A team of researchers led by Dr. Yasutaka Kakui from Waseda Institute for Advanced Study, Waseda University; Frank Uhlmann at the Chromosome Segregation Laboratory, The Francis Crick Institute; and Toru Hirota, from the Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research, set out to decode this enigma.

How did it all start? For Kakui, it was his fascination for chromosomes that motivated him to take up this research. “How is genomic DNA stored within cells? This is an ancient, unsolved question. To expand our knowledge of how cells accurately pass on genetic information to successive generations, we need to understand the molecular basis for chromosome formation.” And that is what drove this study, the findings of which have been published in Cell Reports.

During mitosis, DNA undergoes significant compaction to form chromosomes. A large protein ring complex called condensin plays a key role in the compaction process. It binds at specific sites on DNA and compresses it by forming loops. So, scientists know that condensin is crucial for DNA compaction, which is closely related to chromosomal dimensions — with thicker chromosomes being more compacted. They also know that the pattern of condensin-binding sites is species-specific. But the exact role of condensin and chromatin contacts in determining chromosomal dimensions is, as yet, unclear.

The researchers explored various facets of condensin and chromatin contacts to address the questions at hand. They employed Hi-C and super-resolution microscopy to analyze the correlation between mitotic chromatin contacts and chromosomal arm length in both budding and fission yeasts, S. cerevisiae and S. pombe, respectively. Conclusive evidence was found indicating that the distance between chromatin contacts is directly proportional to arm length in both interphase and mitosis. Hence, shorter arms have short range contacts and longer arms have long range contacts. This was found to be species-specific.

Now, longer distances of chromatin contacts lead to larger chromatin loops, both of which are indicators of wider chromosomal arms. The authors thus investigated both budding and fission yeasts to conclude that within a species, longer chromosomal arms were always wider. Motivated by the successful observation in the yeasts, they extended their study to human cells, to find the same correlations. “We made the unexpected discovery that longer chromosomal arms are always thicker throughout eukaryotic species, which helps us understand how mitotic chromosomes form during cell divisions,” explains Kakui. Their study would be the first to conclusively establish that chromosomal arm length determines mitotic chromosome width.

This study has provided unique insights into mitotic chromosomal structure that challenge the current perspectives on mitotic chromosome formation. Kakui summarizes, “Our findings would open a novel way to avoid chromosome miscarriage, a probable cause for the formation of cancer cells and/or birth defects such as Down syndrome, through controlling mitotic chromosome structure. This can potentially change medical treatments for cancer therapy and/or fertility treatments.”

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Now, studying mice with an autoimmune disease similar to multiple sclerosis (MS), researchers at Washington University School of Medicine in St. Louis have shown that the same approach can be used to eliminate unwanted cells that cause autoimmunity. The findings, available online in Science Immunology, extend the powerful tool of immunotherapy to a class of diseases that are often debilitating and difficult to treat.

“We were able to use CAR-T cells to eliminate just the immune cells that are causing the autoimmunity and not other immune cells you might need to protect against viruses or other infection,” said co-senior author Chyi-Song Hsieh, MD, PhD, the Alan A. and Edith L. Wolff Professor of Rheumatology and a professor of medicine and of pathology & immunology. “Our CAR-T cells were very effective at treating mice that have an MS-like disease.”

At the heart of CAR-T therapy are the immune system’s T cells, crucial elements of the body’s defense force. T cells respond to threats such as bacteria, viruses and cancerous cells by coordinating an immune assault and killing foreign organisms and infected or cancerous cells.

But every once in a while, T cells mistake healthy cells for infected cells and turn their weapons on the body’s own cells and tissues, triggering an autoimmune disease. MS is marked by rogue T cells that trigger the destruction of myelin, the protective covering over nerves. As myelin is eaten away, communication between the brain and spinal cord and the rest of the body becomes unreliable, and people begin experiencing symptoms such as fatigue, pain, tingling, vision problems and loss of coordination. Immunosuppressive drugs can quash the self-destructive activity of rogue T cells, but such drugs also suppress helpful T cells and put people at risk of severe infections.

In CAR-T cancer therapies, doctors take a patient’s own T cells, modify them to recognize and vigorously attack his or her specific cancer, and then put them back in the body on a seek-and-destroy mission. Inspired by this approach, the researchers set out to create CAR-T cells equipped to seek out and destroy the rogue T cells that cause MS. The idea was to make CAR-T cells that would function akin to a police department’s internal affairs office, rooting out the bad apples in the T cells defense force while leaving good T cells in place to protect the body.

“Having MS can really erode your quality of life, and while current therapies slow down the course of the disease, they don’t cure it and they have side effects,” said co-senior author Gregory F. Wu, MD, PhD, an associate professor of neurology and of pathology & immunology. “I believe that this is a fully treatable disease, and CAR-T cells may be the way toward much better therapeutics.”

Along with Hsieh and Wu, the research team included co-authors Nathan Singh, MD, an assistant professor of medicine, and Takeshi Egawa, MD, PhD, an associate professor of pathology & immunology.

First, the researchers made some bait. They designed a molecule by combining a fragment of a protein found in myelin with a protein that activates T cells. Only T cells that target myelin — the bad apples, so to speak — would respond to this hybrid molecule. Then, they loaded the bait molecule onto a kind of T cell known as killer T cells. Any rogue T cells that took the bait would be eliminated by the killer T cells.

That was the idea, at least. To see whether it worked, the researchers turned to mice with an MS-like condition. Treating such mice with the engineered CAR-T cells prevented disease in those that had yet to develop problems, and reduced signs of disease in those that were already showing neurological effects.

“We’re working on improving the CAR-T cells, to get them to kill more efficiently and last longer so that we can get better treatment outcomes,” Hsieh said. “Right now, there’s no way to tell who is going to get MS or when, so preventing disease in people isn’t realistic, but we could treat it, and I think the CAR-T approach looks very promising.”

The beauty of the CAR-T approach is that by swapping out the protein fragment in the bait molecule, killer T cells can be redirected toward different rogue immune cells to treat different diseases.

“I see patients in the clinic who have a rare disease known as myelin oligodendrocyte glycoprotein (MOG) antibody disease that is very similar to MS,” Wu said. “Unlike MS, which is complicated, we know exactly what the target is in MOG antibody disease. I wish I could just get rid of these self-reactive cells for my patients, but we’ve had no way to do that. Now, we are working toward using the patient’s own immune cells to create CAR-T cells that would eliminate those self-reactive T cells.”

A new study by scientists at University of California — Berkeley, has found that 39 out of 43 coastal airports in California have assets exposed to projected flooding that could disrupt their operations in the next 20 to 40 years. Sarah Lindbergh of University of California, Berkeley, will present her team’s findings during the Society for Risk Analysis Annual Meeting, Dec. 4-8 in Tampa, Florida.

Lindbergh and her colleagues at UC Berkeley conducted a statewide assessment of California’s airport infrastructure exposure to projected coastal flooding (from storm surge and sea-level rise) up to the year 2100. Their research combines a novel coastal flooding exposure assessment of the airports with a policy review of more than 100 state legislature and planning documents to address the importance of collaborative climate adaptation.

The flooding exposure assessment is the first of its kind, using geospatial tools to look beyond each airport’s perimeter to include its entire interconnected infrastructure — including road access, ground-based navigation, and communications systems. “It’s important to recognize that critical assets for airport operations may lie outside airport boundaries,” explains Lindbergh.

The analysis indicates that 39 out of 43 public coastal California airports have assets exposed to coastal flooding by 2100. (This number is much higher than traditional risk assessments that have only considered assets within an airport’s perimeters.) “Although we do not know how these newly identified exposures translate into impact,” says Lindbergh, “we were surprised to see that most of the airport assets could see a flooding event sooner than 2100 — in the next 20 years.”

Sixteen of the 39 airports have assets exposed within their boundaries (i.e. runways and taxiways), while the remaining 23 have assets outside of their jurisdiction that are at risk from flooding (such as road access to the airport and navigation systems). The list includes Los Angeles International Airport (LAX), ranked among the top five busiest airports in the world.

The researchers also examined how airport assets exposed to flooding transfer risks to nine of the state’s key multimodal, interregional transportation corridors (which include connected highways and railways). The ripple effects on the transportation of both goods and people could include delays, congestion, and cancellations. Their report identifies critical airports within these corridors to be prioritized for adaptation, particularly those within the San Francisco Bay — Central Valley — Los Angeles corridor (such as San Francisco International Airport and Oakland International Airport) and also Murray Field Airport in Eureka within the San Francisco Bay — North Coast transportation corridor.

The team’s state policy review revealed that market and regulatory incentives for airport infrastructure (maintenance, upgrade, and replacement) are mostly bound to an airport’s perimeters. This limits the ability for diverse infrastructure stakeholders to understand and act on their collective exposure to hazards such as coastal flooding. “Most policies are still being designed to mitigate risk and promote adaptation at the single asset level — for example, one airport at a time,” says Lindbergh.

She and her colleagues argue that measuring the exposure of interconnected infrastructure can help direct state-level policies that promote collaborative climate adaptation plans. “Our study pushes people to think beyond their boundaries and jurisdictions,” says Lindbergh.

Her presentation, “Cross-sectoral and multiscalar exposure assessment to advance climate adaptation policy: the case of future coastal flooding of California’s airports” on Monday, December 5th at 3:30 is part of a session on “Risk from Extreme Storm Events.”

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This work appeared Dec. 1 in the journal Nature Methods.

Imaging deep tissues with light is challenging. Visible light is often quickly absorbed and scattered by structures and molecules in the body, preventing researchers from seeing deeper than a millimeter within a tissue. If they do manage to probe further, substances like collagen or melanin often muddy the image, creating the equivalent of background noise through their natural fluorescence.

“Biological molecules naturally absorb and emit light in the visible spectrum, which is about 350 to 700 nanometers,” said Junjie Yao, assistant professor of biomedical engineering at Duke. “So when using it to image deep tissue, it’s like trying to observe the stars in daylight. The signals get flooded out.”

To wade out from these muddied waters, Yao and his collaborator Vladislav Verkhusha, professor of genetics at Albert Einstein College of Medicine, New York developed a protein that absorbs and emits longer wavelengths of light in the near-infrared (NIR) spectrum.

“Tissue is the most transparent in the 700-1300 nanometer window of NIR light,” said Yao. “At those wavelengths, light can penetrate deeper into a tissue, and because there is less natural background fluorescence to filter out, we can take longer exposures and capture clearer images.”

Verkhusha and his lab used a process called directed molecular evolution to engineer their proteins, using photoreceptors normally found in bacteria as the basis for the structure. These photoreceptors are useful for imaging research because they can switch between a silent and active state when hit with a specific wavelength of light. They can bind with biliverdin, a biomolecule that appears in high quantities in mammalian and human tissues.

“We studied the structure of the biliverdin to determine how the photoreceptor would best attach to the biomolecule,” explained Verkhusha. “After we understood the binding process, we carefully introduced substitutions of key parts of the molecule connecting to the biliverdin to increase the electron binding, which is necessary to obtain the red-shifted fluorescence. Last, we performed random mutagenesis followed by high-throughput screenings so the proteins would evolve and increase their brightness.”

The brightest found protein, termed miRFP718nano, is easily produced in cells and tissues and emits light just outside of the visible range. But while the NIR activation itself is helpful, what happens after the initial burst of activity holds even more promise for biomedical imaging.

“We’ve seen that the NIR range can be broken up into two main zones,” explained Yao. “When NIR light first hit these proteins, they emit light in the first zone, which is about 700-900 nanometers. But as they decay, the wavelength gradually gets longer, like the tail behind a comet. That’s when they begin to emit light in the second NIR zone, which is from 900-1300 nanometers.”

In this second zone, all benefits from using the shorter wavelength, zone one NIR light are enhanced: light can penetrate tissue two times deeper, background fluorescence is significantly dimmed, and image resolution can be two to three times clearer, allowing for detailed images of complex structures.

As a proof of concept, Yao and his team at Duke used an imaging technique called short-wavelength infrared (SWIR) to test the efficacy of the new protein. This process sends NIR zone-one light deep into the tissue to activate the fluorescent proteins. As the proteins decay, they emit NIR zone-two light that provides information about the structure and composition of the targeted tissues and cells that can be translated into high-resolution images.

After introducing engineered miRFP718nano proteins into their animal models, the team used them to capture images of microbes in the mouse digestive tract, visualize cells in a mouse mammary gland and even track changes to inflammation in a mouse liver. All the images captured were clearer and more detailed than images made using a standard NIR zone-one imaging protein.

Yao and Verkhusha are optimistic that their continued partnership will be a boon for their work in both biomedical imaging and protein engineering. As Verkhusha continues to refine and improve the fluorescent proteins and biosensors, Yao is excited to use the new tool to visualize the brain more closely and to potentially track the movement of cancer cells.

“This is an exciting new front of our decade-long collaboration because we can use the imaging tools to guide the protein engineering decisions, and we can use the advanced protein engineering to improve the imaging capabilities,” Yao said.

This work was supported by grants from the US National Institutes of Health (GM122567, EB028143, NS111039, NS115581), the Chan Zuckerberg Initiative (226178), the Cancer Foundation Finland and Magnus Ehrnrooth Foundation, and the NIH Intramural Research Program for the Vaccine Research Center of the National Institute of Allergy and Infectious Diseases.

BSIs with various microbial pathogens can rapidly escalate to life-threatening sepsis when the body is overwhelmed by the multiplying invaders and shuts down its organs’ functions. In 2017, there were 48.9 million cases and 11 million sepsis-related deaths worldwide. Importantly, almost half of all global sepsis cases occurred among children, with an estimated 20 million cases and 2.9 million global deaths in those under five years of age.

To prevent BSIs from progressing to full-blown sepsis, the infection-causing bacterial or fungal species must be identified as fast as possible. Only then can optimal pathogen-tailored antibacterial or antifungal treatments be applied in time. The conventional method used in clinical laboratories to identify the causative pathogenic species is long and laborious, requiring two time-consuming culture steps that take at least 1 to 3 days to complete.

“For all patients with sepsis, their chances of surviving dramatically shrink the longer it takes to identify the infection-causing pathogen(s) and thus, receive the most promising antimicrobial treatment,” said Nigel Klein, M.D., Ph.D., pls, a Professor of Infectious Disease and Immunology at GOSH, and a senior author on the study. “At Great Ormond Street Hospital we have been working to demonstrate both the importance rapid diagnosis and the fact that with innovative approaches we can identify the causative organism in between 40 minutes and six hours. Compared to adult patients, sepsis in infants and small children progresses much faster, and therefore there is a real need for diagnostic methods that support early detection. Accurate diagnosis is even more significant due to the availability of only small blood volumes from paediatric patients which can make re-sampling challenging.”

In 2020, senior authors Klein and Elaine Cloutman-Green, Ph.D., a Consultant Clinical Scientist and Infection Control Doctor at GOSH, began collaborating with Lead Staff Scientist Michael Super, Ph.D. and Founding Director Donald Ingber, M.D., Ph.D. at Harvard’s Wyss Institute to solve this problem. “Based on our earlier success with FcMBL in isolating pathogens from joints as well as bovine and human blood with extraordinary efficiencies, we hypothesized that building an FcMBL-mediated pathogen capture into a modified clinical blood culture protocol could shorten the time and reduce the size of the required patient samples to yield the same results that time-consuming blood culture protocols provide,” said Super.

In the pathogen identification process currently performed in clinical settings, first, blood samples are added to bottles containing liquid media in which infectious microbes, if present, are amplified to a certain density. Then, the amplified microbes are grown on solid media as isolated colonies whose constituent cells eventually can be identified with a highly sensitive, yet fast and relatively inexpensive analytical method know as MALDI-TOF mass spectrometry (MS). “Indeed, isolating the infectious microbes directly from grown liquid blood cultures using FcMBL makes them available for MALDI-TOF MS analysis much earlier,” added Super.

FcMBL is the key component of a broad-spectrum pathogen capture technology. It consists of a genetically engineered human immune protein called mannose-binding lectin (MBL) that is fused to the Fc fragment of an antibody molecule to produce the resulting FcMBL protein. In this configuration, the MBL portion of FcMBL can capture more than 100 [CHECK WITH MIKE] different microbial species with high efficiency, including virtually all of the bacterial and fungal pathogens causing sepsis. FcMBL’s Fc portion can be used to couple it to magnetic beads, allowing the captured pathogens to be quickly pulled out of patient samples and liquid blood cultures.

In the earlier stages of the project, the Wyss team provided purified bead-coupled FcMBL to the GOSH team, which had access to blood samples from pediatric patients at the hospital. At later stages, the sepsis and infectious disease company BOA Biomedical, co-founded by Super and Ingber to commercialize the Wyss Institute’s FcMBL technology, provided the FcMBL reagent and critical expertise to the project. BOA Biomedical meanwhile developed the manufacturing capabilities for FcMBL that the Food and Drug Administration (FDA) in the US and other federal health agencies require for producing therapeutic and diagnostic products.

“Sepsis is the leading killer in hospitals, and rapidly initiating the right antibiotic saves lives. Using work originally developed at the Wyss Institute, BOA Biomedical’s revolutionary FcMBL technology helps to quickly and accurately identify the pathogen causing sepsis, ushering in a new era of targeted antimicrobial therapy to help individual patients and curb society’s deadly antimicrobial resistance problem,” stated Mike McCurdy, M.D., Chief Medical Officer of BOA Biomedical.

In addition to using the gold standard two-step blood culture in combination with MALDI-TOF MS pathogen identification, the team also included the Bruker Corporation’s MBT Sepsityper® kit as a comparison. Brought to market in 2021, the MBT Sepsityper® essentially eliminates the time-consuming second microbial culture step by lysing microbial cells from the liquid culture and spinning the fragments down in a centrifuge before analyzing them by MALDI-TOF mass spectrometry analysis. Although it accelerates the overall diagnostic process, the MBT Sepsityper® methodproduces lower microbial detection rates than those obtained with the conventional culture method, which means that it may still fail to identify the infection-causing pathogen in a significant fraction of blood samples.

“Our FcMBL approach has opened up the opportunity to identify pathogenic organisms to guide treatment 24 to 48 hours earlier than would be possible using standard culture techniques. It has also enabled us to use this identification to make any ongoing culture for antibiotic sensitivities more tailored to the needs of the patient. This method isn’t tied into a specific platform or manufacturer, and thus we see clear potential for it to become a new standard processing step for clinical pathogen detection,” said Cloutman-Green.

“The FcMBL method identified 94.1% of microbial species found in clinical blood culture analysis with samples from 68 pediatric patients,” said first author Kerry Kite, who performed her graduate work with Klein and Cloutman-Green. “We were able to identify more infectious species in positive liquid blood cultures using the FcMBL method than with the MBT Sepsityper® method (25 of 25 vs 17 of 25), and this trend was even further pronounced in the case of the common fungal pathogen Candida (24 of 24 vs 9 of 24).” Candida species account for about 5% of all cases of severe sepsis and are the fourth most common pathogen isolated from patients’ bloodstreams in the United States. Not only do infections with Candida and other fungi require specific antifungal treatments, distinguishing among the various types of pathogenic fungi helps direct the appropriate antimicrobial therapy. Specifically in neonatal intensive care units, Candidainfections are a major cause of morbidity and mortality, killing as many as 40% of infants and often causing neurodevelopmental impairments in those that survive.

“By continuously adapting the powerful FcMBL pathogen capture technology to unmet and pressing diagnostic needs, such as the rapid diagnosis of sepsis in pediatric patients, we hope to profoundly alter the frequently dismal prospects of patients of all ages,” said Ingber. “Our ultimate goal is to be able to accurately and even more rapidly identify pathogens directly in small samples of blood without the need for any additional microbial cultures.” Ingber is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s Hospital, and the Hansjörg Wyss Professor of Bioinspired Engineering at the Harvard John A. Paulson School of Engineering and Applied Sciences.

The study was also authored by Sahil Loomba and Thomas Elliott at Imperial College London; Francis Yongblah, Lily Gates and Dagmar Alber at GOSH; George Downey and James Hill at BOA Biomedical; and Shanda Lightbown and Thomas Doyle at the Wyss Institute. The authors were supported in their work by the clinical microbiology staff at GOSH, as well as Erika Tranfield with MALDI-TOF MS expertise. At GOSH, critical financial help for the project from the Benecare Foundation, philanthropists Luca Albertini and Professor Pauline Barrieu, as well the Office of Vice-President (Advancement) at University College London was coordinated by Simona Santojanni. At the Wyss Institute, the study was funded by the Defense Advanced Research Projects Agency (DARPA) under Cooperative Agreement Number W911NF-16-C-0050, and the Wyss Institute’s technology translation engine. Additional support was provided by BOA Biomedical.