TL;DR
- Researchers have developed a new way to deliver molecular therapies to cells. The system, called SEND, can be programmed to encapsulate and deliver different RNA cargoes.
- Unprecedented visualizations of SARS-CoV-2 have allowed researchers to discover how the virus enters and infects healthy human cells. Supercomputing movies have revealed how glycans — molecules that make up a sugary residue around the edges of the SARS-CoV-2 spike protein — act as infection ‘gates’ that open to allow access to our cell’s receptors.
- Researchers have identified what may be the key molecular mechanism responsible for COVID-19 mortality — an enzyme related to neurotoxins found in rattlesnake venom.
- New research shows that hamsters inoculated with spike protein gene mutants show resistance to subsequent infection with both the parental strain and the currently emerging SARS-CoV-2 alpha and gamma variants.
- Researchers have developed a method to engineer new functionalities into cells.
- Ancient-looking fish known as bowfin are guarding genetic secrets that that can help unravel humanity’s evolutionary history and better understand its health. Researchers are now decoding some of those secrets and have assembled the most complete picture of the bowfin genome to date.
- Researchers have built the world’s smallest mechanically interlocked biological structure, a deceptively simple two-ring chain made from tiny strands of amino acids called peptides.
- Scientists have helped to fill the gaps in the rhino evolutionary family tree by analyzing genomes of all five living species together with the genomes of three ancient and extinct species.
- Researchers have isolated genetic material from exuviae (discarded exoskeletons) left after insects like cicadas molt. They tested five different methods of amplifying the DNA sample by PCR, and were able to isolate nuclear DNA of good enough quality for repetitive loci known as microsatellites to be genotyped. This work is a significant contribution to insect sciences because these methods can be used for any insect species that molts.
- A team of scientists has conducted a comprehensive analysis reconstructing how kidneys form their filtering units, known as nephrons. The team studied hundreds of human and mouse nephrons at various points along their typical developmental trajectories, comparing important processes that have been conserved during the nearly 200 million years of evolution since humans and mice diverged from their common mammalian ancestor. The study details the similar genetic machinery that underpins nephron formation in humans and mice, enabling other groups of scientists to follow the logic of these developmental programs to make new types of kidney cells.
- And more!
Overview
Genetic technology is defined as the term which includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do and how DNA can be modified to add, remove or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
- The valuation of the genetic engineering market is projected to escalate to USD 6.90 MN by the end of 2027.
- Global Genetic Engineering Market is projected to grow at 12.48% CAGR during the assessment period (2017–2027).
- North America holds the largest share in the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
- Another research provider, MarketsandMarkets, forecasts the genome editing, genome engineering market to grow from USD 3.19 billion in 2017 to USD 6.28 billion by 2022, at a compounded annual growth rate (CAGR) of 14.5% during the forecast period. The key factors propelling market growth are rising government funding and growth in the number of genomics projects, high prevalence of infectious diseases (like COVID-19) and cancer, technological advancements, increasing production of genetically modified (GM) crops, and growing application areas of genomics.
Latest News & Research
Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery
by Michael Segel, Blake Lash, Jingwei Song, Alim Ladha, Catherine C. Liu, Xin Jin, Sergei L. Mekhedov, Rhiannon K. Macrae, Eugene V. Koonin, Feng Zhang in Science
Researchers from MIT, the McGovern Institute for Brain Research at MIT, the Howard Hughes Medical Institute, and the Broad Institute of MIT and Harvard have developed a new way to deliver molecular therapies to cells. The system, called SEND, can be programmed to encapsulate and deliver different RNA cargoes. SEND harnesses natural proteins in the body that form virus-like particles and bind RNA, and it may provoke less of an immune response than other delivery approaches.
The new delivery platform works efficiently in cell models, and, with further development, could open up a new class of delivery methods for a wide range of molecular medicines — including those for gene editing and gene replacement. Existing delivery vehicles for these therapeutics can be inefficient and randomly integrate into the genome of cells, and some can stimulate unwanted immune reactions. SEND has the promise to overcome these limitations, which could open up new opportunities to deploy molecular medicine.
“The biomedical community has been developing powerful molecular therapeutics, but delivering them to cells in a precise and efficient way is challenging,” said CRISPR pioneer Feng Zhang, senior author on the study, core institute member at the Broad Institute, investigator at the McGovern Institute, and the James and Patricia Poitras Professor of Neuroscience at MIT. “SEND has the potential to overcome these challenges.”
The team describes how SEND (Selective Endogenous eNcapsidation for cellular Delivery) takes advantage of molecules made by human cells. At the center of SEND is a protein called PEG10, which normally binds to its own mRNA and forms a spherical protective capsule around it. In their study, the team engineered PEG10 to selectively package and deliver other RNA. The scientists used SEND to deliver the CRISPR-Cas9 gene editing system to mouse and human cells to edit targeted genes.
First author Michael Segel, a postdoctoral researcher in Zhang’s lab, and Blake Lash, second author and a graduate student also in the group, said PEG10 is not unique in its ability to transfer RNA. “That’s what’s so exciting,” said Segel. “This study shows that there are probably other RNA transfer systems in the human body that can also be harnessed for therapeutic purposes. It also raises some really fascinating questions about what the natural roles of these proteins might be.”
The PEG10 protein exists naturally in humans and is derived from a “retrotransposon” — a virus-like genetic element — that integrated itself into the genome of human ancestors millions of years ago. Over time, PEG10 has been co-opted by the body to become part of the repertoire of proteins important for life.
Four years ago, researchers showed that another retrotransposon-derived protein, ARC, forms virus-like structures and is involved in transferring RNA between cells. Although these studies suggested that it might be possible to engineer retrotransposon proteins as a delivery platform, scientists had not successfully harnessed these proteins to package and deliver specific RNA cargoes in mammalian cells.
Knowing that some retrotransposon-derived proteins are able to bind and package molecular cargo, Zhang’s team turned to these proteins as possible delivery vehicles. They systematically searched through these proteins in the human genome for ones that could form protective capsules. In their initial analysis, the team found 48 human genes encoding proteins that might have that ability. Of these, 19 candidate proteins were present in both mice and humans. In the cell line the team studied, PEG10 stood out as an efficient shuttle; the cells released significantly more PEG10 particles than any other protein tested. The PEG10 particles also mostly contained their own mRNA, suggesting that PEG10 might be able to package specific RNA molecules.
To develop the SEND technology, the team identified the molecular sequences, or “signals,” in PEG10’s mRNA that PEG10 recognizes and uses to package its mRNA. The researchers then used these signals to engineer both PEG10 and other RNA cargo so that PEG10 could selectively package those RNAs. Next, the team decorated the PEG10 capsules with additional proteins, called “fusogens,” that are found on the surface of cells and help them fuse together.
By engineering the fusogens on the PEG10 capsules, researchers should be able to target the capsule to a particular kind of cell, tissue, or organ. As a first step towards this goal, the team used two different fusogens, including one found in the human body, to enable delivery of SEND cargo.
“By mixing and matching different components in the SEND system, we believe that it will provide a modular platform for developing therapeutics for different diseases,” said Zhang.
SEND is composed of proteins that are produced naturally in the body, which means it may not trigger an immune response. If this is demonstrated in further studies, the researchers say SEND could open up opportunities to deliver gene therapies repeatedly with minimal side effects. “The SEND technology will complement viral delivery vectors and lipid nanoparticles to further expand the toolbox of ways to deliver gene and editing therapies to cells,” said Lash.
Next, the team will test SEND in animals and further engineer the system to deliver cargo to a variety of tissues and cells. They will also continue to probe the natural diversity of these systems in the human body to identify other components that can be added to the SEND platform.
“We’re excited to keep pushing this approach forward,” said Zhang. “The realization that we can use PEG10, and most likely other proteins, to engineer a delivery pathway in the human body to package and deliver new RNA and other potential therapies is a really powerful concept.”
SARS-CoV-2 Bearing a Mutation at the S1/S2 Cleavage Site Exhibits Attenuated Virulence and Confers Protective Immunity
by Michihito Sasaki, Shinsuke Toba, Yukari Itakura, Herman M. Chambaro, Mai Kishimoto, Koshiro Tabata, Kittiya Intaruck, Kentaro Uemura, Takao Sanaki, Akihiko Sato, William W. Hall, Yasuko Orba, Hirofumi Sawa in mBio
Previous research has shown that the spike (S) protein of -CoV-2 binds to a host cell receptor, facilitating viral entry. Research has also shown that SARS-CoV-2 variants that lose the furin cleavage site at the spike protein (S gene mutants) emerge rapidly during propagation in Vero cells (lineage of cells used in cell cultures).
New research shows that hamsters inoculated with S gene mutants show resistance to subsequent infection with both the parental strain and the currently emerging SARS-CoV-2 alpha and gamma variants (B.1.1.7 variant, first identified in the U.K. and P.1. variant, first identified in Brazil, respectively). The research highlights the potential benefits of S gene mutants as immunogens (antigens that can trigger an immune response).
“SARS-CoV-2 S gene mutants may be used as immunogens for live-attenuated vaccines, similar to the current yellow fever vaccine,” said Hirofumi Sawa, Ph.D., M.D., study principal investigator in the Division of Molecular Pathobiology, International Institute for Zoonosis Control, at Hokkaido University, in Sapporo Japan, and with One Health Research Center at Hokkaido University.
In the new study, researchers set out to further characterize SARS-CoV-2 S gene mutants properties through animal experiments using hamsters. All infected animals were maintained in isolators at the biosafety level-3 facility. “Our experiments were conducted in accordance with set guidelines. Because we had to move animals with the isolators into the safety cabinet to monitor the animals, we did a lot of heavy lifting on a daily basis,” said lead study author Michihito Sasaki, Ph.D., D.V.M., a lecturer in the Division of Molecular Pathobiology, International Institute for Zoonosis Control, at Hokkaido University.
The researchers found that the SARS-CoV-2 S gene mutants are weakened variants but can induce protective immunity against infection with clinical strains of SARS-CoV-2. “Because these variants rapidly emerge through SARS-CoV-2 propagation in some cell lines, including Vero cells, researchers should be alert to the possibility of unexpected contamination with these variants,” said Dr. Sasaki.
The researchers say their next steps are to uncover the mechanism of severe COVID-19 and develop new therapeutic strategies for COVID-19.
“To overcome the COVID-19 pandemic, a multisectoral and transdisciplinary approach under the ‘One Health’ umbrella is needed,” said Dr. Sawa. “At our International Institute for Zoonosis Control, we endeavor to establish effective strategies for prediction, prevention and control of zoonotic diseases, including COVID-19.”
A glycan gate controls opening of the SARS-CoV-2 spike protein
by Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Evan Seitz, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, Rommie E. Amaro in Nature Chemistry
Since the early days of the COVID pandemic, scientists have aggressively pursued the secrets of the mechanisms that allow severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to enter and infect healthy human cells.
Early in the pandemic, University of California San Diego’s Rommie Amaro, a computational biophysical chemist, helped develop a detailed visualization of the SARS-CoV-2 spike protein that efficiently latches onto our cell receptors.
Now, Amaro and her research colleagues from UC San Diego, University of Pittsburgh, University of Texas at Austin, Columbia University and University of Wisconsin-Milwaukee have discovered how glycans — molecules that make up a sugary residue around the edges of the spike protein — act as infection gateways.
A research study led by Amaro, co-senior author Lillian Chong at the University of Pittsburgh, first author and UC San Diego graduate student Terra Sztain and co-first author and UC San Diego postdoctoral scholar Surl-Hee Ahn, describes the discovery of glycan “gates” that open to allow SARS-CoV-2 entry.
“We essentially figured out how the spike actually opens and infects,” said Amaro, a professor of chemistry and biochemistry and a senior author of the new study. “We’ve unlocked an important secret of the spike in how it infects cells. Without this gate the virus basically is rendered incapable of infection.”
Amaro believes the research team’s gate discovery opens potential avenues for new therapeutics to counter SARS-CoV-2 infection. If glycan gates could be pharmacologically locked in the closed position, then the virus is effectively prevented from opening to entry and infection.
The spike’s coating of glycans helps deceive the human immune system since it comes across as nothing more than a sugary residue. Previous technologies that imaged these structures depicted glycans in static open or closed positions, which initially didn’t draw much interest from scientists. Supercomputing simulations then allowed the researchers to develop dynamic movies that revealed glycan gates activating from one position to another, offering an unprecedented piece of the infection story.
“We were actually able to watch the opening and closing,” said Amaro. “That’s one of the really cool things these simulations give you — the ability to see really detailed movies. When you watch them you realize you’re seeing something that we otherwise would have ignored. You look at just the closed structure, and then you look at the open structure, and it doesn’t look like anything special. It’s only because we captured the movie of the whole process that you actually see it doing its thing.”
“Standard techniques would have required years to simulate this opening process, but with my lab’s ‘weighted ensemble’ advanced simulation tools, we were able to capture the process in only 45 days,” said Chong.
The computationally intensive simulations were first run on Comet at the San Diego Supercomputer Center at UC San Diego and later on Longhorn at the Texas Advanced Computing Center at UT Austin. Such computing power provided the researchers with atomic-level views of the spike protein receptor binding domain, or RBD, from more than 300 perspectives. The investigations revealed glycan “N343” as the linchpin that pries the RBD from the “down” to “up” position to allow access to the host cell’s ACE2 receptor. The researchers describe N343 glycan activation as similar to a “molecular crowbar” mechanism.
Jason McLellan, an associate professor of molecular biosciences at UT Austin and his team created variants of the spike protein and tested to see how a lack of the glycan gate affected the RBD’s ability to open. “We showed that without this gate, the RBD of the spike protein can’t take the conformation it needs to infect cells,” McLellan said.
The bowfin genome illuminates the developmental evolution of ray-finned fishes
by Andrew W. Thompson, M. Brent Hawkins, Elise Parey, Dustin J. Wcisel, Tatsuya Ota, Kazuhiko Kawasaki, Emily Funk, Mauricio Losilla, Olivia E. Fitch, Qiaowei Pan, Romain Feron, Alexandra Louis, Jérôme Montfort, Marine Milhes, Brett L. Racicot, Kevin L. Childs, Quenton Fontenot, Allyse Ferrara, Solomon R. David, Amy R. McCune, Alex Dornburg, Jeffrey A. Yoder, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Matthew P. Harris, Ingo Braasch in Nature Genetics
As we live and breathe, ancient-looking fish known as bowfin are guarding genetic secrets that that can help unravel humanity’s evolutionary history and better understand its health.
Michigan State researchers Ingo Braasch and Andrew Thompson are now decoding some of those secrets. Leading a project that included more than two dozen researchers spanning three continents, the Spartans have assembled the most complete picture of the bowfin genome to date.
“For the first time, we have what’s called a chromosome-level genome assembly for the bowfin,” said Braasch, an assistant professor of integrative biology in the College of Natural Science. “If you think of the genome like a book, what we had in the past was like having all the pages ripped out in pieces. Now, we’ve put them back in the book.”
“And in order,” added Thompson, a postdoctoral researcher in Braasch’s lab and the first author of the new research.
This is really important information for a few reasons, the duo said, and it starts with the bowfin being what Charles Darwin referred to as a “living fossil.” The bowfin, or dogfish, looks like an ancient fish.
This doesn’t mean that the bowfin hasn’t evolved since ancient times, but it has evolved more slowly than most fishes. This means that the bowfin has more in common with the last ancestor shared by fish and humans, hundreds of millions of years ago, than, say, today’s zebrafish.
Zebrafish — which are modern, so-called teleost fishes — are a notable example because they’re widely used by scientists as a model to test and develop theories about human health. Having more genetic information about the bowfin helps make the zebrafish a better model.
“A lot of research on human health and disease is done on model organisms, like mice and zebrafish,” Thompson said. “But once you identify important genes and the elements that regulate those genes in zebrafish, it can be hard to find their equivalents in humans. It’s easier to go from zebrafish to bowfin to human.”
For example, one particularly interesting gene is one that’s used in developing the bowfin’s gas bladder, an organ the fish uses to breathe and store air. Scientists believe that the last common ancestor shared by fish and humans had air-filled organs like these that were evolutionary predecessors to human lungs.
In their new study, the Spartan researchers could see that a certain genetic process in the bowfin’s gas bladder development bore striking similarities to what’s known about human lung development. A similar process is also present in the modern teleost fishes, but it’s been obscured by eons of evolution.
“When you looked for the human genetic elements of this organ development in zebrafish, you couldn’t find it because teleost fishes have higher rates of evolution,” Thompson said. “It’s there in modern fishes, but it’s hidden from view until you see it in bowfin and gar.”
The gar is another air-breathing fish with “living fossil” status that’s studied by Braasch and his team. With both the gar and bowfin genomes, the team was able to show where these genetic elements linked to gas bladder and lung formation were hiding out in the modern teleost fishes. The ancient fish enable researchers to build a better bridge between the established modern fish model organisms and human biology.
“You don’t want to base that bridge on one species,” said Braasch, who added this finding also strengthens the implications for evolutionary history. “This is another piece of the puzzle that suggests the common ancestor of fish and humans had an air-filled organ and used it for breathing at the water surface, quite similar to what you see in bowfin and gar.”
Although these findings have insights that are pertinent to all of humanity, Spartans might feel a special affinity for the bowfin. For starters, male fish turn their fins and throats a bright shade of green during spawning season. Also, famed biologist William Ballard of Dartmouth College studied bowfin development from eggs to larval fish at Michigan State’s W.K. Kellogg Biological Station during the 1980s. This was what he called his “Odyssey of Strange Fish,” and Braasch’s team now uses his work to guide their genomic analyses of bowfin development.
Bowfins are native to Michigan. They could be in the Red Cedar River on MSU’s campus now, according to Thompson, but they also can be quite elusive and, sometimes, very aggressive. This made collaborations essential for securing specimens. With colleagues at Nicholls State University in Louisiana, the team caught bowfins for genome sequencing. Amy McCune, a collaborator and professor at Cornell University, knew where to find bowfin eggs in upstate New York and had a graduate student gifted at securing these unique samples for investigating bowfin development.
The Spartans also had connections at other universities and institutions with experts in bowfin biology, chromosome evolution and more. All told, the team included researchers from six states as well as France, Japan and Switzerland. Back in East Lansing, graduate students Mauricio Losilla and Olivia Fitch, research technologist Brett Racicot, and Kevin Childs, director of the MSU Genomics Core facility, also contributed to the study, which comes with an interesting twist at the end.
Almost all vertebrate creatures that grow paired limbs or fins share a common gene.
“Humans use it, mice use it. All fishes that have been studied so far use it,” Braasch said. “The naïve expectation would be that bowfin do, too.”
But that’s not what the team found. The bowfin, the “living fossil,” has evolved a different way of growing its paired fins.
“For whatever reason, it changed its genetic programming. Even ‘living fossils’ keep evolving. They’re not frozen in time,” Braasch said. “It’s sort of a cautionary tale that we shouldn’t take these things for granted. You have to look trait by trait, gene by gene and across many different species to paint the complete picture.”
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
by Shanlin Liu, Michael V. Westbury, Nicolas Dussex, Kieren J. Mitchell, Mikkel-Holger S. Sinding, Peter D. Heintzman, David A. Duchêne, Joshua D. Kapp, Johanna von Seth, Holly Heiniger, Fátima Sánchez-Barreiro, Ashot Margaryan, Remi André-Olsen, Binia De Cahsan, Guanliang Meng, Chentao Yang, Lei Chen, Tom van der Valk, Yoshan Moodley, Kees Rookmaaker, Michael W. Bruford, Oliver Ryder, Cynthia Steiner, Linda G.R. Bruins-van Sonsbeek, Sergey Vartanyan, Chunxue Guo, Alan Cooper, Pavel Kosintsev, Irina Kirillova, Adrian M. Lister, Tomas Marques-Bonet, Shyam Gopalakrishnan, Robert R. Dunn, Eline D. Lorenzen, Beth Shapiro, Guojie Zhang, Pierre-Olivier Antoine, Love Dalén, M. Thomas P. Gilbert in Cell
There’s been an age-old question going back to Darwin’s time about the relationships among the world’s five living rhinoceros species. One reason answers have been hard to come by is that most rhinos went extinct before the Pleistocene. Now, researchers have helped to fill the gaps in the rhino evolutionary family tree by analyzing genomes of all five living species together with the genomes of three ancient and extinct species.
The findings show that the oldest split separated African and Eurasian lineages about 16 million year ago. They also find that — while dwindling populations of rhinos today have lower genetic diversity and more inbreeding than they did in the past — rhinoceroses have historically had low levels of genetic diversity.
“We can now show that the main branch in the rhinoceroses’ tree of life is among geographic regions, Africa versus Eurasia, and not between the rhinos that have one versus two horns,” says Love Dalén of the Centre for Palaeogenetics and the Swedish Museum of Natural History. “The second important finding is that all rhinoceroses, even the extinct ones, have comparatively low genetic diversity. To some extent, this means that the low genetic diversity we see in present-day rhinos, which are all endangered, is partly a consequence of their biology.
“All eight species generally displayed either a continual but slow decrease in population size over the last 2 million years, or continuously small population sizes over extended time periods,” said Mick Westbury of the University of Copenhagen, Denmark. “Continuously low population sizes may indicate that rhinoceroses in general are adapted to low levels of diversity.”
This notion is consistent with an apparent lack of accumulated deleterious mutations in rhinos in recent decades. Westbury says that rhinos may have purged deleterious mutations in the last 100 years, allowing them to remain relatively healthy, despite low genetic diversity.
The new study was inspired at a scientific meeting. Dalén and Tom Gilbert, University of Copenhagen, had been working separately on different rhino species. They realized that if they joined forces, along with colleagues around the world, they could do a comparative study of all living rhinos together with the three species that went extinct during the last Ice Age.
There were some challenges to overcome, says Shanlin Liu, China Agricultural University, Beijing. “When we decided to put together all the rhinoceroses’ data and conduct a comparative genomics study, we also confronted the ‘big data’ problem,” Liu explained.
The genome data represented different data types, in part due to the inclusion of both modern and ancient DNA. The team had to develop new analysis tools to take those differences into account. The new approaches and tools they developed can now be applied to studies in other taxonomic groups.
Dalén says that the findings are “partly good news, and partly not.” It appears that low levels of genetic diversity in rhinos is part of their long-term history and hasn’t led to an increase in health problems related to inbreeding and disease-causing mutations.
“However, we also find that present-day rhinos have lower genetic diversity, and higher levels of inbreeding, compared to our historical and prehistoric rhinoceros genomes,” he says. “This suggests that recent population declines caused by hunting and habitat destruction have had an impact on the genomes. This is not good, since low genetic diversity and high inbreeding may increase the risk of extinction in the present-day species.”
The findings do have some practical implications for rhino conservation, the researchers say.
“Now we know that the low diversity we see in contemporary individuals may not be indicative of an inability to recover, but instead a natural state of rhinoceros,” Westbury says. “We can better guide recovery programs to focus on increasing population size rather than individual genetic diversity.”
The team hopes that the new findings will be useful for continued study of rhinoceroses and their conservation. Dalén reports that his team is now working on a more in-depth study of the extinct woolly rhinoceros. Meanwhile, Westbury is involved in comparing the genomes of African black rhinoceros sampled from before the recent decrease in population size to those of contemporary individuals.
“We hope that this will provide a framework to better understand where translocated populations may have arisen from, direct changes in genetic diversity, and whether any populations may have been lost forever because of humans,” Westbury said.
Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation
by Christopher D. Reinkemeier, Edward A. Lemke in Cell
Researchers at the Institute of Molecular Biology (IMB) and Johannes Gutenberg University Mainz (JGU) have developed a method to engineer new functionalities into cells.
Numerous processes occur inside living cells, from DNA replication and repair to protein synthesis and recycling. In order to organise this plethora of reactions, they must be separated in three-dimensional space. One way eukaryotic cells do this is by extruding a piece of membrane to form a membrane-enclosed space — an organelle — in which specific functions can take place. Alternatively, the cell can also segregate molecules into distinct areas (so-called membraneless organelles) through phase separation, a phenomenon similar to the separation of vinegar and oil in a salad dressing. Such membraneless organelles have advantages: as they are not separated from the rest of the cell by a membrane barrier, large molecules can get in and out more easily. Membrane-enclosed organelles therefore operate like separate “rooms” in a cell, while membraneless organelles operate like different corners of the same room.
One of the most important processes in the cell is protein synthesis, where the RNA code is translated into a protein code, which contains the blueprint for making proteins. These codes are like the languages of the cell. If an organelle could be engineered and dedicated to translate the RNA code in new ways (i.e. use a different language), the functions of the resulting protein could also be changed, endowing it with unique properties that could be used, for example, to switch its functions on or off, or to allow the protein to be visualised in living cells.
In 2019, Prof. Edward Lemke and his research team succeeded in creating an artificial membraneless organelle that translated the RNA code using a new code, or language, without interfering with RNA translation in the rest of the cell. Now Edward and a student from his lab, Christopher Reinkemeier, have further built on this success by creating film-like organelles that can be used to subdivide cell processes into even smaller spaces.
“The biggest gain is that we were able to create extremely small reaction spaces — this way we can have several of them in a cell at the same time,” explains Prof. Lemke. “We have converted the large 3D organelles into 2D organelles on a membrane surface, and can even run complicated biochemical reactions in these thin layers.”
Using these thinner organelles, the same cell can now translate the RNA code into three different languages — thus creating three different proteins — in different “corners of the same room,” without the translations interfering with each other. This means that the same protein can now have three different functions, depending on which “corner” it was made in.
This novel method not only allows scientists to engineer proteins with unique functions, but also helps them to better understand how eukaryotic cell functions evolve.
“We can find out more about how complicated functions occur in the membrane space, what unique functionalities the membrane has, and what special reaction spaces are created there when you concentrate proteins using 2D phase separation,” says Dr Reinkemeier. “Through engineering these film-like organelles, we can also better understand how nature also uses such mechanisms to create proteins with new functions.”
Group IIA secreted phospholipase A2 is associated with the pathobiology leading to COVID-19 mortality
by Justin M. Snider, Jeehyun Karen You, Xia Wang, Ashley J. Snider, Brian Hallmark, Manja M. Zec, Michael C. Seeds, Susan Sergeant, Laurel Johnstone, Qiuming Wang, Ryan Sprissler, Tara F. Carr, Karen Lutrick, Sairam Parthasarathy, Christian Bime, Hao H. Zhang, Chiara Luberto, Richard R. Kew, Yusuf A. Hannun, Stefano Guerra, Charles E. McCall, Guang Yao, Maurizio Del Poeta, Floyd H. Chilton in Journal of Clinical Investigation
An enzyme with an elusive role in severe inflammation may be a key mechanism driving COVID-19 severity and could provide a new therapeutic target to reduce COVID-19 mortality, according to a study.
Researchers from the University of Arizona, in collaboration with Stony Brook University and Wake Forest University School of Medicine, analyzed blood samples from two COVID-19 patient cohorts and found that circulation of the enzyme — secreted phospholipase A2 group IIA, or sPLA2-IIA — may be the most important factor in predicting which patients with severe COVID-19 eventually succumb to the virus.
sPLA2-IIA, which has similarities to an active enzyme in rattlesnake venom, is found in low concentrations in healthy individuals and has long been known to play a critical role in defense against bacterial infections, destroying microbial cell membranes.
When the activated enzyme circulates at high levels, it has the capacity to “shred” the membranes of vital organs, said Floyd (Ski) Chilton, senior author on the paper and director of the UArizona Precision Nutrition and Wellness Initiative housed in the university’s College of Agriculture and Life Sciences.
“It’s a bell-shaped curve of disease resistance versus host tolerance,” Chilton said. “In other words, this enzyme is trying to kill the virus, but at a certain point it is released in such high amounts that things head in a really bad direction, destroying the patient’s cell membranes and thereby contributing to multiple organ failure and death.”
Together with available clinically tested sPLA2-IIA inhibitors, “the study supports a new therapeutic target to reduce or even prevent COVID-19 mortality,” said study co-author Maurizio Del Poeta, a SUNY distinguished professor in the Department of Microbiology and Immunology in the Renaissance School of Medicine at Stony Brook University.
“The idea to identify a potential prognostic factor in COVID-19 patients originated from Dr. Chilton,” Del Poeta said. “He first contacted us last fall with the idea to analyze lipids and metabolites in blood samples of COVID-19 patients.”
Del Poeta and his team collected stored plasma samples and went to work analyzing medical charts and tracking down critical clinical data from 127 patients hospitalized at Stony Brook University between January and July 2020. A second independent cohort included a mix of 154 patient samples collected from Stony Brook and Banner University Medical Center in Tucson between January and November 2020.
“These are small cohorts, admittedly, but it was a heroic effort to get them and all associated clinical parameters from each patient under these circumstances,” Chilton said. “As opposed to most studies that are well planned out over the course of years, this was happening in real time on the ICU floor.”
The research team was able to analyze thousands of patient data points using machine learning algorithms. Beyond traditional risk factors such as age, body mass index and preexisting conditions, the team also focused on biochemical enzymes, as well as patients’ levels of lipid metabolites.
“In this study, we were able to identify patterns of metabolites that were present in individuals who succumbed to the disease,” said lead study author Justin Snider, an assistant research professor in the UArizona Department of Nutrition. “The metabolites that surfaced revealed cell energy dysfunction and high levels of the sPLA2-IIA enzyme. The former was expected but not the latter.”
Using the same machine learning methods, the researchers developed a decision tree to predict COVID-19 mortality. Most healthy individuals have circulating levels of the sPLA2-IIA enzyme hovering around half a nanogram per milliliter. According to the study, COVID-19 was lethal in 63% of patients who had severe COVID-19 and levels of sPLA2-IIA equal to or greater than 10 nanograms per milliliter.
“Many patients who died from COVID-19 had some of the highest levels of this enzyme that have ever been reported,” said Chilton, who has been studying the enzyme for over three decades.
The role of the sPLA2-IIA enzyme has been the subject of study for half of a century and it is “possibly the most examined member of the phospholipase family,” Chilton explained.
Charles McCall, lead researcher from Wake Forest University on the study, refers to the enzyme as a “shredder” for its known prevalence in severe inflammation events, such as bacterial sepsis, as well as hemorrhagic and cardiac shock.
Previous research has shown how the enzyme destroys microbial cell membranes in bacterial infections, as well as its similar genetic ancestry with a key enzyme found in snake venom.
The protein “shares a high sequence homology to the active enzyme in rattlesnake venom and, like venom coursing through the body, it has the capacity to bind to receptors at neuromuscular junctions and potentially disable the function of these muscles,” Chilton said.
“Roughly a third of people develop long COVID, and many of them were active individuals who now can’t walk 100 yards. The question we are investigating now is: If this enzyme is still relatively high and active, could it be responsible for part of the long COVID outcomes that we’re seeing?”
Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides
by Hendrik V. Schröder, Yi Zhang, A. James Link in Nature Chemistry
Researchers at Princeton University have built the world’s smallest mechanically interlocked biological structure, a deceptively simple two-ring chain made from tiny strands of amino acids called peptides.
In a paper, the team detailed a library of such structures made in their lab — two interlocked rings, a ring on a dumbbell, a daisy chain and an interlocked double lasso — each around one billionth of a meter in size. The study also demonstrates that some of these structures can toggle between at least two shapes, laying the groundwork for a biomolecular switch.
“We’ve been able to build a bunch of structures that no one’s been able to build before,” said A. James Link, professor of chemical and biological engineering, the study’s principal investigator. “These are the smallest threaded or interlocking structures you can make out of peptides.”
To craft these gadgets, dubbed mechanically interlocked peptides, or MIPs, the researchers used genetic engineering to manipulate individual amino acids in a naturally occurring lasso peptide, microcin J25, and direct the peptide to self-assemble into new shapes.
They also bypassed the need for the harsh solvents and metal ions used in building similar synthetic molecular architectures, work that was the focus of the 2016 Nobel Prize in chemistry. This work, using a single-pot protocol in water, leverages minimal control over the peptides’ own form-finding program to create an entirely new class of technology.
“It’s really building a bridge between the biological world,” Link said, “and what until now has been the playground of synthetic chemistry.”
Efficient PCR Amplification Protocol of Nuclear Microsatellites for Exuviae-Derived DNA of Cicada, Yezoterpnosia nigricosta
by Keisuke Yumoto, Takashi Kanbe, Yoko Saito, Shingo Kaneko, Yoshiaki Tsuda in Frontiers in Insect Science
Research into insect species can benefit from genetic studies. However, genetic samples can often be difficult to collect in a non-invasive manner, especially when the insects are only found in a particular location or are endangered.
Some insects, such as cicadas, shed their outer hard “exoskeleton” as part of their normal growth in a process known as molting. The structures that are left behind are called exuviae. Cicada exuviae are left on tree trunks and are easy to collect. Exuviae have been used for some genetic research in the past on mitochondria, small and ubiquitous parts of the cell, but no previous studies have been able to isolate and sequence nuclear DNA from exuviae.
When only a very small DNA sample is available, the size of the sample can be increased, or “amplified,” by a process known as PCR, or polymerase chain reaction. PCR can make millions of copies of a small sample of DNA to give a large enough sample for detailed study. Now, a team from the University of Tsukuba have tested five different PCR methods to amplify the DNA isolated from exuviae for sequencing.
The team focused on sequencing microsatellites, regions of the genome where a particular DNA pattern is repeated many times. These regions are promising targets because they can be amplified from just a small amount of DNA, and the process is cost efficient. Microsatellites also show a great deal of variation and are already used in molecular ecology studies as effective genetic markers.
First, the team isolated DNA from cicada exuviae and amplified the samples using the different PCR methods. They then compared the results with those taken from adult insects, to check the quality of the samples produced. The best results were seen from the PCR reaction that used an enzyme called TaKaRa LA Taq polymerase, which resulted in a DNA sample comparable to the sample isolated from adult insects. The best results were also seen from fresh exuviae.
“Our work shows that DNA that has been isolated from cicada exuviae can be amplified by PCR, and that cicada exuviae give samples of good enough quality to allow multiple independent nuclear DNA microsatellite marker loci to be genotyped. This approach will be very useful to evaluate population genetic structure and demography of forest insect species in relation to conservation and the ecosystem under ongoing climate change,” explains senior author Yoshiaki Tsuda.
This study makes a significant contribution to insect sciences because the methods here are applicable not only to cicadas but also to any other insect species that molt to leave exuviae.
Spatial transcriptional mapping of the human nephrogenic program
by Nils O. Lindström, Rachel Sealfon, Xi Chen, Riana K. Parvez, Andrew Ransick, Guilherme De Sena Brandine, Jinjin Guo, Bill Hill, Tracy Tran, Albert D. Kim, Jian Zhou, Alicja Tadych, Aaron Watters, Aaron Wong, Elizabeth Lovero, Brendan H. Grubbs, Matthew E. Thornton, Jill A. McMahon, Andrew D. Smith, Seth W. Ruffins, Chris Armit, Olga G. Troyanskaya, Andrew P. McMahon in Developmental Cell
When it comes to building a kidney, only nature possesses the complete set of blueprints. But a USC-led team of scientists has managed to borrow some of nature’s pages through a comprehensive analysis of how kidneys form their filtering units, known as nephrons.
The study from Andy McMahon’s lab in the Department of Stem Cell Biology and Regenerative Medicine at USC was led by Nils Lindström, who started the research as a postdoctoral fellow and is now an assistant professor in the same department. The study also brought in the expertise of collaborators from Princeton University and the University of Edinburgh in the UK.
The team traced the blueprints for how cells interact to lay the foundations of the human kidney, and how abnormal developmental processes could contribute to disease. Their findings are publicly available as part of the Human Nephrogenesis Atlas, which is a searchable database showing when and where genes are active in the developing human kidney, and predicting regulatory interactions going on in developing cell types.
“There’s only one way to build a kidney, and that’s nature’s way,” said McMahon, who is the director of the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC. “Only by understanding the logical framework of normal embryonic development can we improve our ability to synthesize cell types, model disease and ultimately build functional systems to replace defective kidneys.”
To reconstruct nature’s molecular and cellular blueprints, the team studied hundreds of human and mouse nephrons at various points along their typical developmental trajectories. This allowed the researchers to compare important processes that have been conserved during the nearly 200 million years of evolution since humans and mice diverged from their common mammalian ancestor.
The study details the similar genetic machinery that underpins nephron formation in humans and mice, enabling other groups of scientists to follow the logic of these developmental programs to make new types of kidney cells. All told, there are at least 20 specialized cell types that form the kidney’s intricate tubular network, which helps maintain the body’s fluid and pH balance, filter the blood, and concentrate toxins into the urine for excretion.
“By generating detailed views of the beautifully complex process by which human nephrons form, we aim to enhance our understanding of development and disease, while guiding efforts to build synthetic kidney structures,” said Lindström.
The scientists were also able to determine the precise positions of expressed genes with known roles in Congenital Abnormalities of the Kidney and Urinary Tract (CAKUT). In specific types of cells, the researchers identified networks of interacting genes. Based on these associations, the team predicted new candidate genes to explore in CAKUT and other kidney diseases.
“Our approach of inferring spatial coordinates for genes expressed in individual cells could be widely used to create similar atlases of other developing organ systems — something that is an important focus of many research groups around the world,” said Lindström. “The study exemplifies the impact of collaborative science bringing together expertise across the US and Europe to connect developmental anatomy with cutting-edge molecular, computational and microscopy tools.”
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