UNC’s novel way to visualize the human proteome could lead to improved clinical laboratory tests along with the development of new therapies
Diagnostic testing based on proteomics is considered to be a field with immense potential in diagnostics and therapeutics. News of a research breakthrough into how scientists can visualize protein activity within cells will be of major interest to the pathologists, PhDs, and medical laboratory scientists who specialize in clinical laboratory testing involving proteins.
Proteins are essential to all life and to the growth, maintenance, and repair of the human body. So, a thorough understanding of how they function within living cells would be essential to informed medical decision-making as well. And yet, how proteins go about doing their work is not well understood.
That may soon change. Scientists at the University of North Carolina (UNC) School of Medicine have developed an imaging method that could provide new insights into how proteins alter their shapes within living cells. And those insights may lead to the development of new therapies and medical treatments.
Dubbed “binder-tag” by the UNC scientists, their new technique “allows researchers to pinpoint and track proteins that are in a desired shape or ‘conformation,’ and to do so in real time inside living cells,” according to a UNC Health news release.
Two labs in the UNC School of Medicine’s Department of Pharmacology collaborated to develop the binder-tag technique:
“No one has been able to develop a method that can do, in such a generalizable way, what this method does. So, I think it could have a very big impact,” said lead author of the UNC study Klaus Hahn PhD (above), in the news release. “With this method we can see, for example, how microenvironmental differences across a cell affect, often profoundly, what a protein is doing,” he added. This research may enlarge scientists’ understanding of how the human proteome works and could lead to new medical laboratory tests and therapeutic drugs. (Photo copyright: UNC School of Medicine.)
How Binder-Tag Works
During their study, the UNC scientists developed binder-tag “movies” that allow viewers to see how the binder-tag technique enables the tracking of active molecules in living cells.
The technique involves two parts: a fluorescent binder and a molecular tag that is attached to the proteins of interest.
When inactive, the tag is hidden inside the protein, but when the protein is ready for action it changes shape and exposes the tag.
The binder then joins with the exposed tag and fluoresces. This new fluorescence can easily be tracked within the cell.
Nothing else in the cell can bind to the binder or tag, so they only light up when in contact on the active protein.
This type of visualization will help researchers understand the dynamics of a protein in a cell.
“The method is compatible with a wide range of beacons, including much more efficient ones than the interacting beacon pairs required for ordinary FRET [fluorescence resonance energy transfer]. Binder-tag can even be used to build FRET sensors more easily. Moreover, the binder-tag molecules were chosen so that nothing in cells can react with them and interfere with their imaging role,” Hahn said in the news release.
“Only upon exposure can the peptide specifically interact with a reporter protein (the binder). Thus, simple fluorescence localization reflects protein conformation. Through direct excitation of bright dyes, the trajectory and conformation of individual proteins can be followed,” the UNC researchers wrote in Cell. “The simplicity of binder-tag can provide access to diverse proteins.”
The UNC researchers’ binder-tag technique is a way to overcome the dire challenge of seeing tiny and hard-working proteins, Cosmos noted. Typical light microscopy does not enable a view of molecules at work. This paves the way for the new binder-tag technique, UNC pointed out.
“With this method, we can see, for example, how microenvironmental differences across a cell affect—and often profoundly—what a protein is doing,” Hahn said. “For a lot of protein-related diseases, scientists haven’t been able to understand why proteins start to do the wrong thing. The tools for obtaining that understanding just haven’t been available.”
More Proteins to Study
More research is needed before the binder-tag method can be used in diagnostics. Meanwhile, the UNC scientists intend to show how binder-tag can be applied to other protein structures and functions.
“The human proteome has between 80,000 and 400,000 proteins, but not all at one time. They are expressed by 20,000 to 25,000 human genes. So, the human proteome has great promise for use in diagnostics, understanding disease, and developing therapies,” said Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
Medical scientists and diagnostics professionals will want to stay tuned to discover more about the tiny—though mighty—protein’s contributions to understanding diseases and patient treatment.
Tiny sensors with Bluetooth technology that measure useful biomarkers may eliminate need for invasive blood draws used for clinical laboratory tests
What if a baby’s pacifier could be used to measure electrolyte levels in newborns? An international research team has developed just such a device, and it has the potential to reduce invasive blood collections required to provide specimens for clinical laboratory testing of critical biomarkers. At the same time, this device may allow continuous monitoring of electrolyte levels with wireless alerts to caregivers.
Typical blood draws for NICU babies can cause information gaps as they are usually only performed twice a day. This can be problematic in cases where more frequent monitoring of these biomarkers is required to monitor the infant’s condition.
“We know that premature babies have a better chance of survival if they get a high quality of care in the first month of birth,” said Jong-Hoon Kim, PhD, Associate Professor at the WSU School of Electrical Engineering and Computer Science, in a WSU news release. “Normally, in a hospital environment, they draw blood from the baby twice a day, so they just get two data points. This device is a non-invasive way to provide real-time monitoring of the electrolyte concentration of babies.”
The smart pacifier (above) developed by researchers at the Washington State University School of Electrical Engineering and Computer Science—in collaboration with scientists in two South Korean institutions—provides continuous monitoring of sodium and potassium ion levels. This can help detect and prevent potentially dangerous dehydration issues in NICU babies without invasive blood draws for traditional clinical laboratory testing. (Photo copyright: University of Washington.)
How the Smart Pacifier Works
The miniature system developed by the WSU researchers utilizes a typical, commercially available pacifier outfitted with ion-selective sensors, flexible circuits, and microfluidic channels that monitor salivary electrolytes. These flexible, microfluidic channels attract the saliva when the pacifier is in the infant’s mouth which enables continuous and efficient saliva collection without the need for any type of pumping system. The gathered data is relayed wirelessly to caregivers using Bluetooth technology.
When the researchers tested their smart pacifier on infants, they discovered that the results captured from the device were comparable to information obtained from normal blood draws and standard clinical laboratory tests. Kim noted in the press release that technology currently in use to test infant saliva for electrolytes tend to be bulky, rigid devices that require a separate sample collection.
“You often see NICU pictures where babies are hooked up to a bunch of wires to check their health conditions such as their heart rate, the respiratory rate, body temperature, and blood pressure,” said Kim in the press release. “We want to get rid of those wires.”
The researchers intend to make the components for the device more affordable and recyclable. They also plan to perform testing for their smart pacifier on larger test groups to prove efficacy and hope the gadget will help make NICU treatment less disruptive for infant patients.
Going as far back as 2013, Dark Daily has covered research into the use of sensors placed in wearables and disposables to detect and monitor health issues.
“It should be noted that the ability to put reliable diagnostic sensors in disposables like diapers has been around for almost a decade and does not seem to have caught on with either caregivers or the public,” said Robert Michel, Editor-in-Chief of Dark Daily and its sister publication, The Dark Report. “Because the researchers who developed the pacifier are attempting to solve a problem for NICU babies, this solution might find acceptance.”
This is another example of how researchers are thinking outside the box as to how to measure critical biomarkers without the need to send a specimen to the core clinical laboratory and wait hours—sometimes overnight—for results.
Screening and analysis of ocean samples also identified a possible missing link in how the RNA viruses evolved
An international team of scientists has used genetic screening and machine learning techniques to identify more than 5,500 previously unknown species of marine RNA viruses and is proposing five new phyla (biological groups) of viruses. The latter would double the number of RNA virus phyla to 10, one of which may be a missing link in the early evolution of the microbes.
Though the newly-discovered viruses are not currently associated with human disease—and therefore do not drive any current medical laboratory testing—for virologists and other microbiologists, “a fuller catalog of these organisms is now available to advance scientific understanding of how viruses evolve,” said Dark Daily Editor-in-Chief Robert Michel.
“While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively unstudied,” wrote four microbiologists from Ohio State University (OSU) who participated in the study in an article they penned for The Conversation.
The OSU study authors included:
Ahmed Zayed, PhD, research scientist, Dept. of Microbiology, OSU.
Matthew Sullivan, PhD, Professor of Microbiology and Director of the Center of Microbiome Science at OSU.
“RNA viruses are clearly important in our world, but we usually only study a tiny slice of them—the few hundred that harm humans, plants and animals,” explained Matthew Sullivan, PhD (above), Director, Center of Microbiome Science, in an OSU news story. Sullivan led the OSU research team. “We wanted to systematically study them on a very big scale and explore an environment no one had looked at deeply, and we got lucky because virtually every species was new, and many were really new,” he added. (Photo copyright: University of Ohio.)
RNA versus DNA Viruses
In contrast to the better-understood DNA virus, an RNA virus contains RNA instead of DNA as its genetic material, according to Samanthi Udayangani, PhD, in an article she penned for Difference Between. Examples of RNA viruses include:
One major difference, she explains, is that RNA viruses mutate at a higher rate than do DNA viruses.
The OSU scientists identified the new species by analyzing a database of RNA sequences from plankton collected during a series of ocean expeditions aboard a French schooner owned by the Tara Ocean Foundation.
“Plankton are any aquatic organisms that are too small to swim against the current,” the authors explained in The Conversation. “They’re a vital part of ocean food webs and are common hosts for RNA viruses.”
The team’s screening process focused on the RNA-dependent RNA polymerase (RdRp) gene, “which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells,” according to the OSU news story.
“RdRp is supposed to be one of the most ancient genes—it existed before there was a need for DNA,” Zayed said.
The RdRp gene “codes for a particular protein that allows a virus to replicate its genetic material. It is the only protein that all RNA viruses share because it plays an essential role in how they propagate themselves. Each RNA virus, however, has small differences in the gene that codes for the protein that can help distinguish one type of virus from another,” the study authors explained.
The screening “ultimately identified over 44,000 genes that code for the virus protein,” they wrote.
Identifying Five New Phyla
The researchers then turned to machine learning to organize the sequences and identify their evolutionary connections based on similarities in the RdRp genes.
“The more similar two genes were, the more likely viruses with those genes were closely related,” they wrote.
The technique classified many of the sequences within the five previously known phyla of RNA viruses:
But the researchers also identified five new phyla—including two dubbed “Taraviricota” and “Arctiviricota”—that “were particularly abundant across vast oceanic regions,” they wrote. Taraviricota is named after the Tara expeditions and Arctiviricota gets its name from the Arctic Ocean.
They speculated that Taraviricota “might be the missing link in the evolution of RNA viruses that researchers have long sought, connecting two different known branches of RNA viruses that diverged in how they replicate.”
In addition to the five new phyla, the researchers are proposing at least 11 new classes of RNA viruses, according to the OSU story. The scientists plan to issue a formal proposal to the International Committee on Taxonomy of Viruses (ICTV), the body responsible for classification and naming of viruses.
Studying RNA Viruses Outside of Disease Environments
“As the COVID-19 pandemic has shown, RNA viruses can cause deadly diseases. But RNA viruses also play a vital role in ecosystems because they can infect a wide array of organisms, including microbes that influence environments and food webs at the chemical level,” wrote the four study authors in The Conversation. “Mapping out where in the world these RNA viruses live can help clarify how they affect the organisms driving many of the ecological processes that run our planet. Our study also provides improved tools that can help researchers catalog new viruses as genetic databases grow.”
This remarkable study, which was partially funded by the US National Science Foundation, will be most intriguing to virologists and microbiologists. However, clinical laboratories also should be interested in the fact that the catalog of known viruses has just expanded by 5,500 types of RNA viruses.
With Millennials soon to make up the majority of the medical laboratory workforce, it’s only natural that digital networking is gaining momentum at events like the Executive War College
At any hour during the in-person event in New Orleans, attendees scheduled meetups, participants asked questions to conference organizers, and users discussed important clinical laboratory and anatomic pathology topics. All of those interactions occurred within the Whova meeting application, which served as the Executive War College’s virtual guide.
In many ways, widespread use of the meeting app reflects a younger crowd that lives life on mobile phones. It’s not all that different than the changing face of the clinical lab industry as laboratory veterans retire and new faces come in, said Robert Michel, Founder of the Executive War College (EWC) and Editor-in-Chief of Dark Daily’s sister publication The Dark Report.
“It’s clear from the soaring use of our conference’s meeting app at the Executive War College that a younger generation is changing how business is conducted during and after a lab industry conference,” he observed. “Generation X and Millennials are steadily influencing how people network at live events.”
“It is remarkable that, among the 900 attendees at this year’s event, there were more than 750,000 impressions involving the sponsors and companies supporting this year’s conference,” said Robert Michel (above), Editor-in-Chief of Dark Daily and Founder of the Executive War College. “It shows that these attendees are serious about identifying solutions and vendors who can help them solve the various pain points in their laboratories.” (Photo copyright: Dark Intelligence Group.)
88% of Attendees at Executive War College Used the Event App
Usage numbers aggregated during the EWC conference of people who downloaded and used the meeting app speak for themselves:
A large majority of attendees (88%) downloaded the app.
Users sent 11,398 messages in the app.
There were 136 community board discussions posted.
Users created 80 meetups, with 677 people attending those gatherings.
There were 764,745 sponsor impressions in the app (in other words, clicks on a sponsor link or attendees navigating to sponsor material).
What the numbers don’t convey is that the conference’s meeting app was also fun to use!
Butterworth spoke during a special session at the Executive War College. She also took the No. 1 spot on the meeting app’s leaderboard for the event, collecting an impressive 225,900 points. Users gained points for the leaderboard based on activities they completed in the app.
Spirited competition ensued among the leaderboard’s top users, who jockeyed for position as the conference progressed. Plenty of off-topic conversations took place in the app as well, as attendees helped each other navigate New Orleans with tips about restaurants, local cemetery tours, or where to work out.
The leaderboard on the Whova meeting application (above) at the conclusion of this year’s Executive War College on Laboratory and Pathology Management showed the top point gainers. (Photo copyright: Dark Intelligence Group.)
Clinical Laboratory Sponsors Reached Out to Attendees in New Ways
For sponsors and other vendors visiting the conference, the meeting app provided a different avenue to approach attendees beyond the typical networking that takes place during breaks, cocktail receptions, luncheons, and off-site parties.
For example, some sponsors shared white papers or YouTube videos via the app’s community boards or asked questions about topics of interest. Additionally, sponsors could respond directly to queries from attendees.
“At the Executive War College, there was clearly a sustained exchange between vendors looking to engage business development opportunities and participants who have pain points that need to be addressed and are looking for solutions,” Michel said.
The next Executive War College will return to New Orleans on April 25-26, 2023. Click on this link to access early registration discounts.
Supplychain shortages involving clinical laboratory products may not ease up any time soon, as China’s largest shipping province is once again in COVID-19 lockdown
Following two years of extremely high demand, pathology laboratories as well as non-medical labs in the United Kingdom (UK) and Europe are experiencing significant shortages of laboratory resources as well as rising costs. That’s according to a recently released survey by Starlab Group, a European supplier of lab products.
In its latest annual “mood barometer” survey of around 200 lab professionals in the UK, Germany, Austria, Italy, and France, Starlab Group received reports of “empty warehouses” and a current shortage of much needed lab equipment, reportedly as a result of rising costs, high demand, and stockpiling of critical materials needed by pathology laboratories during the COVID-19 pandemic, according to Laboratory News.
The survey respondents, who represented both medical laboratories and research labs, noted experiencing more pressure from staff shortages and insufficient supplies required to meet testing demands in 2021 as compared to 2020. For example, only 23% of respondents said they had enough liquid handling materials—such as protective gloves and pipettes—in 2021, down from 39% who responded to the same question in 2020.
“The entire laboratory industry has been in a vicious circle for two years. While more and more materials are needed, there’s a lack of supplies. At the same time, laboratories want to stockpile material, putting additional pressure on demand, suppliers, and prices,” Denise Fane de Salis, Starlab’s UK Managing Director and Area Head for Northern Europe, told Process Engineering. “Institutes that perform important basic work cannot keep up with the price competition triggered by COVID-19 and are particularly suffering from this situation,” she added.
“COVID-19 is the largest, but by no means the only challenge facing Europe’s laboratories,” Denise Fane de Salis (above), Starlab’s UK Managing Director and Area Head for Northern Europe, told Laboratory News. “The mood barometer we commissioned once again clearly shows that we need to look at the entire range of laboratory work. The laboratory sector is not only essential in medicine and research. Diagnostics have long since encompassed almost all areas of life and the economy.” Those in this country responsible for clinical laboratory supply chains should consider what Salis is advising. (Photo copyright: Starlab UK.)
Lab Supply Shortages Worsen in 2021
With a UK office in Milton Keynes, Starlab’s network of distributors specialize in liquid handling products including pipette tips, multi-channel pipettes, and cell culture tubes, as well as PCR test consumables and nitrile and latex gloves.
According to Laboratory News, Starlab’s 2021 annual survey, released in March 2022, found that:
64% cited late deliveries contributing to supply woes.
58% noted medical labs getting preference over research labs, up from 46% in 2020.
57% said demand for liquid handling products was the same as 2020.
30% of respondents said material requirements were up 50% in 2021, compared to 2020.
76% reported dealing with rising prices in lab operations.
29% expect their need for materials to increase by 25% in 2022, and 3% said the increase may go as high as 50%.
17% of respondents said they foresee challenges stemming from staff shortages, with 8% fearing employee burnout.
UK-European Medical Laboratories on Waiting Lists for Supplies
Could import of lab equipment and consumables from Asia and other areas outside UK have contributed to the shortages?
“A substantial portion of the world’s clinical laboratory automation, analyzers, instruments, and test kits are manufactured outside UK. Thus, UK labs may face a more acute shortage of lab equipment, tests, and consumables because governments in countries that manufacture these products are taking ‘first dibs’ on production, leaving less to ship to other countries,” said Robert Michel, Editor-in-Chief of Dark Daily and our sister publication The Dark Report.
Indeed, a statement on Starlab’s website describes challenges the company faces meeting customers’ requests for supplies.
“The pandemic also has an impact on our products that are manufactured in other countries. This particularly affects goods that we ship from the Asian region to Europe by sea freight. Due to the capacity restrictions on the ships, we expect additional costs for the transport of goods at any time. Unfortunately, the situation is not expected to ease for the time-being,” Starlab said.
Furthermore, economists are forecasting probable ongoing supply chain effects from a new SARS-CoV-2 outbreak in China.
Lockdown of China’s Largest Shipping Province Threatens Supply Chains Worldwide
According to Bloomberg News, “Shenzhen’s 17.5 million residents [were] put into lockdown on [March 13] for at least a week. The city is located in Guangdong, the manufacturing powerhouse province, which has a gross domestic product of $1.96 trillion—around that of Spain and South Korea—and which accounts for 11% of China’s economy … Guangdong’s $795 billion worth of exports in 2021 accounted for 23% of China’s shipments that year, the most of any province.”
Bloomberg noted that “restrictions in Shenzhen could inflict the heaviest coronavirus-related blow to growth since a nationwide lockdown in 2020, with the additional threat of sending supply shocks rippling around the world.”
“Given that China is a major global manufacturing hub and one of the most important links in global supply chains, the country’s COVID policy can have notably spillovers to its trading partners’ activity and the global economy,” Tuuli McCully, Head of Asia-Pacific Economies, Scotiabank, told Bloomberg News.
Wise medical laboratory leaders will remain apprised of supply chain developments and possible lockdowns in Asia while also locating and possibly securing new sources for test materials and laboratory equipment in anticipation of future supply shortages.
