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A team of researchers led by professors Wybren Jan Buma at the University of Amsterdam and Vasilios Stavros at the University of Warwick (U.K.) have laid the groundwork for using urocanic acid and its derivatives as a novel class of sunscreen filters. Urocanic acid is a naturally occurring UV-A and UV-B absorbing compound found in the skin.

The team investigated the light-adsorbing, “sun-blocking” properties of urocanic acid and its derivatives, both in isolated molecules and in solutions. They present their results in two papers published in the journal Physical Chemistry Chemical Physics.

According to Wybren Jan Buma, professor of Molecular Photonics at the UvA’s Van ‘t Hoff Institute for Molecular Sciences, the two papers provide detailed insight into the light-conversion mechanism of urocanic acid.

“This is an excellent starting point for further optimization of its photoactive properties,” he says. “We envision many specific applications of urocanic acid and its derivatives, notably in safe UV filters.”

He expects that urocanic acid can meet the need for better, safer and more efficient sunscreen agents, replacing synthetic filters that are under discussion because of potential adverse effects on health and environment.

By  University of Amsterdam

Article can be accessed on: phys.org

Some sequences in the genome cause genes to be switched on or off. Until now, each of these gene switches, or so-called enhancers, was thought to have its own place on the DNA. Different enhancers are therefore separated from each other, even if they control the same gene, and switch it on in different parts of the body.

A recent study from the University of Bonn and the LMU Munich challenges this idea. The findings are also important because gene switches are thought to play a central role in evolution. The study has been published in the journal Science Advances.

The blueprint of plant and animal forms is encoded in their DNA. But only a small part of the genome—about two percent in mammals—contains genes, the instructions for making proteins. The rest largely controls when and where these genes are active: how many of their transcripts are produced, and thus how many proteins are made from these transcripts.

Some of these regulatory sequences, called “enhancers,” work like dimmer switches used to modulate the light in our living room. Indeed, they specifically increase the expression of a particular gene, where and when this gene is required. Genes controlling morphology often respond to several independent enhancers, each determining the expression of the gene in a different body part.

By University of Bonn

Article can be accessed on: phys.org

Tucked away on the kitchen countertop sits a bubbling, living goop in a jar. Each day, a mixture of flour and water feeds the beige concoction, commencing a ritualistic dance that summons wild yeast and bacteria from the air. This transformation turns simple ingredients into a tangy, fermenting marvel embraced by professional bakers and home chefs alike to create rustic bread loaves.

Cooking is deeply rooted in science. Replacing eggs in baking with aquafaba from cooked legumes or using baking soda to increase the pH of onions for faster caramelization are just a couple examples of how a deeper understanding of physical and chemical principles can transform the cooking process.

In his laboratory at Stanford University, chef-turned-scientist Vayu Hill-Maini loves to experiment with the science of food. He draws on his experiences in the kitchen and scientific training in biochemistry and microbiology to address challenges facing the food system. Specifically, his team uses filamentous fungi—molds and mushrooms—as a platform to address these goals and transform food waste into tasty meals. He believes that mastering food preservation, waste minimization, and alternative ingredients can lead to more sustainable culinary practices, reducing the environmental impact of the modern food system. For Hill-Maini, one man’s trash is another man’s dinner.

From Chef to Scientist, Food is a Common Ground

For many, the kitchen is a sacred space, a warm haven where the scents of simmering spices and baked bread mingle with laughter, familiar faces, and memories. “Food is deeply meaningful and deeply personal and deeply connected to who I am and how I see the world,” said Hill-Maini, who noted the influence of his global upbringing. Born in Stockholm to a Cuban and Norwegian father and a mother who is of Indian descent from Kenya, food became his bridge to connecting with these diverse cultures.

At the age of 18, Hill-Maini moved to the US to pursue a career as a chef. After a few years working in a sandwich shop in New York City, Hill-Maini returned to school, enrolling at Carleton College. He recalled how difficult it was to connect with the overly theoretical material taught in the introductory biology, chemistry, and physics classes; he craved more hands-on learning that would allow him to tap into his creative side. During the summer after his freshman year, he visited the Fundación Alícia, started by Ferran Adrià, a three-star Michelin chef and pioneer in molecular gastronomy, a scientific approach to cooking that explores the chemical and physical properties of food to create innovative dishes.

“It was a space that really embraced science as a way to create new food innovations,” said Hill-Maini.

He returned to university with a fresh perspective on his studies, recognizing that science served as a lens through which he could understand and connect with his passion; organic chemistry provided a foundation for understanding smell and sensation while biology was a vehicle for exploring the human experience and nutrition. His budding interests were met with support from mentors who encouraged him to continue his studies, which led him to pursue a PhD in biochemistry at Harvard University.

“I never really dreamt or considered it, until these experiences led me there,” said Hill-Maini.

There, he studied how gut bacteria break down food and drugs and explored how the emergence of cooking in human evolution may have shifted the structure and function of the gut microbiome. His graduate studies led him to a postdoctoral fellowship at the University of California, Berkeley (UC Berkeley), where he worked with bioengineer Jay Keasling to develop synthetic biology tools for manipulating microbial metabolism.

As he continued to immerse himself in the realms of biochemistry and microbiology, Hill-Maini saw an opportunity to combine his passions for science and cooking, envisioning innovative solutions to the pressing challenges facing the food system.

By Danielle Gerhard, PhD

Article can be accessed on: The Scientist

The genome serves as the blueprint for the body, influencing every trait from the shape of the face to the arches of the feet, and even the development of certain diseases. While some disorders, like cystic fibrosis, are linked to single genes and can be reliably predicted based on a person’s genetic data, many others—such as autism spectrum disorder, Alzheimer’s disease, depression, and obesity— are not.

For the past 15 years, scientists have used genome-wide association studies (GWAS) to compare genomes of large groups of people to identify hundreds of thousands of genetic variants that are associated with a trait or disease. This method has helped scientists unravel the underlying biology and risk factors of complex diseases and has also led to the discovery of novel drug targets. Despite these advancements, GWAS studies have their limitations, which scientists have tried to address with the help of artificial intelligence (AI). However, in two studies published in Nature Genetics, researchers at the University of Wisconsin-Madison identified pervasive biases these new approaches can introduce when working with large but incomplete datasets.

GWAS rely on large biobanks with extensive patient data. However, these repositories could be lacking anything from blood reports, scans, and patient history to family data. Even with a thorough survey, challenges such as the lack of data on late onset diseases in a cohort of young participants can throw a wrench into researchers’ plans.

By Sahana Sitaraman, PhD

Article can be accessed on: The Scientist

Researchers led by Osaka University in Japan have conducted the first human trial using induced pluripotent stem-cell-derived corneal epithelium to treat limbal stem cell deficiency, offering a potential new avenue for restoring vision.

Limbal stem cell deficiency (LSCD) is a severe ocular condition where the loss of functioning adult stem cells at the cornea’s edge leads to vision impairment due to the invasion of fibrotic conjunctival tissue over the cornea. Limbal stem cells normally perform repair functions by differentiating into corneal epithelium. Without them, the integrity and transparency of the corneal surface becomes compromised, leading to fibrotic tissue buildup, and ultimately, vision loss.

Traditional treatments often involve grafts from the patient’s healthy eye or donors, but these methods carry risks like immunological rejection, or require the removal of healthy tissue.

In a study titled “Induced pluripotent stem-cell-derived corneal epithelium for transplant surgery: a single-arm, open-label, first-in-human interventional study in Japan,” published in The Lancet, researchers conducted transplants of pluripotent stem cell (iPSC)-derived corneal epithelial sheets (iCEPS) as a potential treatment for LSCD.

Four patients with LSCD participated in the study. After removing any fibrotic tissue, the team transplanted allogeneic iCEPS onto the affected eyes. All surgeries were performed without human leukocyte antigen (HLA) matching. Half the patients received low-dose cyclosporine (typically used to mitigate organ rejection after a transplant), while the other half received no immunosuppressive agents beyond corticosteroids.

Two years of monitoring revealed no severe adverse events. Minor adverse events were managed effectively and without lasting effects.

By Justin Jackson , Medical Xpress

Article can be accessed on: MedicalXpress

Researchers at the University of São Paulo (USP) in Brazil have developed a novel nanotechnology-based solution for the removal of micro- and nanoplastics from water. Their research is published in the journal Micron.

Tiny plastic particles are ubiquitous in the world today and may currently be one of the most important environmental problems, after the climate emergency and the accelerating extinction of species and ecosystems.

Microplastics are in the soil, water and air, and in the bodies of animals and humans. They come from everyday consumer goods and from wear-and-tear on larger materials. They are found everywhere and in every kind of environment. A major source is the water used to wash clothes made of synthetic fibers. Microplastics currently cannot be filtered out of wastewater and eventually penetrate the soil, water table, rivers, oceans and atmosphere.

Defined as fragments of up to 1 millimeter, microplastics proper are a well-identified and visible problem. Nanoplastics, however, are a thousand times smaller and are proving an even more insidious hazard, since they can pass through key biological barriers and reach vital organs. A recent study, for example, detected their presence in the human brain.

“Nanoparticles aren’t visible to the naked eye or detectable using conventional microscopes, so they’re very hard to identify and remove from water treatment systems,” said Henrique Eisi Toma, a professor at the Institute of Chemistry (IQ-USP) and last author of the Micron article.

By FAPESP

Article can be accessed on: phys.org

It’s the first Spring Friday of 2024 and 75 enthusiastic plant biotechnology researchers converge at the Wits professional development hub (pdh) for a full day of discussions about microbes that affect plants: the good and the bad.

A diverse audience hears about the potential of microbial communities surviving in harsh environments, of fungi that live inside plants with possible human health benefits, of devastating viruses and bacteria; and how plants can prepare themselves for future pathogen attack and respond quicker (analogous to human vaccination).

Constructive discussions follow the presentations with suggestions for improved experimental design, follow-up work, and importantly- how potential solutions can be scaled to field settings.

Seven universities, two science councils, an IP law firm, science vendors and the SA biodiversity institute ensure a highly multidisciplinary audience.

The event sponsor, inqaba biotec, donated a sequencing prize for the best motivation to utilize their newly installed PacBio Revio and Onso sequencers at their Pretoria headquarters. This includes machine time and consumables. These sequencers have the capacity to unravel the highly complex and large genomes of plants as well as their associated microbes.

Some key takeaways from the event:

1. Young plant biotechnology researchers are doing great research with cutting-edge tools;
2. There are numerous beneficial microorganisms under study and their potential for commercialization should be investigated;
3. The level of interaction and collaborative spirit among the younger researchers are very encouraging.
   

The ACGT thanks Proffs Chrissie Rey and Timothy Sibanda for co-organizing the event.

We look forward to the next instalment, focusing on Genome Editing, in early 2025.

Story by Dr. John Becker

Over one hundred years ago, when Santiago Ramón y Cajal observed neurons microscopically, he saw fibrillous and spotted structures inside their nuclei. Researchers later discovered that these nuclear compartments, dubbed nuclear bodies, lacked membranes but contained clusters of molecules that participated in specific functions. One such nuclear body, the speckle, contains spliceosomes that are known to be involved in mRNA splicing. Disruption of speckles leads to a range of diseases and developmental disorders, yet how speckles drive splicing remains unclear.

One idea has been that speckles are splicing factories. The splicing reaction would happen inside the speckle, and then the spliced product would leave. “What people found is that’s not what happens,” said Mitchell Guttman, a molecular biologist at the California Institute of Technology. “The reason for their highest concentration of splicing factors is very much like the same reason that, if I look for where’s the highest concentration of bed sheets in your house, it’s not going to be on your bed, it’s going to be in your linen closet, right? The location where you store them when you’re not using them. And the same was thought to be true for nuclear speckles.”

The idea that speckles might be storage sites for spliceosomes triggered Guttman to look deeper into how nuclear organization might affect the splicing process. In a recent article, he showed that when genes are preferentially positioned near speckles, mRNA splicing is significantly more efficient.

By Karen Kelley Perkins, PhD

Article can be accessed on: The Scientist

When a chef develops a new recipe, they methodically add and remove individual ingredients to see how each of them alters the final dish. When scientists try to understand the role of genes in the body, they employ a similar tactic using genome editing. Currently, the most popular tool in their toolbox is CRISPR, with applications ranging from cancer therapeutics to treatments for genetic diseases like sickle cell anemia and β-thalassemia. However, this genome editing staple still has its limitations.

“It’s really hard to pack the genes encoding these proteins into the viruses that are used for their delivery into the cells,” said Tautvydas Karvelis, a genome biologist at Vilnius University. Even when CRISPR nucleases are directly delivered into cells, their large protein sizes present limitations.  For example, the commonly used Cas9 is about 1,400 amino acid residues long.

In a recent study published in Nature Methods, Gerald Schwank, a genome biologist at the University of Zurich, and his team described a tiny, but efficient, nuclease that works as well as some of the current Cas proteins but is less than half their size.

“It’s like a new class of tools that can be used for genome editing, not just as a principle,” said Karvelis, who was not involved in the study.

In 2021, Karvelis discovered a compact RNA-guided protein capable of cutting DNA: TnpB. Compared to other CRISPR nucleases, TnpB is much smaller with approximately 400 amino acid residues. However, TnpB has a lower editing efficiency and limited target range.

By Sahana Sitaraman, PhD

Article can be accessed on: The Scientist

A team of researchers have worked together to identify possible genes associated with certain metabolites molecules involved in the body’s biochemical processes and cardiovascular risk.

The scientists analyzed the levels of 187 such compounds in plasma samples from 4,974 participants in the Catalan GCAT cohort. They integrated this data with other genetic databases from European individuals, reaching a total of 40,000, and re-analyzed the data. As a result, they identified 44 genetic regions associated with these metabolites.

To identify how these genetic regions influence metabolites, the findings were combined with gene expression panels from 58 different tissue and cell types. The researchers were able to pinpoint the genes that, through modulation of their expression, are responsible for the levels of these molecules in the body.

This same methodology was applied to data from three European studies involving around 700,000 participants, aiming to study the relationship between gene expression and cardiovascular events, such as heart attacks.

Finally, the researchers explored the causal relationship between gene expression, metabolite levels, and cardiovascular risk through a genetic mediation analysis. Thanks to these various analyses, the researchers have identified a potential molecular mechanism by which six genetic loci (genetic regions) are associated with cardiovascular risk through the metabolites they regulate. In this way, this study, published in Genome Medicine highlights new genetic targets with therapeutic potential.

By Germans Trias i Pujol Research Institute

Article can be accessed on: MedicalXpress