Scientists Peer Inside An Asteroid (Planetary Science)

New findings from NASA’s OSIRIS-REx mission suggest that the interior of the asteroid Bennu could be weaker and less dense than its outer layers–like a crème-filled chocolate egg flying though space.

The results appear in a study published today in the journal Science Advances and led by the University of Colorado Boulder’s OSIRIS-REx team, including professors Daniel Scheeres and Jay McMahon. The findings could give scientists new insights into the evolution of the solar system’s asteroids–how bodies like Bennu transform over millions of years or more.

OSIRIS-REx rendezvoused with Bennu, an asteroid orbiting the sun more than 200 million miles from Earth, in late 2018. Since then, the spacecraft, built by Colorado-based Lockheed Martin, has studied the object in more detail than any other asteroid in the history of space exploration.

So far, however, one question has remained elusive: What’s Bennu like on the inside?

Scheeres, McMahon and their colleagues on the mission’s radio science team now think that they have an answer–or at least part of one. Using OSIRIS-REx’s own navigational instruments and other tools, the group spent nearly two years mapping out the ebbs and flows of Bennu’s gravity field. Think of it like taking an X-ray of a chunk of space debris with an average width about the height of the Empire State Building.

“If you can measure the gravity field with enough precision, that places hard constraints on where the mass is located, even if you can’t see it directly,” said Andrew French, a coauthor of the new study and a former graduate student at CU Boulder, now at NASA’s Jet Propulsion Laboratory (JPL).

What the team has found may also spell trouble for Bennu. The asteroid’s core appears to be weaker than its exterior, a fact that could put its survival at risk in the not-too-distant future.

“You could imagine maybe in a million years or less the whole thing flying apart,” said Scheeres, a distinguished professor in the Ann and H.J. Smead Department of Aerospace Engineering Sciences.

Evolution of asteroids

Of course, that’s part of the fun of studying asteroids. Scheeres explained that Bennu belongs to a class of smaller bodies that scientists call “rubble pile” asteroids–which, as their name suggests, resemble loosely held-together mounds of debris.

Asteroids also change over time more than people think.

“None of them have sat out there unchanging since the dawn of the solar system,” Scheeres said. “They’re being changed by things like sunlight affecting how they spin and collisions with other asteroids.”

To study how Bennu and other similar asteroids may change, however, he and his colleagues needed to take a peek inside.

This is where the team got lucky. When OSIRIS-REx first arrived at Bennu, the spacecraft spotted something unusual: Over and over again, tiny bits of material, some just the size of marbles, seemed to pop off the asteroid and into space. In many cases, those particles circled Bennu before falling back down to the surface. Members of the mission’s radio science team at JPL were able to witness how the body’s gravity worked first-hand–a bit like the apocryphal story of Isaac Newton inferring the existence of gravity after observing an apple falling on his head.

“It was a little like someone was on the surface of the asteroid and throwing these marbles up so they could be tracked,” Scheeres said. “Our colleagues could infer the gravity field in the trajectories those particles took.”

Squishy center

In the new study, Scheeres and his colleagues combined those records of Bennu’s gravity at work with data from OSIRIS-REx itself–precise measurements of how the asteroid tugged on the spacecraft over a period of months. They discovered something surprising: Before the mission began, many scientists had assumed that Bennu would have a homogenous interior. As Scheeres put it, “a pile of rocks is a pile of rocks.”

But the gravity field measurements suggested something different. To explain those patterns, certain chunks of Bennu’s interior would likely need to be more tightly packed together than others. And some of the least dense spots in the asteroid seemed to lie around the distinct bulge at its equator and at its very core.

“It’s as if there is a void at its center, within which you could fit a couple of football fields,” Scheeres said.

The asteroid’s spin may be responsible for that void. Scientists know that the asteroid is spinning faster and faster over time. That building momentum could, Scheeres said, be slowly pushing material away from the asteroid’s center and toward its surface. Bennu, in other words, may be in the process of spinning itself into pieces.

“If its core has a low density, it’s going to be easier to pull the entire asteroid apart,” Scheeres said.

For the scientist, the new findings are bittersweet: After measuring Bennu’s gravity field, Scheeres and his team have mostly wrapped up their work on the OSIRIS-REx mission.

Their results have contributed to the mission’s sample analysis plan, which is currently in development. The returned sample will be analyzed to determine the cohesion between grains–a key physical property that affects the mass distribution observed in the team’s study.

“We were hoping to find out what happened to this asteroid over time, which can give us better insight into how all of these small asteroids are changing over millions, hundreds of millions or even billions of years,” Scheeres said. “Our findings exceeded our expectations.”

Provided by University Of Colorado at Boulder

SwRI Scientists Study The Rugged Surface Of Near-Earth Asteroid Bennu (Planetary Science)

As the days count down to NASA’s OSIRIS-REx spacecraft’s Touch-And-Go asteroid sample collection attempt, Southwest Research Institute scientists have helped determine what the spacecraft can expect to return from the near-Earth asteroid Bennu’s surface. Three papers published online by Science on Oct. 8 discuss the color, reflectivity, age, composition, origin and distribution of materials that make up the asteroid’s rough surface.

As NASA’s OSIRIS-REx spacecraft’s Touch-And-Go asteroid sample collection attempt approaches, Southwest Research Institute scientists have helped determine what the spacecraft can expect to return from the near-Earth asteroid Bennu’s surface. SwRI scientists also played a role in sample site selection, including the primary site Nightingale shown here. ©NASA/Goddard/University of Arizona

On October 20, the spacecraft will descend to the asteroid’s boulder-strewn surface, touch the ground with its robotic arm for a few seconds and collect a sample of rocks and dust – marking the first time NASA has grabbed pieces of an asteroid for return to Earth. SwRI scientists played a role in the selection of the sample sites. The first attempt will be made at Nightingale, a rocky area 66 feet in diameter in Bennu’s northern hemisphere. If this historic attempt is unsuccessful, the spacecraft will try again at a secondary site.

Since the spacecraft arrived at Bennu in 2018, scientists have been characterizing the asteroid’s composition and comparing it to other asteroids and meteorites. The mission discovered carbon-bearing compounds on Bennu’s surface, a first for a near-Earth asteroid, as well as minerals containing or formed by water. Scientists also studied the distribution of these materials, globally and at the sample sites

“Our recent studies show that organics and minerals associated with the presence of water are scattered broadly around Bennu’s surface, so any sample returned to Earth should contain these compounds and minerals,” said SwRI’s Dr. Vicky Hamilton, a coauthor on all three papers. “We will compare the sample’s relative abundances of organics, carbonates, silicates and other minerals to those in meteorites to help determine the scenarios that best explain Bennu’s surface composition.”

Asteroid Bennu is a dark, rubble pile held together by gravity and thought to be the collisional remnant of a much larger main-belt object. Its rubble-pile nature and heavily cratered surface indicates that it has had a rough-and-tumble life since being liberated from its much larger parent asteroid millions or even billions of years ago.

“Boulders strewn about near the Nightingale site have bright carbonate veins,” Hamilton said. “Bennu shares this compositional trait with aqueously altered meteorites. This correlation suggests that at least some carbonaceous asteroids were altered by percolating water in the early Solar System.”

The boulders on Bennu have diverse textures and colors, which may provide information about their variable exposure to micrometeorite bombardment and the solar wind over time. Studying color and reflectance data provide information about the geologic history of planetary surfaces.

“Bennu’s diverse surface includes abundant primitive material potentially from different depths in its parent body plus a small proportion of foreign materials from another asteroid family littered about its surface,” said SwRI’s Dr. Kevin Walsh, a coauthor of one of the papers. “In addition, both the primary and back-up sample sites, Nightingale and Osprey, are situated within small spectrally reddish craters that are thought to be more pristine, having experienced less space weathering than most of Bennu’s bluish surface.”

The OSIRIS-REx team is also comparing Bennu to Ryugu, another near-Earth asteroid. Both asteroids are thought to have originated from primitive asteroid families in the inner main belt. The Japan Aerospace Exploration Agency launched Hayabusa2 in 2014 and rendezvoused with near-Earth asteroid Ryugu in 2018. After surveying the asteroid for a year and a half, the spacecraft collected samples and is expected to return to Earth December 6, 2020.

The sample returned by OSIRIS-REx, combined with the surface context maps OSIRIS-REx has collected, will improve interpretations of available ground and space telescope data for other primitive dark asteroids. Comparing returned Bennu samples with those of Ryugu will be instrumental for understanding the diversity within, and history of, asteroid families and the entire asteroid belt.

Provided by Southwest Research Institute

How An Egg Cell’s “Operating Manual” Sets The Stage For Fertility? (Biology)

Genetic instructions immature egg cells go through step by step as they mature into functionality revealed in unprecedented detail.

Recently published work from Carnegie’s Allan Spradling and Wanbao Niu revealed in unprecedented detail the genetic instructions immature egg cells go through step by step as they mature into functionality. Their findings improve our understanding of how ovaries maintain a female’s fertility.

An illustration of gene expression underlying wave1 and wave2 follicle production. Each dot on the diagram mathematically summarizes the gene expression of individual ovarian helper cells that surround developing egg cells in two-dimensional gene space. Developing cells fall into clusters indicated by a common color and clusters are present in the ovary only at single developmental times (i.e. E14.5, E16.5, etc.) indicated for cells within the dashed zones. It can be seen that each time zone houses precisely two types of follicle cells, which were found to come from future wave 1 follicles (4, odd numbers >4) or wave 2 two follicles (even numbers >4). ©Figure is courtesy of Allan Spradling and Wanbao Niu. Underlying image purchased from Shutterstock. Composite created by Navid Marvi.

The general outline of how immature egg cells are assisted by specific ovarian helper cells starting even before a female is born is well understood. But Spradling and Niu mapped the gene activity of thousands of immature egg cells and helper cells to learn how the stage is set for fertility later in life.

Even before birth, “germ” cells assemble a finite number of cell clusters called follicles in a female’s ovaries. Follicles consist of an immature egg cell and some “helper” cells, which guide the egg through its maturation process. It is from a follicle that a mature egg cell bursts during ovulation.

“Follicles are slowly used up during a female’s reproductive lifespan and menopause ensues when they run out. Understanding what it takes for follicles to form and develop successfully, helps us learn how damaged genes or adverse environmental factors, including a poor diet, can interfere with fertility,” explained Spradling. “By documenting the follicle’s genetic operating manual, problems in egg development that might lead to birth defects –as a result of mutations or due to bad nutrition– can be better understood and reduced.”

Spradling and Niu sequenced 52,500 mouse ovarian cells at seven stages of follicle development to determine the relative expression of thousands of genes and to characterize their roles.

The study also illuminated how mammalian ovaries produce two distinct types of follicles and Spradling and Niu were able to identify many differences in gene activity between them.

The first, called wave 1 follicles, are present in the ovary even before puberty. In mice, they generate the first fertile eggs; their function in humans is poorly understood, but they may produce useful hormones. The second type, called wave 2 follicles, are stored in a resting state but small groups are activated to mature during a female’s hormonal cycle, ending in ovulation. The findings help clarify each type’s roles.

Spradling and Niu’s work and all its underlying data were published by Proceedings of the National Academy of Sciences.

“We hope our work will serve as a genetic resource for all researchers who study reproduction and fertility,” concluded Spradling.

References: Wanbao Niu and Allan C. Spradling, “Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary”, PNAS August 18, 2020 117 (33) 20015-20026; first published August 5, 2020; https://doi.org/10.1073/pnas.2005570117 link: https://www.pnas.org/content/117/33/20015

Provided by Carnegie Institute For Science

Quality Control Mechanism Closes The Protein Production ‘On-Ramps’ (Neuroscience)

Newly discovered quality control system in the protein production assembly line has implications for neurogenerative disease.

Recent work led by Carnegie’s Kamena Kostova revealed a new quality control system in the protein production assembly line with possible implications for understanding neurogenerative disease.

An illustration of stalled ribosomes as stalled cars on a freeway. New work shows that factors GIGYF2 and 4EHP prevent translation from being initiated on problematic messenger RNA fragments. This is akin to closing an on-ramp to prevent additional traffic backups after an incident. Artwork courtesy of Kamena Kostova and Navid Marvi.

The DNA that comprises the chromosomes housed in each cell’s nucleus encodes the recipes for how to make proteins, which are responsible for the majority of the physiological actions that sustain life. Individual recipes are transcribed using messenger RNA, which carries this piece of code to a piece of cellular machinery called the ribosome. The ribosome translates the message into amino acids–the building blocks of proteins.

But sometimes messages get garbled. The resulting incomplete protein products can be toxic to cells. So how do cells clean up in the aftermath of a botched translation?

Some quality assurance mechanisms were already known–including systems that degrade the half-finished protein product and the messenger RNA that led to its creation. But Kostova led a team that identified a new tool in the cell’s kit for preventing damage when protein assembly goes awry. Their work was published by Molecular Cell.

Using CRISPR-Cas9-based genetic screening, the researchers discovered a separate, and much needed, device by which the cell prevents that particular faulty message from being translated again. They found two factors, called GIGYF2 and 4EHP, which prevent translation from being initiated on problematic messenger RNA fragments.

“Imagine that the protein assembly process is a highway and the ribosomes are cars traveling on it,” Kostova explained. “If there’s a bad message producing incomplete protein products, it’s like having a stalled car or two on the road, clogging traffic. Think of GIGYF2 and 4EHP as closing the on-ramp, so that there is time to clear everything away and additional cars don’t get stalled, exacerbating the problem.”

Loss of GIGYF2 has previously been associated with neurodegenerative and neurodevelopmental problems. It is possible that these issues are caused by the buildup of defective proteins that occurs without the ability to prevent translation on faulty messenger RNAs.

References: Kelsey L. Hickey, Kimberley Dickson, J. Zachery Cogan, “GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control”, VOLUME 79, ISSUE 6, P950-962.E6, SEPTEMBER 17, 2020 DOI:https://doi.org/10.1016/j.molcel.2020.07.007

Provided by Carnegie Institution For Science

Treating Cystic Fibrosis With mRNA Therapy Or CRISPR (Medicine)

The potential for treating cystic fibrosis (CF) using mRNA therapies or CRISPR gene editing is possible regardless of the causative mutation. CF clinical trials showing that a genotype-agnostic gene therapy for CF is possible are reviewed in the peer-reviewed journal Human Gene Therapy. Click here to read the full-text article free on the Human Gene Therapy website through November 4, 2020.

Human Gene Therapy. Field and provides all-inclusive access to the critical pillars of human gene therapy: research, methods, and clinical applications. ©Mary Ann Liebert, Inc., publishers

“Treating CF by delivering mRNA that encodes CFTR has the potential to work in any CF patient, independent of the underlying mutation,” state James Dahlman, Georgia Institute of Technology, and coauthors. “Another potential treatment is utilizing mRNA encoding nucleases such as CRISPRCas9 accompanied by gRNA and using them to edit DNA in target cells.”

Challenges remain to be able to utilize these approaches successfully. First among them is the need to identify drug delivery systems that can reach pulmonary epithelial cells at low doses.

“CF was the first disease target in humans for several vector platforms, including rAAV and rAd. It is gratifying to see these newer technologies applied to CF, particularly to the 5% of patients whose mutations are resistant to CFTR modulator drugs,” according to Editor-in-Chief of Human Gene Therapy Terence R. Flotte, MD, Celia and Isaac Haidak Professor of Medical Education and Dean, Provost, and Executive Deputy Chancellor, University of Massachusetts Medical School.

References: Alejandro Da Silva Sanchez, Kalina Paunovska, Ana Cristian, and James E. Dahlman, “Treating Cystic Fibrosis with mRNA and CRISPR”, Human Gene Therapy 2020 31:17-18, 940-955. Link: https://www.liebertpub.com/doi/10.1089/hum.2020.137# doi: https://doi.org/10.1089/hum.2020.137

Provided by Mary Ann Liebert, Inc., publishers

New Perspectives To Treat Neuropschychiatric Diseases (Neuroscience)

Molecular differences in neurons that may support drug development for the treatment of psychiatric disorders.

Researchers at the Institute of Biology, Eötvös Loránd University (ELTE), Budapest, Hungary, studied the major types of neurons of the prefrontal cortex of the brain in an international collaboration. The research team has identified molecular differences in neurons that may support drug development for the treatment of psychiatric disorders such as schizophrenia or depression.

It has long been known that the prefrontal cortex in the frontal lobe is responsible for nervous system processes related to decision-making, planning, or central constructive functions. Dysfunctions of this part of the brain play role in several psychiatric illnesses and can also cause neuropsychiatric conditions such as autism, schizophrenia, or depression.

The proper functioning of the prefrontal cortex is largely based on the balanced communication between its two major types of neurons, the excitatory pyramidal cells and the inhibitory interneurons.

The researchers at the Institute of Biology, Faculty of Science, Eötvös Loránd University (ELTE), led by Gábor Juhász, James Eberwine (University of Pennsylvania) and Tamás Bártfai (Scripps Research), studied the messenger RNA (mRNA) set of these two types of cortical neurons by the so-called single-cell sequencing for several years.

The mRNAs transmit genetic information from DNA to ribosomes, the sites of protein synthesis. Researchers at ELTE mapped these molecules in excitatory pyramidal cells and inhibitory interneurons. The essence of the single-cell sequencing method is that by examining the cells individually, it is possible to identify and quantify the mRNAs of the cells and thus estimate the type and amount of proteins that each cell synthesizes at a given time.

“Single-cell mRNA sequencing has been used primarily for neuronal classification in the previous nervous systems studies, whereas in the present work, we have focused specifically on the mRNA set of the two, functionally clearly distinguishable neuronal cell types. We have looked especially for mRNAs encoding cell surface proteins. This was of particular importance, since cell surface proteins such as neurotransmitter receptors and ion channels play essential role in the adequate communication between neurons, and on the other hand, these proteins might be available for pharmaceutical drugs” said Gábor Juhász, one of the leaders of the research.

Out of the detected more than 19,000 different mouse mRNAs, the scientists have looked for mRNAs that are preferentially expressed in one of the examined types of neurons and that encode proteins located on the surface of the cells. A large number of cell type-specific mRNAs has been identified, which were present in at least tenfold higher amount in one of the cell types than in the other, so it can be assumed that the encoded cell surface proteins are also present in higher amount. This is an important step providing an accurate picture of the cell surface proteins that can be used to treat certain psychiatric disorders by selectively influencing the function of the studied cell types. These findings will also help to better understand the mechanism of action of clinically used nervous system drugs.

References: Lilla Ravasz, Katalin Adrienna Kékesi, Dániel Mittli, Mihail Ivilinov Todorov, Zsolt Borhegyi, Mária Ercsey-Ravasz, Botond Tyukodi, Jinhui Wang, Tamás Bártfai, James Eberwine, Gábor Juhász, Cell Surface Protein mRNAs Show Differential Transcription in Pyramidal and Fast-Spiking Cells as Revealed by Single-Cell Sequencing, Cerebral Cortex, , bhaa195, https://doi.org/10.1093/cercor/bhaa195

Provided by ELTE, Faculty Of Science

Experimental Glioblastoma Therapy Shows Curative Powers In Mice Models (Neuroscience)

Houston Methodist researchers found that mice harboring human glioblastoma tumors in their brains had greatly enhanced survival and weight gain when given a newly developed prodrug. This mitochondrial-targeted prodrug – an inactive compound that cancer cells selectively metabolize to produce an active toxic drug – also greatly improves outcomes when coupled with standard therapies of radiation and/or chemotherapy. The drug selectively targets and destroys the DNA inside the glioblastoma cell mitochondria (the energy factory of the cancer cell) leaving normal cells intact.

In an Oct. 8 study published online in Molecular Cancer Therapeutics, a journal of the American Association for Cancer Research, investigators used a second generation prodrug called MP-Pt(IV) to target the deadly cells of glioblastoma tumors, a brain cancer that is almost always fatal and has no cure. Life expectancy in humans with glioblastoma ranges from a few months to two years.

Human glioma cells were removed from patients during surgical excision and isolated within 10 minutes after removal. The glioblastoma cells were injected into the brains of 48 female mice for a 300-day study. The prodrug was well tolerated, and, when given on its own, extended survival by more than a factor of three. However, when combined with standard chemotherapy and radiotherapy, the drug was curative in nature, allowing 90% of mice to survive, thrive and gain weight during the 10 months of observation.

“This study tells us that adding MP-Pt(IV) to a chemoradiotherapy protocol could address a critical need in glioblastoma treatment,” said David S. Baskin, M.D., FACS, FAANS, corresponding author and director of the Kenneth R. Peak Center for Brain and Pituitary Tumor Treatment in the Department of Neurosurgery at Houston Methodist. “We now know that MP-Pt(IV) is an excellent candidate for preclinical development.”

References: Sudhir Raghavan, David S Baskin and Martyn A Sharpe, “MP-Pt(IV): A MAOB-sensitive mitochondrial-specific prodrug for treating glioblastoma”, Mol Cancer Ther October 8 2020 DOI: 10.1158/1535-7163.MCT-20-0420 link: https://mct.aacrjournals.org/content/early/2020/10/06/1535-7163.MCT-20-0420

Provided by Houston Methodist

A New Assembler For Decoding Genomes Of Microbial Communities Developed (Biology)

Researchers from the Center for Algorithmic Biotechnology at St Petersburg University, as part of a group of Russian and American scientists, have developed the metaFlye assembler. It is designed to assemble DNA samples from microbial communities. With its help, it is possible to solve a wide range of fundamental and applied problems, among which is the control of the process of treating patients and even the creation of new drugs.

The metaFlye assembler is designed to assemble DNA samples from microbial communities. With its help, it is possible to solve a wide range of fundamental and applied problems, among which is the control of the process of treating patients and even the creation of new drugs. ©SPbU

At present, to study the DNA of any living organism, scientists around the world use complex biotechnological instruments – DNA sequencers. These special machines cannot ‘read’ the genome from start to finish (like people read books). They do it in separate short fragments – reads. Combining reads into longer fragments, and ideally into a single sequence of the original genome, is an extremely complex computational problem. It is like assembling a million-piece puzzle. The problem is complicated by the fact that genomes often contain a large number of identical repetitive sequences, which often exceed the length of reads. It is possible to cope with this challenging problem using specialised software – genome assemblers.

Several dozen different assemblers are being developed in leading bioinformatics laboratories around the world, and they are available to scientists. This diversity is because the algorithms that assemblers are based on need to be adapted to: different types of input data obtained on different types of DNA sequencers; and different organisms. For example, approaches for assembling bacterial genomes may not be suitable at all for assembling the human genome and vice versa. Additionally, the developers of genomic assemblers are constantly striving to improve their solutions so that: their programmes run faster and use less memory; and the resulting assemblies are longer and more accurate than those produced by the competing software.

The new metaFlye assembler is designed for assembling metagenomes. These are DNA samples from microbial communities obtained from various environments, such as the deep sea, soil in a park, or human gut. Having received an assembly of such a sample, it is possible to determine what kind of and how many organisms are presented in it. Using additional assembly analysis, it is often possible to find out: what these organisms can feed on; how they interact; and what substances they synthesise. All this information can be used in the future, for example: to search for new drugs of natural origin; to determine the reasons underlying the extreme soil fertility; when checking the course of treating patients; and in solving many other fundamental and applied problems.

The metaFlye assembler is designed for data obtained using the current state-of-the-art sequencing technology – long-read sequencing. There are already several metagenomic assemblers working with short-read sequencing, or next-generation sequencing (NGS) data generated on Illumina instruments. Among these assemblers there is the metaSPAdes assembler. It was developed at the Center for Algorithmic Biotechnology at St Petersburg University in 2016. There are also software for assembling isolate genomes from long reads. metaFlye makes it possible to take advantage of the new technology for complex metagenomic data. It is the first metagenome assembler specially designed to work with Oxford Nanopore and PacBio technologies.

‘The impetus to develop metaFlye was the absence of a specific metagenomic assembler for long-read technology,’ says Mikhail Rayko, one of the project’s authors, a senior research fellow at the Center for Algorithmic Biotechnology at St Petersburg University. ‘This technology has already changed dramatically the whole modern genomic science. We have learned to obtain much more complete assemblies. For example, with its help, many missing fragments of the human genome have recently been sequenced and localised. The original Flye tool was used for that, and the members of our laboratory also took part in this project. However, such data have just begun to appear for metagenomes, and, of course, special tools are needed for processing it.’

Work on metaFlye started about two years ago. It is four years if we count from the creation of its predecessor, the genomic assembler Flye, on the basis of which the new project was implemented.

‘In our study, published in the journal Nature Methods, we used metaFlye and other assemblers to analyse several simulated (i.e., computer generated, without real DNA sequencing) and real metagenomic samples from the gastrointestinal tract of a human, a cow and a sheep,’ says Alexey Gurevich, a co-author of the assembler and a senior research fellow at the Center for Algorithmic Biotechnology at St Petersburg University. ‘A sample of the sheep microbiome is perhaps of principal interest. It was first obtained and studied in this work, while the initial sequencing data for the other two samples were taken from the works of third-party authors. metaFlye made it possible to assemble an order of magnitude more viral genomes and one and a half times more plasmids in this sample than when using the best existing analogue programmes.’

Another intriguing result was that it was possible to assemble in the sample the genomes of not only bacteria and archaea, but also eukaryotes. At the same time, bioinformatics analysis revealed that almost half of eukaryotic genomic fragments belong to representatives of nematodes, or roundworms. This result fully complies with the autopsy report of the animal, which showed signs of parasitic infection.

‘The metaFlye assembler is a tool for solving a wide range of tasks. It will be available to all researchers working with such data. Of the specific projects carried out in our laboratory, we use the assembler to study the soil composition in Chernevaya taiga – a unique biocoenosis of Western Siberia with abnormally high fertility,’ says Alexey Gurevich.

The publication about metaFlye is the result of a collaboration of 11 Russian and American scientists from: St Petersburg University; the University of California San Diego (UCSD); Bioinformatics Institute (St Petersburg); and US Research Centers for Dairy Forage and Meat Animal. The metaFlye assembler itself is being mainly developed in UCSD. Its developer and main author of the publication is Mikhail Kolmogorov, a postdoc at UCSD. The research supervisor of the project is Pavel Pevzner, Professor at UCSD and Chief Advisor of the Center for Algorithmic Biotechnology at St Petersburg University.

References: Mikhail Kolmogorov et al, metaFlye: scalable long-read metagenome assembly using repeat graphs, Nature Methods (2020). DOI: 10.1038/s41592-020-00971-x

Provided by St. Petersburg State University

Genomic Study Reveals Evolutionary Secrets Of Banyan Tree (Botany)

The banyan fig tree Ficus microcarpa is famous for its aerial roots, which sprout from branches and eventually reach the soil. The tree also has a unique relationship with a wasp that has coevolved with it and is the only insect that can pollinate it.

The banyan tree Ficus macrocarpa produces aerial roots that give it its distinctive look. A new study reveals the genomic changes that allow the tree to produce roots that spring from its branches. ©Photo by Gang Wang

In a new study, researchers identify regions in the banyan fig’s genome that promote the development of its unusual aerial roots and enhance its ability to signal its wasp pollinator.

The study, published in the journal Cell, also identifies a sex-determining region in a related fig tree, Ficus hispida. Unlike F. microcarpa, which produces aerial roots and bears male and female flowers on the same tree, F. hispida produces distinct male and female trees and no aerial roots.

Understanding the evolutionary history of Ficus species and their wasp pollinators is important because their ability to produce large fruits in a variety of habitats makes them a keystone species in most tropical forests, said Ray Ming, a plant biology professor at the University of Illinois, Urbana-Champaign who led the study with Jin Chen, of the Chinese Academy of Sciences. Figs are known to sustain at least 1,200 bird and mammal species. Fig trees were among the earliest domesticated crops and appear as sacred symbols in Hinduism, Buddhism and other spiritual traditions.

The relationship between figs and wasps also presents an intriguing scientific challenge. The body shapes and sizes of the wasps correspond exactly to those of the fig fruits, and each species of fig produces a unique perfume to attract its specific wasp pollinator.

To better understand these evolutionary developments, Ming and his colleagues analyzed the genomes of the two fig species, along with that of a wasp that pollinates the banyan tree.

“When we sequenced the trees’ genomes, we found more segmental duplications in the genome of the banyan tree than in F. hispida, the fig without the aerial roots,” Ming said. “Those duplicated regions account for about 27% of the genome.”

The duplications increased the number of genes involved in the synthesis and transport of auxins, a class of hormones that promote plant growth. The duplicated regions also contained genes involved in plant immunity, nutrition and the production of volatile organic compounds that signal pollinators.

“The levels of auxin in the aerial roots are five times higher than in the leaves of trees with or without aerial roots,” Ming said. The elevated auxin levels appear to have triggered aerial root production. The duplicated regions also include genes that code for a light receptor that accelerates auxin production.

When they studied the genome of the fig wasp and compared it with those of other related wasps, the researchers observed that the wasps were retaining and preserving genes for odorant receptors that detect the same smelly compounds the fig trees produce. These genomic signatures are a signal of coevolution between the fig trees and the wasps, the researchers report.

Ming and his colleagues also discovered a Y chromosome-specific gene that is expressed only in male plants of F. hispida and three other fig species that produce separate male and female plants, a condition known as dioecy.

“This gene had been duplicated twice in the dioecious genomes, giving the plants three copies of the gene. But Ficus species that have male and female flowers together on one plant have only one copy of this gene,” Ming said. “This strongly suggests that this gene is a dominant factor affecting sex determination.”

Provided by University Of Illinois