GN/ Peering inside cells to see how they respond to stress
Genetics biweekly vol.46, 13th October — 27th October
TL;DR
- The heat shock response of cells is a classic model of biological adaptation, part of the fundamental processes of life — conserved in creatures from single-celled yeast to humans — that allow our cells to adjust to changing conditions in their environment. For years, scientists have focused on how different genes respond to heat stress to understand this survival technique. Now, thanks to the innovative use of advanced imaging techniques, researchers are getting an unprecedented look at the inner machinery of cells to see how they respond to heat stress.
- The legendary Alexander Fleming, who famously discovered penicillin, once said ‘never to neglect an extraordinary appearance or happening.’ And the path of science often leads to just that. New research is turning the page in our understanding of harmful bacteria and how they turn on certain genes, causing disease in our bodies.
- Researchers have discovered how the fungus Candida albicans enters the brain, activates two separate mechanisms in brain cells that promote its clearance, and, important for the understanding of Alzheimer’s disease development, generates amyloid beta (Ab)-like peptides, toxic protein fragments from the amyloid precursor protein that are considered to be at the center of the development of Alzheimer’s disease.
- Synthetic biologists report on a new approach to attacking tumors. They have engineered tumor-colonizing bacteria (probiotics) to produce synthetic targets in tumors that direct CAR-T cells to destroy the newly highlighted cancer cells.
- Genomic analysis in snakes shows link between neutral, functional genetic diversity.
- Researchers have obtained new insights into how African-American and Hispanic-American people’s genes influence their ability to use Omega-3 and Omega-6 fatty acids for good health. The findings are an important step toward “precision nutrition” — where a diet tailored to exactly what our bodies need can help us live longer, healthier lives.
- A group of international scientists have mapped the genetic, cellular, and structural makeup of the human brain and the nonhuman primate brain. This understanding of brain structure allows for a deeper knowledge of the cellular basis of brain function and dysfunction, helping pave the way for a new generation of precision therapeutics for people with mental disorders and other disorders of the brain.
- Researchers have extracted and analyzed DNA from fruit flies housed in museum collections in Lund, Stockholm and Copenhagen. Surprisingly, the researchers found the fruit flies collected in Sweden in the early 1800s were more genetically similar to 21st century flies than the Swedish samples from the 1930s.
- A new CRISPR-based gene-editing tool has been developed which could lead to better treatments for patients with genetic disorders. The tool is an enzyme, AsCas12f, which has been modified to offer the same effectiveness but at one-third the size of the Cas9 enzyme commonly used for gene editing. The compact size means that more of it can be packed into carrier viruses and delivered into living cells, making it more efficient.
- Nitrogen is an essential nutrient for plant growth, but the overuse of synthetic nitrogen fertilizers in agriculture is not sustainable. A team of bacteriologists and plant scientists discuss the possibility of using genetic engineering to facilitate mutualistic relationships between plants and nitrogen-fixing microbes called ‘diazotrophs.’ These engineered associations would help crops acquire nitrogen from the air by mimicking the mutualisms between legumes and nitrogen-fixing bacteria.
- 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
Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates
by Asif Ali, Rania Garde, Olivia C. Schaffer, Jared A. M. Bard, Kabir Husain, Samantha Keyport Kik, Kathleen A. Davis, Sofia Luengo-Woods, Maya G. Igarashi, D. Allan Drummond, Allison H. Squires, David Pincus in Nature Cell Biology
Imagine the life of a yeast cell, floating around the kitchen in a spore that eventually lands on a bowl of grapes. Life is good: food for days, at least until someone notices the rotting fruit and throws them out. But then the sun shines through a window, the section of the counter where the bowl is sitting heats up, and suddenly life gets uncomfortable for the humble yeast. When temperatures get too high, the cells shut down their normal processes to ride out the stressful conditions and live to feast on grapes on another, cooler day.
This “heat shock response” of cells is a classic model of biological adaptation, part of the fundamental processes of life — conserved in creatures from single-celled yeast to humans — that allow our cells to adjust to changing conditions in their environment. For years, scientists have focused on how different genes respond to heat stress to understand this survival technique. Now, thanks to the innovative use of advanced imaging techniques, researchers at the University of Chicago are getting an unprecedented look at the inner machinery of cells to see how they respond to heat stress.
“Adaptation is a hidden superpower of the cells,” said Asif Ali, PhD, a postdoctoral researcher at UChicago who specializes in capturing images of cellular processes. “They don’t have to use this superpower all the time, but once they’re stuck in a harsh condition, suddenly, there’s no way out. So, they employ this as a survival strategy.”
Ali works in the lab of David Pincus, PhD, Assistant Professor of Molecular Genetics and Cell Biology at UChicago, where their team studies study how cells adapt to stressful and complex environments, including the heat shock response. In the new study, they combined several new imaging techniques to show that in response to heat shock, cells employ a protective mechanism for their orphan ribosomal proteins — critical proteins for growth that are highly vulnerable to aggregation when normal cell processing shuts down — by preserving them within liquid-like condensates.
Once the heat shock subsides, these condensates get dispersed with the help of molecular chaperone proteins, facilitating integration of the orphaned proteins into functional mature ribosomes that can start churning out proteins again. This rapid restart of ribosome production allows the cell to pick back up where it left off without wasting energy. The study also shows that cells unable to maintain the liquid state of these condensates don’t recover as quickly, falling behind by ten generations while they try to reproduce the lost proteins.
“Asif developed an entirely new cell biological technique that lets us visualize orphaned ribosomal proteins in cells in real time, for the first time,” Pincus said. “Like many innovations, it took a technological breakthrough to enable us to see a whole new biology that was invisible to us before but has always been going on in cells that we’ve been studying for years.”
Ribosomes are crucial machines inside the cytoplasm of all cells that read the genetic instructions on messenger RNA and build chains of amino acids that fold into proteins. Producing ribosomes to perform this process is energy intensive, so under conditions of stress like heat shock, it’s one of the first things a cell shuts down to conserve energy. At any given time though, 50% of newly synthesized proteins inside a cell are ribosomal proteins that haven’t been completely translated yet. Up to a million ribosomal proteins are produced per minute in a cell, so if ribosome production shuts down, these millions of proteins could be left floating around unattended, prone to clumping together or folding improperly, which can cause problems down the line.
Instead of focusing on how genes behave during heat shock, Ali and Pincus wanted to look inside the machinery of cells to see what happens to these “orphaned” ribosomal proteins. For this, Ali turned to a new microscopy tool called lattice light sheet 4D imaging that uses multiple sheets of laser light to create fully dimensional images of components inside living cells.
Since he wanted to focus on what was happening to just the orphaned proteins during heat shock, Ali also used a classic technique called “pulse labeling” with a modern twist: a special dye called a “HaloTag” to flag the newly synthesized orphan proteins. Often when scientists want to track the activity of a protein inside a cell, they use a green fluorescent protein (GFP) tag that glows bright green under a microscope. But since there are so many mature ribosomal proteins in a cell, using GFPs would just light up the whole cell. Instead, the pulse labelling with HaloTag dye allows researchers to light up just the newly created ribosomes and leave the mature ones dark.
Using these combined imaging tools, the researchers saw that the orphaned proteins were collected into liquid-like droplets of material near the nucleolus (Pincus used the scientific term “loosely affiliated biomolecular goo”). These blobs were accompanied by molecular chaperones, proteins that usually assist the ribosomal production process by helping fold new proteins. In this case, the chaperones seemed to be “stirring” the collected proteins, keeping them in a liquid state and preventing them from clumping together.
This finding is intriguing, Pincus said, because many human diseases like cancer and neurodegenerative disorders are linked to misfolded or aggregated clumps of proteins. Once proteins get tangled together, they stay that way too, so this “stirring” mechanism seems to be another adaptation.
“I think a very plausible general definition for cellular health and disease is if things are liquid and moving around, you are in a healthy state, once things start to clog up and form these aggregates, that’s pathology,” Pincus said. “We really think we’re uncovering the fundamental mechanisms that might be clinically relevant, or at least, at the mechanistic heart of so many human diseases.”
In the future, Ali hopes to employ another imaging technique called cryo-electron tomography, an application using an electron microscope while cell samples are frozen to capture images of their interior components at an atomic level of resolution. Another advantage of this technique is that it allows researchers to capture 3D images inside the cell itself, as opposed to separating and preparing proteins for imaging.
Using this new tool, the researchers want to peer inside the protein condensates to see if they are organized in a way that helps them easily disperse and resume activity once the heat shock subsides.
“I have to believe they’re not just jumbled up and mixed together,” Pincus said. “What we’re hoping to see within what looks like a disorganized jumbled soup, there’s going to be some structure and order that helps them start regrowing so quickly.”
VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities
by Taylor M. Gerson, Audrey M. Ott, Monika M. A. Karney, Jillian N. Socea, Daren R. Ginete, Lakshminarayan M. Iyer, L. Aravind, Ronald K. Gary, Helen J. Wing in mBio
The legendary Alexander Fleming, who famously discovered penicillin, once said “never to neglect an extraordinary appearance or happening.” And the path of science often leads to just that. New UNLV research is turning the page in our understanding of harmful bacteria and how they turn on certain genes, causing disease in our bodies.
A team of interdisciplinary scientists, led by professor and microbiologist Helen Wing, focuses on Shigella — a lethal bacterial pathogen that causes abdominal cramping, fever, and diarrhea. The Centers for Disease Control and Prevention estimates that Shigella cases lead to 600,000 deaths globally each year.
Shigella contains a major ‘switch’ protein (VirB), which triggers the bacterium to cause disease in humans. VirB does this by binding to Shigella’s DNA, activating the disease. The researchers showed that it is possible that interfering with VirB’s binding process can prevent Shigella from making us sick.
“When molecular substitutions are made in VirB, this protein loses the ability to turn on virulence genes in Shigella, therefore making Shigella non-infectious,” said Taylor Gerson, a fourth-year Ph.D. student at UNLV and the study’s first author.
Traditionally, proteins that control how harmful a disease is, such as VirB, have been underappreciated. The goal of the team’s microbiology lab is to better understand these ‘switch’ proteins, which turn an otherwise harmless bacteria into an aggressive pathogen.
“I think our research has a broader impact,” said Monika Karney, a UNLV lab technician and study co-author. “What we’re seeing with this one protein in this one bacterium — there’s room for it to be applied to other proteins in other clinically relevant bacteria.”
The implications this research has for other pathogens remain to be seen, but the hope is that it is a major stepping stone toward putting a big red “X” through some of the diseases plaguing many parts of the world.
“We study these molecules to understand how they function in disease, so that other labs may look into finding drugs that kill these pathogens,” said Wing. “Understanding these proteins and what they interact with is critical.”
Integral to the research is CPT, or cytidine triphosphate, and its role in the binding process. The molecule is traditionally used as a building block for making DNA and RNA, and is needed by VirB for this process. Interfering with that binding process is what ultimately opens the door for future treatment strategies and potentially minimizes the impacts of harmful bacteria, such as Shigella.
Toll-like receptor 4 and CD11b expressed on microglia coordinate eradication of Candida albicans cerebral mycosis
by Yifan Wu et al in Cell Reports
Previous research has implicated fungi in chronic neurodegenerative conditions such as Alzheimer’s disease, but there is limited understanding of how these common microbes could be involved in the development of these conditions.
Working with animal models, researchers at Baylor College of Medicine and collaborating institutions discovered how the fungus Candida albicans enters the brain, activates two separate mechanisms in brain cells that promote its clearance, and, important for the understanding of Alzheimer’s disease development, generates amyloid beta (Ab)-like peptides, toxic protein fragments from the amyloid precursor protein that are considered to be at the center of the development of Alzheimer’s disease.
“Our lab has years of experience studying fungi, so we embarked on the study of the connection between C. albicans and Alzheimer’s disease in animal models,” said corresponding author Dr. David Corry, Fulbright Endowed Chair in Pathology and professor of pathology and immunology and medicine at Baylor. He also is a member of Baylor’s Dan L Duncan Comprehensive Cancer Center. “In 2019, we reported that C. albicans does get into the brain where it produces changes that are very similar to what is seen in Alzheimer’s disease. The current study extends that work to understand the molecular mechanisms.”
“Our first question was, how does C. albicans enter the brain? We found that C. albicans produces enzymes called secreted aspartic proteases (Saps) that breakdown the blood-brain barrier, giving the fungus access to the brain where it causes damage,” said first author Dr. Yifan Wu, postdoctoral scientist in pediatrics working in the Corry lab.
Next, the researchers asked, how is the fungus effectively cleared from the brain? Corry and his colleagues had previously shown that a C. albicans brain infection is fully resolved in otherwise healthy mice after 10 days. In this study, they reported that this occurred thanks to two mechanisms triggered by the fungus in brain cells called microglia.
“The same Saps that the fungus uses to break the blood-brain barrier also break down the amyloid precursor protein into AB-like peptides,” Wu said. “These peptides activate microglial brain cells via a cell surface receptor called Toll-like receptor 4, which keeps the fungi load low in the brain, but does not clear the infection.”
C. albicans also produces a protein called candidalysin that also binds to microglia via a different receptor, CD11b. “Candidalysin-mediated activation of microglia is essential for clearance of Candida in the brain,” Wu said. “If we take away this pathway, fungi are no longer effectively cleared in the brain.”
“This work potentially contributes an important new piece of the puzzle regarding the development of Alzheimer’s disease,” Corry said. “The current explanation for this condition is that it is mostly the result of the accumulation of toxic Ab-like peptides in the brain that leads to neurodegeneration. The dominant thinking is that these peptides are produced endogenously, our own brain proteases break down the amyloid precursor proteins generating the toxic Ab peptides.”
Here, the researchers show that the Ab-like peptides also can be generated from a different source — C. albicans. This common fungus, which has been detected in the brains of people with Alzheimer’s disease and other chronic neurodegenerative disorders, has its own set of proteases that can generate the same Ab-like peptides the brain can generate endogenously.
“We propose that the brain Ab-peptide aggregates that characterize multiple Candida-associated neurodegenerative conditions including Alzheimer’s disease, Parkinson’s disease and others, may be generated both intrinsically by the brain and by C. albicans,” Corry said. “These findings in animal models support conducting further studies to evaluate the role of C. albicans in the development of Alzheimer’s disease in people, which can potentially lead to innovative therapeutic strategies.”
Probiotic-guided CAR-T cells for solid tumor targeting
by Rosa L. Vincent, Candice R. Gurbatri, Fangda Li, Ana Vardoshvili, Courtney Coker, Jongwon Im, Edward R. Ballister, Mathieu Rouanne, Thomas Savage, Kenia de los Santos-Alexis, Andrew Redenti, Leonie Brockmann, Meghna Komaranchath, Nicholas Arpaia, Tal Danino in Science
For several years, researchers have been successfully using chimeric antigen receptor (CAR) T cells to target specific antigens found on blood cells as a cure for patients with leukemia and lymphoma. But solid tumors, like breast and colon cancers, have proven to be more difficult to home in on. Solid tumors contain a mix of cells that display different antigens on their surface-often shared with healthy cells in the body. Thus, identifying a consistent and safe target has impeded the success of most CAR-T cell therapy for solid tumors at the first phase of development.
Synthetic biologists at Columbia Engineering report today a new approach to attacking tumors. They have engineered tumor-colonizing bacteria (probiotics) to produce synthetic targets in tumors that direct CAR-T cells to destroy the newly highlighted cancer cells.
“Our probiotic platform enables CAR-T cells to attack a broad range of tumor types,” said Tal Danino, associate professor of biomedical engineering, who led the study. “Traditional CAR-T therapies have relied on targeting natural tumor antigens. This is the first example of pairing engineered T cells with engineered bacteria to deliver synthetic antigens safely, systemically, and effectively to solid tumors. This could have a significant impact on the treatment of many cancers.”
Danino’s lab has essentially created a universal CAR-T cell that attacks a universal antigen, by programming the tumor-seeking bacteria to paint solid tumors with a synthetic marker that the CAR-T cells can recognize. The researchers expect that, with further refinements, this platform will enable the treatment of any solid tumor type without the need to identify a specific tumor antigen — thus bypassing the need to generate a custom CAR-T cell product for each cancer type and each patient.
This probiotic-guided CAR-T cell (ProCAR) platform is the first time that scientists have not only successfully combined engineered probiotics with CAR-T cells, but have also demonstrated the first evidence of CARs responding to synthetic antigens produced directly within the tumor.
“Combining the advantages of tumor-homing bacteria and CAR-T cells provides a new strategy for tumor recognition, and this builds the foundation for engineered communities of living therapies,” said the study’s co-lead author Rosa Vincent, a PhD student working in Danino’s lab. “We chose to bridge the individual limitations of these two cell therapies by combining the best features of each — using bacteria to place the targets, and T cells to destroy the malignant cells.”
The platform has proven to be safe and effective across multiple models of human and mouse cancers in both immunocompromised and immune-healthy mice. In fact, the study shows that human T cells in particular benefit so much from the presence of immunostimulatory bacteria within the tumor that their tumor-killing functions are further enhanced.
“Overall, our ProCAR platform represents a new strategy for enhancing the effectiveness of CAR-T cell therapy in solid tumors,” said Danino, who is also affiliated with the Herbert Irving Comprehensive Cancer Center and Data Science Institute. “While we’re still in the research phase, it could open up new avenues for cancer therapy.”
Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake
by Samarth Mathur, Andrew J. Mason, Gideon S. Bradburd, H. Lisle Gibbs in Proceedings of the National Academy of Sciences
In the world of threatened and endangered species conservation, the genomic revolution has raised some complicated questions: How can scientists justify assessing species genetic diversity without consulting entire genomes now that they can be sequenced? But then again, how can scientists justify the time and expense of genome sequencing when age-old measures of neutral genetic diversity are much cheaper and easier to obtain? A new study suggests making a transition from “old school” genetics to “new school” genomics for species conservation purposes probably isn’t necessary in all cases.
Researchers found the functional genetic diversity they detected by analyzing gene variations in fully sequenced genomes of 90 Eastern massasauga rattlesnakes correlated nicely with the neutral genetic diversity seen across broad sections of those same genomes containing no protein-coding genes — similar to the type of genetic material historically used to assess genetic diversity.
“If we’re worried about the genetic health of populations, neutral diversity can give us a pretty good answer, as has long been argued. We have directly tested that for this species,” said H. Lisle Gibbs, professor of evolution, ecology and organismal biology at The Ohio State University and senior author of the study.
“Hopefully for many other small species that live in small, isolated populations, it’s a good news story in that neutral genetic diversity measured using much less expensive and more easily accessible techniques than sequencing their whole genomes gives us important information about their genetic health.”
The point of assessing genetic diversity in a small, isolated animal (or plant) population is to get an idea of how well its members are able to adapt to changing conditions through their “good” mutations, and determining the level of need for conservation measures that will give them a fighting chance to carry on. Other species are deemed threatened or endangered because the inbreeding that happens in a small population is expected to let damaging (“bad”) gene mutations pile up, lowering chances for species survival.
Historically, genetic diversity has been estimated by searching easy-to-measure DNA regions unrelated to protein-coding genes. A higher level of diversity in these regions suggests more genetic variation in genes that encode proteins — a sign, but not firm evidence, that the species’ genes are changing to allow for adaptation to future environmental changes.
“With genomic information, we can now for the first time do things like go after specific variants in specific genes across the entire genome, which we’ve never been able to do before. And that’s what we were able to do,” Gibbs said. “There’s no expectation that this be done for every single species — that would be cost prohibitive and impossible. So we are trying to provide a model for how one can do these things in any endangered species.”
As part of this work, Gibbs’ lab was the first to sequence the genome of the Eastern massasauga rattlesnake, which was listed as threatened under the Endangered Species Act in 2016 because of loss and fragmentation of its wetland habitat. They then compared 90 of those sequences to sequenced genomes of 10 Western massasauga rattlesnakes, a common species with no limitations on breeding opportunities and large populations.
For this study, the researchers made use of that analysis to create two “boxes” in which to classify Eastern massasauga functional mutations: gene changes seen in massasaugas that implied either strong positive selection, and therefore contained beneficial mutations, or strong negative selection, and, accordingly, contained deleterious mutations. For comparison, the region they assigned as neutral consisted of sections of the genome located far away from functional genes.
“Those were our three types of variation. The prediction is that if measuring the neutral variation is accurate, then if there’s lots of neutral variation, then there should be lots of good variation present in the population and not very much bad variation,” Gibbs said. “And that’s because in big populations, natural selection is efficient, leading to all the bad stuff being purged and the good stuff retained.
“But then bad things happen when populations shrink because genetic drift, and random processes, start to become important and interfere with how effectively natural selection can purge things, allowing bad mutations to increase in frequency or maintain high frequencies of good mutations. So that’s the model that we have for how population size affects how evolution acts on these two kinds of mutations.”
There is a caveat to the finding, he said: They also show evidence that neutral genetic diversity may not be so useful for predicting the future because conditions on the ground aren’t yet captured in species’ genes.
“When we study patterns of diversity that we see in nature, we’re looking at what I call the ghost of evolution past over many previous generations. But humans have started to have an impact within the last 200 years, so when you do genetics and conservation, you have to be aware of this lag,” he said. “The patterns may no longer be relevant to what is going to happen in the future. You can still use neutral variation, but be aware it may not be as predictive as it used to be.”
Genome-wide association studies and fine-mapping identify genomic loci for n-3 and n-6 polyunsaturated fatty acids in Hispanic American and African American cohorts
by Chaojie Yang, Jenna Veenstra, Traci M. Bartz, et al in Communications Biology
University of Virginia School of Medicine researchers have obtained new insights into how African-American and Hispanic-American people’s genes influence their ability to use Omega-3 and Omega-6 fatty acids for good health. The findings are an important step toward “precision nutrition” — where a diet tailored to exactly what our bodies need can help us live longer, healthier lives.
Omega-3 and Omega-6 are “healthy fats.” We can get them from foods, but many people also take them as supplements. Omega-3 helps keep the immune system healthy and may lower the risk of heart disease, while Omega-6 promotes immune health and offers other benefits. These fatty acids also play important roles in the proper functioning of our cells. People with higher levels of the fatty acids circulating in their bloodstreams are thought to be at reduced risk of heart disease, type 2 diabetes, Alzheimer’s disease, breast cancer and other serious illnesses.
There has been substantial research into how genes influence the body’s ability to use Omega-3 and Omega-6 among people of European descent, but there has been much less study among Americans of Hispanic and African descent. UVA’s Ani W. Manichaikul, PhD, and colleagues set out to address that disparity. Their new findings reveal broad similarities among the groups but also some important differences — differences the researchers say highlight the need to conduct genetic studies in diverse groups of people.
“People of diverse ancestries have some distinct features in their DNA, and we can find this genetic variation if we include diverse participants in research,” said Manichaikul, of UVA’s Center for Public Health Genomics and Department of Public Health Sciences. “The results from this study bring us a step closer to considering a full spectrum of genetic variation to predict which individuals are at increased risk of fatty acid deficiencies.”
To better understand these genetic differences, Manichaikul and colleagues looked at data collected from more than 1,400 Hispanic-Americans and more than 2,200 African-Americans. This data was obtained through the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, an international group created to facilitate large-scale genetic analyses.
Manichaikul and colleagues report that prior genetic findings on fatty-acid metabolism in people of European ancestry often held true for Hispanic- and African-descended people. For example, one location on a particular chromosome had been identified as an important hub for the regulation of fatty acid use in Europeans, and that hub proved important for people of Hispanic and African descent too. There were several such shared genetic influences across the three groups. But Manichaikul and her team also found notable differences, with several previously unknown genetic sources of variation in fatty-acid levels among both Hispanic-Americans and African-Americans.
The differences the researchers detected in Hispanic-Americans and African-Americans help explain why their bodies use fatty acids differently. They also suggest answers to questions such as why Hispanic people with significant American Indigenous ancestry often have lower levels of fatty acids in their blood.
The researchers say their new findings lay the groundwork for future studies to examine how fatty-acid differences may influence the outcomes of diseases such as cancer, or how they affect immune system function. We might then use “precision nutrition” — a carefully tailored diet or strategic supplementation — to improve those outcomes.
“Our study found new fatty acid-related genetic variation that we have never found in our earlier studies that did not include as much genetic diversity,” Manichaikul said. “In our future research, we will continue to include as much ancestral and genetic diversity as possible, so that we can learn how the vast array of variations in human DNA affect people’s health.”
A quest into the human brain
by Mattia Maroso in Science
A group of international scientists have mapped the genetic, cellular, and structural makeup of the human brain and the nonhuman primate brain. This understanding of brain structure, allows for a deeper knowledge of the cellular basis of brain function and dysfunction, helping pave the way for a new generation of precision therapeutics for people with mental disorders and other disorders of the brain.
“Mapping the brain’s cellular landscape is a critical step toward understanding how this vital organ works in health and disease,” said Joshua A. Gordon, M.D., Ph.D., director of the National Institute of Mental Health. “These new detailed cell atlases of the human brain and the nonhuman primate brain offer a foundation for designing new therapies that can target the specific brain cells and circuits involved in brain disorders.”
The 24 papers in this latest BRAIN Initiative Cell Census Network (BICCN) collection detail the exceptionally complex diversity of cells in the human brain and the nonhuman primate brain. The studies identify similarities and differences in how cells are organized and how genes are regulated in the human brain and the nonhuman primate brain. For example:
- Three papers in the collection present the first atlas of cells in the adult human brain, mapping the transcriptional and epigenomic landscape of the brain. The transcriptome is the complete set of gene readouts in a cell, which contains instructions for making proteins and other cellular products. The epigenome refers to chemical modifications to a cell’s DNA and chromosomes that alter the way the cell’s genetic information is expressed.
- In another paper, a comparison of the cellular and molecular properties of the human brain and several nonhuman primate brains (chimpanzee, gorilla, macaque, and marmoset brains) revealed clear similarities in the types, proportions, and spatial organization of cells in the cerebral cortex of humans and nonhuman primates. Examination of the genetic expression of cortical cells across species suggests that relatively small changes in gene expression in the human lineage led to changes in neuronal wiring and synaptic function that likely allowed for greater brain plasticity in humans, supporting the human brain’s ability to adapt, learn, and change.
- A study exploring how cells vary in different brain regions in marmosets found a link between the properties of cells in the adult brain and the properties of those cells during development. The link suggests that developmental programming is embedded in cells when they are formed and maintained into adulthood and that some observable cellular properties in an adult may have their origins very early in life. This finding could lead to new insights into brain development and function across the lifespan.
- An exploration of the anatomy and physiology of neurons in the outermost layer of the neocortex — part of the brain involved in higher-order functions such as cognition, motor commands, and language — revealed differences in the human brain and the mouse brain that suggest this region may be an evolutionary hotspot, with changes in humans reflecting the higher demands of regulating humans’ more complex brain circuits.
The core aim of the BICCN, a groundbreaking effort to understand the brain’s cellular makeup, is to develop a comprehensive inventory of the cells in the brain — where they are, how they develop, how they work together, and how they regulate their activity — to better understand how brain disorders develop, progress, and are best treated.
“This suite of studies represents a landmark achievement in illuminating the complexity of the human brain at the cellular level,” said John Ngai, Ph.D., director of the NIH BRAIN Initiative. “The scientific collaborations forged through BICCN are propelling the field forward at an exponential pace; the progress — and possibilities — have been simply breathtaking.”
The census of brain cell types in the human brain and the nonhuman primate brain presented in this paper collection serves as a key step toward developing the brain treatments of the future. The findings also set the stage for the BRAIN Initiative Cell Atlas Network, a transformative project that, together with two other large-scale projects — the BRAIN Initiative Connectivity Across Scales and the Armamentarium for Precision Brain Cell Access — aim to revolutionize neuroscience research by illuminating foundational principles governing the circuit basis of behavior and informing new approaches to treating human brain disorders.
Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution
by Max Shpak, Hamid R. Ghanavi, Jeremy D. Lange, John E. Pool, Marcus C. Stensmyr in PLOS Biology
Back when the biggest fly enthusiasts of 19th century Sweden — Carl Fredrik Fallén, for one, and later Johan Wilhelm Zetterstedt — were collecting insects for what would become Lund University’s entomological collections, they wondered exactly what was that buzzing coming from their can of raisins.
Skip forward 200 years, and the humble fruit fly, known better to geneticists as Drosophila melanogaster, is one of the most thoroughly studied animals on the planet. And DNA from Fallén and Zetterstedt’s centuries-old curiosities are still revealing new insights into the fly’s evolution as it spread alongside people to new parts of the world.
Researchers from the University of Wisconsin-Madison and Lund University extracted and analyzed DNA from fruit flies housed in museum collections in Lund, Stockholm and Copenhagen. The flies are museum specimens collected by naturalists in Europe as early as the first decade of the 19th century and as recently as the 1930s.
The early fly-finders considered any insects they could get their hands on worth keeping — Fallén’s specimens indeed include some that appear to have been enjoying his raisins — but they probably couldn’t have conceived of Drosophila’s importance to science.
“This species has been a key player in basic biological science for well over a century now,” says John Pool, UW-Madison professor of genetics. “We’ve turned to it to learn things about the basic rules of life, what genetic variation looks like in natural populations, how different evolutionary forces shape diversity. And that’s just in my field.”
That means the genes of fruit flies may have been sequenced, catalogued and described more often than any other animal. But those samples came from modern specimens. Because a fruit fly lives about 50 days, the new DNA samples come from some very ancient relatives of the flies buzzing around our fruit bowls these days.
“It’s not so unusual to get useful DNA from very old specimens of our hominid ancestors or other animals,” Pool says. “But the number of generations — about 3,000 — that have elapsed in fly populations since some of these we’ve sequenced were alive is about the same number of our generations since humans emerged from Africa.”
Lund zoologist Marcus Stensmyr recovered genetic material from the museum flies by soaking them in a solution that breaks open cell membranes to free up large molecules inside. The flies were washed and dried and returned to the museum collection. Their DNA was extracted from the solution and analyzed at UW-Madison.
Surprisingly, the researchers found the fruit flies collected in Sweden in the early 1800s were more genetically similar to 21st century flies than the Swedish samples from the 1930s. That’s likely due to the older flies’ place in Drosophila history as some of the first arrivals so far north of their original range in Southern Africa. For some time, they were a small outpost, in which random mutations would make larger differences in the population — more of what’s called “genetic drift” — as the 1800s became the 1900s. Swedish flies would get less unique, though, when their numbers were reinforced from the broader European gene pool.
“There would have been a vast increase in fruit shipping between the 1930s and the present and, generally, more human transport that probably increased opportunities for longer distance Drosophila migration,” Pool says. “So, what we think we are seeing between the 1930s and the present is the effect of that migration basically homogenizing genetic variation.”
By comparing changes across the centuries of fly samples now at their disposal, the researchers also identified a handful of genes showing signs of evolutionary pressure.
“That was a key interest of our study, to try to figure out which genes may have been the most important in helping this fly population adapt to very novel climate and a novel environment,” Pool says.
Differences between DNA from 1930s specimens and their present-day kin revealed the emergence of a gene called Cyp6g1 that’s known now to make the flies more resistant to the pesticide DDT.
“That was our top result for the more recent time interval,” Pool says. “And that made perfect sense, in terms of when DDT was introduced.”
That would be in the 1940s, not long after the study’s most recent museum sources of Drosophila were still airborne. Earlier than that, important genetic shifts show a gene called Ahcy aiding the 19th century flies’ adaptation to cooler temperatures and shorter days — important factors in the fly’s reproductive cycles — in Sweden (and other high-latitude homes).
Another gene, ChKov1, was thought to be insecticide-related, but DNA from museum flies collected in the 1800s showed that the gene evolved before the relevant insecticides were even invented. Previous work by other researchers had suggested ChKov1 also conferred resistance to a virus, called sigmavirus, believed to have appeared in flies about 200 years ago.
“Our results strongly favor the viral resistance hypothesis over the insecticide resistance hypothesis,” Pool says. “So, that’s an example of a gene that was already suggested to be under natural selection, but we learned some new things about it by having these temporal samples.”
It’s a testament to both the work done long ago by curious scientists breaking new ground in their field and present-day practitioners using modern technology to much the same effect.
“This is an example of what millions of museum specimens all around the world could tell us about the changes that have taken place in many different species,” says Pool.
An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis
by Tomohiro Hino, Satoshi N. Omura, Ryoya Nakagawa, et al in Cell
A new CRISPR-based gene-editing tool has been developed which could lead to better treatments for patients with genetic disorders. The tool is an enzyme, AsCas12f, which has been modified to offer the same effectiveness but at one-third the size of the Cas9 enzyme commonly used for gene editing. The compact size means that more of it can be packed into carrier viruses and delivered into living cells, making it more efficient. Researchers created a library of possible AsCas12f mutations and then combined selected ones to engineer an AsCas12f enzyme with 10 times more editing ability than the original unmutated type. This engineered AsCas12f has already been successfully tested in mice and has the potential to be used for new, more effective treatments for patients in the future.
By now you have probably heard of CRISPR, the gene-editing tool which enables researchers to replace and alter segments of DNA. Like genetic tailors, scientists have been experimenting with “snipping away” the genes that make mosquitoes malaria carriers, altering food crops to be more nutritious and delicious, and in recent years begun human trials to overcome some of the most challenging diseases and genetic disorders. The potential of CRISPR to improve our lives is so phenomenal that in 2020, researchers Jennifer Doudna and Emmanuelle Charpentier, who developed the most precise version of the tool named CRISPR-Cas9, were awarded the Nobel Prize in chemistry.
But even Cas9 has limitations. The common way to deliver genetic material into a host cell is to use a modified virus as a carrier. Adeno-associated viruses (AAVs) are not harmful to patients, can enter many different types of cells to introduce CRISPR enzymes like Cas9, and have a lower likelihood of provoking an undesired immune response compared to some other methods. However, like any parcel delivery service, there is a size limit. “Cas9 is at the very limit of this size restriction, so there has been a demand for a smaller Cas protein that can be efficiently packaged into AAV and serve as a genome-editing tool,” explained Professor Osamu Nureki from the Department of Biological Sciences at the University of Tokyo.
Its large size means that Cas9 can lack efficiency when used for gene therapy. So, a large multi-institutional team worked to develop a smaller Cas enzyme that is just as active, but more efficient. The researchers selected an enzyme called AsCas12f, from the bacteria Axidibacillus sulfuroxidans. The advantage of this enzyme is that it is one of the most compact Cas enzymes found to date and less than one-third the size of Cas9. However, in previous tests it showed barely any genome activity in human cells.
“Using a screening method called deep mutational scanning, we assembled a library of potential new candidates by substituting each amino acid residue of AsCas12f with all 20 types of amino acids on which all life is based. From this, we identified over 200 mutations that enhanced genome-editing activity,” explained Nureki. “Based on insights gained from the structural analysis of AsCas12f, we selected and combined these enhanced-activity amino acid mutations to create a modified AsCas12f. This engineered AsCas12f has more than 10 times the genome-editing activity compared to the usual AsCas12f type and is comparable to Cas9, while maintaining a much smaller size.”
The team has already carried out animal trials with the engineered AsCas12f system, partnering it with other genes and administering it to live mice. Administering treatments directly into the body is preferable to extracting cells, editing them in a lab and reinserting them into patients, which is more time-intensive and costly. The success of the tests showed that engineered AsCas12f has the potential to be used for human gene therapies, such as treating hemophilia, a disease in which the blood does not clot normally.
The team discovered numerous potentially effective combinations for engineering an improved AsCas12f gene-editing system, so the researchers acknowledge the possibility that the selected mutations may not have been the most optimal of all the available mixes. As a next step, computational modeling or machine learning could be used to sift through the combinations and predict which might offer even better improvements.
Scripting a new dialogue between diazotrophs and crops
by Sanhita Chakraborty, Maya Venkataraman, Valentina Infante, in Trends in Microbiology
Nitrogen is an essential nutrient for plant growth, but the overuse of synthetic nitrogen fertilizers in agriculture is not sustainable. In a review article, a team of bacteriologists and plant scientists discuss the possibility of using genetic engineering to facilitate mutualistic relationships between plants and nitrogen-fixing microbes called “diazotrophs.” These engineered associations would help crops acquire nitrogen from the air by mimicking the mutualisms between legumes and nitrogen-fixing bacteria.
“Engineering associative diazotrophs to provide nitrogen to crops is a promising and relatively quickly realizable solution to the high cost and sustainability issues associated with synthetic nitrogen fertilizers,” writes the research team, led by senior author Jean-Michel Ané of the University of Wisconsin-Madison.
Diazotrophs are species of soil bacteria and archaea that naturally “fix” atmospheric nitrogen into ammonium, a source that plants can use. Some of these microbes have formed mutualistic relationships with plants whereby the plants provide them with a source of carbon and a safe, low-oxygen home, and in return, they supply the plants with nitrogen. For example, legumes house nitrogen-fixing microbes in small nodules on their roots. However, these mutualisms only occur in a small number of plants and a scant number of crop species. If more plants were able to form associations with nitrogen fixers, it would lessen the need for synthetic nitrogen fertilizers, but these sorts of relationships take eons to evolve naturally.
How to enhance nitrogen fixation in non-legume crops is an ongoing challenge in agriculture. Several different methods have been proposed, including genetically modifying plants so that they themselves produce nitrogenase, the enzyme that nitrogen fixers use to convert atmospheric nitrogen into ammonium, or engineering non-legume plants to produce root nodules.
An alternative method — the topic of this review — would involve engineering both plants and nitrogen-fixing microbes to facilitate mutualistic associations. Essentially, plants would be engineered to be better hosts, and microbes would be engineered to release fixed nitrogen more readily when they encounter molecules that are secreted by the engineered plant hosts.
“Since free-living or associative diazotrophs do not altruistically share their fixed nitrogen with plants, they need to be manipulated to release the fixed nitrogen so the plants can access it,” the authors write.
The approach would rely on bi-directional signaling between plants and microbes, something that already occurs naturally. Microbes have chemoreceptors that allow them to sense metabolites that plants secrete into the soil, while plants are able to sense microbe-associated molecular patterns and microbe-secreted plant hormones. These signaling pathways could be tweaked via genetic engineering to make communication more specific between pairs of engineered plants and microbes.
The authors also discuss ways to make these engineered relationships more efficient. Since nitrogen fixation is an energy-intensive process, it would be useful for microbes to be able to regulate nitrogen fixation and only produce ammonium when necessary.
“Relying on signaling from plant-dependent small molecules would ensure that nitrogen is only fixed when the engineered strain is proximal to the desired crop species,” the authors write. “In these systems, cells perform energy-intensive fixation only when most beneficial to the crop.”
Many nitrogen-fixing microbes could provide additional benefits to plants beyond nitrogen fixation, including promoting growth and stress tolerance. The authors say that future research should focus on “stacking” these multiple benefits. However, since these processes are energy-intensive, the researchers suggest developing microbial communities made up of several species that each provide different benefits to “spread the production load among several strains.”
The authors acknowledge that genetic modification is a complex issue, and the large-scale use of genetically modified organisms in agriculture would require public acceptance. “There needs to be transparent communication between scientists, breeders, growers, and consumers about the risks and benefits of these emerging technologies,” the authors write.
There’s also the issue of biocontainment. Because microbes readily exchange genetic material within and between species, measures will be needed to prevent the spread of transgenic material into native microbes in surrounding ecosystems. Several such biocontainment methods have been developed in the laboratory, for example, engineering the microbes so that they are reliant on molecules that are not naturally available, meaning that they will be restricted to the fields in which the engineered host plants are present, or wiring the microbes with “kill switches.” The authors suggest that these control measures might be more effective if they are layered, since each measure has its limitations, and they stress the need to test these engineered plant-microbe mutualisms under the variable field conditions in which crops are grown.
“The practical use of plant-microbe interactions and their laboratory-to-land transition are still challenging due to the high variability of biotic and abiotic environmental factors and their impact on plants, microbes, and their interactions,” the authors write. “Trials in highly controlled environments such as greenhouses often translate poorly to field conditions, and we propose that engineered strains should be tested more readily under highly replicated field trials.”
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