Wednesday, June 07, 2023

Older trees accumulate more mutations than their younger counterparts

A study demonstrated that long-lived tropical trees accumulate more somatic mutations, providing insights into potential mechanisms underlying genetic variation.

Peer-Reviewed Publication

ELIFE

A study of the relationship between the growth rate of tropical trees and the frequency of genetic mutations they accumulate suggests that older, long-lived trees play a greater role in generating and maintaining genetic diversity than short-lived trees.

The study, published today as a Reviewed Preprint in eLife, provides what the editors describe as compelling evidence that tree species acquire mutations at a similar yearly rate, independent of cell division and regardless of their growth rate.

The findings may be used to inform ecosystem conservation strategies, particularly in the tropical forests of southeast Asia, which are under threat from climate change and deforestation.

“Biodiversity ultimately results from mutations that provide genetic variation for organisms to adapt to their environment,” explains co-lead author Akiko Satake, a Professor in the Department of Biology, Faculty of Science, Kyushu University, Japan. “However, how and when these mutations occur in natural environments is poorly understood.”

Somatic mutations are spontaneous changes in an organism’s DNA that occur during its lifespan. They can arise due to external factors such as ultraviolet radiation, or internal factors such as DNA replication errors. It is not clear which of these factors causes mutations more frequently, particularly in tropical ecosystems and trees, which are not as well characterised as their more temperate counterparts.

To understand this better, Satake and colleagues examined the rates and patterns of somatic mutations in two species of tropical trees native to central Borneo, Indonesia: the slow-growing Shorea laevis (S. laevis), and the fast-growing S. leprosula. The species S. leprosula grows more than three times faster than S. laevis.

Comparing the somatic mutations of the two tree species allowed the team to gain insights into the impact of growth rate on the accumulation of these mutations, and its potential role in driving evolution and species diversity. They collected seven DNA samples from the leaves at the highest level of the tree branches, as well as samples from the trunk of each tree, totalling 32 samples. The length and diameter of the trees at breast height was used to determine the average age of each species in the sampling area. S. laevis trees were on average 256 years old, whereas S. leprosula trees were on average 66 years old.

To identify the mutations present, the team constructed a reference genetic dataset for each tree species, using the DNA collected from the leaves. The genome sequence was determined using a technique called long-read PacBio RS II and short-read Illumina sequencing. The team extracted DNA twice from each sample, allowing them to pinpoint single nucleotide variants (SNVs) within the same individual by identifying those that were identical between the two samples. The majority of mutations were found to be present within a single tree branch. However, some mutations were found across multiple branches, implying that they had been transmitted between branches at some point during the tree’s growth.

In both species, the team noticed a linear increase in the number of mutations with physical distance between branches. The rate of mutations per metre was on average 3.7 times greater in the slow-growing S. leavis than in the fast-growing S. leprosula, suggesting that slow-growing trees accumulate more somatic mutations. However, when accounting for the differences in growth rates, and calculating the rate of mutations per year, the two species had equal rates. This finding suggests that somatic mutations accumulate in a clock-like manner as a tree ages, independent of DNA replication and growth rate.

“We also found that somatic mutations are neutral within an individual – that is, they are neither beneficial nor detrimental to survival. However, those mutations transmitted to the next generation are subject to strong natural selection during seed germination and growth,” says co-lead author Ryosuke Imai, Post-doctoral Fellow in the Department of Biology, Faculty of Science, Kyushu University. “This suggests that somatic mutations accumulate with time, and older trees contribute more towards generating genetic variation and adaptation to their environment, thereby increasing the chances of their species’ survival.”

Imai and colleagues encourage further research into this area. In particular, they say that mathematical modelling would be required to consider the asymmetric division of cells during elongation and branching in order to further validate the findings.

“In trees, somatic mutations can be transmitted to seeds, resulting in rich genetic variations within subsequent generations,” states one of the author Masahiro Kasahara, Associate Professor in the department of computational biology and medical sciences, the University of Tokyo, Japan. “As the tropical rainforests of southeast Asia face the threats of climate change and deforestation, our study suggests that long-lived trees may play a crucial role in maintaining and increasing the genetic variation of these tropical systems.”

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About eLife

eLife transforms research communication to create a future where a diverse, global community of scientists and researchers produces open and trusted results for the benefit of all. Independent, not-for-profit and supported by funders, we improve the way science is practised and shared. From the research we publish, to the tools we build, to the people we work with, we’ve earned a reputation for quality, integrity and the flexibility to bring about real change. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

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JOURNAL

eLife

DOI

10.7554/eLife.88456.1

ARTICLE TITLE

The molecular clock in long-lived tropical trees is independent of growth rate

ARTICLE PUBLICATION DATE

6-Jun-2023

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Developing countries need greater recognition for research into UN Sustainable Development Goals (SDGs)

Reports and Proceedings

DIGITAL SCIENCE

White paper cover — IMAGE: THE WHITE PAPER "RESEARCH IN THE CONTEXT OF THE UNITED NATIONS SUSTAINABLE DEVELOPMENT GOALS IN THE DEVELOPED AND DEVELOPING WORLD: EVIDENCE FROM THE PAST 15 YEARS" HAS BEEN PRESENTED AT THE 2023 GLOBAL SUSTAINABLE DEVELOPMENT CONGRESS. view more
CREDIT: TIMES HIGHER EDUCATION/DIGITAL SCIENCE/PRINCE SULTAN UNIVERSITY.

Developing nations need greater visibility, acknowledgement and support for their research into the United Nations’ Sustainable Development Goals (SDGs), according to the authors of a major analysis of the past 15 years of worldwide research into SDGs.

The analysis – the most comprehensive of its kind to date – has formed the basis of a new White Paper, which calls for equity for developing nations within the world’s research ecosystem, particularly as those nations are often hardest hit by the issues the UN’s Global Goals are aimed at addressing.

Announced at the recent Global Sustainable Development Congress run by the Times Higher Education (THE), the white paper has been co-authored by researchers from Prince Sultan University, data experts from research technology company Digital Science, and THE.

Commissioned by THE, and using data from Dimensions, the white paper – Research in the Context of the United Nations Sustainable Development Goals in the Developed and Developing World: Evidence From the Past 15 Years – reveals significant gaps in research funding, collaboration and assessment between developed and developing countries.

The white paper unveils the unique challenges confronting lower income countries in attaining visibility and acknowledgment for their contributions towards the SDGs. The authors have sought to redress this imbalance through a series of recommendations, including:

Targeted interventions to support lower-income countries, promote research infrastructure, and provide funding opportunities to bolster their research capacities and collaborations.
Continued use of THE Impact Rankings to help address global inequalities and promote strong SDG partnerships between regions.
Use of comprehensive and (if needed) bespoke metrics that capture the multidimensional aspects of research impact aligned with the SDGs, to provide valuable insights and guide policy-making and funding decisions.
Incentives at local and international levels to accelerate SDG research and research collaboration between high-income and lower-income countries, to help uplift scholars from countries that suffer from structural, historical and contemporary imbalances of power in the global research ecosystem.

Co-author Ann Campbell, Technical Solutions Manager – Dimensions & Altmetric, Digital Science says: “Our analysis shows there is a significant gap between higher and lower income nations in relation to SDG research. We can see evidence of growing SDG research in lower income nations over the past 15 years and indeed rising international collaboration within these regions, however, the playing field is far from level. It is encouraging to see that with further collaboration from all sides, it is possible to create a more equitable research landscape, one in which research from lower income countries is both valued and acknowledged for its crucial role in addressing global challenges and advancing the SDGs.”

Co-author Professor Mohammad Nurunnabi, Director of the Center for Sustainability and Climate, Prince Sultan University says: “The SDGs cannot be achieved without the effective involvement of the higher education sector. Policymakers should come together to provide more guidelines to address the gap of research which could be a catalyst to solve many global issues and challenges. Prince Sultan University is strongly committed to this and hence the white paper series could be an eye opener for policymakers.”

Co-author Dr Ishan Cader, Director of Consultancy, THE says: “At the moment, scholars from developing countries are massively under-represented in the global research discourse on sustainability and they suffer from a lack of visibility and promotion. I believe that universities and governments have a moral and ethical duty to ensure that research from the developing world is promoted and funded.”

Phil Baty, Chief Global Affairs Officer, THE says: “University research is absolutely fundamental to achieving the UN’s Sustainable Development Goals – and that research needs to be highly collaborative, crossing borders and transcending geopolitics. Most importantly, we need to tap into expertise and research leadership right across the world – from the global north and the global south, which is on the front-line of our most pressing threats, like the climate crisis.”

Research in the Context of the United Nations Sustainable Development Goals in the Developed and Developing World: Evidence From the Past 15 Years is available on the website of the 2023 Global Sustainable Development Congress.

White paper authors: Professor Mohammad Nurunnabi (Prince Sultan University), Dr Sanjida Haque (Prince Sultan University), Ms Ann Campbell (Digital Science), Dr Juergen Wastl (Digital Science), Dr Ishan Cader (Times Higher Education).

Figure 1 and Figure 2 from the white paper: Research grants by year, organized by country income. Source: Dimensions.

CREDIT

Times Higher Education/Digital Science/Prince Sultan University.

About Prince Sultan University

Prince Sultan University (PSU) is the first private non-profit institution in Saudi Arabia. The Center for Sustainability and Climate (CSC) of Prince Sultan University is committed to the United Nations Sustainable Development Goals (SDGs) through effective institutional resources management, innovative teaching and learning, research, national and international partnerships, continuous studies, and outreach.

The mission is to support Saudi Arabia’s Vision 2030 and the PSU’s strategic directions, transforming commitments into action and building a decarbonized, more sustainable world, driving technological and economic transformations to realize sustainable competitive advantage. To coordinate, promote, and accelerate interdisciplinary research and training on sustainability and climate, and the role of humans in the environment. Prince Sultan University is the First Saudi University to Pledge Net Zero Carbon University by 2060.

About Digital Science

Digital Science is a technology company working to make research more efficient. We invest in, nurture and support innovative businesses and technologies that make all parts of the research process more open and effective. Our portfolio includes admired brands including Altmetric, Dimensions, Figshare, ReadCube, Symplectic, IFI CLAIMS Patent Services, Overleaf, Ripeta, Writefull, and metaphacts. We believe that together, we can help researchers make a difference. Visit www.digital-science.com and follow @digitalsci on Twitter or on LinkedIn.

About Dimensions

Part of Digital Science, Dimensions is the largest linked research database and data infrastructure provider, re-imagining research discovery with access to grants, publications, clinical trials, patents and policy documents all in one place. www.dimensions.ai

About Times Higher Education

We are THE, the trusted global data partner for higher education. Drawing on five decades of expertise in the sector, millions of individual data points and with more unique institutions participating in our flagship university rankings than any other, we offer deeper and richer insight into university performance than anyone else. From powerful data-driven insights and strategic consultancy support to agenda-setting events and hiring solutions, our products and services enable everyone in higher education to make smarter, more informed decisions.   

For more information, visit timeshighereducation.com or find us on Twitter: @timeshighered @THEworldunirank and @THEuniadvice

Media contacts

Simon Linacre, Head of Content, Brand & Press, Digital Science: Mobile: +44 7484 381477, s.linacre@digital-science.com

David Ellis, Press, PR & Social Manager, Digital Science, Mobile +61 447 783 023: d.ellis@digital-science.com

For more information, or to request an interview with Ishan or Phil, please contact Ben Miller: communications@timeshighereducation.com or ben.miller@timeshighereducation.com

The University of Manchester lead innovation in clean hydrogen production

Business Announcement

UNIVERSITY OF MANCHESTER

A new technology that offers a cost-effective way to produce synthetic gas and pure hydrogen with nearly zero direct carbon dioxide emissions will be developed and delopyed by an international team of scientists, led by The University of Manchester.

The RECYCLE (REthinking low Carbon hYdrogen production by Chemical Looping rEforming) project will construct and test a fully integrated innovative hydrogen production pilot unit based at the University.

The technology uses special reactors called fixed bed reactors to convert different materials into hydrogen gas. The process also effectively captures and separates carbon dioxide.

It offers a competitive solution for the production of low carbon hydrogen using both natural gas, biobased streams and waste materials to provide low cost hydrogen.

The £5.1 million collaborative project is funded by the Department for Energy Security and Net Zero as part of the Net Zero Innovation Portfolio (NZIP), and involves five world-leading industrial partners in the area of engineering for sustainable development, including: Johnson Matthey, TotalEnergies OneTech, Kent, Helical Energy and Element Energy.

Dr Vincenzo Spallina, Senior Lecturer at The University of Manchester and Principal Investigator of the RECYCLE project, said: “The feasibility study carried out during Phase 1 demonstrated great potential for low carbon hydrogen in the UK market and it has huge implications for several industrial stakeholders.

“This project will demonstrate its feasibility at a pre-commercial scale to increase awareness of the next steps towards commercial implementation. The demonstration plant will be installed in the James Chadwick Building where we are currently renovating the existing pilot hall area to establish the Sustainable Industrial Hub for Research and Innovation on sustainable process technologies.

“Our students will have the fantastic opportunity to see the next-generation hydrogen plant in operation as a unique teaching and learning experience.”

Professor Alice Larkin, Head of the School of Engineering at The University of Manchester, added: “Our University is committed to achieving zero carbon emissions by 2038 as part of its Environmental Sustainability Strategy and supported by activity through our Advanced Materials and Energy research beacons.

“This collaborative project will boost the prestige of our academic community to secure clean and sustainable development through Science and Innovation in close partnerships with industries.”

In the recently published Powering Up Britain: Energy Security Plan, the UK government expects to have two gigawatts of low-carbon hydrogen production capacity in operation or construction by 2025 and 10 gigawatts in 2030, subject to affordability and value for money.

The RECYCLE project represents an opportunity to to show continued innovation in the development of resilient and cost effective solutions for a low carbon future.

Minister for Energy Efficiency and Green Finance Lord Callanan said: “Hydrogen, known as the super fuel of the future, is critical to delivering UK energy security and clean, sustainable growth. “I’m delighted that we have awarded funding to The University of Manchester so that they can build and test their first-of-a-kind hydrogen technology. This will generate opportunities for UK businesses to export their expertise around the world whilst supporting our ambition to have amongst the cheapest energy in Europe.”

The final demonstration of the project is planned for the second half of 2024 in the pilot area of the James Chadwick Building at The University of Manchester.

Electrical synapses in the neural network of insects found to have unexpected role in controlling flight power

Researchers of Mainz University and Humboldt-Universität zu Berlin revealed previously unknown function of electrical synapses, thus deciphering the neural circuit used to regulate insect wingbeat frequency

Peer-Reviewed Publication

JOHANNES GUTENBERG UNIVERSITAET MAINZ

A team of experimental neurobiologists at Johannes Gutenberg University Mainz (JGU) and theoretical biologists at Humboldt-Universität zu Berlin has managed to solve a mystery that has been baffling scientists for decades. They have been able to determine the nature of the electrical activity in the nervous system of insects that controls their flight. In a paper recently published in Nature, they report on a previously unknown function of electrical synapses employed by fruit flies during flight.

The fruit fly Drosophila melanogaster beats its wings around 200 times per second in order to move forward. Other small insects manage even 1,000 wingbeats per second. It is this high frequency of wingbeats that generates the annoying high-pitched buzzing sound we commonly associate with mosquitoes. Every insect has to beat its wings at a certain frequency to not get “stuck” in the air, which acts as a viscous medium due to their small body size. For this purpose, they employ a clever strategy that is widely used in the insect world. This involves reciprocal stretch activation of the antagonistic muscles that raise and depress the wings. The system can oscillate at high frequencies, thus producing the high rate of wingbeats required for propulsion. The motor neurons are unable to keep pace with the speed of the wings so that each neuron generates an electrical pulse that controls the wing muscles only about every 20th wingbeat. These pulses are precisely coordinated with the activity of other neurons. Special activity patterns are generated in the motor neurons that regulate the wingbeat frequency. Each neuron fires at a regular rate but not at the same time as the other neurons. There are fixed intervals between which each of them fires. While it has been known since the 1970s that neural activity patterns of this kind occur in the fruit fly, there was no explanation of the underlying controlling mechanism.

Neural circuit regulates insect flight

Collaborating in the RobustCircuit Research Unit 5289 funded by the German Research Foundation, researchers at Johannes Gutenberg University Mainz and Humboldt-Universität zu Berlin have finally managed to find the solution to the puzzle. "Wing movement in the fruit fly Drosophila melanogaster is governed by a miniaturized circuit solution that comprises only a very few neurons and synapses," explained Professor Carsten Duch of JGU's Faculty of Biology. And it is extremely probable that this is not just the case in the fruit fly. The researchers presume that the more than 600,000 known species of insects that rely on a similar method of propulsion also employ a neural circuit of this kind.

Drosophila melanogaster is the ideal subject for research in the field of neurobiology as it is possible to genetically manipulate the various components of its neural circuit. Individual synapses can be switched on and off and even the activity of individual neurons can be directly influenced, to name just two examples. In this case, the researchers used a combination of these genetic tools to measure the activity and electrical properties of the neurons in the circuit. Thus they were able to identify all the cells and synaptic interactions of the neural circuit that are involved in the generation of flight patterns. As a result, they found that the neural network regulating flight is composed of just a small number of neurons that communicate with each other through electrical synapses only.

New concepts of information processing by the central nervous system

It had previously been assumed that when one neuron fired, inhibitory neurotransmitter substances were released between neurons of the flight network, thus preventing these from firing at the same time. Using experimentation and mathematical modeling, the researchers have been able to show that such a sequential distribution of pulse generation can also occur when neural activity is directly controlled electrically, without the presence of neurotransmitters. The neurons then create a special kind of pulse and 'listen' closely to each other, especially if they have just been active.

Mathematical analyses predicted that this would not be possible with "normal" pulses. Hence, it would appear unlikely that transmission between neurons in a purely electrical form would result in this sequenced firing pattern. In order to test this theoretical hypothesis experimentally, certain ion channels in the neurons of the network were manipulated. As expected, the activity pattern of the flight circuit became synchronized – just as the mathematical model had predicted. This experimental manipulation caused significant variations in the power generated during flight. It is thus apparent that the desynchronization of the activity pattern determined by the electrical synapses of the neural circuit is necessary to ensure that the flight muscles are able to generate a consistent power output.

The findings of the team based in Mainz and Berlin are particularly surprising given that it was previously thought that interconnections by electrical synapses actually result in a synchronized activity of neurons. The activity pattern generated by the electrical synapses detected here indicates that there may well be forms of information processing by the nervous system that are as yet unexplained. The same mechanism may not only play a role in thousands of other insect species but also in the human brain, where the purpose of electrical synapses is still not fully understood.