Novel enzyme found in gut bacteria could revolutionize prebiotic research

Certain glycans — sugar-like compounds with carbohydrate chains — containing galactose, may exhibit potential prebiotic properties that support human health. Identifying enzymes capable of breaking down these glycans is essential for unlocking their full potential. In a new study, researchers discovered a novel enzyme in the human gut that specifically targets a previously unexplored glycan called β-1,2-galactooligosaccharide, known for their prebiotic benefits. This discovery can open new avenues in prebiotic research, potentially enhancing human health.

Carbohydrate chains, or glycans, are complex sugar-like compounds that play important roles in various biological processes and structures in our bodies. Galactosides are a type of glycan found in plants, animals, and microorganisms. For example, galactosides are present in plant cell walls and in certain types of beneficial sugars known as prebiotic oligosaccharides, which support gut health. Many glycans containing galactose are also added to processed foods like juice and powdered milk due to their potential health benefits. Studying the enzymes that break down these glycans is essential for understanding their prebiotic mechanisms and for improving the way they can be used in food and health products.

β-Galactosidases are enzymes that release galactose from galactosides. However, different β-galactosidases target specific galactosides. These enzymes are found in the intestines of mammals, such as in the human gut bacteria Bifidobacterium, which helps digest complex carbohydrates. Recent studies have shown that another gut bacterium, Bacteroides xylanisolvens, has the potential to utilize a broad range of carbohydrates, though little is known about its exact abilities.

In a groundbreaking study, a research team led by Associate Professor Masahiro Nakajima from the Department of Applied Biological Science, Faculty of Science and Technology at the Tokyo University of Science (TUS), Japan, discovered a novel β-galactosidase enzyme in B. xylanisolvens. This enzyme specifically targets unique galactose-containing glycans which may possess prebiotic properties. The team included Mr. Yutaka Nakazawa from TUS, Associate Professor Hiroyuki Nakai from Niigata University, and Assistant Professor Tomohiko Matsuzawa from Kagawa University. This study was published online in Communications Biology on January 16, 2025.

Discussing the motivation behind their study, Dr. Nakajima explains, “Although there are numerous types of glycans with diverse and complex structures, many glycans still have unknown functionality and potential uses. Since enzymes are essential for the synthesis of glycans, the search for new enzymes is extremely important. Our novel enzyme could be used to synthesize large amounts of unique glycans with prebiotic properties that may be beneficial to human health.”

B. xylanisolvens contains multiple genes encoding β-galactosidases. The researchers identified that one of these genes, Bxy_22780, encodes a novel β-galactosidase. Initially, the enzyme showed no activity towards natural β-galactosides. However, when reactions were conducted in the presence of a nucleophile mutant, α-D-galactosyl fluoride (α-GalF) as a donor substrate, and galactose or D-fucose as an acceptor substrate, the team successfully detected reaction products. Nuclear magnetic resonance studies confirmed that the disaccharide produced in the reactions was β-1,2-galactobiose.

Further studies on the specificity of the Bxy_22780 enzyme revealed that it is highly specific for galactooligosaccharides (GOS), which is a mixture of oligosaccharides with various linkages. Notably, this enzyme exclusively targets GOS that have a specific type of chemical bond, called β-1,2-galactosidic linkages. Kinetic analysis also revealed that this enzyme effectively acts on β-1,2-galactobiose and β-1,2-galactotriose. To understand why the enzyme is selective, the researchers examined the structure of the enzyme using X-ray diffraction studies. They discovered that the enzyme binds to a molecule called methyl β-galactopyranose at a key site called subsite +1. The structure showed that the molecule’s chemical group is positioned in a way that is perfectly suited for breaking down these particular sugar chains. This unique structure explains why the enzyme is highly specific for β-1,2-galactooligosaccharides.

“β-1,2-Galactooligosaccharides and the enzymes are rarely reported. Our discovery is a crucial step toward understanding the functions of these unique glycans, whose roles are largely unknown,” explains Dr. Nakajima. “Furthermore, while there is currently no evidence that β-1,2-galactooligosaccharides possess prebiotic properties, they hold potential in this regard. This enzyme could also open new therapeutic avenues for treating diseases like Chagas disease, caused by a parasite that produces glycans containing these structures.This novel enzyme could therefore not only help improve human gut health but also contribute to developing new life-saving drugs.”

The discovery of Bxy_22780 marks a significant breakthrough in prebiotic research, unlocking exciting opportunities for improving human health. This enzyme could drive the development of innovative prebiotic products to enhance gut health and support digestive functions, offering new opportunities in the food and supplement industries.

Genetic mixing: The secret to killer whale resilience and adaptability

An international team of marine biologists have published research in Molecular Ecology that shows the benefits of gene flow between geographically distant and genetically different killer whale populations.

The study highlights that about 20% of the genetic makeup of southwestern Australian killer whales can be traced back to Antarctic ancestors, with gene flow occurring both historically and recently in the past century.

This influx of genetic material helps reduce the risk of inbreeding and boosts the population’s genetic health, perhaps increasing their ability to adapt to shifting environmental conditions.

“Despite their low densities, killer whale populations in low-latitude oceans maintain exceptionally high genetic diversity, driven by sporadic gene flow from distinct lineages — and this is evident in Australasian killer whales” says lead author Isabella Reeves, PhD Candidate at Flinders University, and part of the Cetacean Research Centre, and the Southern Shark Ecology Group based at Flinders.

“We even identified the presence of great-grandparents from Antarctica in the southwestern Australian killer whales. This sporadic mixing with other populations acts as a mechanism to maintain long-term genetic health and survival. It reduces the effects of inbreeding, promotes a rare natural genetic rescue effect, and increases the population’s ability to adapt.”

Such natural genetic mechanisms are crucial in an era of rapid environmental change.

“This genetic mixing is supporting the long-term viability of these populations, helping safeguard these whales, hopefully in the future of environmental change, but future research will tell,” says Reeves.

The study provides rare evidence of mechanisms in wild populations that promote population health and resilience. It also illustrates how natural genetic rescue protects the genetic integrity of the population, and may enhance their capacity to evolve and thrive in the face of environmental challenges.

This genetic evidence of population health aligns with nearly 15 years of ecological research led by John Totterdell from the Cetacean Research Centre.

“Southwestern Australian killer whales thrive in a nutrient-rich environment, feeding on a diverse range of prey and forming one of the largest aggregations in the Southern Hemisphere,” says Mr Totterdell.

“They calve regularly and maintain consistent body condition, painting a picture of a robust and healthy population.

“Evolutionary history-based studies such as this provide valuable insights into the processes that have shaped modern populations.

“By understanding the genetic past of these killer whale populations, we gain a clearer picture of their present-day resilience and the factors contributing to their continued survival and adaptability.”

The study underscores the critical role of gene flow in enhancing genetic diversity and increasing the adaptive potential of populations.

It also highlights that populations have the capacity to naturally evolve mechanisms to maintain their health, a crucial trait for survival in the face of environmental change.

Transposons Hijack Telomeres to Persist in Bacterial DNA

Transposons are critical drivers of bacterial evolution that have been studied for many decades and have been the subject of Nobel Prize winning research. Now, researchers from Cornell University have uncovered mechanisms by which these mobile genetic elements integrate into the chromosomes of bacteria with linear genomes.

Their findings, published in Science in a paper titled, “Telomeric transposons are pervasive in linear bacterial genomes,“ reveal that transposons can target and insert themselves into chromosome ends, or telomeres, a strategy that influences genome stability and bacterial adaptation.

“Bacteria are like these little tinkerers,” noted Joseph Peters, PhD, professor of microbiology at Cornell University. “They’re always collecting these mobile DNA pieces, and they’re making new functions all the timeeverything in antibiotic resistance is really about mobile genetic elements and almost always transposons that can move between bacteria.”

Bacterial telomeres

While most bacterial DNA is in the form of plasmids, there are some that have linear DNA that contain telomeres. Though the presence of telomeres at the ends of the linear DNA is similar to eukaryotes, the structure and maintenance of these DNA ends are unique. This study utilized two different types of bacteria, each representing a different type of telomere: hairpin-shaped telomeres or telomeres with a terminal protein.   

Cyanobacteria transposons have hairpin-shaped telomers, which, as Peters puts it, “solves the replication problem” of a double-end break, allowing the polymerase to wrap around the end of the DNA during replication. This prevents the need for telomerase to maintain the length of the telomere. 

He continued that the second telomeric transposon mechanism is found in Streptomyces, which has aided in the development of many antibiotics. Their telomeres “have an end binding protein that binds to the end, so that makes it not look like a double-strand break, and it itself is able to recruit or make its own primer and recruit a polymerase to solve the end replication problem.” 

“In each one of these cases, whether it’s a hairpin or these end binding, they have cis-acting sequences that that system recognizes,” Peters concluded. “So, it’s independent to each individual telomere.” 

Tracking transposons in telomeres

The research group focuses on how pieces of DNA move around. Their exploration of transposon movement into telomeres was realized by data mining transposon sequences in relation to telomere sequences in Genbank. Leveraging advanced sequencing technologies, the researchers identified several families of transposons in cyanobacteria and Streptomyces 

Typically, transposons have protein-binding sequences on either end. However, the researchers found that these telomeric transposons have single-sided binding sequences and replace the bacterium’s own telomere. This effectively allows the transposon to function as the telomere, making it an essential component of the bacterial genome.  

The team is the first to document these telomeric transposons in bacteria. Peters explained that transposons are insidious, utilizing the telomeres as a safety net for the bacterium to not remove the transposon. “It’s the ultimate parasite because the cell can’t get rid of the transposon because it controls the end. If it killed the transposon, it would lose the telomere, and it would die,” he told GEN. 

Modern tech to study ancient systems 

Advancements in artificial intelligence (AI) and bioinformatics have played a key role in the team’s discoveries. Peters’ team is excited about the progress in computational tools available for researchers. “We absolutely use AlphaFold all the way,” Peters said about the AI system.  

Additional new computational tools have revolutionized genomic analyses. Peters described how his team has used programs including BLAST searches and HHpred because, compared with humans (and with other programs over time), their algorithms are “much, much better at finding matches, even when there’s almost no amino acid sequence, because somehow it’s able to predict something.” 

As technology advances, DNA synthesis accessibility has become a game-changer in the field. In the not-so-distant past, the process of creating novel sequences and inserting them into plasmids was technically and financially challenging.  

“Another huge thing that I think isn’t really said enough is this idea of DNA synthesis has really been coming down in price,” Peters explained. “Now you can go to one of these biotech companies, and you can get it made and it’s already in plasmids!”  

This, he noted, makes the process of moving from hypothesis building to experimentation much faster.  

From bacterial immunity to human health 

Beyond an advance in understanding evolution, these findings could have practical applications in biotechnology and medicine. The study uncovered a subfamily of telomere-targeting transposons that had utilized a CRISPR system. While CRISPR is typically utilized in bacteria to fight off viral attacks, this subfamily of transposons uses CRISPR to target and integrate into chromosome ends, further supporting prior research from Peters’ lab. 

“These transposons captured CRISPR-Cas systems to be able to use them as ways to identify and self-program to sites they really want to go into,” Peters told GEN. “It was this totally ingenious way that they evolved on their own.” 

As interest in harnessing transposon systems for gene-editing applications grows, researchers recognize both the promise and the challenges ahead. “It’s a good inspiration for ideas.” However, he added that it doesn’t solve all of the problems. Nor can it be put into humans to cure everything.  

He described how gene editing comes in three groups: base editing, prime editing, and large-program gene delivery. Transposons, he said, are a good inspiration for the third group: “These elements are just really ready for that.” 

Looking ahead, he hopes to apply transposon-based systems to gene editing. Peters explained that many genetic diseases have single nucleotide errors in the DNA sequence. Based on the current path to creating disease treatments, each individual genetic change through base or prime editing would require a unique set of trials. Instead, Peters emphasizes that broadening the scope of genetic replacement would be a better and more streamlined solution. “You really want to replace that exon, because then you can cure a hundred diseases at one time.”  

However, delivery systems remain a key challenge. “To really meet the potential for all these, you really need some kind of delivery [mechanism] that can allow this cargo range,” Peters noted. “I think it is safe to say that a lot of these things are aspirational, and that we are going to make a great machine that we don’t know how to deliver yet.” 

Despite these hurdles, Peters remains optimistic. “That’s still a challenge. There’s a lot of money and a lot of companies going into that. So, I think that is something that will be solved.” 

Gut Microbe Composition During Infancy May Protect Against Diabetes in Later Life

Scientists headed by a team at the University of Utah Health have reported on research in mice suggesting that microbiome composition during infancy can shape development of pancreatic insulin-producing cells, leading to long-term changes in metabolism and impacting on diabetes risk later in life. The study, reported in Science by research co-lead June Round, PhD, professor of pathology at University of Utah Health, and colleagues, identified what the team describes as “a critical neonatal window in mice when microbiota disruption results in lifelong metabolic consequences stemming from reduced β cell development.”

Round suggests that understanding how the microbiome impacts metabolism could potentially lead to microbe-based treatments to prevent type 1 diabetes. “What I hope will eventually happen is that we’re going to identify these important microbes, and we’ll be able to give them to infants so that we can perhaps prevent this disease from happening altogether.”

In their published paper, titled “Neonatal fungi promote lifelong metabolic health through macrophage-dependent β cell development,” the team concluded that their results “… identify fungi as critical early-life commensals that promote long-term metabolic health …”

“Loss of early-life microbial diversity is correlated with diabetes, yet mechanisms by which microbes influence disease remain elusive,” the scientists explained. The body’s control of blood sugar depends on the hormone insulin, which is produced solely by pancreatic β cells, and diabetes develops when there is insufficient insulin. “Loss of insulin production or responsiveness is the basis of diabetes,” they stated.

β cell mass expands rapidly after birth, the team continued, and coincident with this postnatal β cell expansion, “… the composition of gut microbiota during the postnatal period also diversifies in phases, with each new phase dominated by distinct taxa.” Acquiring a sufficiently diverse microbiota appears to protect against childhood diabetes, the team further stated, “… however, the mechanisms involved are not known, and we cannot yet attribute specific mechanisms of disease susceptibility or protection to specific microbes.”
For their newly reported study, the team sought to test the hypothesis that mouse postnatal β cell development is linked to the presence of specific microbes during defined windows of microbial colonization. They systematically deleted and restored microbiota during certain windows of pre- and postnatal life in mice. The results identified a 10-day period before weaning when the resident microbes are required to establish normal β cell mass. “These observations were replicated using antibiotic and antifungal drugs, indicating that both bacteria and fungi promote host β cells,” the team noted in their research article summary.
The results indicated that mice exposed to broad-spectrum antibiotics in early life have worse metabolic health in the long term. If the mice received antibiotics during the 10-day window shortly after birth, they developed fewer β cells. The antibiotic-treated mice also had higher levels of blood sugar and lower levels of insulin in adulthood. “This, to me, was shocking and a bit scary,” said Round. “It showed how important the microbiota is during this very short early period of development.” 

The investigators in addition found that fecal samples from human infants, 7 to 12 months of age, stimulated mouse β cell mass, whereas samples from other age groups did not. “Mice that were colonized with samples obtained from children between 7 and 12 months of age had significantly more insulin-expressing tissue and serum insulin than did mice colonized from donors of any other age group.” This finding suggests that humans may also exhibit a window of colonization by β cell–promoting microbes, the authors suggested.

By testing in mice a variety of antibiotics that affect different types of microbes, the researchers pinpointed several specific microorganisms that increased the amount of insulin-producing tissue and the level of insulin in the blood. Intriguingly, they found one of these metabolism-boosting microbes to be a largely unstudied fungus called Candida dubliniensis, which isn’t found in healthy human adults but may be more common in infants.

The experiments showed that C. dubliniensis exposure in early life also dramatically reduced the risk of type 1 diabetes in at-risk male mice. When male mice that were genetically predisposed to develop type 1 diabetes were colonized by a metabolically “neutral” microbe in infancy, they developed the disease 90% of the time. In contrast, mice that were colonized with the C. dubliniensis fungus developed diabetes less than 15% of the time.

Exposure to C. dubliniensis could even help a damaged pancreas recover, the study results suggested. When researchers introduced the fungus to adult mice in which insulin-producing cells had been killed off, the insulin-producing cells regenerated and metabolic function improved. The researchers emphasized that this is highly unusual, as this kind of cell normally doesn’t grow during adulthood.

The C. dubliniensis fungus appears to support insulin-producing cells via its effects on the immune system. Previous research has shown that immune cells in the pancreas can promote the development of their insulin-producing neighbors. The researchers found that mice without a microbiome have fewer immune cells in the pancreas and worse metabolic function in adulthood.

When such mice were given a booster of C. dubliniensis in early lifeboth their pancreatic immune cells and their metabolic function were restored back to normal. The studies showed that C. dubliniensis could only promote the growth of insulin-producing cells in mice that have macrophages, showing that the fungus promotes metabolic health by affecting the immune system. “Here we identify a previously unknown microbiota-mediated mechanism to influence β cell development through macrophage seeding of the islet,” they stated, noting that the results indicated that it is increased numbers of islet macrophages, rather than their functional state, that drive β cell proliferation.

The scientists emphasized that there are probably other microbes that confer similar benefits as C. dubliniensis. The new insights could help scientists better understand how similar health cues from other microbes might function. “We don’t know a lot about how the microbiome is impacting early-life health,” said Jennifer Hill, PhD, first author on the study, who led the research as a postdoctoral scientist in the Round Lab at the U. Hill is now an assistant professor in molecular, cellular, and developmental biology at University of Colorado Boulder. “But we’re finding that these early-life signals do impact early development, and then, on top of that, have long-term consequences for metabolic health.”

The newly reported findings, the researchers suggest, could ultimately help doctors reduce the risk of type 1 diabetes—or potentially even restore lost metabolic function in adulthood—by providing specific gut microbes that help the pancreas grow and heal.

If the benefits seen in mice hold true in humans, microbe-derived molecules might eventually help restore pancreatic function in people with diabetes. Hill added, “One possibility in the far future is that maybe signals like these could be harnessed not only as a preventative but also as a therapeutic to help later in life.” However, Hill also cautions that treatments that help β cells regenerate in mice historically have not led to improvements in human health.

Jazz to Acquire Chimerix for $935M, Expanding Rare Oncology Portfolio

Jazz Pharmaceuticals has agreed to acquire Chimerix for approximately $935 million, the companies said Wednesday, in a deal designed to bolster the buyer’s rare oncology portfolio with a treatment under FDA Priority Review and potential approval this summer for a form of glioma.

Chimerix’s lead clinical pipeline candidate is dordaviprone, a first-in-class small molecule treatment designed to selectively target the mitochondrial protease ClpP and dopamine receptor D2 (DRD2). Dordaviprone is being developed for H3 K27M-mutant diffuse glioma, a rare, high-grade brain tumor that most commonly affects children and young adults.

The FDA has set a target Prescription Drug User Fee Act (PDUFA) action date of August 18 for dordaviprone after the agency accepted the company’s New Drug Application (NDA) under Priority Review for accelerated approval.

If approved, dordaprivone would be the first FDA-approved drug for recurrent H3 K27M-mutant diffuse glioma, with the current standard of care now limited to radiation therapy.

“Adding dordaviprone to our oncology R&D pipeline will further diversify our portfolio with a medicine that addresses a significant unmet need with no other FDA-approved therapies and limited treatment options for this patient population,” Bruce Cozadd, Jazz’s co-founder, chairperson, and CEO, said in a statement.

He added that dordaviprone could also contribute durable revenue beginning in the near-term. Chimerix projected in 2001 that the drug—then known as ONC201—would generate more than $500 million in global peak sales in H3 K27M-mutant diffuse glioma, the first of several potential indications.

Chimerix revealed that projection in January 2021 when it announced it had acquired the drug and the rest of the pipeline of Oncoceutics for $78 million upfront—half in Chimerix stock, the other half in cash—plus up to $360 million in payments for ONC201 and two other programs tied to achieving development, regulatory, and sales milestones.

“We are encouraged by the dordaviprone clinical trial results to date and look forward to closing the proposed acquisition and working with our new colleagues from Chimerix to fully leverage our combined R&D and commercial expertise to deliver this novel therapy to patients, beginning as early as the second half of this year,” Cozadd added.

That could be one of Cozadd’s last major acts at the day-to-day helm of Jazz. In December, Cozadd told Jazz’s board that he intends to retire as CEO once it chooses a successor, something expected by the end of this year.

The board is undertaking a formal search process to identify a new CEO—though Cozadd would continue to serve as chairperson of the board of directors. Cozadd co-founded Jazz in 2003, serving as executive chairman until being appointed chairperson and CEO in 2009.

“Durable growth driver”

“We see this acquisition adding a durable growth driver to JAZZ’s oncology franchise,” Jessica Fye, an analyst with J.P. Morgan, wrote Wednesday in a research note. “We also see the deal as consistent with JAZZ’s recent commentary signaling BD [business development] as an area of (continued) high priority, even with the CEO transition on the horizon.”

In addition, dordaviprone is also being developed for newly diagnosed, non-recurrent H3 K27M-mutant diffuse glioma following radiation treatment, for which the treatment is under study in the ongoing Phase III ACTION trial (NCT05580562). Should dordaprivone win approval for that indication, it would potentially extend use of the drug into the front-line setting.

At $8.55 per share cash, the purchase price marks a 72% premium from Chimerix’s closing price Tuesday of $4.96. Investors reacted to news of the company’s acquisition by Jazz Pharma with a buying surge that sent Chimerix shares soaring 70% to $8.44 Wednesday in late trading as of 3:40 p.m. ET.

Shares of Chimerix have zoomed nearly 10-fold since December, when the company announced plans to seek accelerated approval for dordaviprone. Chimerix also said at the time that it intended to pursue a rare pediatric disease priority review voucher. A 2024 study has pegged the average value of a PRV at $100 million, though individual vouchers have sold for between $67.5 million and $350 million.

Jazz said it will begin an all-cash tender offer to acquire all outstanding shares of Chimerix’s common stock. Upon successful completion of the tender offer, Jazz said, it would acquire all shares not acquired in the tender through a second-step merger for the same price per share as was paid in the tender offer.

Jazz expects to fund the transaction through existing cash and investments. The company finished 2024 with $2.413 billion in cash and cash equivalents, plus $580 million in investments—nearly double the $1.6 billion in cash, cash equivalents, and investments the company reported at the end of 2023.

Both Jazz and Chimerix have approved the acquisition deal, which is expected to close in the second quarter. The deal is subject to customary closing conditions that include the tender of a majority of the outstanding shares of Chimerix’s voting common stock.

“We are excited to reach this agreement with Jazz Pharmaceuticals as they bring global scale to broaden our dordaviprone commercial strategy,” stated Mike Andriole, Chimerix’s president and CEO. “This announcement is the culmination of years of scientific work by our incredibly talented team and will deliver significant and certain value to our shareholders.”

Solanum Pan-Genome Unveils Paralogs’ Role in Genome Engineered Crops

Advancements in genomics, next-generation sequencing, and genome editing are driving forward a new era of crop breeding. About 75% of the world’s food comes from 12 plants. However, scientists estimate up to 30,000 species are edible. One opportunity in broadening our food supply lies in exchanging genotype-to-phenotype knowledge between globally and locally cultivated crops. However, many genetic variants are species-specific. And methods of selecting for advantageous traits can produce different results in related species.

“There’s a lot of wonderful food crops out there,” said Zachary Lippman, PhD, Cold Spring Harbor Laboratory (CSHL) professor & HHMI investigator. “How many of them have not received the attention they would benefit from, compared to ‘major’ crops?”

Now, CSHL researchers and colleagues around the globe have established a pan-genome of the crop-rich genus Solanum. The team sequenced dozens of complete genomes for the plant genus that includes tomatoes, potatoes, and eggplants. The new, high-quality pan-genome was then used to map the genes behind specific traits of agricultural significance across the genus, and target those genes to create desirable mutations.

This work is published in Nature in the paper, “Solanum pan-genetics reveals paralogues as contingencies in crop engineering.”

The team’s research reveals the importance of understanding the evolution of paralog genes in predicting genome editing outcomes. How paralogs relate to physical changes across species has not been deeply studied—until now. And, in this study, the biggest breakthroughs came from the African eggplant: a tomato relative indigenous to the sub-Saharan region, African eggplant varies highly in fruit shape, color, and size.

The authors wrote, “Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression, and function. By augmenting our pan-genome with African eggplant cultivars and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size.”

Lippman and longtime collaborator Michael Schatz, PhD, professor of computational biology and oncology at Johns Hopkins University, turned to a breeder in Uganda to exchange ideas and expertise. Mapping tens of thousands of paralogs, the team identified a previously unknown gene in African eggplant that affects fruit size. The paralog has the same function in tomatoes. The researchers discovered they could influence tomato size by editing it.

“Reciprocal exchange between indigenous and major crops creates new, predictable paths for better breeding,” said Benoit. “This is key to boost the diversity and resilience of the food system.”

The findings, the authors suggest, demonstrate that “paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.”

“Crop diversity benefits nutrition, choice, and health,” Lippman added. “Determining how related paralogs function across species could help improve crop yields, flowering times, and food selection. In other words, it’s a win-win-win for scientists, farmers, and consumers everywhere.”

Making the Big Move: Techniques Evolve to Transfer Large DNA Cargos

Existing gene-editing technologies have led to significant advances in both medicine and food production. However, momentum appears to be slowing, particularly in health applications, as early hype is giving way to the realism of how difficult therapeutic development is turning out to be. Simply put, although major progress is being made, the field is struggling to put gene-editing tools into the healthcare market.

On the bright side, the safety issues that arise in medical research are not as large of a concern in the agricultural field, which continues to make steady progress. But scientists in both health and agriculture are delving deeper to uncover new solutions to tackle the tough issues. Building blocks such as recombinases, integrases, and transposases are being reexamined and enhanced with the use of AI to make them more specific and effective. New platforms are being introduced to insert larger DNA segments that potentially have a greater impact on both the human healthcare and agricultural fields.

Although the rate of progress may have slowed, new gene editing tool discoveries have the possibility to catapult the field into yet another growth spurt. As with all new scientific approaches it takes time and effort, but the results may be well worth it.

Mining for recombinases

The agriculture sector presents a particular set of needs. For example, traditional crop breeding is slow and requires screening of thousands of variants, but no high-throughput screening process exists. Decreasing the number of progeny would help expedite new trait creation.

Compared to therapy development, off-target effects in agricultural applications are not as limiting. More variation increases the chances of finding a new plant or trait. Once desired mutations are identified gene editing can be used to generate them more precisely. “We needed a technology that would allow us to efficiently and precisely insert large DNA cargoes into a ‘safe harbor’ region in the genome,” explained Kevin Zhao, PhD, co-founder and CTO, Qi Biodesign.

Prime Root editors are fundamentally based on recombinase technologies. While these enzymes allow large DNA insertions, they only recognize specific recombinase recognition sites. “These recombinase recognition sites rarely occur in nature where we want to insert our genes,” Zhao said. “So we need to first integrate these recombinase recognition sites into the targeted region then utilize recombinases for performing large DNA integration.”

The challenge is assembling the different pieces, the small recognition site and the large cargo, to generate a final gene edit. “The recombinase step limits Prime Root editors. We hypothesized that this was due to the recombinases themselves so we evolved these enzymes and also used protein structure-based AI predictions to mine for new ones to increase overall editing efficiency,” added Zhao.

Previous mining has traditionally been based on sequence similarity. Since the structure of a protein dictates its function, new proteins can be missed using this traditional sequence-based approach.

Recombinase efficiency increases allow Qi Biodesign to insert 20-30 kb (5 or 6 genes) at one time at one location across a variety of different crop genetics. In addition, a large team at Qi Biodesign works on plant transformation, another bottleneck in plant breeding innovations.

Gene-edited crops are regulated differently than traditional GMOs: the regulations are clearer and becoming more streamlined. Yet it remains a challenge to bring these crops to market. ”A lot of work is needed to get the world on the same page,” emphasized Zhao. “Agriculture products are commodities. Approval needs to be global.” Currently, Qi-Biodesign has 5 approvals in China and 1 in the U.S.

Re-inventing integrases

Despite remarkable advancements, existing genome engineering technologies integrate DNA randomly, require double-strand DNA breaks that risk unintended mutations, or are constrained by the size of DNA cargo they can insert.

KOMO Biosciences, under the leadership of its CEO Jennifer Manning, is pioneering a transformative solution to these challenges with its next-generation, precision genome-engineering platform.

KOMO’s innovation is its high-efficiency serine integrases that enable precise, site-specific integration, which offer a new standard for precision and reliability. Site-specific recombination enables precise modifications of the genome by facilitating the exchange of DNA segments between specific sequences.

This process is mediated by site-specific recombinases (SSRs), enzymes that recognize defined DNA sites, cleave the DNA backbone, exchange strands, and rejoin them. These natural systems play essential roles in bacterial genome replication, differentiation, and the movement of mobile genetic elements.

Among SSRs, serine integrases are particularly effective at inserting large DNA sequences into designated genomic sites. In addition, serine integrases function independently of cellular repair mechanisms, reducing the risk of unintended mutations. They do not require sequence homology between the donor and target DNA, making them highly versatile for genome engineering applications.

A key advantage of serine integrase-mediated recombination is that it does not induce DNA damage or rely on host cell factors, thereby avoiding the activation of error-prone repair pathways. This is particularly important for maintaining genomic integrity, as disruptions in pathways such as p53-mediated DNA damage response can lead to unintended selection for cells with impaired p53 function.

The first application of KOMO’s integrase technology is the development of rapid, stable, clonal cell lines, to be followed by genomically-directed serine integrases for in vivo cell therapy. “We believe that KOMO’s technology has the potential to significantly accelerate therapeutic development, improve the scalability and predictability of manufacturing, and reduce complex supply chains,” Manning explained. “This will improve access to and affordability of life-saving therapeutics.”

De novo on-off switches

“We are all painfully aware that most of the genome-editing tools we have today are great, but just not good enough,” said Jeff Graf, PhD, co-founder, Atelas Biosciences. “We still lack a tool that is both highly specific and highly efficacious. In addition, even the best of the second-generation tools, such as prime editing, cannot perform large DNA rewriting or large DNA insertions.”

Safety relies on the specificity and effectiveness of the tool. Although off-target edits, programmability, and targetability are all important, maintaining a high editing rate ranks higher because of its broad impact.

Atelas Biosciences is developing a technology that relies on existing building blocks. “Our technology ticks all the boxes,” said Graf. “It has high integration efficiency, is fully programmable, works in any tissue, and is specific. We incorporated all of the factors that influence safety to innovate a best-in-class genome editor that is also versatile and simple.”

The platform is based on well-characterized nucleases and transposases with the addition of another novel building block, a mechanism of control that activates and deactivates the transposition activity. “In the same system you have the functionality of the nuclease to go to the right place in the genome due to a RNA guide, and the activity of the transposase to insert large pieces of DNA,” said Luis Iniesta, co-founder, Atelas Biosciences.

The control mechanism is a unique AI-generated, de novo protein function that is inserted into the system and acts as an on-off switch for the transposase activity. This allows the transposase activity to be controlled by the nuclease activity in such a way that there are no unspecific transposition events. Activity only occurs when the nuclease has arrived at the correct location in the genome.

The high activity and large fragment insertion ability of the transposase is maintained and combined with nucleases that are specific and programmable, thus providing efficacious and specific DNA insertion. This targeted, highly-efficient, large insertion DNA gene-editing tool has many potential applications in both agriculture and human therapy development.

Symbiosis Pharmaceutical Services and Enzene Pass Regulatory Reviews

Symbiosis Pharmaceutical Services completed its latest inspection by the FDA of its facilities in Scotland. Headquartered in Stirling, U.K., and specializing in the manufacture and fill/finish of pharmaceuticals and biopharmaceuticals for clinical trials and the supply of commercial markets, the CDMO recorded zero GMP observations from the FDA during the inspection in January.

The FDA inspection was conducted over a seven-day period and focused on the ongoing fill/finish of commercial supplies of an AAV viral vector biologics product for a U.S. pharma client. The inspection outcome validated Symbiosis’s robust quality management systems, ensures continued adherence to FDA regulations, and reinforces the capability of Symbiosis to deliver high-quality biopharmaceutical sterile manufacturing solutions globally, according to Colin MacKay, CEO of Symbiosis.

“In a rapidly evolving biopharmaceutical landscape, regulatory rigor and GMP operational performance are enduring priorities for the company and a fundamental part of our business and cultural ethos,” said MacKay.

The company continues its physical and operational expansion with the commissioning of its new automated sterile GMP manufacturing facility, close to its existing facilities in Stirling. This will increase the company’s commercial-scale sterile manufacturing capabilities, enabling it to support a growing number of clients globally through the clinical and commercial injectable drug product lifecycle challenges, continued MacKay.

Enzene receives European GMP certification

Separately, Enzene, an India-headquartered CDMO working with fully-connected continuous biologics manufacturing technology, said that its two facilities in Pune, India, have received European Union (EU) GMP certification to provide commercial-scale microbial and mammalian drug substance supply and drug product fill/finish and packaging.

“The European Union’s GMP certification provides existing and potential customers with tangible evidence that Enzene meets the stringent quality and safety standards required by the European Medicines Agency and marks another step on Enzene’s journey to providing comprehensive solutions to clients in Europe and beyond,” according to an Enzene spokesperson.

Enzene officials also say facilities provide fully integrated services to address the market for challenging diseases and innovative treatments. Pune was also the first site in the company’s network to feature Enzene’s modular EnzeneX™ 2.0 platform, which reduces the equipment footprint compared with that of conventional fed-batch systems.

The platform is capable of clinical phase cGMP supply from as low as 30-L scale, with variable bioreactor capacity to accommodate scale-on and scale-out expansion, reported the company spokesperson, who added that Enzene will soon launch a new $50-million manufacturing facility in Hopewell, NJ, introducing the company’s patented fully-connected continuous manufacturing (FCCM™) platform to the United States.

Roche Continues Regulatory Run With Acute Stroke Expansion for Heart Attack Drug

TNKase is the first stroke drug to win FDA approval in nearly three decades.

The FDA signed off Monday on the use of Roche’s thrombolytic drug TNKase to treat acute ischemic stroke in adult patients.

According to Roche subsidiary Genentech, which announced the label expansion on Monday, TNKase is the first new drug for stroke in almost 30 years. Roche and Genentech also own Activase, the only other acute ischemic stroke (AIS) drug approved by the FDA.

Delivered intravenously, TNKase is a tissue plasminogen activator that works by kicking off a cascade that culminates in dissolving blood clots. In AIS, this mechanism helps prevent the formation of blockages that can constrict the flow of blood to various regions of the brain. TNKase was first approved in 2000 to lower the risk of death in patients with acute heart attack.

Monday’s label expansion was backed by data from a large multicenter trial that established the non-inferiority of TNKase to Activase. Data published in July 2022 in The Lancet showed that 36.9% of patients treated with TNKase had no to nonsignificant disability as measured by the modified Rankin Scale, a validated tool that doctors use to assess global disability in stroke patients.

In comparison, 34.8% of comparators in the Activase arm reached the same outcome. The risk difference estimate was 2.1%, which satisfied the threshold of non-inferiority.

In a statement on Monday, Genentech Chief Medical Officer Levi Garraway called TNKase’s label expansion a “significant step forward” for the company and for patients, for whom the drug can provide “a faster and simpler administration, which can be critical for anyone who is dealing with an acute stroke.”

Monday’s label expansion also continues Roche’s regulatory run in recent months.

Last month, for instance, the company’s SMN2 splicing modifier Evrysdi became the first FDA-approved tablet for spinal muscular atrophy, a rare motor disorder. The pill “combines established efficacy with convenience,” Garraway said at the time, and is expected to make the drug easier to take for patients.

Months earlier, in September 2024, Roche—alongside partner Sanofi—won the FDA’s approval for the industry’s first biologic treatment for chronic obstructive pulmonary disease. Dupixent, a blockbuster anti-IL4-alpha antagonist, was cleared for the lung condition after Phase III trials demonstrated a 30% to 34% drop in the rate of exacerbations versus placebo.

In April 2024, Roche’s Genentech also snagged approval for Alecensa as the first and only ALK inhibitor for the adjuvant treatment of ALK-positive non-small cell lung cancer patients with early-stage disease who had undergone surgical resection.

Boots recalls paracetamol over labelling error

The High Street pharmacy chain Boots is asking customers to return packs of 500-milligram paracetamol tablets because a labelling error incorrectly states they are a different painkiller, aspirin.

More than 110,000 packs, with the batch number 241005 and expiry date “12/2029” on the bottom, are affected.

Customers can receive a full refund without a receipt.

Boots and the supplier, Aspar Pharmaceuticals Limited, have begun a full investigation.

The outer cardboard packaging is correctly labelled: “Paracetamol 500mg Tablets” but the inner foil blister pack of pills instead reads: “Aspirin 300mg Dispersable Tablets”.

The affected packs should not be used or kept, even if the error is known, as this could lead to an incorrect dose.

And anyone who has bought this product for someone else should tell them as soon as possible.

‘Seek advice’

Dr Stephanie Millican, from the Medicines and Healthcare Products Regulatory Agency (MHRA), said: “Patient safety is always our priority.

“It is vitally important that you check the packaging of your Boots Paracetamol 500mg Tablets 16s – and if the batch number is 241005, you should stop using the product and return it to a Boots store for a full refund.

“If you are unsure which pack you have purchased or have taken Boots Paracetamol 500mg Tablets and experienced any side effects, seek advice from a healthcare professional.

“Please report any suspected adverse reactions via the MHRA’s Yellow Card scheme.

“If you have any questions or require further advice, please seek advice from your pharmacist or other relevant healthcare professional.”

Paracetamol is an effective painkiller for mild or moderate pain. It may be better than aspirin for headaches, toothache, sprains and stomach ache.

Aspirin may be better than paracetamol for period pain or migraines, says the NHS.

Aspirin stops your body making compounds called prostaglandins and this lowers the pain and reduces swelling and high temperature.

Ibuprofen – another type of painkiller, known as a non-steroidal anti-inflammatory drug or NSAID – works in a similar way to aspirin.

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