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First ever ‘pioneer’ factor found in plants enables cells to change their fate

To start the process of unpacking tightly bundled genetic material, plants depend on the LEAFY pioneer protein, according to work

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To start the process of unpacking tightly bundled genetic material, plants depend on the LEAFY pioneer protein, according to work led by biologist Doris Wagner

Cells don’t express all the genes they contain all the time. The portion of our genome that encodes eye color, for example, doesn’t need to be turned on in liver cells. In plants, genes encoding the structure of a flower can be turned off in cells that will form a leaf.

These unneeded genes are kept from becoming active by being stowed in dense chromatin, a tightly packed bundle of genetic material laced with proteins.

In a new study in the journal Nature Communications, biologists from the University of Pennsylvania identify a protein that enables plant cells to reach these otherwise inaccessible genes in order to switch between different identities. Called a “pioneer transcription factor,” the LEAFY protein gets a foothold in particular portions of the chromatin bundle, loosening the structure and recruiting other proteins that eventually allow genes to first be transcribed into RNA and then translated into proteins.

“The programs that are not needed in a given cell or tissue or condition are effectively shut off by various chromatin modifications that make them very inaccessible,” says biologist Doris Wagner of the School of Arts & Sciences, senior author on the work. “The question has always been, How do you go from shut to open? We found that LEAFY, this protein that we already knew was important in reprogramming plant cells, is one of these pioneer transcription factors that get a foot in the door, as it were, to alter the program of cells.”

Pioneer transcription factors were first characterized by Penn faculty member Kenneth Zaret of the Perelman School of Medicine, whose own work has examined these regulatory proteins in animals, such as in the context of liver development. Early in her time at Penn, Wagner heard Zaret give a talk about his work in this area and grew curious about looking for similar factors in plants, given that flexible gene expression is so critical to their survival.

Indeed, plants must switch between expressing whole sets of different genes all the time. In rich soils, they may grow more branches to get bigger, while in a drought they may express more genes associated with developing flowers, so they can set seed and reproduce before they succumb.

How plant cells determine their identity and fate has been a focus of Wagner’s work since the start of her career, and so has LEAFY. During her postdoc days, Wagner showed that LEAFY could reprogram root cells to produce flowers. “That gave us a good clue that LEAFY might have this ‘pioneer’ activity, but we had to look more closely to prove it,” she says.

To do so, Wagner and colleagues first used isolated protein and strands of genetic material to show that LEAFY, though not other transcription factors, bound to nucleosomes, subunits of chromatin where DNA spools on a cluster of proteins called histones. Specifically, the binding occurred at the gene AP1, which is known to be activated by LEAFY to prompt plants to make flowers.

To confirm that this connection was true in a living organism, the researchers took plant roots and applied a compound that causes them to flower spontaneously. When flowering, they found that not only did LEAFY bind strongly to AP1 but that the binding site was also occupied by a histone. “This tells us that the histones and LEAFY are really occupying the same portion of DNA,” Wagner says.

Furthermore, they showed that chromatin structure began to open up at the AP1 region when LEAFY was activated, a key facet of what pioneer transcription factors do. This opening was limited, and full loosening of chromatin took days. What did happen quickly, the researchers found, was that LEAFY displaced a linker histone protein, creating a small local opening that also allowed other transcription factors to nose their way into the DNA.

Though pioneer transcription factors had been proposed to exist in plants, the new work provides the first concrete support backing this conception for LEAFY. And Wagner believes there are others. “If necessary, plants can alter their entire body plan or generate an entire plant from a little piece of leaf,” she says. “We predict setting this in motion will require pioneer transcription factors. So plants may actually have more of these factors than animals.”

In upcoming work, she and her team hope to delve more deeply into the processes that precede and follow this “pioneering” activity of LEAFY: Does anything restrict its activity and how do the other factors that it recruits fully unpack the hidden-away genes? “It would be great to find out both sides of this equation,” Wagner says.

The findings have significance in agriculture and breeding, where LEAFY is already manipulated to encourage earlier flowering, for example. And as more is understood about pioneer transcription factors in plants, Wagner can envision a fine tuning of other aspects of plant growth and activity, which could be leveraged to help crops adapt to new environmental conditions, such as those being ushered in by climate change.

###

Doris Wagner is the Robert I. Williams Term Professor of Biology in the University of Pennsylvania School of Arts & Sciences.

Wagner’s coauthors are gradute students Run Jin and Samantha Klasfeld, postdocs Yang Zhu and Jun Xiao, former graduate student Soon-Ki Han, undergraduate Adam Konkol of Penn’s School of Arts & Sciences, and former Zaret lab graduate student Meilin Fernandez Garcia of Penn’s Perlman School of Medicine.

This research was funded by the National Science Foundation Division of Integrated Organismal Systems (grants 1557529 and 1905062).

https://penntoday.upenn.edu/news/first-ever-pioneer-factor-found-plants-enables-cells-change-their-fate

In a new study in the journal Nature Communications, biologists from the University of Pennsylvania identify a protein that enables plant cells to reach these otherwise inaccessible genes in order to switch between different identities. Called a “pioneer transcription factor,” the LEAFY protein gets a foothold in particular portions of the chromatin bundle, loosening the structure and recruiting other proteins that eventually allow genes to first be transcribed into RNA and then translated into proteins.

Source: https://bioengineer.org/first-ever-pioneer-factor-found-in-plants-enables-cells-to-change-their-fate/

first-ever-‘pioneer’-factor-found-in-plants-enables-cells-to-change-their-fate

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Diving into devonian seas: Ancient marine faunas unlock secrets of warming oceans

Credit: Syracuse University Members of Syracuse University’s College of Arts and Sciences are shining new light on an enduring mystery–one

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Members of Syracuse University’s College of Arts and Sciences are shining new light on an enduring mystery–one that is millions of years in the making.

A team of paleontologists led by Professor Cathryn Newton has increased scientists’ understanding of whether Devonian marine faunas, whose fossils are lodged in a unit of bedrock in Central New York known as the Hamilton Group, were stable for millions of years before succumbing to waves of extinctions.

Drawing on 15 years of quantitative analysis with fellow professor Jim Brower (who died in 2018), Newton has continued to probe the structure of these ancient fossil communities, among the most renowned on Earth.

The group’s findings, reported by the Geological Society of America (GSA), provide critical new evidence for the unusual, long-term stability of these Devonian period communities.

Such persistence, Newton says, is a longstanding scientific enigma. She and her colleagues tested the hypothesis that these ancient communities displayed coordinated stasis–a theory that attempts to explain the emergence and disappearance of species across geologic time.

Newton and Brower, along with their student Willis Newman G’93, found that Devonian marine communities vary more in species composition than the theory predicts. Newton points out that they sought not to disprove coordinated stasis but rather to gain a more sophisticated understanding of when it is applicable. “Discovering more about the dynamics of these apparently stable Devonian communities is critical,” she says. “Such knowledge has immediate significance for marine community changes in our rapidly warming seas.”

Since geologist James Hall Jr. first published a series of volumes on the region’s Devonian fossils and strata in the 1840s, the Hamilton Group has become a magnet for research scientists and amateur collectors alike. Today, Central New York is frequently used to test new ideas about large-scale changes in Earth’s organisms and environments.

During Middle Devonian time (approximately 380-390 million years ago), the faunal composition of the region changed little over 4-6 million years. “It’s a significant amount for marine invertebrate communities to remain stable, or ‘locked,’” explains Newton, a professor in the Department of Earth and Environmental Sciences.

She, Brower and student researchers spent years examining eight communities of animals that once dwelled in a warm, shallow sea on the northern rim of the Appalachian Basin (which, eons ago, lay south of the equator). When the organisms died, sediment from the seafloor began covering their shells and exoskeletons. Minerals from the sediment gradually seeped into their remains, causing them to fossilize. The process also preserved many of them in living position, conserving original shell materials at some sites.

These fossils currently populate exposed bedrock throughout Central New York, ranging from soft, dark, deep-water shale to hard, species-rich, shelf siltstone. “Communities near the top of the bedrock exhibit more taxonomic and ecological diversity than those at the bottom,” Newton says. “We can compare the community types and composition through time. They are remarkable sites.”

Coordinated stasis has been a source of contention since 1995, when it was introduced. At the center of the dispute are two model-based explanations: environmental tracking and ecological locking.

Environmental tracking suggests that faunas follow their environment. “Here, periods of relative stasis are flanked by coordinated extinctions or regional disappearances. When the environment changes, so do marine faunas,” says Newton, also Professor of Interdisciplinary Sciences and Dean Emerita of Arts and Sciences.

Ecological locking, in contrast, views marine faunas as tightly structured communities, resistant to large-scale taxonomic change. Traditionally, this model has been used to describe the stability of lower Hamilton faunas.

Newton and her colleagues analyzed more than 80 sample sites, each containing some 300 specimens. Special emphasis was placed on the Cardiff and Pecksport Members, two rock formations in the Finger Lakes region that are part of the ancient Marcellus subgroup, famed for its natural gas reserves.

“We found that lower Hamilton faunas, with two exceptions, do not have clear counterparts among upper ones. Therefore, our quantitative tests do not support the ecological locking model as an explanation for community stability in these faunas,” she continues.

Newton considers this project a final tribute to Newman, a professor of biology at the State University of New York at Cortland, who died in 2014, and Brower, who fell seriously ill while the manuscript was being finalized. “Jim knew that he likely would not live to see its publication,” says Newton, adding that Brower died as the paper was submitted to GSA.

She says this new work extends and, in some ways, completes the team’s earlier research by further analyzing community structures in the Marcellus subgroup. “It has the potential to change how scientists view long-term stability in ecological communities.”

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The group’s findings, reported by the Geological Society of America (GSA), provide critical new evidence for the unusual, long-term stability of these Devonian period communities.

Source: https://bioengineer.org/diving-into-devonian-seas-ancient-marine-faunas-unlock-secrets-of-warming-oceans/

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Pioneering research unravels hidden origins of Eastern Asia’s ‘land of milk and honey’

Credit: Dr Shufeng Li A study has revealed for the first time the ancient origins of one of the world’s

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A study has revealed for the first time the ancient origins of one of the world’s most important ecosystems by unlocking the mechanism which determined the evolution of its mountains and how they shaped the weather there as well as its flora and fauna.

It was previously thought Southern Tibet and the Himalaya were instrumental in turning the once barren land of eastern Asia into lush forests and abundant coastal regions which became home to a rich array of plant, animal and marine life, including some of the world’s rarest species. But new findings, published today in the journal Science Advances, conversely show Northern Tibet played the more influential role in this transformation which began more than 50 million years ago.

Scientists from a UK-China partnership used an innovative climate model to simulate vegetation and plant diversity, combined with spectacular new fossil finds, to discover how this unique biodiversity hotspot evolved.

Lead author, Dr Shufeng Li, a visiting scientist at the University of Bristol in the UK and associate professor at Xishuangbanna Tropical Botanical Garden (XTBG) Institute in Yunnan, China, said: “Until now it was unknown why the climate changed from that of a dry, arid, almost desert-like ecosystem to that of a lush, wet ecosystem where a vast array of plant, animal, and marine life can be found, including some of the world’s rarest species.

“We conducted 18 sensitivity experiments using different Tibetan topographies representing various late Paleogene to early Neogene conditions, which test almost all possible Tibetan growth evolution scenarios.”

The findings showed that from the late Paleogene to the early Neogene age, some 23-40 million years ago, the growth of the north and northeastern portion of Tibet was the most important factor because it increased rainfall, especially winter rainfall, over eastern Asia where dry winter conditions existed before.

This allowed the development of a stable, wet and warm climate, conducive to the evolution of vast and varied plants and animal species which formed the biodiversity hotspot known today for supplying more than a billion people with fresh water and providing ingredients used for lifesaving pharmaceutical drugs. Rare species of monkey, tiger, leopard, bear, fox, mongoose, hedgehog, seal, dolphin, and sea lion all live in this abundant ecosystem.

Earlier research has mainly investigated the impact of Tibetan mountain building much further to the South when India collided with Asia around 55 million years ago, leading to the rise of the Himalaya mountains and, eventually, the vast arid Tibetan Plateau. However, recent work is increasingly showing the creation of the modern Tibetan plateau was complex, and did not rise as one monolithic block as originally believed.

Co-author Professor Paul Valdes, Professor of Physical Geography at the University of Bristol who led the modelling group, said: “Most previous studies have focused on Southern Tibet and the Himalaya, but our results indicate it is the growth of northern Tibet which is really important.

“The topography of northern Tibet decreases the East Asian winter monsoon winds in the southern part of China, causing wetter winters in eastern Asia and this allows the expansion of vegetation and biodiversity.”

So enigmatic was the drastic change that even in Chinese folklore this area is known as the ‘Land of Fish and Rice’, due to its immense productivity.

“Without the growth in Northern Tibetan mountains, none of this would exist. But our research should also be taken as a cautionary tale,” Professor Valdes explained.

“A unique set of tectonic and stable climatic conditions over millions of years allowed the development of this rare species rich region of South East Asia. However, global warming, harmful intensive agricultural techniques, forest clearing and lack of integrated conservation to preserve this unique ecosystem means once it is gone, it is gone for good.”

Professor Zhekun Zhou, of the Chinese Academy of Sciences’ XTBG, who led on the fossil analysis, said: “So effectively, without northern Tibetan growth, there would be no ‘land of milk and honey’ in eastern Asia. This research represents a significant breakthrough in understanding how this remarkably rich region of mountainous terrain and diverse plant life formed.”

###

Paper

‘Orographic evolution of northern Tibet shaped vegetation and plant diversity in eastern Asia’ by Shufeng Li et al in Science Advances

Notes to editors:

A selection of images, including captions and credit details, can be found here: Dr Li Shufeng and Professor Paul Valdes are available for interview:

https://drive.google.com/drive/folders/1jS58Q9m2kAzoj1mrrtHhvhRbdWa-CG08?usp=sharing

Lead and corresponding author: Dr Li Shufeng – Xishuangbanna Tropical Botanical Garden (XTGB) Institute, Chinese Academy of Sciences, Yunnan.

Email – XTGB: [email protected] and Bristol: [email protected]

Co-author: Prof. Paul Valdes – University of Bristol, School of Geographical Sciences

Email: [email protected]

Source: https://bioengineer.org/pioneering-research-unravels-hidden-origins-of-eastern-asias-land-of-milk-and-honey/

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Focusing on field analysis

Microscopy systems using customized chips could expand on-site identification of pathogensCredit: Viri et al. The development of cost-efficient, portable microscopy

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Microscopy systems using customized chips could expand on-site identification of pathogens

Credit: Viri et al.

The development of cost-efficient, portable microscopy units would greatly expand their use in remote field locations and in places with fewer resources, potentially leading to easier on-site analysis of contaminants such as E. coli in water sources as well as other practical applications.

Current microscopy systems, like those used to image micro-organisms, are expensive because they are optimized for maximum resolution and minimal deformation of the images the systems produce. But some situations do not require such optimization–for instance, simply detecting the presence of pathogens in water. One potential approach to developing a low-cost portable microscopy system is to use transparent microspheres in combination with affordable low-magnification objective lenses to increase image resolution and sensitivity.

A group of researchers from Ecole Polytechnique Federale de Lausanne (EPFL) in Switzerland published a study on such an assembly composed of barium titanate spheres that are partially embedded in thin polymeric membranes. The result of their work, appearing in SPIE’s new Journal of Optical Microsystems, is a proposed method to fabricate microfluidic chips using the assembly for enhanced detection of bacteria. Such customized chips with fluidic and optical components already integrated have many benefits when combined with portable low-end imagers for analyses at remote sites or in resource-limited regions.

“Cost reduction and portability are of benefit to the proliferation of analytical devices, especially in limited-resource contexts, and the integration of affordable micro-optical elements directly onto microfluidic chips can highly contribute to this,” said Martin Gijs, a professor at EPFL and an author of the published work.

The assembly’s ability to enhance bacteria detection paves the way for other applications friendly to use at remote sites. Additionally, the researchers revealed an opportunity to customize specific functional microfluidic elements. Such integrations could bring to fruition applications such as on-site antibiotic testing.

Given falling costs of the components and fabrication methods, the researchers’ proposed fabrication protocol could be adapted easily for a wide variety of microfluidic chips with integrated optical elements. Considered along with the lower cost of low-end imaging systems, the approach could sharply increase the use of such microscopy systems in low-resource locations for on-site analyses.

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Read the open access paper: Vittorio Viri, Daniel Migliozzi, and Martin A.M. Gijs, “Integration of polymeric membrane/dielectric sphere assemblies in microfluidic chips for enhanced-contrast imaging with low-magnification systems,” J. Opt. Microsys. 1(1), 014001 (2021) doi 10.1117/1.JOM.1.1.014001.

A group of researchers from Ecole Polytechnique Federale de Lausanne (EPFL) in Switzerland published a study on such an assembly composed of barium titanate spheres that are partially embedded in thin polymeric membranes. The result of their work, appearing in SPIE’s new Journal of Optical Microsystems, is a proposed method to fabricate microfluidic chips using the assembly for enhanced detection of bacteria. Such customized chips with fluidic and optical components already integrated have many benefits when combined with portable low-end imagers for analyses at remote sites or in resource-limited regions.

Source: https://bioengineer.org/focusing-on-field-analysis/

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