GN/ New method to help with analysis of single cell data
Genetics biweekly vol.48, 14th November — 30th November
TL;DR
- CITE-seq (cellular indexing of transcriptomes and epitopes) is an RNA sequencing-based method that simultaneously quantifies cell surface protein and transcriptomic data within a single cell readout. The ability to study cells concurrently offers unprecedented insights into new cell types, disease states or other conditions. While CITE-seq solves the problem of detecting a limited number of proteins while using single-cell sequencing in an unbiased way, one of its limitations is the high levels of background noise that can hinder analysis.
- Researchers have determined the gene mutation responsible for an observable trait in bison — albinism.
- Unlike humans, zebrafish can completely regenerate their hearts after injury. They owe this ability to the interaction between their nervous and immune systems, as researchers now report.
- Some patients with myelodysplastic syndromes, like acute myeloid leukemia, benefit from a chemotherapy drug called decitabine that stunts cancer growth. But many others are resistant to decatibine’s effects or become resistant over time. Researchers have uncovered a “genomic tug of war” in animal studies that could influence how well certain patients — or certain cancers — respond to decitabine.
- For over 20 years, a research team has studied the common bluetail damselfly. Females occur in three different color forms — one with a male-like appearance, something that protects them from mating harassment. In a new study, an international research team found that this genetic color variation that is shared between several species arose through changes in a specific genomic region at least five million years ago.
- A new theoretical model helps explain how epigenetic memories, encoded in chemical modifications of chromatin, are passed from generation to generation. Within each cell’s nucleus, researchers suggest, the 3D folding patterns of its genome determines which parts of the genome will be marked by these chemical modifications.
- Researchers have rediscovered and successfully cultivating Rhabdamoeba marina — a rare marine amoeba that has only been reported in two cases in the past century. Using this culture strain, they performed a comprehensive analysis of its genetic sequence, revealing for the first time the phylogenetic position of this enigmatic amoeba, and proposed a novel taxonomic classification based on their research findings.
- Scientists take a look at data that has so far been mostly discarded as contamination, revealing the previously underestimated role of extracellular vesicles (EVs). These are important for the exchange of genetic information between cells and thus for the microbial community in the sea.
- Researchers have discovered previously unknown changes in a specific type of liver cells, potentially opening avenues for a new treatment for liver fibrosis, a potentially life-threatening condition. Currently, there are no drugs available to treat liver fibrosis.
- A genetic breakthrough has opened new opportunities for iron-fortified vegetables and cereal crops to help address the global health issue of anemia.
- 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
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro
by Yuan Yin, Masanao Yajima, Joshua D Campbel in Nucleic Acids Research
CITE-seq (cellular indexing of transcriptomes and epitopes) is an RNA sequencing-based method that simultaneously quantifies cell surface protein and transcriptomic data within a single cell readout. The ability to study cells concurrently offers unprecedented insights into new cell types, disease states or other conditions.
While CITE-seq solves the problem of detecting a limited number of proteins while using single-cell sequencing in an unbiased way, one of its limitations is the high levels of background noise that can hinder analysis.
To rectify this problem, researchers from Boston University Chobanian & Avedisian School of Medicine and Collage of Arts and Sciences have developed a novel tool which can identify and remove unwanted background noise that comes from various sources.
“We created DecontPro, a statistical model that decontaminates two sources of contamination that were observed empirically in CITE-seq data,” explains corresponding author Joshua Campbell, PhD, associate professor of medicine at the School. “It can be used as an important quality assessment tool that will aid in the downstream analysis and help researchers to better understand the molecular cause of disease,” he said.
The researchers examined several publicly available datasets that profiled different types of tissue with CITE-seq and found a novel type of artifact, which they called a “spongelet.” The spongelets contributed a large amount of background noise in several datasets. The researchers found that DecontPro can estimate and remove different sources of background noise, including contamination from spongelets, from ambient material that may be present in the cell suspension, or from non-specific binding of antibodies.
Masanao Yajima, PhD, professor of the practice in the department of mathematics and statistics states, “DecontPro is a Bayesian hierarchical model. We carefully constructed it so that it can tease apart the signals from noise in single-cell datasets without being overly aggressive.”
Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation
by Sam Stroupe, Carly Martone, Blake McCann, Rytis Juras, Helena Josefina Kjöllerström, Terje Raudsepp, Donald Beard, Brian W Davis, James N Derr in G3: Genes, Genomes, Genetics
A research team led by scientists from the Texas A&M School of Veterinary Medicine & Biomedical Sciences (VMBS) has developed the most comprehensive genome yet for the North American bison, bringing the animal’s genetic roadmap up to date with the latest genome sequencing technology. In doing so, the research team also discovered the gene responsible for albinism in bison.
The study — recently published in G3: Genes, Genomes, and Genetics — details the development of this high-resolution reference genome, which the researchers then used to produce the first test for genetic mutations, starting with the mutation responsible for albinism.
Albinism, a rare condition characterized by a lack of pigment in an animal’s body, making them look white with red eyes, has historical significance in that albino bison have been recognized as a religious symbol for some Native American Indigenous tribes. The study also lays the framework for determining other genetic variations that impact important bison traits, such as those that contribute to the health and production value of this species.
Dr. James Derr, a VMBS professor of veterinary pathobiology and genetics who led the research team that created the first bison genome back in 2015, assembled the team that developed this new reference genome. This team includes assistant professor of genetics Dr. Brian Davis, graduate student Sam Stroupe, and representatives from Texas Parks and Wildlife and the National Park Service.
“Because reference genomes can help researchers identify and characterize genes that are responsible for a large number of traits, this technology is used to do all kinds of things, including diagnosing health conditions and developing targeted treatments,” Davis said.
The newest bison reference genome was developed using technology that allows researchers to create genomes based on DNA from hybrids, which are animals with DNA from two different species. In this case, the researchers used DNA from a type of bison-cow hybrid called an F1, or individuals with a perfect 50–50 split between its parents’ DNA. In general, F1 hybrids between bison and cattle are rare but have historically happened, since we now know that most bison herds in North America contain descendants of hybrids between bison and cattle — a discovery that Derr and his research partners made last year.
“One day we got a call from Texas Parks and Wildlife saying they knew someone who had an F1 hybrid,” Derr said. “It was the first fully documented, first-generation F1 hybrid I have seen in 25 years of working with bison. That’s why we were able to do this.”
To create the new bison genome, the researchers first sequenced the genome of the F1 hybrid as well as the bison mom and the domestic cattle father. With this information, they were able to separate bison DNA from the cattle DNA regions in the hybrid.
Since the cattle genome is already very advanced, it provided a reference for creating the new bison genome, helping to guide researchers in developing the complete high-resolution reference bison genome. To prove the utility of the new genome, the team set out to discover which gene mutation was responsible for albinism in bison and to create a genetic test that could be used to identify carriers of that mutation. The discovery is the first time anyone has successfully determined the gene mutation responsible for an observable trait in bison.
“We knew albinism was an inherited recessive trait, but we didn’t know which gene was responsible,” Stroupe said. “So, we sequenced the DNA from a few albino bison and compared them to those of normal coloration to find the mutation that causes albinism. As it turns out, the mutation causes an important enzyme to cease functioning correctly, which leads to the lack of skin pigmentation.”
Many North American Indigenous peoples regard white bison as sacred entities with prophetic spiritual associations. While not all white bison have albinism, the birth of one is cause for celebration in some communities. Despite this cultural significance, Derr isn’t suggesting that people try to produce albino bison using genetic testing.
“Sadly, albino bison are often not very healthy,” Derr said. “They tend to develop skin cancers, and they can develop other health problems as they age.”
Albino bison are also different from white or tan bison that result from crossing bison with white cattle, particularly Charolais. These bison lack the red eyes and pink nose of true albinos. Now that a more accurate bison genome exists, scientists can learn more about the genetic makeup of North America’s bison population.
“The development of this new reference genome and the identification of a causative genetic mutation is exciting news for bison,” Derr said. “It opens the doors for new discoveries and insights into bison genetics. “Overall, this is a vital step toward the future conservation management of the United States’ national mammal,” he said.
Alpha-1 adrenergic signaling drives cardiac regeneration via extracellular matrix remodeling transcriptional program in zebrafish macrophages
by Onur Apaydin, Akerke Altaikyzy, Alessandro Filosa, Suphansa Sawamiphak in Developmental Cell
Unlike humans, zebrafish can completely regenerate their hearts after injury. They owe this ability to the interaction between their nervous and immune systems, as researchers led by Suphansa Sawamiphak from the Max Delbrück Center now report.
Each year, more than 300,000 people in Germany have a myocardial infarction — the technical term for heart attack. The number of people surviving a heart attack has increased significantly, but this severe cardiac event causes irreparable damage to their hearts. A heart attack occurs when blood vessels that supply blood and oxygen to the heart muscle become blocked, causing part of the heart muscle tissue to die. This damage is permanent because the human heart has no ability to grow new heart muscle cells. Instead, connective tissue cells known as fibroblasts migrate into the damaged area of the heart muscle. They form scar tissue that weakens the pumping power of the heart. Previous attempts to use stem cells to treat infarction-damaged hearts have not been very successful.
The team led by Dr. Suphansa Sawamiphak, head of the Cardiovascular-Hematopoietic Interaction Lab at the Max Delbrück Center, is looking at the process from a different angle. “We know that both signals from the autonomic nervous system and the immune system play a pivotal role in scarring and regeneration,” says Sawamiphak. “So it stands to reason that the communication between the autonomic nervous and immune systems determines whether heart muscle scarring will occur or whether the heart muscle can recover.” It is also known that macrophages play a role in both processes. But how is this decision made?
To address this question, the researchers are studying zebrafish larvae. The fish can be easily modified and are also optically transparent, making internal processes easy to observe in the living organism. “Plus, they can fully regenerate their heart after an injury,” says Onur Apaydin, first author of the study.
The researchers used zebrafish larvae whose heart muscle cells produce a fluorescent substance, making it easy to detect them under a microscope. They then induced an injury similar to a myocardial infarction in the larval hearts and blocked several receptors on the surface of the macrophages. The result was that adrenergic signals from the autonomic nervous system determined whether the macrophages multiplied and migrated into the damaged site. These signals also played an important role in regenerating heart muscle tissue.
In the next step, the researchers engineered genetically modified zebrafish in which the adrenergic signal reached the macrophages but could not be transmitted from the receptor into the cell’s interior. “This showed that signal transmission is crucial for heart regeneration,” says Apaydin. If signaling is interrupted, the scarring process is triggered instead.
“Our findings indicate that this is a key regulator of crosstalk between the nervous and immune systems,” says Apaydin. When macrophages are activated by the adrenergic signals of the autonomic nervous system, they in turn communicate with fibroblasts. Fibroblasts that promote regeneration alter the extracellular matrix at the damaged site. This ultimately creates a microenvironment conducive to the growth of blood and lymph vessels and to the development of new heart vessels. If, on the other hand, the signal is blocked, fibroblasts infiltrate the site and cause scarring — similar to what occurs in the human heart after a heart attack.
“We next want to examine in detail how signaling differs between zebrafish and humans,” says Sawamiphak. “This will help us understand why heart muscle tissue is unable to regenerate in humans.” The team also hopes to identify potential targets for influencing the interaction between the nervous and immune systems in a way that promotes the regeneration of heart muscle tissue and the maintenance of heart function in heart attack patients.
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression
by Fanju W. Meng, Kristin E. Murphy, Claire E. Makowski, Benjamin Delatte, Patrick J. Murphy in Development
Some patients with myelodysplastic syndromes, like acute myeloid leukemia, benefit from a chemotherapy drug called decitabine that stunts cancer growth. But many others are resistant to decatibine’s effects or become resistant over time. Wilmot Cancer Institute researchers have uncovered a “genomic tug of war” in animal studies that could influence how well certain patients — or certain cancers — respond to decitabine.
In a study, Wilmot investigators found that decitabine causes different regions of DNA to engage in a tug of war for a gene activator, called H2A.Z. If too little of this gene activator is around, gene expression grinds to a halt, causing cells to die. However, many types of cancer have very high levels of H2A.Z, which may help them overcome this decitabine-induced tug of war, allowing the cancer to grow.
“Two years ago, we published a paper where we identified different subtypes of breast cancer based on the amount of H2A.Z in tumors,” said Patrick Murphy, PhD, assistant professor of Biomedical Genetics and Biology at the University of Rochester Medical Center and member of Wilmot’s Genetics, Epigenetics, and Metabolism program, who led the studies. “If our findings bear out in humans, we may be able to classify patients based on how much H2A.Z is in their tumor, and then decide whether or not this therapy is going to be more or less effective. So it could eventually be used alongside personalized medicine diagnostics.”
H2A.Z is a histone — a class of proteins that DNA wraps around. Different types of histones spool the DNA more tightly, keeping it protected, or loosely, allowing the DNA to be read and turned into proteins that carry out the many functions of a cell.
H2A.Z binds DNA loosely, helping to turn on nearby genes. For a long time, it was believed to only bind to regions of DNA that contain the code for proteins. However, Murphy and postdoctoral associate Fanju Meng, PhD, discovered that H2A.Z also binds to non-coding “junk DNA” in zebrafish.
“That was when we first started wondering, maybe it’s not doing what we think it’s doing, or maybe it’s doing something extra,” said Murphy. “We always thought of H2A.Z as a factor that goes to genes and helps turn them on. So when we started seeing it at different places, we started asking more questions.”
Research dating back to the early 2000’s has hinted at a murky link between H2A.Z and decitabine. More recent studies also show that decitabine can turn on portions of non-coding “junk DNA,” but those studies stopped short of explaining exactly how that happens.
Treating the embryos with decitabine drew H2A.Z toward non-coding regions of DNA, reactivating them, and away from coding DNA, which curtailed gene expression, killed cells, and stunted embryo growth. In embryos that expressed high levels of H2A.Z — mimicking some cancers — there was enough H2A.Z to bind at both coding and non-coding regions and gene expression and embryo development were normal.
The same effect was seen with a toxic chemical, called TDCIPP, which is widely used in flame retardants and pesticides and has been found in human urine and breastmilk. The toxin caused H2A.Z to shift from coding to non-coding DNA regions, reducing gene expression and disrupting embryo development. But embryos that overexpressed H2A.Z were able to overcome the tug of war and were protected from the negative effects of the toxin.
“These external stressors — decitabine and TDCIPP — hijack essential aspects of cellular machinery to cause cell death,” said Murphy. “Our study identifies critical vulnerabilities which can be taken advantage of to improve future cancer therapeutics.”
Further research is needed, however, to confirm that this mechanism also happens in humans and to figure out how junk DNA sequences are able to hijack H2A.Z. As a first step in that direction, Murphy and Meng will soon study this mechanism in mouse embryonic stem cells — making the jump into mammals.
The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies
by Beatriz Willink, Kalle Tunström, Sofie Nilén, Rayan Chikhi, Téo Lemane, Michihiko Takahashi, Yuma Takahashi, Erik I. Svensson, Christopher West Wheat in Nature Ecology & Evolution
For over 20 years, a research team at Lund University in Sweden has studied the common bluetail damselfly. Females occur in three different colour forms — one with a male-like appearance, something that protects them from mating harassment. In a new study, an international research team found that this genetic colour variation that is shared between several species arose through changes in a specific genomic region at least five million years ago.
The question of how and why genetic variation arises and is maintained over long periods of time is of key importance to evolutionary biology, population genetics and conservation biology. In all populations of limited size, genetic variation is lost over time. It is therefore important to understand both the mechanisms that give rise to new genetic variation, and the mechanisms that act to maintain variation. This has significance both for conservating species and for the future evolutionary potential of populations to adapt to rapidly changing environments.
In the new study, a research team mapped the extensive and striking colour variation among the females of the bluetail damselfly (Ischnura elegans).
“In this damselfly species, there are three genetically determined colour forms in the females, one of which makes them look like males. These male-like females have an advantage because they avoid excessive mating harassment from the males. Our study clarifies when, how and why this variation arose, and shows that this variation has been maintained over long evolutionary time periods through so-called balanced natural selection,” says Erik Svensson, biology professor at Lund University.
By sequencing the DNA of the three colour forms of the bluetail damselfly and comparing it to the two colour forms in its closely related tropical relative Ischnura senegalensis, the researchers were able to demonstrate that this genetic colour variation in females arose at least five million years ago; through several different mutations in a specific genetic region on the damselfly’s thirteenth chromosome.
“The great colour variation in insects fascinates the general public, and raises questions about the function of colour signals and its evolutionary consequences for partner choice and conflicts between the sexes,” says Erik Svensson.
Having located the gene behind the female colour variation, the researchers can now go further and identify different genotypes in the males, and in the aquatic larval stage of these insects. The males lack visible colour forms, but the researchers plan to investigate whether the colour gene affects other characteristics of the larvae and males, including survival and behaviors.
“We now have a good knowledge base for investigating the colour variation over longer evolutionary time scales among other species of this damselfly genus, which occurs in Europe, Africa, Asia, Australia, North and South America. These new genetic results help us understand both the evolutionary processes that take place within a species, and what happens over longer evolutionary macroevolutionary time scales of tens of millions of years and across several different species,” concludes Erik Svensson.
Design principles of 3D epigenetic memory systems
by Jeremy A. Owen, Dino Osmanović, Leonid Mirny in Science
Every cell in the human body contains the same genetic instructions, encoded in its DNA. However, out of about 30,000 genes, each cell expresses only those genes that it needs to become a nerve cell, immune cell, or any of the other hundreds of cell types in the body.
Each cell’s fate is largely determined by chemical modifications to the proteins that decorate its DNA; these modification in turn control which genes get turned on or off. When cells copy their DNA to divide, however, they lose half of these modifications, leaving the question: How do cells maintain the memory of what kind of cell they are supposed to be?
A new MIT study proposes a theoretical model that helps explain how these memories are passed from generation to generation when cells divide. The research team suggests that within each cell’s nucleus, the 3D folding pattern of its genome determines which parts of the genome will be marked by these chemical modifications. After a cell copies its DNA, the marks are partially lost, but the 3D folding allows each daughter cell to easily restore the chemical marks needed to maintain its identity. And each time a cell divides, chemical marks allow a cell to restore its 3D folding of its genome. This way, by juggling the memory between 3D folding and the marks, the memory can be preserved over hundreds of cell divisions.
“A key aspect of how cell types differ is that different genes are turned on or off. It’s very difficult to transform one cell type to another because these states are very committed,” says Jeremy Owen PhD ’22, the lead author of the study. “What we have done in this work is develop a simple model that highlights qualitative features of the chemical systems inside cells and how they need to work in order to make memories of gene expression stable.”
Within the cell nucleus, DNA is wrapped around proteins called histones, forming a densely packed structure known as chromatin. Histones can display a variety of modifications that help control which genes are expressed in a given cell. These modifications generate “epigenetic memory,” which helps a cell to maintain its cell type. However, how this memory is passed on to daughter cells is somewhat of a mystery.
Previous work by Mirny’s lab has shown that the 3D structure of folded chromosomes is partly determined by these epigenetic modifications, or marks. In particular, they found that certain chromatin regions, with marks telling cells not to read a particular segment of DNA, attract each other and form dense clumps called heterochromatin, which are difficult for the cell to access.
In their new study, Mirny and his colleagues wanted to answer the question of how those epigenetic marks are maintained from generation to generation. They developed a computational model of a polymer with a few marked regions, and saw that these marked regions collapse into each other, forming a dense clump. Then they studied how these marks are lost and gained.
When a cell copies its DNA to divide it between two daughter cells, each copy gets about half of the epigenetic marks. The cell then needs to restore the lost marks before the DNA is passed to the daughter cells, and the way chromosomes were folded serves as a blueprint for where these remaining marks should go.
These modifications are added by specialized enzymes known as “reader-writer” enzymes. Each of these enzymes is specific for a certain mark, and once they “read” existing marks, they “write” additional marks at nearby locations. If the chromatin is already folded into a 3D shape, marks will accumulate in regions that already had modifications inherited from the parent cell.
“There are several lines of evidence that suggest that the spreading can happen in 3D, meaning if there are two parts that are near each other in space, even if they’re not adjacent along the DNA, then spreading can happen from one to another,” Owen says. “That is how the 3D structure can influence the spreading of these marks.”
This process is analogous to the spread of infectious disease, as the more contacts that a chromatin region has with other regions, the more likely it is to be modified, just as an individual who is susceptible to a particular disease is more likely to become infected as their number of contacts increases. In this analogy, dense regions of heterochromatin are like cities where people have many social interactions, while the rest of the genome is comparable to sparsely populated rural areas.
“That essentially means that the marks will be everywhere in the dense region and will be very sparse anywhere outside it,” Mirny says.
The new model suggests possible parallels between epigenetic memories stored in a folded polymer and memories stored in a neural network, he adds. Patterns of marks can be thought of as analogous to the patterns of connections formed between neurons that fire together in a neural network.
“Broadly this suggests that akin to the way neural networks are able to do very complex information processing, the epigenetic memory mechanism we described may be able to process information, not only store it,” he says.
While this model appeared to offer a good explanation for how epigenetic memory can be maintained, the researchers found that eventually, reader-writer enzyme activity would lead to the entire genome being covered in epigenetic modifications. When they altered the model to make the enzyme weaker, it didn’t cover enough of the genome and memories were lost in a few cell generations.
To get the model to more accurately account for the preservation of epigenetic marks, the researchers added another element: limiting the amount of reader-writer enzyme available. They found that if the amount of enzyme was kept between 0.1 and 1 percent of the number of histones (a percentage based on estimates of the actual abundance of these enzymes), their model cells could accurately maintain their epigenetic memory for up to hundreds of generations, depending on the complexity of the epigenetic pattern.
It is already known that cells begin to lose their epigenetic memory as they age, and the researchers now plan to study whether the process they described in this paper might play a role in epigenetic erosion and loss of cell identity. They also plan to model a disease called progeria, in which cells have a genetic mutation that leads to loss of heterochromatin. People with this disease experience accelerated aging.
“The mechanistic link between these mutations and the epigenetic changes that eventually happen is not well understood,” Owen says. “It would be great to use a model like ours where there are dynamic marks, together with polymer dynamics, to try and explain that.”
Rhabdamoeba marina is a heterotrophic relative of chlorarachnid algae
by Takashi Shiratori, Ken‐ichiro Ishida in Journal of Eukaryotic Microbiology
Researchers at the University of Tsukuba have rediscovered and successfully cultivating Rhabdamoeba marina — a rare marine amoeba that has only been reported in two cases in the past century. Using this culture strain, they performed a comprehensive analysis of its genetic sequence, revealing for the first time the phylogenetic position of this enigmatic amoeba, and proposed a novel taxonomic classification based on their research findings.
Rhabdamoeba marina (R. marina) is a small marine amoeba, first discovered and described in England in 1921. The amoeboid cells of R. marina, characterized by their near immobility, can produce flagellated cells with two rearward-extending flagella through budding under conditions of prey scarcity. Despite these distinct characteristics, the taxonomic classification of R. marina has remained unverified because only two cases have been documented, including the original description. Researchers successfully established a culture strain of R. marina from seawater sourced from the coast of Tottori Prefecture, Japan.
Analyzing the genetic sequence of this strain, they found that R. marina does not align with its previously assumed taxonomic group but is closely related to chlorarachnid algae within the phylum Cercozoa. Therefore, the researchers have advocated for the reclassification of R. marina into the class Chlorarachnea.
Through this study, the gene sequence of R. marina — a scarcely encountered and rare amoeba — has been unveiled for the first time, and its phylogenetic position has been clarified. The study highlights the importance of observing environmental samples for the rediscovery of unicellular organisms such as R. marina that lack genetic data. Such efforts are indispensable for understanding microbial diversity.
Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space
by Dominik Lücking, Coraline Mercier, Tomas Alarcón-Schumacher, Susanne Erdmann in ISME Communications
There is a lively exchange of genetic information between the numerous microorganisms in the oceans. This so-called horizontal gene transfer (HGT) is crucial for the evolution of many organisms and is, for example, also the most important mechanism for the spread of antibiotic resistance in bacteria. Until now, it was assumed that direct contacts between cells, free DNA or viruses were primarily responsible for the exchange of genes. A study led by Susanne Erdmann from the Max Planck Institute for Marine Microbiology in Bremen now shows that so-called extracellular vesicles are also very important for the transfer of genetic information in the sea and thus for the life of its smallest inhabitants.
Most viruses are tiny. Up to 10 million of them can be found in every drop of seawater. They can not only pack up their own genetic material (their genome), but also parts of their host’s DNA — i.e. the DNA of the organism they have infected — and transport it into other cells.
Studying viruses is challenging. Seawater samples have to be filtered through filters with a pore size of only 0.2 µm (which is about 300 times less than the thickness of a human hair) to separate the viruses from the cells. In addition to viruses, these filtered samples also contain so-called gene transfer agents (GTAs) and extracellular vesicles (EVs). GTAs are virus-like particles that exclusively package host DNA, and EVs are small vesicles enveloped by a membrane that detach from the cell surface of the host. These EVs can contain a variety of molecules. In addition to enzymes, nutrients and RNA, they often transport fragments of DNA.
Erdmann and her team have now shown that, other than previously assumed, there is a lot of host DNA in the filtered seawater samples that is not transported by viruses. Proving this was extremely complicated. “After sequencing, i.e. reading out the host DNA, we can no longer recognize how it got into our sample,” explains Erdmann, head of the Max Planck Research Group Archaea Virology at the Max Planck Institute in Bremen. “There is no feature to assign a sequence to a specific transport mechanism.” To solve this problem, the researchers used a trick. In a first step, they assigned each DNA sequence to a host from which it originally stems. Then they determined a main transport mechanism for each host as far as possible — i.e. by viruses, GTAs or EVs. This enabled them to assign a potential transport mechanism to a specific DNA sequence. “The result was surprising: Apparently, a large proportion of the DNA was not transported via classical routes, but via extracellular vesicles,” says Erdmann.
“Extracellular vesicles were long regarded as cellular waste. Only in the last fifteen years scientists were able to show their various functions for the cell. Our study clearly highlights the fundamental role that EVs play for the exchange of genetic material between cells,“ explains Dominik Lücking, PhD student in Erdmanns group and first author of the study. Thus, the authors suggest to change terminology: „Traditionally, we are talking of a virome, a metagenome enriched with viruses, when extracting and sequencing the DNA from the 0.2 µm fraction”, says Lücking. However, that way we are missing out on the variety of the other, non-virus-like particles in this fraction, such as EVs. Thus, we suggest to call this fraction ‘protected extracellular DNA’, or peDNA.”
The study presented here lays the foundation for future research on peDNA across all ecosystems, in the ocean and beyond. “The new nomenclature will enable us to talk more clearly about the mechanisms and processes not covered by the term virome,” says Erdmann. Future research can use this study as a guideline to assess the role of extracellular vesicles in other environments, such as soil and freshwater systems or the human gut. „In view of the significance of horizontal gene transfer in many ecosystems, we are very sure that there are quite a few more surprises on the way ahead of us,“ Erdmann concludes.
Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module
by Sofie M. Bendixen, Peter R. Jakobsgaard, et al in Journal of Hepatology
Hormone therapy may be associated with menopause and fertility treatment, but now an SDU-led research team reports that certain intestinal hormones seem to have a beneficial effect on the processes behind the formation of scar tissue in the liver (liver fibrosis).
Liver fibrosis may occur as a result of liver diseases such as metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH), and currently, there is no medical treatment to cure liver fibrosis. Doctors often try to address the underlying causes of the diseases, such as obesity and diabetes, and these treatments may lead to improved liver function over several years but they do not eliminate fibrosis.
The processes that initiate the formation of scar tissue in the liver, i.e., fibrosis, are cellular. In their new study, a Danish/American research team, led by Associate Professor Kim Ravnskjaer from the Department of Biochemistry and Molecular Biology and the ATLAS center of excellence, reports that they have found previously unknown changes in the cell types responsible for fibrosis formation. These are the liver’s so-called stellate cells, named for their star-like appearance.
“We have found a way to inactivate these cells and thus halt the fibrogenic process. This may offer a real opportunity for halting the formation of scar tissue,” explains Kim Ravnskjaer.
One way to deactivate stellate cells is to expose them to certain intestinal hormones, the team discovered.
“We have focused mainly on the intestinal hormone called vasoactive intestinal polypeptide (VIP), which is naturally present in the intestine and neurons, from where it is released when we eat. The liver’s stellate cells, in particular, have a high expression of specific VIP receptors on their surface. VIP stimulates the liver’s blood supply but also appears to keep the stellate cells inactive,” says Kim Ravnskjaer.
The researchers believe that their work could provide the basis for the treatment of liver fibrosis.
“This could result in new ways to treat patients. For example, one could develop synthetic hormones designed to target the receptors on specific cells,” Ravnskjaer adds.
Research on liver fibrosis is ongoing worldwide, with many efforts focused on developing effective drugs. Unfortunately, these often come with serious side effects and for this reason, they are not approved.
“If we target these drugs more towards the cell changes we have discovered, we might be able to avoid many of the side effects,” says Kim Ravnskjaer.
The results of the research team were initially seen in mice that for a year were fed what the scientist refers to as “a pretty bad western diet”; high in fat and sugar.
“When we discovered these cell changes in diseased liver tissue from mice, we went on to look for them in diseased liver tissue from humans. We examined tissue from liver patients from two hospitals in Denmark, and we found the same cell changes in all tissue samples,” Ravnskjaer says.
The researchers will now continue studying stellate cells and their surface receptors in patient samples. “The more precisely we can target the right cells, the fewer side effects and the better for the patient,” says Kim Ravnskjaer, emphasizing that a new drug based on these discoveries are still years away.
Genetic basis of the historical iron‐accumulating dgl and brz mutants in pea
by Sophie A. Harrington, Marina Franceschetti, Janneke Balk in The Plant Journal
A genetic breakthrough has opened new opportunities for iron-fortified vegetables and cereal crops to help address the global health issue of anemia.
John Innes Centre researchers used a newly available map of the pea-genome to identify the underlying genetic sequence responsible for two high-iron mutations in peas.
ProfessorJanneke Balk, a group leader at the John Innes Centre and an author of the research said: “There are a number of intriguing opportunities arising from this research but probably the most exciting outcome is that knowledge of these mutations could inform gene editing strategies to increase iron in a wide range of crops.”
The discovery may help address the persistent problem of iron deficiency, a nutritional health issue that particularly affects girls and women in the UK and other parts of the world. This problem is likely to get worse as people eat less meat because of climate change concerns. Iron deficiency anemia is a condition where a lack of iron in the body leads to a reduction in the number of red blood cells which help store and carry oxygen. Staple foods like wheat flour and breakfast cereals are regularly fortified to ensure that we consume enough iron each day to stave off this important nutritional shortfall.
To make the discovery John Innes Centre Researchers used an RNA sequencing technique which looks for the genes expressed in high iron pea plants and compares these with wild type plants that have normal levels of iron. Using computational mapping techniques and plant experiments, the team in the group of Dr Balk have identified the exact mutations and their locations on the pea genome. By identifying the minute changes in the genetic code that have caused these high-iron phenotypes, the research has unlocked new opportunities for biofortification — enhancing the nutritional value of food.
Possible commercial applications include breeding pea shoots with 10 times more iron, or supplements with a natural, more bioavailable form of iron without some of the side effects associated with chemically derived iron supplements. Even more exciting is that this knowledge of these genes, which are highly conserved across the plant kingdom, could help biofortify other crops such as wheat and barley using gene-editing and other modern breeding techniques.
The two high-iron pea varieties have been critical in research over the past 30 years to better understand how plants transport iron from the roots and make it available for other organs, including seeds. Plants must regulate iron uptake because too much is lethal. The identified mutations are valuable because they maintain high levels of iron accumulation but not so much that the iron becomes very toxic to the plant.
These mutations have been at the centre of a long-standing mystery. Because of the large size of the pea genome, researchers had not been able to find the mutations which cause iron accumulation. However, 4 years ago the first draft of the whole pea genome sequence was put together and this greatly helped Professor Balk and her team. This new research adds to that history, reflects Professor Balk: “I have been associated with the field of iron homeostasis in plants for 20 years and every conference I went to, or in papers, these two genes are mentioned but people did not have the mutations.”
“Now that we have identified these mutated genes, we can start making advances in both scientific understanding and practical improvements in producing food with higher more bioavailable iron content.”
The two high iron mutations at the centre of this longstanding genetic puzzle were created in the 1990s by two different research groups, in Germany and the USA. Soon after they published their findings, the groups donated some of the pea seeds to the BBSRC-funded Germplasm Resources Unit, a national capability resource based at the John Innes Centre. The seed stocks were maintained and kept viable over several decades.
Professor Balk commented: “This was important to the success of our research because the seeds from one of the mutants loses viability after a couple of years. It shows the key role of seed banks and maintaining historical collections.”
Subscribe to Paradigm!
Medium. Twitter. Telegram. Telegram Chat. Reddit. LinkedIn.
Main Sources
Research articles
