Showing posts sorted by date for query CRISPR. Sort by relevance Show all posts
Showing posts sorted by date for query CRISPR. Sort by relevance Show all posts

Friday, September 20, 2024

 

CRISPR/Cas9 modifies euglena to create potential biofuel source



Mutant microalgae produce wax esters for biofuel feedstock with improved cold flow


Osaka Metropolitan University

Modifying euglena for biofuel-ready wax esters 

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Genome editing of Euglena gracilis led to stable mutants that produced wax esters with shorter carbon chains, giving the esters properties more suitable for use in biofuel.

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Credit: Osaka Metropolitan University




News about biofuels sometimes mentions used cooking oil as a feedstock, but if these substances contain animal fat, they can solidify in colder temperatures. This happens because, chemically, the fatty acids of these and many other saturated fats have long carbon chains with single bonds. Enter the euglena. An Osaka Metropolitan University team has found a way to have one species of this microalgae produce wax esters with shorter carbon chains than usual.

Using CRISPR/Cas9 to edit the genome of Euglena gracilis, Dr. Masami Nakazawa and her team at the Graduate School of Agriculture’s Department of Applied Biochemistry produced stable mutants that created wax esters two carbons shorter than the wild-type species.

This improvement in the cold flow of the wax esters makes them more applicable as feedstock for biofuels. Among the factors favorable to using Euglena gracilis as a biofuel source are its ability to grow easily through photosynthesis and anaerobic production of wax esters.

“This achievement is expected to serve as a fundamental technology for replacing some petroleum-based production of wax esters with biological sources,” Dr. Nakazawa affirmed.

The findings were published in Bioresource Technology.

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About OMU 

Established in Osaka as one of the largest public universities in Japan, Osaka Metropolitan University is committed to shaping the future of society through “Convergence of Knowledge” and the promotion of world-class research. For more research news, visit https://www.omu.ac.jp/en/ and follow us on social media: XFacebookInstagramLinkedIn.

Monday, September 16, 2024

 Research shows brain synchronization between humans and dogs

By 

Reviewed by Danielle Ellis, B.Sc.

Sep 16 2024

Study reveals how mutual gazing and petting synchronize human and dog brains, while autism-related gene mutations in dogs reduce this connection. 

Study: Disrupted Human–Dog Interbrain Neural Coupling in Autism-Associated Shank3 Mutant Dogs. Image Credit: sergey kolesnikov/Shutterstock.com
Study: Disrupted Human–Dog Interbrain Neural Coupling in Autism-Associated Shank3 Mutant Dogs. Image Credit: sergey kolesnikov/Shutterstock.com

In a recent study published in Advanced Science, researchers studied cross-species interbrain connections between dogs and humans. They also investigated whether autism-related gene abnormalities in dogs impede social interaction between human-dog pairs.

Background

The human-dog connection has developed with time, with dogs tamed for their protective and hunting capacities. They have become valuable members of households, offering companionship and emotional support. Interspecies partnerships generate mutual benefit but seldom approach the extent of communication between humans and dogs. Dogs can read, comprehend, and react to various human emotions and linguistic signs via facial expressions, behaviors, and voice tones. However, the brain mechanisms underlying interspecies social communication remain unknown.

About the study

In the present study, researchers investigated the brain processes enabling human-dog communication. They explored the influence of autism-related gene alterations in dogs on social interactions between the two species.

Non-invasive wireless electroencephalograms (EEG) concurrently detected brain activity in beagles (research canines) and humans during social interactions. To validate the findings, researchers assessed interbrain correlations between different areas of the brain under three situations. The situations included no social interactions in separate spaces, with social interaction in one room and without social engagement in one room. Social interactions included petting and mutual gazing.

Researchers compared interbrain coupling during complete social interactions (mutual gaze + petting) to partial social interactions (mutual gaze or petting alone) to evaluate the synergistic effects of mutual gaze and petting on interbrain coupling. They also investigated brain activity associations between dogs and human participants from different trials and recorded the brain activities of the two species during social interactions for five days to evaluate the impact of social familiarity on interbrain neural coupling.

Subsequently, researchers conducted an additional five-day investigation to assess the durability or changes in interbrain interactions across prolonged periods. Linear regressions investigated the association between the duration of social interactions and interbrain activity. Generalized partial directed coherence (GPDC) algorithms assessed the directionality of interbrain activity coupling.

Researchers developed an autism spectrum disorder (ASD) model for dogs with SH3 and multiple ankyrin repeat domain 3 (Shank3) mutations using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (Cas9) genome editing.

Behavioral studies such as the three-chamber test and human-dog interaction experiments revealed autism-like symptoms in the mutants. Over five days, researchers explored the interbrain neuronal connection between mutant canines and humans. Theta/beta wave ratios (TBR) indicated attention problems in the mutants during the social interactions between humans and dogs.

Researchers also explored the effects of lysergic acid diethylamide (LSD), a psychedelic, on brain function. They delivered a single dosage of 7.5 μg/kg bodyweight of LSD intramuscularly and observed its effects after 24 hours.

Results

Petting and mutual gazing resulted in interbrain synchronization in the parietal and frontal areas of the brain during human-dog interactions, respectively. These brain areas are involved in joint attention. The interbrain association in these brain areas of dogs and humans caused by mutual gazing or stroking alone was much lower than that during combined social interactions, including petting and mutual gazing.

Over five days, the synchronization intensity increased as the human-dog dyad became more familiar. Linear regression analyses revealed a strong positive association between social contact time, interbrain activity correlations, and GPDC values. After a week of social contacts, logistic growth curve regressions revealed that interbrain correlation in the frontal and parietal areas had plateaued. 

Interbrain correlations between humans and dogs in various sessions were much lower than in the same interaction sessions. The findings demonstrate that reciprocal involvement between dogs and humans is vital for interbrain neural connections. During the human-dog social interactions, the human takes the lead, and the dog follows. The mutant canines displayed lower attention and eliminated interbrain connections. A single dosage of LSD corrected the problems.

Conclusions

The study found that interbrain neural synchronizations between family dogs and human beings are identical to those observed during human-human interactions. The frontoparietal network is essential for interbrain activity coordination and sensory information attention. Dogs with Shank3 mutations demonstrated poor brain circuitry and attention, comparable to those with ASD. A single dosage of LSD restored reduced interbrain connection and joint attention in the mutant dogs, indicating that LSD may improve social impairment in ASD patients.

 The findings point to possible interbrain neural activity biological markers for autism spectrum disorder diagnosis and the development of designed non-hallucinogenic LSD analogs to address social deficiencies. Further research into brain coupling may improve the knowledge of the neurological mechanisms that underpin social interactions between regularly developing humans and those with mental illnesses like ASD.

Journal reference:

A Boy And His Dog (1975) Official Trailer

Tuesday, September 10, 2024

Nigeria: 

Oluwatayo Ajayi-Moses Unveils Plans to Tackle Plant Disease That Threatens Food SecurityFacebookTwitterWhatsApp

Oluwatayo Ajayi-Moses, a dedicated researcher in genomics, phenomics, and bioinformatics, is on a mission to tackle one of the most pressing challenges in agriculture today: plant diseases that threaten food security.

With over ten years of experience in microbiological techniques and currently pursuing a Ph.D. at North Dakota State University, Ajayi-Moses is leveraging cutting-edge scientific methods to safeguard crops and enhance food production.

Ajayi-Moses's passion lies in decoding the genetic mysteries of small grains to develop more resilient crops. Through his work, he aims to mitigate the effects of plant pathogens, ensuring a stable and secure food supply for the United States and beyond. His research focuses on identifying genetic markers that can help in breeding disease-resistant plants, ultimately reducing the need for chemical pesticides and fostering sustainable farming practices.

As a researcher specializing in plant molecular genetics and bioinformatics, my goal is to develop innovative solutions to combat plant diseases and enhance food security.

His impactful research involves utilizing advanced techniques such as genomic library preparation, molecular cloning, and CRISPR-Cas9 gene editing. These methods allow him to investigate and manipulate the genetic material of plants, aiming to enhance their resistance to diseases and environmental stressors. Ajayi-Moses has a proven track record of scientific excellence, with thirteen published scientific articles and presentations at international conferences, highlighting his contributions to the fields of plant genetics and agricultural biotechnology.

With extensive experience as a Graduate Research Assistant at the Small Grains Genotyping Laboratory, under the U.S. Department of Agriculture, Ajayi-Moses collaborates with multidisciplinary teams to conduct genomic analyses on small grains. His work is crucial in identifying genetic diversity and agronomic traits that can be harnessed to improve crop resilience and yield.

My specialties include genomic data analysis, high-throughput data analysis, and bioinformatics. I also have extensive experience in computational biology, Python programming, R Studio, and molecular diagnostics.

During his academic tenure, Ajayi-Moses has also demonstrated strong leadership skills, serving as President of the Genomics Phenomics and Bioinformatics Student Association at North Dakota State University. His commitment to advancing plant science research is evident in his proactive approach to mentoring students and his active participation in various academic societies.

Ajayi-Moses's ability to translate complex genomic data into practical agricultural solutions has positioned him as a leading figure in plant disease research. His dedication to enhancing food security through innovative genetic research aligns with the national interest, as it contributes to the sustainability of the agricultural sector and the well-being of the U.S. population.

With a robust background in microbiology, genomics, and bioinformatics, Ajayi-Moses is driving forward the frontier of plant science, making significant strides in the fight against plant diseases. His work not only has the potential to revolutionize crop protection but also to ensure a more resilient and secure food future for generations to come.

Monday, September 09, 2024

Gene therapy restores vision in first-ever trial for rare, inherited blindness



Patients born with a certain genetic blindness experienced the world in an entirely new way after a single treatment with gene therapy developed at UF.


University of Florida




After the treatment, one patient saw her first star. Another saw snowflakes for the first time. Other patients were newly able to navigate outside of the home or to read the labels on their child’s Halloween candy.

The cause of these seemingly miraculous improvements? A gene therapy developed by University of Florida scientists, which restored useful vision to most patients with the rare, inherited blindness known as Leber congenital amaurosis type I, or LCA1, in a small trial. 

Those who received the highest dose of the gene therapy saw up to a 10,000-fold improvement in their light sensitivity, were able to read more lines on an eye chart, and improved in their ability to navigate a standardized maze. For many patients, it was akin to finally turning on dim lights after trying to navigate their homes in the pitch black for years, the researchers said.

The trial also tested the safety profile of the treatment. Side effects were largely limited to minor surgical complications. The gene therapy itself caused mild inflammation that was treated with steroids.

“This is the first time that anyone with LCA1 has ever been treated, and we showed a very clean safety profile, and we also showed efficacy. These results pave the way for advancing the therapy in a phase 3 clinical trial and eventually commercializing it,” said Shannon Boye, Ph.D., chief of the Division of Cellular and Molecular Therapy at UF, co-author of the study and co-founder of Atsena Therapeutics, the UF spinoff that developed the gene therapy and funded the study.

“Atsena is pleased to advance the foundational work that Shannon and Sanford Boye developed in their laboratory many years ago and thrilled that the 12-month data from our ongoing clinical trial have been published in a prestigious medical journal,” said Kenji Fujita, M.D., chief medical officer of Atsena Therapeutics and co-author of the study. “We look forward to sharing further results from this program as we continue progressing what has the potential to be a breakthrough in treating blindness in children and adults with LCA1.”

Shannon Boye, UF professor of pediatrics and Sanford Boye, associate scientist of pediatrics, and their collaborators at the University of Pennsylvania and Oregon Health and Science University published the results of the clinical trial Sept. 5 in the journal The Lancet.

LCA1 is rare. Only about 3,000 people have the condition across both Europe and the U.S. It is caused by having two defective copies of the gene GUCY2D, which is required for the light-sensitive cells in the eyes to function properly. People with the disease tend to have severely impaired vision that makes it difficult or impossible to drive, read, or navigate the world visually. 

Shannon Boye has been developing the gene therapy targeting LCA1 for more than 20 years, since she enrolled as a graduate student at UF in 2001. In collaboration with her husband Sanford Boye, Shannon Boye’s lab developed the virus-based transport system that is essential for delivering functioning copies of the GUCY2D gene into the correct cells in the eyes. The Boyes founded Atsena Therapeutics in 2019 to bring the LCA1 treatment and other gene therapies to market.

“Most pharmaceutical companies are not interested in treating these rare diseases, because they are not strong revenue generators,” Sanford Boye said. “But we think these patients deserve attention, because we have treatments that work and provide really meaningful improvements to their quality of life.”

The study enrolled 15 subjects for treatment at the University of Pennsylvania or Oregon Health and Science University. Subjects received one of three different doses of the therapy to identify the safest and most effective dose for future trials. All patients received the treatment in one eye, which involved a surgical injection in the retina.

Researchers followed the patients for a year to test their vision in the treated eye compared to the untreated eye. Subjects who received higher doses saw greater improvements in their vision. 

The researchers expect the gene therapy to last indefinitely, requiring just a single treatment per eye. So far, they have seen visual improvements last at least five years.

Broad access to the treatment will require approval by the FDA following a phase 3 clinical trial, which tests the therapy in a larger population of patients. 

Saturday, August 31, 2024

 

Genomic dark matter solves butterfly evolutionary riddle



New study reveals how an unexpected genetic mechanism influences the evolution of butterfly wing coloration




George Washington University

A Longwing Butterfly Resting on a Lantana flower 

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Depicted is a longwing butterfly resting on a Lantana flower. Its wing patterns have been modified through CRISPR gene editing, which removed a crucial RNA molecule, leading to a loss of melanic scales.

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Credit: Luca Livraghi, a postdoctoral scientist at GW




[Note: High-resolution images related to this research available for download at this linkCaption and credit information provided.]  

WASHINGTON (August 30, 2024) — A team of international researchers has uncovered a surprising genetic mechanism that influences the vibrant and complex patterns on butterfly wings. In a study published in the Proceedings of the National Academy of Sciences, the team, led by Luca Livraghi at the George Washington University and the University of Cambridge, discovered that an RNA molecule, rather than a protein as previously thought, plays a pivotal role in determining the distribution of black pigment on butterfly wings.

Precisely how butterflies are able to generate the vibrant patterns and colors on their wings has fascinated biologists for centuries. The genetic code contained within the cells of developing butterfly wings dictates the specific arrangement of the color on the wing’s scales—the microscopic tiles that form wing patterns—similar to the arrangement of colored pixels to form a digital image. Cracking this code is fundamental to understanding how our own genes build our anatomy. In the lab, researchers can manipulate that code in butterflies with gene-editing tools and observe the effect on visible traits, such as coloration on a wing.

Scientists have long known that protein-coding genes are crucial to these processes. These types of genes create proteins that can dictate when and where a specific scale should generate a particular pigment. When it comes to black pigments, researchers thought this process would be no different, and initially implicated a protein-coding gene. The new research, however, paints a different picture.

The team discovered a gene that produces an RNA molecule—not a protein—controls where dark pigments are made during butterfly metamorphosis. Using the genome-editing technique CRISPR, the researchers demonstrated that when you remove the gene that produces the RNA molecule, butterflies completely lose their black pigmented scales, showing a clear link between RNA activity and dark pigment development.

“What we found was astonishing,” said Livraghi, a postdoctoral scientist at GW. “This RNA molecule directly influences where the black pigment appears on the wings, shaping the butterfly’s color patterns in a way we hadn’t anticipated.”

The researchers further explored how the RNA molecule functions during wing development. By examining its activity, they observed a perfect correlation between where the RNA is expressed and where black scales form.

“We were amazed that this gene is turned on where the black scales will eventually develop on the wing, with exquisite precision” said Arnaud Martin, associate professor of biology at GW. “It is truly an evolutionary paintbrush in this sense, and a creative one, judging by its effects in several species.” 

The researchers examined the newly discovered RNA in several other butterflies whose evolutionary history diverged around 80 million years ago. They found that in each of these species, the RNA had evolved to control new placements in the patterns of dark pigments.

"The consistent result obtained from CRISPR mutants in several species really demonstrate that this RNA gene is not a recent invention, but a key ancestral mechanism to control wing pattern diversity," said Riccardo Papa, professor of biology at the University of Puerto Rico - Río Piedras.

“We and others have now looked at this genetic trait in many different butterfly species, and remarkably we are finding that this same RNA is used again and again, from longwing butterflies, to monarchs and painted lady butterflies,” said Joe Hanly, a postdoctoral scientist and visiting fellow at GW. “It’s clearly a crucial gene for the evolution of wing patterns. I wonder what other, similar phenomena biologists might have been missing because they weren’t paying attention to the dark matter of the genome.” 

The findings not only challenge long-standing assumptions about genetic regulation but also open up new avenues for studying how visible traits evolve in animals. 

The study, “A long noncoding RNA at the cortex locus controls adaptive coloration in butterflies,” was published on August 30, 2024 in the Proceedings of the National Academy of Sciences. The research was supported by the National Science Foundation and the Biotechnology and Biological Sciences Research Council.

-GW-

Wednesday, August 28, 2024

 

Bacterial cells transmit memories to offspring


Temporary stress can cause heritable changes without altering the genetics, study finds



Peer-Reviewed Publication

Northwestern University

Inherited memories 

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An artistic illustration of how cells retain and even pass down memories to their offspring.

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Credit: Camila Felix/Northwestern University




Bacterial cells can “remember” brief, temporary changes to their bodies and immediate surroundings, a new Northwestern University and University of Texas-Southwestern study has found.

And, although these changes are not encoded in the cell’s genetics, the cell still passes memories of them to its offspring — for multiple generations.

Not only does this discovery challenge long-held assumptions of how the simplest organisms transmit and inherit physical traits, it also could be leveraged for new medical applications. For example, researchers could circumvent antibiotic resistance by subtly tweaking a pathogenic bacterium to render its offspring more sensitive to treatment for generations.

The study will be published Wednesday (Aug. 28) in the journal Science Advances.

“A central assumption in bacterial biology is that heritable physical characteristics are determined primarily by DNA,” said Northwestern’s Adilson Motter, the study’s senior author. “But, from the perspective of complex systems, we know that information also can be stored at the level of the network of regulatory relationships among genes. We wanted to explore whether there are characteristics transmitted from parents to offspring that are not encoded in DNA, but rather in the regulatory network itself. We found that temporary changes to gene regulation imprint lasting changes within the network that are passed on to the offspring. In other words, the echoes of changes affecting their parents persist in the regulatory network while the DNA remains unchanged.”

Motter is the Charles E. and Emma H. Morrison Professor of Physics at Northwestern’s Weinberg College of Arts and Sciences and director of the Center for Network Dynamics. The study’s co-first authors are postdoctoral fellow Thomas Wytock and graduate student Yi Zhao, who are both members of Motter’s laboratory. The study also involves a collaboration with Kimberly Reynolds, a systems biologist at the University of Texas Southwestern Medical Center. 

Learning from a model organism

Since researchers first identified the molecular underpinnings of genetic code in the 1950s, they have assumed traits are primarily — if not exclusively — transmitted through DNA. However, after the completion of the Human Genome Project in 2001, researchers have revisited this assumption. 

Wytock cites the World War II Dutch famine as a famous example pointing to the possibility of heritable, non-genetic traits in humans. A recent study showed that the children of men, who were exposed to the famine in utero, exhibited an increased tendency to become overweight as adults. But isolating the ultimate causes for this type of non-genetic inheritance in humans has proved challenging.

“In the case of complex organisms, the challenge lies in disentangling confounding factors such as survivor bias,” Motter said. “But perhaps we can isolate the causes for the simplest single-cell organisms, since we can control their environment and interrogate their genetics. If we observe something in this case, we can attribute the origin of non-genetic inheritance to a limited number of possibilities — in particular, changes in gene regulation.”

The regulatory network is analogous to a communication network that genes use to influence each other. The research team hypothesized that this network alone could hold the key to transmitting traits to offspring. To explore this hypothesis, Motter and his team turned to Escherichia coli (E. coli), a common bacterium and well-studied model organism.

“In the case of E. coli, the entire organism is a single cell,” Wytock said. “It has many fewer genes than a human cell, some 4,000 genes as opposed to 20,000. It also lacks the intracellular structures known to underlie the persistence of DNA organization in yeast and the multiplicity of cell types in higher organisms.Because E. coli is a well-studied model organism, we know the organization of the gene regulatory network in some detail.” 

Reversible stress, irreversible change

The research team used a mathematical model of the regulatory network to simulate the temporary deactivation (and subsequent reactivation) of individual genes in E. coli. They discovered these transient perturbations can generate lasting changes, which are projected to be inherited for multiple generations. The team currently is working to validate their simulations in laboratory experiments using a variation of CRISPR that deactivates genes temporarily rather than permanently.

But if the changes are encoded in the regulatory network rather than the DNA, the research team questioned how a cell can transmit them across generations. They propose that the reversible perturbation sparks an irreversible chain reaction within the regulatory network. As one gene deactivates, it affects the gene next to it in the network. By the time the first gene is reactivated, the cascade is already in full swing because the genes can form self-sustaining circuits that become impervious to outside influences once activated.

“It’s a network phenomenon,” said Motter, who is an expert in the dynamic behaviors of complex systems. “Genes interact with each other. If you perturb one gene, it affects others.”

Although his team is deactivating genes to test the hypothesis, Motter is clear that different types of perturbations could cause a similar effect. “We also could have changed the cell’s environment,” he said. “It could be the temperature, the availability of nutrients or the pH.” 

The study also suggests that other organisms have the necessary elements to exhibit non-genetic heritability. “In biology, it’s dangerous to assume anything is universal,” Motter contends. “But, intuitively, I do expect the effect to be common because E. coli’s regulatory network is similar or simpler than those found in other organisms.”

The study, “Irreversibility in bacterial regulatory networks,” was supported by the National Science Foundation (award number MCB-2206974).