Blog

  • HS2 already billions over budget with work ‘just over halfway done’, says rail boss | HS2

    HS2 already billions over budget with work ‘just over halfway done’, says rail boss | HS2

    HS2 construction contracts priced at £19.5bn have already cost £26bn despite being “just over halfway done”, the boss of the high-speed rail project has told MPs.

    Civil engineering to build tunnels and cuttings for the 100-mile line should be almost finished but is closer to 60% complete, while only a third of the wider project – including laying tracks and wiring – is done, the transport select committee heard on Wednesday.

    Mark Wild, chief executive of HS2 Ltd, said that while budget estimates had suffered from “optimism bias”, the company had “lost control of the programme”. He told the committee that the rush to start work in 2020 without balancing the risks in the contracts was the major reason for costs spiralling upwards.

    Contracts were signed off in April 2020 and construction formally began five months later, before designs were finalised and local planning consents were in place, he said.

    Wild, who started work last December, is currently engaged in a “reset” of construction, which he said would include reshaping his direct staff at HS2 Ltd, coming up with a credible schedule and budget, and renegotiating contracts in the autumn.

    He said: “The bottom line is that, at the notice to proceed, the contractors could not price the risk. What we’re seeing is the crystallisation of risk: they should have cost £19.5bn, and we’ve already spent £26bn and we’re just over halfway done … Between 50% and 100% is the likely overspend.”

    An artist’s impression of an HS2 train produced by the high-speed rail company in 2023. Illustration: HS2/PA

    The line between London and Birmingham – initially designated phase one, but now the entirety of HS2 – was originally planned to open in 2026.

    The schedule was subsequently postponed to between 2029 and 2033. But on Wild’s advice, Heidi Alexander, the transport secretary, told parliament last month that there was “no route” to full HS2 services until after 2033.

    Wild told the committee: “If you lose control of the programme, you end up at the extreme end of optimism bias, which ends up in delusion … The problem with HS2 is we lost control of the programme.”

    He added that Covid and inflation caused by Russia’s invasion of Ukraine had both had a significant impact on time and costs, but that HS2 had failed to manage costs.

    He said the company was “unbalanced” and had “a significant gap” in its frontline workforce managing contractors, as well as having “too many consultants who’ve been there for too long”.

    “We’ve ended up … locked in our own bureaucracy,” he said.

    Also giving evidence, Lord Hendy said politicians had to be ultimately accountable for the decisions made. The rail minister told the committee it was unclear why political leaders had decided HS2 should be an “exceptionally fast railway”.

    skip past newsletter promotion

    While accepting that higher speed did increase potential capacity, he added: “It is hard to understand why there was such zealotry about the highest-speed railway in a relatively small country.”

    HS2 trains will have a maximum speed of 225 miles an hour, though Wild suggested last month they start running at lower speeds to reduce the period needed for testing and potentially run services sooner.

    Wild told the committee he was confident that HS2 could “get a reset” and that the company would keep budgets under control by no longer allowing “gold plating” or “first-of-a-kind technology” on the project.

    He added that he was dealing with contractors who “are working across government and are part of a much bigger game than just HS2”.

    With major contracts to be awarded on work such as the Sizewell C nuclear plant and upgrading the National Grid, Hendy said he believed firms would “lean in” to Wild’s plans.

    He said some examples of what Wild called “gold plating” had already been scrubbed from the project, such as “air-conditioned platforms” as part of the first design for HS2’s London Euston terminus.

    “Even Saudi Arabia doesn’t have air-conditioned platforms,” he said.

    Continue Reading

  • Stonepeak to Acquire a Co-Control Stake in IFCO from ADIA

    Stonepeak to Acquire a Co-Control Stake in IFCO from ADIA

    Stonepeak to join existing IFCO investor Triton, who remains a committed partner to the Company

    MUNICH & NEW YORK & PULLACH, FRANKFURT AM MAIN – July 9, 2025 – Stonepeak, a leading alternative investment firm specializing in infrastructure and real assets, today announced that it has entered into a definitive agreement under which Stonepeak will acquire an ~50% co-controlling stake in IFCO Group (“IFCO” or “the Company”), a leading global provider of reusable packaging solutions for fresh foods, from a wholly-owned subsidiary of the Abu Dhabi Investment Authority (“ADIA”). Triton, a leading European mid-market sector-specialist investor and existing investor in IFCO, will remain a committed partner to the Company. Together, Stonepeak and Triton will have joint and equal ownership and governance of IFCO.

    Founded in 1992, IFCO today manages a global logistics system that utilizes over 400 million reusable packaging containers (“RPCs”) to enable more than 2.5 billion annual shipments of fresh fruits, vegetables, and other perishables from producers to retailers through a closed-loop, circular supply chain. The Company operates a network of approximately 140 service centers to wash and repair RPCs between trips. IFCO’s reusable solutions offer clear advantages over single-use packaging, providing cost, sustainability, and automation benefits to leading food retailers and producers. With a team of approximately 2,000 employees, the Company runs a global operation serving over 300 retailers and 18,000 growers in more than 50 countries.

    “With the support of ADIA and Triton, IFCO has gone through a successful strategic and operational transformation and delivered strong growth. We want to thank both investors for their contribution and welcome Stonepeak as a new partner alongside Triton. Stonepeak’s expertise in critical infrastructure and proven investment strategy paired with Triton’s long years of sector experience and focus on digitalisation and sustainability will contribute largely to IFCO’s further growth, strengthening our market leading position globally,” commented Michael Pooley, Chief Executive Officer of IFCO.

    “As the operator of the largest and most established logistics network for reusable packaging in the grocery supply chain globally, IFCO represents a critical component of the logistics infrastructure delivering fresh produce,” said Nikolaus Woloszczuk, Senior Managing Director at Stonepeak. “Its leadership position is underpinned by its network and scale, which deliver cost and sustainability advantages over single-use cardboard for retailers and growers. We believe the Company’s high-quality, market-leading platform has meaningful embedded and adjacent growth opportunities, and we are excited to partner with Triton and the IFCO team to accelerate this next chapter of growth at IFCO. With IFCO’s strong and growing presence in North America, the Company fits squarely within our infrastructure investment strategy for the region.”

    “We thank ADIA for its support of IFCO and the trustful collaboration with Triton over the last six years and are looking forward to continuing our investment journey with Stonepeak. Together we share the same ambition to create value for our investors and portfolio companies. IFCO is at the core of Triton’s Business Services investment strategy, where we have many years of experience and in-depth sector know-how. We thank the IFCO management team and all employees for the great journey and their excellent contribution so far and will remain a committed investor as we are very excited about the Company prospects,” adds Stephan Förschle, Partner and Co-Head of Business Services at Triton.

    Hamad Shahwan Aldhaheri, Executive Director of the Private Equities Department at ADIA, said, “ADIA invested alongside Triton in IFCO’s carve-out from Brambles in 2019. Since then, IFCO has built solid foundations for the future, based on strong operational performance and enhanced digital capabilities, and is well positioned for growth. We wish the Company, Triton, and Stonepeak continued success in the years ahead.”

    The transaction is subject to customary regulatory approvals and is expected to be completed in the fourth quarter of 2025.

    Citi is serving as financial advisor and Kirkland & Ellis is serving as legal counsel to Stonepeak. Bank of America and Morgan Stanley & Co. International PLC are serving as financial advisors and Latham & Watkins as legal counsel to ADIA and Triton. Freshfields Bruckhaus Deringer is serving as legal counsel to ADIA.

    About IFCO
    IFCO is a leading global provider of reusable packaging solutions for fresh foods, empowering customers to participate in the circular economy in 50+ countries. IFCO operates a pool of over 400 million reusable packaging containers (RPCs) globally, which are used for over 2.5 billion shipments of fresh fruits and vegetables, meat, poultry, seafood, eggs, bread, and other items from suppliers to grocery retailers every year. IFCO RPCs ensure a better fresh food supply chain by protecting freshness and quality and lowering costs, food waste and environmental impact compared to single-use packaging.

    About Stonepeak
    Stonepeak is a leading alternative investment firm specializing in infrastructure and real assets with approximately $73 billion of assets under management. Through its investment in defensive, hard-asset businesses globally, Stonepeak aims to create value for its investors and portfolio companies, with a focus on downside protection and strong risk-adjusted returns. Stonepeak, as sponsor of private equity and credit investment vehicles, provides capital, operational support, and committed partnership to grow investments in its target sectors, which include transport and logistics, digital infrastructure, energy and energy transition, and real estate. Stonepeak is headquartered in New York with offices in Houston, Washington, D.C., London, Hong Kong, Seoul, Singapore, Sydney, Tokyo, Abu Dhabi, and Riyadh. For more information, please visit www.stonepeak.com.

    About Triton
    Founded in 1997 and owned by its partners, Triton is a leading European mid-market sector-specialist investor. Triton focuses on investing in businesses that provide mission critical goods and services in its three core sectors of Business Services, Industrial Tech, and Healthcare.

    Triton has over 150 investment professionals and value creation experts across 11 offices and invests through three complementary “All Weather” strategies: Mid-Market Private Equity, Smaller Mid-Cap Private Equity, and Opportunistic Credit.

    About ADIA
    Established in 1976, the Abu Dhabi Investment Authority (“ADIA”) is a globally-diversified investment institution that prudently invests funds on behalf of the Government of Abu Dhabi through a strategy focused on long-term value creation. For more information: https://www.adia.ae

    Contacts

    For IFCO
    Inigo Canalejo
    Vice President, ESG and Strategic Marketing
    media@ifco.com

    For Stonepeak
    Kate Beers / Maya Brounstein
    corporatecomms@stonepeak.com
    +1 (646) 540-5225

    For Triton
    media@triton-partners.com

    Continue Reading

  • Perplexity launches Comet, an AI-powered web browser

    Perplexity launches Comet, an AI-powered web browser

    Perplexity on Wednesday launched its first AI-powered web browser, called Comet, marking the startup’s latest effort to challenge Google Search as the primary avenue people use to find information online.

    At launch, Comet will be available first to subscribers of Perplexity’s $200-per-month Max plan, as well as a small group of invitees that signed up to a waitlist.

    Here’s what a New tab looks like for me on CometImage Credits:Screengrab/Maxwell Zeff / Perplexity

    Comet’s headline feature is Perplexity’s AI search engine, which is pre-installed and set as the default, putting the company’s core product — AI generated summaries of search results — front and center.

    Users can also access Comet Assistant, a new AI agent from Perplexity that lives in the web browser and aims to automate routine tasks. Perplexity says the assistant can summarize emails and calendar events, manage tabs, and navigate web pages on behalf of users. Users can access Comet Assistant by opening a sidecar on any web page, which lets the AI agent see what’s on the web page and answer questions about it.

    Comet Assistant in your email inboxImage Credits:Perplexity

    Perplexity has released several products and initiatives in recent months, but none feel quite as consequential as Comet. The company’s CEO, Aravind Srinivas, has significantly hyped Comet’s launch in particular, perhaps because he sees it as vital in Perplexity’s battle against Google.

    With Comet, Perplexity is aiming to reach users directly without having to go through Google Chrome, the most popular browser currently. While AI-powered browsers present uncharted territory for many users, Google itself seems convinced this is the direction browsers are headed: The Search giant has deployed several AI integrations into Chrome in recent months, not to mention AI mode, an AI search product with a striking resemblance to Perplexity.

    Srinivas said in March that his goal with Comet was to “develop an operating system with which you can do almost everything,” enabling Perplexity’s AI to help users across apps and websites. Becoming the default browser for users can translate to “infinite retention,” Srinivas said in June, which would ostensibly lead to more requests on Perplexity.

    Perplexity’s Comet Assistant can open new tabs for youImage Credits:Perplexity

    That said, Comet is entering a crowded arena. While Google Chrome and Apple’s Safari hold most of the market, The Browser Company launched an AI-powered browser, Dia, in June that seems to offer many of the same features as Comet. OpenAI has also reportedly considered launching its own browser to compete with Google, and has even hired some key members from the original Google Chrome team in the last year.

    Comet could get an initial leg up in the browser wars if a meaningful chunk of Perplexity users sign up for the product. Srinivas recently said that Perplexity saw 780 million queries in May 2025, and that the company’s search products are seeing more than 20% growth month-over-month.

    Taking on Google Search is no small task, but Perplexity seems to have the right idea by launching a browser of its own. But the startup’s team may find it even harder to convince users to switch browsers than weaning them off Google Search.

    Hands on with Comet

    The most unique aspect of this browser seems to be Comet Assistant. During our testing, we found Comet’s AI agent to be surprisingly helpful for simple tasks, but it quickly falls apart when given more complex requests. Using Comet Assistant to its fullest potential also requires you to hand over an uncomfortable level of access to Perplexity.

    My favorite way to use Comet Assistant, so far, is loading it in the sidecar while I’m browsing the web. Perplexity’s on-browser AI agent can automatically see what I’m looking at, so I can simply ask it questions without needing to open a new window or copy and paste text or links. It’s right there, and it always has the context for what I’m looking at.

    Comet Assistant can see your web pageImage Credits:Perplexity

    Comet Assistant was able to answer questions about posts on social media, YouTube videos, and even sentences I just wrote in a Google Doc. I imagine this will streamline workflows for millions of people that are sending screenshots, files, and links to ChatGPT all day.

    Next, I tried getting Comet Assistant to look through my Google Calendar. But before I could do so, I had to give Perplexity significant access to my Google Account — a lot of access. Just look at how long this list is.

    Image Credits:Screengrab/Maxwell Zeff / Perplexity

    I have to say, giving Perplexity permission to view my screen, send emails, look at my contacts, and add events to my Calendar made me a little uneasy. But it seems AI agents need this kind of access to be useful.

    Nevertheless, Comet Assistant did a reasonably good job looking through my Calendar. It notified me about some upcoming events, and offered me some advice on when to leave my home, and how to navigate public transit, to get to those events.

    The assistant was also able to summarize emails I received that morning from noteworthy senders — in my case, important startups and tech companies with upcoming news. I’ve found that AI agents have a very difficult time parsing through what’s important in an email inbox, but Comet Assistant fared pretty well.

    But Comet Assistant fails at more complicated tasks. For example, I tried asking it to help me find a long-term parking spot at San Francisco’s airport for an upcoming trip, specifically places with good reviews that cost less than $15 a day.

    The assistant offered up several options that seemed to fit the criteria, so I asked it to book me a spot at one of the locations for the dates I’d be away. The agent navigated the parking lot’s website for me, entered in dates, and even some of my information, then asked me to review what it did and check out.

    Turns out, Comet Assistant hallucinated and entered completely wrong dates, later telling me that the dates I wanted were booked, but still wanted to have me complete the check-out anyways. I had to tell the AI agent that the dates were non-negotiable, and asked it to find another location. It ran into the same problem again.

    AI agents that mess up key details like this are not new. My experience with OpenAI’s agent, Operator, and Perplexity’s previous shopping agent yielded similar results. Clearly, hallucinations stand in the way of these products becoming real tools. Until AI companies can solve them, AI agents will still be a novelty for complex tasks.

    Nevertheless, Comet does seem to offer some new capabilities that may just give Perplexity a leg up over the competition in the modern browser wars.

    Continue Reading

  • Thierno Barry: Everton sign Villarreal striker for £27m

    Thierno Barry: Everton sign Villarreal striker for £27m

    Everton have completed the signing of Thierno Barry from Villarreal for £27m.

    The France Under-21 striker has signed a four-year contract with the Toffees until the end of June 2029.

    Barry had a £34.5m release clause in his Villarreal contract, but Everton negotiated a lower fee for the 22-year-old, who scored 11 goals and provided four assists in 38 games last season as the Spanish club finished fifth in La Liga to qualify for the Champions League.

    He will add to Everton’s attacking resources after Dominic Calvert-Lewin left at the end of his contract.

    “I’m very happy,” Barry told Evertontv. “It’s very exciting to be here.

    “Everton is a big club in the Premier League. They have a good history and good players have played here, like Wayne Rooney and Romelu Lukaku.

    “When I was young, I liked to watch these players, now I want to do like these players who have gone before.”

    Forward Armando Broja also exited when his loan ended, returning to Chelsea without the deal being made permanent.

    Barry was born in Lyon and left French club Sochaux aged 19 to play in the Belgian second division with Beveren.

    The following season, he moved to Swiss Super League club Basel, before joining Villarreal in August 2024 in a deal worth about £13m.

    Continue Reading

  • Black holes could act as cosmic supercolliders – Physics World

    Black holes could act as cosmic supercolliders – Physics World






    Black holes could act as cosmic supercolliders – Physics World


















    Skip to main content



    Discover more from Physics World


    Copyright © 2025 by IOP Publishing Ltd and individual contributors

    Continue Reading

  • 8-year-old with rare, fatal disease shows dramatic improvement on experimental treatment

    8-year-old with rare, fatal disease shows dramatic improvement on experimental treatment

    The 8-year-old boy declined rapidly over only a few months. In August 2023, he was running and playing soccer, but by September, involuntary muscle contractions took hold of both his ankles. By October, he’d lost the ability to run and play sports, and by late November, he fell down frequently enough that physical therapists advised his family to get him a wheelchair.

    Genetic testing confirmed the cause of the child’s sudden deterioration: He carried two mutant copies of a gene called HPDL. The HPDL protein helps make an antioxidant, called coenzyme Q10, that is critical to the functioning of mitochondria, the powerhouses of cells.

    Continue Reading

  • Research finds 18-million-year-old enamel proteins in mammal fossils — Harvard Gazette

    Research finds 18-million-year-old enamel proteins in mammal fossils — Harvard Gazette

    Proteins degrade over time, making their history hard to study. But new research has uncovered ancient proteins in the enamel of the teeth of 18-million-year-old fossilized mammals from Kenya’s Rift Valley, opening a window into how these animals lived and evolved.

    In their new paper in Nature, researchers from Harvard and the Smithsonian Museum Conservation Institute  discuss their findings.

    “Teeth are rocks in our mouths,” explained Daniel Green, field program director in the Department of Human Evolutionary Biology and the paper’s lead author. “They’re the hardest structures that any animals make, so you can find a tooth that is a hundred or a hundred million years old, and it will contain a geochemical record of the life of the animal.”

    That includes what the animal ate and drank, as well as its environment.

    “In the past, we thought that mature enamel, the hardest part of teeth, should really have very few proteins in it at all,” said Green. However, utilizing a newer proteomics technique called liquid chromatography tandem mass spectrometry, the team was able to detect “a great diversity of proteins … in different biological tissues.”

    “The technique involves several stages where peptides are separated based on their size or chemistry so that they can be sequentially analyzed at higher resolutions than was possible with previous methods,” explained Kevin T. Uno, associate professor in HEB and one of the paper’s corresponding authors.

    “We and other scholars recently found that there are dozens — if not even hundreds — of different kinds of proteins present inside tooth enamel,” said Green.

    With the realization that many proteins are found in contemporary teeth, the researchers turned to fossils, collaborating with the Smithsonian and the National Museum of Kenya for access to fossilized teeth, particularly those of early elephants and rhinos.

    Formed approximately 16 million years ago, the Buluk site in Kenya is found in one of the most remote and inhospitable places in the rift, but has yielded an extraordinary diversity of fossil fauna.

    Photo by Ellen Miller

    As herbivores, they had large teeth to grind the plants that made up their diets. These mammals, Green said, “can have enamel two to three millimeters thick. It was a lot of material to work with.”

    What they found — peptide fragments, chains of amino acids, that together form proteins as old as 18 million years — was “field-changing,” according to Green.

    “Nobody’s ever found peptide fragments that are this old before,” he said, calling the findings “kind of shocking.”

    Until now, the oldest prior findings were put at about 3.5 million years old, he said.

    “With the help of our colleague Tim Cleland, a superb paleoproteomicist at the Smithsonian, we’re pushing back the age of peptide fragments by five or six times what was known before.”

    The newly discovered peptides cover a range of proteins that perform different functions, altogether known as the proteome, Green said.

    “One of the reasons that we’re excited about these ancient teeth is that we don’t have the full proteome of all proteins that could have been found inside the bodies of these ancient elephants or rhinoceros, but we do have a group of them.”

    With such a collection, “There might be more information available from a group of them than just one protein by itself.”

    This research “opens new frontiers in paleobiology, allowing scientists to go beyond bones and morphology to reconstruct the molecular and physiological traits of extinct animals and hominins,” said Emmanuel K. Ndiema, senior research scientist at the National Museum of Kenya and paper co-author. “This provides direct evidence of evolutionary relationships. Combined with other characteristics of teeth, we can infer dietary adaptations, disease profiles, and even age at death — insights that were previously inaccessible.”

    In addition to shedding light on the lives of these creatures, it helps place them in history.

    “We can use these peptide fragments to explore the relationships between ancient animals, similar to how modern DNA in humans is used to identify how people are related to one another,” Uno said.

    “Even if an animal is completely extinct — and we have some animals that we analyze in our study who have no living descendants — you can still, in theory, extract proteins from their teeth and try to place them on a phylogenetic tree,” said Green.

    Such information “might be able to resolve longstanding debates between paleontologists about what other mammalian lineages these animals are related to using molecular evidence.”

    Although this research began as “a small side project” of a much larger project involving dozens of institutions and researchers from around the world, said Green, “We were surprised at just how much we found. There really are a lot of proteins preserved in these teeth.”


    This research was partially funded by the National Science Foundation and Smithsonian’s Museum Conservation Institute.


    Continue Reading

  • New Research Questions Severity of Withdrawal From Antidepressants – The New York Times

    1. New Research Questions Severity of Withdrawal From Antidepressants  The New York Times
    2. Largest review of antidepressants to date finds most people do not experience severe withdrawal  Medical Xpress
    3. 5 Ways to Stop Antidepressants Safely  Everyday Health
    4. Antidepressant withdrawal: new review downplays symptoms but misses the mark for long-term use  The Conversation
    5. Getting off antidepressants isn’t as risky as is widely believed, review suggests  STAT

    Continue Reading

  • Owen signs new Brentford deal | Brentford FC

    Owen signs new Brentford deal | Brentford FC

    Brentford B midfielder Riley Owen has put pen to paper on a new deal with the club, signing on until at least the summer of 2026.

    Across 40 matches last season, he played 90 minutes in 28 of them, becoming a reliable presence in the heart of the midfield. Often operating in a deeper role, his calmness in possession and ability to progress play under pressure stood out.

    And it’s been a steady rise for Owen since signing with the club after a successful trial period in August 2023, with the midfielder enjoying back-to-back strong seasons under former Brentford B head coach Neil MacFarlane’s leadership.

    Brentford technical director Lee Dykes said: “Riley is a player with a high technical level and has the ability to influence games from midfield.

    “He has excelled in the B team, and we believe we can help him develop to another level over the next few years.”

    Having signed a contract extension, Owen sees the decision as a reflection of his development so far and a platform for what’s to come.

    “I’ve grown a lot since I joined the club,” he said. “I want that to continue, wherever and whatever that looks like. I’m just focused on giving my all and making the most of whatever comes next.

    “I played most of the games and was one of the main players in midfield.

    “We had hoped to win the Premier League Cup as well as the U21 PDL title, but overall, it was a good season, for the team and for me personally, so I’m very happy about it.”

    Trusted with responsibility in the centre of the pitch, he formed a solid partnership with team-mate Ethan Brierley, who completed a season-long loan deal to Exeter City in June, with both players taking on key roles across the campaign.

    “We worked well together, me and Ethan,” he added. “I’m really pleased for him that he’s out on loan now and getting the chance to show what he can do. We both took on a lot in midfield and had real trust in each other.

    “I’m happy for all the boys who’ve gone out on loan – these are good opportunities and I know they’ll take them.

    “For me, I’m just focused on continuing to grow, whether that’s training more with the first team, going on loan, or developing further here with the B team.”

    Continue Reading

  • Tomato genes point to new medicines

    Tomato genes point to new medicines

    COLD SPRING HARBOR, N.Y., July 9, 2025 /PRNewswire/ — Picture juicy red tomatoes on the vine. What do you see? Some tomato varieties have straight vines. Others are branched. The question is why. New research from Cold Spring Harbor Laboratory (CSHL) provides the strongest evidence to date that the answer lies in what are called cryptic mutations. The findings have implications for agriculture and medicine, as they could help scientists fine-tune plant breeding techniques and clinical therapeutics.

    Cryptic mutations are differences in DNA that don’t affect physical traits unless certain other genetic changes occur at the same time. CSHL Professor & HHMI Investigator Zachary Lippman has been researching cryptic mutations’ effects on plant traits alongside CSHL Associate Professor David McCandlish and Weizmann Institute Professor Yuval Eshed. Their latest study, published in Nature, reveals how interactions between cryptic mutations can increase or decrease the number of reproductive branches on tomato plants. Such changes result in more or fewer fruits, seeds, and flowers. The interactions in question involve genes known as paralogs.

    “Paralogs emerge across evolution through gene duplication and are major features of genetic networks,” Lippman explains. “We know paralogs can buffer against each other to prevent gene mutations from affecting traits. Here, we found that collections of natural and engineered cryptic mutations in two pairs of paralogs can impact tomato branching in myriad ways.”

    One crucial component of the project was the pan-genome Lippman and colleagues completed for Solanum plants around the globe, including cultivated and wild tomato species. Where genomes typically encompass one species, pan-genomes capture DNA sequences and traits across many species. The pan-genome pointed Lippman’s lab toward natural cryptic mutations in key genes controlling branching. Lippman lab postdoc Sophia Zebell then engineered other cryptic mutations using CRISPR. That enabled Lippman’s lab to count the branches on more than 35,000 flower clusters with 216 combinations of gene mutations. From there, McCandlish lab postdoc Carlos Martí-Gómez used computer models to predict how interactions between specific combinations of mutations in the plants would change the number of branches.

    “We can now engineer cryptic mutations in tomatoes and other crops to modify important agricultural traits, like yield,” Lippman says.

    Additionally, the kind of modeling done here could have many other applications. McCandlish explains: “When making mutations or using a drug that mimics the effects of a mutation, you often see side effects. By being able to map them out, you can choose the manner of controlling your trait of interest that has the least undesirable side effects.”

    In other words, this research points not only to better crops but also better medicines. So, you see tomatoes? Science sees tomorrow.

    About Cold Spring Harbor Laboratory
    Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,000 people including 600 scientists, students and technicians. For more information, visit www.cshl.edu.

    SOURCE Cold Spring Harbor Laboratory

    Continue Reading