Enabling early detection of cancer

With his group’s new method and the use of artificial intelligence, G.V. Shivashankar hopes to improve tumor diagnosis.
Photo Credit: Paul Scherrer Institute/Markus Fischer

Blood cells reveal tumors in the body. Researchers at the Paul Scherrer Institute achieve an advance with the development of a test for early diagnosis of cancer.

The ability to detect a developing tumor at a very early stage and to closely monitor the success or failure of cancer therapy is crucial for a patient’s survival. A breakthrough on both counts has now been achieved by researchers at the Paul Scherrer Institute PSI. Researchers led by G.V. Shivashankar, head of PSI‘s Laboratory for Nanoscale Biology and professor of Mechano-Genomics at ETH Zurich, were able to prove that changes in the organization of the cell nucleus of some blood cells can provide a reliable indication of a tumor in the body. With their technique – using artificial intelligence – the scientists were able to distinguish between healthy and sick people with an accuracy of around 85 percent. Besides that, they managed to correctly determine the type of tumor disease – melanoma, glioma, or head and neck tumor. “This is the first time anyone, worldwide, has achieved this,” Shivashankar says happily. The researchers have published their results in the journal npj Precision Oncology.

New Insights into Ecosystem Functions

The mastermind behind the new statistical method: mathematician and statistician Anne Chao from National Tsing Hua University in Taiwan. Here she is in the university forest of the University of Würzburg on an experimental test plot.
Photo Credit: Simon Thorn/JMU

A DFG research group led by the University of Würzburg has developed a method that makes it possible to analyze the relationship between biodiversity within and between ecosystems and the multifunctionality of entire landscapes.

Ecosystems fulfil a number of vital tasks: They store carbon, clean polluted water, pollinate plants and so on. How well an ecosystem can fulfil these tasks depends largely on its biodiversity, i.e. the variety of plants, animals and microorganisms that live in it. Until now, scientists have only been able to understand the exact nature of this relationship at a local level, for example in relation to individual forest areas, meadows and ponds. The DFG (German Research Foundation) research group BETA-FOR, led by the University of Würzburg (JMU), has now succeeded in developing a statistical method that for the first time can also analyze the contributions of biodiversity between local ecosystems to the multifunctionality of entire landscapes.

Flowers Were More Diverse 100 Million Years Ago Than They Are Today

In black and white: three fossil flowers from the Early Cretaceous (Glandulocalyx, Normanthus,Platydiscus; enlarged). In colour: four present-day species (Cymbidium, Primula,Hyacinthoides, and Passiflora)
Illustration Credit: Julia Asenbaum

Angiosperm flowers reached their greatest morphological diversity early in their evolutionary history

An international team of researchers around botanists at the University of Vienna, Austria, has now analyzed the morphological diversity of fossilized flowers and compared it with the diversity of living species. Their results were quite exciting: Flowering plants had already produced a large number of different flower types shortly after their emergence in the Cretaceous period, and this earliest floral diversity was greater than that today. The study has just been published in the prestigious journal New Phytologist.

With at least 300,000 species, flowering plants (angiosperms) are by far the largest group of plants living today. They first appeared at least 140 million years ago, when dinosaurs roamed the Earth. In recent decades, many fossilized flowers from different geological time periods have been discovered and described, giving us a glimpse of past diversity. But how does this past diversity compare to the present one? And – what has happened to flower morphology over time? An international research team from the National Autonomous University of Mexico, the Botanic Gardens of Sydney, Australia, and the University of Vienna, Austria, has tackled precisely these questions – and found answers.

Viking dentistry was surprisingly advanced

Teeth from individuals among the Viking Age population of Varnhem in Västergötland, Sweden, are clinically examined by Carolina Bertilsson at the Institute of Odontology.
Photo Credit: Yoichi Ishizuka

Widespread caries and toothache – but also some dental work and filing of front teeth. Viking Age teeth from Varnhem bear witness to surprisingly advanced dentistry. This has been shown in a study carried out at the University of Gothenburg.

The study examined 3,293 teeth from 171 individuals among the Viking Age population of Varnhem in Västergötland, Sweden. The site is known for extensive excavations of Viking and medieval environments, including tombs where skeletons and teeth have been preserved well in favorable soil conditions.

The research team from the University of Gothenburg’s Institute of Odontology worked with an osteologist from Västergötland’s Museum. The skulls and teeth were transported to Gothenburg, where all the examinations were carried out.

The teeth underwent clinical examinations using standard dentistry tools under bright light. A number of X-ray examinations were also performed using the same technique used in dentistry, where the patient bites down on a small square imaging plate in the mouth.

Ribosomal protein exhibits remarkable evolutionary transformation

The cryo-EM maps and atomic models showing the structure of ribosomal protein msL1 in the ribosome from microsporidian parasites V. necatrix (first row), and protein msL2 in the ribosome from microsporidian parasites E. cuniculi (second row).
Illustration Credit: Leon Schierholz

A team of researchers from the Universities of Newcastle and Umeå has discovered that a ribosomal protein exhibits a remarkable evolutionary transformation, with its three-dimensional structure changing drastically while its sequence remains relatively conserved.

The protein, known as msL1/msL2, is found in ribosomes of parasitic microorganisms called microsporidia, and it is suggested to play a role in stabilizing the highly reduced protein synthesis machinery in these unique organisms. 

“Despite its conserved sequence, msL1/msL2 adopts distinct folds in two different microsporidian species, Encephalitozoon cuniculi, and Vairimorpha necatrix. This structural divergence is particularly striking given that the two proteins share approximately 41% sequence similarity,” comments Léon Schierholz, one of the authors from Umeå University.  

Aquatic Insects in Restored Streams Need More Rocks to Lay Their Eggs

A caddisfly egg mass sits on the underside of a protruding rock.
Photo Credit: Brad Taylor, NC State University.

Likening it to providing more runways at busy airports, researchers at North Carolina State University found in a new study that adding protruding rocks to restored streams can help attract female aquatic insects that lay their eggs on the rock bottoms or sides.

More eggs that hatch into larval insects is great news for stream restoration because the re-establishment of organisms, such as insects, is often slower than expected in restored streams, says Brad Taylor, associate professor of applied ecology at NC State and corresponding author of a paper describing the research. A thriving population of stream insects generally portends good water quality, overall stream health, and provides food for fish, amphibians, reptiles, and even birds, he adds.

Most stream insects use rocks protruding above the water as runways to land on, then crawl underwater and attach their eggs to the underside of the rocks. Because restored streams sometimes fail to regain their abundance of aquatic insects even decades following restoration, researchers were interested in testing whether increasing egg-laying habitat the rock landing areas would increase the abundance and diversity of insect eggs and larvae.

Taylor and NC State graduate student Samantha Dilworth selected 10 restored streams in northwestern North Carolina and added protruding rocks gathered near the streams to five of them; the other five restored streams did not receive additional rocks.

UNC Researchers Reveal Prevalence of Persistent Symptoms in Patients with Microscopic Colitis

Walker Redd, MD, a clinical outcomes and epidemiology fellow in the Division of Gastroenterology and Hepatology, Department of Medicine.
Photo Credit: Courtesy of University North Carolina, School of Medicine

It’s a hidden cause of diarrhea and the development of the disease is poorly understood. Multiple factors work against the diagnosis of microscopic colitis, an inflammatory digestive disease, because the symptom distress compared to patients with other causes of chronic diarrhea remains unknown. Now, a new study published in journal Gastro Hep Advances, shows patients may be unsure of a diagnosis based on their colonoscopy results, patients may not be prescribed the proper medications, and many patients may remain symptomatic one year after colonoscopy.

The study, led by corresponding author Walker Redd, MD, a clinical outcomes and epidemiology fellow in the Division of Gastroenterology and Hepatology at the UNC School of Medicine, involved a cohort of patients from April 1, 2015 to December 22, 2020 enrolled at UNC Hospitals in Chapel Hill, NC. Patients participating in a follow-up survey included 74 with biopsy-confirmed microscopic colitis and 162 patients experiencing other causes of chronic diarrhea (diarrhea controls) after colonoscopy at a one-year follow-up.

“We thought it was important to better understand the burden of symptoms among those patients with microscopic colitis within the context of all patients undergoing colonoscopy to evaluate diarrhea,” Redd said.

Sugar analysis could reveal different types of cancer

By analyzing changes in glycan structures in the cell, researchers can detect different types of cancer.
Photo Credit: Mikhail Nilov

In the future, a little saliva may be enough to detect an incipient cancer. Researchers at the University of Gothenburg have developed an effective way to interpret the changes in sugar molecules that occur in cancer cells.

Glycans are a type of sugar molecule structure that is linked to the proteins in our cells. The structure of the glycan determines the function of the protein. It has been known for a while that changes in glycan structure can indicate inflammation or disease in the body. Now, researchers at the University of Gothenburg have developed a way to distinguish different types of structural changes, which may provide a precise answer to what will change for a specific disease.

“We have analyzed data from about 220 patients with 11 differently diagnosed cancers and have identified differences in the substructure of the glycan depending on the type of cancer. By letting our newly developed method, enhanced by AI, work through large amounts of data, we were able to find these connections,” says Daniel Bojar, associate senior lecturer in bioinformatics at the University of Gothenburg and lead author of the study published in Cell Reports Methods.

What Happens in the Brain While Daydreaming?

The findings provide a clue that daydreams may play a role in brain plasticity
Image Credit: Scientific Frontline 

You are sitting quietly, and suddenly your brain tunes out the world and wanders to something else entirely — perhaps a recent experience, or an old memory. You just had a daydream.

Yet despite the ubiquity of this experience, what is happening in the brain while daydreaming is a question that has largely eluded neuroscientists.

Now, a study in mice, published Dec. 13 in Nature, has brought a team led by researchers at Harvard Medical School one step closer to figuring it out.

The researchers tracked the activity of neurons in the visual cortex of the brains of mice while the animals remained in a quiet waking state. They found that occasionally these neurons fired in a pattern similar to one that occurred when a mouse looked at an actual image, suggesting that the mouse was thinking — or daydreaming — about the image. Moreover, the patterns of activity during a mouse’s first few daydreams of the day predicted how the brain’s response to the image would change over time.

The research provides tantalizing, if preliminary, evidence that daydreams can shape the brain’s future response to what it sees. This causal relationship needs to be confirmed in further research, the team cautioned, but the results offer an intriguing clue that daydreams during quiet waking may play a role in brain plasticity — the brain’s ability to remodel itself in response to new experiences.

Enzymes Can’t Tell Artificial DNA From the Real Thing

Like adding new letters to an existing language’s alphabet to expand its vocabulary, adding new synthetic nucleotides to the genetic alphabet could expand the possibilities of synthetic biology. This image shows a rendering of RNA polymerase (center) and a synthetic nucleotide (lower right).
Image Credit: UC San Diego Health Sciences

The genetic alphabet contains just four letters, referring to the four nucleotides, the biochemical building blocks that comprise all DNA. Scientists have long wondered whether it’s possible to add more letters to this alphabet by creating brand-new nucleotides in the lab, but the utility of this innovation depends on whether or not cells can actually recognize and use artificial nucleotides to make proteins.

Now, researchers at Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego have come one step closer to unlocking the potential of artificial DNA. The researchers found that RNA polymerase, one of the most important enzymes involved in protein synthesis, was able to recognize and transcribe an artificial base pair in exactly the same manner as it does with natural base pairs.

The findings, published in Nature Communications, could help scientists create new medicines by designing custom proteins.