For metalloproteins to work properly, they must be paired with the correct metal ion — hemoglobin can only function with iron Yet, protein-metal binding is normally governed by a strict order, called the Irving-Williams Series, which dictates that copper ions should bind to proteins over other metals.

In other words, if a cell contained equal amounts of different metal ions, most cellular proteins and other components would bind to copper, clogging up cellular machinery in the process. This is why organisms spend considerable energy keeping very strict controls over how much free copper is present in cells.

Now researchers in the University of California San Diego’s Division of Physical Sciences have reported a new protein-design strategy to sidestep the Irving-Williams Series. The findings were published earlier this week in the journal Nature.

Professor of Chemistry and Biochemistry Akif Tezcan and postdoctoral scholar Tae Su Choi designed a flexible protein that selectively binds other metal ions over copper, paving the way for the design of novel functional proteins and metal sequestration agents. Choi and Tezcan discovered that selective binding to non-copper metals required the artificial protein to present a very specific combination of amino acids and geometries to discriminate against copper. This discovery required an uncommon design approach.

“Protein design typically involves trying to craft a discrete protein structure that can perform a certain function, such as catalysis. This approach is inherently deterministic and follows the sequence of one design-one structure-one function,” stated Tezcan. “Best case scenario, you obtain the structure and function that is designed. However, this approach doesn’t leave much room for the discovery of new design principles or unexpected outcomes, which are potentially more significant than what was originally planned.”

Tezcan and Choi took a probabilistic approach instead. At the outset, their designed protein wasn’t engineered to possess a singular structure that selectively binds to a certain type of metal. They created a flexible system that could arrange itself in multiple ways to bind different metal ions in different geometries. It was this flexibility that led them to an outcome they did not originally plan for.

“In analyzing these systems, we saw that proteins were binding to cobalt and nickel ions ahead of copper, which is not the natural order of things,” stated Choi. “We created an hypothesis and tested new variants. After extensive analysis, we realized we could construct a protein environment where copper was disfavored.”

“This is an example of designing a pathway rather that a target,” explained Tezcan. “I personally think that this is a more exciting way to go about the protein design problem. By incorporating an element of flexibility into the design, we leave open the possibility of different outcomes and new design principles we couldn’t have known beforehand.”

Research on selective metal binding and protein design has importance beyond a better understanding of the fundamentals of life. It can also lay the foundation for more efficient processes during environmental remediation, such as when certain metals need to be sequestered in contaminated water. Protein design is also a critical part of pharmaceutical research and development.

“We were intrigued by the question ‘Can we design proteins that can selectively bind to metals or have catalytic reactions in ways that evolution has not yet invented?'” said Choi. “Just because biology doesn’t do it, it doesn’t mean it’s not possible.”

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Materials provided by University of California – San Diego. Original written by Michelle Franklin. Note: Content may be edited for style and length.

‘We correctly diagnosed all patients with conditions that were already known, including Huntington’s disease, fragile X syndrome, hereditary cerebellar ataxias, myotonic dystrophies, myoclonic epilepsies, motor neuron disease and more,’ says Dr Ira Deveson, Head of Genomics Technologies at the Garvan Institute and senior author of the study.

The diseases covered by the test belong to a class of over 50 diseases caused by unusually-long repetitive DNA sequences in a person’s genes — known as ‘Short Tandem Repeat (STR) expansion disorders’.

‘They are often difficult to diagnose due to the complex symptoms that patients present with, the challenging nature of these repetitive sequences, and limitations of existing genetic testing methods,’ says Dr Deveson.

The study, published today in Science Advances, shows that the test is accurate, and allows the team to begin validations to make the test available in pathology services around the world.

A patient who participated in the study, John, first realised something wrong when he experienced unusual problems balancing during a ski lesson.

‘It was very worrying having symptoms that, over the years, increased in severity; from being active and mobile to not being able to walk without support. I had test after test for over ten years and absolutely no answers as to what was wrong,’ says John, who was eventually diagnosed with a rare genetic disease called CANVAS, which affects the brain.

‘It was reassuring to finally confirm my diagnosis genetically, and it’s exciting to know that, in the near future, others with these types of conditions will be able to get a diagnosis quicker than I did,’ he says.

‘For patients like John, the new test will be a game-changer, helping to end what can often be a taxing diagnostic odyssey,’ says Dr Kishore Kumar, a co-author of the study and clinical neurologist at the Concord Hospital.

Repeat expansion disorders can be passed on through families, can be life threatening and generally involve muscle and nerve damage, as well as other complications throughout the body.

Quicker, more-accurate diagnosis for patients avoids ‘diagnostic odyssey’

Current genetic testing for expansion disorders can be ‘hit and miss’, says Dr Kumar. ‘When patients present with symptoms, it can be difficult to tell which of these 50-plus genetic expansions they might have, so their doctor must decide which genes to test for based on the person’s symptoms and family history. If that test comes back negative, the patient is left without answers. This testing can go on for years without finding the genes implicated in their disease. We call this the ‘diagnostic odyssey’, and it can be quite stressful for patients and their families,’ he says.

‘This new test will completely revolutionise how we diagnose these diseases, since we can now test for all the disorders at once with a single DNA test and give a clear genetic diagnosis, helping patients avoid years of unnecessary muscle or nerve biopsies for diseases they don’t have, or risky treatments that suppress their immune system,’ says Dr Kumar.

Although repeat expansion disorders cannot be cured, a quicker diagnosis can help doctors identify and treat disease complications earlier, such as heart issues associated with Friedreich’s ataxia.

Scanning for known and novel diseases

Using a single DNA sample, usually extracted from blood, the test works by scanning a patient’s genome using a technology called Nanopore sequencing.

‘We’ve programmed the Nanopore device to hone in on the roughly 40 genes known to be involved in these disorders and to read through the long, repeated DNA sequences that cause disease,’ he says. ‘By unravelling the two strands of DNA and reading the repeated letter sequences (combinations of A, T, G or C), we can scan for abnormally long repeats within the patient’s genes, which are the hallmarks of disease.’

‘In the one test, we can search for every known disease-causing repeat expansion sequence, and potentially discover novel sequences likely to be involved in diseases that have not yet been described,’ says Dr Deveson.

Upscaling to wider use in the next five years

The Nanopore technology used in the test is smaller and cheaper than standard tests, which the team hopes will smooth its uptake into pathology labs. ‘With Nanopore, the gene sequencing device has been reduced from the size of a fridge to the size of a stapler, and costs around $1000, compared with hundreds of thousands needed for mainstream DNA sequencing technologies’ says Dr Deveson.

The team expects to see their new technology used in diagnostic practice within the next two to five years. One of the key steps towards that goal is to gain appropriate clinical accreditation for the method.

Once accredited, the test will also transform research into genetic diseases, says Dr Gina Ravenscroft, a co-author of the study and a researcher working on rare disease genetics at the Harry Perkins Institute of Medical Research.

‘Adult-onset genetic disorders haven’t received as much research attention as those that appear in early life,’ she says. ‘By finding more people with these rare adult-onset diseases, and those who may be pre-symptomatic, we’ll be able to learn more about a whole range of rare diseases through cohort studies, which would otherwise be hard to do.’

The work was supported predominantly by philanthropic funding from The Kinghorn Foundation.

Published today in Science Advances, the study found that the DNA-binding dye performed well in processed clinical tissue samples and generated high-quality images via superresolution fluorescence microscopy.

“My lab is focused on developing microscopy techniques to visualize the invisible,” said senior author Yang Liu, Ph.D., associate professor of medicine and bioengineering at the University of Pittsburgh. “We are one of the first groups to explore the capabilities of superresolution microscopy in the clinical realm. Previously, we improved its throughput and robustness for analysis of clinical cancer samples. Now, we have a DNA dye that is easy to use, which solves another big problem in bringing this technology to patient care.”

Inside the cell’s nucleus, DNA strands are wound around proteins like beads on a string. Pathologists routinely use traditional light microscopes to visualize disruption to this DNA-protein complex, or chromatin, as a marker of cancer or precancerous lesions.

“Although we know that chromatin is changed at the molecular scale during cancer development, we haven’t been able to clearly see what those changes are. This has bothered me for more than 10 years,” said Liu, who is also a member of the UPMC Hillman Cancer Center. “To improve cancer diagnosis, we need tools to visualize nuclear structure at much greater resolution.”

In 2014, the Nobel Prize-winning invention of superresolution fluorescence microscopy was a major step towards making Liu’s vision reality. A molecule of interest is labelled with a special fluorescent dye that flashes on and off like a blinking star. Unlike traditional fluorescence microscopy, which uses labels that glow constantly, this approach involves switching on only a subset of the labels at each moment. When several images are overlayed, the complete picture can be reconstructed — at a much higher resolution than previously possible.

Until now, the problem was that fluorescent dyes didn’t work well on DNA or in processed clinical cancer samples. So, Liu and her team formulated a new label called Hoechst-Cy5 by combining the DNA-binding molecule Cy5 and a fluorescent dye called Hoechst with ideal blinking properties for superresolution microscopy.

After showing that the new label produced higher resolution images than other dyes, the researchers compared colorectal tissue from normal, precancerous and cancerous lesions. In normal cells, chromatin is densely packed, especially at the edges of the nucleus. Condensed DNA glows brightly because a higher density of labels emits a stronger signal, while loosely packed chromatin produces a dimmer signal.

The images show that as cancer progresses, chromatin becomes less densely packed, and the compact structure at the nuclear border is severely disrupted. While these findings indicate that the new label can distinguish normal tissue from precancerous and cancerous lesions, Liu said that superresolution microscopy is unlikely to replace traditional microscopes for such routine clinical diagnoses. Instead, this technology could shine in risk stratification.

“Early-stage lesions can have very different clinical outcomes,” said Liu. “Some people develop cancer very quickly, and others stay at the precursor stage for a long time. Stratifying cancer risk is a major challenge in cancer prevention.”

To see if chromatin structure could hold clues about future cancer risk, Liu and her team evaluated patients with Lynch syndrome, a heritable condition that increases the risk of several cancer types, including colon cancer. They looked at non-cancerous colorectal tissue from healthy people without Lynch syndrome and Lynch patients with or without a personal history of cancer.

The differences were striking. In Lynch patients who previously had colon cancer, chromatin was much less condensed than in healthy samples, suggesting that chromatin disruption could be an early sign of cancer development — even in tissue that looks completely normal to pathologists.

For Lynch patients without a personal history of cancer, some will go on to develop cancer, while others will not.

“We see a much larger spread in this group, which is very interesting,” said Liu. “Some patients resemble healthy controls, and some are closer to Lynch patients who previously had cancer. We think that patients with more open chromatin are those who are more likely to develop cancer. We need to follow these patients over time to measure outcomes, but we’re pretty excited that chromatin disruption in normal cells could potentially predict cancer risk.”

In future work, Liu and her team are interested in examining chromatin structure in endometrial tissue from Lynch patients, who also have elevated risk of endometrial cancer. The researchers also received funding recently to look at sputum samples from smokers for early detection of lung cancer.

Other authors who contributed to this study were Jianquan Xu, Ph.D., Xuejiao Sun, M.S., Hongqiang Ma, Ph.D., Rhonda M. Brand, Ph.D., Douglas Hartman, M.D., and Randall E. Brand, M.D., all of Pitt; and Mingfeng Bai, Ph.D., and Kwangho Kim, Ph.D., both of Vanderbilt University.

This work was funded by the National Institutes of Health (R01CA254112, R33CA225494 and R01CA232593).

In The Physics Teacher, by AIP Publishing, scientists from Carleton College and the University of Colorado Boulder are helping to change this narrative by presenting discussions and activities on DEI as a fundamental and essential part of physics training beyond the introductory physics level.

“Diversity, equity, and inclusion are a part of being a physicist, just as much as knowing about quantum mechanics or using an oscilloscope,” said author Martha-Elizabeth Baylor.

The team created two separate approaches for DEI curriculum at the intermediate level in 30-person and 75- to 120-person classrooms. The former replaced one question on a weekly homework assignment with a reflection essay on a topic important to physicists. The latter included activities and discussions during a two-day unit on representation.

“On the whole, students respond positively to covering this material in a physics class,” said author Jessica Hoehn. “They are eager for these conversations.”

The reflection essays in the first approach were a small component of a larger “Practicing Professionalism” framework, which explored what physicists know, do, and care about. Meanwhile, the second approach tested students on the ideas within their DEI activities and discussions, just as it would with other course content.

Baylor said students began the term by writing themselves out of the definition of a physicist. However, that changed by the end of the class.

“Many students come to see that the physics community thinks about the things that they think about, the things they care about,” said Baylor. “They find that anybody can be a physicist. They just have to care about physics, choose to do physics, and choose that as part of their identity.”

For women in these classes in particular, a large theme emerged: Their feelings about being in physics were particular to the cultural environment in the U.S.

The authors believe instructors can look at each curriculum and design their own lessons that they are comfortable enacting. The individual reflection activities in the first approach may be an easier start for instructors who want to engage with students on an individual basis, rather than lead a class discussion.

The researchers recommend looking at their resources for ideas, then gathering feedback and iteratively improving the curriculum. They hope to help other instructors frame physics as a human endeavor.

“We’re doing this, because if you enter the physics community, you need to be able to engage intelligently and respectfully in these conversations,” said Baylor.

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Materials provided by American Institute of Physics. Note: Content may be edited for style and length.

More recently, however, cancer surgeons have discovered that CLND has the potential to cause more problems than it solves. In most cases, patients do better on immunotherapy alone than they do when their surgery involves removal of the lymph nodes, due to potential complications from lymph node surgery.

In a paper published in February in the Annals of Surgical Oncology, University of Colorado (CU) Cancer Center members Martin McCarter, MD, Camille Stewart, MD, Karl Lewis, MD, William Robinson, MD, Ana Gleisner, MD, PhD, and Rene Gonzalez, MD — along with CU School of Medicine resident Robert Torphy, MD, PhD — reviewed their patient data to determine if immunotherapy alone resulted in better outcomes than CLND.

“In the few years prior to immunotherapy being available, some surgical trials were done asking if regional node dissection by itself improves overall survival for the patients,” says McCarter, a professor of surgical oncology at the CU School of Medicine. “And the answer came back: no, it did not improve survival. That had been the standard forever, because we didn’t have other effective therapies, but once the definitive trials were done, we learned that CLND wasn’t helping, it wasn’t improving survival. Subsequent trials demonstrated that immunotherapy can improve survival in metastatic melanoma.”

Better outcomes with immunotherapy

For the study, Torphy, working with McCarter and the other researchers, looked at data on 90 patients who underwent sentinel lymph node biopsy (a procedure to determine if a skin melanoma has spread microscopically) only for stage III melanoma but did not undergo CLND. Of those patients, 56 received immunotherapy and 34 did not. Those who received immunotherapy had better rates of distant metastasis-free survival, meaning their cancer was less likely to come back.

“As treatments for melanoma have evolved, the standard of care may be evolving as well,” McCarter says. “This study took a look at the patients who had a sentinel lymph node biopsy, so we knew the patient had a positive melanoma metastasis to their regional node. Those folks historically used to go on and get the completion lymph node dissection, but recently, people started to forego doing that lymph node dissection, which did not improve survival, and instead moved directly to immunotherapy, which did improve survival in other clinical trials. We proved that this is acceptable, that we’re not causing more harm to patients by doing it, and that those who do go on to get the immunotherapy seem to benefit from it.”

The de-escalation movement

Forgoing CLND is part of a recent movement in cancer treatment known as de-escalation (or de-implementation) — giving patients only the surgery absolutely necessary to treat their immediate disease. It’s especially important when it comes to lymph node surgery, McCarter says, as on top of the risks inherent to all surgeries, CLND has a 20% to 30% risk of permanent lymphedema, potentially harmful tissue swelling caused by an accumulation of protein-rich fluid that’s usually drained through the body’s lymphatic system.

“If you could avoid that complication and not compromise a patient’s survival, that would be beneficial,” McCarter says. “That’s what we guessed was happening outside of definitive clinical trial evidence, and that’s what we were able to show. We know that we often overtreat patients, and this fits in that paradigm of finding ways to de-escalate unnecessary therapies, which has been done in breast cancer and other cancers as well.”

Changing course

The CU researchers hope the study begins to move the needle for cancer surgeons for whom CLND is still routine, despite the earlier studies showing that the additional surgery was not improving survival.

“Previous clinical trials with the use of adjuvant immunotherapy for melanoma had required a CLND,” McCarter says. “This study used real-world data from our stage III melanoma patients who were treated with immunotherapy without having a prior CLND.

“It takes years to change people’s practice patterns. I still have conversations with community surgeons who treat melanoma, asking me, ‘Should I be doing these regional node dissections?’ even though this data has been out for five to 10 years now,” McCarter continues. “They’re afraid to give up what they used to do, and they’re afraid that they are doing a disservice to the patients or not giving them the best chance, when in reality, our understanding of cancer biology has evolved. We now have effective immunotherapy, which is overcoming some of the limitations of surgery while improving outcomes.”

Dr. Cynthia Hipwell is studying friction at the finger-device level, while Dr. Jonathan Felts is researching friction in the interaction between single skin cells and the glass of the touchscreen interface. The two are bringing together their respective areas of expertise to apply friction principles at the microscopic level to finger-device interaction mechanics.

Hipwell highlighted the significance of the pursuit by comparing it to the technologies currently available for conveying immersive and accurate information through high-fidelity audio and video.

“We can view digitally recorded or remotely transmitted audio and video on a screen with great detail,” said Hipwell, Oscar S. Wyatt, Jr. ’45 Chair II professor. “We do not yet have that same capability with touch on a touchscreen. Imagine you could feel the skin of a snake that lives on another continent or the fabric of clothes you want to buy online.”

Another application of this technology, which has received high levels of interest recently, is the augmentation of immersive virtual environments, such as the proposed metaverse.

“The touch sensations that would be required to really immerse yourself into a reality that is fully digital requires huge advancements in touch perception,” said Felts, associate professor and Steve Brauer, Jr. ’02 Faculty Fellow. “What we’ve done is essentially created an entirely new way to modulate the perception of touch that hasn’t existed before.”

The team is working to show that it is possible to mimic the unique mechanical and thermal sensations associated with different surface textures and shapes. Their recent publication in the journal Science Robotics demonstrates the potential for translating these sensations on a touchscreen by using temperature variation alone, rather than expressing them through ultrasonic vibrations or electroadhesion methods.

“We were actually surprised by the magnitude of the friction increase we were able to achieve,” Hipwell said. “Its magnitude is competitive with current surface haptic devices, meaning that there is another option for friction modulation in surface-haptic device rendering.”

Another exciting development, Hipwell said, is that their research has shown that it is possible to localize the friction to the outer layer of the skin and, at least at swipe speeds, control friction without making the device feel hot.

As the research continues, Felts said many of the questions remaining involve how readily the approach can be incorporated into consumer devices and commercialized.

“Can it be scaled down? Can it respond quickly enough? Can it mimic a wide range of surfaces? Can it be affordable? We think these are fair criticisms, yet we look forward to using this phenomenon to improve our basic understanding of haptic feedback and pursuing miniaturization and commercialization avenues,” he said.

The team is continuing their work to address challenges facing the approach by further exploring the complexities of the finger-device interface and variations that occur due to environmental and skin-property differences. They also hope to look at design improvements for miniaturization and integration into touchscreens.

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Materials provided by Texas A&M University. Original written by Steve Kuhlmann. Note: Content may be edited for style and length.

This scenario is not as impossible as it seems. Too small to withstand a rhythmic strum or sliding bowstring, DNA is a powerhouse for storing audio files and all kinds of other media.

“DNA is nature’s original data storage system. We can use it to store any kind of data: images, video, music — anything,” said Kasra Tabatabaei, a researcher at the Beckman Institute for Advanced Science and Technology and a coauthor on this study.

Expanding DNA’s molecular makeup and developing a precise new sequencing method enabled a multi-institutional team to transform the double helix into a robust, sustainable data storage platform.

The team’s paper appeared in Nano Letters in February 2022.

In the age of digital information, anyone brave enough to navigate the daily news feels the global archive growing heavier by the day. Increasingly, paper files are being digitized to save space and protect information from natural disasters.

From scientists to social media influencers, anyone with information to store stands to benefit from a secure, sustainable data lock box — and the double helix fits the bill.

“DNA is one of the best options, if not the best option, to store archival data especially,” said Chao Pan, a graduate student at the University of Illinois Urbana-Champaign and a coauthor on this study.

Its longevity rivaled only by durability, DNA is designed to weather Earth’s harshest conditions — sometimes for tens of thousands of years — and remain a viable data source. Scientists can sequence fossilized strands to uncover genetic histories and breathe life into long-lost landscapes.

Despite its diminutive stature, DNA is a bit like Dr. Who’s infamous police box: bigger on the inside than it appears.

“Every day, several petabytes of data are generated on the internet. Only one gram of DNA would be sufficient to store that data. That’s how dense DNA is as a storage medium,” said Tabatabaei, who is also a fifth-year Ph.D. student.

Another important aspect of DNA is its natural abundance and near-infinite renewability, a trait not shared by the most advanced data storage system on the market today: silicon microchips, which often circulate for just decades before an unceremonious burial in a heap of landfilled e-waste.

“At a time when we are facing unprecedented climate challenges, the importance of sustainable storage technologies cannot be overestimated. New, green technologies for DNA recording are emerging that will make molecular storage even more important in the future,” said Olgica Milenkovic, the Franklin W. Woeltge Professor of Electrical and Computer Engineering and a co-PI on the study.

Envisioning the future of data storage, the interdisciplinary team examined DNA’s millennia-old MO. Then, the researchers added their own 21st-century twist.

In nature, every strand of DNA contains four chemicals — adenine, guanine, cytosine, and thymine — often referred to by the initials A, G, C, and T. They arrange and rearrange themselves along the double helix into combinations that scientists can decode, or sequence, to make meaning.

The researchers expanded DNA’s already broad capacity for information storage by adding seven synthetic nucleobases to the existing four-letter lineup.

“Imagine the English alphabet. If you only had four letters to use, you could only create so many words. If you had the full alphabet, you could produce limitless word combinations. That’s the same with DNA. Instead of converting zeroes and ones to A, G, C, and T, we can convert zeroes and ones to A, G, C, T, and the seven new letters in the storage alphabet,” Tabatabaei said.

Because this team is the first to use chemically modified nucleotides for information storage in DNA, members innovated around a unique challenge: not all current technology is capable of interpreting chemically modified DNA strands. To solve this problem, they combined machine learning and artificial intelligence to develop a first-of-its-kind DNA sequence readout processing method.

Their solution can discern modified chemicals from natural ones, and differentiate each of the seven new molecules from one another.

“We tried 77 different combinations of the 11 nucleotides, and our method was able to differentiate each of them perfectly,” Pan said. “The deep learning framework as part of our method to identify different nucleotides is universal, which enables the generalizability of our approach to many other applications.”

This letter-perfect translation comes courtesy of nanopores: proteins with an opening in the middle through which a DNA strand can easily pass. Remarkably, the team found that nanopores can detect and distinguish each individual monomer unit along the DNA strand — whether the units have natural or chemical origins.

“This work provides an exciting proof-of-principle demonstration of extending macromolecular data storage to non-natural chemistries, which hold the potential to drastically increase storage density in non-traditional storage media,” said Charles Schroeder, the James Economy Professor of Materials Science and Engineering and a co-PI on this study.

DNA literally made history by storing genetic information. By the looks of this study, the future of data storage is just as double-helical.

Additional UIUC collaborators include Aleksei Aksimentiev, the Center for Biophysics and Quantitative Biology; and Alvaro Hernandez, the Roy J. Carver Biotechnology Center. Partner institutions include the University of Massachusetts at Amherst and Stanford University. For a full list of collaborators and their affiliations, please consult the published work.