Archive for the ‘bioengineering’ category

Nov 23, 2020

[email protected] Lab: Engineering the Fruit Fly Genome

Posted by in categories: bioengineering, biotech/medical, genetics, science

Although Drosophila is an insect whose genome has only about 14,000 genes, roughly half the human count, a remarkable number of these have very close counterparts in humans; some even occur in the same order in the fly’s DNA as in our own. This, plus the organism’s more than 100-year history in the lab, makes it one of the most important models for studying basic biology and disease.

To take full advantage of the opportunities offered by Drosophila, researchers need improved tools to manipulate the fly’s genes with precision, allowing them to introduce mutations to break genes, control their activity, label their protein products, or introduce other inherited genetic changes.

“We now have the genome sequences of lots of different animals — worms, flies, fish, mice, chimps, humans,” says Roger Hoskins of Berkeley Lab’s Life Sciences Division. “Now we want improved technologies for introducing precise changes into the genomes of lab animals; we want efficient genome engineering. Methods for doing this are very advanced in bacteria and yeast. Good methods for worms, flies, and mice have also been around for a long time, and improvements have come along fairly regularly. But with whole genome sequences in hand, the goals are becoming more ambitious.”

Nov 23, 2020

A ‘crisper’ method for gene editing in fungi

Posted by in categories: bioengineering, biotech/medical, food, genetics

O,.o Circa 2019

CRISPR/Cas9 is now a household name associated with genetic engineering studies. Through cutting-edge research described in their paper published in Scientific Reports, a team of researchers from Tokyo University of Science, Meiji University, and Tokyo University of Agriculture and Technology, led by Dr Takayuki Arazoe and Prof Shigeru Kuwata, has recently established a series of novel strategies to increase the efficiency of targeted gene disruption and new gene “introduction” using the CRISPR/Cas9 system in the rice blast fungus Pyricularia (Magnaporthe) oryzae. These strategies include quicker (single-step) gene introduction, use of small homologous sequences, and bypassing of certain prerequisite host DNA “patterns” and host component modification.

The team led by Dr Arazoe and Prof Kuwata has devised simple and quick techniques for gene editing (target gene disruption, sequence substitution, and re-introduction of desired genes) using CRISPR/Cas9 in the rice blast fungus Pyricularia (Magnaporthe) oryzae, a type of filamentous fungus. Spurred on by encouraging results, the researchers surmise, “Plants and their pathogens are still coevolving in nature. Exploiting the mutation mechanisms of model pathogenic fungi as a genome editing technique might lead to the development of further novel techniques in genetic engineering.”

The working component of the CRISPR/Cas9 system binds to the target gene region (DNA) and causes a site-specific double-stranded break (DSB) in the DNA. Effective binding of this component requires a certain “motif” or “pattern” called the protospacer-adjacent motif (PAM), which follows downstream of the target gene region.

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Nov 23, 2020

High-Efficiency CRISPR/Cas9-Mediated Gene Editing in Honeybee (Apis mellifera) Embryos

Posted by in categories: bioengineering, biotech/medical, food, genetics

The honeybee (Apis mellifera) is an important insect pollinator of wild flowers and crops, playing critical roles in the global ecosystem. Additionally, the honeybee serves as an ideal social insect model. Therefore, functional studies on honeybee genes are of great interest. However, until now, effective gene manipulation methods have not been available in honeybees. Here, we reported an improved CRISPR/Cas9 gene-editing method by microinjecting sgRNA and Cas9 protein into the region of zygote formation within 2 hr after queen oviposition, which allows one-step generation of biallelic knockout mutants in honeybee with high efficiency. We first targeted the Mrjp1 gene. Two batches of honeybee embryos were collected and injected with Mrjp1 sgRNA and Cas9 protein at the ventral cephalic side and the dorsal posterior side of the embryos, respectively. The gene-editing rate at the ventral cephalic side was 93.3%, which was much higher than that (11.8%) of the dorsal-posterior-side injection. To validate the high efficiency of our honeybee gene-editing system, we targeted another gene, Pax6, and injected Pax6 sgRNA and Cas9 protein at the ventral cephalic side in the third batch. A 100% editing rate was obtained. Sanger sequencing of the TA clones showed that 73.3% (for Mrjp1) and 76.9% (for Pax6) of the edited current-generation embryos were biallelic knockout mutants. These results suggest that the CRISPR/Cas9 method we established permits one-step biallelic knockout of target genes in honeybee embryos, thereby demonstrating an efficient application to functional studies of honeybee genes. It also provides a useful reference to gene editing in other insects with elongated eggs.

Nov 23, 2020

Gene editing technologies and applications for insects

Posted by in categories: bioengineering, biotech/medical, cybercrime/malcode, genetics

Initially discovered in bacteria, CRISPR-based genome editing endonucleases have proven remarkably amenable for adaptation to insects. To date, these endonucleases have been utilized in a plethora of both model and non-model insects including diverse flies, bees, beetles, butterflies, moths, and grasshoppers, to name a few, thereby revolutionizing functional genomics of insects. In addition to basic genome editing, they have also been invaluable for advanced genome engineering and synthetic biology applications. Here we explore the recent genome editing advancements in insects for generating site-specific genomic mutations, insertions, deletions, as well as more advanced applications such as Homology Assisted Genome Knock-in (HACK), potential to utilize DNA base editing, generating predictable reciprocal chromosomal translocations, and development gene drives to control the fate of wild populations.

Nov 22, 2020

COVID-19 Researchers Identify Features of a Virus Super-Spreader

Posted by in categories: bioengineering, biotech/medical, computing

Sneezes from people who have congested noses and a full set of teeth travel about 60% farther than from people who don’t, according to a new study.

New research from the University of Central Florida has identified physiological features that could make people super-spreaders of viruses such as COVID-19.

In a study appearing this month in the journal Physics of Fluids, researchers in UCF’s Department of Mechanical and Aerospace Engineering used computer-generated models to numerically simulate sneezes in different types of people and determine associations between people’s physiological features and how far their sneeze droplets travel and linger in the air.

Nov 22, 2020

Cracking the Secrets of an Emerging Branch of Physics: Exotic Properties to Power Real-World Applications

Posted by in categories: bioengineering, nuclear energy, physics

In a new realm of materials, PhD student Thanh Nguyen uses neutrons to hunt for exotic properties that could power real-world applications.

Thanh Nguyen is in the habit of breaking down barriers. Take languages, for instance: Nguyen, a third-year doctoral candidate in nuclear science and engineering (NSE), wanted “to connect with other people and cultures” for his work and social life, he says, so he learned Vietnamese, French, German, and Russian, and is now taking an MIT course in Mandarin. But this drive to push past obstacles really comes to the fore in his research, where Nguyen is trying to crack the secrets of a new and burgeoning branch of physics.

“My dissertation focuses on neutron scattering on topological semimetals, which were only experimentally discovered in 2015,” he says. “They have very special properties, but because they are so novel, there’s a lot that’s unknown, and neutrons offer a unique perspective to probe their properties at a new level of clarity.”

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Nov 20, 2020

It Sure Looks Like Humans Have Found a Way to Reverse Aging

Posted by in categories: bioengineering, biotech/medical, life extension

A landmark study shows this age-old tech is the key.

The cure for aging has long been the Holy Grail of medicine. Emerging technologies, like the gene editing tool CRISPR, have opened the floodgates to what may be possible for the future of medical science. The key to slowing down aging, however, may lie in a simple and age-old technique.

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Nov 18, 2020

Synthetic biology crucial to human missions to Mars

Posted by in categories: bioengineering, biological, chemistry, genetics, space travel

In Project Apollo, life support was based on carrying pretty much everything that astronauts needed from launch to splashdown. That meant all of the food, air, and fuel. Fuel in particular took up most of the mass that was launched. The enormous three-stage Saturn-V rocket was basically a gigantic container for fuel, and even the Apollo spacecraft that the Saturn carried into space was mostly fuel, because fuel was needed also to return from the Moon. If NASA’s new Orion spacecraft takes astronauts back to the Moon, they’ll also use massive amounts of fuel going back and forth; and the same is true if they journey to a near-Earth asteroid. However, once a lunar base is set up, astronauts will be able use microorganisms carried from Earth to process lunar rock into fuel, along with oxygen. The latter is needed not just for breathing, but also in rocket engines where it mixes with the fuel.

Currently, there are microorganisms available naturally that draw energy from rock and in the process release chemical products that can be used as fuel. However, as with agricultural plants like corn and soy, modifying such organisms can potentially make a biologically-based lunar rock processing much more efficient. Synthetic biology refers to engineering organisms to pump out specific products under specific conditions. For spaceflight applications, organisms can be engineered specifically to live on the Moon, or for that matter on an asteroid, or on Mars, and to synthesize the consumables that humans will need in those environments.

In the case of Mars, a major resource that can be processed by synthetic biology is the atmosphere. While the Martian air is extremely thin, it can be concentrated in a biological reactor. The principal component of the Martian air is carbon dioxide, which can be turned into oxygen, food, and rocket fuel by a variety of organisms that are native to Earth. As with the Moon rocks, however, genetic techniques can make targeted changes to organisms’ capabilities to allow them to do more than simply survive on Mars. They could be made to thrive there.

Nov 18, 2020

Bioethicist: We Should Give Sex Robots to Lonely Seniors

Posted by in categories: bioengineering, ethics, robotics/AI, sex

Newfound Autonomy

There are ways that a robot companion could outperform humans, Jecker says, by providing sympathetic and patient support free of judgment and condescension around the clock.

“It relates to issues of dignity,” Jecker told the Times. “The ability to be sexual at any age relates to your ability to have a life. Not just to survive, but to have a life, and do things that have value. Relationships. Bodily integrity. These things are a matter of dignity.”

Nov 11, 2020

DARPA Selects Teams to Modify Skin Microbiome for Disease Prevention

Posted by in categories: bioengineering, biotech/medical, health, military

ReVector researchers have expertise in synthetic biology, human microbiome, and mosquito studies.

The American Society for Microbiology estimates that there are trillions of microbes living in or on the human body that constitute the human microbiome1. The human skin microbiome (HSM) acts as a barrier between humans and our external environment, protecting us from infection, but also potentially producing molecules that attract mosquitos. Mosquitos are of particular concern to the Department of Defense, as they transmit pathogens that cause diseases such as chikungunya, Zika, dengue, West Nile virus, yellow fever, and malaria. The ReVector program aims to maintain the health of military personnel operating in disease-endemic regions by reducing attraction and feeding by mosquitos, and limiting exposure to mosquito-transmitted diseases.

Genome engineering has progressed to the point where editing the HSM to remove the molecules that attract mosquitos or add genes that produce mild mosquito repellants are now possible. While the skin microbiome has naturally evolved to modulate our interactions with the environment and organisms that surround us, exerting precise control over our microbiomes is an exciting new way to provide protection from mosquito-borne diseases.

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