Tyler O'Neal, Staff Editor ENGINEERING

Salk prof Michael shines a light into black holes in the Arabidopsis genome

Salk scientists, collaborating with researchers from the University of Cambridge and Johns Hopkins University, have sequenced the genome of the world’s most widely used model plant species, Arabidopsis thaliana, at a level of detail never previously achieved. The study, published in Science on November 12, 2021, reveals the secrets of Arabidopsis chromosome regions called centromeres. The findings shed light on centromere evolution and provide insights into the genomic equivalent of black holes. Todd Michael

“Just over 20 years ago the Arabidopsis genome was published, and it has been the gold standard plant genome since giving rise to amazing advances from models to crops,” says Todd Michael, a research professor in the Plant Molecular and Cellular Biology Laboratory. “Our new assembly resolves the final missing pieces of the genome, paving the way for exciting research on chromosome architecture and evolution, which will be critical for our efforts to engineer plants to address climate change in the future.”

Arabidopsis thaliana was adopted as a model plant due to its short generation time, small size, ease of growth, and prolific seed production through self-pollination. Its fast life cycle and small genome make it well suited for genetics research and to map key genes that underpin traits of interest. It has led to a multitude of discoveries and in 2000 it became the first plant to have its genome sequenced. This initial genome release was of an excellent standard in the chromosome arms, where most of the genes are located, but was unable to assemble the highly repetitive and complex regions known as centromeres, telomeres, and ribosomal DNA. Now, due to advances in sequencing technologies, these challenging regions have been assembled for the first time.

The study is the first to successfully perform long-read sequencing and assembly of the Arabidopsis thaliana centromeres. Since the genome was first sequenced in 2000, long-read sequencing technologies have advanced, allowing researchers to see the genome in greater than 100,000 nucleotide pieces, instead of 100-200 nucleotide pieces. These data, combined with algorithmic advances that assemble the reads, means that the “genomic jigsaw puzzle” is suddenly now completable.

“The centromeres are some of the most interesting, but also the most difficult, regions of the genome to analyze —they are like endless ‘blue sky’ within a jigsaw puzzle,” says co-corresponding author Professor Mike Schatz, from Johns Hopkins University. “Fortunately, advances in sequencing paired with advances in the computational methods for genome assembly now make it possible to accurately assemble even the most challenging of sequences,” such as the genetic makeup of the centromere. Arabidopsis thaliana plant.

For decades, researchers have been trying to understand the paradox of how and why centromeric DNA evolves with extraordinary rapidity, whilst remaining stable enough to perform its job during cell division. In contrast, other ancient parts of the cell that have conserved roles, such as ribosomes, which make proteins from mRNA, tend to be very slow evolving. Yet the centromere, despite its conserved role in cell division, is the fastest evolving part of the genome. This study, by revealing the genetic and epigenetic topography of Arabidopsis centromeres, marks a step-change in our understanding of this paradox.

As part of the study, the compiled centromere maps provide new insights into the “repeat ecosystem” found in the centromere. The maps reveal the architecture of the repeat arrays, which has implications for how they evolve, and for the chromatin and epigenetic states of the centromeres. Moving forward the scientists want to use these maps as a foundation to understand how and why centromeres are evolving so rapidly.

“It’s fantastic to be able to see into the centromeres for the first time and use this to understand their unusual modes of evolution,” says co-corresponding author Professor Ian Henderson, from the University of Cambridge’s Department of Plant Sciences.

Next, the scientists will be looking at using this approach to map centromeres from diverse Arabidopsis species, and ultimately more widely throughout plants.

Other scientists include Bradley W. Abramson, Nolan Hartwick and Kelly Colt of Salk; Matthew Naish, Piotr Wlodzimierz, Andrew J. Tock, Christophe Lambing, Pallas Kuo and Natasha Yelina of the University of Cambridge; Michael Alonge of Johns Hopkins University; Anna Schmücker, Bhagyshree Jamge and Frédéric Berger of the Austrian Academy of Sciences; Terezie Mandáková and Martin A. Lysak of Masaryk University in the Czech Republic; Lisa Smith and Jurriaan Ton of the University of Sheffield; Tetsuji Kakutani of the University of Tokyo; Robert A. Martienssen of the Howard Hughes Medical Institute; Korbinian Schneeberger of LMU Munich; and Alexandros Bousios of the University of Sussex.

NSF renews funding for Two-Dimensional Crystal Consortium

Tyler O'Neal, Staff Editor ENGINEERING

Penn State facility enables the development of new ultra-thin materials for advanced electronics

The National Science Foundation (NSF) announced a renewal of funding for the Materials Innovation Platform (MIP) national user facility at Penn State's Materials Research Institute (MRI), the Two-Dimensional Crystal Consortium (2DCC). The 2DCC is one of four MIPs in the United States and was awarded $20.1 million over five years, an increase of 13% above the initial award in 2016.

MIPs are NSF facilities focused on a specific topic that is funded to stimulate materials research innovation and foster the growth of a national community of users to develop next-generation materials. These groups seek to substantially increase the rate at which new materials and new materials phenomena are discovered. The 2DCC at Penn State follows the "materials by design" concept, combining synthesis, characterization, and theory/simulation applied to targeted outcomes to accelerate materials discovery.

The 2DCC received its first five years of funding in 2016, which was used to nucleate and grow the MIP by developing state-of-the-art equipment for thin film deposition with integrated characterization tools, establishing a bulk growth facility, developing new computational tools and a facility-wide database, and initiating an external user program. In 2020, the 2DCC underwent a renewal process for the second five years of funding.

"Over the past five years, the 2DCC has established itself as a premier facility for the synthesis of wafer-scale 2D films and bulk crystals with unique quantum properties," said Joan Redwing, director of the 2DCC and synthesis lead, and professor of materials science and engineering and electrical engineering.

Two-dimensional (2D) materials are atomically thin layers that, due to the restricted electron and atom motion, have physical characteristics that are not present in three dimensions. The 2DCC focuses on the bulk and thin-film synthesis of 2D chalcogenides, i.e., layered compounds of transition elements such as selenium and sulfur. By controlling the growth of these materials on the atomic level, new materials can be created with unique properties and exotic quantum states that hold the potential for revolutionary new device technologies, such as flexible electronics and quantum computing.

"As an inaugural Materials Innovation Platform, 2DCC MIP exemplifies the power of the Materials Genome Initiative approach with close experiment-theory interactions," said Charles Ying, program director for MIPs and National Facilities and Instrumentation with the Division of Materials Research of the National Science Foundation. "Multi-year efforts of studying and refining growth conditions have paid off, leading to reproducible synthesis of 2D materials that have already benefited more than 100 scientists nationwide. The new experimental and data tools will bring 2DCC to a new level in its second five years."

As a core component of the 2DCC's efforts in synthesizing ground-breaking 2D chalcogenide materials, the 2DCC offers a user program that advances 2D materials research across the U.S., not just at Penn State.

"Researchers outside of Penn State at other universities, companies, or national labs can come on-site to receive training in the facility and carry out their research or request samples grown by 2DCC staff," said Redwing. "In addition to the user program, we also have an in-house team of researchers who collaborate with users on their projects. We've sponsored over 125 user projects in our facility since we started in 2016. So, a big part of the MIP is indeed the user program."

The Penn State MIP has proven to be very beneficial for the development of 2D materials.

"Even before the MIP, Penn State had a number of faculty working on 2D material research," said Redwing. "But getting the MIP funded enabled us to expand and more deeply integrate that activity and initiate research collaborations with other universities and national labs through our user program. It's really helped to make Penn State one of the main centers of activity in 2D materials in the world."

During its first five years, the 2DCC has managed to meet challenges of complexity, scale, and even an unexpected obstacle that affected the entire globe.

"The discovery of high-performance materials is a complex process, and the framework of the MIP integrates research methodologies that efficiently aid the optimal synthesis of 2D materials, with a teaming of theory, synthesis science, in situ metrologies, and machine learning from the large data sets," said Clive Randall, director of MRI and distinguished professor of materials science and engineering. "In addition, the outreach has been very impressive, aiding researchers from all over the United States, and even globally. The 2DCC also maintained their mission during the COVID crisis, including holding a virtual research experience for undergraduates program in the summer of 2020."

The 2DCC is one of four user facilities in MRI, along with the Materials Characterization Lab, the Nanofabrication Lab, and the Materials Computation Center. The 2DCC research staff includes 17 faculty and 13 doctorate-level researchers. Graduate students are also involved in the in-house research program.

Along with Redwing, the 2DCC executive leadership team includes Nitin Samarth, associate director and characterization lead and professor and George A. and Margaret M. Downsbrough Department Head in Physics; Vincent Crespi, theory lead and distinguished professor of physics, materials science and engineering and chemistry; Joshua Robinson, director of user programs and professor of materials science and engineering; Eric Hudson, director of education, outreach and diversity programs and associate professor of physics; Zhiqiang Mao, bulk growth lead and professor of physics; Roman Engel-Herbert, industry lead and associate professor of materials science and engineering and physics; Adri van Duin, distinguished professor of mechanical engineering, chemistry, materials science & engineering, chemical engineering and engineering science and mechanics; Jun Zhu, professor of physics; Wes Reinhart, assistant professor of materials science and engineering and Institute for Computational and Data Sciences faculty co-hire; and Kevin Dressler, operations and user facilities director and affiliate assistant professor of civil engineering.

"The 2DCC has created this critical mass of research activity that has brought considerable attention to Penn State and MRI over the last five years," said Redwing. "The funding we received for new equipment, research support, and other activities has established Penn State and MRI as one of the leading institutes for 2D materials research."

With the renewed funding, the 2DCC will work to build on the progress made in 2D materials research through new collaborations and the existing ones created in the MIP's first five years. Plans for the next five years include the addition of a double crucible Bridgman system for synthesis of bulk crystals with improved composition control, development of an integrated etch/deposition tool for the synthesis of 2D metals, and an expansion of the facility database to enable materials discovery through data science methods.

"We are very proud of the 2DCC leadership, researchers, and staff who have partnered with the NSF to develop, refine and model the MIP program as one of the inaugural awardees back in 2016," said Randall. "We are looking forward to this next era and the scientific discoveries that will inevitable come with the multiple university partnerships which will emerge via the MIP program."

ASME’s Engineering for Change Research Fellowship Program cohort doubles with Autodesk Foundation support

Tyler O'Neal, Staff Editor ENGINEERING

In a unique collaboration between two nonprofit organizations, Autodesk Foundation has invested in the American Society of Mechanical Engineers (ASME)’s Engineering for Change (E4C) Research Fellowship Program, doubling the 2021 cohort from 25 to 50 fellows and expanding the reach and impact of Autodesk Foundation’s Impact Internship Program.

Autodesk Foundation is the philanthropic arm of Autodesk, Inc., a global developer of design software for the architecture, engineering, construction, media and entertainment, and manufacturing industries. Autodesk Foundation allocates resources, including capital, technology, and industry expertise, toward creating a more sustainable and equitable future.

Autodesk Foundation’s Impact Internship program connects innovators and entrepreneurs in the Autodesk Foundation portfolio with emerging engineers.

This combined internship initiative gives more emerging engineers the opportunity to apply their technical expertise to solving some of the world’s most pressing social and environmental issues, while also developing leadership skills and advancing career readiness. This year, E4Chas received nearly 650 applications from interested candidates in 80 countries – an increase of 50% compared with the previous year. 

E4C’s Fellows will be matched with Autodesk Foundation portfolio organizations on projects that address the United Nations Sustainable Development Goals. Projects include proving the affordability of greenhouses for small shareholder farmers in India, product design of electric motorbikes, and developing a holistic design approach for sustainable construction projects.

Fellows advance their career path through 400 hours of research, 30 hours of networking online with their peers and expert advisors, and 30 hours of learning modules designed to enhance their knowledge in the sector. In addition, the Autodesk Foundation will provide software training to the Fellows as needed for their research collaborations, on Autodesk tools including AutoCAD, BIM 360, Dynamo, Revit, Inventor, and Fusion 360. Fellows publish the results of their technical research, expert interviews, and share their insights on E4C’s online platform, reaching a global community of more than one million innovators and influencers in sustainable development.

“Autodesk Foundation’s substantial investment in this signature ASME philanthropic initiative is a powerful endorsement of our mission to advance engineering for the benefit of humanity,” said Kathleen Lobb, managing director of ASME philanthropy and executive director of the ASME Foundation. “E4C Fellowships are a mainstay of our Engineering Global Development portfolio, which is just one of the ways ASME and the ASME Foundation inspire, engage, and empower next generation engineers.”

"We are proud to collaborate with ASME and E4C on Autodesk Foundation's Impact Internship Program this year. With ASME and E4C's expertise and network, we're able to connect our portfolio with a global cohort of emerging engineers to solve some of the world's most pressing social and environmental problems," said Christine Stoner, head of engagement at Autodesk Foundation.

Since 2016, the E4C Research Fellowship has provided opportunities for 86 fellows from 23 countries to create social impact. The highly competitive program attracts hundreds of applicants each year. More than half of all E4C Fellows are women, addressing the critical need to expand diversity in engineering for sustainable development where only 13 percent of engineers are women.