobi launches DQL to scan, interrogate petabyte-scale data lakes

According to the latest research, there will be about 175 zettabytes (ZB) of data worldwide by 2025 compared to 64.2ZB in 2020. Not surprisingly, as a result, 95% of businesses cite the need to manage unstructured data as a problem for their business. 

Both of Datadobi’s products, DobiMigrate and DobiProtect, have been designed to scan large file systems containing billions of files to help organizations harness the power of unstructured data. Each of these scans produces huge lists of file paths and their metadata in a proprietary format to allow performant and storage-efficient handling, analysis, and comparison of the files to enhance unstructured data management.

Historically, these scan files were only used for doing data migration or protection for customers…until now. 

What is Datadobi Query Language? (DQL)

Over the last several months as the COVID-19 pandemic drove digital transformation and increased the amount of unstructured data within networks, enterprises began asking us for access to the scans to analyze and reorganize unstructured data lakes. 

For a customer to dissect the composition of the data, however, it requires some serious data reduction and aggregation in that set of billions of files. This created the need for a tool to query, aggregate, and reduce the amount of information about the data lake so it is consumable by the IT administrator. 

Datadobi has officially developed Datadobi Query Language (DQL) to enhance the file system assessment service to optimize and organize data lakes internally. DQL within the file system assessment service offers complete flexibility around how the software can interrogate the customer data set and enables tremendous data reduction to make it manageable for the customer to handle its multi-petabyte data lake. 

DQL is a query framework that can look for many aspects in a data lake such as: 

  • Identifying cold data sets — data that is infrequently accessed
  • Identifying old data sets —data that was created or modified some time ago
  • Identifying data sets owned by a specific user or group, e.g. by users who no longer work at the company
  • Identifying shares, exports, or directories trees that are homogeneous (cold, old, owner, file types) and can be handled as one data set e.g. to take specific lifecycle actions upon

How DQL Fits into Datadobi’s Existing Products and Services 

As mentioned above, DQL is used to customize Datadobi’s file system assessment service.  

For background, Datadobi created the file system assessment offering last year as a service for customers that can be used before they plan a data migration or reorganization. 

DQL is now an essential part of the file system assessment service because it enables assessments to be customizable. Using the pre-migration service enhanced with DQL, customers can learn to understand what’s on their storage system, and based on the partitioning of their system in data sets, make a plan of what to migrate where. 

On a similar note, DQL is an essential part of Datadobi’s vendor-neutral data mobility engine. DQL sits within the engine technology to scan file systems, move data, analyze the file metadata of large data lakes, and simplify how IT administrators can look at their data and identify logical subsets of data. 

The volume of data is only expected to grow over the next few years. IT administrators need a data management solution that can transform data into digestible material to allow curated decisions on storage options for migration and protection to be made.