TL;DR
- Scientists have developed a new method to determine how proteins are organized on the surface of cells. Insights gained with the technology could lead to the development of novel drugs to fight cancer.
- Scientists have used gene editing technology to create female-only and male-only mice litters with 100% efficiency.
- Researchers have identified the first non-coding RNA that controls formation of chromosome loops, which govern gene expression. Jpx RNA was previously thought to be involved only in X chromosome inactivation, a necessary step in development of female embryos. This discovery could create new targets for drug developers.
- Scientists have discovered a new route to produce complex antibiotics exploiting gene editing to re-program pathways to future medicines urgently required to combat antimicrobial resistance, treat neglected diseases and prevent future pandemics.
- A new study uses novel single-cell profiling techniques to reveal how plants add new cell layers that help them resist climate stressors like drought or flooding. The research focuses on corn in an effort to create a cell-by-cell map of the plant’s root system, which mediates drought stress and absorbs nutrients and fertilizer from the soil.
- Researchers have developed a method to precisely and rapidly correct genetic alterations in the cultured patient cells.
- The majority of dog breeds are highly inbred, contributing to an increase in disease and health care costs throughout their lifespan, according to new research.
- Biologists have discovered how a pathogenic fungus can bypass the immune system of plants. By releasing an ‘effector’ molecule, it avoids elimination at a critical stage in its reproduction cycle.
- Scientists have collaborated to build a structurally-motivated deep learning method built from recent advances in neural language modeling. The team’s deep-learning model, called D-SCRIPT, was able to predict protein-protein interactions (PPIs) from primary amino acid sequences.
- Using artificial intelligence and deep learning, researchers have developed a neural network that ‘hallucinates’ the structures of new protein molecules. The scientists made up completely random protein sequences and introduced mutations into them until the neural network predicted they would fold into stable structures. The software was not guided toward a particular outcome; the proteins were just what the computer dreams up. Next step: using deep learning to try to design proteins with particular functions, such as enzymes or drugs.
- 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
Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Maik Müller, Fabienne Gräbnitz, Niculò Barandun, Yang Shen, Fabian Wendt, Sebastian N. Steiner, Yannik Severin, Stefan U. Vetterli, Milon Mondal, James R. Prudent, Raphael Hofmann, Marc van Oostrum, Roman C. Sarott, Alexey I. Nesvizhskii, Erick M. Carreira, Jeffrey W. Bode, Berend Snijder, John A. Robinson, Martin J. Loessner, Annette Oxenius, Bernd Wollscheid in Nature Communications
Biological cells have multiple functions, and they need to communicate with each other to coordinate them. Molecules on the cell surface are central to this process. For decades, biologists have been studying such surface proteins and it is becoming increasingly clear that not only their presence but also their organisation on the cell’s surface is crucial to the function of a cell.
“Proteins aren’t simply distributed evenly and independently of one another across the cell’s surface; instead, they’re organised into molecular communities. In these communities, proteins often work together to fulfil cellular functions,” explains Bernd Wollscheid, Professor at ETH Zurich’s Institute of Translational Medicine. Together with a large interdisciplinary team that includes further researchers from ETH Zurich and other institutions, Wollscheid’s doctoral student Maik Müller has now developed a technology that can be used to discover the organisation of cell surface molecules.
With this technology called LUX-MS, the researchers can determine with nanometer-scale precision how proteins integrate into an organisation on the cell surface — in other words, which proteins are in proximity to each other. So far, scientists were able to measure interactions of individual proteins that have a high affinity for each other, as well as for molecules that reside inside the cell. However, the new method is the first to enable scientists to specifically detect the organisation of the entirety of cell surface molecules. Wollscheid refers to this entirety as the “surfaceome.” The term is composed of the word “surface” and the suffix “-ome,” that is also used in terms such as genome or proteome.
With a twinkle in his eye, Wollscheid explains the principle behind the method as follows: “We specifically modify a particular surface molecule so that it likes to ‘give kisses’ to molecules in its proximity, and then we check the other surface molecules for traces of lipstick.” In more technical terms, a small chemical compound is attached to a protein of interest. When irradiated with light, this compound produces small amounts of what are known as reactive oxygen molecules, that oxidise surface proteins in the immediate vicinity. Using a specific enrichment method and mass spectrometry in combination with statistical data analysis, the scientists can ultimately identify which molecules have been oxidised.
To determine the distance between the protein of interest and the other molecules, the researchers repeat their experiments under slightly modified conditions that affect the amount and survival time of the reactive oxygen molecules. These include the length of irradiation with light and the choice of medium in which the cells are cultured. The more reactive oxygen is locally generated and the longer that process continues, the wider the area in which surface molecules get oxidised.
Wollscheid and his colleagues will now use the technology to compare cells from healthy and diseased people. “We’re trying to understand how a disease changes the organisation of proteins at the cellular level — for example, when a healthy cell transforms into a cancer cell,” Wollscheid says. The scientists are in the process of creating a reference map of healthy cells. They then plan to use it to identify differences in the organisation of protein communities on the surface of diseased cells.
Knowing which molecules exist on cell surfaces and how they are organised could become significant in areas such as the development of novel drugs to fight cancer. Modern cancer drugs employ a cell-killing agent is often coupled to an antibody that recognises a surface molecule that is present in large quantities on cancer cells. This means the cancer cells are killed with a reasonable degree of specificity. However, many cancer-specific surface molecules are also found on healthy cells, albeit at lower concentrations, provoking these drugs to also kill some healthy cells.
If two molecules were found to be adjacent only on a diseased but not on a healthy cell, drugs could be developed that recognise these two molecules together. The drug would then kill a cell only if both molecules were present on the cell and adjacent to each other. This is precisely the information that the new technology provides.
In the published work, the scientists showed that the scope for using this method goes beyond the investigations of which cell surface molecules are next to each other. They also tagged viruses and drugs with the small chemical compound that produces reactive oxygen. This allows the researchers to study the binding events of viruses or drugs to cells. Furthermore, the method makes it possible to investigate which protein communities are involved in the interaction between two different cells. The scientists demonstrated this using the example of communication between immune cells.
“In this way, the new method can help to understand how drugs work and how viruses or immune cells recognise other cells,” says ETH doctoral student Müller. “The method is therefore of great benefit for research at universities and in industry.”
CRISPR-Cas9 effectors facilitate generation of single-sex litters and sex-specific phenotypes
by Charlotte Douglas, Valdone Maciulyte, Jasmin Zohren, Daniel M. Snell, Shantha K. Mahadevaiah, Obah A. Ojarikre, Peter J. I. Ellis, James M. A. Turner in Nature Communications
Scientists at the Francis Crick Institute, in collaboration with University of Kent, have used gene editing technology to create female-only and male-only mice litters with 100% efficiency.
This proof of principle study, demonstrates how the technology could be used to improve animal welfare in scientific research and perhaps also agriculture.
In scientific research and also farming, there is often a need for either male or female animals. For example, laboratory research into male or female reproduction requires only animals of the sex being studied. And in farming, only female animals are required for egg production and in dairy herds. This means it is common practice for animals of the unrequired sex to be culled after birth.
The researchers’ new method uses a two-part genetic system to inactivate embryos shortly after fertilisation, allowing only the desired sex to develop. Such a genetically-based method to control the sex of offspring could drastically reduce culling in both industries.
The embryo selection is based on the fact that there are two elements of CRISPR-Cas9 — the Cas9 enzyme that cuts the DNA, allowing scientists to alter specific regions, and the guide RNA which carries the Cas9 to the right location on the genome. The team placed one element of the system on the father’s X or Y chromosome, meaning that it will only be inherited by female or male embryos respectively. The other element is contributed by the mother, and is inherited by all embryos.
They targeted the Top1 gene, which is essential to DNA replication and repair. When an embryo formed from a sperm and egg, each containing one half of CRISPR-Cas9, the gene-editing was triggered in the embryo and it was not able to develop beyond a very early stage of around 16 to 32 cells.
Using this method, the researchers were able to control, with 100% effect, the sex of a litter. To produce a male-only litter, the researchers edited the father’s X chromosome, meaning only females inherited the deleterious mutation, and for a female-only litter, they edited the Y chromosome.
Surprisingly, the method did not lead to a 50% decrease in the number of offspring produced, rather the litter sizes were between 61% — 72% of the control litters. The researchers suggest this is because animals such as mice produce more eggs than required during each ovarian cycle, allowing for a proportion of them to be lost during early development without reducing litter size. This means that in situations where one sex is needed, fewer breeding animals will be required in order to produce the same number of the desired sex of offspring. As the Top1 gene is well conserved across mammals, these results may also be applicable to other animals.
Charlotte Douglas, first author and former PhD student and postdoctoral scientist at the Crick, says: “This method works as we split the genome editing process in half, between a male and female, and it is only when the two halves meet in an embryo through breeding, that it is activated. Embryos with both halves cannot develop beyond very early cell stages.
“We’ve also shown this process works successfully in different combinations — introducing either the Cas9 or the guide RNA elements on to the mother’s or father’s chromosomes.”
As the offspring which survive only contain half of the CRISPR-Cas9 elements within their genome, this acts as a control preventing the sex-selection being passed down to further generations, unless they are selectively bred with an individual of the opposite sex containing the other half. This is different to genetic engineering through ‘gene-drive’ methods, which seek to spread a genetic mutation widely amongst a population.
There are also no harmful effects of the gene edit in the surviving offspring.
James Turner, author and group leader of the Sex Chromosome Biology Laboratory at the Crick says: “This work could have immediate and valuable impact in scientific laboratories, as we’ve shown how it is safe and effective in mice, a common mammal used in medical and scientific research. While a lot of research needs both sexes, there are areas of study where only one is needed. For example, when studying the reproductive system, sex-specific diseases, or certain hormones.”
Peter Ellis, author and senior lecturer in molecular genetics and reproduction at University of Kent, says: “The implications of this work are potentially far-reaching when it comes to improving animal welfare, but should be considered at ethical and regulatory levels.
Ground tissue circuitry regulates organ complexity in maize and Setaria
by Carlos Ortiz-Ramírez, Bruno Guillotin, Xiaosa Xu, Ramin Rahni, Sanqiang Zhang, Zhe Yan, Poliana Coqueiro Dias Araujo, Edgar Demesa-Arevalo, Laura Lee, Joyce Van Eck, Thomas R. Gingeras, David Jackson, Kimberly L. Gallagher, Kenneth D. Birnbaum in Science
A new study uses novel single-cell profiling techniques to reveal how plants add new cell layers that help them resist climate stressors like drought or flooding. The research focuses on corn — a critically important crop around the world — in an effort to create a cell-by-cell map of the plant’s root system, which mediates drought stress and absorbs nutrients and fertilizer from the soil.
“We discovered how corn expands its cortex tissue, which makes up much of the crop’s root system. Adding layers to the cortex tissue is a key evolutionary feature that generates ways for plants to tolerate drought and flooding and improve nutrient uptake,” said Kenneth Birnbaum, a professor in New York University’s Department of Biology and Center for Genomics and Systems Biology and the senior author of the paper.
“These traits will be critical targets to allow plants to withstand global warming and reduce the carbon footprint of crops,” added Birnbaum, whose lab at NYU led the project in collaboration with researchers at Cold Spring Harbor Laboratory and the University of Pennsylvania.
To create a single-cell map of the corn root, the researchers first broke apart the root using cell-wall digesting enzymes to generate single, free-floating cells. New approaches then allowed them to analyze mRNA content of individual cells — distinguishing molecular features that lead to specific types of specialized cells — using miniaturized droplet-based single cell-sequencing techniques.
They next mapped the cells back to their location in the corn root, akin to assembling a 10,000-piece jigsaw puzzle without a guide. To solve the puzzle, the researchers used fluorescent dyes that penetrated into root tissues at variable depths to label and isolate different layers, like separating the layers of an onion, giving them gene landmarks to map the single cells.
“This second layer of information essentially gave us the puzzle box that allowed us to precisely map cells to their appropriate location in order to recreate a 3D model of gene expression throughout the entire corn root,” said Carlos Ortiz Ramirez of the NYU Center for Genomics and Systems Biology and UGA Laboratorio Nacional de Genómica para la Biodiversidad in Mexico, who was the first author of the study.
The new map of the corn root revealed previously undescribed cellular specialization in the cortex of the root. The cortex is particularly important because it comprises the bulk of the early corn root and has more than 10 layers. In addition, the cortex cellular subtypes are of critical importance for traits that help crop plants cope with environmental stressors. For example, the inner cortex layer is where symbiotic fungi exchange nutrients with the plant, and increased cooperation could help lessen the carbon footprint of agriculture. Middle layers of cortex create air tunnels that enable gas exchange during flooding, while on-demand expansion of the cortex can reduce water loss during drought stress.
“Using our 3D model of the corn root, we mapped out four distinct cortex layer signatures that could provide important genetic targets for further improvement in symbiosis, flooding, and drought,” said Ortiz Ramirez.
Furthermore, the group found clues within the new map of the root about how corn could generate the extra layers of cortex. In particular, the key gene regulator known as SHORT ROOT (SHR), whose function is similar across different plants, was in an intriguing position that was different from other plants with just one layer of cortex.
In Arabidopsis, a small flowering plant commonly used as a model organism in plant biology, SHR was one of the first transcription factors shown to move from cell to cell, allowing inner cell types to give instructions to middle layers to create a new tissue. That makes SHR a type of local organizer, directing root tissues to assemble around a core pattern. However, in corn, the single-cell map revealed that SHR was in a new position right next to the multiple layers of cortex, a convenient “jumping off” point to expand the multiple cortex layers. Indeed, the researchers tracked SHR protein movement and found that it was hypermobile, moving not just one layer but multiple layers through the cortex.
Moreover, mutations that disturbed SHR function in both corn and the corn relative foxtail millet had a severely reduced number of cortex layers. This demonstrates how SHR kept its primary role in expanding tissue layers and generating new cell identities but switched its location to add new cell types that ultimately allow corn to cope with environmental stresses.
“Identifying SHR has a key regulator of cortex expansion is an important first step,” said Birnbaum. “Moving forward, tweaking these regulators could provide tools to alter the number of cortex layers or subtypes that could enhance their ability to withstand climate stressors like drought, or improve nitrogen uptake, allowing plants to use less fertilizer or grow in nutrient-poor soil.”
The effect of inbreeding, body size and morphology on health in dog breeds
by Danika Bannasch, Thomas Famula, Jonas Donner, Heidi Anderson, Leena Honkanen, Kevin Batcher, Noa Safra, Sara Thomasy, Robert Rebhun in Canine Medicine and Genetics
Dog breeds are often recognized for distinctive traits — the short legs of a dachshund, wrinkled face of a pug, spotted coat of a Dalmatian. Unfortunately, the genetics that give various breeds their particular attributes are often the result of inbreeding.
In a recent study, an international team of researchers led by University of California, Davis, veterinary geneticist Danika Bannasch show that the majority of canine breeds are highly inbred, contributing to an increase in disease and health care costs throughout their lifespan.
“It’s amazing how inbreeding seems to matter to health,” Bannasch said. “While previous studies have shown that small dogs live longer than large dogs, no one had previously reported on morbidity, or the presence of disease. This study revealed that if dogs are of smaller size and not inbred, they are much healthier than larger dogs with high inbreeding.”
The average inbreeding based on genetic analysis across 227 breeds was close to 25%, or the equivalent of sharing the same genetic material with a full sibling. These are levels considered well above what would be safe for either humans or wild animal populations. In humans, high levels of inbreeding (3–6%) have been associated with increased prevalence of complex diseases as well as other conditions.
“Data from other species, combined with strong breed predispositions to complex diseases like cancer and autoimmune diseases, highlight the relevance of high inbreeding in dogs to their health,” said Bannasch, who also serves as the Maxine Adler Endowed Chair in Genetics at the UC Davis School of Veterinary Medicine.
The researchers partnered with Wisdom Health Genetics, a world leader in pet genetics, to obtain the largest sample size possible for analysis. Wisdom Health’s database is the largest dog DNA database in the world, helping researchers collect data from 49,378 dogs across 227 breeds — primarily from European sources.
So, what makes a dog breed more inbred than others? Bannasch explained that it’s often a combination of a small founding population followed by strong selection for particular traits in a breed — often based on looks rather than purpose. While she has always had an interest in the population structure of some of these breeds, she became particularly interested in the Danish-Swedish farmdog several years ago. She fell in love with their compact size, disposition and intelligence, and ended up importing one from Sweden.
Bannasch discovered that Danish-Swedish farmdogs have a low level of inbreeding based on their history of a relatively large founding population of 200, and being bred for function, rather than a strong artificial selection for looks. And according to the insurance health data on breeds collected from Agria Insurance Sweden and hosted online by the International Partnership for Dogs, the farmdog is one of the healthiest breeds.
The study also revealed a significant difference in morbidity between brachycephalic (short skull and snout) and non-brachycephalic breeds. While that finding wasn’t unexpected, the researchers removed brachycephalic breeds from the final analysis on effects of inbreeding on health.
In the end, Bannasch said she isn’t sure there is a way out of inbred breeds. People have recognized that creating matches based solely on pedigrees is misleading. The inbreeding calculators don’t go back far enough in a dog’s genetic line, and that method doesn’t improve overall high levels of population inbreeding. There are other measures that can be taken to preserve the genetic diversity and health of a breed, she said. They include careful management of breeding populations to avoid additional loss of existing genetic diversity, through breeder education and monitoring of inbreeding levels enabled by direct genotyping technologies.
Outcrosses are being proposed or have already been carried out for some breeds and conditions as a measure to increase genetic diversity, but care must be taken to consider if these will effectively increase overall breed diversity and therefore reduce inbreeding, Bannasch said. In particular, in the few breeds with low inbreeding levels, every effort should be made to maintain the genetic diversity that is present.
De novo protein design by deep network hallucination
by Ivan Anishchenko, Samuel J. Pellock, Tamuka M. Chidyausiku, Theresa A. Ramelot, Sergey Ovchinnikov, Jingzhou Hao, Khushboo Bafna, Christoffer Norn, Alex Kang, Asim K. Bera, Frank DiMaio, Lauren Carter, Cameron M. Chow, Gaetano T. Montelione, David Baker. in Nature
Just as convincing images of cats can be created using artificial intelligence, new proteins can now be made using similar tools. Researchers describe the development of a neural network that “hallucinates” proteins with new, stable structures.
Proteins, which are string-like molecules found in every cell, spontaneously fold into intricate three-dimensional shapes. These folded shapes are key to nearly every biological process, including cellular development, DNA repair, and metabolism. But the complexity of protein shapes makes them difficult to study. Biochemists often use computers to predict how protein strings, or sequences, might fold. In recent years, deep learning has revolutionized the accuracy of this work.
“For this project, we made up completely random protein sequences and introduced mutations into them until our neural network predicted that they would fold into stable structures,” said co-lead author Ivan Anishchenko, He is an acting instructor of biochemisty at the University of Washington School of Medicine and a researcher in David Baker’s laboratory at the UW Medicine Institute for Protein Design.
“At no point did we guide the software toward a particular outcome,” Anishchenko said, “ These new proteins are just what a computer dreams up.”
In the future, the team believes it should be possible to steer the artificial intelligence so that it generates new proteins with useful features.
“We’d like to use deep learning to design proteins with function, including protein-based drugs, enzymes, you name it,” said co-lead author Sam Pellock, a postdoctoral scholar in the Baker lab.
The research team, which included scientists from UW Medicine, Harvard University, and Rensselaer Polytechnic Institute (RPI), generated two thousand new protein sequences that were predicted to fold. Over 100 of these were produced in the laboratory and studied. Detailed analysis on three such proteins confirmed that the shapes predicted by the computer were indeed realized in the lab.
“Our NMR [nuclear magnetic resonance] studies, along with X-ray crystal structures determined by the University of Washington team, demonstrate the remarkable accuracy of protein designs created by the hallucination approach,” said co-author Theresa Ramelot, a senior research scientist at RPI in Troy, New York.
Gaetano Montelione, a co-author and professor of chemistry and chemical biology at RPI, noted. “The hallucination approach builds on observations we made together with the Baker lab revealing that protein structure prediction with deep learning can be quite accurate even for a single protein sequence with no natural relatives. The potential to hallucinate brand new proteins that bind particular biomolecules or form desired enzymatic active sites is very exciting.”
“This approach greatly simplifies protein design,” said senior author David Baker, a professor of biochemistry at the UW School of Medicine who received a 2021 Breakthrough Prize in Life Sciences. “Before, to create a new protein with a particular shape, people first carefully studied related structures in nature to come up with a set of rules that were then applied in the design process. New sets of rules were needed for each new type of fold. Here, by using a deep-learning network that already captures general principles of protein structure, we eliminate the need for fold-specific rules and open up the possibility of focusing on just the functional parts of a protein directly.”
An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation
by Nick C. Snelders, Gabriella C. Petti, Grardy C. M. van den Berg, Michael F. Seidl, Bart P. H. J. Thomma in Proceedings of the National Academy of Sciences
A team of biologists has identified that the pathogenic fungus Verticillium dahliae, responsible for wilt disease in many crops, secretes an ‘effector’ molecule to target the microbiome of plants to promote infection. The research was performed by the team of Alexander von Humboldt Professor Dr Bart Thomma at the University of Cologne (UoC) within the framework of the Cluster of Excellence on Plant Sciences (CEPLAS) in collaboration with the team of Dr Michael Seidl at the Theoretical Biology & Bioinformatics group of Utrecht University in the Netherlands.
Scientists increasingly recognize that an organism’s microbiome — the totality of bacteria and other microbes living in and on it — is an important component of its health. For humans as well as other animals, particular microbes inhabiting the gut and the skin have beneficial effects. This is similarly true for plants. Moreover, it has been established that plants can ‘recruit’ beneficial microbes from their environment, for instance from the soil surrounding the roots, to help them withstand disease.
At the UoC, together with Dr Nick Snelders lead author of the study Dr Thomma hypothesized that if plants can do this, perhaps some pathogens have ‘learned’ to perturb this ‘cry for help’ and disturb the plant’s microbiome in order to promote invasion. Thus, in addition to the direct suppression of the plant host’s immune responses, these pathogens can suppress immunity indirectly by affecting the plant’s healthy microbiome.
Verticillium dahliae is a well-known pathogen of many plants, including greenhouse crops like tomatoes and lettuce, but also olive trees, ornamental trees and flowers, cotton, potatoes, and others. The current study shows that the fungus secretes the antimicrobial protein VdAMP3 in order to manipulate the plant’s microbiome as an effector.
Generally, effector molecules target components of the host immune system, leading to immune suppression. The authors have now shown that these targets extend to inhabitants of the host’s microbiome: during host colonization, the VdAMP3 molecule suppresses beneficial organisms in the microbiome of the plant, leading to microbiome disturbance or ‘dysbiosis’, so that the fungus can complete its life cycle and produce progeny that can spread and start new infections.
‘In terms of evolution, the molecule that is secreted is very old. Homologs also occur in organisms that are not pathogenic on plants,’ said Thomma. ‘It looks like Verticillium “used” the molecule to “exploit” it during the process of disease development on the host. Interestingly, the molecule does not act like a broad-spectrum antibiotic that targets any microbe, but specifically against “competitor” fungi that have abilities to hinder Verticillium.’
Initially, the researchers wanted to find out whether Verticilium had ‘effectors’ in its arsenal that have antimicrobial activity. Different candidates were then tested for their ability to inhibit the growth of test microbes in the laboratory. VdAMP3 was one of these potential candidates. Follow-up experiments then showed that without the ‘effector’, other fungi — antagonists — could thrive and suppress the formation of Verticillium reproduction structures. VdAMP3 is mainly active in later stages of disease development, when Verticillium needs to produce these new reproduction structures to start infections of new hosts. However, this is not the first such molecule the scientists have identified: A year ago, they found a molecule that does not act against competing fungi, like VdAMP3, but against bacterial competitors.
‘Together, these findings demonstrate that pathogens use various molecules at various stages of the disease process to manipulate the healthy microbiome of a host to cause disease. This shows that it is important to look beyond the “binary interaction” between a pathogen and a host if we want to understand disease. Rather, we must take the entire microbiome of the host into account as well, looking at the host as a “holobiont” — the ecological unit formed by the host and all the organisms living in and on it,’ Thomma added.
In the long term, a better understanding of these mechanisms will help to develop more resilient plants and better strategies for crop protection. In the face of a growing world population, limited farmland, and the need to reduce environmental impact and pollution, one of the major aims of plant scientists is to increase the yield of field crops while minimizing our ecological footprint on the environment. ‘Learning more about these effector molecules that help pathogenic fungi infect crop plants may lead to new ways to safeguard against them,’ said Snelders.
In future studies, the authors aim to find further effector proteins with selective antimicrobial activity — from Verticillium, but also from other pathogens that have other infection strategies.
‘Unravelling how these molecules work, and how they can inhibit the one microbe while not affecting the other is important to discover novel mechanisms to target microbes, which may ultimately even lead to the development of novel antibiotics,’ Snelders concluded.
Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops
by Hyun Jung Oh, Rodrigo Aguilar, Barry Kesner, Hun-Goo Lee, Andrea J. Kriz, Hsueh-Ping Chu, Jeannie T. Lee in Cell
An important player in the healthy development of female embryos turns out also to play a key role in regulating the behavior of chromosome loops and gene expression in both sexes, according to a new study by researchers at Massachusetts General Hospital (MGH). These findings could help create new targets for drug development.
Chromosomes are long, string-like structures made up of DNA, RNA and proteins. A chromosome must fold into a loop in order to fit into the nucleus of a cell. These loops bring together distant genetic material. “Genes and control elements — sequences that regulate genes — have to communicate with one another for the cell to work properly,” says the senior author of the paper, Jeannie Lee, MD, PhD, of the Department of Molecular Biology at MGH. “Chromosome looping is kind of like bringing people together in a conference room so they can talk to one another.”
These interactions within a chromosome loop regulate gene expression, that is, whether a gene is turned “on” and thus producing proteins or turned “off.” Chromosome loops are in constant flux, growing and contracting as they change their composition of genes in response to environmental stimuli and the body’s developmental needs. Returning to the conference room metaphor, a protein called CTCF acts as a door, explains Lee, and it was already known that a chromosome loop may have multiple sets of double doors — some open, some closed. “But what wasn’t known is how these doors open and close,” explains Lee. “Who are the gatekeepers?”
The answer proved to be a surprise. Lee and her team discovered that a form of RNA known as Jpx is a gatekeeper that regulates the behavior of CTCF in chromosome looping. Jpx RNA was no stranger to Lee and her fellow investigators. Eight years ago, they showed that this noncoding form of RNA is a key player in the phenomenon known as X chromosome inactivation, which is essential for normal development in all female mammals, including humans. Jpx RNA helps count X chromosomes in female cells very early in development; if two are detected, one X chromosome is inactivated, or silenced. However, Lee’s group, which included postdoctoral fellow Hyun Jung Oh, PhD, first author of the study, found that Jpx RNA also determines what combination of double doors are open at any given time by “evicting” CTCF from the chromatin (a substance within a chromosome).
“Jpx regulates whether multiple doors are open or just one, as well as which panels of double doors are open, left or right,” says Lee. “By regulating that process, Jpx determines how big the chromatin loop is and, therefore, which genes around the loop are expressed.”
Jpx is the first form of RNA to be identified as playing a vital role in regulating the behavior of CTCF, but there will be many others, predicts Lee. That’s exciting, she says, because there are probably 10 times more varieties of RNA than there are proteins. While Jpx regulates genes involved in early in the development of an embryo, other RNAs awaiting discovery may regulate the formation of chromosome loops that influence the risk for cancer, autoimmune disorders and other diseases, says Lee. Identifying these RNA could speed the development of effective new medications.
Simultaneous high-efficiency base editing and reprogramming of patient fibroblasts
by Sami Jalil, Timo Keskinen, Rocío Maldonado, Joonas Sokka, Ras Trokovic, Timo Otonkoski, Kirmo Wartiovaara in Stem Cell Reports
Researchers in the University of Helsinki and University Hospital Helsinki have developed a method to precisely and rapidly correct genetic alterations in the cultured patient cells.
The method produces genetically corrected autologous pluripotent stem cells from a 2–3 mm skin biopsy from patients with different genetic diseases. The corrected stem cells are essential in the research and for the development of new therapies for the diseases in question.
The scientists based the new method on previous groundbreaking research in the fields of stem cells and gene editing, including two Nobel-prize awarded techniques. The first technique is the invention of induced pluripotent stem cells, iPSCs from differentiated cells, which won the Nobel in 2012. The other technique is the CRISPR-Cas9 “gene scissors” innovation, which got the prize in 2020. The new method combines these techniques to correct gene alterations that cause inherited diseases and at the same time creates fully functional new stem cells.
The long-term goal of the researchers is to produce autologous cells with therapeutic properties. The use of the patient’s own corrected cells could help in avoiding the immunological challenges hampering the organ and tissue transplantation from a donor. The new method was developed by an Argentinian PhD student Sami Jalil in the Biomedicum Helsinki Stem Cell Center.
There are more than 6000 known inherited diseases, which are caused by different gene alterations. Some of them are currently treated with a cell or organ transplant from a healthy donor, if available.
“Our new system is much faster and more precise than the older methods in correcting the DNA errors, and the speed makes it easier and diminishes also the risk of unwanted changes,” says adjunct professor Kirmo Wartiovaara, who has supervised the work.
“In perfect conditions, we have reached up to 100 % efficacy, although one has to remember that the correction of cultured cells is still far away from proven therapeutic applications. But it is a very positive start,” Wartiovaara adds.
Gene editing enables rapid engineering of complex antibiotic assembly lines
by Wei Li Thong, Yingxin Zhang, Ying Zhuo, Katherine J. Robins, Joanna K. Fyans, Abigail J. Herbert, Brian J. C. Law, Jason Micklefield in Nature Communications
Scientists have discovered a new route to produce complex antibiotics exploiting gene editing to re-programme pathways to future medicines urgently required to combat antimicrobial resistance, treat neglected diseases and prevent future pandemics.
Researchers from The University of Manchester have discovered a new way of manipulating key assembly line enzymes in bacteria which could pave the way for a new generation of antibiotic treatments.
New research describes how CRISPR-cas9 gene editing can be used to create new nonribosomal peptide synthetase (NRPS) enzymes that deliver clinically important antibiotics. NRPS enzymes are prolific producers of natural antibiotics such as penicillin. However, up until know, manipulating these complex enzymes to produce new and more effective antibiotics has been a major challenge.
The UK government suggest, antimicrobial resistance (AMR) infections are estimated to cause 700,000 deaths each year globally and are predicted to rise to 10 million, costing the global economy $100 trillion, by 2050. AMR also threatens many of the UN’s Sustainable Development Goals (SDGs), with an extra 28 million people that could be forced into extreme poverty by 2050 unless AMR is contained.
The Manchester team says the gene editing process could be used to produce improved antibiotics and possibly lead to the development of new treatments helping in the fight against drug-resistant pathogens and illnesses in the future. Jason Micklefield, Professor of Chemical Biology at the Manchester Institute of Biotechnology, UK, explains: “The emergence of antibiotic-resistant pathogens is one of the biggest threats we face today.”
“The gene editing approach we developed is a very efficient and rapid way to engineer complex assembly line enzymes that can produce new antibiotic structures with potentially improved properties.”
Microorganisms in our environment, such as soil dwelling bacteria, have evolved nonribosomal peptide synthetase enzymes (NRPS) that assemble building blocks called amino acids into peptide products which often have very potent antibiotic activity. Many of the most therapeutically important antibiotics, used in the clinic today, are derived from these NRPS enzymes (e.g. penicillin, vancomycin and daptomycin).
Unfortunately, deadly pathogens are emerging which are resistant to all of these existing antibiotic drugs. One solution could be to create new antibiotics with improved properties that can evade the resistance mechanisms of the pathogens. However, the nonribosomal peptide antibiotics are very complex structures which are difficult and expensive to produce by normal chemical methods. To address this, the Manchester team use gene editing to engineer the NRPS enzymes, swapping domains that recognise different amino acid building, leading to new assembly lines that can deliver new peptide products.
Micklefield added: “We are now able to use gene editing to introduce targeted changes to complex NRPS enzymes, introducing alternative amino acids precursors into peptide structures. We are optimistic that our new approach could lead to new ways of making improved antibiotics which are urgently needed to combat emerging drug-resistant pathogens.”
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions
by Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger in Cell Systems
In research, Professor Lenore Cowen of the Tufts Department of Computer Science and colleagues from Massachusetts Institute of Technology (MIT) collaborated to design a structurally-motivated deep learning method built from recent advances in neural language modeling. The team’s deep-learning model, called D-SCRIPT, was able to predict protein-protein interactions (PPIs) from primary amino acid sequences.
Those predictions allow researchers to model PPI networks with a clustering method and enable the detection of functional subnetworks, or modules. Scientists study organisms’ PPI networks as a means of understanding their signaling circuitry, which could lead to better prediction of cell behavior and gene functions, while finding functional modules in PPI networks could help researchers reach stronger understandings of cellular functional organization.
Cowen along with researchers Sam Sledzieski, Rohit Singh, and renowned computational biologist Bonnie Berger from MIT’s Computer Science and Artificial Intelligence Lab found that the D-SCRIPT model, trained on more than 38,000 human PPIs, was better able to generalize when compared to the current state-of-the-art approach (the deep-learning method PIPR), and therefore could characterize fly proteins. They also applied D-SCRIPT to screen for PPIs related to cow digestion and identified functional gene modules that related to immune response and metabolism.
The researchers concluded that the D-SCRIPT model trained on human PPI data could be applied to many species of interest — critically, even those that have been rarely studied or that lack PPI data.
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