TL;DR
- Scientists have created a new technology that rapidly detects the SARS-CoV-2 virus. The new SENSR was developed using CRISPR gene-editing technology as a rapid diagnostic that eventually could be used in homes, airports and other locations.
- Medical researchers have developed a new drug-like molecule that can counteract the effects of mutated epigenetic regulators, which are known to drive certain types of cancer including lymphoma.
- A team of researchers has demonstrated the existence of an internal diffusion barrier in the brain of fruit flies — in addition to the already known blood-brain barrier.
- The potential of DNA structural properties in single-molecule electronics has finally been harnessed by researchers in a single-molecule junction device that shows spontaneous self-restoring ability. Additionally, the device, based on a ‘zipper’ DNA configuration, shows unconventionally high electrical conductivity, opening doors to the development of novel nanoelectronic devices.
- It is essential for cells to control precisely which of the many genes of their genetic material they use. This is done in so-called transcription factories, molecular clusters in the nucleus. Researchers have now found that the formation of transcription factories resembles the condensation of liquids. Their findings will improve the understanding of causes of diseases and advance the development of DNA-based data storage systems.
- Using nanopore DNA sequencing technology, researchers have managed to scan a single protein. The new single-molecule peptide reader marks a breakthrough in protein identification, and opens the way towards single-molecule protein sequencing and cataloguing the proteins inside a single cell.
- Researchers used transcriptomics (a type of gene sequencing) calibrated using information from the fossil record to create the first phylogenetic reconstruction of the insect order Odonata (dragonflies and damselflies), covering 105 species. The reconstruction of the evolutionary history allowed robust estimations of the species divergence time and the timing of evolutionary changes, such as the development of egg-laying organs.
- A new finding offers researchers a direct way to investigate oxidative stress and its damaging effects in aging, cancer and other diseases.
- Depending on the outcome of social conflicts, ants of the species Harpegnathos saltator do something unusual: they can switch from a worker to a queen-like status known as gamergate. Now, researchers have made the surprising discovery that a single protein, called Kr-h1, responds to socially regulated hormones to orchestrate this complex social transition.
- What can sponges tell us about the evolution of the brain? Sponges have the genes involved in neuronal function in higher animals. But if sponges don’t have brains, what is the role of these? Scientists imaged the sponge digestive chamber to find out.
- 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
Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2
by Daniel J. Brogan, Duverney Chaverra-Rodriguez, Calvin P. Lin, Andrea L. Smidler, Ting Yang, Lenissa M. Alcantara, Igor Antoshechkin, Junru Liu, Robyn R. Raban, Pedro Belda-Ferre, Rob Knight, Elizabeth A. Komives, Omar S. Akbari in ACS Sensors
Blending experts from molecular genetics, chemistry and health sciences, researchers at the University of California San Diego have created a rapid diagnostic technology that detects SARS-CoV-2, the coronavirus that causes COVID-19.
The new SENSR (sensitive enzymatic nucleic acid sequence reporter) is based on CRISPR gene-editing technology that allows speedy detection of pathogens by identifying genetic sequences in their DNA or RNA.
Currently, many human pathogens are detected using a method known as real-time polymerase chain reaction. While highly accurate and sensitive, such diagnostics are time consuming and require specialized laboratory equipment, limiting their use to health and specialized facilities. SENSR is designed to simplify the SARS-CoV-2 detection process with a goal of eventual adaptation for in-home use.
While the Cas9 enzyme has been used extensively in CRISPR genetic engineering research, scientists have recently employed other enzymes such as the Cas12a and Cas13a for the development of highly accurate CRISPR-based diagnostics. Developed in a similar vein, SENSR is the first SARS-CoV-2 diagnostic to leverage the Cas13d enzyme (specifically a ribonuclease effector called “CasRx”).
The researchers believe that in order to maximize CRISPR’s capabilities and expand the genetics-based diagnostics pipeline, any Cas enzymes that can complement or supplement existing systems should be explored.
“CRISPR has significantly advanced our capabilities for rapid identification of infected individuals and offers point-of-care testing in low-resource settings that previously wasn’t possible,” said UC San Diego Biological Sciences Professor Omar Akbari, the study’s senior author. “SENSR further opens the toolbox for CRISPR diagnostic systems and will help detect emerging pathogens before they become pandemics.”
In developing SENSR, Akbari’s molecular genetics lab worked in conjunction with Professor Elizabeth Komives’ lab in the Department of Chemistry and Biochemistry (Division of Physical Sciences) to purify SENSR proteins and Rob Knight’s lab in the Department of Pediatrics (School of Medicine and Center for Microbiome Innovation) to test SARS-CoV-2 samples.
Early tests in SENSR’s development demonstrated SARS-CoV-2 detection in less than an hour. The researchers note in the paper that further development is needed, but the technology has the potential to become a “powerful molecular diagnostic with numerous applications.”
Eventually, Akbari envisions SENSR becoming important in locations such as airports so that passengers can quickly determine whether they might be carrying a virus.
“We need to keep innovating in the detect-and-protect arena to come up with more tools so when there is another pandemic, we will have scalable point-of-care diagnostics systems in place for rapid distribution,” said Akbari.
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
by Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, Gerd Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert in Molecular Systems Biology
It is essential for cells to control precisely which of the many genes of their genetic material they use. This is done in so-called transcription factories, molecular clusters in the nucleus. Researchers of Karlsruhe Institute of Technology (KIT), Friedrich-Alexander-Universität Erlangen-Nuremberg (FAU), and Max Planck Center for Physics and Medicine (MPZPM) have now found that the formation of transcription factories resembles the condensation of liquids. Their findings will improve the understanding of causes of diseases and advance the development of DNA-based data storage systems.
Human genetic material contains more than 20,000 different genes. But each cell only uses a fraction of the information stored in this genome. Hence, cells have to control precisely which genes they use. If not, cancer or embryonal growth disorder may develop. So-called transcription factories play a central role in the selection of active genes. “These factories are molecular clusters in the nucleus that combine the correct selection of active genes and the read-out of their sequence at a central location,” Lennart Hilbert explains. The Junior Professor for Systems Biology/Bioinformatics at the Zoological Institute (ZOO) of KIT also heads a working group at KIT’s Institute of Biological and Chemical Systems — Biological Information Processing (IBCS-BIP).
For decades, cellular and molecular biologists have studied how transcription factories are set up and taken into operation within a few seconds. Results obtained so far suggest relevance of processes known from industrial and technical polymer and liquid materials only. Current research focuses on phase separation as a central mechanism. In everyday life, phase separation can be observed when separating oil from water. It has not yet been clear, however, how exactly phase separation contributes to the setup of transcription factories in living cells.
Researchers from KIT’s Institute of Biological and Chemical Systems (IBCS), Zoological Institute (ZOO), Institute of Applied Physics (APH), and Institute of Nanotechnology (INT), in cooperation with scientists from FAU and MPZPM in Erlangen and the University of Illinois at Urbana-Champaign/USA, have now gained new findings on the formation of transcription factories: It is similar to the condensation of liquids. The first co-authors are Agnieszka Pancholi of IBCS-BIP and ZOO and Tim Klingberg of FAU and MPZPM.
In their publication, the researchers point out that condensation to form transcription factories resembles steamy glasses or windows. Liquid condenses in the presence of a receptive surface only, but then very quickly. In the living cell, specially marked areas of the genome are used as condensation surfaces. The liquid-coated areas allow for the adhesion of relevant gene sequences and additional molecules that eventually activate the adhering genes. These findings were obtained by interdisciplinary cooperation. Zebrafish embryos were studied with latest light microscopes developed by Professor Gerd Ulrich Nienhaus’s Chair at APH. These observations were then linked to computer simulations at the FAU Chair for Mathematics headed by Professor Vasily Zaburdaev. Combination of observations and simulations makes the condensation process reproducible and explains how living cells can set up transcription factories rapidly and reliably.
New understanding of condensed liquids in living cells recently resulted in entirely new approaches to treating cancer and diseases of the nervous system. These approaches are now being pursued by startups developing new drugs. Other research activities focus on the use of DNA sequences as digital data storage systems. Meanwhile, principle feasibility of DNA-based data storage systems has been demonstrated by several working groups. Reliable storage and read-out of information in such DNA storage media still represent big challenges.
“Our work shows how the biological cell organizes such processes rapidly and reliably. The computer simulations and functional concepts developed by us can be transferred directly to artificial DNA systems and can support their design,” Lennart Hilbert says.
Single-molecule junction spontaneously restored by DNA zipper
by Takanori Harashima, Shintaro Fujii, Yuki Jono, Tsuyoshi Terakawa, Noriyuki Kurita, Satoshi Kaneko, Manabu Kiguchi, Tomoaki Nishino in Nature Communications
In every advanced organism, the molecule called DNA (deoxyribonucleic acid, to use its full name) forms the genetic code. Modern-day technology takes DNA one step beyond living matter; scientists have established that the intricate structures of DNA have made it possible for it to be used in new-age electronic devices with junctions comprising just a single DNA molecule. However, as with any ambitious endeavor, there are impediments to overcome. It turns out that the single-molecule conductance falls off sharply with the length of the molecule so that only extremely short stretches of DNA are useful for electrical measurements. Is there a way around this problem?
There is, indeed, suggest researchers from Japan in a new breakthrough study. They have managed to achieve an unconventionally high conductivity with a long DNA molecule-based junction in a “zipper” configuration that also shows a remarkable self-restoring ability under electrical failure.
How did the researchers achieve this feat? Dr. Tomoaki Nishino from Tokyo Tech, Japan, who was part of this study, explains, “We investigated electron transport through the single-molecule junction of a ‘zipper’ DNA that is oriented perpendicular to the axis of a nanogap between two metals. This single-molecule junction differs from a conventional one not only in the DNA configuration but also in orientation relative to the nanogap axis.”
The team used a 10-mer and a 90-mer DNA strand (which indicate the number of nucleotides, basic building blocks of DNA, comprising the molecule length) to form a zipper-like structure and attached them to either a gold surface or to the metal tip of a scanning tunneling microscope, an instrument used to image surfaces at the atomic level. The separation between the tip and the surface constituted the “nanogap” that was modified with the zipper DNA.
By measuring a quantity called “tunneling current” across this nanogap, the team estimated the conductivity of the DNA junctions against a bare nanogap without DNA. Additionally, they carried out molecular dynamics simulations to make sense of their results in light of the underlying “unzipping” dynamics of the junctions.
To their delight, they found that that the single-molecule junction with the long 90-mer DNA showed an unprecedented high conductance. The simulations revealed that this observation could be attributed to a system of delocalized π-electrons that could move around freely in the molecule. The simulations also suggested something even more interesting: the single-molecule junction could actually restore itself i.e., go from “unzipped” to “zipped,” spontaneously after an electrical failure! This showed that the single-molecule junction was both resilient and easily reproducible.
In the wake of these discoveries, the team is excited about their future ramifications in technology. An optimistic Dr. Nishino speculates, “The strategy presented in our study could provide a basis for innovations in nanoscale electronics with superior designs of single-molecule electronics that could likely revolutionize nanobiotechnology, medicine, and related fields.”
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
by Jacob M. Musser, Klaske J. Schippers, et al. in Science
As you read these lines the highly sophisticated biological ‘machine’ that is your brain is at work. The human brain is made up of approximately 86 billion neurons and controls not only our bodily functions from vision to movement but also provides consciousness and understanding.
Despite its central importance the brain’s origins have not yet been uncovered. The first animal brains appeared hundreds of millions of years ago. Today, only the most primitive animal species, such as aquatic sponges, lack brains. Paradoxically, these species may hold the key to unlock the mystery of how neurons and brains first evolved.
Individual neurons in a brain communicate via synapses. These connections between cells lie at the heart of brain function and are regulated by a number of different genes. Sponges do not have these synapses, but their genome still encodes many of the synaptic genes. EMBL scientists asked the question why this might be the case.
“We know that these synaptic genes are involved in neuronal function in higher animals. Finding them in primitive species like sponges begs the question: if these animals don’t have brains, what is the role of these genes?” explained Detlev Arendt, EMBL Group Leader and Senior Scientist at EMBL Heidelberg. “As simple as that sounds, answering this question was beyond our technological abilities so far.”
To study the role of these synaptic genes in sponges, the Arendt lab established microfluidic and genomic technologies in the freshwater sponge Spongilla lacustris. Using these techniques, the scientists captured individual cells from several sponges inside microfluidic droplets and then profiled each cell’s genetic activity.
“We showed that certain cells in the sponge digestive chambers activate the synaptic genes. So even in a primitive animal lacking synapses, the synaptic genes are active in specific parts of its body,” said Jacob Musser, Research Scientist in the Arendt group and lead author on the study.
Sponges use their digestive chambers to filter out food from the water and interact with environmental microbes. To understand what the cells expressing synaptic genes do, the Arendt group joined forces with six EMBL teams as well as collaborators in Europe and worldwide. Working with EMBL’s Electron Microscopy Core Facility, Yannick Schwab’s team and Thomas Schneider’s group operating synchrotron beamlines at EMBL Hamburg the researchers developed a new correlative imaging approach. “By combining electron microscopy with X-ray imaging on a synchrotron beamline we were able to visualize the stunning behaviour of these cells,” Dr Schwab explained.
The scientists captured three-dimensional snapshots of cells crawling throughout the digestive chamber to clear out bacterial invaders and sending out long arms that enwrap the feeding apparatus of specific digestive cells. This behaviour creates an interface for targeted cell-cell communication, as it also happens across synapses between neuronal cells in our brains.
“Our results point to the cells regulating feeding and controlling the microbial environment as possible evolutionary precursors for the first animal brains,” Dr Musser said. “Truly food for thought!”
Reprogramming CBX8-PRC1 function with a positive allosteric modulator
by Junghyun L. Suh, Daniel Bsteh, Bryce Hart, Yibo Si, et al. in Cell Chemical Biology
A decade ago, genome sequencing revealed a big surprise: about 50 percent of human cancers are linked to mutations in what are known as epigenetic regulators, which control the activity of genes.
In a new study, a team of scientists led by Oliver Bell from USC and Stephen V. Frye from the University of North Carolina at Chapel Hill developed a new drug-like molecule that can counteract the effects of mutated epigenetic regulators, which are known to drive certain types of cancer including lymphoma.
In healthy cells, epigenetic regulators play an essential role: turning on and off the activity of hundreds of genes in the precisely orchestrated sequence that directs normal human development. One of these epigenetic regulators, EZH2, controls the transient inactivation of specific? genes in order to permit the maturation of immune cells. However, mutated EZH2 may cause persistent repression of these genes, thus preventing the immune cells from developing normally and ultimately leading them to transform into cancerous malignancies.
The good news is that in contrast to many other types of mutations, cancer-causing mutations in epigenetic regulators are potentially reversible by therapeutic drugs. With this in mind, first author Junghyun L. Suh and the research team set out to design a drug-like molecule to reverse the cancer-causing gene repression by EZH2.
Suh and her colleagues started by considering the mechanism by which EZH2 controls gene repression. EZH2 acts as a “writer” that marks which genes will be repressed. A second epigenetic regulator called CBX8 serves as a “reader” that interprets these repressive marks, and recruits additional regulatory machinery that actually turns off the genes.
Compared to the writer, the reader CBX8 seems to be equally critical for the proliferation of cancer cells, but is more dispensable for the function of healthy cells. This means that drugs targeting the reader would be expected to have fewer toxic side effects on the healthy cells throughout a patient’s body.
To specifically target CBX8, the researchers first engineered mouse stem cells in which they could easily screen a large number of drug-like molecules. These engineered stem cells relied on CBX8 reading the marks deposited by EZH2 to repress a gene producing a visible green fluorescent protein (GFP). If the stem cells showed activation of the telltale green glow, the scientists knew that a drug-like molecule had successfully prevented CBX8 from reading the repressive marks.
The researchers then parlayed their knowledge of CBX8 into several iterations of drug-like molecules that targeted this particular reader. They took into account CBX’s intricate protein structure, as well as the way that it binds to DNA and reads repressive marks. When they had succeeded in synthesizing a potent molecule that worked well in the engineered mouse cells, they moved on to testing in human cancer cells.
“When we exposed human lymphoma and colorectal cancer cells to our newly synthesized drug-like molecule in the laboratory, the malignant cells ceased to proliferate and began to behave more like healthy cells,” said the study’s co-corresponding author Oliver Bell, who is an assistant professor of biochemistry and molecular medicine, and stem cell biology and regenerative medicine at the Keck School of Medicine of USC, and a member of the USC Norris Comprehensive Cancer Center.
“Our CBX8-targeted molecule has the most powerful effect that we’ve seen so far in terms of blocking the reader’s function,” added co-corresponding author Stephen V. Frye, who is the Fred Eshelman Distinguished Professor and Co-director of the Center for Integrative Chemical Biology and Drug Discovery at the University of North Carolina at Chapel Hill. “This opens a path to exploring related cancer therapies, as well as to enhancing our understanding of epigenetic regulation in normal human development.”
Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics
by Manpreet Kohli, Harald Letsch, Carola Greve, Olivier Béthoux, et al. in iScience
Many people hate insects, but the iridescent colors and elegant flying style of dragonflies and damselflies have made them firm favorites worldwide. They have been around in some form for hundreds of millions of years, but the evolutionary history of these relics of prehistoric life has been poorly understood — until now.
In newly published study, researchers including a member of the University of Tsukuba have applied transcriptomics, a type of gene sequencing, to reconstruct the phylogeny of the insect order Odonata. By calibrating this sequencing using the fossil record, they have been able to determine when dragonflies and damselflies first emerged.
Transcriptomics is the study of the collection of ribonucleic acid (RNA) — known as the transcriptome — that is present in a cell at any given time. This RNA contains a wealth of information and can be used to determine relationships among different members of a species. Understanding these relationships is essential for reconstructing evolutionary histories, or phylogenies, which are essentially like a family tree in a genetic sense.
“This is the first transcriptome-based phylogenetic reconstruction of the order Odonata,” says one of the authors of the study Professor Ryuichiro Machida. “We analyzed a total of 2,980 protein-coding genes in 105 species, covering all but two of the order’s families.”
There are thousands of living (extant) species of Odonata, but few have been analyzed in a phylogenetic context, and most species have been identified or differentiated on the basis of physical characteristics, such as wing patterns or larvae appearance. Although comparing appearances can be useful for extant species, it’s not always as helpful when trying to reconstruct evolutionary histories — that’s where transcriptomics and fossil calibration are useful.
“A robust and reliable phylogenetic reconstruction is essential for dependable estimates of species divergence times,” explains Machida. “Different fossil calibration schemes can be applied, but these can greatly impact the range of estimated dates. We used a comprehensive fossil dataset combining newly assessed fossils with data from the literature to produce a well-resolved and robustly time-calibrated phylogeny for Odonata.”
This reconstruction provides the most comprehensive divergence time estimates for Odonata to date, meaning the researchers were able to determine when dragonflies and damselflies first appeared (around 200 million years ago). They were even able to estimate the time at which certain evolutionary characteristics developed, such as ovipositors (tube-shaped organs for laying eggs). Species that once flourished but have since died out were also identified. Given that these species can now only be identified in the fossil record, transcriptomics and phylogenetic reconstructions provide a unique opportunity to better understand the connections between extant and extinct species. Studies of a similar nature could shed light on equally obscured genetic histories for other species.
Drosophila ßHeavy-Spectrin is required in polarized ensheathing glia that form a diffusion-barrier around the neuropil
by Nicole Pogodalla, Holger Kranenburg, Simone Rey, Silke Rodrigues, Albert Cardona, Christian Klämbt in Nature Communications
The neurons, located in the brain are interconnected in a complex pattern and establish special communication points, the synapses. All neurons require a constant environment in order to function reliably. To ensure this, the brain is surrounded by the so-called blood-brain barrier. It ensures, for example, that the nutrient balance always remains the same and that harmful influences do not reach the neurons. This applies to all animals including humans. For insects, a team led by Nicole Pogodalla and Prof. Dr. Christian Klämbt from the Institute of Neuro- and Behavioral Biology at the University of Münster (Germany) has now shown that there is also a second barrier in the brain. Here glial cells, too, ensure a spatial separation of different functional compartments, which is essential for reliable functioning of the nervous system.
The research team studied the insect brain using larvae of the fruit fly (Drosophila melanogaster) as an example and focused on the role of glial cells. Early in development these cells help to establish the correct neuronal network and later glial cells play important roles in controlling the transmission of signals between neurons. In all invertebrates, as well as in primitive vertebrates, glial cells also define the outer boundary of the nervous system — the blood-brain barrier.
Deep in the fly brain, all synapses are located in a special region called the neuropil. The neuropil is separated from the zone containing the cell bodies of the neurons by a small set of surrounding glial cells, that were in the focus of Nicole Pogodalla. She developed a new experimental approach — dye injections into living larval brains — and combined this with cell type specific ablation experiments to show that these glial cells actually form a diffusion barrier, i. e. regulate the distribution of molecules.
Since all other cellular barriers in the body are formed by polarized cells that have an “up” and a “down,” the research team next examined glial cell polarity. Using advanced confocal image analysis as well as electron microscopy work in combination with state-of-the-art molecular genetics, the researchers uncovered that the ensheathing glial cells are indeed polarized. They showed that this polarization is functionally important, as defects in polarity lead to both an altered cell shape and cause a significant behavioral phenotype in fly larvae: Movement of larvae with defective or absent glial cells is impaired, and crawling speed is reduced.
In the current paper, the research team also describes the importance of extracellular matrix — the tissue lying between cells -, membrane lipids and membrane proteins, as well as the function of the cytoskeleton in the formation of the barrier-forming glial cells. The study includes extensive electron microscopy data obtained in a collaboration with Dr. Albert Cardona at the HHMI Janelia Research Campus in Ashburn, VA 20147, USA.
SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells
by Ying Wang, Frederick S. Yen, Xiphias Ge Zhu, Rebecca C. Timson, Ross Weber, Changrui Xing, Yuyang Liu, Benjamin Allwein, Hanzhi Luo, Hsi-Wen Yeh, Søren Heissel, Gokhan Unlu, Eric R. Gamazon, Michael G. Kharas, Richard Hite, Kıvanç Birsoy in Nature
Many of the processes that keep us alive also put us at risk. The energy-producing chemical reactions in our cells, for example, also produce free radicals — unstable molecules that steal electrons from other molecules. When generated in surplus, free radicals can cause collateral damage, potentially triggering malfunctions such as cancer, neurodegeneration, or cardiovascular disease.
Cells solve this problem by synthesizing antioxidants, compounds that neutralize free radicals. In a new study, Rockefeller scientists identify a key molecule that ferries glutathione, the body’s major antioxidant, into the cell’s mitochondria, where free radicals are produced en masse. The discovery opens new possibilities for investigating oxidative stress and its damaging effects.
“With the potential transporter identified, we can now control the amount of glutathione that enters mitochondria and study oxidative stress specifically at its source,” says Kivanç Birsoy, Chapman Perelman Assistant Professor at The Rockefeller University.
To avoid oxidative stress, cells need to properly balance the levels of free radicals and antioxidants within their mitochondria, where energy production happens. Because glutathione is produced outside of mitochondria, in the cell’s cytosol, the scientists wanted to know how it gets transported into these tiny powerhouses in the first place.
To shed light on this process, Birsoy’s team monitored protein expression in cells in response to glutathione’s levels. “We hypothesized that glutathione is shuttled by a transporter protein whose production is regulated by glutathione,” Birsoy says. “So if we lower the levels of glutathione, the cell should compensate by upregulating the transporter protein.”
The analysis pointed to SLC25A39, a protein in the mitochondrial membrane whose function was hitherto unknown. The researchers found that blocking SLC25A39 reduced glutathione inside the mitochondrion, without affecting its levels elsewhere in the cell. Other experiments showed that mice cannot survive without SLC25A39. In animals engineered to lack this protein, red blood cells quickly die by oxidative stress due to their failure to bring glutathione into mitochondria.
The identification of the transporter may lead to a better understanding of a variety of disease pathways linked to oxidative stress, including those involved in aging and neurodegeneration. “These conditions could potentially be treated or prevented by stimulating antioxidant transport into mitochondria,” Birsoy says. Moreover, the team is now exploring whether SLC25A39 might hold promise as a drug target for cancer, by helping to induce fatal oxidative stress in tumor cells. “In cancer, we would want to prevent antioxidants from getting into mitochondria, and the transporter protein may be our way to do that,” Birsoy says.
Kr-h1 maintains distinct caste-specific neurotranscriptomes in response to socially regulated hormones
by Janko Gospocic, Karl M. Glastad, Lihong Sheng, Emily J. Shields, Shelley L. Berger, Roberto Bonasio in Cell
Depending on the outcome of social conflicts, ants of the species Harpegnathos saltator do something unusual: they can switch from a worker to a queen-like status known as gamergate. Now, researchers have made the surprising discovery that a single protein, called Kr-h1 (Kru-ppel homolog 1), responds to socially regulated hormones to orchestrate this complex social transition.
“Animal brains are plastic; that is, they can change their structure and function in response to the environment,” says Roberto Bonasio of the University of Pennsylvania Perelman School of Medicine. “This process, which also takes place in human brains — think about the changes in behavior during adolescence — is crucial to survival, but the molecular mechanisms that control it are not fully understood. We determined that, in ants, Kr-h1 curbs brains’ plasticity by preventing inappropriate gene activation.”
In an ant colony, workers maintain the colony by finding food and fighting invaders, whereas the queen’s main task is to lay eggs. And, yet, it is the same genetic instructions that give rise to these very different social roles and behaviors. By studying ants, Bonasio and colleagues, including Shelley Berger, also at the University of Pennsylvania, wanted to understand how turning certain genes “on” or “off” affects brain function and behavior. Because Harpegnathos adults can switch from a worker to a gamergate, they were perfect for such studies.
So that they could study the underlying molecular events that cause such a switch, the research team, led by co-first authors Janko Gospocic and Karl Glastad, developed a method for isolating neurons from the ants and keeping them alive in plastic dishes in the lab. This allowed the team to explore how the cells responded to changes in their environment, including hormone levels.
These studies further identify that two hormones, juvenile hormone and ecdysone, which are present at different levels in the bodies of workers and gamergates, produced distinct patterns of gene activation in the brains of the two castes. The biggest surprise was that both hormones influenced the cells by activating a single protein, Kr-h1.
“This protein regulates different genes in workers and gamergates and prevents the ants from performing ‘socially inappropriate’ behaviors,” Berger says. “That is to say, Kr-h1 is required to maintain the boundaries between social castes and to ensure that workers continue to work while gamergates continue to act like queens.”
“We had not anticipated that the same protein could silence different genes in the brains of different castes and, as a consequence, suppress worker behavior in gamergates and gamergate behavior in workers,” Bonasio adds. “We thought that these jobs would be assigned to two or more different factors, each of them only present in one or the other brain.”
The findings reveal important roles for socially regulated hormones and gene regulation in the ability of animal brains to switch from one genetic mode and social caste to another. “The key message is that, at least in ants, multiple behavioral patterns are simultaneously specified in the genome and that gene regulation can have a great impact on which behavior that organism carries out,” Berger says. “In other words, the parts of both Dr. Jekyll and Mr. Hyde are already written into the genome; everyone can play either role, depending on which gene switches are turned on or off.”
The researchers think the implications may go much farther than understanding behavioral plasticity in ants and other insects. “It is tempting to speculate that related proteins might have comparable functions in more complex brains, including our own,” says Bonasio. “Discovering these proteins might allow us to one day restore plasticity to brains that have lost it, for example aging brains.”
The discovery that a single factor can suppress different sets of genes and behaviors in different brains raises important questions about how the dual function of this protein and others like it might be regulated. In future studies, the researchers plan to explore the role of Kr-h1 in other organisms. They say they also want to explore how the environment impacts gene regulation at the epigenetic level — through the presence or absence of certain chemical marks on DNA — and how this in turn impacts brain plasticity and behavior.
Multiple rereads of single proteins at single–amino acid resolution using nanopores
by Henry Brinkerhoff, Albert S. W. Kang, Jingqian Liu, Aleksei Aksimentiev, Cees Dekker in Science
Using nanopore DNA sequencing technology, researchers from TU Delft and the University of Illinois have managed to scan a single protein: by slowly moving a linearized protein through a tiny nanopore, one amino acid at the time, the researchers were able to read off electric currents that relate to the information content of the protein. The new single-molecule peptide reader marks a breakthrough in protein identification, and opens the way towards single-molecule protein sequencing and cataloguing the proteins inside a single cell.
Proteins are the workhorses of our cells, yet we simply don’t know what proteins we all carry with us. A protein is a long peptide string made of 20 different types of amino acids, comparable to a necklace with different kinds of beads. From the DNA blueprint, we are able to predict of which amino acids a protein consists. However, the final protein can greatly differ from the blueprint, for example due to post-translational modifications. Current methods to measure proteins are expensive, limited to large volumes, and they cannot detect many rare proteins. With nanopore-based technology, one is already able to scan and sequence single DNA molecules. The team led by Cees Dekker (TU Delft) now adapted this technique to instead scan a single protein, one amino acid at a time.
“Over the past 30 years, nanopore-based DNA sequencing has been developed from an idea to an actual working device,” Cees Dekker explains. “This has even led to commercial hand-held nanopore sequencers that serve the billion-dollar genomics market. In our paper, we are expanding this nanopore concept to the reading of single proteins. This may have great impact on basic protein research and medical diagnostics.”
The new technique reveals characteristics of even single amino acids within a peptide, but how? Lead author of the paper Henry Brinkerhoff, who pioneered this work as a postdoc in Dekker’s lab, explains: “Imagine the string of amino acids in one peptide molecule as a necklace with different-sized beads. Then, imagine you turn on the tap as you slowly move that necklace down the drain, which in this case is the nanopore. If a big bead is blocking the drain, the water flowing through will only be a trickle; if you have smaller beads in the necklace right at the drain, more water can flow through. With our technique we can measure the amount of water flow (the ion current actually) very precisely.” Cees Dekker enthusiastically adds: “A cool feature of our technique is that we were able to read a single peptide string again and again: we then average all the reads from that one single molecule, and thus identify the molecule with basically 100% accuracy.”
This results in a unique read-off which is characteristic for a specific protein. When the researchers changed even one single amino acid within the peptide (‘a single bead within the necklace’), they obtained very different signals, indicating the extreme sensitivity of the technique. The group led by Alek Aksimentiev at the University of Illinois performed molecular dynamics simulations that showed how the ion current signals relate to the amino acids in the nanopore.
The new technique is very powerful for identifying single proteins and mapping minute changes between them — much like how a cashier in the supermarket identifies each product by scanning its barcode. It also may provide a new route towards full de novo protein sequencing in the future.
Henry Brinkerhoff clarifies: “Our approach might lay a basis for a single-protein sequencer in the future, but de novo sequencing remains a big challenge. For that, we still need to characterize the signals from a huge number of peptides in order to create a ‘map’ connecting ion current signals to protein sequence. Even so, the ability to discriminate of single-amino-acid substitutions in single molecules is a major advance, and there are many immediate applications for the technology as it is now.”
Using the current nanopore peptide reader, researchers can start analyzing what proteins float around in our cells. After synthesis in cells, proteins still undergo changes that affect their function, called post-translational modifications. The resulting millions of protein variants are difficult to measure, and could be considered the ‘dark matter of biology’.
Cees Dekker: “To continue the metaphor: after a necklace with its beads is made, it will still be changed: some red beads get a phosphoryl attached to it, some blue beads a sugar group, etc. These changes are crucial to protein function, and also a marker for diseases such as cancer. We think that our new approach will allow us to detect such changes, and thus shine some light on the proteins that we carry with us.”
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