Genetics biweekly vol.34, 26th July — 9th August
TL;DR
- A research team led by André Marques at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, has uncovered the profound effects of an atypical mode of chromosome arrangement on genome organization and evolution. Their findings are published in the journal Cell.
- Genetic analyses of baboons in Kenya reveals that most of them carry traces of hybridization in their DNA. As a result of interbreeding, about a third of their genetic makeup consists of genes from another, closely-related species. Fifty years of observations turned up no obvious signs that hybrids fare any worse than their counterparts. But the new findings suggest that appearances can be deceiving.
- Researchers generated rat sperm cells inside sterile mice using a technique called blastocyst complementation. The advance appears in the journal Stem Cell Reports.
- Scientists have found that muscle fibers in Japanese Fire-bellied Newts have an intrinsic ability to dedifferentiate, or reprogram, and contribute to limb regeneration. The results indicate that changes in the niche (the environment outside the cell) during metamorphosis and body growth are needed to unleash this ability. This study provides a key basis for future research on dedifferentiation, and could contribute to medical treatments for muscle damage and disease.
- New research shows that one fruit fly species contains whole genomes of a kind of bacteria, making this finding the largest bacteria-to-animal transfer of genetic material ever discovered. The new research also sheds light on how this happens.
- Scientists have created a probiotic to restore bile salt metabolism found in the gastrointestinal tract, to counter the onset and effects of Clostridium Difficile Infection (CDI).
- Researchers from the Nara Institute of Science and Technology (NAIST) have used elastic shell theory to describe how the stiffness of plant cell walls depends on their elasticity and internal turgor pressure. By utilizing atomic force microscopy (AFM) combined with finite element computer simulations, they were able to show that cell stiffness is very sensitive to internal turgor pressure.
- An international research team has deciphered the mechanism by which the fungus Cryptococcus neoformans is resistant to fungus-specific drugs. It is a yeast-like fungus that can infect humans. Specific drugs, named antifungals, are available for treatment, but they don’t always work — a phenomenon similar to antibiotic resistance. A team from Duke University in the USA and Ruhr-Universität Bochum (RUB) has used genetic, bioinformatic and microbiological techniques to decipher the mechanism underlying this resistance.
- Scientists have published new research showing light-activated proteins can help normalize dysfunction within cells. The technique helps naturally balance mitochondria.
- Plant biologists have defined the high-efficiency ‘hacks’ that cannabis cells use to make cannabinoids (THC/CBD). Although many biotechnology companies are currently trying to engineer THC/CBD outside the plant in yeast or cell cultures, it is largely unknown how the plant does it naturally.
- 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
Repeat-based holocentromeres influence genome architecture and karyotype evolution
by Paulo G. Hofstatter, Gokilavani Thangavel, Thomas Lux, Pavel Neumann, Tihana Vondrak, Petr Novak, Meng Zhang, Lucas Costa, Marco Castellani, Alison Scott, Helena Toegelová, Joerg Fuchs, Yennifer Mata-Sucre, Yhanndra Dias, André L.L. Vanzela, Bruno Huettel, Cicero C.S. Almeida, Hana Šimková, Gustavo Souza, Andrea Pedrosa-Harand, Jiri Macas, Klaus F.X. Mayer, Andreas Houben, André Marques in Cell
A research team led by André Marques at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, has uncovered the profound effects of an atypical mode of chromosome arrangement on genome organization and evolution. Their findings are published in the journal Cell.
In each individual cell in our body, our DNA, the molecule carrying the instructions for development and growth, is packaged together with proteins into structures called chromosomes. Full sets of chromosomes together constitute the genome, the entire genetic information of an organism. In most organisms, including us, chromosomes appear as X-shaped structures when they are captured in their condensed, duplicated states in preparation for cell division. Indeed, these structures may be among the most iconic in all of science. The X shape is due to a constricted region called the centromere that serves to connect sister chromatids, which are identical copies formed by the DNA replication of a chromosome. Most studied organisms are “monocentric,” meaning that centromeres are restricted to a single region on each chromosome. Several animal and plant organisms, however, show a very different centromere organization: instead of one solitary constriction as in the classic X-shaped chromosomes, chromosomes in these organisms harbor multiple centromeres that are arranged in a line from one end of a sister chromatid to the other. Thus, these chromosomes lack a primary constriction and the X shape, and species with such chromosomes are known as “holocentric,” from the ancient Greek word hólos meaning “whole.”
A new study led by André Marques from the Max Planck Institute for Plant Breeding Research in Cologne, Germany, now reveals the striking effects of this non-classical mode of chromosome organization on genome architecture and evolution.
To determine how holocentricity affects the genome, Marques and his team used highly accurate DNA sequencing technology to decode the genomes of three closely related holocentric beak-sedges, grass-like flowering plants found worldwide that are often the first conquerors of new habitats. For reference, the team also decoded the genome of their most closely related monocentric relative. Thus, comparing the holocentric beak-sedges with their monocentric relative allowed the authors to attribute any differences they observed to the effects of holocentricity.
Their analyses reveal striking differences in genome organization and chromosome behavior in holocentric organisms. They found that centromere function is distributed across hundreds of small centromere domains in holocentric chromosomes. While in monocentric organisms, genes are largely concentrated distant from centromeres and the regions immediately around them, in holocentric species they are uniformly distributed over the whole length of chromosomes. Further, in monocentric species chromosomes are known to engage in a high degree of intermingling with each other during cell division, a property that appears to play a role in regulating gene expression. Notably, these long-range interactions were sharply diminished in the beak-sedges with holocentromeres. Thus, holocentricity fundamentally affects genome organization as well as how chromosomes behave during cell division.
In holocentric organisms, almost any given chromosomal fragment will harbor a centromere and will thus have proper centromere function, which is not true for monocentric species. In this way, holocentromeres have been thought to stabilize chromosomal fragments and fusions and thus promote rapid genome evolution, or the ability of an organism to make prompt, wholesale changes to its DNA. In one of the beak-sedges they analyzed, Marques and his team could show that chromosome fusions facilitated by holocentromeres allowed this species to maintain the same chromosome number even after quadruplication of the entire genome. In another of their analyzed beak-sedges, a species with only two chromosomes, the lowest of any plant, holocentricity was found to be responsible for the dramatic reduction in chromosome number. Thus, holocentric chromosomes may allow the formation of news species through rapid evolution at genome-level.
According to Marques, “Our study shows that the transition to holocentricity has greatly influenced the way genomes are organized and regulated as well as allowing genomes to evolve rapidly through fusing their chromosomes together.”
The team’s findings also show exciting implications for plant breeding, which typically relies on the ability to swap DNA and genes between chromosomes and organisms.
“Holocentric plants allow the swapping of DNA in the vicinity of centromeres, something which is normally suppressed in monocentric species. Understanding how holocentrics do this could allow us to ‘unlock’ those genes in monocentric species and make them accessible for the breeding of better- performing, more resistant crop species.”
Selection against admixture and gene regulatory divergence in a long-term primate field study
by Tauras P. Vilgalys, Arielle S. Fogel, Jordan A. Anderson, Raphael S. Mututua, J. Kinyua Warutere, I. Long’ida Siodi, Sang Yoon Kim, Tawni N. Voyles, Jacqueline A. Robinson, Jeffrey D. Wall, Elizabeth A. Archie, Susan C. Alberts, Jenny Tung in Science
New genetic analyses of wild baboons in southern Kenya reveals that most of them carry traces of hybridization in their DNA. As a result of interbreeding, about a third of their genetic makeup consists of genes from another, closely-related species.
The study took place in a region near Kenya’s Amboseli National Park, where yellow baboons occasionally meet and intermix with their anubis baboon neighbors that live to the northwest.
Researchers have monitored these animals on a near-daily basis since 1971, noting when they mated with outsiders and how the resulting offspring fared over their lifetimes as part of the Amboseli Baboon Research Project, one of the longest-running field studies of wild primates in the world.
Yellow baboons have yellow-brown fur with white cheeks and undersides. Anubis baboons have greenish-grey fur and males with shaggy manes around their heads. Although they are distinct species that diverged 1.4 million years ago, they can hybridize where their ranges overlap.
By all accounts, the offspring of these unions manage just fine. Fifty years of observations turned up no obvious signs that hybrids fare any worse than their counterparts. Some even fare better than expected: baboons that carry more anubis DNA in their genome mature faster and form stronger social bonds, and males are more successful at winning mates.
The research sheds light on how the diversity of species on Earth is maintained even when the genetic lines between species are blurry, said Duke University professor Jenny Tung, who led the project with her doctoral students Tauras Vilgalys and Arielle Fogel.
Interspecies mating is surprisingly common in animals, said Fogel, who is a PhD candidate in the Duke University Program in Genetics and Genomics. Some 20% to 30% of apes, monkeys and other primate species interbreed and mix their genes with others.
Even modern humans carry around a mix of genes from now-extinct relatives. As much as 2% to 5% of the DNA in our genomes points to past hybridization with the Neanderthals and Denisovans, ancient hominins our ancestors encountered and mated with as they migrated out of Africa into Europe and Asia. Those liaisons left a genetic legacy that still lingers today, affecting our risk of depression, blood clots, even tobacco addiction or complications from COVID-19.
The researchers wanted to understand the possible costs and benefits of this genetic mixing in primates, including humans. But modern humans stopped interbreeding with other hominins tens of thousands of years ago, when all but one species — ours — went extinct. The wild baboons of Amboseli, however, make it possible to study primate hybridization that is still ongoing.
The researchers analyzed the genomes of some 440 Amboseli baboons spanning nine generations, looking for bits of DNA that may have been inherited from anubis immigrants.
They found that all baboons in the Amboseli basin of southern Kenya today are a mix, with anubis DNA making up about 37% of their genomes on average. Some have anubis ancestry due to interbreeding that occurred fairly recently, within the last seven generations. But for nearly half of them the mixing happened further back, hundreds to thousands of generations ago.
During that time, the data show that certain bits of anubis DNA came at a cost for the hybrids who inherited them, affecting their survival and reproduction in such a way that these genes are less likely to show up in their descendants’ genomes today, said Vilgalys, now a postdoctoral scholar at the University of Chicago.
Their results are in line with genetic research in humans, which suggests that our early ancestors paid a price for hybridizing too. But exactly what Neanderthal and Denisovan genes did to cause them harm has been hard to tease out of the limited fossil and DNA evidence that’s available.
The researchers say that the baboons at Amboseli offer clues to the costs of the hybridization. Using RNA sequencing to measure gene activity in the baboons’ blood cells, the researchers found that natural selection is more likely to weed out bits of borrowed DNA that act as switches, turning other genes on and off.
The next step, Fogel said, is to pin down more precisely what is ultimately affecting these hybrid baboons’ ability to survive and reproduce.
Genomic data allows researchers to look back many more generations and study historical processes that can’t be seen directly in the field, Vilgalys said.
“But you need to look at the animals themselves to understand what genetic changes actually mean,” Tung said. “You need both fieldwork and genetics to get the whole story.”
“We’re not saying this is what Neanderthal and Denisovans genes did in humans,” added Tung, now at the Max Planck Institute for Evolutionary Anthropology in Germany. “But the baboon case makes it clear that genomic evidence for costs to hybridization can be consistent with animals that not only survive, but often thrive.”
Exclusive generation of rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells
by Joel Zvick, Monika Tarnowska-Sengül, Adhideb Ghosh, Nicola Bundschuh, Pjeter Gjonlleshaj, Laura C. Hinte, Christine L. Trautmann, Falko Noé, Xhem Qabrati, Seraina A. Domenig, Inseon Kim, Thomas Hennek, Ferdinand von Meyenn, Ori Bar-Nur in Stem Cell Reports
Researchers generated rat sperm cells inside sterile mice using a technique called blastocyst complementation. The advance appears August 4 in the journal Stem Cell Reports.
“Our study shows that we can use sterile animals as hosts for the generation of germ cells from other animal species,” says senior author Ori Bar-Nur, a stem cell biologist at ETH Zurich. “Aside from a conceptual advancement, this notion can be utilized to produce endangered animal species gametes inside more prevalent animals. Other implications may involve an improved method to produce rat transgenic models for biomedical research.”
Pluripotent stem cells (PSCs) provide a powerful tool for biomedical research, but the generation of gametes in the form of eggs or sperm cells from PSCs is a highly challenging endeavor. In prior studies, researchers used a technique called blastocyst complementation to generate rat organs in mice using PSCs and mutated mouse embryos that cannot produce specific organs. Building on this work, Bar-Nur and his collaborators wondered whether it would be possible to generate rat sperm inside mice that carry a genetic mutation that otherwise renders them sterile.
To test this idea, the researchers injected rat PSCs into mouse embryos to produce mouse-rat chimeras. An essential gene for sperm production was mutated in the mouse blastocysts. The rat stem cells developed together with the mouse cells, thereby generating a chimeric animal composed of genotypes from the two species. As a consequence of the genetic sterility-inducing mutation, an empty niche developed inside the testes, which enabled the rat cells to colonize them and exclusively generate rat sperm in mouse-rat chimeras. The sperm cells could fertilize rat egg cells, but the embryos did not develop normally or give rise to live offspring.
“We were surprised by the relative simplicity by which we could mix the two species to produce viable mouse-rat chimeras. These animals, by large, appeared healthy and developed normally, although they carried both mouse and rat cells in a chimeric animal,” Bar-Nur says. “The second surprise was that indeed all the sperm cells inside the chimeras were of rat origin. As such, the mouse host environment, which was sterile due to a genetic mutation, was still able to support efficient sperm cell production from a different animal species.”
Although the researchers were able to generate rat sperm cells that morphologically appeared indistinguishable from normal rat sperm cells, these cells were immotile and the fertilization rates of rat eggs was significantly lower in comparison to rat sperm cells produced in rats. Nonetheless, the work provides a proof-of-principle that one can generate sperm cells of one animal species in another by mixing the two species in an artificially generated organism called a chimera. Using sterile mice for genetically modified rat PSCs may speed up the production of transgenic rats to model human diseases in biomedical research.
Moving forward, the researchers will try to produce live animals from rat sperm cells that have been produced in mouse-rat chimeras. “We will need to improve the technique and demonstrate that rat sperm produced in mice can give rise to adult rats when fertilizing rat eggs,” Bar-Nur says.
A more distant plan is to adapt this technique for the production of gametes from endangered rodent species to support animal species conservation efforts.
“For example, to the extent we can procure stem cells from an endangered rodent, which at some point in time might become extinct, we may be able to employ the same method to produce its germ cells via chimera production with mice,” Bar-Nur says. “However, it is important to note that several scientific hurdles will need to be overcome to adapt this technique to other animal species. In addition, one still needs to showcase the production of female reproductive cells (i.e., eggs) in female sterile mice, especially if we envision utilizing this technology for species conservation efforts.”
The latent dedifferentiation capacity of newt limb muscles is unleashed by a combination of metamorphosis and body growth
by Zhan Yang Yu, Shota Shiga, Martin Miguel Casco-Robles, Kazuhito Takeshima, Fumiaki Maruo, Chikafumi Chiba in Scientific Reports
Unknown to passersby, a modest little creature with amazing abilities lives and breeds in the forests and paddy fields of Japan. Now, researchers from Japan have discovered how these amphibians’ superpowers are unleashed.
In a study published this month in Scientific Reports, researchers from the University of Tsukuba have revealed that during limb regeneration in newts, two developmental processes — metamorphosis and body growth — are needed to provide the right conditions for muscle cells to be redeployed within the limb stump.
Newts, which are a semiaquatic type of salamander, are like most other amphibians in that they undergo metamorphosis. But unlike their relatives, newts are capable of repeated limb regeneration — even in the adult stage after they have undergone metamorphosis. In some newt species, individuals that have already metamorphosed regenerate muscle via dedifferentiation or reprogramming of muscle fibers in the limb stump, and mobilization of these fibers, to create muscle in the regenerating limb.
“Unlike cell differentiation, where cells become more specialized, cell dedifferentiation is a process via which they become less specialized,” says senior author of the study, Professor Chikafumi Chiba. “Prior to our study, it was unknown whether metamorphosis or body growth was the key developmental process for muscle dedifferentiation.”
The researchers investigated muscle cell dedifferentiation in the Japanese Fire-bellied Newt, Cynops pyrrhogaster, by tracking muscle fibers during limb regeneration while body growth and metamorphosis were experimentally delayed or advanced. The results suggest that metamorphosis and body growth are both needed for muscle differentiation.
Conversely, when larval newt muscles were cultured with a physiologically active thyroid hormone, tracking of the muscle fibers showed that these fibers can dedifferentiate independently of body growth and metamorphosis. These results indicate that newt muscle fibers have an inherent capacity to dedifferentiate, but that both body growth and metamorphosis are required for the fibers to activate this secret ability.
“We suggest that the developmental changes in the extracellular environment, or niche, inhibit the activity of myogenic stem cells — cells that can differentiate into muscle fibers — and promote the latent ability of muscle fibers to dedifferentiate. This way, the stem cells are compensated for by dedifferentiation, allowing newts to regenerate limb muscles throughout their life cycle,” says Professor Chiba.
The results of this study provide an important foundation for future research on extracellular environments as well as the molecular mechanisms of dedifferentiation, such as the gene regulation that underpins this phenomenon. This research will also contribute to a deeper understanding of regeneration, and possible even to potential future medical treatments such as new therapies for diseases and muscle damage.
Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement
by Eric S. Tvedte, Mark Gasser, Xuechu Zhao, Luke J. Tallon, Lisa Sadzewicz, Robin E. Bromley, Matthew Chung, John Mattick, Benjamin C. Sparklin, Julie C. Dunning Hotopp in Current Biology
A fruit fly genome is not just made up of fruit fly DNA — at least for one fruit fly species. New research from the University of Maryland School of Medicine’s (UMSOM) Institute for Genome Sciences (IGS) shows that one fruit fly species contains whole genomes of a kind of bacteria, making this finding the largest bacteria-to-animal transfer of genetic material ever discovered. The new research also sheds light on how this happens.
The IGS researchers, led by Julie Dunning Hotopp, PhD, Professor of Microbiology and Immunology at UMSOM and IGS, used new genetic long-read sequencing technology to show how genes from the bacteria Wolbachia incorporated themselves into the fly genome up to 8,000 years ago.
The researchers say their findings show that unlike Darwin’s finches or Mendel’s peas, genetic variation isn’t always small, incremental, and predictable.
Scientist Barbara McClintock first identified “jumping genes” in the 1940s like those that can move around within or transfer into other species genomes. However, researchers continue to discover their significance in evolution and health.
“We did not have the technology previously to unequivocally demonstrate these genomes-inside-genomes showing such extensive lateral gene transfer from the bacteria to the fly,” explained Dr. Dunning Hotopp. “We used state-of-the-art long-read genetic sequencing to make this important discovery.”
In the past, researchers had to break DNA into short pieces in order to sequence it. Then they needed to assemble them, like a jigsaw puzzle, to look at a gene or section of DNA. Long-read sequencing, however, allows for sequences more than 100,000 DNA letters, turning a million-piece jigsaw puzzle into one made for toddlers.
In addition to the long reads, the researchers validated junctions between integrated bacteria genes and the host fruit fly genome. To determine if the bacteria genes were functional and not just DNA fossils, the researchers sequenced the RNA from fruit flies specifically looking for copies of RNA that were created from templates of the inserted bacterial DNA. They showed the bacteria genes were encoded into RNA and were edited and rearranged into newly modified sequences indicating that the genetic material is functional.
An analysis of these unique sequences revealed that the bacteria DNA integrated into the fruit fly genome in the last 8,000 years — exclusively within chromosome 4 — expanding the chromosome size by making up about 20 percent chromosome 4. Whole bacterial genome integration supports a DNA-based rather than an RNA-based mechanism of integration.
Dr. Dunning Hotopp and colleagues found a full bacterial genome of the common bacteria Wolbachia transferred into the genome of the fruit fly Drosophila ananassae. They also found nearly a complete second genome and much more with almost 10 copies of some bacterial genome regions.
“There always have been some skeptics about lateral gene transfer, but our research clearly demonstrates for the first time the mechanism of integration of Wolbachia DNA into this fruit fly’s genome,” Dr. Dunning Hotopp said.
“This new research shows basic science at its best,” said Dean E. Albert Reece, MD, PhD, MBA, who is also Executive Vice President for Medical Affairs, UM Baltimore, the John Z. and Akiko K. Bowers Distinguished Professor, and Dean, University of Maryland School of Medicine. “It will make a contribution to our understanding of evolution and may even prove to help us understand how microbes contribute to human health.”
Wolbachia is an intracellular bacteria that infects numerous types of insects. Wolbachia transmits its genes maternally through female egg cells. Some research has showed that these infections are more mutualistic than parasitic, giving insects advantages, such as resistance to certain viruses.
Sequenced just three years before the human genome, fruit flies have long been used in genomic research because of the abundance of common fly-human genetic similarities. In fact, 75 percent of genes causing human disease can also be found in the fruit fly.
Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism
by Elvin Koh, In Young Hwang, Hui Ling Lee, Ryan De Sotto, Jonathan Wei Jie Lee, Yung Seng Lee, John C. March, Matthew Wook Chang in Nature Communications
Scientists from the Yong Loo Lin School of Medicine, National University of Singapore (NUS Medicine) have created a probiotic to restore bile salt metabolism, found in the gastrointestinal tract, to counter the onset and effects of Clostridium Difficile Infection (CDI).
CDI is the infection of the large intestine or colon that leads to infectious diarrhea, caused by an infectious bacterium known as Clostridium. Most cases of CDI have been observed to occur in those who have been taking antibiotics or just finished their course of antibiotics.
The administration of antibiotics in the treatment of CDI causes an imbalanced gut microbiome, known as dysbiosis, which can disrupt other microbiome processes such as bile salt metabolism. The dysregulation of bile salt metabolism can activate dormant Clostridioides difficile spores, leading to CDI, causing severe diarrhea and colitis — inflammation of the large intestine, or a reinfection of CDI.
A team of researchers, led by Associate Professor Matthew Chang, from the Synthetic Biology Translational Research Programme at NUS Medicine and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), engineered a probiotic that can detect the occurrence of antibiotic-induced microbiome imbalance and express an enzyme that can regulate the bile salt metabolism upon detection. This probiotic contains a genetic circuit that comprises a genetically encoded sensor, amplifier and actuator.
The team used an E. coli probiotic strain as the host because of its proven safety record in humans and its gram-negative nature makes it compatible with the current CDI therapy that uses antibiotics targeting gram-positive bacteria. The sensor in this probiotic, detects the presence of sialic acid, a gut metabolite that is indicative of microbiome imbalance. The actuator produces an enzyme that can regulate the bile salt metabolism, activated by the sensor, and it reduces the germination of the Clostridioides difficile spores that causes CDI, when induced by the sialic acid sensor. The team also included an amplifier in the probiotic which amplifies the activation by the sensor and increases the production of the enzyme, reducing the germination of the Clostridioides difficile spores by 98%. Experiments showed that the probiotic significantly reduced CDI in laboratory models, as demonstrated by a 100% survival rate and improved clinical outcomes.
Assoc Prof Chang is encouraged by this advancement that sheds more light on the gut environment and how it can be manipulated to create less invasive treatment strategies.
He says, “This scientific innovation gives a better understanding on how we can control the microenvironment in the body, without needing to exert direct lethality to kill the Clostridioides difficile bacterium, give additional drugs, or use invasive methods to rid the infection. Our perspectives have shifted towards studying how we can come up an antimicrobial strategy to complement and assist the natural biological processes in the body to help limit the onset of infection. This is useful when considering the development or improvement of future therapeutics for CDI.”
Elastic shell theory for plant cell wall stiffness reveals contributions of cell wall elasticity and turgor pressure in AFM measurement
by Satoru Tsugawa, Yuki Yamasaki, Shota Horiguchi, Tianhao Zhang, Takara Muto, Yosuke Nakaso, Kenshiro Ito, Ryu Takebayashi, Kazunori Okano, Eri Akita, Ryohei Yasukuni, Taku Demura, Tetsuro Mimura, Ken’ichi Kawaguchi, Yoichiroh Hosokawa in Scientific Reports
Scientists from Nara Institute of Science and Technology (NAIST) have used elastic shell theory to describe how the stiffness of plant cell walls depends on their elasticity and internal turgor pressure. By utilizing atomic force microscopy (AFM) combined with finite element computer simulations, they were able to show that cell stiffness is very sensitive to internal turgor pressure.
Many people will have fond memories from their school days looking at onion peels under a microscope. While the individual cells might have seemed then like simple rectangles, the stability of plant cells reflects complex combinations of forces. In addition to the cell membrane which is similar in animals, plant cells also have a rigid cell wall that provides structural integrity. Turgor, meaning the normal rigidity of cells due to the pressure from its contents, is also a critical factor in maintaining balance with the environment. Too little pressure can cause the cell to shrink. Cells can regulate their turgor pressure osmotic flows that tend to balance the salt concentrations between the interior and the outside of the wall. However, the resulting mechanical properties of plant cells remain nebulous. For example, using AFM alone to determine the stiffness from cell wall deformation makes it difficult to separate the contributions from the tension of the cell wall, cell geometry and turgor pressure.
Now, a team of researchers led by NAIST has used finite element method (FEM) simulations to verify a new formula based on elastic shell theory. This allowed them to interpret the apparent stiffness observed using AFM. The team studied onion epidermal cells, which are a model system for understanding the physical properties of plant cells.
“Looking at the force versus indentation data suggested that the standard equations were not sufficient for interpreting the apparent stiffness of plant cells,” senior author Yoichiroh Hosokawa says.
Based on the FEM simulations, the elastic shell theory equation was shown to be better at describing the AFM response of the onion cells, compared with the conventional model used for objects without internal turgor pressure. Moreover, their findings suggest that tension caused by turgor pressure regulates cell stiffness, which can be modified by slight changes, on the order of 0.1 megapascals.
“Our theoretical analysis paves the way for a more complete understanding of the forces inherent in a plant cell,” Hosokawa says.
The work helps generalize our understanding of stiffness for living systems. This knowledge can be applied to help ensure that plants maintain their structure even under stressful situations, such as during periods of water deprivation.
Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans
by Shelby J. Priest, Vikas Yadav, Cullen Roth, Tim A. Dahlmann, Ulrich Kück, Paul M. Magwene, Joseph Heitman in Nature Microbiology
An international research team has deciphered the mechanism by which the fungus Cryptococcus neoformans is resistant to fungus-specific drugs. It is a yeast-like fungus that can infect humans. Specific drugs, named antifungals, are available for treatment, but they don’t always work — a phenomenon similar to antibiotic resistance. A team from Duke University in the USA and Ruhr-Universität Bochum (RUB) has used genetic, bioinformatic and microbiological techniques to decipher the mechanism underlying this resistance.
“The results are highly relevant for combating fungal infections in clinical practice, veterinary medicine and agriculture,” says Professor Ulrich Kück, Senior Professor in General and Molecular Botany at RUB. He cooperated for the project with the Bochum researcher Dr. Tim Dahlmann and the team headed by Professor Dr. Joe Heitman, who is currently based at Duke University in North Carolina and has been a visiting professor at RUB on several occasions.
“In the western hemisphere, the number of people with a lowered immune defence is increasing, because life expectancies are rising rapidly and treatment with immunosuppressants after organ transplants is becoming more common,” explains Ulrich Kück. “This is associated with an increase in fungal infections.”
Cryptococcus neoformans is one of the most significant human pathogenic fungi responsible for so-called cryptococcosis. It triggers acute infections in immunocompromised patients; and the mortality rate may be as high as 70 per cent. This is because fungal strains that are resistant to the drugs often evolve in hospitals, which makes treatment more difficult. So far, it was unclear which cellular and genetic mechanisms lead to this resistance.
So-called transposons, however, were known to play a role in the resistances. Transposons are jumping genes, i.e. DNA segments that can change their position in the genome and thus affect the function of genes. If a transposon jumps into a gene that’s critical for susceptibility to a drug, it’s possible for resistance to emerge. The mobility of the transposons is controlled by regulatory RNAs, so-called small interfering RNA, or siRNA for short.
In their current study, the researchers discovered gene mutations in resistant isolates that led to siRNA control being switched off. By introducing an intact copy of the gene, it was possible to restore siRNA control; as a result, the researchers were able to prevent the transposons from jumping and shed light on the cause of resistance. Due to their small size, the gene segments that code for siRNAs are not easy to find in the genome. Tim Dahlmann managed to locate them with special bioinformatic analyses. By identifying the resistance mechanisms, it will be possible to use them for the treatment of mycoses in humans in the future.
A polarized supercell produces specialized metabolites in cannabis trichomes
by Samuel J. Livingston, Kim H. Rensing, Jonathan E. Page, A. Lacey Samuels in Current Biology
For the first time, plant biologists have defined the high-efficiency “hacks” that cannabis cells use to make cannabinoids (THC/CBD). Although many biotechnology companies are currently trying to engineer THC/CBD outside the plant in yeast or cell cultures, it is largely unknown how the plant does it naturally.
“This really helps us understand how the cells in cannabis trichomes can pump out massive quantities of tetrahydrocannabinol (THC) and terpenes — compounds that are toxic to the plant cells at high quantities — without poisoning itself,” says Dr. Sam Livingston, a botanist at the University of British Columbia who led the research.
“This new model can inform synthetic biology approaches for cannabinoid production in yeast, which is used routinely in biotechnology. Without these ‘tricks’ they’ll never get efficient production.”
For centuries, humans have cultivated cannabis for the pharmacological properties that result from consuming its specialized metabolites, primarily CBD and terpenoids. Today, production within the $20 billion global cannabis market largely relies on the biological activity of tiny cell clusters, called glandular trichomes, found mainly on the plant’s flowers.
The study, published in Current Biology, reveals the microenvironments in which THC is produced and transported in cannabis trichomes, and sheds light on several critical points in the pathway of making THC or CBD within the cell.
Dr. Livingston and co-author Dr. Lacey Samuels used rapid freezing of cannabis glandular trichomes to immobilize the plant’s cellular structures and the metabolites in situ. This enabled them to investigate cannabis glandular trichomes using electron microscopes that revealed cell structure at the nano level, showing that the metabolically active cells in cannabis form a “supercell” that acts as a tiny metabolic biofactory.
Until now, synthetic biology approaches have focused on optimizing the enzymes responsible for making THC/CBD — like building a factory with the most efficient machinery to make as much product as possible. However, these approaches haven’t developed an efficient way to move intermediate substances from one enzyme to another, or from inside the cell to the outside of the cell where final products can be collected. This research helps to define the subcellular “shipping routes” that cannabis uses to create an efficient pipeline from raw materials to end products without accumulating toxins or waste products.
“For more than 40 years, everything that we thought about cannabis cells was inaccurate because it was based on dated electron microscopy,” says Dr. Samuels, a plant cell biologist at UBC. “This work defines how cannabis cells make their product. It’s a paradigm shift after many years, producing a new view of cannabinoid production. This work has been challenging, partly the result of legal prohibition and also due to the fact that no protocol for the genetic transformation of cannabis has been published.”
Light-activated mitochondrial fission through optogenetic control of mitochondria-lysosome contacts
by Kangqiang Qiu, Weiwei Zou, Hongbao Fang, Mingang Hao, Kritika Mehta, Zhiqi Tian, Jun-Lin Guan, Kai Zhang, Taosheng Huang, Jiajie Diao in Nature Communications
New research from the University of Cincinnati shows early indications that light can be used as a treatment for certain diseases, including cancer.
Researchers from UC, the University of Illinois Urbana-Champaign and the University at Buffalo published the results of their study demonstrating light-activated proteins can help normalize dysfunction within cells in the journal Nature Communications.
The research centers on the functions of mitochondria, organelles within a cell that act as the cell’s “power plant” and source of energy. Organelles are tiny specialized structures that perform various jobs inside cells.
Jiajie Diao, PhD, one of the study’s authors, said hundreds of mitochondria are constantly coming together (a process called fusion) and dividing into smaller parts (a process called fission) to stay balanced in healthy cells. But when mitochondria are not functioning properly, there is an imbalance of this process of fission and fusion.
This imbalance can lead to a number of mitochondrial diseases, including neurodegenerative diseases like dementia and certain cancers.
Diao said previous research found that another organelle within cells called a lysosome can play a role in mitochondria fission. When a mitochondria comes in contact with a lysosome, the lysosome can act like a pair of scissors and cut the mitochondria into smaller pieces.
The current research focused on jump-starting the fission process by bringing the lysosomes and mitochondria together within cells. This was accomplished using a technique known as optogenetics, which can precisely control specific cell functions using light.
“Many proteins in plants are light sensitive, informing plants whether it is day or night. Optogenetics borrows these light-sensitive proteins from plants and uses them in animal cells,” said Kai Zhang, PhD, associate professor at the University of Illinois Urbana-Champaign and study co-author, who developed the optogenetic tools for controlling mitochondria and lysosomes with blue light. “By attaching such proteins to organelles, one can use light to control the interaction between them, such as mitochondria and lysosomes shown in this work,” he said.
The researchers attached two separate proteins to mitochondria and lysosomes within stem cells. When stimulated by blue light, the proteins naturally bind to each other to form one new protein, which also brings the mitochondria and lysosome into contact. Once they are brought together, the lysosome can cut the mitochondria, achieving fission.
“We found that it can recover the mitochondrial function,” said Diao, associate professor in the Department of Cancer Biology in UC’s College of Medicine and a University of Cincinnati Cancer Center member. “Some of the cells can even go back to normal. This proves that by just using some simple light stimulation we can at least partially recover the mitochondrial function of the cell.”
Diao said this technique could be especially useful for patients with dramatically oversized mitochondria that need to be divided into smaller pieces to achieve normal cell function. The technique could also be aimed at cancer cells, continually separating the mitochondria into smaller and smaller pieces until they can no longer function.
“Eventually the cancer cells will be killed because mitochondria is their energy,” Diao said. “Without normal functional mitochondria, all of the cancer cells will be killed.”
Since the proteins are activated by light, Diao said it allows for a more targeted approach to specific cells. Only cells exposed to the light are affected, meaning healthy cells nearby do not have their mitochondria unbalanced through the technique.
There are currently other processes that can be used to induce mitochondrial fission, but Diao said the optogenetic method is safer since it does not involve any chemicals or toxic agents.
“What we have is actually the natural process, we’re just making it faster,” Diao said. “So it’s not like a chemical or a therapy or a radiotherapy where you need to reduce the side effects.”
Diao said his team is already at work on using the same technique to encourage fusion to address issues when mitochondria are unbalanced because they are too small and not coming together as they should within cells.
Further research from Zhang’s lab will also include developing new optogenetic systems working with different colors of light, including green, red and infrared, since a longer wavelength will be needed to penetrate human tissue.
“We would like to further expand the toolbox by introducing multicolor optogenetic systems to give us multiple ways to control how organelles behave and interact,” Zhang said. “For instance, one color makes organelles come together, while the other color forces them apart. This way, we can precisely control their interactions.”
From the current research using human stem cells, the team hopes to progress to test its efficacy using animal models on the way to eventually test the technique in humans through clinical trials. At the same time, Diao said other research groups are studying the use of magnetic fields and acoustic vibrations instead of light to accomplish similar results.
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